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. 2004 Aug;186(16):5460–5472. doi: 10.1128/JB.186.16.5460-5472.2004

TABLE 3.

Gene cluster analysis of the microarray data

Group and name (alias) Group or gene product description Mi value in expta:
1 2 3 4 5
A Genes differentially expressed dependent on SinI and ExpR
    SMc02726 Putative iron transport protein 2.26 0.04 0.05 2.29 0.08
    SMc04059 Hypothetical protein 2.14 0.28 0.34 1.00 −0.80
    SMc04114 (pilA1) Putative pilin subunit protein 1.50 −0.09 0.21 1.58 −0.85
    SMb20557 Conserved hypothetical protein −1.00 −0.30 1.54 −1.02 −0.16
    SMb21309 (expE6) Putative membrane protein −1.07 −0.23 0.32 −1.28 0.00
    SMc04170 Putative two-component receiver domain protein −1.07 0.28 0.53 −1.47 0.04
    SMb21310 (expE5) Putative membrane-anchored protein −1.15 0.07 0.39 −1.01 0.02
    SMb21544 Hypothetical exported protein −1.20 1.03 −1.08 −1.13
    SMb20951 (exoI) Putative periplasmic protein −1.29 0.05 −0.47 −1.69 −0.21
    SMb20391 Putative cellulose synthase catalytic subunit protein −1.30 0.00 −0.10 −1.59 0.12
    SMb21319 (expA1) Putative membrane-anchored protein −1.31 0.19 0.26 −1.93 0.50
    SMb21311 (expE4) Putative glycosyltransferase, forming α-glycosyl linkages protein −1.36 −0.21 0.26 −2.06 0.10
    SMb21402 Hypothetical calcium binding protein −1.46 −0.03 0.12 −1.12 0.69
    SMb21318 (expC) Putative glycosyltransferase, forming α-glycosyl linkages protein −1.50 −0.08 0.27 −2.22 0.38
    SMb20909 Hypothetical protein −1.58 0.04 0.04 −1.85 −0.55
    SMb20952 Hypothetical protein −1.68 −0.32 0.94 −2.15 0.14
    SMb21321 (expA4) Putative membrane-anchored protein −2.03 −0.04 0.20 −3.26 −0.26
    SMb20932 (exsH) Endo-1,3-1,4-β-glycanase, C-terminal secretion signal protein −2.07 −0.05 0.34 −2.46 0.46
    SMa2111 Hypothetical protein −2.18 −0.04 −0.16 −1.46 0.58
    SMb21312 (expE3) Putative methyltransferase protein −2.44 −0.30 0.40 −3.26 0.31
    SMb21323 (expA6) Putative protein, probably exported to periplasm −2.47 0.02 0.12 −3.22 −0.41
    SMb21317 (expG) Transcriptional activator of exopolysaccharide II synthesis, MarR family protein −2.62 0.07 0.48 −2.62 0.32
    SMc04171 Putative hemolysin-type calcium-binding protein −2.73 −0.06 0.08 −2.75 0.24
    SMb21681 Hypothetical protein −3.06 0.02 0.49 −3.03 0.21
    SMb21543 Putative outer membrane secretion protein −3.15 0.01 0.57 −3.35 0.52
    SMb21314 (expE1) Putative secreted calcium-binding protein −3.18 −0.03 0.57 −3.50 0.54
B Genes differentially expressed dependent on SinI and SinR and independent of ExpR
    SMc01403 Putative transcription regulator protein 0.16 1.76 1.40 1.53 0.42
    SMc00779 Putative FAD-dependent oxidoreductase protein 0.47 1.33 1.55 −0.86 0.28
    SMc00672 (hisX) Histidine-binding periplasmic signal peptide protein 0.14 1.04 1.25 0.76 0.76
C Genes differentially expressed dependent on SinR and independent of SinI
    SMa0089 Conserved hypothetical protein −0.08 0.04 4.21 0.14 −0.15
    SMc02111 Conserved hypothetical protein −0.57 −0.25 2.67 −0.16 −0.17
    SMa1727 Putative hydrolase 0.07 0.09 2.36 0.00 −0.39
    SMa1262 Conserved hypothetical protein 0.08 −0.07 1.99 0.50 0.02
