Supporting information for Xu et al. (2003) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0337479100
Table 3. Three hundred highly expressed genes in rabbit ileal loops as determined by analysis of RNA versus gDNA
Gene description | Gene ID | Density of genespring |
Protein synthesis | ||
ribosomal protein L11 (rplK) | VC0324 | 4.3 |
ribosomal protein L1 (rplA) | VC0325 | 6.7 |
ribosomal protein L10 (rplJ) | VC0326 | 12.8 |
ribosomal protein L7/L12 (rplL) | VC0327 | 3.3 |
ribosomal protein S7 (rpsG) | VC0360 | 4.7 |
ribosomal protein S6 (rpsF) | VC0366 | 4.4 |
ribosomal protein L21 (rplU) | VC0435 | 12.4 |
ribosomal protein L27 (rpmA) | VC0436 | 3.5 |
ribosomal protein S1 (rpsA) | VC1915 | 13.2 |
ribosomal protein L32 (rpmF) | VC2025 | 3.2 |
ribosomal protein S2 (rpsB) | VC2260 | 4.5 |
ribosomal protein L17 (rplQ) | VC2570 | 4.8 |
ribosomal protein S4 (rpsD) | VC2572 | 9.6 |
ribosomal protein S11 FRAMESHIFT (rpsK) | VC2573 | 11.9 |
ribosomal protein S13 (rpsM) | VC2574 | 16.6 |
ribosomal protein L36 (rpmJ) | VC2575 | 5.1 |
ribosomal protein L15 (rplO) | VC2577 | 5.8 |
ribosomal protein L30 (rpmD) | VC2578 | 3.6 |
ribosomal protein S5 (rpsE) | VC2579 | 5.4 |
ribosomal protein L18 (rplR) | VC2580 | 5.5 |
ribosomal protein L6 (rplF) | VC2581 | 8.1 |
ribosomal protein S8 (rpsH) | VC2582 | 9.6 |
ribosomal protein S14 (rpsN) | VC2583 | 10.3 |
ribosomal protein L5 (rplE) | VC2584 | 12.1 |
ribosomal protein L24 (rplX) | VC2585 | 10.8 |
ribosomal protein L14 (rplN) | VC2586 | 8.1 |
ribosomal protein S17 (rpsQ) | VC2587 | 4.7 |
ribosomal protein L29 (rpmC) | VC2588 | 6.6 |
ribosomal protein L16 (rplP) | VC2589 | 6.5 |
ribosomal protein S3 (rpsC) | VC2590 | 3.8 |
ribosomal protein L22 (rplV) | VC2591 | 4.7 |
ribosomal protein S19 (rpsS) | VC2592 | 4.9 |
ribosomal protein L2 (rplB) | VC2593 | 7.9 |
ribosomal protein L23 (rplW) | VC2594 | 4.3 |
ribosomal protein L4 (rplD) | VC2595 | 4.8 |
ribosomal protein L3 (rplC) | VC2596 | 6.3 |
ribosomal protein S10 (rpsJ) | VC2597 | 6.1 |
ribosomal protein L35 (rpmI) {Vibrio cholerae} | VCA0289 | 5.1 |
elongation factor Tu (tufB) | VC0321 | 8.0 |
elongation factor TU (tufA) | VC0362 | 8.0 |
elongation factor G (fusA) | VC2342 | 4.7 |
elongation factor G (fusA) | VC0361 | 3.6 |
threonyl-tRNA synthetase (thrS) | VCA0287 | 3.1 |
tRNA delta(2)-isopentenylpyrophosphate transferase (MiaA) | VC0346 | 3.5 |
initiation factor IF3, POINTMUTATION (infC) | VCA0288 | 10.2 |
Protein fate | ||
protease DegS (degS) {Escherichia coli} | VC0565 | 4.7 |
protease, putative {Escherichia coli} | VC0652 | 3.9 |
peptidase, M20A family | VC1343 | 3.7 |
preprotein translocase, SecG subunit | VC0640 | 4.3 |
preprotein translocase, SecY subunit | VC2576 | 9.2 |
