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

Abstract

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.

How many α-amylase GH families are there in the CAZy database?

“…Although the first actinobacterial sequence (from a Brevibacterium genus) was recently classified in this family [1], from its creation, GH126 was known as prokaryotic with members solely originating from the phylum Firmicutes [115]. However, a recent in silico study, aimed to disclose potential GH126 members outside of Firmicutes, convincingly identified 17 bacterial proteins from several other phyla (Proteobacteria, Actinobacteria and Bacteroidetes), hence expanding the taxonomic occurrence [116]. Seven CSRs were proposed for family GH126, along with elucidating evolutionary relationships within the family [115].…”

Nanomaterials: An Efficient Support to Immobilize Microbial α–Amylases for Improved Starch Hydrolysis

“…[21] However, recent in silico study helped to expand its taxonomic coverage outside the phylum Firmicutes too, mainly belonging to Proteobacteria, Actinobacteria, and Bacteroidetes. [22] Reportedly, several members in GH13 family have been assigned to subfamilies as per Stam et al [23] For instance, GH13_43 was assigned by 𝛼-amylase of the halophilic archaeon Haloarcula hispanica [24] and further assignment of subfamily numbers to recently identified members may facilitate the researchers in future.…”

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“…The starch degrading or modifying enzymes are distributed in GH families 3,13,14,15,31,57,63,77,97,119,122,126,and 133 (Table 1). Mostly useful amylolytic enzymes are commonly found in GH13, GH57, GH119, and GH126 family (Lombard et al, 2014;Janeček et al, 2014;Kerényiová and Janeček, 2020a). The family GH57 was established more than twenty years ago when the threedimensional structure of some α-amylases and related enzymes were elucidated that contained a (β/α)7-barrel (an irregular TIM-barrel domain) in their configuration (Sarian et al, 2017).…”

“…The family GH126 was created by Ficko-Blean in the year 2011 (Ficko-Blean et al, 2011). Up to July 2020, this family counts more than 1000 sequences exclusively from the bacteria under the phylum Firmicutes (Kerényiová and Janeček, 2020a). The in silico study had revealed that this family has relationships with other GH families.…”