Biological Context
Lead Research Organisation:
John Innes Centre
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The vast wealth of natural products discovered so far, and the far greater numbers predicted from genome sequences, potentially provide entirely new opportunities for biological discoveries. Many of these molecules are likely to have roles in the environment – for example in deterring or killing competitors, facilitating symbioses, acquiring nutrients, and attracting dispersal agents. By shedding light on the roles and targets of natural products and the contexts in which they are produced, we will provide new understanding of the biology of the producing organisms and the ecological niches they occupy and also accelerate the discovery of new bioactive molecules as antibiotics, therapeutics, agrichemicals, food ingredients and industrial raw materials. This research both draws on and feeds into product and pathway discovery research in the Project “Products and pathways”. Research in the Biological context Project stems in part from new discoveries in established areas of strength: bacterial growth and differentiation and the biology of proteins that are targets for antibiotics. The Project also takes a major new direction: the exploration of small-molecule interactions between microbes and other organisms in the soil. This is an area of strong synergy with other JIC research in Plant Health, and with the University of East Anglia.
The outcomes of this Project are relevant for both the development and discovery of antibiotics and the search for new agrichemicals and interventions. Better understanding of the role of natural products in microbial interactions will underpin the identification of new antimicrobial molecules and biocontrol strains for the control of crop pests and diseases: a subject of particular concern given increasing legislative restrictions on the use of previously-allowed agrichemicals.
The outcomes of this Project are relevant for both the development and discovery of antibiotics and the search for new agrichemicals and interventions. Better understanding of the role of natural products in microbial interactions will underpin the identification of new antimicrobial molecules and biocontrol strains for the control of crop pests and diseases: a subject of particular concern given increasing legislative restrictions on the use of previously-allowed agrichemicals.
Planned Impact
unavailable
Organisations
- John Innes Centre (Lead Research Organisation)
- California State University, Bakersfield (Collaboration)
- Binghamton University (Collaboration)
- Fundacion MEDINA (Collaboration)
- Indian Institute of Science Bangalore (Collaboration)
- University of York (Collaboration)
- VCS Potatoes (Collaboration)
- Uppsala University (Collaboration)
- University of Leon (Collaboration)
- University of Ljubljana (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- Macquarie University (Collaboration)
- Jagiellonian University (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- University College London (Collaboration)
- University of Western Australia (Collaboration)
- University of Perth (Collaboration)
- CARDIFF UNIVERSITY (Collaboration)
- Isomerase Therapeutics (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Commonwealth Scientific and Industrial Research Organisation (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- University of Toronto (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
Publications
Aron AT
(2020)
Reproducible molecular networking of untargeted mass spectrometry data using GNPS.
in Nature protocols
Bax BD
(2019)
DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
in Journal of molecular biology
Becher PG
(2020)
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal.
in Nature microbiology
Branch HA
(2022)
Discussions of the "Not So Fit": How Ableism Limits Diverse Thought and Investigative Potential in Evolutionary Biology.
in The American naturalist
Bush M
(2022)
Hyphal compartmentalization and sporulation in Streptomyces require the conserved cell division protein SepX
in Nature Communications
Bush MJ
(2017)
Multi-layered inhibition of Streptomyces development: BldO is a dedicated repressor of whiB.
in Molecular microbiology
Bush MJ
(2017)
Multi-layered inhibition of Streptomyces development: BldO is a dedicated repressor of whiB.
in Molecular microbiology
Bush N
(2020)
Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance
in Molecules
Bush, N.G.
(2018)
DNA in a twist? How topoisomerases solve topological problems in DNA
in The Biochemist
| Description | KEY FINDINGS APRIL 2017 - MARCH 2018 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANISATION. CONTROL OF THE INITIATION OF STREPTOMYCES DEVELOPMENT. (Schumacher et al., 2017. Nucleic Acids Res. 45: 6923-6933. doi: 10.1093/nar/gkx287; Bush et al., 2017. Mol. Microbiol. 104: 700-711. doi: 10.1111/mmi.13663). Streptomyces are ubiquitous soil bacteria that undergo a complex developmental transition coinciding with their production of antibiotics. This transition is controlled by binding of a novel tetrameric form of the second messenger, 3'-5' cyclic diguanylic acid (c-di-GMP) to the master repressor, BldD. In all domains of life, nucleotide-based second messengers allow a rapid integration of external and internal signals into regulatory pathways that control cellular responses to changing conditions. c-di-GMP can assume alternative oligomeric states to effect different functions, binding to effector proteins as monomers, intercalated dimers, or, uniquely in the case of BldD, as a tetramer. However, at physiological concentrations c-di-GMP is a monomer and little is known about how higher oligomeric complexes assemble on effector proteins and if intermediates in assembly pathways have regulatory significance. We have now demonstrated that c-di-GMP binds BldD using an ordered, sequential mechanism and that BldD function necessitates the assembly of the tetrameric c-di-GMP-BldD complex. BldD-(c-di-GMP) sits on top of the regulatory network that controls differentiation in Streptomyces, repressing a large regulon of developmental genes when the bacteria are growing vegetatively. In this way, BldD functions as an inhibitor that blocks the initiation of sporulation. We have reported the identification and characterization of BldO, an additional developmental repressor that acts to sustain vegetative growth and prevent entry into sporulation. However, unlike the pleiotropic regulator BldD, we have shown that BldO functions as the dedicated repressor of a single key target gene, whiB, and that deletion of bldO or constitutive expression of whiB is sufficient to induce precocious hypersporulation. THE ROLE OF DYNAMIN MEMBRANE-REMODELLING PROTEINS IN BACTERIA. (Schlimpert et al., 2017. PNAS 114: E6176-E6183. doi/10.1073/pnas.1704612114). Bacterial dynamins were discovered ~10 years ago and the explosion in genome sequencing has shown that they radiate throughout the bacteria, being present in >1000 species. In eukaryotes, dynamins play critical roles in the detachment of endocytic vesicles from the plasma membrane, the division of chloroplasts and peroxisomes, and both the fusion and fission of mitochondria. However, in evolutionary terms, dynamins are of bacterial origin, and yet the biological functions of bacterial dynamins remain poorly understood. We have now demonstrated a novel and critical role for dynamins in developmentally regulated cell division in Streptomyces, reminiscent of the essential role of eukaryotic dynamins in the division of chloroplasts and mitochondria. CONTROL OF THE OXIDATIVE STRESS RESPONSE IN STREPTOMYCES. Feeney et al., 2017. mBio 8: e00815-17. doi:10.1128/mBio.00815-17). The major oxidative stress response in Streptomyces is controlled by the sigma factor SigR and its cognate antisigma factor RsrA, and SigR activity is tightly controlled through multiple mechanisms at both the transcriptional and post-translational levels. Here we show that sigR has a highly unusual GTC start codon, and that this leads to another level of SigR regulation, in which SigR translation is repressed by Translation Initiation Factor 3 (IF3). Changing the GTC to a canonical start codon causes SigR to be overexpressed relative to RsrA, resulting in unregulated and constitutive expression of the SigR regulon. Similarly, introducing IF3* mutations that impair its ability to repress SigR translation has the same effect. Thus, the non-canonical GTC sigR start codon and its repression by IF3 are critical for the correct and proper function of the oxidative stress regulatory system. sigR and rsrA are cotranscribed and translationally coupled, and it had therefore been assumed that SigR and RsrA are produced in stoichiometric amounts. Instead, we have shown that RsrA can be transcribed and translated independently of SigR, that RsrA is normally produced in excess of SigR, and we have characterized the factors that determine SigR:RsrA stoichiometry. CHROMOSOME ORGANIZATION. (Tran et al., 2017. Cell Rep. 20: 2057-2071. doi: 10.1016/j.celrep.2017.08.026). SMC proteins, also known as cohesin and condensin in eukaryotes, is crucial for chromosome organization in all living organisms. But how SMC translocates on a protein-laden chromosome is poorly investigated. Whether SMC impacts DNA-translocating proteins such as RNA polymerase and is, in turn, influenced by such proteins, is not well understood. How different cellular processes share the same DNA but avoid, or resolve, conflicts is a question that arises in all cells and all domains of life. Our study provided the first concrete experimental evidence that the translocation of bacterial SMC on the chromosome is strongly influenced by RNA polymerases. We showed that highly-transcribed genes oriented to collide head-on with translocating SMC slow down and potentially stop SMC translocation. This might have contributed to the selection for highly-transcribed genes to be co-oriented with the direction of SMC movement. Broadly, our work demonstrated a tight interdependence of bacterial chromosome organization and the highly non-random global pattern of transcription. Further, we demonstrate that the translocation of bacterial SMC is directional, from the bacterial centromere site parS progressively to the replication terminus, extruding out DNA in a loop as a result of this directional movement. The finding that bacterial SMC translocation is directional has significant implications for how eukaryotic cohesin and CTCF may work together to extrude DNA loops (Rao et al 2015 Cell, Sanborn et al 2015 PNAS, Fudenberg et al 2016 Cell Rep). CAULOBACTER AS A MODEL SYSTEM. Our findings were greatly aided by the use of Caulobacter as a model system. Caulobacter is easily synchronized, enabling us to generate genome-wide data for a homogenous population of G1-phase cells that each contain a single chromosome. As there is no active DNA replication in these cells, we were able to isolate and specifically study the effect of transcription on SMC translocation and global chromosome organization, without confounding effects from replication-transcription conflicts. Such a "clean" arrangement cannot be achieved in other traditional model bacteria such as Escherichia coli, Bacillus subtilis, or Streptomyces. Our work took advantage of the genetic tractability of Caulobacter but produced findings that should be of broad relevance to researchers studying chromosome organization and chromosome segregation in a wide range of bacterial species. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS. DNA GYRASE AS AN ANTIBIOTIC TARGET. (Webber et al., 2017. J Antimicrob Chemother. 72: 2755-2763. doi: 10.1093/jac/dkx201; Ghilarov et al., 2017. Structure 25: 1549-1561.e5. doi: 10.1016/j.str.2017.08.006; Chan et al., 2017. PNAS. 114: E4492-E4500. doi: 10.1073/pnas.1700721114; Wallace et al., 2018. Chem Commun. 54: 1869-1872. doi: 10.1039/c7cc09518j; Colgan et al., 2018. Mol Microbiol. Jan 20. doi: 10.1111/mmi.13911). This work concerns the physiological roles of bacterial DNA gyrase and its interactions with inhibitors, towards the aim of developing novel antibiotics and herbicides. We showed in Salmonella enterica serovar Typhimurium, which exists at low pH in macrophage vacuoles, that the physiological effects can be attributed, at least in part, to the effect of low pH on gyrase's supercoiling activity. Further, in Escherichia coli, we showed that mutations in gyrase conferring quinolone resistance have a fitness cost that is manifested by a decrease in susceptibility to triclosan. In collaboration with GSK and Sanofi we have identified a novel drug-binding pocket in gyrase that accommodates thiophene compounds, which can be exploited in the development of new antibacterial agents. With Arabidopsis thaliana gyrase we have found that, like its bacterial counterparts, it can be inhibited by quinolone antibiotics, such as ciprofloxacin, and that these compounds also have herbicidal activity. Analogues of ciprofloxacin have been prepared with increased herbicidal activity and diminished antibacterial activity. We have been developing the bacterial toxin microcin B17 as a potential substitute for quinolones and have discovered how it is proteolytically processed during its biosynthesis. To aid drug discovery in the gyrase (and topoisomerase) area we have developed a rapid high-resolution method for resolving DNA topoisomers, using microcapillary electrophoresis. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS. USING CHEMICAL ECOLOGY AND GENOMICS TO DISCOVER NEW ANTIBIOTICS. (Qin et al., 2017. Chem Sci. 8(4):3218-3227. doi: 10.1039/c6sc04265a; Holmes et al., 2018. J Biotechnol. 265: 116-118. doi: 10.1016/j.jbiotec.2017.11.011; Scott et al., 2017. Nat Commun. 8: 15935. doi: 10.1038/ncomms15935). Using a chemical ecology/genomics guided approach we discovered a new class of polyketide antibiotics that we named the formicamycins. The formicamycins are active against drug resistant pathogens, including clinical isolates of MRSA and VRE, and display an extremely high barrier for the selection of resistant isolates. We identified the BGC encoding formicamycin production and were able to interrogate the biosynthetic pathway. Future work will extend these findings: our key aims are to produce new analogues with improved properties, and identify the molecular target/mode of action as part of our efforts to generate next generation antibiotics active against drug resistant organisms. In parallel work we delineated the entire biosynthetic pathway to the unusual antibiotic obafluorin produced by Pseudomonas fluorescens and identified a new family of l-threonine transaldolase enzymes which have potential synthetic utility (10.1038/ncomms15935). More recently we uncovered the likely molecular target of obafluorin and have preliminary data suggesting a novel mode of action which has value for the design of next generation versions of obafluorin with activity against drug resistant pathogens. THE WAX MOTH AS A MODEL SYSTEM. (Ignasiak and Maxwell, 2017a. BMC Microbiol. 