Re-engineering robustness in to industrial antibiotic producing Streptomyces strains
Lead Research Organisation:
University of Strathclyde
Department Name: Inst of Pharmacy and Biomedical Sci
Abstract
Currently around two-thirds of our antibiotics are made by the soil bacterium Streptomyces. Industrial Streptomyces usually undergo several rounds of random mutagenesis to improve their production characteristics becoming highly-adapted to industrial culture conditions. There is a problem, however, highly-adapted strains are less flexible limiting alterations to production processes and the introduction of sustainable feedstocks. This project will identify genes used by the bacteria to adapt to certain feedstocks and develop new, rapid methods to repair genes lost or damaged genes during mutagenesis, maintaining performance and increasing the flexibility of high-producing strains. This is important because the generation of industrial strains is time consuming and labour intensive. Understanding what limits flexibility in high-yielding antibiotic producers and repairing these mutations will make it easier and greener to make future antibiotics and combat antimicrobial resistance.
Organisations
People |
ORCID iD |
| Paul Hoskisson (Principal Investigator) | |
| Iain Hunter (Co-Investigator) |
Publications
Barona-Gómez F
(2023)
On the evolution of natural product biosynthesis.
in Advances in microbial physiology
Bizior A
(2023)
Prokaryotic ammonium transporters: what has three decades of research revealed?
in Microbiology (Reading, England)
Bottura B
(2022)
Intra-Colony Channel Morphology in Escherichia Coli Biofilms is Governed by Nutrient Availability and Substrate Stiffness
in SSRN Electronic Journal
Bottura B
(2024)
Quantifying the fractal complexity of nutrient transport channels in Escherichia coli biofilms under varying cell shape and growth environment.
in Microbiology (Reading, England)
Bruce J
(2022)
Editorial overview: Eco-evolutionary dynamics in microbiology comes of age
in Current Opinion in Microbiology
E McHugh R
(2023)
Optimisation of aurodox production by Streptomyces goldiniensis.
Feeney MA
(2022)
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.
in Microbial genomics
Fernández-Martínez LT
(2024)
Microbial Primer: Bacterial growth kinetics.
in Microbiology (Reading, England)
| Title | Supplementary data for McHugh et al., 2022 - Biosynthesis of aurodox, a Type III secretion system inhibitor from Streptomyces goldiniensis. |
| Description | The global increase in antimicrobial-resistant infections means that there is a need to develop new antimicrobial molecules and strategies to combat the issue. Aurodox is a linear polyketide natural product that is produced by Streptomyces goldiniensis, yet little is known about aurodox biosynthesis or the nature of the biosynthetic gene cluster (BGC) that encodes its production. To gain a deeper understanding of aurodox biosynthesis by S. goldiniensis, the whole genome of the organism was sequenced, revealing the presence of an 87 kb hybrid Polyketide Synthase/Non-Ribosomal Peptide Synthetase (PKS/NRPS) BGC. The aurodox BGC shares significant homology with the kirromycin BGC from S. collinus T? 365; however, the genetic organisation of the BGC differs significantly. The candidate aurodox gene cluster was cloned and expressed in a heterologous host to demonstrate that it was responsible for aurodox biosynthesis and disruption of the primary PKS gene (aurAI) abolished aurodox production. These data support a model whereby the initial core biosynthetic reactions involved in aurodox biosynthesis follow that of kirromycin. Cloning aurM* from S. goldiniensis and expressing this in the kirromycin producer S. collinus T? 365 enabled methylation of the pyridone group, suggesting this is the last step in biosynthesis. This methylation step is also sufficient to confer the unique Type III Secretion System inhibitory properties to aurodox. |
| Type Of Art | Image |
| Year Produced | 2022 |
| URL | https://figshare.com/articles/figure/Supplementary_data_for_McHugh_et_al_2022_-_Biosynthesis_of_auro... |
| Description | We have developed in collaboration with The Game Doctor Limited a game that allows 11-18 year old students and interested parties to simulate the antibiotic discovery process from isolation of bacteria through to chemical analysis - the app is soft launched (march 2nd 2021) but we will be using a stronger social media presence during science week (5-14th March 2021) in the UK to promote the game - it is available as an iPhone/iPad app App: https://apps.apple.com/gb/app/dr-dirt/id1543940322 WebGL version: https://www.drdirt.co.uk |
| First Year Of Impact | 2021 |
| Sector | Education |
| Impact Types | Cultural |
| Title | 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces |
| Description | This file is intended as supplementary information for a forthcoming publication: 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/8223787 |
| Title | 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces |
| Description | This file is intended as supplementary information for a forthcoming publication: 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/8223786 |
| Title | Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386 - ACMI-D-22-00033R1 |
