TABLE 4.

Results of microarray analysis showing LiaR-dependent marker genes that are induced/repressed more than 3-fold

Gene(s)Fold change in:aFunction, homology, remarkb,cReference
ΔliaF mutantΔliaR mutant
Induced
    liaIH310 ± 49Membrane protein, phage-shock protein homolog22
    liaGFSR75 ± 12Unknown (liaG), negative regulator (liaF), TCS (liaSR)29
    gerAC-gerAB-gerAA18 ± 3.26.7 ± 1.8Spore germination, polar effect49
    yhcYZ-yhdA24 ± 2.3Putative TCS and azoreductase45
    yhdB-yhdC3.6 ± 0.3Unknown, polar effect
    ydhE15 ± 0.8Putative macrolide glycosyltransferase
    yqjU6.7 ± 1.5Unknown
    wapA-yxxG6.3 ± 0.9Cell wall-associated protein13
    yxiF-yxzC-yxiG-yxiH-yxzG-yxiI-yxiJ-yxiK-yxiL6.4 ± 1.1Unknown
    yxiM-deaD4.5 ± 0.6Unknown, ATP-dependent RNA helicase34
    ytrABCDEF4.1 ± 0.9Acetoin utilization, stress inducible62
Repressed
    hag3.3 ± 0.05Flagellin protein18
    yvzB3.3 ± 0.04Similar to flagellin21
    srfAA-srfAB-comS-comAC-comAD5.3 ± 0.03Surfactin synthetase, regulation of competence50, 52
    yxkC4 ± 0.02Unknown
    pel5.8 ± 0.03Pectate lyase51
    catD-catE4.8 ± 0.04Catechol catabolism, dioxygenase56
  • a Values (relative to wild-type levels) are averages and standard deviations of the results from three independent biological replicates. All genes listed had a Cyber-T Bayesian P value of <0.001 (see Materials and Methods for experimental details).

  • b TCS, two-component system that includes histidine kinase and response regulator.

  • c Positive polar effect was indicated by strong expression of upstream genes.