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. 2009 Feb 17;77(5):1866–1880. doi: 10.1128/IAI.01496-08

TABLE 2.

Hfq-regulated genesa

Locus Gene product Gene KEGG classification Change (fold)b
Defined medium Agar plates Broth
Genes significantly downregulated in the hfq mutant (n = 16)
    FTL_0194 Cytochrome o ubiquinol oxidase subunit IV cyoD Metabolism 0.21 0.42
    FTL_0195 Protoheme IX farnesyltransferase cyoE Metabolism 0.28 0.32
    FTL_0221 Amino acid permease 0.50 0.41
    FTL_0317 Hypothetical protein 0.41 0.41 0.36
    FTL_0392 Type IV pilus fiber building block protein 0.42 0.47 0.33
    FTL_0421 Conserved hypothetical lipoprotein lpnA 0.46 0.31 0.47
    FTL_0568 Transposase isftu2 0.84 0.48 0.47
    FTL_0570 Hypothetical protein 0.34 0.42 0.39
    FTL_0898 Host factor I for bacteriophage Qβ replication hfq 0.12 0.04 0.08
    FTL_0899 Protease, GTP-binding subunit hflX 0.37 0.47 0.75
    FTL_1016 Short-chain dehydrogenase 0.31 0.50 0.48
    FTL_1394 Galactose-proton symporter, major facilitator superfamily transport protein galP2 0.47 0.49
    FTL_1504 Peroxidase/catalase katG Metabolism 0.37 0.49 0.64
    FTL_1555 Hypothetical membrane protein 0.53 0.49 0.36
    FTL_1678 Conserved membrane hypothetical protein 0.53 0.47 0.36
    FTL_1764 Pseudo 0.13 0.37
Genes significantly upregulated in the hfq mutant (n = 88)
    FTL_0045 Orotidine 5′-phosphate decarboxylase pyrF Metabolism 2.60 3.30
    FTL_0046 Dihyroorotate dehydrogenase pyrD Metabolism 2.58 3.44
    FTL_0117/ FTL_1163 Hypothetical protein 4.83 3.92 3.72
    FTL_0118/ FTL_1164 Hypothetical protein 3.24 1.91 2.28
    FTL_0119/ FTL_1165 Hypothetical protein 4.21 3.19 2.68
    FTL_0120/ FTL_1166 Hypothetical protein 6.02 5.82 2.46
    FTL_0121/ FTL_1167 Hypothetical protein 7.72 4.08 4.55
    FTL_0122/ FTL_1168 Conserved hypothetical protein 9.35 6.49 4.94
    FTL_0123/ FTL_1169 Hypothetical protein 3.49 4.03 3.53
    FTL_0124/ FTL_1170 Hypothetical protein 5.21 5.35 3.64
    FTL_0125/ FTL_1171 Hypothetical protein pdpB 10.7 6.00 5.15
    FTL_0126/ FTL_1172 Hypothetical protein pdpA 8.19 3.63 3.69
    FTL_0237 50S ribosomal protein L4 Genetic information processing 1.23 2.61 2.51
    FTL_0239 50S ribosomal protein L2 rplB Genetic information processing 2.24 2.77
    FTL_0240 30S ribosomal protein S19 Genetic information processing 1.23 2.48 3.26
    FTL_0242 30S ribosomal protein S3 rpsC Genetic information processing 2.93 2.64
    FTL_0261 DNA-directed RNA polymerase, alpha subunit Metabolism and genetic information processing 1.25 2.66 3.30
    FTL_0396 Fusion protein PurC/PurD Metabolism 1.46 2.45 2.16
    FTL_0414 GTP-binding protein engA 2.75 3.46 1.53
    FTL_0437 Riboflavin biosynthesis protein RibF ribF Metabolism 3.27 5.02 2.06
    FTL_0460 Hypothetical protein 3.31 2.74 2.71
    FTL_0461 Hypothetical protein 1.88 2.60 2.22
    FTL_0534 1-Deoxy-d-xylulose 5-phosphate reductoisomerase dxr Metabolism 2.97 3.69 1.62
    FTL_0535 Outer membrane protein 2.14 5.31
    FTL_0603 O-antigen flippase wzx 2.02 3.43
    FTL_0604 Glycosyltransferase wbtK 1.67 2.04 2.01
    FTL_0605 Glucose-1-phosphate thymidylyltransferase wbtL Metabolism 2.95 2.24
    FTL_0669 Exodeoxyribonuclease V, beta chain recB Genetic information processing 1.75 2.17 2.23
    FTL_0670 Exodeoxyribonuclease V, alpha subunit recD Genetic information 4.16 4.04 1.77
    FTL_0737 Hypothetical membrane protein     processing 5.81 4.63 1.79
    FTL_0739 Glucose-inhibited division protein A gidA Cellular processes 3.18 2.03
    FTL_0788 Glutamine amidotransferase class II family protein 4.09 3.28 1.94
    FTL_0797 Type IV pili associated protein Genetic information processing 2.99 2.35 1.32
    FTL_0798 Type IV pilus glycosylation protein Genetic information processing 4.06 3.38 1.81
    FTL_0827 Type IV pilus polytopic inner membrane protein Genetic information processing 2.32 4.31 2.32
    FTL_0882 Apolipoprotein N-acyltransferase 6.09 7.01
    FTL_0883 Metal ion transporter protein Environmental 3.33 3.15 1.74
