Bioinformatic Survey of S-Layer Proteins in Bifidobacteria

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.

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

“…Moreover, exposure to 0.5 mM silver nitrate induced the upregulation of the basic membrane protein A (Hfx-2019-SC1-cds278), as well as the S-layer domain COG136-containing protein (Hfx-2019-SC5-cds185; Table 6 ). Previous studies have suggested that the COG1361 domain is involved in the synthesis of the cell membrane and S-layer components in thermoacidophilic archaea [ 105 , 106 ]. In addition to reinforcing cellular structures, the overexpression of these enzymes can facilitate the production of components responsible for coating and stabilizing the observed extracellular silver nanoparticles [ 107 ].…”

Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria

“…Another explanation could be a higher abundance of hydrophobic surface (S)-layer proteins on the cell surface of BB-12. In general, S-layer proteins can form a protective coating around the peptidoglycan layer in Gram-positive bacteria ( 61 ), but very little is known about S-layer proteins in bifidobacteria ( 62 ). According to genome annotation, BB-12 possesses 2 S-layer homology domain-containing proteins (BIF_01636, BIF_01633).…”

“…According to genome annotation, BB-12 possesses 2 S-layer homology domain-containing proteins (BIF_01636, BIF_01633). In addition, BB-46 harbors 1 gene annotated as ABC transporter permease (I3242_02465) that shows 99% sequence identity with an S-layer protein of B. longum DJO10A ( 62 ). These S-layer proteins of BB-12 and BB-46 have a similar percentage of hydrophobic amino acids (40 to 42%).…”

Acceptive Immunity: The Role of Fucosylated Glycans in Human Host–Microbiome Interactions

“…Bifidobacteria and lactobacilli use various adhesive proteins, which are often glycosylated and can modulate the immune response. Part of bifidobacteria (e.g., some strains of B. adolescentis , B. longum , B. breve , B. catenulatum , B. pseudocatenulatum ) [ 109 ] and lactobacilli (e.g., some strains of L. acidophilus , L. helveticus , L. crispatus , L. amylovorus , L. gallinarum , L. gasseri , L. johnsonii ) [ 110 ] can form a protein layer (S-layer protein, Slp) on the cell surface [ 109 , 111 ]. slp genes are expressed constitutively.…”