17: 223. doi: 10.1186/s12866-017-1133-0; Ignasiak and Maxwell, 2017b. BMC Res Notes. 10: 428. doi: 10.1186/s13104-017-2757-8). We have been developing the greater wax moth larva (Galleria mellonella) as a system that can be used for antibacterial drug discovery, and shown that it can be used as a surrogate for rodents in infectivity trials and toxicity testing. Moreover, we have shown that the Galleria gut microbiome can be used in the discovery process for new, plant-based, antibiotics. IDENTIFICATION OF THE BIOSYNTHETIC GENE CLUSTER FOR BICYCLOMYCIN. (Vior et al. 2018. Appl. Environ. Microbiol., in the press). Bicyclomycin is an antibiotic that is a promising candidate for treating multi-drug resistant bacterial infections. Our identification of the biosynthetic gene cluster for bicyclomycin revealed that this gene cluster is found in the genomes of a wide variety of bacteria, including hundreds of sequenced isolates of the human pathogen Pseudomonas aeruginosa. This represents a highly unusual transfer of an intact gene cluster between Gram-positive and Gram-negative bacteria, and we showed that the P. aeruginosa gene cluster produces authentic bicyclomycin. This discovery provides the basis for further investigations into how and why this antibiotic pathway has become distributed across such diverse bacteria, and whether it has a role in P. aeruginosa infection. ACTIVATION OF SILENT ANTIBIOTIC BIOSYNTHETIC GENE CLUSTERS. (Som et al., 2017. Front Microbiol. 8:1145. doi: 10.3389/fmicb.2017.01145; Som et al., 2017. Microbiology 163: 1415-1419. doi: 10.1099/mic.0.000524). A major aim of our research is to develop methods for the activation of silent or cryptic biosynthetic gene clusters (BGCs) in order to illuminate the natural products chemical 'dark matter' encoded in actinobacterial genomes, and to increase the production of compounds otherwise produced at trace levels. We have now shown that the highly conserved actinobacterial two component system mtrAB is important in coordinating antibiotic production with development, and that mtrAB manipulation leads to the significant increase in antibiotic production and a shift in the global metabolome. We will exploit these findings for the discovery of new molecules from environmental isolates, and the anticipate it will form part of a toolkit for cryptic BGC activation useful to researchers generally. KEY FINDINGS APRIL 2018 - MARCH 2019 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANISATION. CONTROL OF THE INITIATION OF DEVELOPMENT IN ANTIBIOTIC-PRODUCING STREPTOMYCES. (Schumacher et al., 2018. Nat. Commun. 9: 1139. doi: 10.1038/s41467-018-03576-3; Schumacher et al., 2018. Nucleic Acids Res. 46: 7405-7417. doi: 10.1093/nar/gky493; Bush et al., 2019. mBio 10: e02812-18. doi.org/10.1128/mBio.02812-18). The complex life cycle of the antibiotic-producing bacteria Streptomyces involves two distinct filamentous cell forms: the growing or vegetative hyphae and the reproductive or aerial hyphae, which differentiate into long chains of spores. Genetic studies identified the transcription factors that control entry into development, which are called Bld (bald) regulators because mutations in the corresponding genes prevent formation of the hair-like aerial hyphae. One of these regulators, BldC, is a small, 68-residue protein with a winged Helix-Turn-Helix (wHTH) motif, related to those found in MerR-family proteins. The basic structure of classical MerR proteins is a dimer consisting of two identical subunits, each composed of an N-terminal wHTH DNA-binding domain, a C-terminal effector-recognition domain and an interconnecting linker region that consists of a long a-helix that interacts with the same helix in the other subunit, forming an antiparallel coiled-coil responsible for homodimerization. MerR transcription factors bind to palindromic DNA sequences as homodimers. However, unlike classical members of the MerR family, BldC has neither an effector domain nor the dimerization helix, and BldC behaves as a monomer in free solution. As a consequence, how BldC might bind DNA was unclear. To address this question, we carried out biochemical and structural studies to characterize the binding of BldC to the promoters of two known target genes. These studies showed that BldC binds DNA in a completely different way to classical MerR regulators, instead involving asymmetric, cooperative, head-to-tail oligomerization on DNA direct repeats with concomitant pronounced DNA distortion. The number of direct repeats present in BldC-binding sites is variable, thus allowing cooperative, head-to-tail binding of additional BldC monomers. Since BldC-like proteins radiate throughout the bacteria, this study identified BldC as the founding member of a new structural family of transcription factors. Although this work provided a clear mechanistic understanding of how BldC binds DNA, there was less insight into its biological role and impact on Streptomyces development. Accordingly, we exploited the benefits of the model species, Streptomyces venezuelae, which sporulates in liquid culture, to study the biological role of BldC. Using ChIP-seq coupled with RNA-seq, we identified the genes under BldC control and showed that BldC can function both as a repressor and as an activator of transcription. We showed that bldC mutants are bald because they enter development prematurely, bypassing the formation of aerial hyphae. This correlates with the premature expression of BldC target genes with key roles in development, chromosome condensation and segregation, and sporulation-specific cell division, suggesting that BldC-mediated repression is critical to maintain a sustained period of vegetative growth prior to sporulation. A second Bld regulator, BldN, is an extracytoplasmic function (ECF) s factor that plays a pivotal role in the onset of development by directing transcription of the rodlin and chaplin genes, which encode the proteins required to form an external hydrophobic sheath that permits the reproductive aerial hyphae to escape surface tension and grow into the air. BldN activity is in turn controlled by an anti-s factor, RsbN. RsbN shows no sequence similarity to known anti-s factors and binds and inhibits BldN in an unknown manner. We determined the 2.23 Å structure of the RsbN-BldN complex. The structure shows that BldN harbours s2 and s4 domains that are individually similar to other ECF s domains, which bind -10 and -35 promoter regions, respectively. The anti-s RsbN consists of three helices, with a3 forming a long helix embraced between BldN s2 and s4 while RsbN a1-a2 dock against s4 in a manner that would block -35 DNA binding. RsbN binding also freezes BldN in a conformation inactive for simultaneous -10 and -35 promoter interaction and RNAP binding. Strikingly, RsbN is structurally distinct from previously solved anti-s proteins. Thus, we have characterized the molecular determinants controlling a central Streptomyces developmental switch and shown that RsbN is the founding member of a new structural class of anti-s factor. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS. DNA GYRASE FUNCTION AND ANTIBIOTIC TARGETING. (Stracy, et al., 2019. Nucleic Acids Res, 47: 210-220; doi: 10.1093/nar/gky1143; Bush, et al., 2018. The Biochemist, 40; 26-31; Jeannot, et al., 2018. J Med Chem, 61: 3565-3581; doi: 10.1021/acs.jmedchem.7b01892; Germe, et al., 2018. Nucleic Acids Res, 46; doi: 4114-412810.1093/nar/gky181; Mori, et al., 2018. Tuberculosis, 112: 98-109; doi: 10.1016/j.tube.2018.08.004; Maxwell, et al., 2018. In Fong, I. W., Shlaes, D. and Drlica, K. (eds.), Antimicrobial resistance and implications for the 21st century. Springer, Switzerland; doi: 10.1007/978-3-319-78538-7). Working with groups in York, Oxford and Poznan (Poland) we have used high-speed single-molecule imaging in live Escherichia coli to show preferential association of gyrase at the DNA replication fork and demonstrated that the enzyme also performs a significant role in vivo in maintaining the level of negative supercoiling. In work partly funded by the EU in two consortia (mm4tb & ENABLE), we have investigated novel compounds that target gyrase as potential antibiotics. Imidazopyrazinones (IPYs), developed by Sanofi, were found to bind to gyrase at the quinolone pocket but to make different contacts, such that cross-resistance was only partial. The antimalarial compound, pyronaridine, showed modest activity against DNA gyrase from Mycobacterium tuberculosis, but higher activity versus RNA polymerase. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS. CHEMICAL WARFARE BETWEEN LEAFCUTTER ANT SYMBIONTS AND A CO-EVOLVED PATHOGEN. (Heine et al., 2018. Nat. Commun. 9:2208; doi: 10.1038/s41467-018-04520-1). Acromyrmex leafcutter ants form a mutually beneficial symbiosis with the cultivar fungus Leucoagaricus gongylophorus and with Pseudonocardia bacteria. Both are vertically transmitted and actively maintained by the ants. The fungus garden is manured with freshly cut leaves and provides the sole food for the ant larvae, while Pseudonocardia cultures are reared on the ant cuticle and make antifungal metabolites to help protect the cultivar against disease. If left unchecked, specialized parasitic Escovopsis fungi can overrun the fungus garden and lead to colony collapse. Our interdisciplinary approach showed that Escovopsis upregulates the production of two specialized metabolites when it infects the cultivar. These compounds inhibit Pseudonocardia and one, shearinine D, also reduces worker behavioural defences and is ultimately lethal when it accumulates in ant tissues. Our results are consistent with an active evolutionary arms race between Pseudonocardia and Escovopsis, which modifies both bacterial and behavioural defences such that colony collapse is unavoidable once Escovopsis infections escalate. ANTIBIOTIC AND TOXIN ACTION AND DISCOVERY. (Ignasiak & Maxwell, 2018. BMC Microbiol, 18: 228. doi: 10.1186/s12866-018-1377-3; Farrell, et al., 2018. J Antimicrob Chemother, 73; 2284-2297. doi: 10.1093/jac/dky208; Iyer, et al., 2018. Cell, 173: 1123-1134. doi: 10.1016/j.cell.2018.04.037). To further develop Galleria mellonella (greater wax moth) as a model system for studying the effects of antibiotics on the human infant gut microbiome, we have assessed the effects of treating larvae with oxytetracycline and found that it affects the composition and diversity of the insects' gut microbiome. We have investigated antibiotic compounds that have been reported in the literature and not developed as clinical antibiotics, generating an antibiotic database (Antibiotic DB) towards the goal of revitalising the drug pipeline. Investigations of the natural product toxin Microcin B17, produced by Escherichia coli in the human gut, have shown that it can trigger an intestinal inflammation response that is associated with inflammatory bowel disease. DISCOVERY OF NOVEL RIBOSOMALLY SYNTHESISED AND POST-TRANSLATIONALLY MODIFIED PEPTIDES. (Santos-Aberturas et al., 2018. bioRxiv 494286. doi: 10.1101/494286). To enable the discovery of novel ribosomally synthesised and post-translationally modified peptides (RiPPs), we have developed a genome mining tool, RiPPER (https://github.com/streptomyces/ripper), which enables the family-independent identification of RiPP precursor peptides from genomic data. This will support our efforts to understand the natural products made by bacteria during their interactions with other organisms. We used this tool to show that thioamidated RiPP natural products are likely to be widely distributed and diverse, despite currently being incredibly rare. To illustrate this, we characterise the structure and biosynthetic pathway to a new thioamidated natural product family, the thiovarsolins. RiPPER has enabled the bioinformatic identification of many novel gene clusters that are in the process of being investigated. KEY FINDINGS APRIL 2019 - MARCH 2020 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANISATION. c-di-GMP ARMS AN ANTI-s TO CONTROL THE DIFFERENTIATION OF THE REPRODUCTIVE AERIAL HYPHAE INTO SPORES IN STREPTOMYCES (Gallagher et al., 2020. Molecular Cell 77: 586-599. doi.org/10.1016/j.molcel.2019.11.006). The dramatic phenotypic consequences of altered c-di-GMP levels in Streptomyces, where high c-di-GMP levels trap the bacteria in vegetative growth and low c-di-GMP levels cause precocious hypersporulation suggested that this signaling molecule must directly interact with the regulatory network controlling the life cycle. We previously showed that showed that c-di-GMP controls the activity of the master regulator BldD to control entry into development and the formation of the reproductive aerial hyphae (Tschowri et al., 2014). By contrast, what controls the final stage of development, the differentiation of the reproductive aerial hyphae into spores, has been unknown. The sporulation-specific s factor, sWhiG, is known to play a key role in this stage of development, but its function has not been subjected to systematic analysis. We have now identified a novel anti-s factor, RsiG, which controls the activity of sWhiG. Strikingly, we show that the interaction between RsiG and sWhiG is mediated by c-di-GMP. Specifically, when 'armed' with a dimer of c-di-GMP, RsiG sequesters sWhiG, blocking the differentiation of the reproductive hyphae into spores. This is the first known instance of c-di-GMP targeting a s factor. Thus, like BldD, the RsiG-sWhiG complex senses changes in c-di-GMP levels to control a specific stage of development. In this complex, RsiG primarily binding the cyclic dinucleotide via two E(X)3S(X)2R(X)3Q(X)3D signatures, one on each helix of its antiparallel coiled coil. This signature is distinct from any previously observed c-di-GMP binding motif. Notably, the anti-s factor RsiG can bind c-di-GMP in the absence of sWhiG, and that binding is specific for this nucleotide. We also show that RsiG must bind c-di-GMP to carry out its function of inhibiting sWhiG activity during vegetative growth, thereby preventing premature expression of the sWhiG regulon. Conservation of the signature c-di-GMP binding motifs in all Streptomyces RsiG homologs suggests that regulation of RsiG-sWhiG complex formation by this second messenger is a general mechanism of developmental control across the genus. As a result of this discovery, it is now clear that c-di-GMP signals through BldD and sWhiG, respectively, to control the two most dramatic transitions of the Streptomyces life cycle, the formation of the reproductive aerial hyphae, and their differentiation into spore chains. CHROMOSOME ORGANIZATION. (Jalal et al., 2020. eLife 9: e53515. doi: 10.7554/eLife.53515). In all living organisms, it is essential to transmit genetic information faithfully to the next generation. The SMC-ParAB-parS system is widely employed for chromosome segregation in bacteria. A DNA-binding protein ParB nucleates on parS sites and must associate with neighbouring DNA, a process known as spreading, to enable efficient chromosome segregation. Despite its importance, how the initial few ParB molecules nucleating at parS sites recruit hundreds of further ParB to spread is not fully understood. Recently, we reconstituted a parS-dependent ParB spreading event using purified proteins from Caulobacter crescentus and showed that CTP is required for spreading. We further showed that ParB spreading requires a closed DNA substrate, and a DNA-binding transcriptional regulator can act as a roadblock to attenuate spreading unidirectionally in vitro. Our biochemical reconstitutions recapitulate many observed in vivo properties of ParB in the past 35 years and open up avenues to investigate the interactions between ParB-parS with ParA and SMC. