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
ypkA3.0814.38+BTTTGTGTGATTAACACCACCTTTD/−462/8.57YPCD1.72cTargeted effector protein kinase YpkApCD1 plasmid
yfiA−5.57−3.47+AAATGTATGATCGAGATCACTTTTR/−84/10.74YPO3279Putative sigma 54 modulation proteinRegulatory functions
rpoH3.232.77+BAAAACGTGATCTAGATTGAACTTD/−152/8.78YPO3811RNA polymerase sigma 32 factorRegulatory functions
−7.03YPO0409 ↑Periplasmic solute-binding proteinTransport/binding proteins
−2.14YPO0410 ↑ABC transporter permease proteinTransport/binding proteins
MDgYPO0411 ↑ABC transporter permease proteinTransport/binding proteins
−3.27−7.43+AAAATTGTGATCTTGGTTACGCCAD/−118/8.76YPO0412 ↑ABC transporter ATP-binding proteinTransport/binding proteins
sdaC4.843.20+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/−283/8.54YPO2255l-Arabinose-binding periplasmic protein precursorTransport/binding proteins
mntH3.0713.31+BAATTAGTGGGCTTGATCACATAAD/−321/9.24YPO2982Manganese transport protein MntHTransport/binding proteins
nupC2.262.55+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/−255/10.35YPO1109 ↓Succinate dehydrogenase cytochrome b556 subunitEnergy metabolism
sdhD−2.77YPO1110 ↓Succinate dehydrogenase hydrophobic membrane anchor proteinEnergy metabolism
sdhA−3.64YPO1111 ↓Succinate dehydrogenase flavoprotein subunitEnergy metabolism
sdhB−3.21YPO1112 ↓Succinate dehydrogenase iron-sulfur proteinEnergy metabolism
sucA−3.04YPO1113 ↓2-Oxoglutarate dehydrogenase E1 componentEnergy metabolism
sucB−3.30YPO1114 ↓Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complexEnergy metabolism
sucC−3.17YPO1115 ↓Succinyl-coenzyme A (succinyl-CoA) synthetase beta chainEnergy metabolism
sucD−3.12YPO1116 ↓Succinyl-CoA synthetase alpha chainEnergy metabolism
cydA−3.24−5.88+AAAACTGTGATTTGACTCACTCTGD/−478/8.4YPO1117 ↓Cytochrome d ubiquinol oxidase subunit IEnergy metabolism
cydB−2.03YPO1118 ↓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/−112/9.62YPO2147d-Amino acid dehydrogenase small subunitDegradation of small molecules
idnO−5.63−2.825+AAAACTGTGATGCAGATCACTATAR/−417/12.73YPO2539 ↓Gluconate 5-dehydrogenaseDegradation of small molecules
idnK−2.25YPO2540 ↓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
ompX2.415.75+BAGTATGTGACCTCCATCACCCAAR/−199/9.34YPO2506PorinCell envelope
aspA−8.16−20.61+ATATCTGTGATTGCTCTCACACTTR/−224/9.8YPO0348Aspartate ammonia lyaseAmino acid biosynthesis
aroH2.0111.92+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/−156/9.93YPO3647 ↓Conserved hypothetical proteinUnknown
−4.09YPO3648 ↓Putative 2-hydroxy-3-oxopropionate reductaseUnknown
−5.72YPO3649 ↓Putative gamma carboxymuconolactone decarboxylaseUnknown
−6.01YPO3650 ↓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.