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. 2017 Mar 20;8:370. doi: 10.3389/fpls.2017.00370

Table 3.

R. solanacearum UY031 genes differentially expressed in potato roots vs. solid rich medium.

Function UY031 NCBI locusa UY031 Prokka locusb GMI1000 locusc Log2FC Gene name Gene product
RALSTONIA SOLANACEARUM VIRULENCE GENES
Type III secretion system and effectors RSUY_RS19685 RSUY_40420 RSp0855 7.80 hrpY Type III secretion system protein HrpY
RSUY_RS19795 RSUY_40640 RSp0877 4.66 popA Type III effector protein PopA
RSUY_RS19790 RSUY_40630 RSp0876 4.27 popB Type III effector protein PopB
RSUY_RS20380 RSUY_41860 RSp1024 3.96 awr5_1 Type III effector protein AWR5
RSUY_RS22080 RSUY_45370 RSp0900 3.94 popF1 Type III effector protein PopF1
RSUY_RS16550 RSUY_33840 RSp0304 3.76 ripD Type III effector protein RipD
RSUY_RS19785 RSUY_40620 RSp0875 3.35 popC Type III effector protein PopC
RSUY_RS19735 RSUY_40520 RSp0865 3.08 hrpK Type III secretion system protein HrpK
RSUY_RS19690 RSUY_40430 RSp0856 2.86 hrpX Type III secretion system protein HrpX
RSUY_RS19770 RSUY_40590 RSp0872 2.69 hrcT HrcT family type III secretion system export apparatus protein
RSUY_RS09370 RSUY_19160 − 2.44 ripV2 Type III effector protein RipV2
RSUY_RS19150 RSUY_39290 RSp0731 −2.61 ripTPS Trehalose-6-phosphate synthase
RSUY_RS21730 RSUY_44630 RSp1374 −2.88 ripS2 Type III effector protein SKWP2
RSUY_RS21610 RSUY_44390 RSp1277 −3.50 ripQ Type III effector protein RipQ
Motility RSUY_RS04635 RSUY_09450 RSc0727 3.14 pilV Type IV pilus modification protein PilV
RSUY_RS22435 RSUY_46110 RSp1412 2.65 flhC Transcriptional activator FlhC
RSUY_RS02415 RSUY_04970 RSc2974 2.62 pilN Tfp pilus assembly protein PilN
RSUY_RS22440 RSUY_46120 RSp1413 2.47 flhD Flagellar transcriptional activator FlhD
RSUY_RS04630 RSUY_09440 RSc0726 2.30 pilW Pilus assembly protein PilW
RSUY_RS02410 RSUY_04960 RSc2975 2.28 pilM Pilus assembly protein PilM
RSUY_RS04330 RSUY_08850 RSc0668 2.20 pilG Two-component system response regulator
RSUY_RS04335 RSUY_08860 RSc0669 1.95 pilH Two-component system response regulator
RSUY_RS11250 RSUY_22930 RSc1986 1.24 fimV Tfp pilus assembly protein FimV
RSUY_RS04590 RSUY_09370 RSc0718 −3.56 pilY Pilus assembly protein PilY
Stress responses RSUY_RS22220 RSUY_45660 RSp1581 3.16 katE Catalase katE
RSUY_RS00425 RSUY_00900 RSc3398 3.10 hmpX flavohemoprotein
RSUY_RS17495 RSUY_35830 RSp0245 2.64 ahpC1 Peroxiredoxin
RSUY_RS17500 RSUY_35840 RSp0246 2.21 ahpF Alkyl hydroperoxide reductase subunit F
RSUY_RS04770 RSUY_09720 RSc0754 1.96 − Peroxidase
RSUY_RS04870 RSUY_09930 RSc0775 1.82 katGb Catalase katGb
RSUY_RS01185 RSUY_02450 RSc3254 −3.11 − alkyl hydroperoxide reductase
Other virulence factors RSUY_RS18925 RSUY_38830 RSp0676 3.71 metE Methionine synthase II (cobalamin-independent)
RSUY_RS01465 RSUY_03030 RSp0693 3.38 hdfA Dioxygenase
