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Table 1 Y. pseudotuberculosis transcriptional variations discussed in this article compared with those recently published for Y. pestis [8]

From: Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression

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)