Starch-binding domains as CBM families–history, occurrence, structure, function and evolution

Janeček, Štefan; Mareček, Filip; MacGregor, E. Ann; Svensson, Birte

doi:10.1016/j.biotechadv.2019.107451

Cited by 99 publications

(119 citation statements)

References 305 publications

Supporting

Mentioning

104

Contrasting

Unclassified

Order By: Relevance

“…As reported by the CAZy database and several studies, β-amylases are secreted mainly by plants, followed by several bacteria, and by a very limited number in fungi (Ray, 2004;Derde et al, 2012;Thalmann et al, 2019). Two CBM families were identified in bacterial β-amylases, i.e., CBM20 from species of Bacillus and Clostridium as well as CBM25 from Paenibacillus, and no CBMs were found in the fungal GH14 β-amylases (see review Janeček et al, 2019).…”

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 87%

“…Based on the domain position, the CBM20s in α-amylases from Aspergillus and Streptomyces are always located at the C-terminal end (Figure 2). This is also true for other starch active enzymes, such as in GH14 (Oyama et al, 1999), GH15 (Bott et al, 2008;Roth et al, 2018), LPMO AA13 (Vu et al, 2014), and in most of the GH13 enzymes (see review Janeček et al, 2019). Based on the CAZy database, only in a few GH13s, the CBM20 is located at the N-terminal end of the catalytic domain, especially the GH13s from green algae (Lombard et al, 2014).…”

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 90%

“…Moreover, some of the Streptomyces amylases have combinations of different CBMs attached: CBM20&CBM25 as well as CBM41&CBM48 (Figures 2B1,B2). In general, the binding modules of the CBM20 family are found in a single copy, while only in a few special cases a CBM20 is present together with other CBMs, such as CBM25, CBM34, and CBM48 (Janeček et al, 2019).…”

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 99%

See 2 more Smart Citations

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Sidar

Albuquerque²,

Voshol³

et al. 2020

Front. Bioeng. Biotechnol.

102

View full text Add to dashboard Cite

Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.

show abstract

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 87%

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 90%

Section: Amylases With Cbm From Aspergillus and Streptomycesmentioning

confidence: 99%

See 1 more Smart Citation

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Sidar

Albuquerque²,

Voshol³

et al. 2020

Front. Bioeng. Biotechnol.

102

View full text Add to dashboard Cite

show abstract

“…Four proteins containing the N-terminal extensions that were cut for making the alignment are marked by an asterisk; the length of the extension being indicated in parentheses. With regard to bootstrap values (not shown to preserve the clarity), they were ≥ 50% for more than 83% of interior branches the presence of some kind of SBDs that have been currently classified in 15 different CBM families in CAZy (Janecek et al 2019). It is, however, worth mentioning that none of the extensions of sequences from the family GH126 studied here was recognized to contain either an SBD, or a CBM in general ( Table 2).…”

Section: In Silico Characterization Of the Family Gh126 Non-catalyticmentioning

confidence: 81%

Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains

Kerényiová

Janeček

2020

3 Biotech

Self Cite

View full text Add to dashboard Cite

The family GH126 is a family of glycoside hydrolases established in 2011. Officially, in the CAZy database, it counts ~ 1000 sequences originating solely from bacterial phylum Firmicutes. Two members, the proteins CPF_2247 from Clostridium perfringens and PssZ from Listeria monocytogenes have been characterized as a probable α-amylase and an exopolysaccharide-specific glycosidase, respectively; their three-dimensional structures being also solved as possessing catalytic (α/α)6-barrel fold. Previously, based on a detailed in silico analysis, the seven conserved sequence regions (CSRs) were identified for the family along with elucidating basic evolutionary relationships within the family members. The present study represents a continuation study focusing on two particular aims: (1) to find out whether the taxonomic coverage of the family GH126 might be extended outside the Firmicutes and, if positive, to deliver those out-of-Firmicutes proteins with putting them into the context of the family; and (2) to identify the family members containing the N- and/or C-terminal extensions of their polypeptide chain, additional to the catalytic (α/α)6-barrel domain, and perform the bioinformatics characterization of the extra domains. The main results could be summarized as follows: (1) 17 bacterial proteins caught by BLAST searches outside Firmicutes (especially from phyla Proteobacteria, Actinobacteria and Bacteroidetes) have been found and convincingly suggested as new family GH126 members; and (2) a thioredoxin-like fold and various leucine-rich repeat motifs identified by Phyre2 structure homology modelling have been recognized as extra domains occurring most frequently in the N-terminal extensions of family GH126 members possessing a modular organization.

show abstract

“…30 CAZymes families altered signi cantly in the RPS diet group, 14 families changed signi cantly in the INU group, and 35 families changed signi cantly in the PEC group. Among these families, CBM26 and CBM41 downregulated in all three diet groups compared with the CON group, they can be considered as families having starch-binding domain (SBD) in the CAZymes database, an SBD is a special case of a carbohydrate-binding domain, it has no enzymatic activity but can attach the catalytic domain to the carbohydrate substrate to hold it and process it at the active site which gave the enzymes the ability to bind onto raw starch [22,23], it may showed these three additive prevented the degradation of starch to a certain degree. And CBM61 increased in the PEC group compared with the CON group.…”

Section: Discussionmentioning

confidence: 99%

Metatranscriptomic analysis of functional response of colonic microbiota to different dietary fibers in growing pigs

Jia

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Dietary fibers are widely considered to be beneficial for health by producing nutrients by gut microbial fermentation while helping with weight management and gut health. So far, the gene expression profiles of CAZymes responsing to different type of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigate the functional response of colonic microbiota to different dietary fibers in pigs based on metatranscriptomic analysis. Results Results showed that the microbial composition and carbohydrate active enzymes (CAZymes) structure of three experimental groups changed significantly compared to the control group (CON). As determined by comparative analysis with the control diet, RPS increased the abundances of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella, and decreased Sutterella. INU increased the relative abundance of Fusobacterium and Rhodococcus, while decreased Bacillus. And pectin treatment increased the relative abundance of Streptococcus and Bacteroidetes group, while decreased the relative abundance of Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum, and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated while GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; as to the PEC group, the gene expression of PL4, AA1, GT32, GH18, GH37, GH101, and GH112 downregulated while CE14, AA3, AA12, GH5, GH102 and GH103 upregulated. Compared to RPS and INU groups, the composition of colonic microbiota in the PEC group had more diverse changes with the variation of carbohydrate active enzymes and Streptococcus as the main contributor to CBM61, which promoted the digestion of pectin greatly. Conclusions The results of this exploratory study displayed a comprehensive overview on the effects of different fibers on gut microbiota and CAZymes in pig colons, which will provide new insights into the impacts of the use of dietary fibers on animal or human health.

show abstract

Starch-binding domains as CBM families–history, occurrence, structure, function and evolution

Cited by 99 publications

References 305 publications

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains

Metatranscriptomic analysis of functional response of colonic microbiota to different dietary fibers in growing pigs

Contact Info

Product

Resources

About