RSUY_RS14015 RSUY_28660 RSc0408 2.22 rpoN1 RNA polymerase sigma-54 factor
RSUY_RS17795 RSUY_36440 RSp1529 1.72 efe 2-oxoglutarate-dependentethylene/succinate-forming enzyme
RSUY_RS04455 RSUY_09100 RSc0693 −2.19 kdtA 3-deoxy-D-manno-octulosonic-acid transferase
Type II Secretion System RSUY_RS01675 RSUY_03470 RSc3109 −2.63 gspJ General secretion pathway protein GspJ
RSUY_RS16275 RSUY_33280 RSp0148 −3.19 gspE General secretion pathway protein GspE
Type VI secretion system RSUY_RS19215 RSUY_39440 RSp0746 2.25 − Type VI secretion protein
Cofactor metabolism and transport RSUY_RS04050 RSUY_08280 RSc2633 −2.92 pabB aminodeoxychorismate synthase component I
Quorum sensing RSUY_RS01010 RSUY_02100 RSc3286 −3.24 solI Acyl-homoserine-lactone synthase
RALSTONIA SOLANACEARUM GENES INVOLVED IN PLANT COLONIZATION
Aminoacid metabolism RSUY_RS21930 RSUY_45070 RSp1263 2.019462 nadB2 L-aspartate oxidase
RSUY_RS04790 RSUY_09760 RSc0758 1.900185 − Tryptophan 2,3-dioxygenase 1
RSUY_RS01705 RSUY_03530 RSc3103 −1.93219 − 4-hydroxyphenylpyruvate dioxygenase
RSUY_RS00955 RSUY_01990 RSc3295 −1.97096 gcvP glycine dehydrogenase
RSUY_RS00965 RSUY_02010 RSc3293 −2.1387 gcvT aminomethyltransferase
RSUY_RS08880 RSUY_18160 RSc1381 −2.22786 − glutathione ABC transporter permease GsiC
RSUY_RS02965 RSUY_06080 RSc2867 −2.45751 dppD1 peptide ABC transporter substrate-bindingprotein
RSUY_RS19000 RSUY_38980 RSp0691 −2.63642 hmgA homogentisate 1,2-dioxygenase
RSUY_RS08860 RSUY_18120 RSc1377 −2.72373 − transcriptional regulator
RSUY_RS00950 RSUY_01980 RSc3296 −2.82715 sdaA2 L-serine ammonia-lyase / L-serine ammonia-lyase
RSUY_RS18995 RSUY_38970 RSp0690 −2.93699 hmgB fumarylacetoacetase
RSUY_RS08895 RSUY_18190 RSc1384 −3.10843 − D-aminopeptidase
RSUY_RS08865 RSUY_18130 RSc1378 −3.44342 − isoaspartyl peptidase
Carbohydrate metabolism RSUY_RS22935 RSUY_47230 RSp1633 −1.90617 xylF D-xylose ABC transporter substrate-bindingprotein
RSUY_RS22945 RSUY_47250 RSp1635 −2.40016 xylH xylose ABC transporter permease
RSUY_RS21965 RSUY_45140 RSp1270 −2.4781 − glycosyl hydrolase
RSUY_RS22940 RSUY_47240 RSp1634 −2.98048 xylG D-xylose ABC transporter ATP-binding protein
RSUY_RS17060 RSUY_34910 RSp0423 −3.65067 − aldolase
RSUY_RS22950 RSUY_47260 RSp1636 −4.75552 − NAD-dependent dehydratase
Transcriptional and response regulators RSUY_RS08455 RSUY_17320 RSc1295 4.365537 − MarR family transcriptional regulator
RSUY_RS22955 RSUY_47270 RSp1637 −1.62836 − LacI family transcriptional regulator
RSUY_RS06090 RSUY_12470 RSc2209 −1.75486 − LysR family transcriptional regulator
RSUY_RS00225 RSUY_00480 RSc0040 −2.26596 − two-component system response regulator
RSUY_RS00910 RSUY_01900 RSc3301 −2.57757 putA trifunctional transcriptional regulator
Siderophore biosynthesis RSUY_RS17055 RSUY_34900 RSp0422 −2.30463 − siderophore biosynthesis protein
