Table 1

Genes up-regulated at 18°C in P. syringae pv. phaseolicola NPS3121
Gen/ORF Gene product Ratio
Cluster 1: Phaseolotoxin production (Pht cluster)
PSPPH_4299 Hypothetical protein (phtU) 11.86
PSPPH_4300 Membrane protein, putative (phtT) 8.70
PSPPH_4301 Adenylylsulfate kinase (phtS) 13.50
PSPPH_4302 Conserved hypothetical protein (phtQ) 6.23
PSPPH_4305 Hypothetical protein (phtO) 8.78
PSPPH_4306 Hypothetical protein (phtM) 15.90
PSPPH_4306 Hypothetical protein (phtM) 7.29
PSPPH_4307 pyruvate phosphate dikinase PEP/pyruvate binding subunit 23.74
PSPPH_4317 Hypothetical protein 11.52
PSPPH_4323 Hypothetical protein 2.13
argK control 3.30
phtA control 4.96
phtD control 6.50
desI control 14.97
phtL control 7.64
phtMN control 1.81
amtA control 10.34
Cluster 2: Genes involved in Non-ribosomal synthesis
PSPPH_4538 transposon Tn7-like transposase protein A 1.67
PSPPH_4539 transposon Tn7-like transposase protein B 1.70
PSPPH_4544 hypothetical protein PSPPH_4544 8.08
PSPPH_4544 hypothetical protein PSPPH_4544 7.26
PSPPH_4546 hypothetical protein 9.44
PSPPH_4549 hypothetical protein PSPPH_4549 9.13
PSPPH_4553 major facilitator family protein 15.83
PSPPH_4554 arginine aminomutase, putative 12.67
PSPPH_4555 conserved hypothetical protein 7.46
Cluster 3: Type VI secretion system
PSPPH_0122 hcp 2.13
PSPPH_0124 hypothetical protein 1.66
PSPPH_0125 icmF 1.94
PSPPH_0131 HsiG 1.61
PSPPH_0135 hypothetical protein 1.64
PSPPH_4978 prophage PSPPH06, putative reverse transcriptase/maturase 1.65
PSPPH_4979 prophage PSPPH06, putative reverse transcriptase/maturase 2.68
PSPPH_4984 prophage PSPPH06, site-specific recombinase, phage integrase family 1.70
Cluster 4: Genes involved in membrane synthesis
PSPPH_1430 leucine-rich repeat domain protein 1.75
PSPPH_1464 lipoprotein, putative 1.66
PSPPH_1708 ABC transporter, periplasmic substrate-binding protein 1.84
PSPPH_2260 UTP-glucose-1-phosphate uridylyltransferase 1.72
PSPPH_2542 membrane protein, putative 1.94
PSPPH_2643 outer membrane efflux protein 1.68
PSPPH_2654 lipoprotein, putative 1.55
PSPPH_2842 lipoprotein, putative 1.55
PSPPH_3226 glycosyl transferase, group 1 family protein 1.72
PSPPH_3288 predicted periplasmic lipoprotein 2.05
PSPPH_3810 lipoprotein 1.71
PSPPH_3916 membrane protein, putative 1.86
PSPPH_4139 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1.55
PSPPH_4669 acetyltransferase, GNAT family 1.73
PSPPH_4682 lipopolysaccharide biosynthesis protein, putative 3.03
PSPPH_5220 inner membrane protein, 60 kDa 1.61
Cluster 5: Genes involved in motility
PSPPH_0730 type IV pilus-associated protein, putative 1.74
PSPPH_0818 type IV pilus prepilin peptidase PilD 1.53
PSPPH_0820 type IV pilus biogenesis protein PilB 1.53
PSPPH_1200 pili assembly chaperone 2.03
PSPPH_3387 flagellar regulator FleQ 1.64
PSPPH_3880 CheW domain protein WspB 1.94
PSPPH_3881 methyl-accepting chemotaxis protein WspA 1.5
Cluster 6: Oxidative stress response genes and iron metabolism
PSPPH_1309 cysteine desulfurase IscS 1.93
PSPPH_1311 iron-sulfur cluster assembly protein IscA 1.69
PSPPH_1909 RNA polymerase sigma-70 family protein. pvdS 1.59
PSPPH_1923 pyoverdine sidechain peptide synthetase I, epsilon-Lys module 1.70
PSPPH_2117 FecR protein superfamily 2.05
PSPPH_3007 iron ABC transporter, permease protein, putative 1.61
PSPPH_3274 catalase KatB 2.31
PSPPH_3274 catalase KatB 1.65
PSPPH_3753 siderophore biosynthesis protein 1.57
Cluster 7: Unknown function
PSPPH_0317 conserved hypothetical protein 1.81
PSPPH_0611 conserved hypothetical protein 2.15
PSPPH_0612 hypothetical protein PSPPH_0612 1.94
