Function of a laminin_G_3 module as a carbohydrate‐binding module in an arabinofuranosidase from <i>Ruminiclostridium josui</i>

Sakka, Makiko; Kunitake, Emi; Kimura, Takeshi; Sakka, Kazuo

doi:10.1002/1873-3468.13283

Cited by 14 publications

(9 citation statements)

References 34 publications

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“…Fast evolution of surface-presented proteins is well-known in pathogens and other bacteria to evade host detection systems and viral attachment sites. Giant ORFs from Omnitrophia frequently encode domains used by eukaryotes for cell adhesion 81,82 . For example, ORFs from Multiplicimicrobium inquinatum (Genome 171) and Omnitrophus fodinae (Genome 190) encode discoidin (PF00754) domains and ORFs from M. inquinatum and SAG-3300015153 (Genome 196) encode laminin_G_3 (PF13385) domains (Supplementary Fig.…”

Section: Genomic Data Suggest Predatory or Parasitic Functionsmentioning

confidence: 99%

Omnitrophota encompasses diverse and hyperactive nanobacteria: Potential metabolisms and host-dependent lifestyles

Seymour

Palmer

Becraft

et al. 2022

Preprint

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Candidate bacterial phylum Omnitrophota has never been grown in axenic culture and is poorly understood. Here, we combined analysis of 421 Omnitrophota genomes representing six classes and 276 species and show that they are prevalent in water, sediments, and soils globally. Fluorescence-activated cell sorting and differential size filtration showed ultra-small (~0.2 μm) cells to be common across the phylum. Reduced genomes in all six classes maintained major biosynthetic and energy conservation pathways, particularly the acetogenic Wood-Ljungdahl pathway or diverse aerobic and anaerobic respirations. However, most genomes also encoded multiple systems typical of bacterial predators and intracellular parasites, suggesting possible predatory or parasitic lifestyles. In support of this, quantitative stable-isotope probing revealed three families with high isotope uptake rates comparable to obligate bacterial predators in diverse soils. Based on their ubiquity, small cell size, high metabolic activity, and genomic repertoire, many Omnitrophota are likely to be ecologically important in a wide range of ecosystems, possibly as predators or parasites.

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Section: Genomic Data Suggest Predatory or Parasitic Functionsmentioning

confidence: 99%

Omnitrophota encompasses diverse and hyperactive nanobacteria: Potential metabolisms and host-dependent lifestyles

Seymour

Palmer

Becraft

et al. 2022

Preprint

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“…Such non-CBM substrate binding modules include "laminin_G_3", "FIVAR", "Big_2", etc., and may alter the affinity or activity of GH catabolic domains with respect to local structural motifs. For example, "laminin_G_3" selectively binds with 3 2 -α-l-arabinofuranosyl-xylobiose and 2 3 ,3 3 -di-α-l-arabinofuranosyl-xylotriose [32],…”

Section: Discussionmentioning

confidence: 99%

“…Such non-CBM substrate binding modules include “laminin_G_3”, “FIVAR”, “Big_2”, etc., and may alter the affinity or activity of GH catabolic domains with respect to local structural motifs. For example, “laminin_G_3” selectively binds with 3 2 -α-l-arabinofuranosyl-xylobiose and 2 3 ,3 3 -di-α-l-arabinofuranosyl-xylotriose [32], suggesting a potential hydrolytic target of branched arabinofuranosyl residues on xylooligomers. “FIVAR” domains have been extensively reported along with CAZymes and are thought to have carbohydrate binding functions, but are not yet well-characterized [33–35].…”

Section: Discussionmentioning

confidence: 99%

Subtle Differences in Fine Polysaccharide Structures Govern Selection and Succession of Human Gut Microbiota

Yao

Deemer

Chen

et al. 2022

Preprint

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Dietary fibers are fermented in the human gut and are known to modulate microbiome composition and metabolic function, but few studies have explored to what extent the small variations in complex fiber structures impact community assembly, microbial division of labor, and organismal metabolic responses across individual microbiome structures. To test the hypothesis that subtle linkage variations in chemical structures of polysaccharides afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fermentation with fecal inocula from individual donors and measured microbial responses using an integrated multi-omics approach. We fermented two sorghum arabinoxylans (SAXs) as model complex polysaccharides, with fecal microbiota from three donors and an artificially high diversity mix of all three. Although differences in sugar linkage profiles across SAXs were subtle, surprisingly, consortia fermenting different AXs revealed distinct species-level genomic diversity and metabolic outcomes with nearly-identical strains on each polysaccharide across inocula. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials; however, CAZyme genes enriched in different AX-fermenting consortia were specific to SAX type and displayed various catabolic domain fusions with diverse accessory motifs, suggesting they may be functionally degenerate and this degeneracy may relate to fine substrate structure. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia, which are present amongst unrelated individuals.

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“…MC68GH43-1 contains a GH43 domain and a GH43_C domain, while MC72GH43-2 additionally contains a laminin_G_3 domain. A laminin_G_3 domain was reported to play a role in substrate binding of an arabinofuranosidase from Ruminococcus josui , specifically with a branched arabinofuranosyl residue of an arabino-oligosaccharide [ 50 ]. Regarding the exo-arabinofuranosidases, MC72GH43-1 also displayed a multi-modular structure, being composed of a GH43 module and a module associated with some GH43 modules, GH43_C2 (Pfam designation PF17851, beta-xylosidase C-terminal concanavalin A-like domain).…”

Section: Discussionmentioning

confidence: 99%

Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases

Liu

Angelov

Feiler

et al. 2022

Biotechnol Biofuels

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Background Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited. Results In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-l-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan). Conclusions We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.

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Function of a laminin_G_3 module as a carbohydrate‐binding module in an arabinofuranosidase from Ruminiclostridium josui

Cited by 14 publications

References 34 publications

Omnitrophota encompasses diverse and hyperactive nanobacteria: Potential metabolisms and host-dependent lifestyles

Omnitrophota encompasses diverse and hyperactive nanobacteria: Potential metabolisms and host-dependent lifestyles

Subtle Differences in Fine Polysaccharide Structures Govern Selection and Succession of Human Gut Microbiota

Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases

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