Bacteria
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| BJKJ01.dat.gz | Other | |||
| BJKJ01.fasta.gz | Fasta.gz | |||
| BJKJ01.master.dat | Other | |||
| BJKK01.dat.gz | Other |
Items per page: 5 1 - 5 of 57 |
Similar Datasets
Project description:Degradation pathway of Green algal polysaccharide ulvan
| PRJDB6910 | ENA
Project description:The marine Flavobacterium Formosa agariphila KMM 3901T is able to use a broad range of different carbohydrates as growth substrates. This is reflected in the strain’s repertoire of 13 polysaccharide utilization loci (PUL) in total. One PUL – termed as PUL H – is responsible for ulvan degradation, which is a widely distributed, algal-derived polysaccharide. The PUL comprises almost 40 genes, coding for transporters, lyases, glycoside hydrolases or sulfatases, among others. These proteins catalyse the breakdown of ulvan or the uptake of degradation products. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed that corresponding PUL encoded proteins were substrate specific up-regulated in ulvan-cultivated cells. The sulphated polysaccharide ulvan also induced the specific expression of proteins necessary for subsequent monosaccharide degradation. Compared to a control (fructose-cultivated cells), expression of PUL H additionally responded to rhamnose, a basic component of ulvan, indicating that this monosaccharide might signal ulvan availability in the environment. Our proteome analyses proofed a substrate specific expression of proteins involved in ulvan utilization and allowed us to deduce a comprehensive degradation pathway for this complex marine polysaccharide.
2019-07-25 | PXD009299 | Pride
Project description:Seaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics (RNA-seq) and proteomics (LC-MS) approach.
2024-04-03 | GSE252125 | GEO
Project description:Genomic diversity and evolution of algal-polysaccharide degrading marine bacteria
| PRJEB23587 | ENA
Project description:Adaptations of Alteromonas sp. 76-1 to polysaccharide degradation: A CAZyme plasmid for ulvan degradation and two alginolytic systems
| PRJEB28726 | ENA
Project description:Elucidation of quaternary amine degradation pathway in the methanogen Methanolobus vulcani B1d
2019-06-26 | MSV000084013 | MassIVE
Project description:Seaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics and proteomics approach. Feeding piglets with seaweed and enzyme supplementation resulted in reduced macronutrient availability, leading to protein degradation through the proteasome (PSMD2), with resulting amino acids being utilized as an energy source (GOT2, IDH3B). Moreover, mineral element accumulation (iodine and bromine) contributed to increased oxidative stress, evident from elevated levels of antioxidant proteins like catalase, as a response to maintain tissue homeostasis. The upregulation of the gene AQP7, associated with the osmotic stress response, further supports these findings. Consequently, an increase in chaperone activity, including HSP90, was required to repair damaged proteins. Our results suggest that enzymatic supplementation may exacerbate the effects observed from feeding U. lactuca alone, potentially due to side effects arising from cell wall degradation during digestion.
2024-02-27 | PXD043394 | Pride
Project description:A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all the co-cultivated algal cells within a short time. However, the regulation of molecular mechanism is rarely understood. Here, proteomic analysis was applied to investigate the algicidal process of Trametes versicolor F21a. Our results showed that 3,754 fungal proteins were identified, among which 2,809 unique proteins could be quantified during the process. 30 isoenzymes with the capacity of degradation biomass, belonging to Glycoside Hydrolases, Auxiliary Activities, Carbohydrate Esterases and Polysaccharide Lyases, were significantly up-regulated, suggesting that these enzymes probably employed synergistic mechanisms in degrading algal cells. Additionally, peptidase, exonuclease, manganese peroxidase and cytochrome c peroxidase were also up-regulated. 10% of the significantly up-regulated proteins were extracellular enzymes. Gene Ontology (GO) and KEGG pathway enrichment analysis demonstrated that the enriched metabolic pathways mainly contained carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, as well as several amino acid biosynthesis pathways, which implied that these pathways should play vital roles in the synthesis of needed nutrition for the fungal mycelia via components of algal cells. Moreover, the fungal NmrA-like transcriptional regulator which represses the nitrogen metabolite was also enriched and might be a key regulator in eliminating algal cells
2018-04-13 | PXD005568 | Pride
Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide. Simple two-way comparisons between pectin or xylan sources (treatment) and glucose or xylose (control), collected during mid- and late-log phase. Three replicates per condition.
2015-10-28 | E-GEOD-74379 | biostudies-arrayexpress
Project description:We set out to investigate the genetic adaptions of the known marine fungus Paradendryphiella salina CBS112865 to the degradation of brown macro-algae, expecting to find a repertoire of carbohydrate active enzymes highly specialized to the degradation of algal polysaccharides. We performed whole genome, transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina growing on three species of brown algae and under carbon starvation. The genome comparison to close terrestrial fungal relatives, revealed P. salina to have a similar, but reduced carbohydrate active enzyme (CAZyme) profile, except for the presence of three putative alginate lyase 7 genes, most likely acquired via ancient horizontal gene transfer event from a marine bacterium and a polysaccharide lyase 8 gene with similarity to ascomycete chondroitin AC lyases. The proteomic analysis revealed both PL7 and PL8 enzymes to be highly abundant in the algal fermentations together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the base CAZyme repertoire of saprobic and plant pathogenic ascomycetes with the necessary addition of alginate lyases provide the fungi with the enzymatic capabilities to thrive on brown algae polysaccharides and even cope with the algal defense mechanisms.
2019-11-13 | PXD012152 | Pride