TABLE 1.

Collection of 37 members of minimal CRP regulon in Yersinia pestis bv. microtus

Gene nameMean fold change in mRNA levelaEMSA resultbCRP regulationcCRP sitedPositioneGene IDfProtein productFunctional class
MicroarrayRT-PCR
pst −18.28−12.59+ATAAGAGTGATTCAGATCACAAAAD/−152/11.15YPPCP1.05cPesticinpPCP1 plasmid
pla −8.89−19.26+AATTATGTGACTTTGCTCACATAAR/−148/11.95YPPCP1.07Plasminogen activatorpPCP1 plasmid
ypkA 3.0814.38+BTTTGTGTGATTAACACCACCTTTD/−462/8.57YPCD1.72cTargeted effector protein kinase YpkApCD1 plasmid
yfiA −5.57−3.47+AAATGTATGATCGAGATCACTTTTR/−84/10.74YPO3279Putative sigma 54 modulation proteinRegulatory functions
rpoH 3.232.77+BAAAACGTGATCTAGATTGAACTTD/−152/8.78YPO3811RNA polymerase sigma 32 factorRegulatory functions
−7.03 YPO0409 ↑ Periplasmic solute-binding proteinTransport/binding proteins
−2.14 YPO0410 ↑ ABC transporter permease proteinTransport/binding proteins
MDg YPO0411 ↑ ABC transporter permease proteinTransport/binding proteins
−3.27−7.43+AAAATTGTGATCTTGGTTACGCCAD/−118/8.76 YPO0412 ↑ ABC transporter ATP-binding proteinTransport/binding proteins
sdaC 4.843.20+BCAATTGAGATCACGATCACGGTAD/−308/9.19YPO1321Serine transporterTransport/binding proteins
ptsG −10.34−2.20+AAATGTTTGATTGCCGTCACGTTTR/−166/9.35YPO1608PTS system, glucose-specific IIBC componentTransport/binding proteins
araF −2.44−3.58+AAACTTTTGACTGACATCACAAAAR/−283/8.54YPO2255 l-Arabinose-binding periplasmic protein precursorTransport/binding proteins
mntH 3.0713.31+BAATTAGTGGGCTTGATCACATAAD/−321/9.24YPO2982Manganese transport protein MntHTransport/binding proteins
nupC 2.262.55+BAATTAGTGGGCTTGATCACATAAR/−136/9.24YPO2983Nucleoside permeaseTransport/binding proteins
−5.14−3.59+AAAAATGAGAGGTATATCTCAATTD/−327/9.93YPO3633Putative periplasmic binding proteinTransport/binding proteins
gntT −4.00−2.05+AGAGATGTGACTTTTATCACAACAD/−124/9.78YPO3954Gluconate permeaseTransport/binding proteins
−3.09−2.08+ATAATTGTGGTGTAGATCTCATAAD/−265/9.92YPO4037Sugar-binding periplasmic proteinTransport/binding proteins
sdhC −2.69−3.11+AAAATCGTGATCCTAATCACTGTTD/−255/10.35 YPO1109 ↓ Succinate dehydrogenase cytochrome b556 subunitEnergy metabolism
sdhD −2.77 YPO1110 ↓ Succinate dehydrogenase hydrophobic membrane anchor proteinEnergy metabolism
sdhA −3.64 YPO1111 ↓ Succinate dehydrogenase flavoprotein subunitEnergy metabolism
sdhB −3.21 YPO1112 ↓ Succinate dehydrogenase iron-sulfur proteinEnergy metabolism
sucA −3.04 YPO1113 ↓ 2-Oxoglutarate dehydrogenase E1 componentEnergy metabolism
sucB −3.30 YPO1114 ↓ Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complexEnergy metabolism
sucC −3.17 YPO1115 ↓ Succinyl-coenzyme A (succinyl-CoA) synthetase beta chainEnergy metabolism
sucD −3.12 YPO1116 ↓ Succinyl-CoA synthetase alpha chainEnergy metabolism
cydA −3.24−5.88+AAAACTGTGATTTGACTCACTCTGD/−478/8.4 YPO1117 ↓ Cytochrome d ubiquinol oxidase subunit IEnergy metabolism
cydB −2.03 YPO1118 ↓ Cytochrome d ubiquinol oxidase subunit IIEnergy metabolism
pepT −2.75−2.14+AAATATTTGATCATGATCACTTCCD/−58/8.46YPO1631Peptidase TDegradation of macromolecules
