Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei

Abstract

Lactobacillus casei has traditionally been recognized as a probiotic, thus needing to survive the industrial production processes and transit through the gastrointestinal tract before providing benefit to human health. The two-component signal transduction system (TCS) plays important roles in sensing and reacting to environmental changes, which consists of a histidine kinase (HK) and a response regulator (RR). In this study we identified HKs and RRs of six sequenced L. casei strains. Ortholog analysis revealed 15 TCS clusters (HK-RR pairs), one orphan HKs and three orphan RRs, of which 12 TCS clusters were common to all six strains, three were absent in one strain. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. Some TCS clusters are involved with the response under the stress of the bile salts, acid, or oxidative, which contribute to survive the difficult journey through the human gastrointestinal tract. Computational predictions of 15 TCSs were verified by PCR experiments. This genomic level study of TCSs should provide valuable insights into the conservation and divergence of TCS proteins in the L. casei strains.

Keywords: Comparative genomics; Lactobacillus casei; Probiotic; Two-component signal transduction system.

Fig. 1

Phylogenetic trees of the paired HKs and RRs in the six sequenced L. casei strains. The trees were constructed using MEGA version 4 by applying the neighbor-joining method. The scale bar is shown above the trees and the scale is in units of “substitution/site”

Fig. 2

Domain architectures of histidine kinases representative of each TCS clusters. The pictorial depiction is based on the predictions carried out using the SMART web interface http://smart.embl-heidelberg.de/. The transmembrane helices (TMs) were predicted using the tool TMHMM. C, E and M stand for cytoplasmic, extracytoplasmic and membrane sensing, respectively

Fig. 3

PCR verification of the presence of TCS genes in Lactobacillus casei strains. Agarose gel electrophoresis of PCR products amplified using TCS-2 primers. Lane 1, Lactobacillus casei ATCC334; Lane 2, Lactobacillus casei LC2W; Lane 3, Lactobacillus casei BD00054; Lane 4, Lactobacillus casei BD00090; Lane 5, Lactobacillus casei BD01649; Lane 6, Lactobacillus casei BD01803; Lane 7, Lactobacillus paracasei BD03416; Lane 8, negative control (ddH₂O); M 100 bp DNA Marker