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. 2005 Dec;187(23):8205–8210. doi: 10.1128/JB.187.23.8205-8210.2005

TABLE 1.

Genes that are differentially expressed in S. pneumoniae strains T4 and Tupelo 10 and 20 min after the addition of vancomycina

Identity and function Annotation Gene T4 with vancomycin for:
Tupelo with vancomycin for:
10 min 20 min 10 min 20 min
Stress response
    SP0515 Heat-inducible transcription repressor HrcA hrcA 5.8 −1.0 s 4.7 3.3
    SP0516 Heat shock protein GrpE grpE 6.1 1.2 s 4.8 3.1
    SP0517 DnaK protein dnaK 6.6 2.0 4.6 3.5
    SP0519 DnaJ protein dnaJ 3.9 1.6 s 3.8 3.1
    SP0766 Superoxide dismutase, manganese dependent sodA 1.3 s 1.3 s −1.1 s −3.4
    SP0784 Glutathione reductase gor 2.0 3.3 1.6 s 1.9
    SP1283 Heat shock protein HtpX htpX 1.7 3.5 1.4 s 1.7
    SP1284 LemA protein lemA 1.7 3.5 1.5 s 1.8
    SP1996 Universal stress protein family uspA 2.1 6.0 −1.6 s −2.5
    SP2206 Ribosomal subunit interface protein yfiA 1.7 s 3.3 −1.7 s −2.7
Transcription factors and two-component systems
    SP0386 Sensor histidine kinase HK03 5.3 5.5 4.1 5.3
    SP0387 DNA-binding response regulator RR03 4.7 4.4 4.4 5.1
    SP0727 Transcriptional repressor, putative 1.4 s 4.3 1.4 s 1.3 s
    SP1714 Transcriptional regulator, GntR family 6.8 27.6 9.8 8.1
    SP2000 DNA-binding response regulator RR11 2.7 2.5 3.6 3.3
    SP2001 Sensor histidine kinase HK11 3.4 2.8 3.8 3.7
Aminosugar and cell wall metabolism
    SP0266 Glucosamine-fructose-6-phosphate aminotransferase glmS −8.3 −20.1 −4.2 −3.9
    SP1415 Glucosamine-6-phosphate isomerase nagB 7.8 18.5 3.0 2.0
    SP1975 SpolllJ family protein 2.3 2.3 2.6 3.1
    SP2056 N-Acetylglucosamine-6-phosphate deacetylase nagA 7.1 15.6 2.6 2.4
    SP2217 Rod shape-determining protein MreD, putative −1.5 s −3.1 −1.0 #s −1.1 s
    SP2218 Rod shape-determining protein MreC mreC −1.4 s −2.6 1.1 #s 1.1 s
Nitrogen, purine, and polyamine metabolism
    SP0044 Phosphoribosylaminoimidazole-succinocarboxamide synthase purC −2.7 −3.5 1.1 s −6.5
    SP0045 Phosphoribosylformylglycinamidine synthase, putative −2.0 s −3.1 1.2 s −3.7
    SP0231 Adenylate kinase adk −1.8 s −5.1 −1.6 s −1.6 s
    SP0287 Xanthine/uracil permease family protein −2.4 −6.2 −1.3 s −3.1
    SP0502 Glutamine synthetase, type I glnA −2.2 −3.3 −1.4 s −1.4 s
    SP0916 Lysine decarboxylase cad −2.5 −6.9 −1.7 #s −1.2 #s
    SP0918 Spermidine synthase speE −2.4 −7.8 −2.4 −2.1 s
    SP0920 Carboxynorspermidine decarboxylase nspC −1.9 s −7.2 −2.1 s −2.2
    SP0922 Carbon-nitrogen hydrolase family protein −2.0 −7.0 −2.1 s −2.2
