Table 2

Genes down-regulated at 18°C in P. syringae pv. phaseolicola NPS3121
Gen/ORF Gene product Ratio
Cluster 9: Alginate synthesis
PSPPH_1112 alginate biosynthesis protein AlgX 0.52
PSPPH_1113 alginate biosynthesis protein AlgG 0.19
PSPPH_1114 alginate biosynthesis protein AlgE 0.18
PSPPH_1115 alginate biosynthesis protein AlgK 0.19
PSPPH_1118 alginate biosynthesis protein AlgD 0.46
PSPPH_1119 conserved hypothetical protein 0.46
algD algD (control) 0.25
Cluster 10: Plant-Pathogen interactions
PSPPH_A0075 type III effector HopW1-2, truncated 0.60
PSPPH_A0127 type III effector HopAB1 0.42
PSPPH_A0127 type III effector HopAB1 0.65
PSPPH_A0127 virA type III HopAB1 (control) 0.57
PSPPH_A0120 avrC type III effector AvrB2 (control) 0.53
PSPPH_A0010 avrD type III effector hopD1 (control) 0.56
PSPPH_3992 pectin lyase 0.62
PSPPH_3993 acetyltransferase, GNAT family 0.57
PSPPH_A0072 polygalacturonase 0.50
Cluster 11: Type IV secretion system
PSPPH_B0022 transcriptional regulator, PbsX family 0.65
PSPPH_ B0023 transcriptional regulator 0.64
PSPPH_ B0025 conjugal transfer protein 0.65
PSPPH_ B0027 conjugal transfer protein 0.65
PSPPH_ B0028 conjugal transfer protein 0.61
PSPPH_ B0031 conjugal transfer protein 0.65
PSPPH_ B0032 conjugal transfer protein 0.61
PSPPH_ B0034 conjugal transfer protein 0.62
PSPPH_ B0035 conjugal transfer protein 0.66
PSPPH_ B0036 conjugal transfer protein 0.51
PSPPH_ B0041 conjugal transfer protein 0.58
Cluster 12: Heat-shock proteins
PSPPH_0381 heat shock protein HslVU, ATPase subunit HslU 0.65
PSPPH_0742 clpB protein 0.54
PSPPH_4077 chaperonin, 60 kDa. groEL 0.29
PSPPH_4206 dnaK protein 0.28
PSPPH_4206 dnaK protein 0.57
PSPPH_4207 heat shock protein GrpE 0.65
Cluster 13: Genes related with nucleic acids synthesis
PSPPH_4598 DNA-directed RNA polymerase, beta' subunit 0.59
PSPPH_4599 DNA-directed RNA polymerase, beta' subunit 0.57
PSPPH_2495 DNA polymerase II 0.57
PSPPH_B0043 DNA topoisomerase III 0.64
PSPPH_A0002 Replication protein 0.54
Cluster 14: Unknown function
PSPPH_0220 conserved hypothetical protein 0.64
PSPPH_0609 hypothetical protein PSPPH_0609 0.54
PSPPH_2482 conserved hypothetical protein 0.63
PSPPH_2855 hypothetical protein PSPPH_2855 0.43
PSPPH_3333 conserved hypothetical protein 0.36
PSPPH_3625 conserved hypothetical protein 0.59
PSPPH_4047 conserved hypothetical protein 0.66
PSPPH_A0040 hypothetical protein PSPPH_A0040 0.66
PSPPH_B0048 conserved hypothetical protein 0.60
Cluster 15: Uncharacterized function
PSPPH_0012 glycyl-tRNA synthetase, alpha subunit 0.63
PSPPH_0033 3-oxoadipate enol-lactonase, putative 0.65
PSPPH_0072 membrane protein, putative 0.63
PSPPH_0080 ATP-dependent DNA helicase Rep 0.43
PSPPH_0117 phospholipase D family protein 0.63
PSPPH_0215 aldehyde dehydrogenase family protein 0.35
PSPPH_0296 colicin/pyocin immunity family protein 0.58
