Molecular genetics, chemical biology and industrial applications of microbial natural products
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
Building on JIC’s international reputation in the molecular genetics of actinomycete natural products biosynthesis we will develop new tools & techniques for their discovery and manipulation. Particular areas of expertise include polyketide, non-ribosomal peptide & deoxyhexose pathways, and we aim to identify and delineate new biosynthetic mechanisms and enzymology.
Our approach is two-fold: first to harness known but neglected compounds with potential as anti-infective agents, both anti-proliferative and through the modulation of virulence factors. Secondly, novel compounds have been accessed through our industry contacts and we will expand our interests to identify their molecular targets and mode of action. In all cases we will use bioengineering principles to enable their production for testing and modify their properties to address limitations or enhance properties as required.
Where possible we shall look to target compounds with potential to address diseases that represent emerging public health threats and to these ends will develop our existing collaboration with the Health Protection Agency and the Defence Science and Technology Laboratory. Examples include bacteria such as Legionella, Burkholderia and Mycobacterium tuberculosis, and emerging viruses such as the coronaviruses (e.g. SARS-like coronavirus).
Long term we will expand efforts to incorporate the discovery of natural products which modulate the transcription and translation of key protein targets involved in longevity in model systems. This should be instructive towards understanding the biology of healthy aging as well as the mechanisms of diseases of aging. Natural products have proven fruitful in this arena, e.g. rapamycin & resveratrol. We will build upon an existing collaboration with the Buck Institute of Aging Research in California, and have already identified novel pharmacologic agents that extend the lifespan of model organisms such as yeast and worms
Our approach is two-fold: first to harness known but neglected compounds with potential as anti-infective agents, both anti-proliferative and through the modulation of virulence factors. Secondly, novel compounds have been accessed through our industry contacts and we will expand our interests to identify their molecular targets and mode of action. In all cases we will use bioengineering principles to enable their production for testing and modify their properties to address limitations or enhance properties as required.
Where possible we shall look to target compounds with potential to address diseases that represent emerging public health threats and to these ends will develop our existing collaboration with the Health Protection Agency and the Defence Science and Technology Laboratory. Examples include bacteria such as Legionella, Burkholderia and Mycobacterium tuberculosis, and emerging viruses such as the coronaviruses (e.g. SARS-like coronavirus).
Long term we will expand efforts to incorporate the discovery of natural products which modulate the transcription and translation of key protein targets involved in longevity in model systems. This should be instructive towards understanding the biology of healthy aging as well as the mechanisms of diseases of aging. Natural products have proven fruitful in this arena, e.g. rapamycin & resveratrol. We will build upon an existing collaboration with the Buck Institute of Aging Research in California, and have already identified novel pharmacologic agents that extend the lifespan of model organisms such as yeast and worms
Planned Impact
unavailable
Publications
Aldholmi M
(2020)
Epigenetic modulation of secondary metabolite profiles in Aspergillus calidoustus and Aspergillus westerdijkiae through histone deacetylase (HDAC) inhibition by vorinostat.
in The Journal of antibiotics
Aldholmi M
(2022)
Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis.
in Angewandte Chemie (International ed. in English)
Alt S
(2015)
Biosynthesis of the Novel Macrolide Antibiotic Anthracimycin.
in ACS chemical biology
Batey SFD
(2020)
Chemical warfare between fungus-growing ants and their pathogens.
in Current opinion in chemical biology
Booth TJ
(2020)
Production of novel pladienolide analogues through native expression of a pathway-specific activator.
in Chemical science
Booth TJ
(2016)
Synchronous intramolecular cycloadditions of the polyene macrolactam polyketide heronamide C.
in Chemical communications (Cambridge, England)
Bozhüyük KA
(2019)
Engineering enzymatic assembly lines to produce new antibiotics.
in Current opinion in microbiology
Challis GL
(2016)
Editorial: Biosynthetic assembly lines themed issue.
in Natural product reports
Feeney MA
(2022)
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.
in Microbial genomics
Gomez-Escribano JP
(2021)
Streptomyces venezuelae NRRL B-65442: genome sequence of a model strain used to study morphological differentiation in filamentous actinobacteria.