RSUY_RS03590 RSUY_07350 RSc2729 −2.4997 − membrane protein / membrane protein
RSUY_RS17040 RSUY_34870 RSp0419 −2.75083 − siderophore biosynthesis protein
RSUY_RS17050 RSUY_34890 RSp0421 −2.94313 − siderophore biosynthesis protein
Nitrogen metabolism RSUY_RS14025 RSUY_28680 RSc0406 2.27 ptsN PTS IIA-like nitrogen-regulatory protein PtsN
RSUY_RS17995 RSUY_36860 RSp0980 2.24 narL DNA-binding response regulator
RSUY_RS11470 RSUY_23380 RSc2031 −3.3167 ureE urease accessory protein UreE
Transporters RSUY_RS20760 RSUY_42660 RSp1283 2.005142 − porin
RSUY_RS11090 RSUY_22610 RSc1951 −2.22 − cation acetate symporter
RSUY_RS22930 RSUY_47220 RSp1632 −2.42488 oprB porin
RSUY_RS05795 RSUY_11880 RSc2274 −2.96894 ragC Cation efflux protein
Organic acid metabolism RSUY_RS19540 RSUY_40110 RSp0826 3.403389 − 5-dehydro-4-deoxyglucarate dehydratase
RSUY_RS19480 RSUY_39990 RSp0814 2.44631 mqo malate:quinone oxidoreductase
RSUY_RS11960 RSUY_24410 RSc2358 −1.7429 ppc phosphoenolpyruvate carboxylase
Proteases RSUY_RS12475 RSUY_25460 RSc2465 2.359347 clpS ATP-dependent Clp protease adaptor ClpS
RSUY_RS18550 RSUY_38040 RSp0603 2.211049 − serine protease
RSUY_RS14120 RSUY_28870 RSc0388 −1.98903 − zinc protease
Lipid metabolism RSUY_RS17295 RSUY_35410 − 2.478807 − Acyl-CoA synthetase
RSUY_RS01975 RSUY_04090 RSc3052 −2.40887 glpK glycerol kinase
Energy RSUY_RS08510 RSUY_17430 RSc1305 3.640811 fpr ferredoxin–NADP(+) reductase
RSUY_RS08360 RSUY_17120 RSc1276 3.417949 − cytochrome c oxidase, cbb3-type subunit I
Signal transduction RSUY_RS23055 RSUY_47460 RSc0617 1.988909 − signal peptidase
RSUY_RS01700 RSUY_03520 RSc3104 1.73953 − calcium sensor EFh
Stress related RSUY_RS13090 RSUY_26760 RSc0582 2.610905 − avrD-like protein
RSUY_RS21705 RSUY_44580 RSp1306 −2.11404 speE2 spermidine synthetase
Cofactor metabolism and transport RSUY_RS02845 RSUY_05840 RSc2886 −2.57058 − adenylate cyclase
Recombination and repair RSUY_RS07890 RSUY_16140 RSc1189 −2.09233 − recombinase RecB
Translation RSUY_RS15445 RSUY_31580 RSc0085 −2.70405 cca multifunctional CCA protein
Hypothetical proteins RSUY_RS19605 RSUY_40240 − 4.758974 − hypothetical protein
RSUY_RS17575 RSUY_35990 RSp0261 4.146986 − membrane protein
RSUY_RS16950 RSUY_34650 RSp0403 3.74634 − hypothetical protein
RSUY_RS22040 RSUY_45290 RSp0982 3.589851 − hypothetical protein
RSUY_RS12885 RSUY_26330 RSc0613 3.409348 − hypothetical protein
RSUY_RS08290 RSUY_16960 RSc1262 3.394474 − hypothetical protein
RSUY_RS06775 RSUY_13900 RSc0971 3.025981 − hypothetical protein
RSUY_RS20375 RSUY_41850 − 3.019263 − hypothetical protein
RSUY_RS01105 RSUY_02290 RSc3270 2.806237 − hypothetical protein
RSUY_RS15470 RSUY_31630 RSc0080 2.792044 − hypothetical protein
RSUY_RS14600 RSUY_29830 RSc0297 2.641501 − hypothetical protein
RSUY_RS05760 RSUY_11810 RSc2280 2.552951 − hypothetical protein
RSUY_RS10215 RSUY_20850 RSc1622 2.233892 − hypothetical protein