    SMc00777 Conserved hypothetical protein 0.22 1.88 0.28
    SMa0091 Hypothetical protein 0.00 0.03 1.71 0.04 0.35
    SMb21097 Putative amino acid uptake ABC transporter periplasmic solute-binding protein precursor 0.24 0.00 1.54 −0.08 −0.10
    SMc00670 (hisV) Histidinc transport ATP-binding ABC transporter protein 0.43 0.43 1.44 1.23 0.90
    SMc01843 Probable 5,10-methylenetetrahydrofolate reductase oxidoreductase protein −0.16 0.35 1.39 0.91 0.34
    SMb20836 Hypothetical heme-binding protein 0.18 0.40 1.29 0.75 −0.12
    SMc02087 (gltA) Citrate synthase protein 0.05 −0.03 1.20 0.10 0.39
    SMa0645 Hypothetical protein 0.25 0.60 1.19 −0.05 0.35
    SMc03998 Hypothetical transcription regulator protein 0.26 0.01 1.17 0.29 0.07
    SMb20464 Hypothetical protein −0.18 0.26 1.16 0.23 −0.17
    SMa1036 Hypothetical protein 0.05 0.40 1.14 0.15 −0.38
    SMa1729 Putative periplasmic binding protein 0.18 0.29 1.10 0.30 0.62
    SMa1208 (fixS1) FixS1 nitrogen fixation protein −0.27 0.18 1.07 0.12 0.10
    SMc00665 Hypothetical/unknown protein −0.11 0.27 1.07 0.26 0.21
    SMb21378 Hypothetical protein 0.00 0.58 1.01 0.23 0.42
    SMb20032 Hypothetical protein −0.02 −0.11 −1.10 0.05 −0.95
    SMb20336 Conserved hypothetical protein −0.09 −0.10 −1.61 −0.31 0.82
    SMb20292 Hypothetical immunogenic protein −0.34 −0.11 −2.74 −0.34 0.62
    SMb20335 Conserved hypothetical protein 0.33 −0.19 −3.48 0.01 0.66
D1 Genes differentially expressed dependent on ExpR and independent of SinI
    SMa0445 (TRm1a) TRmla transposase 0.13 0.12 0.18 2.59 1.46
    SMa1030 (TRm1a) TRmla transposase 0.27 0.20 0.15 1.98 1.11
    SMb21440 Hypothetical protein 0.08 −0.13 0.04 1.95 1.82
    SMb20918 (TRm1a) Transposase of insertion sequence ISRm1 ORFA protein 0.09 −0.09 0.20 1.71 1.07
    SMc02079 Putative outer membrane protein 0.06 0.15 0.31 1.68 2.51
    SMc03898 (TRm1a) Transposase for insertion sequence element ISRm1 0.29 −0.15 0.16 1.65 1.06
    SMc01959 (TRm1a) Transposase for insertion sequence element ISRm1 0.24 0.04 0.14 1.55 1.07
    SMc03295 (TRm1a) Transposase for insertion sequence element ISRm1 0.19 0.04 0.01 1.04 1.19
D2 Genes differentially expressed dependent on ExpR in the absence of SinI
    SMb21522 (minE) Putative cell division inhibitor protein −0.08 −0.29 0.07 0.69 1.25
    SMb20837 Hypothetical protein −0.01 −0.15 0.18 0.11 1.13
    SMc03239 (ppa) Probable inorganic pyrophosphatase protein 0.19 0.01 0.81 0.70 1.11
    SMc00198 Hypothetical/unknown protein −0.88 −0.60 −0.44 0.10 1.09
    SMc02298 (TRm1a) Transposase for insertion sequence element ISRm1 0.05 0.19 −0.04 0.72 1.09
    SMb21523 (minD) Putative cell division inhibitor protein 0.20 −0.07 0.40 0.24 1.08
    SMc03900 (ndvA) β-1→2 glucan export ATP-binding protein 0.07 −0.26 0.18 −0.02 1.03
    SMb20946 (exoY) Galactosyltransferase protein −0.14 −0.16 0.90 0.72 1.01
    SMc00912 10-kDa chaperonin A protein −0.41 −0.04 −0.16 −0.12 1.00
    SMc01266 (hemN) Conserved hypothetical protein 0.12 −0.79 −0.50 −0.72 −1.02
    SMc03051 (flbT) Putative flagellin synthesis repressor protein 0.95 0.13 0.39 −0.38 −1.02