    FTL_0884 Hypothetical protein     information processing 1.49 3.09 2.55
    FTL_0885 PhoH-like protein phoH 2.31 4.40 1.77
    FTL_0893 ATP-dependent protease, ATP-binding subunit clpX 2.22 3.42 1.81
    FTL_0894 DNA-binding, ATP-dependent protease La lon 2.16 2.76 1.92
    FTL_0921 Endonuclease III Genetic information 2.78 2.11 1.75
    FTL_0993 HesA/MoeB/ThiF family protein     processing 3.61 3.38 2.75
    FTL_0994 Hypothetical protein 5.66 4.91 2.55
    FTL_1004 d-Alanyl-d-alanine carboxypeptidase vanY 2.44 2.08 1.79
    FTL_1005 Hypothetical protein 10.6 4.06 1.86
    FTL_1043 Hypothetical protein 7.12 5.79 3.75
    FTL_1044 Hypothetical protein 6.70 3.46 4.03
    FTL_1045 Conserved hypothetical lipoprotein 3.27 3.01 2.27
    FTL_1046 d-Alanyl-d-alanine carboxypeptidase (penicillin-binding protein) family protein dacB 11.6 3.70 2.78
    FTL_1049 DNA primase dnaG Genetic information processing 4.16 4.04
    FTL_1050 RNA polymerase sigma-70 factor rpoD Genetic information 2.47 3.04 1.75
    FTL_1064 Hypothetical protein     processing 4.10 4.47 2.10
    FTL_1065 ABC transporter, ATP-binding protein yhbG 2.64 7.30 3.39
    FTL_1066 Fumarylacetoacetate hydrolase family protein 2.37 2.59
    FTL_1067 Hypothetical protein 2.79 5.48 2.32
    FTL_1068 tRNA pseudouridine synthase A truA Genetic information 1.46 3.27 3.56
    FTL_1074 GDSL-like lipase/acylhydrolase family protein     processing 1.72 2.54 2.51
    FTL_1106 Alanyl-tRNA synthetase alaS Metabolism and genetic 2.41 2.80 2.06
    FTL_1108 Cytosol aminopeptidase family protein     information processing 2.49 2.65 1.65
    FTL_1174 Cystathionine beta-synthase (cysteine synthase) cbs Metabolism 6.30 3.86 3.20
    FTL_1177 tRNA modification GTPase trmE 2.71 2.37
    FTL_1190 Chaperone protein GrpE (heat shock protein family 70 cofactor) grpE 2.65 2.03 3.27
    FTL_1228 Hypothetical protein 3.15 1.43 2.41
    FTL_1229 ABC transporter, ATP-binding protein 4.57 1.35 3.29
    FTL_1230 Cysteine desulfurase activator complex subunit SufB 2.49 2.63 1.44
    FTL_1261 Anthranilate synthase component II trpG Metabolism 6.60 3.05 3.42
    FTL_1262 Chorismate binding family protein 10.2 4.00 2.90
    FTL_1266 Lipase/esterase 5.90 2.91
    FTL_1267 Hypothetical protein 3.19 1.88 2.81
    FTL_1271 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase bioA Metabolism 2.71 2.03
    FTL_1273 8-Amino-7-oxononanoate synthase bioF Metabolism 2.57 2.00 1.49
    FTL_1274 Biotin synthesis protein BioC bioC 5.02 3.25 3.12
    FTL_1275 Dethiobiotin synthetase bioD Metabolism 3.23 2.66 3.89
    FTL_1276 Bifunctional protein BirA Metabolism 5.74 2.66
    FTL_1283 Glutamate-1-semialdehyde-2,1-aminomutase hemL Metabolism 2.02 2.90 1.76
    FTL_1284 Glutathione synthetase Metabolism 2.56 4.62 2.20
    FTL_1285 Methionyl-tRNA formyltransferase Metabolism and genetic information processing 5.04 4.87 2.52
    FTL_1372 Hypothetical lipoprotein 2.65 3.61 1.14
    FTL_1396 Galactose-1-phosphate uridylyltransferase galT Metabolism 2.54 2.03 1.28
    FTL_1397 Galactokinase galK Metabolism 3.37 3.93 1.33
    FTL_1484 Methylase Metabolism 4.56 4.53 1.36
    FTL_1530 Pseudo 1.61 2.88 2.36
    FTL_1539 Penicillin-binding protein (peptidoglycan synthetase) ftsI Metabolism and cellular processes 2.39 2.65 1.79
    FTL_1616 Phosphoenolpyruvate carboxykinase pckA Metabolism 2.33 3.78
    FTL_1639 Hypothetical protein 2.59 2.99 1.59
    FTL_1806 Major facilitator superfamily (MFS) transport protein 3.37 5.45 1.22
    FTL_1826 NADH dehydrogenase I, E subunit Metabolism 2.13 2.18 1.72
a

Genes whose expression is significantly changed (at least twofold, as determined using the SAM program) in LVS and the hfq mutant under at least two conditions are included.

b

The values are average changes between the hfq mutant and LVS in all microarrays. Bold type indicates a gene whose expression is significantly changed (as determined using the SAM program), but the change is less than twofold.