Lachnoclostridium phytofermentans
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PROVIDER: PRJNA229109 | ENA |
REPOSITORIES: ENA
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Project description:The complexity of the plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by C. phytofermentans and identify molecular mechanisms that may overcome these limitations. Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end 100bp paired end reads were generated per population resulting in ~300 fold coverage of each site in the genome. A mixture of alleles fixed in the population down to frequencies of 5% could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Protein structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane proteins and the ATPase binding protein. Experimental evolution was effective in identifying molecular constraints on the rate of cellulose and hemicellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates. Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose. Microarray analysis was performed on 1 time point from the evolved lines and the initial founder
2013-11-20 | E-GEOD-52494 | biostudies-arrayexpress
Project description:Clostridium phytofermentans overview
| PRJNA35843 | ENA
Project description:The complexity of the plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by C. phytofermentans and identify molecular mechanisms that may overcome these limitations. Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end 100bp paired end reads were generated per population resulting in ~300 fold coverage of each site in the genome. A mixture of alleles fixed in the population down to frequencies of 5% could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Protein structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane proteins and the ATPase binding protein. Experimental evolution was effective in identifying molecular constraints on the rate of cellulose and hemicellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.
2013-11-20 | GSE52494 | GEO
Project description:Polyhedral microcompartments in Clostridium phytofermentans
| PRJNA109487 | ENA
Project description:Clostridium phytofermentans ferments all major component of the plant cell wall to alcohols and is an emerging model organism for understanding the direct conversion of plant biomass into biofuels. Encoded in the genome of C. phytofermentans are three large genetic loci for the production of polyhedral microcompartments (PMCs) that may function as metabolic centers for the dissimilation of plant cell wall components into primary alcohols. We demonstrate that the PMC encoded by one of these loci acts in the fermentation of fucose and rhamnose to propanol and propionate. The PMC contains a propanediol dehydratase that is part of a new superfamily of enzymes that utilizes S-adenosylmethionine in place of adenosylcobalamin to catalyze radical reactions. Analysis of the C. phytofermentans genome sequence data indicated that the fucose and rhamnose pathways might converge at the point of the enzymes encoded by the PMC loci. When C. phytofermentans is grown on fucose, a 100-200 nm polyhedral body is apparent in electron micrographs, and ethanol and propanol are produced. Microarray experiments revealed that during growth on fucose, three fucose-related operons coding for (i) the PMC shell and metabolic proteins, (ii) cytoplasmic fucose dissimilatory enzymes, and (iii) an ABC transporter system become the dominant transcripts in the cell. Similarly when C. phytofermentans is grown on rhamnose, three rhamnose-related operons coding for (i) the PMC shell and metabolic proteins, (ii) cytoplasmic rhamnose dissimilatory enzymes, and (iii) an ABC transporter system become the dominant transcripts in the cell. Quite surprisingly, growth on fucose or rhamnose also led to the expression of a broader plant degradative transcriptional response. The expression of cellulose degrading enzymes on fucose and rhamnose is a fundamental difference between C. phytofermentans and its closest relatives, the human gut commensals.
2011-09-01 | GSE13194 | GEO
Project description:Pathways involved in plant decomposition in Clostridium phytofermentans
| PRJNA229108 | ENA
Project description:Clostridium phytofermentans KNHs219
| PRJNA262382 | ENA
Project description:Clostridium phytofermentans ISDg, Cphy_SMC3100 genome sequencing
| PRJNA337250 | ENA
Project description:Clostridium phytofermentans ISDg, Cphy_SGX1100 genome sequencing
| PRJNA337242 | ENA
Project description:Clostridium phytofermentans ISDg, Cphy_SGX3100 genome sequencing
| PRJNA337244 | ENA