in Journal of industrial microbiology & biotechnology
| Description | We have identified the biosynthetic gene cluster for the novel macrolide antibiotic anthracimycin and determined how it is made. A paper was published in ACS Chemical Biology on this work. We supported Prof Mark Buttner with work regarding the biosynthesis of the antibiotic simicyclinone which led to a paper in J. Mol. Biol. Further work on the project led to a better understanding of an enzyme involved in this pathway which led to a second paper published in Cell Chemical Biology. I provided input to a community paper regarding standards on reporting of biosynthetic gene clusters that was published in Nature Chemical Biology. We published a paper in Chemical Communications on the biosynthesis of the polyketide heronamides (work done by a PhD student). Collaborating with Prof Matt Hutchings at UEA we have published papers on the discovery of new antibacterial polyketides from an ant derived Streptomyces strain (Chemical Science 2017) and a second paper examining the biosynthetic potential of two families of any symbionts through comparative genomics (Frontiers in Microbiology 2017). 2018 entry:- We have delineated the biosynthetic pathway to the beta-lactone antibiotic obafluorin and identified a new family of transaldolase enzymes with potential for synthetic biology and the manufacture of high value chemicals. This work will be valuable in genome mining efforts to identify new antibiotic encoding gene clusters and for the biological production of analogues of these potentially valuable molecules. This work was published in Nature Communications during 2017. With our industrial collaborators Isomerase Therapeutics and colleagues at the University of Cambridge we discovered and described a new process for Accelerating the Evolution of modular biosynthetic gene clusters and therefore the biosynthetic pathways for making a range of valuable natural products with clinical and industrial importance. This work was published in Nature Communications and then widely reported. In collaboration with Prof Matt Hutchings at UEA we described the role that the conserved two component system mtrAB plays linking the development cycle of Streptomyces species to the production of antibiotic natural products, and then showed how this can be used to activate or upregulate the production of natural products biosynthesis. This led to two papers being published during 2017. 2019 entry:- We have clarified the chemical ecology behind the phenomenon of colony collapse that affects leacutter ant nests when they are infected with the co-evolved pathogen Escovopsis weberi. This process involves a suite of metabolites with antibacterial activity to inhibit growth of the ant mutualist Pseudonocardia, cytotoxic molecules that are likley to affect all members of the symbiosis, and behaviour modifying molecuels which cause teh ants to neglect their primary hygeine. This work was published in Nature Communications in 2018. We have a significant number of projects that are coming to fruition and will produce both publications and collaboration opportunities for the next year. 2020 Entry:- Using an immunity guided approach we identified the molecular target of the unique beta-lactone antibiotic obafluorin. This will aid in efforts to design new and improved analogues of this compound. This was published in ACS Chemical Biology in 2019. By co-expression of an immunity gene and a pathway specific activator, we successfully awakened a silent (or cryptic) biosynthetic gene cluster for a new lanthipeptide antibiotic that we named kyamicin. At the same time we generated a heterologous expression platform that will allow us to diversify the structure of this and other lanthipeptide antibiotic antibiotics. This was published in Applied & Environmental Microbiology in 2020. Our work on antibiotic production (fasamycin and formicamycin) led to the discovery that a third group of structurally distinct compounds - the formicapyridines - are also derived from the same biosynthetic gene cluster. These are minor, shunt metabolites and our work uncovered a non-catalytic function for ABM domain family monooxygenases - we showed that these proteins are important for maintaining the fidelity of the biosynthetic machinery, minimising the production of side (shunt) products and tuning the maximal activity of the biosynthetic enzyme complex. 2022 Entry:- We have worked with international collaborators on the isolation of new plant derived neoclerodane diterpenoids who examined their activity for the glucose-triggered release of insulin from isolated murine pancreatic islets compared with the standard drug tolbutamide, showing that they have potential for the development of new anti-diabetic drugs. With the Hutchings group at JIC we extended our work on defensive microbiomes, and our findings were consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition. We also worked with the Hutchings group to investigate the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome. We showed that given their saprotrophic nature, and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of streptomycetes as biocontrol strains (and the work can be applied to a wider group of organisms in this regard). |
| Exploitation Route | With this knowledge the production titres of anthracimycin might be improved, and strategies for making new analogues may be developed. Further experiments to understand the fine details of anthracimycin have been designed and are underway in our lab. The new antibiotic natural products isolated from an ant derived strain (the formicamycins) may inspire others to investigate new ecological sources for the discovery of antimicrobials and new chemistry. These molecules themselves might be the first step on developing new antibiotics. Our study of Pseudonocardia symbionts suggests that these organism have the potential to produce new antifungal and antibacterial agents - we are actively following this line of enquiry. 2018 entries:- The L-threonine transaldolase that we uncovered during our study of obafluorin biosynthesis may prove a useful tool for the chiral synthesis of valuable alpha-hydroxy-beta-amino acids. We anticipate that the Accelerated Evolution methodology we published will be used widely for the diversification of natural product molecules produced by modular biosynthetic pathway, in particular polyketide natural products. 2019 entry:- Our understanding of the leadcutetr anst system, and in particular the chemical ecology of this system, is likely to inspire similar studies by other groups and might also provide the basis for control measures against the founding of new leafcutter colonies which can be a signficant nuisance in native countries but for which limited solutinos are available. Several of our ongoing studies have uncovered new moleculat targets and modes of action for atural products. This will be useful for others to develop alternative molecules to inhibit or 'drug' these targets and as such could lead to the identification of new classes of antibiotics. 2020 entry:- Our work provides a number of avenues for other researchers to identify, produce and optimise potential antibiotics. |
