Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum
| Autor: | Murray Moo-Young, Michael E. Pyne, Duane A. Chung, C. Perry Chou, Xuejia Liu |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Mitomycin Prophages Biology Polymerase Chain Reaction Genome Article DNA sequencing Metabolic engineering Industrial Microbiology 03 medical and health sciences Microscopy Electron Transmission CRISPR Clustered Regularly Interspaced Short Palindromic Repeats DNA Restriction-Modification Enzymes Organism Prophage Clostridium Genetics Whole genome sequencing Multidisciplinary Whole Genome Sequencing Virion High-Throughput Nucleotide Sequencing Sequence Analysis DNA Metabolic pathway 030104 developmental biology Fermentation Virus Activation Metabolic Networks and Pathways |
| Zdroj: | Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/srep26228 |
| Popis: | Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided. |
| Databáze: | OpenAIRE |
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