Table 1 Y. pseudotuberculosis transcriptional variations discussed in this article compared with those recently published for Y. pestis [8]
Locus tags | gene transcription fold ratio human plasma/Luria Bertani broth (p-value) | ||||||
|---|---|---|---|---|---|---|---|
Y. pseudotuberculosis | Y. pestis | Gene Name | Putative product/function | Y. pseudotuberculosis | Y. pestis | ||
Iron uptake and storage | |||||||
YPTB1659 | YPO1783 | ftnA | ferritin | 0.180 | (< 0.001) | 0.341 | (0.001) |
YPTB0336 | YPO0279 | hmuV | ABC hemin transporter, ATP-binding subunit HmuV | 1.665 | (0.003) | 1.499 | (0.021) |
YPTB0338 | YPO0281 | hmuT | ABC transporter, periplasmic hemin-binding protein HmuT | 1.684 | (0.016) | 2.149 | (0.001) |
YPTB0339 | YPO0282 | hmuS | possible hemin degradation/transport protein HmuS | 1.577 | (0.022) | 1.984 | (< 0.001) |
YPTB0340 | YPO0283 | hmuR | TonB-dependent outer membrane hemin receptor, HmuR | 7.426 | (< 0.001) | 2.028 | (< 0.001) |
YPTB0739 | YPO3392 | fhuC | putative ABC type hydroxymate-dependent iron transport ATP binding protein | 1.932 | (0.047) | 1.500 | (0.258) |
YPTB0740 | YPO3391 | fhuD | putative ABC type hydroxamate-dependent iron uptake ATP binding protein | 1.836 | (0.021) | 1.174 | (0.486) |
YPTB1341 | YPO1310 | yiuA | putative ABC type periplasmic iron siderophore/cobalamin binding protein | 3.085 | (< 0.001) | 1.737 | (0.027) |
YPTB1343 | YPO1312 | yiuC | putative siderophore/cobalamin ABC transporter, ATP-binding subunit | 2.468 | (< 0.001) | 1.991 | (0.012) |
YPTB1512 | YPO1496 | putative heme-binding protein | 2.456 | (< 0.001) | 0.921 | (0.639) | |
YPTB1513 | YPO1497 | putative ABC transporter ATP-binding protein | 1.877 | (0.009) | 1.408 | (0.113) | |
YPTB1515 | YPO1499 | putative membrane protein | 1.521 | (0.045) | 1.018 | (0.921) | |
YPTB1540 | YPO1528 | ysuF | putative ferric iron reductase | 4.019 | (< 0.001) | 3.137 | (< 0.001) |
YPTB1541 | YPO1529 | ysuJ | putative decarboxylase | 2.092 | (< 0.001) | 1.246 | (0.236) |
YPTB1543 | YPO1531 | ysuH | putative siderophore biosynthetic enzyme | 1.896 | (0.021) | 1.213 | (0.387) |
YPTB1544 | YPO1532 | ysuG | putative siderophore biosynthetic enzyme | 2.403 | (0.005) | 1.830 | (0.006) |
YPTB1549 | YPO1537 | ysuR | putative OMR family iron-siderophore receptor | 2.610 | (< 0.001) | 3.273 | (0.001) |
YPTB2117 | YPO2193 | tonB | TonB protein | 5.464 | (< 0.001) | 2.563 | (0.001) |
YPTB2347 | YPO2439 | yfeA | ABC transporter, periplasmic iron siderophore-binding protein YfeA | 11.88 | (< 0.001) | 10.22 | (< 0.001) |
YPTB2348 | YPO2440 | yfeB | ABC chelated iron transporter, ATP-binding subunit YfeB | 3.141 | (< 0.001) | 2.772 | (0.001) |
YPTB2349 | YPO2441 | yfeC | ABC chelated iron transporter, permease subunit YfeC | 4.375 | (< 0.001) | 1.817 | (0.017) |
YPTB2350 | YPO2442 | yfeD | ABC chelated iron transporter, permease subunit YfeD | 2.103 | (< 0.001) | 1.369 | (0.195) |
