FIGURE 1.

Protein sequence alignment and molecular phylogenetic analyses of the LsrB and LuxS in XH001. (A) Protein sequence alignment of the XH001 LsrB and representative LsrB species: 1, XH001; 2, S. typhimurium 14028; 3, E. coli MG1655; 4, A. actinomycetecomitans HK1651; 5, and Bacillus anthracis. Alignment was conducted using MEGA7 (Kumar et al., 2016) via ClustalW Omega alignment method (Sievers et al., 2011). The conserved AA residues required for AI-2 binding are highlighted in bold, purple (K35, D116, D166, Q167, P220, and A222) and the corresponding XH001 conserved residue in bold, red. (B) The evolutionary relationship of the LsrB protein among the representative taxa. The evolutionary history was inferred by using the maximum-likelihood method based on the JTT matrix-based model (Jones et al., 1992). The tree with the highest log likelihood (-7027.33) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log-likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 26 amino acid sequences. All positions containing gaps and missing data were masked. There were a total of 284 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 (Kumar et al. (2016). (C) Protein sequence alignment of the XH001 LuxS protein and representative species. Marked in bold, yellow are the requisite amino acid residues (H,H, and C) that constitute the catalytic center of LuxS (Hilgers and Ludwig, 2001) and coordinate the Zn²⁺ ion: 1, XH001; 2, S. typhimurium 14028; 3, E. coli MG1655; 4, A. actinomycetecomitans HK1651; 5, S. mutans UA159. (D) The evolutionary relationship of the luxS protein among the representative taxa. The tree was generated using the same method parameters as (B). The tree with the highest log likelihood (-1292.94) is shown. The analysis involved 5 amino acid sequences and there were a total of 157 positions in the final dataset.