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Supplemental Material for the JI website
Table II. Genes regulated by Irr-Ihk.
SPy# Gene
Encoded protein or homologue
Fold-Change Growth
Transcription (27 total, 23↓ and 4↑)
0164
nusG
transcription anti-termination factor
-1.8
EE
0349
greA
transcription elongation factor
-1.6
LE
0583
stress response transcription regulator
-1.5
LE
0728
septation ring formation regulator
-1.7
LE
0875
two-component sensor histidine kinase
-1.6
LE
1107
two-component sensor histidine kinase
-1.5 & -1.7
EE & LE
1210
putative transcription regulator, gntR family
-2.0
EE
ATP-dependent RNA helicase
-2.6
LE
1427
transcription regulator
-2.4
LE
1556
two-component response regulator
-1.9
EE
transcription regulator
-1.6
EE
1659
ATP-dependent RNA helicase
-2.1
LE
1699
transcription regulator, tetR family
-1.5
LE
-1.9 & -1.6
EE & LE
1415
1605
1717
deaD
rocA
copY
negative transcriptional regulator-copper
transport
1777
codY
transcription pleiotropic repressor
-1.7
LE
1817
scrR
sucrose operon repressor
-1.6
EE
1
1861
transcription regulator
1863
transcription activator regulator protein,
-1.6
LE
-1.7 & -1.6
EE & LE
-1.6
LE
-1.9 & -2.0
EE & LE
merR family
1895
rpoE
DNA-directed RNA polymerase
1934
transcription regulator
1957
putative transcription regulator
-2.6
LE
2053
transcription regulator, sigma-factor N-
-1.7
EE
transcription regulator
-1.7
LE
DNA-directed RNA polymerase alpha
+2.0
EE
two-component response regulator
+1.7
LE
putative positive regulator
+1.8
LE
chromosome segregation protein
+1.5
EE
terminal domain
2054
0080
rpoA
subunit
0528
vicR
0533
2217
spoJ
Virulence-associated (5 total, 4↓ and 1↑)
0738
sagA
streptolysin S
-2.0
EE
1013
fbp
fibronectin-binding protein-like protein A
-1.8
LE
1436
mf3
deoxyribonuclease (DNase)
-1.8
LE
2043
mf
deoxyribonuclease (DNase)
-1.9
EE
67 kDa myosin-crossreactive streptococcal
+1.8
EE
-2.4
EE
0470
antigen
Oxidative stress (5 total, 4↓ and 1↑)
0850
thioredoxin reductase
2
1374
nrdH
1681
glutaredoxin
-2.1 & -2.9
EE & LE
NADH peroxidase
-1.8
EE
1835
trx
thioredoxin
-1.5
EE
0605
bsaA
glutathione peroxidase
+1.7
EE
glucose-inhibited division protein
-1.5
LE
export protein for polysaccharides & teichoic
-1.8
LE
Cell wall synthesis (15 total, 11↓ and 4↑)
0329
gidB
0390
acids
0510
glucosyltransferase
-1.6
LE
0540
putative glycosyltransferase
-2.0
EE
0797
oligosaccharide translocase (flippase)
-1.6
EE
1035
putative UDP-N-acetylmuramyl tripeptide
-1.5
EE
synthetase
1093
D-alanyl-D-alanyl-carboxypeptidase
-1.7
LE
1094
putative polysaccharide deacetylase
-1.9
LE
1205
UDP-N-acetylmuramoylpentapeptide-lysine
-1.9
LE
N(6)-alanyltransferase
1311