YPTB2353 | YPO2445 | yfeE | putative yfeABCD locus regulator | 1.527 | (0.008) | 2.085 | (0.001) |
YPTB3263 | YPO0989 | iucA | possible siderophore biosynthesis protein, IucA familly | 3.789 | (< 0.001) | 2.059 | (0.033) |
YPTB3265 | YPO0992 | iucC | putative siderophore biosynthesis protein IucC | 2.600 | (< 0.001) | 0.920 | (0.711) |
YPTB3266 | YPO0993 | iucD | putative siderophore biosynthesis protein IucD | 2.151 | (0.002) | 0.631 | (0.036) |
YPTB3298 | YPO1011 | putative TonB-dependent O-M, iron siderophore receptor/tranporter | 2.150 | (0.005) | 1.845 | (0.018) | |
YPTB3383 | YPO0682 | exbB | possible MotA/TolQ/ExbB proton channel family protein | 4.165 | (< 0.001) | 3.021 | (< 0.001) |
YPTB3382 | YPO0683 | exbD | pExbD/TolR-family transport protein | 9.811 | (< 0.001) | 3.576 | (< 0.001) |
YPTB3701 | YPO0205 | bfd | putative bacterioferritin-associated ferredoxin | 1.857 | (0.002) | 3.195 | (< 0.001) |
YPTB3700 | YPO0206 | bfr | bacterioferritin | 1.153 | (0.255) | 4.483 | (< 0.001) |
YPTB3767 | YPO0133 | feoA | conserved hypothetical protein | 1.510 | (0.046) | 1.081 | (0.648) |
YPTB3769 | YPO0131 | feoC | conserved hypothetical protein | 1.900 | (0.001) | 1.964 | (0.002) |
YPTB3857 | YPO4022 | putative ABC transporter, periplasmic iron siderophore ferrichrome binding protein | 3.127 | (< 0.001) | 2.157 | (< 0.001) | |
YPTB3858 | YPO4023 | putative ABC iron siderophore transporter, permease subunit | 2.236 | (0.001) | 1.214 | (0.529) | |
YPTB3860 | YPO4025 | putative ABC iron siderophore transporter, ATP-binding subunit | 2.216 | (0.001) | 1.417 | (0.041) | |
YPTB1246 | YPO1207 | katA | putative catalase | 0.324 | (< 0.001) | 0.556 | (0.002) |
YPTB0811 | YPO3319 | katY | putative catalase-hydroperoxidase HPI I | 0.603 | (0.009) | 0.717 | (0.342) |
Biotin operon | |||||||
YPTB1181 | YPO1150 | bioA | putative adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 3.377 | (< 0.001) | 2.512 | (0.002) |
YPTB1183 | YPO1152 | bioF | putative 8-amino-7-oxononanoate synthase | 3.800 | (< 0.001) | 2.595 | (< 0.001) |
YPTB1184 | YPO1153 | bioC | putative biotin synthesis protein BioC | 1.784 | (0.004) | 1.351 | (0.374) |
YPTB1185 | YPO1154 | bioD | putative dethiobiotin synthetase | 2.499 | (0.002) | 1.780 | (0.026) |
Superoxyde dismutases | |||||||
YPTB3925 | YPO4061 | sodA | putative superoxide dismutase [Mn] | 3.101 | (< 0.001) | 1.796 | (0.049) |
YPTB2299 | YPO2386 | sodB | superoxide dismutase [Fe] | 0.090 | (< 0.001) | 0.326 | (< 0.001) |
Ribonucleotides reductases (RNR) | |||||||
YPTB2956 | YPO2650 | nrdI | probable NrdI protein homologue | 2.842 | (0.001) | 8.784 | (< 0.001) |
YPTB2957 | YPO2649 | nrdE | putative ribonucleoside-diphosphate reductase 2 alpha chain | 4.745 | (< 0.001) | 9.007 | (< 0.001) |
