Abstract
Surface layer (S-layer) proteins are one of the most commonly observed cell envelope components in both Archaea and Bacteria. It has versatile functions and holds considerable application potential in biotechnology. Bifidobacteria are representative probiotics conferring health promoting properties. However, there is little study of S-layer in bifidobacteria yet. The distribution and characteristics of S-layer in bifidobacteria are unknown. In this study, search for S-layer protein in the identical protein groups in NCBI yielded 49 hits belonging to bifidobacteria. These proteins were annotated as either “S-layer (domain) protein” or “putative S-layer (y) domain protein” that distributed among 26 species of Bifidobacterium genus. Multiple alignments suggest S-layer proteins are relatively conservative. Phylogenetic analysis of 24 S-layer (domain) protein sequences groups them into three distinct clusters, with the majority species in Cluster-2. S-layer (domain) protein has a universe motif DUF4381, though its function is unknown. Meanwhile, two other motifs CARDB and EphA2_TM involved in cell adhesion and cell signaling respectively, presented in most S-layer (domain) protein in bifidobacteria. All S-layer proteins have a typical N-terminal Sec-dependent signal peptide and a C-terminal trans-membrane region. Homological modeling of representative S-layer proteins from each cluster revealed a few unique structural features. All representative S-layer proteins have a plenty of β-meander motif that exclusively composed by β-barrel structural architectures linked together by hairpin loops.
Highlights
Surface layer (S-layer) are one of the most commonly observed prokaryotic cell surface structures
Search for S-layer protein in the identical protein groups in NCBI yielded 49 hits belonging to bifidobacteria
It is clear that S-layer and putative S-layer proteins distributed in only 26 known species and 1 uncharacterized specie of the genus of Bifidobacterium
Summary
S-layers are one of the most commonly observed prokaryotic cell surface structures They are composed by two-dimensional arrays of proteinaceous subunits (S-layer proteins), presented in almost every taxonomic group of walled Bacteria and almost universal in Archaea [1]. S-layer proteins are one of the most abundant biopolymers on our planet, as they account for approximately ten percent of cellular proteins in Archaea and Bacteria [2] They are generally composed of a single molecular species that can assemble on the cell surface into closed regular arrays. Chemical and genetically analysis of many S-layers has revealed a similar overall composition [4] They are generally composed of a single protein or glycoprotein species with molecular masses ranging from 40 to 170 kDa [5]. It is obvious that common structural principles must exist in S-layer proteins (e.g. the ability to form inter-subunit bonds and to self-assemble into monomolecular arrays, the formation of hydrophilic pores with low unspecific adsorption, and the interaction with underlying cell envelope components)
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