dltB
integral membrane protein
-1.8
EE
1662
mraY
undecaprenyl-phosphate-UDP-MurNAc-
-1.8
EE
+2.1
EE
+1.9
LE
pentapeptide phospho-MurNAc-pentapeptide
transferase
0516
0786
glucosyl transferase
rgpAc rhamnosyltransferase
3
0787
rgpBc rhamnosyltransferase
+1.9
LE
2185
gidA
+1.7
EE
methyltransferase
-1.9
EE
glucose-inhibited division protein
Nucleotide biosynthesis (20 total, 8↓ and 12↑)
0808
0910
parC
DNA topoisomerase IV, subunit C
-1.6
EE
1164
topA
DNA topoisomerase I
-1.6
LE
1368
udk
uridine kinase
-1.6
EE
1375
nrdE.2 ribonucleotide reductase alpha-chain
-1.7
LE
DNA-directed RNA polymerase
-1.6
LE
1630
2105
nrdG
anaerobic ribonucleotide reductase activator
-1.6
LE
2206
guaB
inosine monophosphate dehydrogenase
-2.0
EE
DNA repair protein
+1.8
EE
phosphoribosylaminoimidazole -
+2.1
EE
0021
0024
purC
succinocarboxamide synthase
0032
purD
phosphoribosylamine-glycine ligase
+2.0
EE
0034
purK
phosphoribosylaminoimidazole carboxylase
+1.5
EE
putative methyltransferase
+1.7
EE
II
0406
0781
dnaG
DNA primase
+1.7
LE
0901
pyrE
putative orotate phosphoribosyltransferase
+1.7
EE
1632
gmk
guanylate kinase
+1.7
EE
1906
hsdM
type I site-specific deoxyribonuclease
+1.7
LE
ribonucleotide reductase
+1.5
LE
1984
4
2110
nrdD
anaerobic ribonucleoside-triphosphate
+2.1
EE
+1.6
EE
reductase
2182
holB
replicative DNA helicase
Protein synthesis (48 total, 16↓ and 32↑)
0050
rplD
50S ribosomal protein
-1.5
LE
0069
rpsE
30S ribosomal protein
-1.9
EE
-1.8 & -1.6
EE & LE
-1.7
LE
0502
pre-protein translocase subunit
0821
putative ribosomal protein
1549
ahrC.2 arginine repressor
-1.6
EE
1557
msrA
-1.8
EE
-1.7 & -2.0
EE & LE
1619
peptide methionine sulfoxide reductase
polyribonucleotide nucleotidyltransferase
1652
nadE
NAD+ synthase
-2.0
LE
1672
proB
gamma-glutamyl kinase
-1.9
LE
1842
spi
signal peptidase I
-1.5 & -1.6
EE & LE
glycoprotein endopeptidase
-1.6
LE
50S ribosomal protein
-2.3
LE
1874
1932
rplM
2072
groES heat shock protein
-1.7
EE
2135
replication protein
-1.8
LE
-1.5
LE
2150
ahrC
arginine repressor
2159
rpmF
50S ribosomal protein
-1.7 & -2.3
EE & LE
0049
rplC
50S ribosomal protein
+1.6
EE
0050
rplD
50S ribosomal protein
+1.7
EE
0059
rpmC
50S ribosomal protein
+1.9
EE
5
0060
rpsQ
30S ribosomal protein
+1.5
LE
0062
rplX
50S ribosomal protein
+1.8 & 1.6
EE & LE
0063
rplE
50S ribosomal protein
+2.0
EE
0065
rpsH
30S ribosomal protein
+1.8
EE
0066
rplF
50S ribosomal protein
+1.6
EE
0067
rplR
50S ribosomal protein
+1.6 & 1.6
EE & LE
0071
rpmD
50S ribosomal protein
+1.9
EE
0072
rplO
50S ribosomal protein
+1.9
EE
0075
infA
translation initiation factor
+1.9
EE
0595
lysS
putative lysyl-tRNA synthetase
+1.7 & 1.5
EE & LE
0611
tufA