    SP1180 Ribonucleoside-diphosphate reductase 2, beta subunit nrdF −1.7 −3.4 −1.3 s −1.7
    SP1847 Xanthine phosphoribosyltransferase xpt −2.3 −10.9 1.2 s −3.0
    SP1848 Xanthine permease pbuX −2.4 −11.3 1.2 s −2.3
Fermentation, polysaccharide, and sugar metabolism
    SP0285 Alcohol dehydrogenase, zinc containing 2.3 3.1 −3.4 −3.5
    SP0459 Formate acetyltransferase pfl 1.7 1.9 −2.1 −4.2
    SP1118 Pullulanase, putative −1.6 s −3.9 −1.1 s −1.1 s
    SP1122 Glucose-1-phosphate adenylyltransferase glgC 1.2 s 1.5 s −2.3 s −3.2
    SP1123 Glycogen biosynthesis protein GlgD glgD 1.2 s 1.3 s −2.1 s −3.1
    SP1329 N-Acetylneuraminate lyase 1.7 #s 1.6 #s −2.4 s −4.0
    SP1330 N-Acetylmannosamine-6-P epimerase, putative nanE 1.4 #s 1.7 #s −2.7 s −4.4
    SP1382 Alpha-amylase amy 3.1 6.0 1.2 #s 2.1 #s
    SP1852 Galactose-1-phosphate uridylyltransferase galT 1.0 s −1.0 s −1.9 s −3.3
    SP2026 Alcohol dehydrogenase, iron-containing adhE 2.8 1.4 s −3.4 −3.2
    SP2106 Glycogen phosphorylase family protein 3.3 3.4 −1.0 s −1.2 s
    SP2107 4-Alpha-glucanotransferase malQ 4.3 3.9 −1.0 s −1.2 s
    SP2157 Alcohol dehydrogenase, iron-containing fucO 3.7 5.3 −1.2 #s −1.2 #s
    SP2167 l-Fuculose kinase FucK, putative fucK 2.4 #s 4.1 1.2 #s 1.5 #s
Capsule biosynthesis
    SP0346 Capsular polysaccharide biosynthesis protein Cps4A cps4A −1.4 s −1.8 1.0 s 1.1 s
    SP0347 Capsular polysaccharide biosynthesis protein Cps4B cps4B −1.3 s −1.5 1.1 s 1.1 s
    SP0348 Capsular polysaccharide biosynthesis protein Cps4C cps4C −1.5 s −2.4 −1.0 s 1.1 s
    SP0349 Capsular polysaccharide biosynthesis protein Cps4D cps4D −1.7 −3.1 −1.2 s −1.2 s
    SP0350 Capsular polysaccharide biosynthesis protein Cps4E cps4E −1.9 −4.0 −1.0 #s 1.2 #s
    SP0351 Capsular polysaccharide biosynthesis protein Cps4F cps4F −1.9 −4.3 1.4 #s −1.4 #s
    SP0352 Capsular polysaccharide biosynthesis protein Cps4G cps4G −1.9 s −4.0 1.1 #s 1.1 #s
    SP0353 Capsular polysaccharide biosynthesis protein Cps4H cps4H −1.6 −1.5 1.1 #s −1.0 #s
    SP0357 UDP-N-acetylglucosamine-2-epimerase cps4I −2.0 −6.6 −1.0 #s −1.0 #s
    SP0358 Capsular polysaccharide biosynthesis protein Cps4J cap4J −1.8 s −6.3 1.7 #s 1.0 #s
    SP0359 Capsular polysaccharide biosynthesis protein Cps4K cps4K −1.8 −6.4 1.1 #s −1.3 #s
    SP0360 UDP-N-acetylglucosamine-2-epimerase cps4L −1.7 −5.8 1.2 #s 1.2 #s
Surface proteins
    SP0390 Choline binding protein G cbpG 3.9 4.4 3.4 4.3
    SP0391 Choline binding protein F cbpF 3.2 4.2 3.0 4.5
    SP0462 Cell wall surface anchor family protein −1.5 s −2.6 1.0 #s 1.2 #s
    SP0463 Cell wall surface anchor family protein −1.7 s −3.4 1.5 #s 1.3 #s