YPTB2958 | YPO2648 | nrdF | putative ribonucleoside-diphosphate reductase 2 beta chain | 2.672 | (0.002) | 2.142 | (0.011) |
YPTB2955 | YPO2651 | nrdH | putative glutaredoxin | 1.407 | (0.152) | 3.439 | (< 0.001) |
YPTB1254 | YPO1214 | nrdA | putative ribonucleoside-diphosphate reductase 1 alpha chain | 0.329 | (< 0.001) | 0.668 | (0.085) |
YPTB1253 | YPO1213 | nrdB | putative ribonucleoside-diphosphate reductase 1 beta chain | 0.815 | (0.351) | 0.579 | (0.020) |
YPTB0519 | YPO3454 | nrdD | putative anaerobic ribonucleoside-triphosphate reductase | 0.614 | (0.025) | 0.373 | (< 0.001) |
YPTB0518 | YPO3455 | nrdG | putative anaerobic ribonucleotide reductase activating protein | 0.440 | (0.001) | 0.508 | (0.019) |
Mannose and glucose uptake | |||||||
YPTB1634 | YPO1758 | manX | probable PTS system, mannose-specific IIAB component | 2.673 | (< 0.001) | 3.234 | (< 0.001) |
YPTB1633 | YPO1757 | manY | probable PTS system, mannose-specific IIC component | 1.991 | (0.006) | 2.201 | (< 0.001) |
YPTB1632 | YPO1756 | manZ | probable PTS system, mannose-specific IID component | 3.084 | (< 0.001) | 3.676 | (< 0.001) |
YPTB2463 | YPO1608 | ptsG, | putative PTS system, glucose-specific IIBC component | 4.033 | (< 0.001) | 1.708 | (0.027) |
YPTB2715 | YPO2993 | ptsH | probable PTS system, phosphocarrier protein | 1.697 | (0.002) | 1.422 | (0.109) |
YPTB2716 | YPO2994 | ptsI | putative PTS sytem, enzyme I component | 1.946 | (< 0.001) | 1.351 | (0.038) |
YPTB2717 | YPO2995 | crr | putative PTS system, glucose-specific IIA component, permease | 1.611 | (0.002) | 1.440 | (0.117) |
Sugar metabolism | |||||||
YPTB0074 | YPO0078 | pfkA | putative 6-phosphofructokinase | 1.594 | (0.017) | 1.430 | (0.073) |
YPTB3195 | YPO0920 | fbaA, fba, fda | possible fructose-bisphosphate aldolase class II | 1.325 | (0.049) | 1.504 | (0.104) |
YPTB3196 | YPO0921 | pgk | putative phosphoglycerate kinase | 1.365 | (0.024) | 1.365 | (0.099) |
YPTB1166 | YPO1133 | gpmA, gpm | putative phosphoglycerate mutase 1 | 3.179 | (< 0.001) | 3.650 | (< 0.001) |
YPTB2047 | YPO2064 | pykA | putative pyruvate kinase II | 0.486 | (0.001) | 0.604 | (0.013) |
YPTB2306 | YPO2393 | pykF | probable pyruvate kinase I | 2.282 | (< 0.001) | 1.322 | (0.185) |
YPTB3762 | YPO0138 | pck | putative phosphoenolpyruvate carboxykinase [ATP] | 0.395 | (0.001) | 1.213 | (0.460) |
YPTB2103 | YPO2180 | adhE, ana | putative aldehyde-alcohol dehydrogenase | 2.116 | (0.001) | 3.383 | (< 0.001) |
YPTB0460 | YPO3516 | mdh | putative malate dehydrogenase | 0.665 | (0.010) | 0.394 | (< 0.001) |
YPTB0796 | YPO3335 | fumA, fumB | putative fumarase A fumarate hydratase class I, aerobic isozyme | 0.351 | (< 0.001) | 0.501 | (0.020) |
YPTB0413 | YPO0360 | frdA | putative fumarate reductase flavoprotein subunit | 0.156 | (< 0.001) | 0.299 | (< 0.001) |
YPTB0412 | YPO0359 | frdB | putative fumarate reductase iron-sulfur protein | 0.127 | (< 0.001) | 0.217 | (< 0.001) |
