Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1103758 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28783700_1.fastq.gz | Fastqsanger.gz | |||
| SRR28783700_2.fastq.gz | Fastqsanger.gz | |||
| SRR28783701_1.fastq.gz | Fastqsanger.gz | |||
| SRR28783701_2.fastq.gz | Fastqsanger.gz | |||
| SRR28783702_1.fastq.gz | Fastqsanger.gz |
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Project description:To effectively use methanol derived from CO2 or methane in E. coli, it is crucial to develop a fast-growing strain that can efficiently process methanol. We successfully developed a methylotrophic E. coli strain, SM6, which has a doubling time of 3.5 hours, surpassing the growth rates of typical native methylotrophs. This was achieved through evolutionary engineering that utilized dynamic copy number variation (CNV). The SM6 strain has demonstrated the ability to overcome the issue of formaldehyde-induced DNA-protein cross-linking (DPC) during its evolution, enabling rapid growth in methanol medium. Proteomics are conducted to understand the underlying metabolism / regulation change for the improved growth phenotype.
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Project description:Methanol, being electron-rich and derivable from methane or CO2, is a potentially renewable one-carbon (C1) feedstock for microorganisms. Although the ribulose monophosphate (RuMP) cycle used by methylotrophs to assimilate methanol differs from the typical sugar metabolism by only three enzymes, turning a non-methylotrophic organism to a synthetic methylotroph that grows to a high cell density has been challenging. Here, we reprogrammed E. coli using metabolic robustness criteria followed by laboratory evolution to establish a strain that can utilize methanol as the sole carbon source efficiently. This synthetic methylotroph alleviated a heretofore uncharacterized hurdle, DNA-protein crosslinking (DPC), by insertion sequence (IS) mediated copy number variations (CNV) and balanced the metabolic flux by mutations. Being capable of growing at a rate comparable to natural methylotrophs in a wide-range of methanol concentrations, this synthetic methylotrophic strain illustrates genome editing and evolution for microbial tropism changes, and expands the scope of biological C1 conversion.
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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.
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