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS. IMMUNITY-GUIDED IDENTIFICATION OF THREONYL-tRNA SYNTHETASE AS THE MOLECULAR TARGET OF OBAFLUORIN, A ?ETA LACTONE ANTIBIOTIC. (Scott et al., 2019. ACS Chem. Biol. 14:2663-2671; DOI: 10.1021/acschembio.9b00590). To meet the ever-growing demands of antibiotic discovery new molecules that work in new ways are urgently needed. Many potent natural products with antibacterial activity that were previously discarded by the pharmaceutical industry might provide new opportunities. One such example is the structurally unique molecule obafluorin that is produced by a soil bacterium. Obafluorin is active against many types of bacteria, including important human pathogens, but how it works was unknown. In this paper we reported that obafluorin targets threonyl-tRNA synthetase, an essential enzyme required for protein synthesis in bacteria. Enzymes of this type are the targets of clinically validated drugs, but threonyl-tRNA synthetase has thus far not been exploited. This means obafluorin does not show cross resistance with other clinically used antibiotics. We also reported how the obafluorin producing bacteria remains immune to obafluorin, and it was this knowledge that helped us to identify threonyl-tRNA synthetase as the target in sensitive cells. Our results will aid in the development of improved obafluorin variants that might be useful as antibiotic drugs. DNA GYRASE FUNCTION AND ANTIBIOTIC TARGETING. (Bax et al. 2019. J. Mol. Biol. 431: 3427-3449; doi: 10.1016/j.jmb.2019.07.008; Li et al., 2019. Mol. Microbiol. 111: 1529-1543; doi: 10.1111/mmi.14235; McKie et al. 2020. Genes 11: 92; 10.3390/genes11010092). Drawing on extensive structural and mechanistic data, we have established a model for the topoisomerase catalytic cycle and proposed how metal ions are involved in the DNA cleavage-religation cycle; this has important implications for drug interaction, particularly quinolones. Working with colleagues in China, we have found that QnrB, a protein associated with quinolone resistance, can activate DNA replication initiation via binding to dnaA. A key question with gyrases and other topoisomerases is how to determine cleavage- and binding-site specificities; we have reviewed NGS-based methodologies for doing this. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS. ANTIBIOTIC AND TOXIN ACTION AND DISCOVERY. (Maxwell et al., 2019. J. Mol. Biol. 431: 3367-3369; doi: 10.1016/j.jmb.2019.06.018; Collin & Maxwell, 2019. J. Mol. Biol. 431: 3427-3449; doi: 10.1016/j.jmb.2019.05.050; Ghilarov, et al., 2019. Mol. Cell 73: 749-762; doi: 10.1016/j.molcel.2018.11.032; McCauley, et al., 2019. Cell Chem. Biol. 26: 1274-1282; doi: 10.1016/j.chembiol.2019.06.002; Narramore, et al., 2019. Bioorg. Med. Chem. 27: 3546-3550; doi: 10.1016/j.bmc.2019.06.015). We have evaluated the current status of our knowledge of the molecular basis of antibiotic action and resistance, in particular focussing on the current state of our understanding of the action of the Escherichia coli toxin microcin B17 (MccB17) and its prospects for a role in the development of new antibiotics going forward. Working with labs from Russia and Poland we have gained molecular-level understanding of the biosynthesis of MccB17 through structural work. In terms of novel antibiotics, we have been working with colleagues in Canada and identified a novel antibiotic that is a gyrase inhibitor that appears to have a unique mode of action. With colleagues in Leeds using computational medicinal chemistry, we have established the molecular mechanism of action of a series of novel gyrase ATPase inhibitors. KEY FINDINGS APRIL 2020 - MARCH 2021 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANIZATION BACTERIAL DIFFERENTIATION Ramos-Léon et al. 2020. BioRxiv 10.01.322578. doi:10.1101/2020.10.01.322578 While cell division in model bacterial species like E. coli and B. subtilis is well understood, it is less well characterised in actinobacteria, including industrial and medical important bacteria of the genus Streptomyces and Mycobacterium. We have identified a highly conserved protein that plays an important role in the assembly and function of the bacterial cell division machinery in actinobacteria (doi: https://doi.org/10.1101/2020.10.01.322578). This protein, SepH, directly regulates the function of the key cell division protein FtsZ, thereby promoting the assembly of the cell division machinery and the formation of a division septum. Using a combination of live cell imaging and comparative in vitro approaches, we demonstrate that SepH plays a similar role in morphological diverse actinobacteria including filamentous growing bacteria of the genus Streptomyces and unicellular bacteria such as Mycobacterium smegmatis. Importantly, our results significantly advance the understanding of an essential biological process in this important class of bacteria, which includes major pathogens like the causative agent of TB Mycobacterium tuberculosis. CHROMOSOME ORGANIZATION Jalal et al., 2020. eLife 9: e53515. doi: 10.7554/eLife.53515 Szafran et al., 2020 BioRxiv doi: 10.1101/2020.12.09.403915 Jalal et al., 2021 BioRxiv doi: 10.1101/2021.02.11.430593 In all living organisms, it is essential to transmit genetic information faithfully to the next generation. The SMC-ParA-ParB-parS system is widely employed for chromosome organization and segregation in bacteria. We, in collaboration with Prof. Jakimowicz, investigated the spatial rearrangement of the Streptomyces venezuelae linear chromosome during its sporogenic development. We showed that at entry to sporulation, arms of S. venezuelae chromosomes are spatially separated, but they are closely aligned within the core region during sporogenic cell division. Chromosomal arm alignment is imposed by the segregation protein ParB and SMC. This work is an extension from our previous work on Caulobacter crescentus SMC and we provided further evidence for the conserved roles of SMC in bacterial chromosome organization. A DNA-binding protein ParB nucleates on parS sites and must associate with neighbouring DNA, a process known as spreading, to enable efficient chromosome segregation. Despite its importance, how the initial few ParB molecules nucleating at parS sites recruit hundreds of further ParB to spread is not fully understood. Recently, we reconstituted a parS-dependent ParB spreading event using purified proteins from Caulobacter crescentus and showed that CTP is required for spreading. We further showed that ParB spreading requires a closed DNA substrate, and a DNA-binding transcriptional regulator can act as a roadblock to attenuate spreading unidirectionally in vitro. Our biochemical reconstitutions recapitulate many observed in vivo properties of ParB in the past 35 years and open up avenues to investigate the interactions between ParB-parS with ParA and SMC. Next, we expanded our research to investigate the roles of CTP in nucleoid occlusion and bacterial cell division. We unexpectedly found that CTP couples membrane-binding activity of the nucleoid occlusion factor (Noc) to its spreading activity to ensure a productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity. Our study provided the first evidence for a CTP switch that controls membrane activity, adding the control of membrane association in Noc to the role of ParB-CTP in bacterial chromosome segregation. The implication of our finding is that CTP switches are likely pervasive in biology but have so far been underappreciated. We believe that our work here will motivate a systematic discovery and characterization of other CTPase proteins that will potentially open many new and unexpected horizons in biology. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS DNA TOPOISOMERASE STRUCTURE/FUNCTION AND ANTIBIOTIC TARGETING. Waraich et al. 2020. Biotechniques, 69, 356-362; doi: 10.2144/btn-2020-0059 Bush et al., 2019. Molecules, 25; doi: 10.3390/molecules25235662 Henderson et al. 2020. J Antimicrob Chemother, 75, 2835-2842; doi: 10.1093/jac/dkaa286 Skok et al. 2020. ACS Med. Chem. Letts., 11, 2433-2440; doi: 10.1021/acsmedchemlett.0c00416 Kolaric et al. 2021. Nature Comms., 12, 150; doi: 10.1038/s41467-020-20405-8 Pyne et al. 2021. Nature Comms., 12, 1053; doi: 10.1038/s41467-021-21243-y Although the structure of B-form DNA is well-established, the structure of long, plasmid-sized DNA molecules and their dynamics is challenging to establish. Using atomic-force microscopy, molecular dynamics and SPR, we have observed kinks and defects in supercoiled DNA and how these might influence interactions with enzymes, such as DNA topoisomerases. A key log-jam in antibiotic/anticancer drug screening with topoisomerase targets has been the lack of a useful assay for DNA decatenation. We have addressed this by developing a novel decatenation assay using a singly-linked catenated substrate. Although fluoroquinolones (FQs) are highly successful antibiotics targeted to DNA gyrase, there is an urgent need to develop new agents on account of increasing resistance to FQ compounds. Working with colleagues in industry and academia (in Europe), we have developed several new series of compounds that have efficacy against pathogenic bacteria, in particular Mycobacterium tuberculosis. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS DISCOVERY THAT SIGNALLING BY VOLATILES ATTRACTS SPRINGTAILS AS VECTORS FOR STREPTOMYCES SPORE DISPERSAL Becher et al., 2020. Nature Microbiology 5: 821-829. Streptomyces bacteria are responsible for the characteristic earthy odour of soil. This odour is caused by production of the volatile terpenoids geosmin, which is made by all Streptomyces species, and 2-methylisoborneol (2-MIB), which is made by most species in the genus. This ubiquity suggested that geosmin and 2-MIB must provide a selective advantage for these soil microbes, but the nature of this advantage was unknown. We showed that, unlike other Streptomyces natural products, production of geosmin and 2-MIB is directly under the control of sporulation-specific transcription factors and that emission of these volatiles is confined to immature spores. In a collaboration with Paul Becher and Klas Flärdh (Lund, Sweden), we went on to show that these volatiles attract springtails (Collembola) that feed on Streptomyces colonies and disseminate spores both via their faecal pellets and through adherence to their hydrophobic cuticles. Thus, geosmin and 2-MIB production in immature spores is an integral part of the sporulation process, completing the Streptomyces life cycle by facilitating dispersal of spores by soil arthropods. SUPPRESSION OF PLANT PATHOGENIC BACTERIA Stefanato et al., 2019, bioRxiv, doi: 10.1101/783258 Moffat et al., 2021, Synthetic Biology, doi: 0.1093/synbio/ysab004. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. We therefore genetically and phenotypically characterized the Pseudomonas population in a commercial potato field, where we identified strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. This revealed that hydrogen cyanide and cyclic lipopeptides are key specialized metabolites associated with pathogen inhibition. However, our analysis demonstrated that some strains feature no characterised genetic loci associated with pathogen inhibition, which highlighted the potential for novel determinants of biological activity. We therefore developed an automated transposon mutagenesis screen (in collaboration with the Earlham Institute Biofoundry), which led to the discovery of a new biosynthetic gene cluster associated with S. scabies inhibition. We are currently determining the structure of this molecule and we are applying this methodology to identify strains and natural products that suppress other agriculturally important pathogens. REWIRING THE REGULATION OF THE FORMICAMYCIN BIOSYNTHETIC GENE CLUSTER TO ENABLE THE DEVELOPMENT OF PROMISING NEW ANTIBACTERIAL COMPOUNDS Devine et al., 2021 Cell Chem Biol. 28:1-9. Formicamycins are a new structural class of antibiotics that inhibit the growth of MRSA and these bacteria do not become resistant to formicamycins, even after growing in the presence of sub-inhibitory concentrations. In this work we undertook a detailed analysis of the regulation of formicamycin biosynthesis and used this knowledge to engineer strains which produce formicamycins in liquid culture, and which produce 10-fold more than the wild-type strain. We also made strains which biosynthesise three new formicamycin congeners. Formicamycins are not toxic to mammalian cells and have a naturally high barrier to resistance so they are promising anti-infectives. STREPTOMYCES ENDOPHYTES PROMOTE HOST HEALTH AND ENHANCE GROWTH ACROSS PLANT SPECIES Worsley et al. 2020. Appl Env Microbiol. 86:e01053-20. We isolated and genome sequenced five Streptomyces endophyte strains from the roots of Arabidopsis thaliana and demonstrated that three of them enhance the growth of A. thaliana and another protected the common bread wheat Triticum aestivum against Take-all disease. We also isolated the antifungal compounds that protect wheat seedlings against the Take-all fungus, which is the causative agent of the most economically important disease of wheat in the UK. KEY FINDINGS APRIL 2021 - MARCH 2022 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANIZATION BACTERIAL DIFFERENTIATION HYPHAL COMPARTMENTALIZATION AND SPORULATION IN STREPTOMYCES REQUIRE THE CONSERVED CELL DIVISION PROTEIN SEPX Bush et al. 2022. Nat. Commun. 