| Sectors | Agriculture Food and Drink Chemicals Environment Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| URL | https://www.jic.ac.uk/directory/barrie-wilkinson/ |
| Description | Our work on Gram-negative virulence inhibitors led to a successful application for an MRC DART iCase studentship which started in October 2018. This was joint with the SME Isomerase Therapeutics. |
| First Year Of Impact | 2018 |
| Sector | Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | AMR select committee evidence |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| 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 | Anti-infective discovery from competitive ecosystems |
| Amount | £304,886 (GBP) |
| Funding ID | BB/V005723/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2021 |
| End | 05/2022 |
| Description | Norwich Research Park Translational award |
| Amount | £44,984 (GBP) |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2015 |
| End | 01/2016 |
| Description | Regulation, biosynthesis and mode of action of formicamycins, promising new antibiotics with a high barrier to resistance |
| Amount | £445,991 (GBP) |
| Funding ID | BB/S009000/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2022 |
| 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 | Biosynthesis of natural products from an Australian actinomycete strain library |
| Organisation | BioAustralis |
| Country | Australia |
| Sector | Private |
| PI Contribution | Biosynthesis; genome mining; natural products chemistry |
| Collaborator Contribution | Strain and compound provision; data on metabolite profiles; fermentation data |
| Impact | Successful grant applciations |
| Start Year | 2014 |
| 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 | 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 | 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 | Faculty member at Summer School for Applied Molecular Biology |
| 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 | The 2018 Summer Schools in Applied Molecular Microbiology took place at the Inter-University Centre in Dubrovnik, from 8 - 16 September. It was designed to bring together some pf the mos. talented PhD students and postdocs from around the world and engage with them - we aimed to make them aware of the work done and the John Innes Centre, and to evaluate them as potential future leaders in the field and therefore potential postdocs or faculty members. The focus for this meetingwas 'Microbial Specialised Metabolites: From Genome to Molecule' and recognises the recent development of interest in microbial metabolites that has resulted from the sequencing of small molecule-producing microorganisms, coupled with the explosive development of sequencing technology, bioinformatics and chemical analysis. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/ |
| Description | Faculty member, John Innes Centre/Rudjer Boškovic Summer School in Applied Molecular Microbiology on Microbial |
| 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 | The Summer School in Applied Molecular Microbiology usually takes place every two years, over 10 days in September, at the Inter-University Centre in Dubrovnik, Croatia. It is designed to bring together the most talented PhD students and postdocs from around the world and for the chosen Faculty to engage with them - we aim to make them aware of the work done at the John Innes Centre and to evaluate them as potential future leaders in the field, and therefore potential postdocs or faculty members. The focus for this meeting was 'Microbial Specialised Metabolites: From Genome to Molecule' and recognises the recent development of interest in microbial metabolites that has resulted from the sequencing of small molecule-producing microorganisms, coupled with the explosive development of sequencing technology, bioinformatics and chemical analysis. This year the meeting was held on line due to covid19 restrictions. It was delivered as two afternoon sessions a week for 4 weeks, and new innovations were introduced to enable interactions on line. |
| Year(s) Of Engagement Activity | 2020,2022 |
| URL | https://www.jic.ac.uk/training-careers/summer-schools/applied-molecular-microbiology/2020-applied-mo... |
| Description | Primary school science week |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | I talked with two classes of year 3 children about microbes, presenting fun facts on how they are essential to us but also that there are some microbes that can be dangerous. A slide show was used which was supported with props including agar plates of bacteria to view and smell, microscopes and leafcutter ant micro-colonies. |
| Year(s) Of Engagement Activity | 2015 |
| Description | SAW trust year 6 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | In collaboration with the SAW Trust (science, arts and writing) I delivered two days of cross curriculum teaching/engagement with the two classes of year 6 children at my local school. This was really well received and the children were enthusiastic and came away with a much better appreciation of the science and its relevance to their life. Many of the children said they would like to be scientists when they grow up having never thought about it as an option previously. |
| Year(s) Of Engagement Activity | 2014,2015 |
| 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 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 | School science week - gave one hour presentations on the role of microbes in bioremediation |
| Year(s) Of Engagement Activity | 2017 |
| Description | School visit with SAW Trust |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | SAW Trust event at Monkfield Park Primary School in Cambourne Cambridgeshire. Two days of working with Year 6 classes (one each day) on antibiotics and microbes. |
| Year(s) Of Engagement Activity | 2016 |
| Description | U3A lecture |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Presented to a University of the Third Age Science Group in Sevenoaks Kent. Discussed the issues associated with antimicrobial resistance and work on-going in Norwich to address this and identify new ways to discover antibiotics from natural sources. The talk was interactive and generated much discussion and debate. I was asked to see if another Faculty member might be able to talk to them about GM issues. |
| Year(s) Of Engagement Activity | 2015 |