peptidyl-prolyl cis-trans isomerase A | VC2299 | 2.9 |
Transport and binding proteins | ||
maltose/maltodextrin ABC transporter (malK) | VCA0946 | 3.9 |
maltose ABC transporter, periplasmic mal (malE) | VCA0945 | 8.6 |
maltose ABC transporter, permease protein (malF) | VCA0944 | 4.8 |
maltoporin (ompS) | VCA1028 | 6.6 |
formate transporter 1, putative | VCA0540 | 6.2 |
phosphoenolpyruvate-protein phosphotransferase (ptsl) | VC0965 | 19.8 |
C4-dicarboxylate transporter, anaerobic (dcuA) | VC2699 | 17.1 |
C4-dicarboxylate transporter, anaerobic (dcuB) | VCA0205 | 8.2 |
C4-dicarboxylate transporter, anaerobic (dcuC) | VCA0665 | 5.6 |
phosphocarrier protein HPr (ptsH) | VC0966 | 20.0 |
PTS system, glucose-specific IIBC component (ptsG) | VC2013 | 17.9 |
PTS system, glucose-specific IIA component (ptsN) | VC0964 | 3.3 |
PTS system, IIA component {Escherichia coli} | VCA0245 | 4.3 |
PTS system, nitrogen regulatory IIA component | VC2531 | 2.9 |
peptide ABC transporter, permease protein | VC0172 | 38.9 |
serine transporter (sdaC) | VC1301 | 26.2 |
spermidine/putrescine ABC transporter | VC1427 | 3.2 |
TonB system receptor, putative FRAMESHIFT | VCA0232 | 3.3 |
TonB system receptor, putative | VCA0064 | 4.3 |
ferrous iron transport protein A (feoA) | VC2078 | 8.3 |
ferrous iron transport protein B (feoB) | VC2077 | 8.0 |
TonB system transport protein ExbB1 (exbB1) | VCA0911 | 7.7 |
TonB system transport protein ExbD1 (exbD1) | VCA0912 | 8.5 |
tonB1 protein (tonB1) {Vibrio cholerae} | VCA0910 | 4.7 |
ferric vibriobactin receptor (viuA) | VC2211 | 4.7 |
bacterioferritin (bfr) | VC0365 | 3.3 |
hemin ABC transporter, ATP-binding protein | VCA0915 | 2.9 |
hemin ABC transporter, permease protein | VCA0914 | 4.0 |
hemin ABC transporter, periplasmic hemin-binding protein (hutB) | VCA0913 | 10.2 |
heme transport protein HutA (hutA) {Vibrio cholerae} | VCA0576 | 8.3 |
iron(III) compound receptor | VC0200 | 3.2 |
Na+/H+ antiporter (yqkI) | VC2037 | 3.0 |
NupC family protein | VC2352 | 4.9 |
lipopolysaccharide/O-antigen transport protein (rfbI) | VC0247 | 6.7 |
transporter, putative | VC1314 | 3.2 |
SgaT protein (sgaT) {Escherichia coli} | VCA0246 | 3.7 |
Cellular processes | ||
stringent starvation protein B (sspB) | VC0577 | 4.1 |
stringent starvation protein A (sspA) | VC0576 | 6.1 |
antibiotic synthetase, putative FRAMESHIT | VC2209 | 2.9 |
cardiolipin synthase (cls) | VC1670 | 3.9 |
cell division protein FtsA (ftsA) | VC2398 | 3.5 |
cell division protein FtsZ (ftsz) | VC2397 | 3.3 |
heat shock protein HslJ (hslJ) | VC1663 | 3.4 |
Cellular processes (chemotaxis and motility) | ||
purine-binding chemotaxis protein CheW (cheW) | VC2059 | 3.8 |