PSPPH_0360 periplasmic glucan biosynthesis protein 0.63
PSPPH_1072 oxidoreductase, short chain dehydrogenase/reductase family 0.57
PSPPH_1181 glucose ABC transporter, periplasmic glucose-binding protein, putative 0.65
PSPPH_1211 cytochrome o ubiquinol oxidase, subunit I 0.55
PSPPH_1508 acetyltransferase, GNAT family 0.35
PSPPH_1518 ATP-dependent DNA helicase RecQ 0.53
PSPPH_1575 CAIB/BAIF family protein 0.65
PSPPH_1759 plasmid stabilization system family protein 0.53
PSPPH_1762 transcriptional regulator, AsnC family 0.54
PSPPH_1917 cation ABC transporter, periplasmic cation-binding protein 0.60
PSPPH_1921 peptidase 0.58
PSPPH_1963 electron transfer flavoprotein-ubiquinone oxidoreductase, putative 0.38
PSPPH_2053 membrane protein, putative 0.65
PSPPH_2057 2-methylcitrate synthase 0.62
PSPPH_2159 dehydrogenase, isocitrate/isopropylmalate family 0.60
PSPPH_2246 4-alpha-glucanotransferase 0.66
PSPPH_2695 peptide ABC transporter, permease protein 0.45
PSPPH_2868 major facilitator family transporter 0.63
PSPPH_2892 TonB-dependent siderophore receptor, putative 0.62
PSPPH_2897 yersiniabactin non-ribosomal peptide synthetase 0.40
PSPPH_2899 yersiniabactin polyketide/non-ribosomal peptide synthetase 0.58
PSPPH_2904 isochorismate synthase 0.55
PSPPH_3100 isocitrate dehydrogenase, NADP-dependent 0.63
PSPPH_3251 maleylacetoacetate isomerase 0.53
PSPPH_3528 acetate--CoA ligase 0.52
PSPPH_3558 aconitate hydratase 2 0.61
PSPPH_3782 porin D 0.42
PSPPH_3985 3-oxoacyl-[acyl-carrier protein] reductase 0.54
PSPPH_4221 unnamed protein product 0.44
PSPPH_4654 smtA protein 0.47
PSPPH_4703 coenzyme PQQ biosynthesis protein PqqF 0.32
PSPPH_4805 oxidoreductase FAD-binding domain/oxidoreductase NAD-binding domain/2Fe-2S iron-sulfur cluster binding domain protein 0.55
PSPPH_4833 Rhs family protein 0.33
PSPPH_4859 transporter, BCCT family 0.65
PSPPH_4869 cadmium-translocating P-type ATPase 0.54
PSPPH_4885 D-3-phosphoglycerate dehydrogenase 0.56
PSPPH_4938 amino acid ABC transporter, ATP-binding protein 0.61
PSPPH_4962 prophage PSPPH06, C4-type zinc finger protein, DksA/TraR family 0.35
PSPPH_5024 acetyltransferase, GNAT family 0.64
PSPPH_5027 acetyltransferase, GNAT family 0.64
PSPPH_5170 acyltransferase family protein 0.60
PSPPH_A0062 LysR-family transcription regulator SinR 0.45
PSPPH_A0083 IS801, transposase 0.64
PSPPH_A0109 sulfotransferase, putative 0.49
PSPPH_A0129 Yersinia/Haemophilus virulence surface antigen family 0.53
PSPPH_A0132 ISPsy16, transposase 0.66
PSPPH_A0145 conjugal transfer protein 0.56
PSPPH_B0004 RulB protein 0.63
PSPPH_B0050 relaxase, putative 0.65
PSPPH_B0059 exeA-like protein 0.64

The described functions were obtained from the literature. The down-regulated genes were identified using cutoff criteria ≤ 0.6 of ratio. The ratio is in relation to the 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