translation elongation factor
+1.5
EE
0717
rpmE
50S ribosomal protein
+1.5
EE
0724
rplS
50S ribosomal protein
+2.2
EE
0835
carB
carbamoylphosphate synthetase
+1.7
LE
0740
sagC
streptolysin S biosynthesis protein
+2.2
LE
0870
fms
peptide deformylase
+1.5
EE
0902
amiC
amidase
+1.9
EE
1073
rplL
50S ribosomal protein
+1.6
EE
phosphor-2-dehydro-3-deoxyheptonatre
+1.6
EE
1576
aldolase
1760
dnaK
heat shock protein 70
+1.9
EE
1831
rpsF
30S ribosomal protein
+1.7
EE
1991
trpG
anthranilate synthase component II
+1. 7
EE
6
2082
hutU
2083
urocanate hydratase
+1.6
EE
glutamate formiminotransferase
+1.7
EE
+2.1
EE
2085
fhs.2
formate-tetrahydrofolate ligase
2092
rpsB
30S ribosomal protein
+1.6 & 1.5
EE & LE
2095
pepO
neutral endopeptidase
+1.5
LE
2183
rplI
50S ribosomal protein
+2.1
EE
tRNA-(5-methylaminomethyl-2-
+2.1
EE
2188
thiouridylate)
Transporters (45 total, 24↓ and 21↑)
0196
integral membrane protein
-2.0
LE
0287
ABC transporter
-1.6
LE
-1.6 & -2.0
EE & LE
0323
braB
branched-chain amino acid transport protein
0623
pacL
calcium-transporting ATPase
-1.7
LE
0631
agaV
mannose-specific phosphotransferase system
-2.8
EE
component IIAB
0773
ABC transporter
-1.9
LE
0903
ABC transporter
-1.5
LE
0904
ABC transporter (permease)
-1.5
LE
1018
ABC transport protein (permease)
-1.6
EE
1148
ABC transporter
-1.8
LE
1241
pstB
phosphate ABC transporter
-1.8
LE
1242
pstB2
phosphate ABC transporter
-2.4
EE
1243
pstC
phosphate ABC transporter (permease
-1.6
LE
7
protein)
1245
pstS
phosphate ABC transporter, periplasmic
-1.7
LE
phosphate-binding protein
1255
ABC transporter
-1.9
LE
1315
putative glutamine-binding/transport
-1.6
LE
1506
amino acid ABC transporter
-1.6
LE
1674
ABC transporter
-1.8 & -1.6
EE & LE
glycerol uptake facilitator
-1.5
EE
1695
sodium-dependent phosphate transporter
-1.8
LE
1728
ABC transporter (permease)
-1.6
LE
sucrose-specific PTS permease, enzyme II
-1.6
LE
-1.6
EE
PTS system enzyme IIB
-1.9
EE
short-chain fatty acids transporter
+1.9
LE
0254
sugar ABC transporter
+1.5
EE
0324
sodium/dicarboxylate symporter
+1.6
EE
ferrichrome ABC transporter
+1.6
LE
ABC transporter
+2.2
LE
PTS dependent N-acetyl-galactosamine-IIC
+1.7
EE
0746
streptolysin S export protein SagI
+2.3
LE
0789
ABC-transporter (permease protein)
+2.3
LE
uracil permease
+1.7
EE
PTS enzyme II component B
+2.3
LE
1682
glpF
1815
scrA
1976
msmK sugar-binding ABC transport system
2051
0137
0386
atoE
fhuA
0518
0630
0831
1058
agaW
pyrP
8
1154
sortase
+1.9 & 1.6
EE & LE
1275
amino acid ABC transporter
+1.6 & 1.6
EE & LE
1276
amino acid ABC transporter
+1.9
EE
maltose/maltodextrin ABC transport system
+1.7
LE
1784
ABC transporter
+1.6
LE
1828