YPTB0411 | YPO0358 | frdC | putative fumarate reductase hydrophobic protei | 0.248 | (< 0.001) | 0.403 | (< 0.001) |
YPTB0410 | YPO0357 | frdD | putative fumarate reductase hydrophobic protein | 0.393 | (0.001) | 0.372 | (< 0.001) |
YPTB1145 | YPO1111 | sdhA | putative succinate dehydrogenase flavoprotein subunit | 0.497 | (< 0.001) | 0.124 | (< 0.001) |
YPTB1144 | YPO1110 | sdhD | putative succinate dehydrogenase hydrophobic membrane anchor protein | 0.501 | (< 0.001) | 0.165 | (< 0.001) |
YPTB1143 | YPO1109 | sdhC | putative succinate dehydrogenase cytochrome b-556 subunit | 0.553 | (0.016) | 0.241 | (0.001) |
YPTB1146 | YPO1112 | sdhB | putative succinate dehydrogenase iron-sulfur protein | 0.592 | (0.004) | 0.196 | (< 0.001) |
YPTB1149 | YPO1115 | sucC | putative succinyl-CoA synthetase beta chain | 0.419 | (< 0.001) | 0.205 | (< 0.001) |
YPTB1150 | YPO1116 | sucD | putative succinyl-CoA synthetase alpha chain | 0.525 | (< 0.001) | 0.236 | (0.001) |
YPTB1148 | YPO1114 | sucB | putative dihydrolipoamide succinyltransferase component | 0.610 | (0.014) | 0.267 | (0.003) |
YPTB1147 | YPO1113 | sucA | putative 2-oxoglutarate dehydrogenase E1 component | 0.516 | (0.007) | 0.193 | (< 0.001) |
YPTB0716 | YPO3415 | acnB | putative aconitate hydratase 2 | 0.510 | (< 0.001) | 0.319 | (< 0.001) |
YPTB3656 | YPO3725 | aceA, icl | isocitrate lyase | 2.068 | (0.003) | 1.298 | (0.319) |
YPTB3657 | YPO3726 | aceB, mas | malate synthase A | 1.875 | (0.053) | 1.089 | (0.710) |
YPTB2222 | YPO2300 | fnr, nirR | putative fumarate and nitrate reduction regulatory protein | 0.699 | (0.002) | 0.877 | (0.621) |
YPTB0601 | YPO0458 | arcA | probable response regulator (OmpR family) | 0.464 | (0.001) | 0.705 | (0.036) |
Porins | |||||||
YPTB1964 | YPO1411 | ompC2 | putative outer membrane protein C2, porin | 0.835 | (0.447) | 1.827 | (0.001) |
YPTB1261 | YPO1222 | ompC | putative outer membrane protein C, porin | 0.285 | (< 0.001) | 0.659 | (0.013) |
YPTB1453 | YPO1435 | ompA | putative outer membrane porin A protein | 1.085 | (0.372) | 0.587 | (0.070) |
Chromosomal virulence factors | |||||||
YPTB1668 | YPO3944 | inv | putative invasin | 0.501 | (< 0.001) | 0.993 | (0.976) |
YPTB1334 | YPO1303 | psaA | pH 6 antigen precursor | (< 0.001) | 0.367 | (0.154) | |
YPTB1335 | YPO1304 | psaB | chaperone protein PsaB precursor | 0.216 | (< 0.001) | 0.700 | (0.214) |
YPTB1332 | YPO1301 | psaE | putative regulatory protein | 1.987 | (0.002) | 2.619 | (< 0.001) |
pYV-encoded virulence factors – Type Three Secretion System | |||||||
pYV0062 | YPCD1.36c | yscX | YscX, putative type III secretion protein | 1.629 | (0.009) | 0.873 | (0.444) |
pYV0014 | YPCD1.89 | possible transposase remnant (pseudogene) | 1.789 | (0.025) | 0.786 | (0.899) | |
pYV0076 | YPCD1.49 | lcrF | LcrF, VirF; putative thermoregulatory protein | 1.441 | (0.042) | 1.311 | (0.216) |
