Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

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doi:10.1093/glycob/cwx089

Cited by 149 publications

(66 citation statements)

References 17 publications

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“…Polysaccharide degradation potential of Colwellia echini A3 T . Bioinformatic analyses showed that the genome of C. echini encodes a large number of carbohydrateactive enzymes (CAZymes) (12). In comparisons to phylogenetically related Colwellia species, C. echini A3 T encoded the largest amount of CAZymes (see Table S1A in the supplemental material).…”

Section: Resultsmentioning

confidence: 99%

A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan

Christiansen

Pathiraja

Bech

et al. 2020

mSphere

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Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono-and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium Colwellia echini A3 T is a potent enzyme producer since it completely hydrolyzes agar and -carrageenan. Here, we report that the genome of C. echini A3 T harbors two large gene clusters for the degradation of carrageenan and agar, respectively. Phylogenetical and functional studies combined with transcriptomics and in silico structural modeling revealed that the carrageenolytic cluster encodes furcellaranases, a new class of glycoside hydrolase family 16 (GH16) enzymes that are key enzymes for hydrolysis of furcellaran, a hybrid carrageenan containing both ␤and -carrageenan motifs. We show that furcellaranases degrade furcellaran into neocarratetraose-43-O-monosulfate [DA-(␣1,3)-G4S-(␤1,4)-DA-(␣1,3)-G], and we propose a molecular model of furcellaranases and compare the active site architectures of furcellaranases, -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, C. echini A3 T was shown to encode -carrageenases, -carrageenases, and members of a new class of enzymes, active only on hybrid ␤/-carrageenan tetrasaccharides. On the basis of our genomic, transcriptomic, and functional analyses of the carrageenolytic enzyme repertoire, we propose a new model for how C. echini A3 T degrades complex sulfated marine polysaccharides such as furcellaran, -carrageenan, and -carrageenan. IMPORTANCE Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on -carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of -carrageenan and agar, respectively. As the first, we report on the structure/ function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated ␤/-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 ␤-galactosidases and show that this new class of enzymes is active only on hybrid ␤/-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize ␤/-, -, and -carrageenan.

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Section: Resultsmentioning

confidence: 99%

A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan

Christiansen

Pathiraja

Bech

et al. 2020

mSphere

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“…They have also been found in several PLs and GTs [52]. In addition, CBMs present in proteins without hydrolytic activity are parts of a scaffolding (scaffoldin) subunit that organizes the catalytic subunits into a non-covalent multi-protein complex called a cellulosome [51].…”

Section: Resultsmentioning

confidence: 99%

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Park

Jeong

Kong

2018

IJMS

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Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

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“…All clan GH-A enzymes are predicted to use a canonical Koshland doubledisplacement mechanism employing a covalent glycosyl enzyme intermediate and resulting in overall retention of the anomeric stereochemistry at the site of polysaccharide backbone hydrolysis (39). This was confirmed for BuGH158 by nuclear magnetic resonance (NMR) analysis of the hydrolysis of 2-chloro-4-nitrophenyl laminaribioside (G3G-CNP), which constitutes the first stereochemical determination for the family (Fig.…”

Section: B Uniformis Possesses a Distinct Pul Upregulated During Gromentioning

confidence: 91%

“…Additionally, a conserved asparagine (N136) precedes the general acid/base (E137) and is anticipated to engage in hydrogen-bonding interactions with the substrate (Fig. 4D) (39). Indeed, site-directed mutation of N136, E137, or E220 to alanine completely abolished catalytic activity (data not shown).…”

Section: B Uniformis Possesses a Distinct Pul Upregulated During Gromentioning

confidence: 95%

“…1). In particular, the GH complement was suggestive of a role in ␤(1,3)-glucan hydrolysis: GH16 subfamily 3 (GH16_3 [38]) contains known endo-laminarinases (among other endo-␤-glucanases) (19) and GH3 contains exo-␤glucosidases (among others) (39). Notably, during the course of this study, GH158 emerged as a new family whose founding member was shown to hydrolyze a chemically derivatized ␤(1,3)-glucan in a high-throughput screen (40).…”

Section: B Uniformis Possesses a Distinct Pul Upregulated During Gromentioning

confidence: 99%

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Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

Déjean

Tamura

Cabrera

et al. 2020

mBio

103

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The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL. IMPORTANCE Bacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.

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Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

Cited by 149 publications

References 17 publications

A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan

A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

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