putative transporter
+1.7
EE
1897
putative mechanosensitive ion channel
+1.7
EE
1296
malG
1912
salX
salivaricin A ABC transporter
+1.8
EE
1917
lacE
PTS system, lactose-specific component
+2.4
LE
+1.8 & 1.6
EE & LE
+1.7
LE
V-type Na+ -ATPase
-1.6
EE
0176
PTS system 3-keto-L-gluconate-6-P
-1.6
LE
0251
N-acetylmannosamine-6-P epimerase
-1.7
LE
IIBC
1918
lacF
2194
PTS system, lactose-specific component IIA
ABC transporter
General metabolism (61 total, 29↓ and 32↑)
0149
ntpK
0327
ntpJ
V-type Na+ -ATPase subunit J
-1.7
LE
0341
pgdA
phosphoglycerate dehydrogenase
-1.5
LE
0628
putative oligohyaluronate lyase
-1. 7
EE
0720
putative phosphoesterase
-1.8
LE
0722
chorismate mutase
-1.7
LE
0754
atpE
H+-transporting ATP synthase chain C
-1.9
LE
0883
dyr
dihydrofolate reductase
-1.6
LE
9
1020
putative zinc-dependent hydrolase
-2.3
EE
tributyrin esterase
-1.5
LE
1115
putative lipase/acylhydrolase
-1.8
LE
1119
glutamine aminotransferase, class I
-2.1
EE
1124
putative adenyate cyclase
-1.6 & -1.9
EE & LE
1144
putative acetyltransferase
-2.2
LE
1174
transcarboxylase subunit
-1.8
LE
1177
methylmalonyl-CoA decarboxylase
-2.0
EE
-1.6 & -1.7
EE & LE
1022
estA
1186
citD
citrate lyase acyl carrier protein
1214
lplA
lipoate-protein ligase
-1.6
EE
1233
coaA
pantothenate kinase
-2.1
EE
1250
mreA
FAD synthetase
-1.6
LE
1498
fps
geranyltranstransferase
-1.9
LE
1570
putative acetyltransferase
-2.0
LE
1580
putative acetate kinase
-1.6
LE
1599
beta-glucosidase
-1.8
EE
1678
transaldolase
-1.7 & -2.0
EE & LE
1849
pfl
pyruvate formate-lyase
-1.5
EE
2047
gldA
glycerol dehydrogenase
-1.7
LE
0023
acpP.2 acyl carrier protein
+1.5 & 1.5
EE & LE
0165
nga
nicotine adenine dinucleotide glycohydrolase
+1.5
LE
0308
nicotinate-nucleotide adenylyltransferase
+2.1
EE
0524
acetyl-CoA c-acetyltransferase
+1.5
LE
10
0526
fatty acid CoA ligase
+2.8
LE
0477
phosphohydrolase
+1.6
LE
0720
phosphoesterase
+2.1
EE
fructose-1-phosphate kinase
+1.5
LE
0854
fruB
1096
folC.1 folyl-polyglutamate synthetase
+1.6
EE
1097
folE
GTP cyclohydrolase I
+1.7
EE
1126
putative ATP-NAD kinase
+1.7
EE
1139
4-oxalocrotonate tautomerase
+2.0 & 1.5
EE & LE
1192
citC
citrate lyase synthetase
+1.7
EE
1280
glmS
glucosamine-fructose-6-phosphate
+2.4
EE
amidotransferase
1292
malM
4-alpha-glucanotransferase
+1.5
LE
1544
arcB
ornithine carbamoyltransferase
+2.0
LE
1547
sagP
arginine deaminase
+1.9
LE
1744
accD
acetyl-CoA carboxylase beta subunit
+2.0
EE
1745
accC
acetyl-CoA carboxylase
+1.5
EE
1747
accB
biotin carboxyl carrier protein
+1.7
EE
1748
fabF
beta-ketoacyl-ACP synthase II
+2.1
EE
1749
fabG
beta-ketoacyl-ACP reductase
+1.8
EE
1750
fabD
malonyl CoA-acyl carrier protein
+2.0
EE
transacylase