PSPPH_1142 hypothetical protein PSPPH_1142 1.58
PSPPH_1230 hypothetical protein PSPPH_1230 1.59
PSPPH_1243 conserved hypothetical protein 1.98
PSPPH_1637 hypothetical protein 2.25
PSPPH_1835 conserved hypothetical protein 1.72
PSPPH_1938 conserved hypothetical protein 1.52
PSPPH_2103 conserved hypothetical protein 1.89
PSPPH_2116 conserved hypothetical protein 1.58
PSPPH_2147 hypothetical protein PSPPH_2147 2.51
PSPPH_2578 conserved hypothetical protein 1.53
PSPPH_3212 conserved hypothetical protein 1.53
PSPPH_3262 conserved hypothetical protein 1.60
PSPPH_5014 conserved hypothetical protein 1.52
Cluster 8: Uncharacterized Function
PSPPH_0210 DNA repair protein RadC 1.56
PSPPH_0398 glutamate synthase, large subunit 2.63
PSPPH_0581 radical SAM domain protein 1.53
PSPPH_0620 DNA primase 2.48
PSPPH_0622 O-sialoglycoprotein endopeptidase 1.87
PSPPH_0625 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 1.62
PSPPH_0627 SpoVR like family protein 2.10
PSPPH_0629 protein kinase 1.65
PSPPH_0703 phosphonate ABC transporter permease protein phnE 1.73
PSPPH_1141 ISPsy20, transposase IstB 1.51
PSPPH_1150 conserved domain protein-Divergente HU family 1.61
PSPPH_1179 DNA-binding response regulator GltR 1.54
PSPPH_1244 transcriptional regulator, AsnC family 1.89
PSPPH_1306 RNA methyltransferase, TrmH family, group 1 1.545
PSPPH_1378 Methionyl-tRNA synthetase (Methionine--tRNA ligase)(MetRS) 2.56
PSPPH_1406 ATP-dependent helicase, DinG family 1.77
PSPPH_1468 nucleic acid binding protein 1.58
PSPPH_1595 transcriptional regulator, GntR family 2.58
PSPPH_1661 cvpA family protein 1.66
PSPPH_1746 oxidoreductase, aldo/keto reductase family 1.92
PSPPH_2216 zinc carboxypeptidase domain protein 1.89
PSPPH_2221 precorrin-4 C11-methyltransferase 1.52
PSPPH_2506 L-arabinose ABC transporter, periplasmic L-arabinose-binding protein 1.62
PSPPH_2551 oxidoreductase, putative 1.84
PSPPH_2563 transcriptional regulator, GntR family 1.53
PSPPH_2580 transcriptional regulator, LysR family 1.97
PSPPH_2620 5-methyltetrahydrofolate--homocysteine methyltransferase 1.85
PSPPH_2690 oxidoreductase, FAD-binding, putative 1.56
PSPPH_2781 TspO/MBR family protein 1.99
PSPPH_2840 sodium/hydrogen exchanger family protein 1.55
PSPPH_2847 general secretion pathway protein GspK, putative 1.89
PSPPH_3045 transporter, AcrB/AcrD/AcrF family 1.64
PSPPH_3252 glycolate oxidase, GlcD subunit 1.97
PSPPH_3291 oxidoreductase, molybdopterin-binding 1.88
PSPPH_3294 DNA-binding heavy metal response regulator 1.81
PSPPH_3654 transcriptional regulator, TetR family 1.51
PSPPH_3906 sensor histidine kinase 1.65
PSPPH_3946 DNA repair protein RecO 1.66
PSPPH_3962 DNA-binding response regulator TctD 1.77
PSPPH_4137 histidinol dehydrogenase 1.63
PSPPH_4151 RNA polymerase sigma-54 factor RpoN 1.69
PSPPH_4152 ribosomal subunit interface protein 1.86
PSPPH_4332 DNA repair protein RadA 1.76
PSPPH_4372 RNA 2'-phosphotransferase 1.55
PSPPH_4634 bmp family protein 2.99
PSPPH_4641 YccA 1.68
PSPPH_4717 dethiobiotin synthetase 2.09
PSPPH_4866 proline-specific permease proY 1.54
PSPPH_4925 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit 1.62
PSPPH_5142 oxaloacetate decarboxylase alpha subunit 2.35

The described functions were obtained from the literature. The up-regulated genes were identified using cutoff criteria ≥1.5 of ratio. The ratio is in relation to expression levels obtained between 18°C and 28°C (18°C/28°C). Control: corresponds to genes obtained by PCR amplification that were printed in the microarray.

Arvizu-Gómez et al.

Arvizu-Gómez et al. BMC Microbiology 2013 13:81   doi:10.1186/1471-2180-13-81

Open Data