RSUY_RS12820 RSUY_26200 − 2.213444 − hypothetical protein
RSUY_RS22015 RSUY_45240 RSp1546 2.185718 − hypothetical protein
RSUY_RS01435 RSUY_02950 RSc0616 2.148496 − hypothetical protein
RSUY_RS06705 RSUY_13730 RSc0953 2.116755 − hypothetical protein
RSUY_RS01875 RSUY_03890 RSc3072 2.098485 − hypothetical protein
RSUY_RS04190 RSUY_08560 RSc2555 1.909667 − membrane protein
RSUY_RS05940 RSUY_12170 RSc2238 1.775776 − hypothetical protein
RSUY_RS04990 RSUY_10170 RSc0799 −1.56204 − hypothetical protein
RSUY_RS02135 RSUY_04410 RSc3030 −2.05111 − hypothetical protein
RSUY_RS20585 RSUY_42270 − −2.22451 − membrane protein
RSUY_RS14980 RSUY_30600 RSc0211 −2.4077 − membrane protein
RSUY_RS17045 RSUY_34880 RSp0420 −2.58002 − membrane protein
RSUY_RS15175 RSUY_31000 RSc0146 −2.83465 − hypothetical protein
PUTATIVE VIRULENCE GENES AND PLANT COLONIZATION METABOLIC ACTIVITIES
Transporters RSUY_RS00490 RSUY_01050 RSc3386 3.50 − metal ABC transporter substrate-binding protein
RSUY_RS17605 RSUY_36050 RSp0429 3.24 − MFS transporter
RSUY_RS20020 RSUY_41100 RSp0931 2.92 − ABC transporter
RSUY_RS19045 RSUY_39070 RSp0706 −1.77 − metal-dependent hydrolase
RSUY_RS18205 RSUY_37320 RSp0481 −2.03 − ABC transporter substrate-binding protein
RSUY_RS18195 RSUY_37300 RSp0479 −2.09 − amino acid ABC transporter ATPase
RSUY_RS21220 RSUY_43600 RSp1181 −2.11 − transporter
RSUY_RS18895 RSUY_38770 RSp0670 −2.14 − acriflavine resistance protein B / transporter protein
RSUY_RS17425 RSUY_35690 RSp0234 −2.37 − MFS transporter
RSUY_RS09885 RSUY_20190 RSc1738 −2.40 − ABC transporter ATPbinding protein
RSUY_RS21615 RSUY_44400 RSp1278 −2.49 − MFS transporter
RSUY_RS21315 RSUY_43800 RSp1200 −2.60 − RND transporter
RSUY_RS03020 RSUY_06190 RSc2856 −2.72 − MFS transporter
RSUY_RS01560 RSUY_03230 RSc3134 −2.94 − MFS transporter
RSUY_RS06940 RSUY_14230 RSc1002 −2.95 − membrane protein
RSUY_RS15855 RSUY_32410 − −2.98 oprM RND transporter
RSUY_RS20395 RSUY_41890 − −2.99 ybtP ABC transporter ATP-binding protein
RSUY_RS15985 RSUY_32660 RSp0078 −3.05 − MFS transporter
RSUY_RS18200 RSUY_37310 RSp0480 −3.17 − amino acid ABC transporter permease
RSUY_RS19050 RSUY_39080 RSp0707 −3.19 − ABC transporter ATP-binding protein
RSUY_RS21055 RSUY_43260 RSp1114 −3.35 − RND transporter
RSUY_RS01890 RSUY_03920 RSc3069 −3.50 − MFS transporter
RSUY_RS22255 RSUY_45730 RSp1595 −3.73 − ABC transporter ATP-binding protein
RSUY_RS04055 RSUY_08290 RSc2632 −3.85 − ABC transporter ATP-binding protein
Lipid metabolism RSUY_RS14075 RSUY_28780 RSc0396 3.29 ipk 4-diphosphocytidyl-2C-methyl-D-erythritolkinase
RSUY_RS10705 RSUY_21830 RSc1540 3.14 − acyltransferase
RSUY_RS19325 RSUY_39670 − 2.15 − Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase
RSUY_RS09620 RSUY_19650 RSc1772 −2.06 − alpha/beta hydrolase
RSUY_RS14790 RSUY_30210 RSc0262 −2.17 − glyoxylate/hydroxypyruvate reductase A