1751
fabK
putative trans-2-enoyl-ACP reductase II
+2.0
EE
1754
fabH
beta-ketoacyl-[ACP] synthase III
+1.8
EE
11
1811
scrK
fructokinase
+1.6
EE
1916
lacG
phospho-beta-D-galactosidase
+2.5
LE
1919
lacD.2 tagatose 1,6-diphosphate aldolase
+2.4
LE
1922
lacB.2 galactose-6-phosphate isomerase
+1.7
LE
1990
pabB
+1.7
EE
+1.9 & 1.7
EE & LE
+1.5
LE
abortive-infection phage-resistance protein
-1.6
LE
0100
DNA binding
-1.6
LE
0247
60 KD inner membrane protein, yidC family
-1.6 & -1.8
EE & LE
0199
transposase
-2.0
LE
0428
C3-family ADP-ribosyltransferase
-1.9
LE
0458
putative cell division protein
-1.5
LE
0504
transmembrane RNA-binding protein
-1.5
LE
0552
plasmid stabilization
-1.8
LE
para-aminobenzoate synthetase
2184
phosphoesterase
2186
phosphohydrolase
Miscellaneous (29 total, 22↓ and 7↑)
0035
abiR
0609
ftsW
cell division protein
-2.0
LE
0766
endA
competence-associated membrane nuclease
-1.8
LE
1087
srtG
putative, lantibiotics-associated
-1.7
EE
1201
yxlM
DNA-binding protein
-2.0
LE
1260
putative stress protein, gls24 family
-1.5
EE
1384
putative metalloprotease
-1.6 & -1.7
EE & LE
-1.6
LE
1523
divIB
cell division protein
12
1527
GTP-binding protein
-1.7
EE
1592
putative sugar binding protein
-1.6
LE
1820
stress protein
-1.7
EE
-1.7
EE
1823
comEB late competence protein required for DNA
binding
1851
C3-degrading proteinase
-1.6
LE
1884
membrane protease
-1.7
EE
2045
low temperature requirement C protein
-1.7
LE
0015
ftsH
cell division protein
+1.8
EE
0103
comYC competence protein
+2.1
EE
collagen-like protein
+1.6
EE
1054
1191
oadA
oxaloacetate decarboxylase alpha-chain
+1.5
LE
1497
hlyA1
hemolysin tlyA-related protein
+1.5
EE
1615
comFC late competence protein
+2.2
EE
+1.7
LE
-1.6 & -1.5
EE & LE
2165
DNA segregation ATPase, ftsK/spoIII
Phage-encoded (19 total, 15↓ and 4↑)
0555
portal protein, phage-associated
0658
cro-like protein, phage-associated
-1.7
LE
0670
hypothetical, phage-associated
-1.7
LE
0684
hypothetical, phage-associated
-1.8
LE
0961
hypothetical, phage-associated
-1.6
LE
0962
hypothetical, phage-associated
-1.6
LE
1290
hypothetical, phage-associated
-1.8
LE
13
1447
hypothetical, phage-associated
-2.3
LE
1455
hypothetical, phage-associated
-1.5
LE
1462
hypothetical, phage-associated
-1.7
EE
1464
hypothetical, phage-associated
-1.6
EE
1468
endonuclease, phage-associated
-1.6
LE
1471
hypothetical, phage-associated
-1.5
EE
1477
recombinase, phage-associated
-1.8
LE
2127
hypothetical, phage-associated
-2.8
LE
0957
hypothetical, phage-associated
+1.6
EE
1462
hypothetical, phage-associated
+1.5
LE
1465
structural protein, phage-associated
+1.6
EE
1471
hypothetical, phage-associated
+1.8
LE