    SMc04319 Hypothetical protein −0.02 0.70 0.31 −0.46 −1.02
    SMc03052 (flgD) Putative basal-body rod modification protein 0.79 −0.04 0.30 −0.15 −1.04
    SMc03072 Conserved hypothetical protein 0.29 −0.10 0.38 −0.06 −1.06
    SMc03031 (flgA) Flagellar precursor transmembrane protein 0.58 −0.20 0.24 0.07 −1.14
    SMb21072 Hypothetical membrane protein −0.46 −0.62 −2.05 −1.17
    SMb20651 Hypothetical protein 0.42 0.05 0.51 −1.18
    SMc03034 (flgH) Flagellar L-ring protein precursor basal body L-ring protein 0.71 0.01 0.25 −0.10 −1.21
    SMc00507 Hypothetical/unknown protein 0.18 −0.07 −0.40 −1.48
    SMa1387 Putative LysR-type transcriptional regulator 0.41 −0.06 0.10 0.32 −1.52
    SMc03006 (cheY1) Chemotaxis regulator protein 0.64 0.75 0.18 0.21 −1.62
    SMc03024 (flgF) Flagellar basal-body rod protein 0.09 0.08 0.41 0.21 −1.65
    SMc03050 (flaF) Putative flagellin synthesis regulator protein 0.97 −0.23 0.24 −0.71 −1.74
    SMc03030 (flgG) Flagellar basal-body rod protein 0.77 0.06 0.09 0.02 −1.76
D3 Genes activated or repressed by ExpR in the absence of SinI
    SMc03038 (flaB) Flagellin B protein 1.71 0.14 0.54 −0.54 −2.01
    SMc03037 (flaA) Flagellin A protein 1.61 0.11 0.44 −0.41 −2.04
    SMc03049 (flgL) Putative flagellar hook-associated protein 1.32 −0.14 0.21 −0.74 −1.28
    SMc03048 (flgK) Putative flagellar hook-associated protein 1.25 −0.06 0.42 −0.55 −1.28
    SMc03035 (fliL) Flagellar transmembrane protein 1.19 −0.03 0.19 −0.44 −1.63
    SMc03039 (flaD) Probable flagellin D protein 1.18 0.07 0.48 −0.30 −1.68
    SMc03047 (flgE) Flagellar hook protein 1.13 −0.11 0.32 −0.06 −1.14
    SMc03040 (flaC) Flagellin protein 1.08 0.01 0.21 −0.18 −1.32
    SMc03108 Hypothetical calcium-binding protein −1.57 −0.03 0.10 −0.02 1.59
E1 Genes differentially expressed dependent on ExpR or SinR
    SMc03043 (motC) Chemotaxis precursor (motility protein C) transmembrane 0.77 0.60 1.08 1.00 −0.11
E2 Genes differentially expressed dependent on ExpR or SinR in the absence of SinI
    SMa1541 Putative oxidoreductase 0.39 0.78 1.12 1.10 1.04
    SMc03799 Conserved hypothetical protein 0.24 0.01 −2.05 0.14 −1.22
    SMc04245 (znuA) Probable high-affinity zinc uptake system ABC transporter protein −0.16 0.04 −2.17 −0.15 −1.27
E3 Genes differentially expressed dependent on ExpR or SinR and dependent on SinI or an unknown factor
    SMb20604 Putative urea short-chain amide or branched-chain amino acid uptake ABC transporter permease protein, possibly fusion protein 0.91 1.50 1.42 0.71 2.03
    SMc04127 Putative ATP-binding ABC transporter protein 0.53 1.30 1.17 0.53 1.19
F Genes differentially expressed dependent on SinI and ExpR or an unknown regulatory gene and independent of SinR
    SMc00193 Hypothetical/unknown protein −2.60 −1.09 −0.88 −2.38 −0.66
    SMa2091 Hypothetical protein 0.06 1.13 0.66 1.10 0.42
G Genes differentially expressed dependent on SinI in the absence of ExpR and independent of SinR
    SMc04018 Probable 5′-nucleotidase precursor (signal peptide) protein 4.76
    SMc03987 Putative transport transmembrane protein 3.75
    SMa2055 Hypothetical protein −0.05 1.69
    SMa2019 Putative oxidoreductase 0.33 1.45 0.74 0.07 0.75
