Table 2

LovK-LovR, PhyR, and σT regulate an overlapping set of genesa

LocusAnnotated functionRegulation resultFigure showing validatione
lovKR++bΔphyRcΔsigTd
Down-regulated genes
CC_0163EPS associated protein2.63.5A
CC_0201OmpA-family outer membrane lipoprotein4.73.0F-A, LS1
CC_0280Conserved cell surface protein3522F, A, LS1
CC_0284LovR, receiver proteinNA2.0F, A, L2
CC_0285LovK, cytoplasmic sensor histidine kinaseNA2.8F2
CC_0447Beta-N-acetylhexosaminidae3.6A
CC_0501Hypothetical protein4.4L
CC_0554Conserved hypothetical protein3.53.0
CC_0555FixC-family flavoprotein dehydrogenase2.82.1
CC_0556Conserved hypothetical protein, catalase3.24.3L
CC_0557Conserved hypothetical protein3.43.1L
CC_0558Putative outer membrane lipoprotein4.9(1.8)
CC_0559DPS-family DNA stress protection protein2.62.0FS1
CC_0747OmpA-family outer membrane lipoprotein8.24.7A, L
CC_0938CsbD-related stress response protein2.82.0A, L
CC_1178GsbI general stress protein5416L
CC_1179Hypothetical protein8.93.1A, L
CC_1189CESA-like glycosyltransferase363.4FS1
CC_1356MucR-family transcriptional regulator3292A, L
CC_1532Conserved hypotethical protein6513A, L
CC_2383GalE, UDP-glucose 4-epimerase2.64.6
CC_2384PssZ, polyisoprenylphosphate hexose-1-phosphotransferase4.04.7
CC_2549SOUL domain heme-binding protein2.03.3A, L
CC_2883SigU, ECF-family sigma factor1046.2A, L3
CC_3225PAS-family sensor histidine kinase2.5(1.7)A, L
CC_3466CsbD-related stress response protein2914.7F, LS1
CC_3473Entericidin family protein5.33.0F, LS1
CC_3474PhyK, transmembrane sensor histidine kinase4.05.9
CC_3475SigT, ECF-family sigma factor6.46.0A, L
CC_3476NepR, anti-sigma factor protein2.32.0A, L
CC_3477PhyR, stress regulatory protein1036fH, L
CC_3618Mannose-1-phosphate guanylyltransferase2.42.0
Upregulated genes
CC_0933Ros-MucR-superfamily transcriptional regulator2.12.5A
CC_2610Hemolysin-type calcium binding protein2.1A
CC_3147TonB-dependent outer membrane receptor5.03.6F, AS1
  • a Transcripts regulated >2-fold in at least two transcriptome analyses. The complete set of genes regulated by LovK-LovR or PhyR is presented in Table S2 in the supplemental material.

  • b Fold change compared to empty vector control strain. NA, not applicable.

  • c Fold change compared to phyR overexpression strain. Values in parentheses are for two transcripts weakly regulated by phyR which are regulated by LovK-LovR and by sigT.

  • d Observation of sigT-dependent regulation in reference 2 (A), reference 17 (H), reference 25 (L), or this work (F).

  • e Transcriptional regulation of indicated genes was confirmed using promoter-lacZ fusions. Data are presented in the figure listed.

  • f Calculated from probes complementary to sequences in the 5′ UTR of phyR not present in the overexpression construct.