13: 71. Streptomyces are characterized by two distinct modes of cell division, leading to the partitioning of growing filaments into interconnected compartments via so-called cross-walls and to the septation and release of individual spores that can colonise new environmental niches. While we have made good progress on understanding cell division associated with formation of spores, the formation and biological significance of cell division resulting in cross-walls has remained enigmatic. Our work identified an important cellular component (now called SepX) that is essential for the formation of cross-walls but not for sporulation in Streptomyces. This allowed us for the very first time to experimental probe the importance of cross-walls for growth and development of Streptomyces. We found that cells that lack SepX grow without cross-walls but only poorly, indicating that cross-wall formation is crucial for the fitness of the bacterium. This fitness cost is likely to also affect other cellular processes in Streptomyces such antibiotic production and hence, our work has advanced the understanding of the fundamental biology of Streptomyces bacteria that underpins the production of antibiotics. STRUCTURAL AND FUNCTIONAL EVOLUTION OF A c-di-GMP REGULATORY SWITCH Schumacher, Gallagher, Holmes et al., 2021. PNAS 118: e2105447118. Diverse bacterial lifestyle transitions are controlled by the nucleotide second messenger c-di-GMP, including virulence, motility, and biofilm formation. To control such fundamentally distinct processes, the set of genes under c-di-GMP control must have gone through several shifts during bacterial evolution. We have shown that the RsiG-(c-di-GMP)-WhiG antisigma-sigma switch has been co-opted during evolution to regulate distinct biological functions in unicellular and filamentous bacteria, controlling type IV pilus production in the genus Rubrobacter and the differentiation of reproductive hyphae into spores in the genus Streptomyces. Moreover, biochemical, structural and phylogenetic studies show how the antisigma RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP-binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP-binding motifs, which functions as a monomer. This study thus describes the structural and functional evolution of a c-di-GMP regulatory switch. COMPLETE GENOME SEQUENCE OF THE MODEL STREPTOMYCES SPECIES STREPTOMYCES VENEZUELAE Gomez-Escribano et al., 2021. J. Ind. Microbiol. Biotechnol. 48: kuab035. For over a decade, Streptomyces venezuelae has been used to study the molecular mechanisms that control morphological development in streptomycetes and it is now a well-established model strain. Its rapid growth and ability to sporulate in a near-synchronised manner in liquid culture, unusual among streptomycetes, greatly facilitates the application of modern molecular techniques such as ChIP-seq and RNA-seq, as well as fluorescence time-lapse imaging of the complete Streptomyces life cycle. This work describes a high-quality genome sequence of our isolate of the strain (NRRL B-65442) consisting of an 8.2 Mb chromosome and a 158 kb plasmid, pSVJI1. CHROMOSOME ORGANIZATION Szafran et al., 2021. Nat. Comms. 12: 5222. Jalal et al., 2021. eLife 10: e69676 Jalal et al., Mol. Cell 81: 3623-3636 In all living organisms, it is essential to transmit genetic information faithfully to the next generation. The SMC-ParA-ParB-parS system is widely employed for chromosome organization and segregation in bacteria. We, in collaboration with Prof. Jakimowicz, investigated the spatial rearrangement of the Streptomyces venezuelae linear chromosome during its sporogenic development. We showed that at entry to sporulation, arms of S. venezuelae chromosomes are spatially separated, but they are closely aligned within the core region during sporogenic cell division. Chromosomal arm alignment is imposed by the segregation protein ParB and SMC. This work is an extension from our previous work on Caulobacter crescentus SMC and we provided further evidence for the conserved roles of SMC in bacterial chromosome organization. A DNA-binding protein ParB nucleates on parS sites and must associate with neighbouring DNA, a process known as spreading, to enable efficient chromosome segregation. Despite its importance, how the initial few ParB molecules nucleating at parS sites recruit hundreds of further ParB to spread is not fully understood. Recently, we reconstituted a parS-dependent ParB spreading event using purified proteins from Caulobacter crescentus and showed that CTP is required for spreading. We further solved X-ray crystallography structures of C. crescentus ParB-parS and ParB-CTP?S co-complexes. Our structures show nucleating ParB is an open clamp, in which parS is captured at the DNA-gate. Upon binding CTP, the N-terminal domain self-dimerizes to close the N-terminal-domain-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis likely opens the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling. Next, we expanded our research to investigate the roles of CTP in nucleoid occlusion and bacterial cell division. We unexpectedly found that CTP couples membrane-binding activity of the nucleoid occlusion factor (Noc) to its spreading activity to ensure a productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity. Our study provided the first evidence for a CTP switch that controls membrane activity, adding the control of membrane association in Noc to the role of ParB-CTP in bacterial chromosome segregation. The implication of our finding is that CTP switches are likely pervasive in biology but have so far been underappreciated. We believe that our work here will motivate a systematic discovery and characterization of other CTPase proteins that will potentially open many new and unexpected horizons in biology. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS DNA TOPOISOMERASE STRUCTURE/FUNCTION AND ANTIBIOTIC TARGETING. McKie et al. 2021. Bioessays, 43, e2000286; doi 10.1002/bies.202000286 McKie et al. 2022. eLife, 11; doi: 10.7554/eLife.67021. Orritt et al. 2021. Future Medicinal Chemistry, 13, 2125-2127; doi 10.4155/fmc-2021-0266 Feng et al. 2021. Proc Natl Acad Sci U S A, 118; doi: 10.1073/pnas.2016705118 DNA topoisomerases, enzymes capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. This indispensability is underlined by their role as drug targets, in particular for antibiotics. Using ensemble and single-molecule methods, we have shown that the archaeal enzyme, DNA topoisomerase VI, which is also found in plants and plasmodial parasites, has a key role in the decatenation of entangled DNA. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90 degrees. Building on previous work, we are exploiting a novel allosteric drug-binding pocket in bacterial DNA gyrase and topo IV with a view to developing novel antibiotics inspired by computational medicinal chemistry. Further we have shown that a mycobacterial pentapeptide repeat protein, MfpA, can inhibit gyrase by binding to the ATPase domain and, in so doing, interfere with fluoroquinolone action. These findings provide inspiration for future antibiotic development. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS IDENTIFICATION OF NATURAL PRODUCTS THAT SUPPRESS PLANT PATHOGENIC BACTERIA. Pacheco-Moreno, Stefanato, et al., 2021, eLife 10:e71900. Agricultural soil harbours a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the rhizosphere and have important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. In collaboration with the Malone group (Plant Health ISP, JIC), we genetically and phenotypically characterized the Pseudomonas population in a commercial potato field, where we identified strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. NATURAL PRODUCT ANTIBIOTICS SHAPE THE LEAFCUTTER ANT MICROBIOME Worsley et al., 2021. BMC Biology 19:205. The microbiome on the surface of the leafcutter ant exoskeleton is dominated by antibiotic-producing actinomycete bacteria. The ants vertically transmit a single strain of Pseudonocardia and they specifically recruit multiple Streptomyces species from the environment. In this work we show using RNA stable isotope probing that the ants feed all the bacteria living on their exoskeletons and that the Pseudonocardia strain makes antibiotics that prevent most environmental bacteria from colonising the ant cuticle and stealing this food. These antibiotics also select for Streptomyces bacteria which are naturally antibiotic resistant and also make multiple antibiotics that are useful to the ants. Thus, the ants end up covered in antibiotic-producing bacteria that protect them from disease-causing microbes. To our knowledge, this is the first experimental demonstration of how an animal assembles a microbiome. STREPTOMYCES BACTERIA HAVE EVOLVED TO COLONISE THE ROOT ENDOSPHERE TO ACCESS MORE FOOD Prudence et al., 2021. Env Microbiome 16:1-21 Worsley et al., 2021. Frontiers in Molecular Biosciences 8:541. Streptomyces bacteria are highly enriched in the roots of Arabidopsis thaliana and Triticum aestivum (common bread wheat) plants. Using 13CO2 DNA stable isotope probing, we have shown that, although they can exist solely on root exudates in vitro they are outcompeted for them in the rhizosphere by faster growing proteobacteria. Instead, some Streptomyces species have evolved to enter and live inside the roots where there is less competition and where they feed on plant metabolites. These species are likely symbionts of the plants and provide benefits such as growth promotion and protection against disease in exchange for food and housing. KEY FINDINGS APRIL 2022 - MARCH 2023 OBJECTIVE 1: BACTERIAL DIFFERENTIATION AND CHROMOSOME ORGANIZATION BACTERIAL DIFFERENTIATION Cytoplasmic contractile injection systems mediate cell death in Streptomyces Casu B, JW Sallmen, S Schlimpert* and M. Pilhofer*. (2023). Nat Microbiol (in press). *co-corresponding author This work stems from a collaboration with the lab of M. Pilhofer at ETH Zurich (Switzerland) and describes the structure and novel role of cytoplasmic contractile injection systems (CIS) in Streptomyces. We show that Streptomyces-CIS function via a completely different mechanism distinct from typical CIS involved in interspecies interaction. In Streptomyces, CIS mediate cell death as part of the developmental program and in response to external stressors. Our results provide new functional insights into CISs in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life cycle progression in multicellular bacteria. Genome-Wide Identification of the LexA-Mediated DNA Damage Response in Streptomyces venezuelae Stratton et al. 2022. J Bacteriol. Aug 16;204(8):e0010822. doi: 10.1128/jb.00108-22. Epub 2022 Jul 13. The transcriptional regulator LexA functions as a repressor of the bacterial SOS response, which is a widely conserved stress response that is induced under DNA-damaging conditions. Induction of the SOS results in the expression of genes important for survival and adaptation. We report the regulatory network controlled by LexA in the filamentous antibiotic-producing Streptomyces bacteria and establish the existence of the SOS response in Streptomyces. Collectively, our work reveals significant insights into the DNA damage response in Streptomyces that will promote further studies to understand how these important bacteria adapt to their environment. DNA damage-induced block of sporulation in Streptomyces venezuelae involves downregulation of ssgB Falguera et al. (2022) Microbiology (Reading). Jun;168(6). doi: 10.1099/mic.0.001198 DNA damage often causes an arrest of the bacterial cell cycle to provide time for DNA repair processes to take place to prevent the propagation of damaged DNA to the next generation. In bacteria, the classical SOS DNA damage response mediates this cell cycle checkpoint. However, how this essential cellular process is achieved at the molecular level has remained unclear in the filamentous Streptomyces bacteria. Here, we show that the DNA-damaging agent mitomycin C confers a block in sporulation-specific cell division in Streptomyces venezuelae in a mechanism that involves, at least in part, the downregulation of the key cell division gene ssgB. We also show that this block in sporulation can be partially bypassed by the constitutive production of SsgB although at the cost of reduced viability. This work provides the first molecular insight into how Streptomyces bacteria respond to DNA-damaging growth conditions to ensure their survival. Lilic et al., 2023. Proc. Natl. Acad. Sci. USA. In the press. The transcription factors WhiA and WhiB are both required to express cell division genes in the Actinobacteria. In Streptomyces, WhiA and WhiB co-control the initiation of sporulation-specific cell division, and deletion of either whiA or whiB leads to an identical phenotype in which developmental cell division and chromosome segregation are not initiated. These identical phenotypes arise because WhiA and WhiB function cooperatively to co-control the expression of a common set of WhiA/B target genes, including the critical cell division genes ftsZ, ftsW, ftsK, sepH, and sepX. in vivo DNA binding by WhiA depends on WhiB and vice versa, however, WhiA and WhiB function as monomers and do not interact in the absence of DNA. This represents a unique mechanism of transcriptional activation in bacteria, yet how these factors cooperate at the molecular level is not understood. To address this question, in collaboration with the laboratory of Elizabeth Campbell (Rockefeller University, NYC, USA), we solved cryo-electron microscopy structures of Streptomyces transcriptional regulatory complexes comprising RNA polymerase (RNAP) sA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of sA (sA4) of the sA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between sA4 housekeeping s-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduced or abolished developmental cell division, confirming their significance. In the closely related actinomycete Mycobacterium tuberculosis (Mtb), WhiA and WhiB are essential because they are required for cell division, and mutations in whiA and whiB are positively selected in clinical isolates of Mtb, implicating WhiA/B in virulence and/or resistance to drug treatment. This work thus provides functional insight into the molecular mechanism of a new class of transcription factors in an important bacterial clade that contains the major antibiotic producers while