fadD −2.32−2.13+AAAATAGTGATGTATATCTCAACCD/−132/8.27YPO2074Long-chain-fatty-acid CoA ligaseDegradation of small molecules
dadA −6.38−2.03+AAGATTGTGACTTGTCTCTCAATTR/−112/9.62YPO2147 d-Amino acid dehydrogenase small subunitDegradation of small molecules
idnO −5.63−2.825+AAAACTGTGATGCAGATCACTATAR/−417/12.73 YPO2539 ↓ Gluconate 5-dehydrogenaseDegradation of small molecules
idnK −2.25 YPO2540 ↓ Thermosensitive gluconokinaseDegradation of small molecules
ompC −4.98−3.13+AAAACAGTGAGTTATAGCACATATR/−257/9.4YPO1222Porin OmpCCell envelope
−3.57−2.52+AACTTTGTGACTTAGATCGAATTTR/−226/10.04YPO1411PorinCell envelope
ompX 2.415.75+BAGTATGTGACCTCCATCACCCAAR/−199/9.34YPO2506PorinCell envelope
aspA −8.16−20.61+ATATCTGTGATTGCTCTCACACTTR/−224/9.8YPO0348Aspartate ammonia lyaseAmino acid biosynthesis
aroH 2.0111.92+BGGGAAGTGATGGCGATCACAATAR/−64/8.87YPO2411Phospho-2-dehydro-3-deoxyheptonate aldolaseAmino acid biosynthesis
cspD −3.90−12.93+AAAAGTTTGATGTAGCTAACGCTAR/−185/8.65YPO1366Cold shock proteinAdaptation to atypical conditions
aas −2.54−5.43+AGAAATGCGATGCTACTCACGGTTD/−358/9.38YPO0793Aas bifunctional proteinFatty acid biosynthesis
2.2227.49+BCTTGTGTGATCAATAGCACACTGR/−50/9.16YPO0180Conserved hypothetical proteinUnknown
−6.71−3.93+AAATATGTGCTGGATATAACAGTTD/−130/9.33YPO0400Hypothetical proteinUnknown
−2.24−2.48+AAAATAGTGAGCCAAGTAACAAAAR/−134/8.2YPO0819Putative carbonic anhydraseUnknown
−11.96−23.76+AAGCAAGTGATGTAAATCACAAAAR/−105/8.38YPO1255Hypothetical proteinUnknown
−3.66−4.73+AGTTATGTGATGCAGATCAAATGTD/−37/10.93YPO2436Hypothetical proteinUnknown
−6.90−4.79+AATTTTGTGACGTAGGTCACTGTAR/−202/11YPO2536Putative d-isomer-specific 2-hydroxyacid dehydrogenase family proteinUnknown
−3.00−3.09+AATTGTGTGAATCATGTCACATTGD/−84/10.71YPO2795Hypothetical proteinUnknown
−3.84−6.81+AAAACTGTGATTCTGATCAAGGTTD/−136/10.11YPO3151Conserved hypothetical proteinUnknown
−4.35−33.57+AAATATGTGGGTTATATCACTTTTD/−156/9.93 YPO3647 ↓ Conserved hypothetical proteinUnknown
−4.09 YPO3648 ↓ Putative 2-hydroxy-3-oxopropionate reductaseUnknown
−5.72 YPO3649 ↓ Putative gamma carboxymuconolactone decarboxylaseUnknown
−6.01 YPO3650 ↓ Putative metabolite transport proteinUnknown
  • a The mRNA expression in the crp mutant was compared with that in the WT strain grown in TMH-1 mM cAMP. Positive numbers show increases, while negative numbers show decreases.

  • b +, positive result, indicating that the His-CRP protein binds in vitro to the upstream promoter DNA.

  • c A, positive and direct control by CRP; B, negative and direct control.

  • d Matching of the PSSM consensus of E. coli CRP within the 500-bp promoter regions was performed by the program patser-matrix (see text). The most strongly matched CRP site was indicated with a weight score for each promoter DNA.

  • e Strand/distance of CRP site upstream of transcriptional start site/matching score.

  • f Gene IDs were derived from the genome annotation of Y. pestis CO92. Putative multigene operons are shown in bold, and the arrows indicate the transcriptional organization.

  • g MD, missing data.