    SP0464 Cell wall surface anchor family protein −1.5 s −3.7 1.1 #s −1.3 #s
    SP1002 Adhesion lipoprotein lmb −1.8 s −4.3 1.0 s −1.3 s
Translation and ribosomal proteins
    SP0085 Ribosomal protein S4 rpsD −2.6 −5.0 −1.6 s −2.0
    SP0232 Translation initiation factor IF-1 infA −1.8 −3.0 −1.5 s −1.7
    SP0233 Ribosomal protein L36 rpmJ −1.8 −2.9 −1.6 s −1.9 s
    SP0234 Ribosomal protein S13 rpsM −1.8 −3.3 −1.5 s −1.7
    SP0235 Ribosomal protein S11 rpsK −1.8 −3.3 −1.6 −1.6
    SP0271 Ribosomal protein S12 rpsL −1.8 −3.3 −1.4 s −1.5 s
    SP0272 Ribosomal protein S7 rpsG −1.7 −3.1 −1.4 s −1.4 s
    SP0294 Ribosomal protein L13 rplM −1.8 −3.1 −1.4 s −1.5
    SP0775 Ribosomal protein S16 rpsP −1.7 −3.8 −1.2 s −2.3
    SP0862 Ribosomal protein S1 rpsA −2.2 −3.5 −1.4 s −1.8
    SP0959 Translation initiation factor IF-3 infC −1.8 −4.9 −1.3 s −1.1 s
    SP0960 Ribosomal protein L35 rpmI −1.6 s −3.2 −1.3 s −1.4 s
    SP0961 Ribosomal protein L20 rplT −1.8 −3.2 −1.4 s −1.5 s
    SP1354 Ribosomal protein L7/L12 rplL −1.6 −3.0 −1.6 s −1.6
    SP1355 Ribosomal protein L10 rplJ −1.5 −3.3 −1.5 s −1.2 s
    SP2214 Translation elongation factor Ts tsf −1.2 −3.2 −1.2 s −1.3 s
    SP2215 Ribosomal protein S2 rpsB −1.3 −3.8 −1.2 s −1.3 s
PTS systems and ABC transporters
    SP0090 ABC transporter, permease protein 3.2 5.2 1.3 #s 1.6 #s
    SP0091 ABC transporter, permease protein 2.0 s 3.1 1.2 #s −1.1 #s
    SP0092 ABC transporter, substrate-binding protein 2.9 4.8 1.4 #s 1.3 #s
    SP0282 PTS system, mannose-specific IID component manN −1.2 −1.3 −2.2 s −3.4
    SP0283 PTS system, mannose-specific IIC component manM −2.6 −3.2 −2.3 −3.0
    SP0284 PTS system, mannose-specific IIAB components manL −2.8 −3.8 −1.9 s −3.3
    SP0786 ABC transporter, ATP-binding protein 2.0 3.0 3.2 2.2
    SP0912 ABC transporter, ATP-binding protein 3.2 5.5 1.8 s 1.9 s
    SP0913 ABC transporter, permease protein, putative 3.1 5.0 1.8 s 2.2
    SP0957 ABC transporter, ATP-binding protein 1.2 s 1.2 s −1.9 s −3.1
    SP1032 Iron compound ABC transporter, iron compound-binding protein piuB −1.5 s −2.3 −1.2 s −1.3 s
    SP1033 Iron compound ABC transporter, permease protein piuC −2.0 s −4.3 1.1 #s 1.1 s
    SP1034 Iron compound ABC transporter, permease protein piuD −2.0 s −4.6 −1.1 #s 1.1 s
    SP1035 Iron compound ABC transporter, ATP-binding protein piuA −2.0 s −4.6 −1.1 s −1.1 s
    SP1380 Putative permease 2.0 3.0 2.1 3.3
    SP1381 ABC transporter, ATP-binding protein 2.4 s 5.8 2.0 #s 3.3
    SP1580 Sugar ABC transporter, ATP-binding protein msmK −1.1 s −1.1 s −3.5 −6.6