informing on the adaptive nature of WhiA/B mutations in virulence and antibiotic resistance in a deadly pathogen. CHROMOSOME ORGANIZATION & SEGREGATION Sukhoverkov KV, Jalal ASB, Ault J, Sobott F, Lawson DM, Tung Le* (2023). The CTP-binding domain is disengaged from the DNA-binding domain in a co-crystal structure of Bacillus subtilis Noc-DNA complex. J Biol Chem. 2023 Feb 23:103063. doi: 10.1016/j.jbc.2023.103063 (PDB: 7OL9) McLean TC, Tung Le* (2023) CTP switches in ParABS-mediated bacterial chromosome segregation and beyond. Current Opinion in Microbiology 73:102289. doi:10.1016/j.mib.2023.102289 In Bacillus subtilis, a ParB-like nucleoid occlusion protein (Noc) binds specifically to Noc-binding sites (NBS) on the chromosome to help coordinate chromosome segregation and cell division. Noc does so by binding to cytidine triphosphate (CTP) to form large membrane-associated nucleoprotein complexes to physically inhibit the assembly of the cell division machinery. The site-specific binding of Noc to NBS DNA is a prerequisite for CTP-binding and the subsequent formation of a membrane-active DNA-entrapped protein complex. Here, we solve the structure of a C-terminally truncated B. subtilis Noc bound to NBS DNA to reveal the conformation of Noc at this crucial step. Our structure reveals the disengagement between the N-terminal CTP-binding domain and the NBS-binding domain of each DNA-bound Noc subunit, this is driven, in part, by the swapping of helices 4 and 5 at the interface of the two domains. Site-specific crosslinking data suggest that this conformation of Noc-NBS exists in solution. Overall, our results lend support to the recent proposal that parS/NBS-binding catalyzes CTP-binding and DNA-entrapment by preventing the re-engagement of the CTP-binding domain and the DNA-binding domain from the same ParB/Noc subunit. OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS DNA TOPOISOMERASE STRUCTURE/FUNCTION AND ANTIBIOTIC TARGETING. Cotman et al. 2023. J. Med. Chem., 66, 1380-1425; doi 10.1021/acs.jmedchem.2c01597 Orritt et al. 2022. RSC Med. Chem., 13, 831-839; doi 10.1039/d2md00049k Prescott et al. 2022. FEBS Letts, 596; 3087-3102; doi: 10.1002/1873-3468.14483 DNA topoisomerases, enzymes capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. This indispensability is underlined by their role as drug targets, in particular for antibiotics. Working with teams from Slovenia and Sweden, we have investigated a series of promising novel compounds targeted to bacterial DNA gyrase with promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa that can be further developed as potential clinical antibiotics. Using in silico medicinal chemistry (Univ Leeds) we have further explored the thiophene antibiotics and synthesised novel compounds, some of which have activity against both gyrase and DNA topoisomerase IV from Escherichia coli and Staphylococcus aureus. Work with Kew Gardens has led to new insights into the mechanisms of anti-fungal chalcone compounds. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS. Working with the Malone group (Plant Health ISP, JIC), we have continued to investigate the genetic and metabolic features that enable Pseudomonas bacteria to suppress plant pathogens. Pseudomonas sp. Ps652 was previously identified from a screen of hundreds of Pseudomonas isolates as a potent inhibitor of the potato pathogens Streptomyces scabies (common scab) and Phytophthora infestans (late blight). We used a mixture of transposon mutagenesis and targeted gene deletions to identify the genes that contribute to the suppressive activity of this strain. This led to the discovery of the antimicrobial molecules required for this activity, whose biosynthesis was then investigated. A manuscript is currently in preparation for this study. Research in the Byers Lab has shown that floral traits are not strongly interlinked in orchid flowers, and that levels of interlinking or integration differ by orchid species and in interspecies hybrids. This is in contrast to views of floral traits as being tightly interlinked in these often pollinator-specialized flowers, and suggests that floral traits are loosely related rather than being under tight regulatory control in a "top down" fashion. Research in this area is ongoing. KEY FINDINGS APRIL 2023 - MARCH 2024 OBJECTIVE 2: SMALL-MOLECULE TARGET PROTEINS Uplift from the Wilkinson's group Obafluorin is a broad-spectrum, non-toxic antibacterial natural product that is not cross-resistant with any currently used antibiotics, meaning it has potential as the start point for the development of new antibiotics. Here we build on our previous discoveries regarding the molecular target and mechanism of action by which obafluorin inhibits pathogen growth, showing that its activity and stability are increased in the presence of ferric iron, and determining the mechanisms that underpin these observations. This information is vital for the future development of this chemical class. 1. RSC Chem Biol. 2023 Aug 21;4(11):926-941. doi: 10.1039/d3cb00127j. eCollection 2023 Nov 1. The catechol moiety of obafluorin is essential for antibacterial activity. Sibyl F D Batey , Melissa J Davie , Edward S Hems, Jonathon D Liston, Thomas A Scot, Silke Alt, Christopher S Francklyn, Barrie Wilkinson The resistance of pathogenic bacteria to antibiotics (AMR) is a serious threat to mankind. New compounds with antibiotic potential are urgently needed. The Maxwell group work on DNA topoisomerases, which are key targets for antibiotics in bacteria. One of these enzymes, DNA gyrase, has been highly successful in relation to antibacterial therapy, being the target for the highly successful fluoroquinolone compounds (FQs, such as ciprofloxacin). However, resistance to FQs and other gyrase-targeted compounds is a serious problem. Working as part of an international team including researchers from Slovenia, Italy, Sweden and The Netherlands, they have developed and investigated a range of novel compounds with antibacterial potential that target DNA gyrase. Some of these compounds show promising properties in relation to being clinical antibiotics of the future (1-3). References 1. Cotman, A.E., Durcik, M., Benedetto Tiz, D., Fulgheri, F., Secci, D., Sterle, M., Mozina, S., Skok, Z., Zidar, N., Zega, A. et al. (2023) Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J Med Chem. 2. Durcik, M., Cotman, A.E., Toplak, Z., Mozina, S., Skok, Z., Szili, P.E., Czikkely, M., Maharramov, E., Vu, T.H., Piras, M.V. et al. (2023) New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus. J Med Chem, 66, 3968-3994. 3. Sterle, M., Durcik, M., Stevenson, C.E.M., Henderson, S.R., Szili, P.E., Czikkely, M., Lawson, D.M., Maxwell, A., Cahard, D., Kikelj, D. et al. (2023) Exploring the 5-Substituted 2-Aminobenzothiazole-Based DNA Gyrase B Inhibitors Active against ESKAPE Pathogens. ACS Omega, 8, 24387-24395. OBJECTIVE 3: SMALL-MOLECULE MEDIATED INTERACTIONS BETWEEN MICROBES AND OTHER ORGANISMS. Flowers utilize many signals and cues to attract pollinators, including colour and scent, and these traits can be altered in response to novel pollinator environments. The Byers group demonstrates that in monkeyflowers (Mimulus spp.), parallel shifts from red to yellow colour morphs in two related species are accompanied by shifts in floral scent and shape. These shifts alter bumblebee and hawkmoth pollinator physiological and behavioural responses. However, despite the seeming parallelism of these two transitions from red to yellow, different genetic mechanisms underlie them - in other words, parallel shifts in phenotype are not underlaid by parallel shifts in genotype, and plants therefore are using many different toolkits to accomplish shifts in how they signal to pollinators. |
| Exploitation Route | This section will be competed at a later stage. Research in the Molecules from Nature ISP is broad and cross-disciplinary. It provides major new insights and approaches in our fields of interest, and have implications for other fields including pharmacology, human nutrition, disease diagnosis and prevention, soil ecology, agronomy and plant protection. Our research is thus of potential benefit to a very wide range of academic scientists and other beneficiaries. |
| Sectors | Agriculture Food and Drink Pharmaceuticals and Medical Biotechnology |
| Description | NARRATIVE IMPACT APRIL 2018 - MARCH 2019 MICROCAPILLARY ELECTROPHORESIS AS A TOOL FOR DRUG DISCOVERY (Mitchenall et al., 2018. BMC Res Notes. 11: 37. doi: 10.1186/s13104-018-3147-6). We have shown that the QIAxcel microcapillary electrophoresis system can be used as a drug-discovery tool and has advantages in terms of speed, resolution and cost over conventional gel-based systems. It can be applied to DNA circles of various sizes and can readily be adapted for use in compound screening against topoisomerase targets. Currently unpublished work between Dr Andy Truman (Molecules from Nature ISP), Dr Jake Malone (Plant Health ISP) and VCS Potatoes, an East Anglian agronomy company, has led to numerous successful funding applications. Zespri International Limited (New Zealand) have awarded £76,000 over three years to employ a PhD student to identify biocontrol strains and bioactive NPs from bacterial isolates from kiwi vines that will help combat PsaV, a economically damaging bacterial pathogen of kiwi orchards. Truman has also been awarded a Royal Society Enhancement Award (£170,640) to expand his work on the potato pathogen Streptomyces scabies. This will assess the transcriptional response and metabolism of S. scabies during plant infection. Antibiotics Action - in relation to his work in the area of antibiotic research and development, Maxwell serves on the Scientific Advisory Board of the charity Antibiotic Action (http://antibiotic-action.com/ ), a global public awareness initiative to inform everyone about drug resistance, working with a wide variety of professionals as well as the general public. NARRATIVE IMPACT APRIL 2019 - MARCH 2020 Prof. Tony Maxwell attended the ABX Antibiotic Discovery Accelerator Network meeting at the Eden Project (Cornwall, UK) where, amongst other issues, solutions to the current AMR (antimicrobial resistance) problem were discussed. This led to the submission of a Big Ideas Pipeline proposal to BBSRC: 'A Publicly-funded Research & Development Pipeline for New Antibiotics', which is under discussion by the cross-UKRI team involved in antimicrobial resistance (AMR) research. Dr Andy Truman attended the China-UK AMR Workshop (Beijing, China), where he presented his work on the antibiotic bicyclomycin (collaboration with Xiamen University) and was involved in discussions around strategies for future research into AMR in the UK and China. Dr Andy Truman also participated in the International Research Alliance for Antibiotic Discovery and Development (IRAADD) Workshop Meeting, (Saarbruecken, Germany), where a European strategy for Future AMR research and funding concepts was discussed. A white paper resulting from this network meeting is currently in preparation. Collaborative research between Dr Andy Truman (Molecules from Nature ISP), Dr Jake Malone (Plant Health ISP) and VCS Potatoes (Stefanato et al, 2019, bioRxiv, doi: 10.1101/783258) has led to a follow-on partnership with a UK-based biotechnology company to develop bacterial strains to control plant pathogens. NARRATIVE IMPACT APRIL 2020 - MARCH 2021 Professor Barrie Wilkinson and Dr Andrew Truman organised the Dubrovnik Summer School in Applied Molecular Microbiology. Because of COVID-19, this was run virtually. Details can be found here: https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/2020-applied-molecular-microbiology-summer-school-report/ Prof. Tony Maxwell participated in the UKRI AMR (antimicrobial resistance) consultation and attended the ABX Antibiotic Discovery Accelerator Network meeting (online) where, amongst other issues, solutions to the current AMR (antimicrobial resistance) problem were discussed. Information from these meetings were fed into the AMR on the NRP (Norwich Research Park) group, which is chaired by Maxwell. NARRATIVE IMPACT APRIL 2021 - MARCH 2022 We have identified natural products that suppress plant pathogenic bacteria. We have revealed two novel drug-binding sites in DNA gyrase and DNA topoisomerase IV that can be used by others to design new antibiotics using medicinal chemistry approaches. NARRATIVE IMPACT APRIL 2022 - MARCH 2023 Our collaboration with the Malone group (Plant Health ISP) on using Pseudomonas strains to suppress plant pathogens has led to the generation of a JIC spin-out company, PfBio Ltd, to convert our research findings into agriculturally relevant products. Dr Andrew Truman (MfN ISP) is a co-founder and co-director. The company is currently in the process of securing seed funding, and is in discussion with multiple agricultural and agritech companies in relation to future projects. In addition, Malone and Truman are academic partners in multiple funded collaborations with industrial partners, including a BBSRC-funded partnership with Branston Ltd (UK) to combat crop disease. |
| Sector | Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | Contribution to SAW Antibiotics book |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| URL | http://www.sawtrust.org/buy-the-books/saw-antibiotics/ |
| Description | Submission to Dept of Health and Social consultation/call for evidence: Antimicrobial resistance national action plan |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://www.gov.uk/government/consultations/antimicrobial-resistance-national-action-plan-call-for-e... |
| Description | Discovery of natural products that are critical for controlling plant pathogens (TRUMAN_J17DTP) |
| Amount | £95,000 (GBP) |
| Funding ID | 1937478 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2021 |
| Description | Exploring novel binding pockets in DNA gyrase and DNA topoisomerase IV to address antibiotic resistance |
| Amount | £642,171 (GBP) |
| Funding ID | BB/V006983/ |
| Organisation | University of Leeds |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 06/2021 |
| End | 06/2024 |
| Description | HORTICULTURE: Biological control of potato scab using natural Pseudomonas strains |
| Amount | £40,306 (GBP) |
| Funding ID | BB/X012077/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 10/2023 |
| Description | Research Fellows Enhanced Research Expenses |
| Amount | £167,949 (GBP) |
| Funding ID | RF\ERE\210039 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 12/2023 |
| Description | Research Fellows Enhanced Research Expenses 2021 |
| Amount | £169,985 (GBP) |
