The marine Bacteroidetes Muricauda sp. MAR_2010_75 digests diatom β-mannan
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Muricauda Sp. Mar_2010_75
SUBMITTER: 
Irena Beidler
LAB HEAD: Thomas Schweder
PROVIDER: PXD033586 | Pride | 2022-11-24
REPOSITORIES: Pride
Similar Datasets
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:Bacteroidetes have multiple polysaccharide utilization loci (PUL) which are specific for the decomposition of polysaccharides. The marine Bacteroidetes strain Flavimarina sp. Hel_I_48 encodes two separate PULs which target xylose-containing polysaccharides. We elucidated the specificity of these two PULs by correlating proteome data with biochemical activities of the encoded carbohydrate active enzymes. Proteomics revealed that one PUL targets glucuronoxylans whereas the other PUL targets arabinoxylans.
2023-06-27 | PXD033600 | Pride
Project description:Marine algae convert a substantial fraction of the carbon dioxide they fix into various polysaccharides. Bacteria specialized on the remineralization of these polysaccharides often feature genomic clusters, termed polysaccharide utilization loci (PULs). Such PULs are often prevalent in, but not limited to, marine Flavobacteriia. Since knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia. We obtained 400 PULs, suggesting usage of a large array of polysaccharides, including laminarin, α- and β-mannans, fucose-, xylose-, galactose-, rhamnose- and arabinose-containing substrates, pectins, and chitins. Many of the PULs were novel, some indicating substrates that have rarely been described in marine environments. PUL repertoires of isolates often differed significantly within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD. Respective protein trees revealed clustering according to polysaccharide specificities. Analysis of SusCD expression in multiyear phytoplankton bloom-associated metaproteomes indicated changes in microbial utilization of glucan, ß-mannan and sulfated xylan, suggesting that distinct substrates are temporarily abundant.
2018-08-16 | PXD008238 | Pride
Project description:Proteomes of Bacillus licheniformis DSM13 cultivated with glucose, rhamnose as well as ulvan or two ulvan hydrolysates (UHA and UHB). Hydrolysates were generated using selected Formosa agariphila KM3901 ulvan-PUL encoded enzymes.
2022-11-02 | PXD033411 | 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:Laminarin is a major storage polysaccharide in phytoplankton and an important carbon and energy source for marine microbes. How microbes compete for this labile polysaccharide in nature remains unclear. Here we investigated metaproteomes and metagenomes of bacterioplankton during four consecutive algal blooms in the North Sea to determine key laminarin consumers. We identified two specialized laminarin degraders of the Bacteroidetes group, which reached high abundances year after year. We found that these genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases, sensors and transporters that belonged to the most abundant proteins in the blooms. The respective genes are organized in three polysaccharide utilization loci. Proteomic and biochemical analyses revealed surface tethered enzymes and a laminarinase recombined with a membrane-spanning transporter, which act as a disassembly line and efficiently integrate substrate degradation and uptake in the highly diffusive, aquatic environment. We also show that the bloom bacteria couple laminarin utilization with uptake of cellular building blocks such as amino acids. This study suggests that in addition to genome reduction, enzyme fusions, transporter and enzyme expansion also the tight coupling of the carbon and nitrogen uptake make Formosa spp. efficient laminarin utilizers.
2018-07-31 | PXD007934 | 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.
2015-10-28 | GSE74379 | GEO
Project description:Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria (MHB), using largely uncharacterized mechanisms. In Zobellia galactanivorans, we discovered and characterized the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, providing a model system for carrageenan utilization by MHB. We further demonstrate that carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and several distal genes. The genetic structure of the carrageenan utilization system is well conserved in marine Bacteroidetes, but modified in other MHB phyla. The core system is completed by additional functions which can be assumed by non-orthologous genes in different species. This complex genetic structure is due to multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.
2017-12-06 | GSE101142 | GEO
Project description:About one half of the global, biogenic carbon dioxide fixation into organic matter is driven by microscopic algae in the surface oceans. These microalgal activities generate, among other molecules, polysaccharides that are food for and recycled by bacteria with polysaccharide utilization loci (PULs). These genetic clusters of co-evolved genes, which work together in recognition, depolymerizing and uptake of one type of polysaccharide. However, we rarely know the substrates of PULs present in marine bacteria. Here we investigated the proteomic and physiological response of mannan PULs from marine Flavobacteriia isolated in the North Sea. The genomic clusters of these marine Bacteroidetes are related to PULs of human gut Bacteroides strains, which are known to digest α- and β-mannans from yeasts and plants respectively. Proteomics and defined growth experiments with these types of mannans as sole carbon source confirmed the functional prediction. Our data suggest that biochemical principles established for gut or terrestrial microbes apply to marine bacteria even though the PULs are evolutionary distant. Moreover, our data support discoveries from the 60th reporting mannans in microalgae suggesting that these polysaccharides play an important role in the marine carbon cycle.
2018-10-17 | PXD009066 | Pride
Project description:About one half of the global, biogenic carbon dioxide fixation into organic matter is driven by microscopic algae in the surface oceans. These microalgal activities generate, among other molecules, polysaccharides that are food for and recycled by bacteria with polysaccharide utilization loci (PULs). These genetic clusters of co-evolved genes, which work together in recognition, depolymerizing and uptake of one type of polysaccharide. However, we rarely know the substrates of PULs present in marine bacteria. Here we investigated the proteomic and physiological response of mannan PULs from marine Flavobacteriia isolated in the North Sea. The genomic clusters of these marine Bacteroidetes are related to PULs of human gut Bacteroides strains, which are known to digest α- and β-mannans from yeasts and plants respectively. Proteomics and defined growth experiments with these types of mannans as sole carbon source confirmed the functional prediction. Our data suggest that biochemical principles established for gut or terrestrial microbes apply to marine bacteria even though the PULs are evolutionary distant. Moreover, our data support discoveries from the 60th reporting mannans in microalgae suggesting that these polysaccharides play an important role in the marine carbon cycle.
2018-10-17 | PXD009080 | Pride