    SMa1077 (nex18) Nex18 symbiotically induced conserved protein 0.22 1.15 0.67 1.15 0.48
    SMa0903 Hypothetical protein −0.08 1.13 0.54 −0.63
    SMc00168 (sinI) Putative autoinducer synthase protein 0.60 1.06 −0.19 −0.81 −0.21
    SMa0087 Hypothetical protein 0.24 1.01 0.79 −2.60
H Genes differentially expressed dependent on SinI, SinR, or ExpR
    SMc00477 Conserved hypothetical protein 1.00 1.30 2.06 1.45 1.29
A or F Genes differentially expressed dependent on ExpR and SinI or genes differentially expressed dependent on SinI and ExpR or an unknown regulatory gene and independent of SinR
    SMa1214 (fixQ1) FixQ1 cbb3-type cytochrome oxidase 0.47 −1.20 4.12 −0.53
    SMc03253 Putative l-proline 3-hydroxylase protein 0.16 −0.11 −0.10 3.46 −0.43
    SMc03254 (fixT3) Putative antikinase protein 0.06 −0.34 3.30 0.54
    SMa0762 (fixK2) FixK2 transcription regulator 0.43 0.40 −0.27 3.24 −0.88
    SMa1225 (fixK1) FixK1 transcriptional activator 0.19 0.07 0.41 3.13 −0.51
    SMa0763 Hypothetical protein −0.03 0.07 0.21 2.61 −0.11
    SMa1223 Conserved hypothetical protein (ORF151) 0.06 0.37 0.54 2.06 −0.33
    SMa1092 Hypothetical protein 0.41 0.01 0.43 1.79 −0.61
    SMa1226 (fixT1) FixT1 inhibitor of FixL autophosphorylation 0.27 −0.11 0.77 1.71 −0.05
    SMc02877 Conserved hypothetical protein 0.26 0.99 0.77 1.68 0.52
    SMa1266 HemN coproporphyrinogen III oxidase 0.15 0.33 0.21 1.63 0.27
    SMa0667 Hypothetical protein 0.24 0.78 0.65 1.55 0.43
    SMa1169 Hypothetical protein 0.13 0.57 0.81 1.53 0.38
    SMa1231 Conserved hypothetical protein 0.14 −0.03 0.16 1.53 −0.08
    SMa1995 Putative ABC transporter, permease protein 0.40 0.28 0.32 1.52 −0.19
    SMa1335 Hypothetical protein 0.30 0.05 0.48 1.47 0.40
    SMa1136 Hypothetical protein −0.03 0.47 0.69 1.46 0.52
    SMa0748 Putative MucR family transcriptional regulatory protein −0.18 −0.16 −0.30 1.45 0.94
    SMc01855 Hypothetical transmembrane protein 0.14 −0.08 0.05 1.44 0.47
    SMc04081 (sqdD) Glycosyl transferase (sulfolipid biosynthesis) protein 0.05 0.63 0.50 1.31 0.48
    SMa0765 (fixN2) FixN2 cytochrome c oxidase polypeptide I 0.07 0.19 0.07 1.30 −0.04
    SMc01525 (dppA2) Putative dipeptide binding periplasmic protein 0.79 0.21 0.26 1.30 −0.27
    SMa1615 TRm1a transposase 0.15 0.12 0.22 1.28 0.49
    SMc01947 Conserved hypothetical transmembrane protein −0.30 −0.19 −0.02 1.28 0.15
    SMa0760 (fixT2) FixT2 transcription regulator 0.04 0.17 −0.18 1.26 −0.13
    SMb21234 (TRm1a) Probable transposase of insertion sequence ISRm1 orfA protein −0.09 −0.08 −0.23 1.25 0.72
    SMc01946 (livK) Putative leucine-specific binding protein precursor 0.12 0.12 0.49 1.23 0.82
    SMc03963 (sqdC) Sulfolipid biosynthesis protein 0.07 0.60 0.51 1.21 0.62
    SMc01545 Hypothetical protein −0.14 0.73 0.48 1.19 −0.89
    SMa1132 Hypothetical protein −0.09 0.12 0.23 1.14 −0.35
    SMc02725 (trpE) Anthranylate synthase, glutamine amidotransferase protein 0.37 0.23 0.51 1.14 0.57
    SMa1067 Putative transcriptional regulator −0.02 0.13 0.54 1.11 0.11
    SMc03832 Conserved hypothetical signal peptide protein −0.07 −0.04 0.25 1.11 0.73
