Enhancing the yield of industrial Actinomycete fermentations
Lead Research Organisation:
University of Strathclyde
Department Name: Inst of Pharmacy and Biomedical Sci
Abstract
A new and radical approach to strain construction is needed for the UK to remain competitive in manufacturing off-patent antibiotics. Antibiotic fermentation processes balance nutrients and cell growth rate with the chemical and physical environments. Cellular output is traditionally improved by selecting higher-producing mutants and optimising fermentation media. However, many antibiotics are unstable in the extracellular environment, with well characterised relationships between pH and degradation rate. The pH range for operation of the biological system often conflicts with the optimum for chemical stability of the product. For an established commercial process we propose to utilise recent advances in synthetic biology and genomics to develop a bacterial strain and industrial fermentation process capable of operating at a lower pH, facilitating stability of the desired product.
Technical Summary
A new and radical approach to strain construction is needed for the UK to remain competitive in manufacturing off-patent antibiotics. Antibiotic fermentation processes balance nutrients and cell growth rate with the chemical and physical environments. Cellular output is traditionally improved by selecting higher-producing mutants and optimising fermentation media. However, many antibiotics are unstable in the extracellular environment, with well characterised relationships between pH and degradation rate. The pH range for operation of the biological system often conflicts with the optimum for chemical stability of the product. For an established commercial process we propose to utilise recent advances in synthetic biology and genomics to develop a bacterial strain and industrial fermentation process capable of operating at a lower pH, facilitating stability of the desired product.
Planned Impact
As described in proposal submitted to IUK
People |
ORCID iD |
| Paul Hoskisson (Principal Investigator) | |
| Iain Hunter (Co-Investigator) |
Publications
Chevrette MG
(2020)
Evolutionary dynamics of natural product biosynthesis in bacteria.
in Natural product reports
Feeney MA
(2022)
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.
in Microbial genomics
Fernández-MartÃnez LT
(2019)
Expanding, integrating, sensing and responding: the role of primary metabolism in specialised metabolite production.
in Current opinion in microbiology
Hoskisson P
(2018)
Regulation of specialised metabolites in Actinobacteria - expanding the paradigms
in Environmental Microbiology Reports
Schniete J
(2020)
ActDES - a Curated Actinobacterial Database for Evolutionary Studies
Schniete JK
(2021)
ActDES - a curated Actinobacterial Database for Evolutionary Studies.
in Microbial genomics
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4081595 |
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/3825855 |
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/3825854 |
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/3830391 |
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | The Actinobacteria are a large diverse phylum of bacteria, often with large genomes with a high G+C content. There is great variation in the sequence quality, equivalence of annotation and phylogenetic representation in the sequence databases meaning that evolutionary and phylogenetic studies may be challenging. To address this, we have assembled a curated, high-level, taxa specific, non-redundant database to aid detailed comparative analysis of Actinobacteria. ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. Data summary All genome sequences used in this study can be found in the NCBI taxonomy browser https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi and are summarised along with Accession numbers in Table S1 1. All other data is available on Figshare. a. Perl script files b. List of genomes from NCBI (Actinobacteria database.xlsx) Table S1 c. CVS genome annotation files including the FASTA files of nucleotide and amino acids sequences (612 individual .cvs files - folder cvs) d. BLAST nucleotide database (.fasta file) e. BLAST protein database (.fasta file) f. Table S2 Expansion table genus level (Expansion table.xlsx Tab Genus level) g. Table S2 Expansion table species level (Expansion table.xlsx Tab species level) h. All data for GlcP and Glk data - blast hits from ActDES database, MUSCLE Alignment files and .nwk tree files |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/ActDES_a_Curated_Actinobacterial_Database_for_Evolutionary_Studies/121... |
| Title | ActDES - a Curated Actinobacterial Database for Evolutionary Studies |
| Description | The Actinobacteria are a large diverse phylum of bacteria, often with large genomes with a high G+C content. There is great variation in the sequence quality, equivalence of annotation and phylogenetic representation in the sequence databases meaning that evolutionary and phylogenetic studies may be challenging. To address this, we have assembled a curated, high-level, taxa specific, non-redundant database to aid detailed comparative analysis of Actinobacteria. ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. Data summary All genome sequences used in this study can be found in the NCBI taxonomy browser https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi and are summarised along with Accession numbers in Table S1 1. All other data is available on Figshare. a. Perl script files b. List of genomes from NCBI (Actinobacteria database.xlsx) Table S1 c. CVS genome annotation files including the FASTA files of nucleotide and amino acids sequences (612 individual .cvs files - folder cvs) d. BLAST nucleotide database (.fasta file) e. BLAST protein database (.fasta file) f. Table S2 Expansion table genus level (Expansion table.xlsx Tab Genus level) g. Table S2 Expansion table species level (Expansion table.xlsx Tab species level) h. All data for GlcP and Glk data - blast hits from ActDES database, MUSCLE Alignment files and .nwk tree files |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/ActDES_a_Curated_Actinobacterial_Database_for_Evolutionary_Studies/121... |
| Title | ActDES- a Curated Actinobacterial Database for Evolutionary Studies |
| Description | Supplementary Material for 'ActDES- a Curated Actinobacterial Database for Evolutionary Studies' as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/ActDES-_a_Curated_Actinobacterial_Database_for_Ev... |
| Title | ActDES- a Curated Actinobacterial Database for Evolutionary Studies |
| Description | Supplementary Material for 'ActDES- a Curated Actinobacterial Database for Evolutionary Studies' as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/ActDES-_a_Curated_Actinobacterial_Database_for_Ev... |