Identification of novel β-mannan- and β-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules

2001 ◽  
Vol 356 (3) ◽  
pp. 791-798 ◽  
Author(s):  
Anwar SUNNA ◽  
Moreland D. GIBBS ◽  
Peter L. BERGQUIST
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Experimental Characterization ◽  
Carbohydrate Polymers ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Long Chain

Many glycoside hydrolases, which degrade long-chain carbohydrate polymers, possess distinct catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). On the basis of conserved protein secondary structure, we describe here the identification and experimental characterization of novel type of mannanase-associated mannan-binding module and also characterization of two CBM family 4 laminarinase-associated β-glucan-binding modules. These modules are predicted to belong to a superfamily of CBMs which include families 4, 16, 17, 22 and a proposed new family, family 27.

scholarly journals Characterization of a galactosyl-binding protein module from a Cellvibrio japonicus endo-xyloglucanase defines a new family of Carbohydrate Binding Modules

2020 ◽  
pp. AEM.02634-20
Author(s):  
Mohamed A. Attia ◽  
Harry Brumer
Keyword(s):  
Binding Protein ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Substrate Affinity ◽  
Carbohydrate Binding ◽  
Carbohydrate Active Enzymes ◽  
Plant Polysaccharides ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, e.g. by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is valuable source for CAZyme and CBM discovery and characterization, due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (“X181”), and a Glycoside Hydrolase Family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase [Attia et al. 2018. Biotechnol. Biofuels, 11: 45]. In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest product of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes.Importance This study reveals Carbohydrate Binding Module Family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the Carbohydrate-Active Enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.

scholarly journals Alpha-Agarases Define a New Family of Glycoside Hydrolases, Distinct from Beta-Agarase Families

2007 ◽  
Vol 73 (14) ◽  
pp. 4691-4694 ◽  
Author(s):  
Didier Flament ◽  
Tristan Barbeyron ◽  
Murielle Jam ◽  
Philippe Potin ◽  
Mirjam Czjzek ◽  
...  
Keyword(s):  
Gene Product ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Gene Encoding ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Type 3

ABSTRACT The gene encoding the α-agarase from “Alteromonas agarilytica” (proposed name) has been cloned and sequenced. The gene product (154 kDa) is unrelated to β-agarases and instead belongs to a new family of glycoside hydrolases (GH96). The α-agarase also displays a complex modularity, with the presence of five thrombospondin type 3 repeats and three carbohydrate-binding modules.

scholarly journals A unique combination of glycoside hydrolases in Streptococcus suis specifically and sequentially acts on host-derived αGal-epitope glycans

2020 ◽  
Vol 295 (31) ◽  
pp. 10638-10652
Author(s):  
Ping Chen ◽  
Ran Liu ◽  
Mengmeng Huang ◽  
Jinlu Zhu ◽  
Dong Wei ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Streptococcus Suis ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Unique Combination ◽  
Enzymatic Assays ◽  
Tracheal Epithelial Cells ◽  
Carbohydrate Binding Modules ◽  
Host Signaling ◽  
Important Host

Infections by many bacterial pathogens rely on their ability to degrade host glycans by producing glycoside hydrolases (GHs). Here, we discovered a conserved multifunctional GH, SsGalNagA, containing a unique combination of two family 32 carbohydrate-binding modules (CBM), a GH16 domain and a GH20 domain, in the zoonotic pathogen Streptococcus suis 05ZYH33. Enzymatic assays revealed that the SsCBM-GH16 domain displays endo-(β1,4)-galactosidase activity specifically toward the host-derived αGal epitope Gal(α1,3)Gal(β1,4)Glc(NAc)-R, whereas the SsGH20 domain has a wide spectrum of exo-β-N-acetylhexosaminidase activities, including exo-(β1,3)-N-acetylglucosaminidase activity, and employs this activity to act in tandem with SsCBM-GH16 on the αGal-epitope glycan. Further, we found that the CBM32 domain adjacent to the SsGH16 domain is indispensable for SsGH16 catalytic activity. Surface plasmon resonance experiments uncovered that both CBM32 domains specifically bind to αGal-epitope glycan, and together they had a KD of 3.5 mm toward a pentasaccharide αGal-epitope glycan. Cell-binding and αGal epitope removal assays revealed that SsGalNagA efficiently binds to both swine erythrocytes and tracheal epithelial cells and removes the αGal epitope from these cells, suggesting that SsGalNagA functions in nutrient acquisition or alters host signaling in S. suis. Both binding and removal activities were blocked by an αGal-epitope glycan. SsGalNagA is the first enzyme reported to sequentially act on a glycan containing the αGal epitope. These findings shed detailed light on the evolution of GHs and an important host-pathogen interaction.

scholarly journals Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

2020 ◽  
Vol 8 (4) ◽  
pp. 481 ◽  
Author(s):  
Toshihiko Katoh ◽  
Miriam N. Ojima ◽  
Mikiyasu Sakanaka ◽  
Hisashi Ashida ◽  
Aina Gotoh ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Bifidobacterium Bifidum ◽  
Glycoside Hydrolases ◽  
Altruistic Behavior ◽  
Carbohydrate Binding ◽  
Human Gut ◽  
Genetic Characteristics ◽  
Beneficial Effects ◽  
Carbohydrate Binding Modules ◽  
Enzymatic Machinery

Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder.

scholarly journals A Tomato Endo-β-1,4-glucanase, SlCel9C1, Represents a Distinct Subclass with a New Family of Carbohydrate Binding Modules (CBM49)

2007 ◽  
Vol 282 (16) ◽  
pp. 12066-12074 ◽  
Author(s):  
Breeanna R. Urbanowicz ◽  
Carmen Catalá ◽  
Diana Irwin ◽  
David B. Wilson ◽  
Daniel R. Ripoll ◽  
...  
Keyword(s):  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

scholarly journals Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module (CBM_E1) derived from sugarcane soil metagenome

2014 ◽  
Vol 70 (9) ◽  
pp. 1232-1235 ◽  
Author(s):  
Bruna Medeia Campos ◽  
Thabata Maria Alvarez ◽  
Marcelo Vizona Liberato ◽  
Igor Polikarpov ◽  
Harry J. Gilbert ◽  
...  
Keyword(s):  
Fossil Fuels ◽  
Plant Biomass ◽  
Metagenomic Library ◽  
Glycoside Hydrolases ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Carbohydrate Binding Modules

In recent years, owing to the growing global demand for energy, dependence on fossil fuels, limited natural resources and environmental pollution, biofuels have attracted great interest as a source of renewable energy. However, the production of biofuels from plant biomass is still considered to be an expensive technology. In this context, the study of carbohydrate-binding modules (CBMs), which are involved in guiding the catalytic domains of glycoside hydrolases for polysaccharide degradation, is attracting growing attention. Aiming at the identification of new CBMs, a sugarcane soil metagenomic library was analyzed and an uncharacterized CBM (CBM_E1) was identified. In this study, CBM_E1 was expressed, purified and crystallized. X-ray diffraction data were collected to 1.95 Å resolution. The crystals, which were obtained by the sitting-drop vapour-diffusion method, belonged to space groupI23, with unit-cell parametersa=b=c= 88.07 Å.

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

2018 ◽  
Vol 19 (8) ◽  
pp. 2379 ◽  
Author(s):  
Young-Jin Park ◽  
Yong-Un Jeong ◽  
Won-Sik Kong
Keyword(s):  
Gene Prediction ◽  
Gc Content ◽  
Industrial Applications ◽  
Fungal Species ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
White Rot ◽  
White Rot Fungus ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

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.

α-Glucan Recognition by a New Family of Carbohydrate-Binding Modules Found Primarily in Bacterial Pathogens†

Biochemistry ◽  
2004 ◽  
Vol 43 (49) ◽  
pp. 15633-15642 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Ron Finn ◽  
Juan Ausió ◽  
Alisdair B. Boraston
Keyword(s):  
Bacterial Pathogens ◽  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

scholarly journals The modular architecture of Cellvibrio japonicus mannanases in glycoside hydrolase families 5 and 26 points to differences in their role in mannan degradation

2003 ◽  
Vol 371 (3) ◽  
pp. 1027-1043 ◽  
Author(s):  
Deborah HOGG ◽  
Gavin PELL ◽  
Paul DUPREE ◽  
Florence GOUBET ◽  
Susana M. MARTÍN-ORÚE ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Glycoside Hydrolases ◽  
Crystalline Cellulose ◽  
Carbohydrate Binding ◽  
Molecular Architecture ◽  
Catalytic Domains ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

β-1,4-Mannanases (mannanases), which hydrolyse mannans and glucomannans, are located in glycoside hydrolase families (GHs) 5 and 26. To investigate whether there are fundamental differences in the molecular architecture and biochemical properties of GH5 and GH26 mannanases, four genes encoding these enzymes were isolated from Cellvibrio japonicus and the encoded glycoside hydrolases were characterized. The four genes, man5A, man5B, man5C and man26B, encode the mannanases Man5A, Man5B, Man5C and Man26B, respectively. Man26B consists of an N-terminal signal peptide linked via an extended serine-rich region to a GH26 catalytic domain. Man5A, Man5B and Man5C contain GH5 catalytic domains and non-catalytic carbohydrate-binding modules (CBMs) belonging to families 2a, 5 and 10; Man5C in addition contains a module defined as X4 of unknown function. The family 10 and 2a CBMs bound to crystalline cellulose and ivory nut crystalline mannan, displaying very similar properties to the corresponding family 10 and 2a CBMs from Cellvibrio cellulases and xylanases. CBM5 bound weakly to these crystalline polysaccharides. The catalytic domains of Man5A, Man5B and Man26B hydrolysed galactomannan and glucomannan, but displayed no activity against crystalline mannan or cellulosic substrates. Although Man5C was less active against glucomannan and galactomannan than the other mannanases, it did attack crystalline ivory nut mannan. All the enzymes exhibited classic endo-activity producing a mixture of oligosaccharides during the initial phase of the reaction, although their mode of action against manno-oligosaccharides and glucomannan indicated differences in the topology of the respective substrate-binding sites. This report points to a different role for GH5 and GH26 mannanases from C. japonicus. We propose that as the GH5 enzymes contain CBMs that bind crystalline polysaccharides, these enzymes are likely to target mannans that are integral to the plant cell wall, while GH26 mannanases, which lack CBMs and rapidly release mannose from polysaccharides and oligosaccharides, target the storage polysaccharide galactomannan and manno-oligosaccharides.

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