TABLE 4.
Results of microarray analysis showing LiaR-dependent marker genes that are induced/repressed more than 3-fold
| Gene(s) | Fold change in:a |
Function, homology, remarkb,c | Reference | |
|---|---|---|---|---|
| ΔliaF mutant | ΔliaR mutant | |||
| Induced | ||||
| liaIH | 310 ± 49 | Membrane protein, phage-shock protein homolog | 22 | |
| liaGFSR | 75 ± 12 | Unknown (liaG), negative regulator (liaF), TCS (liaSR) | 29 | |
| gerAC-gerAB-gerAA | 18 ± 3.2 | 6.7 ± 1.8 | Spore germination, polar effect | 49 |
| yhcYZ-yhdA | 24 ± 2.3 | Putative TCS and azoreductase | 45 | |
| yhdB-yhdC | 3.6 ± 0.3 | Unknown, polar effect | ||
| ydhE | 15 ± 0.8 | Putative macrolide glycosyltransferase | ||
| yqjU | 6.7 ± 1.5 | Unknown | ||
| wapA-yxxG | 6.3 ± 0.9 | Cell wall-associated protein | 13 | |
| yxiF-yxzC-yxiG-yxiH-yxzG-yxiI-yxiJ-yxiK-yxiL | 6.4 ± 1.1 | Unknown | ||
| yxiM-deaD | 4.5 ± 0.6 | Unknown, ATP-dependent RNA helicase | 34 | |
| ytrABCDEF | 4.1 ± 0.9 | Acetoin utilization, stress inducible | 62 | |
| Repressed | ||||
| hag | 3.3 ± 0.05 | Flagellin protein | 18 | |
| yvzB | 3.3 ± 0.04 | Similar to flagellin | 21 | |
| srfAA-srfAB-comS-comAC-comAD | 5.3 ± 0.03 | Surfactin synthetase, regulation of competence | 50, 52 | |
| yxkC | 4 ± 0.02 | Unknown | ||
| pel | 5.8 ± 0.03 | Pectate lyase | 51 | |
| catD-catE | 4.8 ± 0.04 | Catechol catabolism, dioxygenase | 56 | |
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.