Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1073563 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27878129_1.fastq.gz | Fastqsanger.gz | |||
| SRR27878129_2.fastq.gz | Fastqsanger.gz | |||
| SRR27878130_1.fastq.gz | Fastqsanger.gz | |||
| SRR27878130_2.fastq.gz | Fastqsanger.gz | |||
| SRR27878131_1.fastq.gz | Fastqsanger.gz |
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Project description:Gut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Individual variation in its composition depends on many factors including dietary factors. We profiled enzymatic activity of fecal microbiota in 63 healthy adult individuals using metaproteomics, and identified Bacteroides and Prevotella –derived microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. One particular profile with many Bacteroides-derived CAZy was identified in one-third of subjects (n=20), and it associated with high abundancy of Bacteroides in most subjects. In other subjects (n=8) with dietary parameters similar to former, microbiota showed intense expression of Prevotella-derived CAZy including exo−beta−(1,4)−xylanase, xylan-1,4−beta−xylosidase, alpha−L−arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with robust representation of Prevotella in gut microbiota, while subjects with intermediate representation of Prevotella showed no CAZy profile. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with robust differences in microbiota composition, the latter with exceptionally high Prevotella abundancy in the gut, are in evidence of individual variation in metabolic adaptation of gut microbiota with an impact on colonizing competence.
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Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization. Growth of Bacteroides thetaiotaomicron in vitro in minimal medium plus different purified complex glycans. Observation of increased gene expression was used to determine genes that are involved in metabolism of each glycan. Two biological replicates each.
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Project description:A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of mostribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates theenzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs hasrevealed a plethora of ways in which dATP inhibits activity by inducing oligomerization andpreventing a productive radical transfer from one subunit to the active site in the other.Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and thebasis for their dATP-dependent inhibition is completely unknown. We present biochemical,biophysical and structural information on the effects of ATP and dATP binding to theanaerobic RNR from Prevotella copri . The enzyme exists in a dimer-tetramer equilibriumbiased towards dimers when two ATP molecules are bound and tetramers when two dATPmolecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully orderedglycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-coneresults in loss of activity and disordering of the GRD. The glycyl radical is formed even in thedATP-bound form, but the substrate does not bind, suggesting that dATP inhibition inanaerobic RNRs acts by disordering of the GRD more than 30 Å away from the dATP molecule,thereby preventing both substrate binding and radical mobilisation. The structures implicatea complex network of activity regulation involving the GRD, the allosteric substratespecificity site and a conserved but previously unseen flap over the active site.
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