| Funding ID | RF\ERE\210084 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 12/2021 |
| End | 12/2023 |
| Description | Royal Society Enhancement Award |
| Amount | £170,640 (GBP) |
| Funding ID | RGF\EA\181083 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 03/2021 |
| Description | Royal Society Research Grant |
| Amount | £19,000 (GBP) |
| Funding ID | RGS\R2\212105 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 01/2023 |
| Description | Royal Society University Research Fellowship Renewal |
| Amount | £483,734 (GBP) |
| Funding ID | URF\R\201020 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 12/2023 |
| Description | Royal Society University Research Fellowships Renewal |
| Amount | £363,410 (GBP) |
| Funding ID | URF\R\180007 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2021 |
| Description | Tackling tricky twists - how does DNA gyrase function inside living cells? |
| Amount | £379,684 (GBP) |
| Funding ID | BB/R001235/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2021 |
| Description | The line of duty: How to segregate a giant linear plasmid in antibiotic-producing Streptomyces |
| Amount | £250,000 (GBP) |
| Organisation | Lister Institute of Preventive Medicine |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2027 |
| Description | Understanding the molecular mechanisms of life, death and survival in multicellular bacteria |
| Amount | £760,344 (GBP) |
| Funding ID | URF\R\231009 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 12/2026 |
| Description | Wellcome Trust Investigator Awards |
| Amount | £1,271,158 (GBP) |
| Funding ID | 221776/Z/20/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 06/2026 |
| Title | QIAxcel |
| Description | We describe the application of the QIAxcel Advanced System, a high-throughput capillary electrophoresis system, to separate DNA topoisomers, and compare this technique with gel electrophoresis. |
| Type Of Material | Biological samples |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | The QIAxcel system has advantages in terms of speed, resolution and cost, and can be applied to DNA circles of various sizes. It can readily be adapted for use in compound screening against topoisomerase targets. |
| Title | RIPPER genome mining |
| Description | RiPPER is a command line computational tool that assists in the identification of biosynthetic gene clusters and associated precursor peptides for RiPPs, a large and important class of natural product. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | This has assisted in research projects in my group and I have had contact with researchers in other groups who have benefited from the tool and the results we have reported from its use. It assisted in the identification of a new family of natural products, the thiovarsolins, which were characterised by my group. The identification of these natural products and the development of the tool were reported in a BioRxiv pre-print (https://www.biorxiv.org/content/10.1101/494286v1) and have just been accepted for publication in Nucleic Acids Research. |
| URL | https://github.com/streptomyces/ripper |
| Title | AntibioticDB |
| Description | Repository of antibiotics developed since 1961. Open-access and searchable |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Provision of database that can be used by other researchers working on antibiotics |
| URL | http://www.antibioticdb.com/ |
| Description | A pipeline for antibiotic disovery |
| Organisation | University of East Anglia |
| Department | School of Biological Sciences UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Natural products chemistry and biosynthesis; actinomycete genetics; genome mining; bioinformatics; anti-infective assays |
| Collaborator Contribution | Entomology; actinomycete biology; genetic regulation; bioinformatics; anti-infective assays |
| Impact | Publications and subseqeunt grant applications |
| Start Year | 2013 |
| Description | Actinobacterial plant pathogen |
| Organisation | California State University, Bakersfield |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are investigating natural products associated with a plant pathogen and their role in pathogenicity. |
| Collaborator Contribution | The partner has generated bacterial mutants and provided expertise in plant pathogenicity assays. |
| Impact | Research is ongoing. Multidisciplinary: plant pathology, genetics, microbiology, chemistry |
| Start Year | 2020 |
| Description | Agnes Noy |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Synthesis of small DNA circles |
| Collaborator Contribution | Simulations |
| Impact | 3papers published so far: 1. A. D. Bates, A. Noy, M. M. Piperakis, S. A. Harris, A. Maxwell, Small DNA circles as probes of DNA topology. Biochem Soc Trans 41, 565-570 (2013). 2. A. Noy, A. Maxwell, S. A. Harris, Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA. Biophys J 112, 523-531 (2017). 3. A. L. B. Pyne et al., Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature communications 12, 1053 (2021). Multidisciplinary: Maxwell - biochemistry; Noy - simulations |
| Start Year | 2011 |
| Description | Anders Karlen |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | We have assayed compounds synthesised by partner |
| Collaborator Contribution | They have synthesised compounds |
| Impact | Publications |
| Start Year | 2014 |
| Description | Andy Bates |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Testing experimental ideas |
| Collaborator Contribution | Discussion of results |
| Impact | Publications |
| Description | Bax |
| Organisation | Cardiff University |
| Country | United Kingdom |
| PI Contribution | We have performed mechanistic enzymology work to complement the structural biology performed by Bax and others. |
| Collaborator Contribution | They have established a crystallography platform to analyse structures of topoisomerase-DNA-drug complexes. That expertise has now been transferred to JIC. |
| Impact | 3 Research publications.: 1. B. D. Bax, G. Murshudov, A. Maxwell, T. Germe, DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion. J Mol Biol 431, 3427-3449 (2019). 2. P. F. Chan et al., Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase. Proc Natl Acad Sci U S A 114, E4492-E4500 (2017). 3. T. Germe et al., A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance. Nucleic Acids Res 46, 4114-4128 (2018). Multi-disciplinary: biochemistry, crystallography, molecular biology |
| Start Year | 2014 |
| Description | Benesch |
| Organisation | University of Oxford |
| Department | Wolfson College |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have provided samples to be analysed by mass spec |
| Collaborator Contribution | They have employed high-resolution non-covalent mass spec methodology to investigate subunit exchange in DNA gyrase |
| Impact | None so far |
| Start Year | 2017 |
| Description | Blumberg |
| Organisation | Harvard University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have provided materials, toxins and DNA constructs to the Harvard team |
| Collaborator Contribution | They discovered that the toxin MccB17 was associated with IBD and carried out the immunology and animal experiments |
| Impact | Paper published: 1. S. S. Iyer et al., Dietary and Microbial Oxazoles Induce Intestinal Inflammation by Modulating Aryl Hydrocarbon Receptor Responses. Cell 173, 1123-1134 e1111 (2018). |
| Start Year | 2017 |
| Description | CSIRO collaboration |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Department | CSIRO Black Mountain Laboratories |
| Country | Australia |
| Sector | Private |
| PI Contribution | My research group hosted a senior researcher for a collaborative research project associated with microbe-plant and microbe-microbe interactions, with a particular focus on Streptomyces strains with inhibitory activity towards fungal pathogens of plants. We provided expertise in Streptomyces genetics, natural product biosynthesis and mass spectrometry. |
| Collaborator Contribution | The CSIRO researcher provided Streptomyces strains with biocontrol activity, as well as extensive expertise in fungal pathogens of crop plants. The bench work for this collaboration was carried out by the CSIRO researcher while they visited JIC. The research visit was for 4 months, but the collaboration is still ongoing. |
| Impact | Manuscript is currently under review. Australian funding: CERC Postdoctoral Fellowship Multi-disciplinary colaboration: microbiology, fungal biology, natural products chemistry, mass spectrometry, plant pathology. |
| Start Year | 2019 |
| Description | Danijel Kikelj |
| Organisation | University of Ljubljana |
| Department | University Medical Centre Ljubljana |
| Country | Slovenia |
| Sector | Hospitals |
| PI Contribution | Assayed compounds synthesised by partner |
| Collaborator Contribution | Synthesised series of compounds for testing by us |
| Impact | Other publications |
| Start Year | 2019 |
| Description | Dmitry Ghilarov |
| Organisation | Jagiellonian University |
| Country | Poland |
| Sector | Academic/University |
| PI Contribution | We hosted to Ghilarov and proved resources for X-ray crystallography |
| Collaborator Contribution | Ghilarov purified and characterized the proteins and carried out the crystallography |
| Impact | 2 papers: 1. D. Ghilarov et al., The Origins of Specificity in the Microcin-Processing Protease TldD/E. Structure 25, 1549-1561 e1545 (2017). 2. D. Ghilarov et al., Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell 73, 749-762 e745 (2019). |
| Start Year | 2017 |
| Description | Earlham Institute Biofoundry |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Development of an assay for strains that inhibit the growth of the plant pathogen Streptomyces scabies |
| Collaborator Contribution | Technical insight and method development relating to the use of a robotic system for the high-throughput screening of Streptomyces inhibition. |
| Impact | Paper: Moffat, A. D., Elliston, A., Patron, N. J., Truman, A. W. & Carrasco Lopez, J. A. A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition. Synth Biol, 6, ysab004 (2021). |
| Start Year | 2018 |
| Description | Fishwick |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been testing compounds synthesised by the med chem research team in Leeds |
| Collaborator Contribution | Using information provided by us, they have been using computational and medicinal chemistry methods to synthesise novel compounds that have antibacterial potential |
| Impact | Grant application to BBSRV funded 2 papers: 1. S. Narramore, C. E. M. Stevenson, A. Maxwell, D. M. Lawson, C. W. G. Fishwick, New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase. Bioorg Med Chem 27, 3546-3550 (2019). 2. K. M. Orritt, A. Maxwell, C. W. Fishwick, M. J. McPhillie, Exploitation of a novel allosteric binding region in DNA gyrase and its implications for antibacterial drug discovery. Future Medicinal Chemistry 13, 2125-2127 (2021). Multidisciplnary: biochemistry, structural biology, medicinal chemistry, computational chemistry |
| Start Year | 2017 |
| Description | Inhibiting bacterial cell division by controlling the essential FtsZ/SepH protein-protein interaction |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Schlimpert group recently reported the identification of the actinobacterial-specific cell division protein SepH, which directly binds the essential bacterial tubulin homolog FtsZ and regulates cell division processes. FtsZ is a GTPase and polymerises into dynamic filaments that assemble into a higher-ordered ring-like structure called the "Z-ring" at the division site, providing a scaffold for the multiprotein division machinery. We characterized SepH from the actinobacterial species Streptomyces venezuelae and Mycobacterium smegmatis, revealing that SepH interacts with FtsZ via a highly conserved helix-turn-helix motif. We further showed that SepH stimulates the formation of FtsZ protofilaments and promotes the lateral interaction of FtsZ filaments in vitro. This promotes the assembly of division-competent Z-rings. The absence of SepH results in failure to efficiently complete cell division, thus making the SepH-FtsZ interaction a promising target for actinobacteria-specific antibiotics. Importantly, the protein-protein interaction under investigation is conserved in medical and industrially important bacteria, including the TB-causing Mycobacteria. The understanding gained from this project will provide new insights into protein-protein interactions essential for bacterial cell division and novel experimental approaches on how to inhibit these, using rationally designed peptides with antimicrobial activity. Identified compounds capable of controlling the protein interaction would be marketable and allow for patentable technology. |
| Collaborator Contribution | The Beekman group is based at the University of East Anglia (School of Pharmacy). Dr Andrew Beekman is an experienced medicinal chemist and expert in protein-protein interaction modulation. His group will design, synthesise and evaluate molecules capable of inhibiting the SepH/FtsZ protein interaction in vitro. |
| Impact | - Successful application for a joint DTP studentship (start date 10/2023), Beekman (primary supervisor)/Schlimpert (secondary supervisor) |
| Start Year | 2023 |
| Description | Isomerase PPIase inhibitors |
| Organisation | Isomerase Therapeutics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Study of putative virulence factors in Gram-negative bacteria. Molecular genetics and in vitro & in vivo bioassays. |
| Collaborator Contribution | Provision of proprietary inhibitor molecules. |
| Impact | None so far |
| Start Year | 2017 |
| Description | Janez Ilas |
| Organisation | University of Ljubljana |
| Country | Slovenia |
| Sector | Academic/University |
| PI Contribution | Assessing novel compounds synthesised by Ilas' team |
| Collaborator Contribution | Synthesis of model compounds; computational design |
| Impact | Paper published: 1. Z. Skok et al., Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS medicinal chemistry letters 11, 2433-2440 (2020). Multi-disciplinary: biochemistry, structural biology, medicinal chemistry |
| Start Year | 2019 |
| Description | Josh Mylne |
| Organisation | University of Western Australia |
| Department | School of Molecular Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We assayed compounds provided by UWA against Arabidopsis gyrase |
| Collaborator Contribution | UWA synthesised new quinolone compounds and tested them in planta |
