Dataset Information

Quantifying variation within the bacterial species E. coli

ABSTRACT: Escherichia coli strains are widely used in academic and applied research as well as in biotechnology for production of various compounds. Despite its status as a model organism, strain-specific differences and their underlying contributing factors are still not well characterized. These differences have a major impact on cell physiology and for the applied purposes of synthetic biology, metabolic engineering, and process design. In this study, strain-specific differences are quantified in seven widely-used applied biotechnology strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics and genome-scale modelling to guide the choice of strain for a given product. Even given the genetic similarity of the strains, mMetabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titre. Further, these differences can be linked to differential regulatory structure. Analysing high flux reactions and the expression levels of their encoding genes revealed a quantitative link between these sets and show that often, these sets are correlated with strain-specific caveats. Integrated modelling also revealed that certain strains are better suited to produce a given compound or express a desired construct considering native expression states of pathways that enable high-production phenotypes. The result of this study is a resource comparing strains in an important model species and a general strategy for choosing a host strain or chassis selection for applied biotechnology.

OTHER RELATED OMICS DATASETS IN: PRJNA314810PRJNA313438

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. W3110 Escherichia coli C Escherichia coli W Escherichia coli DH5[alpha] Escherichia coli BL21 Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE78756 | GEO | 2016/09/22

SECONDARY ACCESSION(S): PRJNA313438

REPOSITORIES: GEO

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Project description:Archer2011 - Genome-scale metabolic model of Escherichia coli (iCA1273) This model is described in the article: The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY, Nielsen LK. BMC Genomics 2011; 12: 9 Abstract: BACKGROUND: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. RESULTS: We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. CONCLUSIONS: The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models. This model is hosted on BioModels Database and identified by: MODEL1507180010. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:The increasing demand for non-food competitive carbon sources such as methanol for biotechnology has brought methanol-utilizing bacteria, so-called methylotrophs, to focus. The product spectrum of natural methylotrophs and their genetic accessibility is limited and as an alternative approach, the introduction of methylotrophic metabolism into a biotechnologically well-established organism, such as Escherichia coli, represents a promising concept. By performing long-term evolution over 600 days, we obtained an E. coli strain that is able to grow on methanol as its sole carbon source at rates comparable to natural methylotrophic organisms. We confirmed that the strain forms its entire biomass from methanol. Furthermore, we sequenced the genome of the evolved strain and compared it to the genome of its ancestor. Intriguingly, we found several hundreds of mutations targeting genes of various functions, such as catalysis and regulation. Like the comparison of the genome before and after evolution, the investigation of the proteome would be of high interest. Proteomics would reveal the consequences of the regulatory mutations found in the genome and provide an overall picture of the adaptations by the cell enabling it to grow on methanol. The increasing demand for non-food competitive carbon sources such as methanol for biotechnology has brought methanol-utilizing bacteria, so-called methylotrophs, to focus. The product spectrum of natural methylotrophs and their genetic accessibility is limited and as an alternative approach, the introduction of methylotrophic metabolism into a biotechnologically well-established organism, such as Escherichia coli, represents a promising concept. By performing long-term evolution over 600 days, we obtained an E. coli strain that is able to grow on methanol as its sole carbon source at rates comparable to natural methylotrophic organisms. We confirmed that the strain forms its entire biomass from methanol. Furthermore, we sequenced the genome of the evolved strain and compared it to the genome of its ancestor. Intriguingly, we found several hundreds of mutations targeting genes of various functions, such as catalysis and regulation. Like the comparison of the genome before and after evolution, the investigation of the proteome would be of high interest. Proteomics would reveal the consequences of the regulatory mutations found in the genome and provide an overall picture of the adaptations by the cell enabling it to grow on methanol.

Project description:AbuOun2009 - Genome-scale metabolic network of Salmonella typhimurium (iMA945) This model is described in the article: Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. AbuOun M, Suthers PF, Jones GI, Carter BR, Saunders MP, Maranas CD, Woodward MJ, Anjum MF. J. Biol. Chem. 2009 Oct; 284(43): 29480-29488 Abstract: Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations. This model is hosted on BioModels Database and identified by: MODEL1507180009. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Quantifying variation within the bacterial species E. coli

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