    SMc04017 (omp10) Probable outer membrane lipoprotein −0.14 0.57 0.34 1.10 −0.05
    SMa1170 (cycB2) Putative CycB2 cytochrome c552 −0.13 −0.02 0.03 1.09 −0.46
    SMc00573 (acpP) Acyl carrier protein −0.29 0.11 −0.33 1.08 −0.44
    SMa0541 Hypothetical protein −0.29 0.41 0.53 1.06 −0.37
    SMa2063 Hypothetical protein −0.06 0.46 0.56 1.06 0.04
    SMc01524 Putative dipeptidase protein 0.45 0.00 0.22 1.05 −0.33
    SMa0900 Possible anti-restriction protein −0.01 0.69 0.74 1.03 0.19
    SMa1957 Hypothetical protein 0.11 0.43 0.43 1.02 0.28
    SMc04007 Conserved hypothetical protein −0.04 0.46 0.34 1.02 −0.16
    SMa1896 Putative methionine sulfoxide reductase 0.25 0.96 0.94 1.00 0.80
    SMc02940 Hypothetical protein 0.37 0.44 0.80 1.00 0.33
    SMc00123 Conserved hypothetical protein −0.39 −0.24 0.18 −1.00 0.01
    SMb21118 Hypothetical protein 0.01 0.02 −0.02 −1.03 −0.61
    SMc00251 Hypothetical protein −0.12 −0.87 0.39 −1.03 −0.12
    SMa1651 Putative ABC transporter, periplasmic solute-binding protein 0.15 0.10 −0.57 −1.09 −0.31
    SMc01585 (cspA3) Putative cold shock transcription regulator protein −0.33 0.04 −0.01 −1.09 −0.34
    SMa2379 Catalase/peroxidase −0.90 −0.19 −0.27 −1.10 −0.03
    SMc04292 (cyaF3) Probable adenylate/guanylate cyclase protein −0.19 0.01 0.53 −1.12 0.22
    SMc04363 Hypothetical protein 0.27 −0.38 −0.05 −1.18 0.10
    SMc04442 Putative acetyltransferase protein −0.08 −0.16 0.31 −1.28 −0.09
    SMb21324 (expA7) Putative glucose-1-phosphate thymidyltransferase protein −0.75 −0.04 0.25 −1.31 −0.11
    SMb20811 Putative protein −0.34 −0.11 0.35 −1.32 −0.47
    SMb21315 (expD2) Putative secretion protein, HlyD family membrane fusion protein, secretes ExpE1 −0.92 −0.12 0.27 −1.33 0.49
    SMa2412 (rhrA) RhrA transcriptional activator −0.23 0.03 0.60 −1.35 0.01
    SMb21552 Putative aminoglycoside 6′-N-acetyltransferase, similar to amikacin resistance protein −0.34 −0.19 −0.13 −1.36 −0.08
    SMb20133 Conserved hypothetical protein −0.96 0.00 0.23 −1.47 0.24
    SMb21320 (expA23) Putative bifunctional glycosyltransferase, forming β-glycosyl and α-glycosyl linkages protein −0.78 −0.01 0.34 −1.48 −0.06
    SMa0357 Hypothetical protein −0.42 −0.22 −1.24 −1.53 −0.86
    SMb21313 (expE2) Putative bifunctional glycosyltransferase, forming α-glycosyl and β-glycosyl linkages −0.89 0.00 0.48 −1.62 0.16
    SMa0125 (groES3) GroES3 chaperonin 0.09 0.24 −0.39 −2.84 −0.47
    SMb21229 Putative calcium-binding exported protein −1.08 0.15 0.12 −0.16 0.57
    SMc00979 Hypothetical transmembrane protein −1.25 0.21 0.14 −0.86 0.34
    SMa1587 (eglC) EglC endo-1,3-1,4-β-glycanase −1.35 −0.12 −0.06 −0.45 0.71
a

Values in boldface italic type indicate genes that meet both M and P criteria; genes were grouped according to these values. Value in boldface roman type indicate genes that meet M but not P criteria. The data presented in this table are the Mi values of each gene. Positive Mi values indicate upregulation in strain 1, and negative Mi values indicate upregulation in strain 2. Cross hybridizations are listed the supplemental data. Experiment parameters for experiments 1 to 5 are as described in Table 2.