RSUY_RS00675 RSUY_01440 RSc3346 −2.24 − alpha/beta hydrolase
RSUY_RS13905 RSUY_28430 RSc0427 −2.30 − beta-ketoacyl-[acyl-carrier-protein] synthaseII
RSUY_RS09090 RSUY_18590 − −2.77 − Lysophospholipase
RSUY_RS01035 RSUY_02150 RSc3283 −2.82 glxR 2-hydroxy-3-oxopropionate reductase
RSUY_RS10955 RSUY_22330 RSc1874 −2.82 − NUDIX hydrolase
RSUY_RS14265 RSUY_29170 RSc0357 −2.86 gpsA glycerol-3-phosphate dehydrogenase (NAD(P)(+))
RSUY_RS11775 RSUY_23990 RSc2091 −3.04 − ABC transporter permease
RSUY_RS15945 RSUY_32580 RSp0036 −3.05 − acyl-CoA dehydrogenase
RSUY_RS21855 RSUY_44890 RSp1245 −3.30 − esterase
RSUY_RS20415 RSUY_41930 − −3.31 − Acyl-coenzyme A synthetase
RSUY_RS21590 RSUY_44350 − −3.32 − Dehydrogenases
RSUY_RS20425 RSUY_41950 − −3.60 − Polyketide synthase
RSUY_RS14720 RSUY_30070 RSc0275 −3.61 − short-chain dehydrogenase
RSUY_RS10105 RSUY_20630 RSc1643 −4.27 ispD 2-C-methyl-D-erythritol 4-phosphatecytidylyltransferase
Other putative virulence factors RSUY_RS16085 RSUY_32860 RSp0112 2.09 − carbonic anhydrase
RSUY_RS00735 RSUY_01550 RSp0085 1.66 − type IV secretion protein Rhs
RSUY_RS00905 RSUY_01890 RSc3302 −2.04 priA primosomal protein N'
RSUY_RS15535 RSUY_31760 RSc0068 −2.06 smf DNA processing protein DprA
RSUY_RS14955 RSUY_30550 RSc0222 −2.29 rtcR Fis family transcriptional regulator
RSUY_RS17190 RSUY_35180 RSp0181 −3.10 − activator of HSP90 ATPase
RSUY_RS14940 RSUY_30520 RSc0226 −3.23 rtcA RNA 3'-terminal phosphate cyclase
Sulfur metabolism and transport RSUY_RS12265 RSUY_25040 RSc2425 3.22 cysI1 Sulfite reductase/sulfite reductase
RSUY_RS07020 RSUY_14390 RSc1019 2.23 nifS Cysteine desulfurase IscS
RSUY_RS12250 RSUY_25010 RSc2422 2.14 cysD Sulfate adenylyltransferase small subunit
RSUY_RS12245 RSUY_25000 RSc2421 1.89 cysN Sulfate adenylyltransferase
RSUY_RS07025 RSUY_14400 RSc1020 1.60 nifU Iron-sulfur cluster scaffold-like protein
RSUY_RS17845 RSUY_36540 RSp1519 −3.36 − Membrane protein
Cofactor metabolism and transport RSUY_RS11705 RSUY_23850 RSc2077 1.85 ilvI acetolactate synthase
RSUY_RS18660 RSUY_38270 RSp0615 −2.97 cbiA cobyrinic acid a,c-diamide synthase
RSUY_RS18690 RSUY_38330 RSp0621 −2.97 cbiL precorrin-2 C(20)-methyltransferase
RSUY_RS18680 RSUY_38310 RSp0619 −3.00 cbiG cobalamin biosynthesis protein CbiG
RSUY_RS03905 RSUY_07990 RSc2663 −3.51 − ATP:cob(I)alamin adenosyltransferase
Phosphate mobilization RSUY_RS10765 RSUY_21950 RSc1529 2.01 pstS1 phosphate ABC transporter substrate-bindingprotein PstS
RSUY_RS07715 RSUY_15790 RSc1160 1.63 suhB Inositol monophosphatase
RSUY_RS10750 RSUY_21920 RSc1532 1.52 pstB phosphate ABC transporter ATP-binding protein
a

According to R. solanacearum UY031 genome annotation available at GenBank (NCBI).

b

According to R. solanacearum UY031 genome annotation from Guarischi-Sousa et al. (2016).

c

According to the homology Supplementary Table 1.