| Impact | 2 papers: 1. K. M. Evans-Roberts et al., DNA Gyrase Is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem 291, 3136-3144 (2016). 2. M. D. Wallace et al., Developing ciprofloxacin analogues against plant DNA gyrase: a novel herbicide mode of action. Chem Commun (Camb) 54, 1869-1872 (2018). Multidisciplinary: biochemistry, plant biology, chemistry |
| Start Year | 2017 |
| Description | Leake |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provision of materials and expertise |
| Collaborator Contribution | They are carrying out high-resolution microscopy experiments using material generated in my lab. |
| Impact | One published paper |
| Start Year | 2017 |
| Description | Lindsay |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been analysing the gut microbiome of Galleria mellonella as a surrogate for the human infant gut microbiome. |
| Collaborator Contribution | Provision of human infant fecal samples and bacteria. Assistance with sequencing. |
| Impact | Paper published: 1. H. C. C. Gooch et al., Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella. International journal of systematic and evolutionary microbiology 71 (2021). |
| Start Year | 2017 |
| Description | Luis Aragon |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been assessing novel nybomycin analogues made by the ICL team |
| Collaborator Contribution | They are using synthetic chemistry to make new analogues of the drug nybomycin |
| Impact | No |
| Start Year | 2019 |
| Description | Macquarie University collaboration |
| Organisation | Macquarie University |
| Department | Department of Chemistry and Biomolecular Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Biosynthetic chemistry and molecular microbiology |
| Collaborator Contribution | Natural products chemistry, structural chemistry |
| Impact | Manuscript in preparation |
| Start Year | 2019 |
| Description | Mark Leake |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Making proteins with fluorescent tags |
| Collaborator Contribution | High-resolution microscopy of bacteria |
| Impact | One paper so far: 1. Stracy, M., Wollman, A.J.M., Kaja, E., Gapinski, J., Lee, J.E., Leek, V.A., McKie, S.J., Mitchenall, L.A., Maxwell, A., Sherratt, D.J. et al. (2019) Single-molecule imaging of DNA gyrase activity in living Escherichia coli. Nucleic Acids Res, 47, 210-220. Multi-disciplinary: Maxwell - biochemistry; Leake - physics |
| Start Year | 2017 |
| Description | Matt Piggott |
| Organisation | University of Perth |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Assessing activity of compounds made by collaborator |
| Collaborator Contribution | Drug synthesis |
| Impact | Not yet |
| Start Year | 2016 |
| Description | Nagaraja |
| Organisation | Indian Institute of Science Bangalore |
| Country | India |
| Sector | Academic/University |
| PI Contribution | Collaborative experiments and provision of materials. Detailed discussions on projects |
| Collaborator Contribution | Collaborative experiments and provision of materials. Detailed discussions on projects |
| Impact | Several research papers: 1. M. Chatterji, S. Unniram, A. Maxwell, V. Nagaraja, The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J. Biol. Chem. 275, 22888-22894 (2000). 2. M. Chatterji, S. Unniraman, A. Maxwell, V. Nagaraja, The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J Biol Chem 275, 22888-22894 (2000). 3. U. H. Manjunatha, A. Maxwell, V. Nagaraja, A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism. Nucleic Acids Res 33, 3085-3094 (2005). 4. U. H. Manjunatha, A. Maxwell, V. Nagaraja, A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism. Nucleic Acids Res 33, 3085-3094 (2005). 5. G. Mori et al., The EU approved antimalarial pyronaridine shows antitubercular activity and synergy with rifampicin, targeting RNA polymerase. Tuberculosis 112, 98-109 (2018). 6. V. Nagaraja, A. A. Godbole, S. R. Henderson, A. Maxwell, DNA topoisomerase I and DNA gyrase as targets for TB therapy. Drug Discov Today 22, 510-518 (2017). 7. A. Sipos et al., Lead selection and characterization of antitubercular compounds using the Nested Chemical Library. Tuberculosis 95 Suppl 1, S200-206 (2015). |
| Description | Neuman |
| Organisation | National Institutes of Health (NIH) |
| Country | United States |
| Sector | Public |
| PI Contribution | We have carried out ensemble biochemical experiments on M mazei topo VI, and provided materials to the NIH team |
| Collaborator Contribution | They have been carrying out single-molecule experiments with M mazei topo VI |
| Impact | 4 paper published: 1. S. J. McKie et al., Topoisomerase VI is a chirally-selective, preferential DNA decatenase. eLife 11 (2022). 2. S. J. McKie, A. Maxwell, K. C. Neuman, Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques. Genes (Basel) 11 (2020). 3. S. J. McKie, K. C. Neuman, A. Maxwell, DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 43, e2000286 (2021). 4. S. L. Pitts et al., Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV. Nucleic Acids Res 39, 4808-4817 (2011). Multidisciplinary: biochemistry, single-molecule techniques |
| Start Year | 2016 |
| Description | Nodwell |
| Organisation | University of Toronto |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | We have performed assays using novel compounds provided by the Canadian team. |
| Collaborator Contribution | They have screened for an characterised novel inhibitors of gyrase |
| Impact | Paper published: 1. S. McAuley et al., Discovery of a Novel DNA Gyrase-Targeting Antibiotic through the Chemical Perturbation of Streptomyces venezuelae Sporulation. Cell chemical biology 26, 1274-1282 e1274 (2019). |
| Start Year | 2018 |
| Description | Pyne |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have provided DNA minicircles for analysis |
| Collaborator Contribution | She has been analysing DNA sample using atomic force microscopy. |
| Impact | Paper published: 1. A. L. B. Pyne et al., Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature communications 12, 1053 (2021). Multidisciplinary: biochemistry, AFM |
| Start Year | 2015 |
| Description | Sarah Harris |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been designing and making small DNA circle substrates |
| Collaborator Contribution | Sarah's group have carried out atomistic simulations |
| Impact | 3 published papers so far: 1. A. D. Bates, A. Noy, M. M. Piperakis, S. A. Harris, A. Maxwell, Small DNA circles as probes of DNA topology. Biochem Soc Trans 41, 565-570 (2013). 2. A. Noy, A. Maxwell, S. A. Harris, Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA. Biophys J 112, 523-531 (2017). 3. A. L. B. Pyne et al., Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature communications 12, 1053 (2021). Multidisciplinary: Maxwell - biochemistry; Harris - simulations |
| Start Year | 2011 |
| Description | Understanding patterns of floral trait evolution in Mimulus section Diplacus |
| Organisation | Binghamton University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have collected floral scent and pigment samples from all but one species of Mimulus section Diplacus as well as F1 crosses to understand how floral traits are related to factors such as pollination system, population range, phylogenetic relatedness, and also to understand the basics of their heritability. |
| Collaborator Contribution | Provision of seed stocks and living plant material for collections. |
| Impact | no outputs yet |
| Start Year | 2022 |
| Description | University of León Collaboration |
| Organisation | Fundacion MEDINA |
| Country | Spain |
| Sector | Charity/Non Profit |
| PI Contribution | This collaboration was started to identify the natural products that were responsible for antifungal activity in Streptomyces clavuligerus following introduction of a regulatory gene into this strain. We also mapped the global changes to metabolism in this strain too using LC-MS. This led to the identification of a wide variety of tunicamycins, where a few specific versions of this molecule exhibited antifungal activity. We helped write the resulting research paper. |
| Collaborator Contribution | The partners led this research project, where they genetically manipulated Streptomyces clavuligerus and assessed changes to gene expression using microarrays. They also assessed the changes in production of other natural products known to be produced by Streptomyces clavuligerus , including the beta-lactam antibiotic cephamycin and the beta-lactamase inhibitor clavulanic acid. They led the writing of the research paper. |
| Impact | A paper was published in Frontiers in Microbiology that reports this work: https://www.frontiersin.org/articles/10.3389/fmicb.2019.00580/abstract |
| Start Year | 2016 |
| Description | University of León Collaboration |
| Organisation | University of Leon |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | This collaboration was started to identify the natural products that were responsible for antifungal activity in Streptomyces clavuligerus following introduction of a regulatory gene into this strain. We also mapped the global changes to metabolism in this strain too using LC-MS. This led to the identification of a wide variety of tunicamycins, where a few specific versions of this molecule exhibited antifungal activity. We helped write the resulting research paper. |
| Collaborator Contribution | The partners led this research project, where they genetically manipulated Streptomyces clavuligerus and assessed changes to gene expression using microarrays. They also assessed the changes in production of other natural products known to be produced by Streptomyces clavuligerus , including the beta-lactam antibiotic cephamycin and the beta-lactamase inhibitor clavulanic acid. They led the writing of the research paper. |
| Impact | A paper was published in Frontiers in Microbiology that reports this work: https://www.frontiersin.org/articles/10.3389/fmicb.2019.00580/abstract |
| Start Year | 2016 |
| Description | VCS Potatoes |
| Organisation | VCS Potatoes |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This is a collaboration to identify Pseudomonas strains that can control potato pathogens. Working with the group of Dr Jake Malone (JIC), we have carried out all scientific aspects of this project, including sampling and genome sequencing of isolated strains, as well as phenotyping, genetics and natural product analysis of these strains. |
| Collaborator Contribution | VCS Potatoes have provided sites for sampling and field trials. Their input also includes technical expertise relating to potato disease and field trials. |
| Impact | Publication: Pacheco-Moreno, A., Stefanato, F. L., Ford, J. J., Trippel, C., Uszkoreit, S., Ferrafiat, L., Grenga, L., Dickens, R., Kelly, N., Kingdon, A. D., Ambrosetti, L., Nepogodiev, S. A., Findlay, K. C., Cheema, J., Trick, M., Chandra, G., Tomalin, G., Malone, J. G. & Truman, A. W. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 10, e71900 (2021). (originally available as a pre-print at bioRxiv: https://doi.org/10.1101/783258). Multidisciplinary: chemistry, informatics, microbiology, agriculture, plant trials, genetics |
| Start Year | 2015 |
| Company Name | Pfbio |
| Description | Pfbio develops biological alternatives to agrochemicals for use in crop farming. |
| Year Established | 2022 |
| Impact | Funding has been obtained from a variety of sources, as well as multiple interactions with companies across agriculture and agritech. Work is already ongoing with a UK plant science research company. |
| Website | http://pfbio.co.uk |
| Description | 2020 Virtual Summer School on Applied Molecular Microbiology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I was on the organising committee for this summer school. This is usually held in person every two years but was held virtually in 2020 due to the pandemic. Along with helping organise this event, I provided a seminar and led multiple small group discussions. This was attended by 40 postgraduate and post-doctoral researchers from around the world to learn about concepts and methods in natural product biosynthesis. Following the summer school, I have been contacted by multiple attendees regarding various aspects of the work I discussed. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/2020-applied-mo... |
| Description | Blog post to explain recent scientific publication to general public |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog post to describe the findings of recent research paper to the wider public. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.jic.ac.uk/news/self-poisoning-for-self-preservation-the-function-of-streptomyces-nano-sy... |
| Description | Chair and Organiser for RSC Directing Biosynthesis V Conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Chaired the organising committee and conference. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.rsc.org/events/detail/22912/Directing%20Biosynthesis%20V |
| Description | Dubrovnik Summer School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I provided a seminar and led multiple small group discussions as part of the Dubrovnik Summer School in Applied Molecular Microbiology. This was attended by 45 postgraduate and post-doctoral researchers from around the world to learn about concepts and methods in natural product biosynthesis. Following the summer school, I have been contacted by multiple attendees regarding various aspects of the work I discussed. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/ |
| Description | Field Perspectives blog article |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A blog article on disability inclusion in fieldwork was published by Field Perspectives, a postdoc-led project funded by the Max Planck Institute of Animal Behavior, and the Centre for the Advanced Study of Collective Behaviour at the University of Konstanz, Germany. |
| Year(s) Of Engagement Activity | 2022 |
| URL | http://fieldperspectives.org/KelseyByers.html |
| Description | ITV news |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview on ITV Anglia news |
| Year(s) Of Engagement Activity | 2023 |