| Description | Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386 Access Microbiology manuscript ACMI-D-22-00033R1 We report the genome sequence of Streptomyces goldiniensis ATCC 21386, a strain which produces the anti-bacterial and anti-virulence polyketide, aurodox. The genome of S. goldiniensis ATCC 21386 was sequenced using a multiplatform hybrid approach, revealing a linear genome of ~10 Mbp with a G+C content of 71 %. The genome sequence revealed 36 putative biosynthetic gene clusters (BGCs), including a large region of 271 Kbp that was rich in biosynthetic capability. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number PRJNA602141. These data represent the FastQ outputs from the Oxford Nanopore sequencing that contributed to the hybrid genome assembly. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Genome_sequence_of_the_aurodox-producing_bacterium_Streptomyce... |
| Title | Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386 - ACMI-D-22-00033R1 |
| Description | Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386 Access Microbiology manuscript ACMI-D-22-00033R1We report the genome sequence of Streptomyces goldiniensis ATCC 21386, a strain which produces the anti-bacterial and anti-virulence polyketide, aurodox. The genome of S. goldiniensis ATCC 21386 was sequenced using a multiplatform hybrid approach, revealing a linear genome of ~10 Mbp with a G+C content of 71 %. The genome sequence revealed 36 putative biosynthetic gene clusters (BGCs), including a large region of 271 Kbp that was rich in biosynthetic capability. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number PRJNA602141.These data represent the FastQ outputs from the Oxford Nanopore sequencing that contributed to the hybrid genome assembly. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Genome_sequence_of_the_aurodox-producing_bacterium_Streptomyce... |
| Title | Sequence and alternative origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002 |
| Description | Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable RK2-derived helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of the helper plasmid pUZ8002, provide details of the sequence relative to the parental RK2 plasmid and a previously published pUZ8002 sequence, providing details on the likely origin and construction of pUZ8002.FilesFig 1 Larcombe et al 2024 pUZ8002 - Snapgene annotated map of the genbank filecircpUZ8002 currated.gbk - Genbank file for the pUZ8002 plasmid |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Sequence_and_alternative_origin_of_the_i_Streptomyces_i_interg... |
| Title | Sequence and alternative origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002 |
| Description | Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable RK2-derived helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of the helper plasmid pUZ8002, provide details of the sequence relative to the parental RK2 plasmid and a previously published pUZ8002 sequence, providing details on the likely origin and construction of pUZ8002.FilesFig 1 Larcombe et al 2024 pUZ8002 - Snapgene annotated map of the genbank filecircpUZ8002 currated.gbk - Genbank file for the pUZ8002 plasmid |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Sequence_and_alternative_origin_of_the_i_Streptomyces_i_interg... |
| Title | Sequence and origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002 |
| Description | Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable RK2-derived helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of the helper plasmid pUZ8002, provide details of the sequence relative to the parental RK2 plasmid and a previously published pUZ8002 sequence, providing details on the likely origin and construction of pUZ8002.FilesFig 1 Larcombe et al 2024 pUZ8002 - Snapgene annotated map of the genbank filecircpUZ8002 curated.gbk - Genbank file for the pUZ8002 plasmidLarcombe_G6V_raw_reads |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Sequence_and_alternative_origin_of_the_i_Streptomyces_i_interg... |
| Title | Sequence and origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002 |
| Description | Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable RK2-derived helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of the helper plasmid pUZ8002, provide details of the sequence relative to the parental RK2 plasmid and a previously published pUZ8002 sequence, providing details on the likely origin and construction of pUZ8002.FilesFig 1 Larcombe et al 2024 pUZ8002 - Snapgene annotated map of the genbank filecircpUZ8002 curated.gbk - Genbank file for the pUZ8002 plasmidLarcombe_G6V_raw_reads |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Sequence_and_alternative_origin_of_the_i_Streptomyces_i_interg... |
| Title | Sequence and origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002 |
| Description | Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable RK2-derived helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of the helper plasmid pUZ8002, provide details of the sequence relative to the parental RK2 plasmid and a previously published pUZ8002 sequence, providing details on the likely origin and construction of pUZ8002.FilesFig 1 Larcombe et al 2024 pUZ8002 - Snapgene annotated map of the genbank filecircpUZ8002 curated.gbk - Genbank file for the pUZ8002 plasmidLarcombe_G6V_raw_reads |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Sequence_and_alternative_origin_of_the_i_Streptomyces_i_interg... |