    SP1688 ABC transporter, permease protein 1.8 s 3.8 1.2 #s −1.5 #s
    SP1689 ABC transporter, permease protein 2.0 s 2.9 1.1 #s −1.1 #s
    SP1690 ABC transporter, substrate-binding protein 2.1 s 3.6 1.5 #s 1.6 #s
    SP1715 ABC transporter, ATP-binding domain and permease 7.9 27.2 9.7 12.2
    SP2002 Putative permease 4.5 4.4 1.8 #s 1.7 #s
    SP2003 ABC transporter, ATP-binding protein 10.3 9.2 4.4 4.9
    SP2108 Maltose/maltodextrin ABC transporter, maltose-binding protein malX 1.7 2.6 −2.7 −4.0
    SP2109 Maltodextrin ABC transporter, permease protein malC 1.6 s 2.1 −2.6 s −3.9
    SP2110 Maltodextrin ABC transporter, permease protein malD 1.6 s 2.4 −1.5 #s −2.5
ClaRH regulon
    SP0282 PTS system, mannose-specific IID component manN −1.2 −1.3 −2.2 s −3.4
    SP0283 PTS system, mannose-specific IIC component manM −2.6 −3.2 −2.3 −3.0
    SP0284 PTS system, mannose-specific IIAB components manL −2.8 −3.8 −1.9 s −3.3
    SP0798 DNA-binding response regulator CiaR ciaR 2.7 2.5 −1.1 s −1.3 s
    SP0799 Sensor histidine kinase CiaH ciaH 2.8 2.2 −1.1 s −1.2
    SP0879 Hypothetical protein 9.9 14.1 1.5 #s 1.2 s
    SP1027 Conserved hypothetical protein 6.1 9.7 1.2 s −1.2 s
    SP2206 Ribosomal subunit interface protein yfiA 1.7 s 3.3 −1.7 s −2.7
    SP2239 HtrA serine protease htrA 5.4 4.1 −1.2 s −1.7
    SP2240 SpoJ protein parB 4.7 3.6 −1.1 s −1.6
Miscellaneous functions
    SP0006 Transcription-repair coupling factor mfd −1.6 s −3.9 −1.1 s −1.3 s
    SP0109 Bacteriocin, putative 1.9 s 3.5 −1.3 s −1.6
    SP0356 O-antigen transporter RfbX, putative −1.8 s −6.5 1.8 # −1.0 #s
    SP0962 Lactoylglutathione lyase gloA −1.8 s −3.6 −1.3 s −1.3
    SP1117 DNA ligase, NAD dependent ligA −1.8 s −4.3 1.0 s −1.0 s
    SP1214 Transulfuration enzyme family protein, authentic point mutation 2.5 s 3.3 1.0 #s 1.3 #s
    SP1325 Oxidoreductase, Gfo/Idh/MocA family 1.9 #s 1.8 # −2.3 s −4.0
    SP1326 Neuraminidase, putative 1.3 #s 2.1 #s −2.6 s −3.7
    SP1328 Sodium:solute symporter family protein 1.4 s 1.4 #s −2.1 s −3.2
    SP1343 Prolyl oligopeptidase family protein 1.9 s 3.2 1.5 #s 1.4 #s
    SP1402 NOL1/NOP2/sun family protein −2.1 s −4.4 −1.1 s −1.7 s
    SP1466 Hemolysin 2.8 6.1 −1.4 s −2.5
    SP1513 ATP synthase F0, A subunit atpB 1.2 s 1.3 s 1.8 s 3.2
    SP1586 ATP-dependent RNA helicase, putative −1.3 s −4.4 1.4 s 1.2 s
    SP1687 Neuraminidase B nanB 2.1 s 3.4 −1.1 #s 1.4 #s
    SP1807 Acetyltransferase, GNAT family 2.1 s 3.3 1.3 #s −1.1 s
Hypothetical proteins
    SP0034 Membrane protein 1.6 1.7 s 2.2 s 3.9
    SP0088 Hypothetical protein 1.5 s 3.2 1.4 #s 1.1 #s
    SP0096 Hypothetical protein 1.8 s 3.2 2.0 #s 1.6 #s