| Description | International Research Alliance for Antibiotic Discovery and Development (IRAADD) Workshop Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attendance and presentation as part of the International Research Alliance for Antibiotic Discovery and Development (IRAADD) Workshop Meeting (Saarbruecken, Germany), which is a Europe-wide network of researchers and industry partners involved in antibiotic discovery and development. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Interview with BBC Radio Five Live for a podcast |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview with BBC Radio Five Live for a podcast relating to the science of weather. In particular, the smell and role of bacterial metabolites. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Interview with science writer (Kat Arney) about antibiotic discovery and combating antimicrobial resistance. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview with science writer (Kat Arney) about antibiotic discovery and combating antimicrobial resistance. In particular a focus on the re-purposing of old antibiotics for treating multi-drug resistant infections. This was in relation to an in-depth article she is preparing on AMR and antibiotic discovery, which was later published in the Daily Mail. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.dailymail.co.uk/health/article-5623417/Could-antibiotics-mens-beards-soil-weapons-battle... |
| Description | Invited lecture, University of Bristol International Day of Persons with Disabilities |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited to give a public lecture for the University of Bristol's International Day of Persons with Disabilities covering research and disability inclusion both . Approximately 30 postgraduate and undergraduate students and faculty attended. Attendees asked many questions and attitudes about disability changed in a positive manner. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited talk at China-UK AMR Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A UKRI-funded workshop held in Beijing to discuss ongoing and recent UK-China research projects on AMR (antimicrobial resistance), as well as future directions and prospects for this research area. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk at Environmental Genomics and Advanced Microbiological Techniques Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Presented a talk about using mass spectrometry-based metabolomics in microbiology to PhD students attending an Environmental Genomics and Advanced Microbiological Techniques Workshop at the University of East Anglia. I received multiple questions after the seminar. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk at Plant-Microbe Interactions Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar provided on Streptomyces-Pseudomonas interactions at a Plant-Microbe Interactions Workshop organised at the John Innes Centre. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk at the University of Leeds |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk for the seminar series in the School of Molecular and Cellular Biology, University of Leeds. Participation in a discussion about my research with a group of MSc students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited talk for Field Inclusive Week |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Approximately 75 attendees (mostly graduate students, faculty, and undergraduate students, but also the general public) attended a talk on inclusive practices in biological fieldwork, particularly aimed at inclusion of researchers with disabilities. Approximately 10 persons reached out afterwards for more information or to continue discussions. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.fieldinclusive.org/past-events/ |
| Description | JIC 50 Open Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Outreach stand for Department of Molecular Microbiology as part of an Open Day in relation to the 50th anniversary of the John Innes Centre in Norwich. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.jic.ac.uk/news-and-events/blog-copy/2017/09/open-day/ |
| Description | John Innes/Rudjer Boškovic Summer School in Applied Molecular Microbiology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I was a co-director of the John Innes/Rudjer Boškovic Summer School in Applied Molecular Microbiology. This is a longstanding workshop targetted at early-career researchers in the field of natural product biosynthesis. 45 students/post-docs are selected from a global application list, who then attend an 8-day course in Dubrovnik (10th and 17th September 2022). The attendees came from 21 different countries. Following the summer school, multiple faculty have been contacted by attendees for advice on projects and collaborations. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/2022-applied-mo... |
| Description | London International Youth Forum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | • Aug 2017 - lecture to students visiting as part of London International Youth Science Form: 'Where will the new antibiotics come from?' |
| Year(s) Of Engagement Activity | 2017 |
| Description | Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | My group participated at The Norwich Science Festival which is regularly occurring local event to showcase and celebrate the scientific research associated with the city. This event is aimed to educate and inspire local public community about the science conducted at the John Innes Centre. Specifically, my group manned a stand themed "Streptomyces: Nature's Doctor. Bringing Microbes into View" to educate the public about Streptomyces bacteria for the production of molecules that are of medical and industrial importance. We combined this more applied aspect with how bacteria and other small organisms can be visualised and studied using light microscopy - a technique that is central to our research program. For this we provided different "microscopes" for the public to use and explore ranging from simple magnifying glasses to a microscope made of LEGO to a more sophisticated microscope that can also be found in the laboratory. The audience was encouraged to inspect Streptomyces bacteria using the different magnification devices. This was particular popular among children. In addition, we provided information material about how Streptomyces bacteria grow and why they are important antibiotic producers. We also had coloring in sheets for children depicting the different stages in the Streptomyces life cycle to educate them about how bacteria grow and how this is connected to what they could see under the microscope. We received a lot of questions from the public about antibiotic resistance and how the work in our lab contributes to finding better antibiotics, clearly showing an overall public interest of the public in these topics. We had about 100 people visiting our stand and we plan to organise similar events in the future. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Observer article |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Article in Observer newspaper |
| Year(s) Of Engagement Activity | 2023 |
| Description | Oral presentation at Directing Biosynthesis VI (Edinburgh, UK) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation provided at Directing Biosynthesis VI, an international meeting focussed on the biosynthesis of natural products. Received some follow up enquiries about the research presented following the talk. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral presentation at EMBO "Bacterial Morphogenesis, Survival and Virulence" Workshop, Goa/India |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation provided at EMBO Workshop, an international meeting focussed on Bacterial Morphogenesis, Survival and Virulence. Received some follow up enquiries about the research presented following the talk. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Oral presentation at the 19th ISBA meeting, Toronto/Canada |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation provided at 19th ISBA meeting, an international meeting focussed on the biology of Actinomycetes. Received some follow up enquiries about the research presented following the talk. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral presentation at the Gordon Research Conference, New Hampshire University/USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation provided at the Gordan Research Conference, an international meeting focussed on bacterial cell biology and development . Received some follow-up enquiries about the research presented following the talk. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation at Science for Innovation Showcase Event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Provided presentation entitled "Discovery and biosynthesis of bacterial peptides with antibacterial and anticancer activities" to an audience of industry and research council representatives invited to the John Innes Centre. Participated in a follow-up panel discussion. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation to Bayer Agronomy team |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation and discussion with the agronomy team at Bayer about biocontrol products |
| Year(s) Of Engagement Activity | 2019 |
| Description | Radio 4 interview and associated press release |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | An interview with Radio 4 Farming Today associated with the publication of our research in eLife (paper details here: https://elifesciences.org/articles/71900) on the suppression of potato pathogens. This research is a collaboration with the Malone group (JIC). The interview and associated media (press releases, LinkedIn, Twitter etc) has resulted in contact from numerous agricultural organisations, as well as students/postdocs interested in working in our research teams. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.jic.ac.uk/news/smart-soil-bugs-offer-farmers-an-ecofriendly-route-to-controlling-crop-di... |
| Description | SAW TRUST Visit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | • Collaborated with a team of scientists, an artist and a writer to plan and deliver a day's learning for a class of 30 pupils • During the morning, the pupils took part in a range of activities designed to inspire them and teach them about bacteria and the antibiotics they produce. • Activities included "Super Soil" (isolating bacteria from soil samples), "Colourful Chromatography" (Separating pigments from sweets), "Magnificent Microscopes" (Understanding magnification and using microscopes on a range of samples and materials), "Beautiful Bacteria" (Looking at bacteria under the microscope and on plates) and "Amazing Ants" (Observing leaf-cutter ants and learning about the antibiotic producing actinomycetes that cover them) • We designed a class lab-book for pupils to complete during each activity and stickers for them to collect • During the writing and art lessons (inspired by the scientific imagery and language), we actively assisted pupils 1:1 as they worked |
| Year(s) Of Engagement Activity | 2022 |
| Description | SAW Trust activity at a School (Thetford) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | A one-day outreach activity organised by Edward Hems (Wilkinson group, JIC) with the SAW Trust, which combines Science, Art and Writing. The day focussed on bacteria and the molecules they make. Two members of the research group participated, where they ran an activity based around "Beautiful Bacteria" - looking at the colours, smells and shapes of bacteria. |
| Year(s) Of Engagement Activity | 2023 |
| Description | School Science week presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Gave a one hour talk on the role that microbes and insects play in the carbon cycle and bioremediation. |
| Year(s) Of Engagement Activity | 2018 |
| Description | School Science week presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | School science week - gave one hour presentations on the role of microbes in bioremediation |
| Year(s) Of Engagement Activity | 2019 |
| Description | School visit (Cambourne Cambs) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Deliver a Science, Arts and Writing workshop event on the topic 'Antibiotics: what they are and where they come from'. Delivered a one day event, to two Year 6 classes (one each day). The event generated significant discussion, and involved hands on learning. |
| Year(s) Of Engagement Activity | 2020,2022,2023 |
| URL | http://sawtrust.org/buy-the-books/saw-antibiotics/ |
| Description | School visit (Cambourne Cambs) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Spent two days presenting a cross curriculum presentation to two classes of Year 6 pupils at a primary school in collaboration with the SAW Trust (http://sawtrust.org/ ). Much debate and discussion about the topics of microbes, antibiotics, ecology and antimicrobial resistance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://sawtrust.org/buy-the-books/saw-antibiotics/ |
| Description | School visit (Cambourne Cambs) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Deliver a Science, Arts and Writing workshop event on the topic 'Antibiotics: what they are and where they come from'. Delivered a one day event, to two Year 6 classes (one each day). The event generated significant discussion, and involved hands on learning. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://sawtrust.org/buy-the-books/saw-antibiotics/ |
| Description | Science Museum Superbugs Late Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | "Antibiotic Hunters" exhibit at a Science Museum Superbug Late Event. This was an adult-only event held in the evening at the Science Museum in London and attended by thousands of people. The exhibit was organised jointly between members of my research group and members of the Wilkinson group (also at JIC). |
| Year(s) Of Engagement Activity | 2018 |
| Description | Tri-Society Diversity Symposium on disability in fieldwork |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Approximately 50 faculty, postdoctoral scholars, postgraduate students, and undergraduates attended a talk on disability in fieldwork at the annual Evolution meeting. Attendees left with an increased understanding of best practices in inclusion in fieldwork. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Tri-Society Diversity Symposium panel |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Approximately 50 persons (faculty, postdocs, postgraduate and undergraduate students) attended an expert panel on inclusion in biological fieldwork. Audience members asked questions related to earlier talks as well as more general questions and left with a more broad understanding of the challenges faced by underrepresented minorities during fieldwork as well as best practices for inclusion. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Year 10 Science Camp Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | A talk on natural product discovery to attendees of the year 10 Science Camp at the John Innes Centre. This was followed by questions on antibiotic and anticancer compound discovery. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.jic.ac.uk/training-careers/work-experience/year-10-science-camp/ |