Lacrimispora sphenoides phytofermentans ASBs410
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA195881 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR1797200_1.fastq.gz | Fastqsanger.gz | |||
| SRR1797200_2.fastq.gz | Fastqsanger.gz | |||
| SRR1797201_1.fastq.gz | Fastqsanger.gz | |||
| SRR1797201_2.fastq.gz | Fastqsanger.gz |
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Project description:Lacrimispora sphenoides JCM 1415 strain:ATCC 19403 Genome sequencing
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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:Genomic analysis of the model lignocellulosic biomass degrading bacteria C. phytofermentans indicates that it can degrade, transport, and utilize a wide-range of carbohydrates as possible growth substrates. Previous experiments characterized the expression of the degradation and transport machinery using custom whole genome oligonucleotide microarrays. The results indicate that C. phytofermentans utilizes ATP-binding cassette (ABC) transporters for carbohydrate uptake and does not use the sole phosphoenolpyruvate-phosphotransferase system (PTS) for any of the tested substrates. While some ABC transporters are specific for a single carbohydrate, the expression profiles indicate that others may be capable of transporting multiple substrates. Distinct sets of Carbohydrate Active Enzymes (CAZy) genes were also up-regulated on specific substrates indicative of C. phytofermentans ability to selectively degrade plant biomass. We also identified a highly expressed cluster of genes which includes seven extracellular glycoside hydrolases and two ABC transporters with unknown specificity. These results lead to the hypothesis that when grown on plant biomass, C. phytofermentans is capable of degrading and transporting all major carbohydrate components of the plant cell. To test this, C. phytofermentans was grown on cornstover and switchgrass. Results from this expression data and HPLC analysis indicates that C. phytofermentans is utilizing multiple substrates. with multiple sugar ABC transporter clusters and glycoside hydrolases being expressed. Interestingly all of the transporters were initially identified on disaccharides or oligio-saccharides, and none of the transporters identified as monosaccharide specific transporters were expressed. This could be an indication that C. phytofermentans prefers to transport oligiosacchrides over monosaccharides. The results presented here corroborate the genomic data which indicates the breath of the carbohydrate degradation, transport, and utilization machinery of C. phytofermentans.
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