pYV0058 | YPCD1.32c | lcrG | LcrG, putative Yop regulator | 1.713 | (0.014) | 0.941 | (0.853) |
pYV0056 | YPCD1.30c | lcrH, sycD | LcrH, SycD; low calcium response protein H | 3.522 | (< 0.001) | 0.898 | (0.480) |
pYV0059 | YPCD1.33c | lcrR | LcrR, hypothetical protein | 1.469 | (0.001) | 0.700 | (0.129) |
pYV0057 | YPCD1.31c | lcrV | LcrV, putative V antigen, antihost protein/regulator | 1.904 | (< 0.001) | 1.302 | (0.051) |
pYV0024 | YPCD1.05c | sycE | SycE, yerA; putative yopE chaperone | 5.781 | (< 0.001) | 1.344 | (0.165) |
pYV0020 | YPCD1.95c | sycH | SycH, putative yopH targeting protein | 5.088 | (< 0.001) | 2.029 | (0.002) |
pYV0017 | YPCD1.91 | putative resolvase | 0.341 | (< 0.001) | 1.152 | (0.705) | |
pYV0075 | YPCD1.48 | virG | VirG; putative Yop targeting lipoprotein | 1.957 | (0.015) | 1.544 | (0.023) |
pYV0055 | YPCD1.29c | yopB | YopB, putative Yop targeting protein | 2.816 | (< 0.001) | 0.956 | (0.758) |
pYV0054 | YPCD1.28c | yopD | YopD, putative Yop negative regulation/targeting component | 2.933 | (< 0.001) | 0.950 | (0.833) |
pYV0047 | YPCD1.26c | yopM | YopM, putative targeted effector protein | 3.467 | (< 0.001) | 1.044 | (0.845) |
pYV0065 | YPCD1.39c | yopN | YopN, LcrE; putative membrane-bound Yop targeting protein | 2.612 | (< 0.001) | 0.878 | (0.475) |
pYV0078 | YPCD1.51 | hypothetical protein | 3.037 | (0.002) | 1.056 | (0.716) | |
pYV0079 | YPCD1.52 | yscC | YscC, putative type III secretion protein | 2.383 | (0.001) | 0.715 | (0.221) |
pYV0080 | YPCD1.53 | yscD | YscD, putative type III secretion protein | 2.541 | (< 0.001) | 0.715 | (0.095) |
pYV0081 | YPCD1.54 | yscE | YscE, putative type III secretion protein | 2.710 | (0.001) | 0.543 | (0.056) |
pYV0082 | YPCD1.55 | yscF | YscF, putative type III secretion protein | 2.116 | (0.017) | 0.616 | (0.135) |
pYV0083 | YPCD1.56 | yscG | YscG, putative type III secretion protein | 2.462 | (< 0.001) | 0.905 | (0.595) |
pYV0085 | YPCD1.58 | yscI | YscI, LcrO; putative type III secretion protein | 1.864 | (0.003) | 1.024 | (0.906) |
pYV0089 | YPCD1.62 | yscM, lcrQ | YscM, LcrQ, putative type III secretion regulatory | 0.678 | (0.036) | 0.755 | (0.052) |
pYV0067 | YPCD1.40 | putative Yops secretion ATP synthase | 2.855 | (< 0.001) | 0.971 | (0.886) | |
pYV0068 | YPCD1.41 | yscO | YscO, putative type III secretion protein | 3.087 | (< 0.001) | 0.974 | (0.913) |
pYV0070 | YPCD1.43 | yscQ | YscQ, putative type III secretion protein | 1.635 | (0.026) | 1.214 | (0.430) |
pYV0071 | YPCD1.44 | yscR | YscR, putative Yop secretion membrane protein | 1.948 | (0.012) | 1.296 | (0.269) |
pYV0072 | YPCD1.45 | yscS | YscS, putative type III secretion protein | 2.331 | (< 0.001) | 1.218 | (0.280) |
pYV-encoded virulence factors – Others | |||||||
pYV0013 | YPCD1.88c | yadA | YadA, Yersinia adhesion | 13.52 | (< 0.001) | 1.040 | (0.861) |