In silico evidence for the horizontal transfer of gsiB, a σ(B)-regulated gene in gram-positive bacteria, to lactic acid bacteria

Abstract

gsiB, coding for glucose starvation-inducible protein B, is a characteristic member of the σ(Β) stress regulon of Bacillus subtilis and several other Gram-positive bacteria. Here we provide in silico evidence for the horizontal transfer of gsiB in lactic acid bacteria that are devoid of the σ(Β) factor.

Fig. 1.

Analysis of the sequences of LAB and non-LAB GsiBs. (A) Multiple-sequence alignment of pPS1 GsiB and related proteins. Gray shading in the alignment reflects the degree of amino acid conservation. Boxes indicate the 20-amino-acid tandem repeats identified manually in the LAB and B. subtilis GsiBs. (B) Consensus sequence created by the WebLogo tool (14) for all 20-mer repeats present in the multiple-sequence alignment. Regions R1 to R5 in the multiple-sequence alignment were used for this analysis.

Fig. 2.

HGT route for the acquisition of GsiB by LAB. (A) Maximum-likelihood phylogenetic tree of pPS1 GsiB and related proteins. (B) Neighbor-joining phylogenetic tree of the 16S rRNA gene sequences of the species carrying GsiBs presented in panel A. Dotted arrows indicate HGT routes predicted by T-REX (26). Phylogenetic analysis was performed at the Phylogeny.fr pipeline (16), as described in the text. The lengths of the curated multiple-sequence alignments used for the construction of phylogenetic trees presented in panels A and B were 73 and 1,449 positions, respectively. Branch support values above 50% are indicated. Brackets highlight the positions of important clades in the phylogenetic trees that are further discussed in the text.

Fig. 3.

Relatedness of the pLS141-1 replicon with the pLS55/pMA67/pSU1/pBHS24 replicon. The phylogenetic tree of pLS141-1 Rep and related proteins was constructed using maximum likelihood at the Phylogeny.fr pipeline (16), as described in the text. The length of the curated multiple-sequence alignment used for the construction of the phylogenetic tree was 214 positions. The bracket and the solid arrow highlight the positions of the Bacillales/Lactobacillus clade and the pLS141-1 protein, respectively, which are further discussed in the text.

Fig. 4.

Promoter regions of the LAB and B. subtilis strain 168 gsiB genes. In LAB, no σ^Β promoters were detected that would satisfy the requirements of the consensus σ^Β sequences GTTTAA (−35 region), and GGG(A/T)A(A/T) (−10 region) determined previously (31). The σ^Β promoter was detected only for the gsiB gene of B. subtilis. In all other cases, the non-σ^Β promoters and ribosome binding site (RBS) sequences were predicted as described before (4). The right arrow indicates the start codons of the genes.