    SP0097 Conserved domain protein 2.0 2.3 3.5 2.3 s
    SP0098 Hypothetical protein 3.2 2.9 3.5 2.6
    SP0099 Hypothetical protein 3.6 3.5 3.8 2.9
    SP0100 Conserved hypothetical protein 3.4 3.6 3.7 2.3
    SP0189 Conserved hypothetical protein 2.9 5.4 2.1 1.7 s
    SP0191 Hypothetical protein 3.3 4.0 2.3 s 2.8
    SP0288 Conserved hypothetical protein −3.2 −5.4 −1.0 #s −1.6 #s
    SP0293 Hypothetical protein 2.2 3.5 1.5 s 1.9
    SP0298 Conserved hypothetical protein 2.2 s 3.1 1.4 #s −1.1 #s
    SP0355 Hypothetical protein −2.0 −6.4 1.2 #s 1.0 #s
    SP0385 Conserved hypothetical protein 5.5 5.9 3.9 5.1
    SP0389 Hypothetical protein 3.4 4.0 2.8 s 3.6
    SP0430 Hypothetical protein −1.5 s −3.3 −1.3 s −1.6 s
    SP0595 Hypothetical protein 1.0 s −3.1 1.1 #s 1.8 #s
    SP0728 Hypothetical protein 1.5 s 3.6 1.3 s 1.2 s
    SP0742 Conserved hypothetical protein 1.9 s 1.6 s −2.2 −3.7
    SP0785 Conserved hypothetical protein 2.2 3.0 3.3 2.4
    SP0787 Conserved hypothetical protein 2.0 s 3.2 3.5 2.2
    SP0879 Hypothetical protein 9.9 14.1 1.5 #s 1.2 s
    SP0910 Conserved hypothetical protein 4.1 8.0 3.2 3.4
    SP0919 Conserved hypothetical protein −2.3 s −6.0 −1.9 s −2.0 #
    SP0921 Conserved hypothetical protein −1.9 s −6.9 −2.3 −2.3
    SP0925 Conserved hypothetical protein 1.7 s 3.2 1.5 #s 1.9 s
    SP0958 Hypothetical protein 1.1 s 1.1 s −2.3 −4.1
    SP1004 Conserved hypothetical protein −1.3 s −4.0 2.4 s 1.3
    SP1027 Conserved hypothetical protein 6.1 9.7 1.2 s −1.2 s
    SP1327 Conserved hypothetical protein 1.3 #s 1.4 #s −2.3 s −3.6
    SP1344 Conserved hypothetical protein 3.1 #s 4.9 1.7 #s 1.2 #s
    SP1465 Hypothetical protein 3.2 7.3 −1.4 s −2.9
    SP1532 Conserved domain protein, authentic frameshift −1.7 s −3.8 −1.1 s −1.2 s
    SP1612 Conserved domain protein 1.2 #s −1.2 s 1.3 #s 3.2
    SP1685 Conserved hypothetical protein 1.1 s 1.5 s −2.2 −3.3
    SP1691 Conserved hypothetical protein 1.8 #s 5.4 1.4 #s 2.2 s
    SP1716 Conserved hypothetical protein natB 3.3 4.2 1.0 s 1.1 s
    SP1972 Membrane protein 2.7 3.4 1.2 s 1.1 s
    SP2004 Hypothetical protein 4.6 4.3 1.7 #s 1.3 #s
    SP2005 Hypothetical protein 6.6 9.5 1.8 #s 1.1 #s
a

Data represent fold increase or decrease in gene expression after treatment. Only genes whose expression changed by at least threefold are shown. Each datum point represents three biological samples and a total of 12 cDNA hybridization spots. A “#” marks data that are based on low signal intensities for the sample and the reference. Data that had analysis of variance P values larger than 0.001 are indicated by an “s.”