Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold

Fujimoto, Zui

doi:10.1271/bbb.130183

Cited by 44 publications

(34 citation statements)

References 92 publications

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“…In bacteria, combinations of such domains have been reported previously, and were shown to be involved in the degradation of insoluble or complex polysaccharides. These GH/ricin B proteins comprise an unusual combination of a carbohydrate-degrading (GH) and a carbohydrate-binding (lectin) domain and in bacterial homologs, the latter has been acknowledged to assist the enzymatic activity [75,76,77]. Both the GH5 and GH27 family are large families of glycoside hydrolases, grouping GHs with diverse enzymatic activities (available online: ) [64,78].…”

Section: Resultsmentioning

confidence: 99%

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Holle

Schutter

Eggermont

et al. 2017

IJMS

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Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

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Section: Resultsmentioning

confidence: 99%

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Holle

Schutter

Eggermont

et al. 2017

IJMS

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“…8) We recently found that the α-repeat of CBM-DK primarily contributes to β-glucan binding, 9) a property different from other CBMs in family 13 from Streptomyces lividans xylanase 10A and Streptomyces olivaceoviridis E-86 xylanase. 10,11) The CBM13 lectinlike xylan binding domain from Streptomyces lividans xylanase 10A was reported to have different repeat preferences for the respective substrates. 12) Based on the available crystal structures, we had hypothesized that the conserved Asp residues, Asp270 in α-repeat, Asp311 in β-repeat, and Asp355 in γ-repeat would contribute to β-glucan binding.…”

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confidence: 99%

Tryptophan introduction can change β-glucan binding ability of the carbohydrate-binding module of endo-1,3-β-glucanase

Miki

Inaba

Maruno

et al. 2017

Bioscience, Biotechnology, and Biochemistry

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Endo-1,3-β-glucanase from Cellulosimicrobium cellulans DK-1 has a carbohydrate-binding module (CBM-DK) at the C-terminal side of a catalytic domain. Out of the imperfect tandem α-, β-, and γ-repeats in CBM-DK, the α-repeat primarily contributes to β-glucan binding. This unique feature is derived from Trp273 in α-repeat, whose corresponding residues in β- and γ-repeats are Asp314 and Gly358, respectively. In this study, we generated Trp-switched mutants, W273A/D314W, D270A/W273A/D314W, W273A/G358W, and D270A/W273A/G358W, and analyzed their binding abilities toward laminarioligosaccharides and laminarin. While the binding affinities of D270A/W273A and W273A mutants were either lost or much lower than that of the wild-type, those of Trp-switched mutants recovered, indicating that a Trp introduction in β- or γ-repeat can substitute the α-repeat by primarily contributing to β-glucan binding. Thus, we have successfully engineered a CBM-DK that binds to laminarin by a mechanism different from that of the wild-type, but with similar affinity.

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“…Populus has all the CAZyme families identified in A. thaliana , whereas one family found in Populus , CBM13, does not have counterparts in A. thaliana (Table ). This domain has a trefoil structure, with three sugar binding domains that can harbor different specificities to mono‐ or disaccharides and that belong to the ricin B lectin family (Fujimoto, ). All identified P. trichocarpa CBM13 gene models clustered at two loci on chromosome 6, and were similar to ricin and abrin‐a, potent plant toxins.…”

Section: Resultsmentioning

confidence: 99%

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data

et al. 2019

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Summary Carbohydrate‐active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long‐term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re‐annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high‐resolution RNA‐Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co‐expression network analysis of CAZymes in wood‐forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue‐specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.

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Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold

Cited by 44 publications

References 92 publications

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Tryptophan introduction can change β-glucan binding ability of the carbohydrate-binding module of endo-1,3-β-glucanase

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data

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