Unknown function (77 total, 62↓ and 15↑)
0105
hypothetical
-1.6 & -1.6
EE & LE
0107
hypothetical
-1.6
EE
0110
hypothetical
-1.8
LE
0116
hypothetical
-1.9
LE
0219
hypothetical
-1.6
LE
0315
hypothetical
-1.6
LE
0367
hypothetical
-1.8
EE
0393
hypothetical
-1.9
EE
0401
hypothetical
-1.6
LE
0407
hypothetical
-1.9 & -1.6
EE & LE
14
0430
hypothetical
-1.6 & -1.6
EE & LE
0439
hypothetical
-1.5 & -1.8
EE & LE
0448
hypothetical
-1.6
LE
0467
hypothetical
-1.9
LE
0480
hypothetical
-1.9
EE
0488
hypothetical
-1.6
EE
0575
hypothetical
-1.6
LE
0580
hypothetical
-1.7
LE
0587
hypothetical
-1.7
LE
0593
hypothetical
-2.0 & -2.1
EE & LE
0622
hypothetical
-1.6 & -1.9
EE & LE
0653
hypothetical
-1.9 & -1.7
EE & LE
0654
hypothetical
-1.8
LE
0798
hypothetical
-2.6
EE
0802
hypothetical
-1.7
EE
0908
hypothetical-membrane spanning
-1.6
LE
0912
hypothetical
-1.6
LE
0914
hypothetical
-1.7 & -1.8
EE & LE
0923
hypothetical
-1.6
LE
1017
hypothetical
-1.6
LE
1044
hypothetical-membrane spanning
-1.7 & -1.5
EE & LE
1048
hypothetical
-1.6
LE
1064
hypothetical
-1.6
EE
15
1146
hypothetical
-1.8
LE
1193
hypothetical
-1.7
LE
1223
hypothetical
-1. 7
EE
1253
hypothetical
-1.5 & -1.6
EE & LE
1322
hypothetical
-2.6
EE
1329
hypothetical
-1.6 & -1.8
EE & LE
1340
hypothetical
-1.9
LE
1344
hypothetical
-1.7
EE
1385
hypothetical
-1.7
LE
1404
hypothetical
-1.6
LE
1425
hypothetical
-1.8
LE
1508
hypothetical
-1.6
LE
1516
hypothetical-integral membrane
-2.2
LE
1534
hypothetical
-1.6
LE
1569
hypothetical
-1.9
LE
1571
hypothetical
-1.9 & -2.3
EE & LE
1675
hypothetical
-2.3 & -2.0
EE & LE
1686
hypothetical
-1.8 & -2.2
EE & LE
1697
hypothetical
-1.6
EE
1698
hypothetical
-1.6
LE
1731
hypothetical
-1.5
LE
1862
hypothetical
-1.5
LE
1936
hypothetical
-1.6
LE
16
1939
hypothetical
-1.6
LE
1945
hypothetical
-1.6
LE
2006
hypothetical
-1.6
EE
2111
hypothetical
-1.6
EE
2165
hypothetical
-1.6
EE
2166
hypothetical
-1.5
EE
0144
hypothetical
+1.7
EE
0315
hypothetical
+3.2
EE
0359
hypothetical
+1.9
EE
0537
hypothetical
+1.8
EE
0604
hypothetical
+2.0
EE
1260
hypothetical
+1.6
LE
1264
hypothetical
+1.6
LE
1277
hypothetical
+1.5 & 1.8
EE & LE
1581
hypothetical
+1.6
EE
1603
hypothetical
+1.6
LE
1607
hypothetical
+2.0
EE
1608
hypothetical
+1.7
EE
1768
hypothetical
+2.0
EE
2112
hypothetical
+1.6
EE
2181
hypothetical
+2.3
EE
Proteins encoded by differentially-expressed genes were identified by annotation or
17
homology to known proteins (http://www.ncbi.nlm.nih.gov/BLAST/) and assigned to
categories based on description in Clusters of Orthologous Groups of proteins (COGs).
EE, early exponential phase of growth (OD600 = 0.35); LE, late exponential phase of
growth (OD600 = 0.75).
18