In-Depth Profiling of the LiaR Response of Bacillus subtilis

Abstract

The Lia system, a cell envelope stress response module of Bacillus subtilis, is comprised of the LiaRS two-component system and a membrane-anchored inhibitor protein, LiaF. It is highly conserved in the Firmicutes bacteria, and all orthologs investigated so far are activated by cell wall antibiotics. In response to envelope stress, the systems in Firmicutes cocci induce the expression of a number of genes that are involved in conferring resistance against its inducers. In contrast, a complete picture of the LiaR regulon of B. subtilis is still missing and no phenotypes could be associated with mutants lacking LiaRS. Here, we performed genome-wide transcriptomic, proteomic, and in-depth phenotypic profiling of constitutive "Lia ON" and "Lia OFF" mutants to obtain a comprehensive picture of the Lia response of Bacillus subtilis. In addition to the known targets liaIH and yhcYZ-yhdA, we identified ydhE as a novel gene affected by LiaR-dependent regulation. The results of detailed follow-up gene expression studies, together with proteomic analysis, demonstrate that the liaIH operon represents the only relevant LiaR target locus in vivo. It encodes a small membrane protein (LiaI) and a phage shock protein homolog (LiaH). LiaH forms large oligomeric rings reminiscent of those described for Escherichia coli PspA or Arabidopsis thaliana Vipp1. The results of comprehensive phenotype studies demonstrated that the gene products of the liaIH operon are involved in protecting the cell against oxidative stress and some cell wall antibiotics. Our data suggest that the LiaFSR system of B. subtilis and, presumably, other Firmicutes bacilli coordinates a phage shock protein-like response.

Lantibiotic Resistance

“…LiaRS-mediated signal transduction is also negatively regulated by LiaF, in a fashion similar to that described for B. subtilis (143). LiaFRS in B. subtilis is seen to regulate expression of itself and liaIH (139), and as seen in L. monocytogenes sv1/2a EGD, this occurs in response to exposure to the cell wall-active antibiotics vancomycin and bacitracin. In L. monocytogenes, however, the expression of 27 genes (143), including a PBP gene (57) and telA, which encodes a protein involved in toxic ion resistance (145), is also regulated.…”

“…In silico analysis could not predict the role of liaI or liaG, though the fact that liaI harbors two transmembrane domains and liaG harbors one transmembrane domain is indicative of membrane localization. However, LiaI seems to be involved in sensing and counteracting membrane damage (139,140). In addition to characterization of the genes within the operon, the promoter of the lia operon and the cis-acting sequences necessary for antibiotic-inducible gene expression were also identified (141).…”

“…Across the Firmicutes, liaG is present only in Bacillus spp. closely related to B. subtilis (139). Systematic deletion of the operon revealed the functions of each gene product.…”

The Bacillus subtilis GntR Family Repressor YtrA Responds to Cell Wall Antibiotics

“…Conversely, in other cases, antibioticinducible genes do not confer an obvious protective effect. For example, no susceptibility changes were observed with the liaIH-null mutant when treated with either vancomycin or nisin, both of which strongly induce these genes (14,44). This may be due, in part, to functional redundancy.…”

Protecting from Envelope Stress: Variations on the Phage-Shock-Protein Theme

“…The operon also encodes the integral membrane protein LiaI and the three-component regulatory system LiaFSR [41] ( Figure 1B). In the absence of stress, a weak, constitutive promoter upstream of liaG (a gene of unknown function) maintains basal levels of the liaGFSR transcript [42].…”