chemotaxis protein CheV, putative {Vibrio cholerae} | VCA0954 | 3.3 |
chemotaxis protein CheY (cheY) | VC2065 | 7.4 |
chemotaxis protein CheZ (cheZ) | VC2064 | 8.3 |
chemotaxis protein CheA (cheA) | VC2063 | 5.2 |
chemotaxis protein CheY, putative | VC1316 | 3.6 |
protein-glutamate methylesterase CheB (cheB) | VC2062 | 5.5 |
twitching motility protein PilT (pilT) | VC0462 | 4.7 |
methyl-accepting chemotaxis protein | VC1898 | 4.2 |
methyl-accepting chemotaxis protein FRAM | VCA1031 | 3.5 |
flagellar hook protein FlgE (flgE) | VC2197 | 4.1 |
flagellin FlaC (flaC) | VC2187 | 12.1 |
flagellin FlaD (flaD) | VC2143 | 8.1 |
flagellin FlaB (flaB) | VC2142 | 5.7 |
flagellar hook-associated protein FliD (fliD) | VC2140 | 3.7 |
basal-body rod modification protein FlgD (flgD) | VC2198 | 3.1 |
sodium-type flagellar protein MotX (motX) | VC2601 | 4.7 |
Energy metabolism | ||
anaerobic glycerol-3-phosphate dehydrogenase, subunit C (glpC) | VCA0749 | 3.3 |
anaerobic glycerol-3-phosphate dehydrogenase, subunit B (glpB) | VCA0748 | 5.3 |
fumarate reductase, flavoprotein subunit (frdA) | VC2656 | 22.1 |
fumarate reductase, iron-sulfur protein (frdB) | VC2657 | 25.5 |
fumarate reductase, 15 kDa hydrophobic protein (frdC) | VC2658 | 12.5 |
fumarate reductase, 13 kDa hydrophobic protein (frdD) | VC2659 | 7.0 |
formate acetyltransferase (pflB) | VC1866 | 31.0 |
alcohol dehydrogenase/acetaldehyde dehydrogenase (adhE) | VC2033 | 54.9 |
iron-containing alcohol dehydrogenase family protein (rfbM) | VC0250 | 3.4 |
acetate kinase (ackA) {Escherichia coli} | VC1098 | 5.6 |
phosphate acetyltransferase (pta) | VC1097 | 3.4 |
glycerol kinase (gplK) {Escherichia coli} | VCA0744 | 3.2 |
sugar isomerase SgaE, AraD/FucA family | VCA0244 | 4.2 |
hexulose-6-phosphate synthase SgbH, putative | VCA0242 | 3.4 |
pyruvate kinase I (pykF) | VC0485 | 8.7 |
glucose-6-phosphate isomerase (pgi) | VC0374 | 6.1 |
enolase (eno) | VC2447 | 7.6 |
2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (sucB) | VC2086 | 3.1 |
6-phosphofructokinase, isozyme I (pfkA) | VC2689 | 5.0 |
Glyceraldehyde 3-phosphate dehydrogenase (gapA) | VC2000 | 27.7 |
2,3-bisphosphoglycerate-independent phosphoglycerate mutase (yibO) | VC0336 | 11.9 |
citrate synthase (gltA) | VC2092 | 3.4 |
phosphomannomutase {Treponema pallidum} | VCA1041 | 4.8 |
phosphomannomutase (rfbB) {Vibrio cholerae} | VC0242 | 5.4 |
glucose-1-phosphate adenylyltransferase (glgC) | VC1727 | 3.6 |
deoxyribose-phosphate aldolase (deoC) | VC2350 | 3.7 |
aspartate ammonia-lyase (aspA) | VC2698 | 40.3 |
tryptophanase (tnaA) {Escherichia coli}, | VCA0161 | 3.5 |
alanine dehydrogenase (ald) | VC1905 | 3.5 |
ATP synthase F1, delta subunit (atpH) | VC2767 | 3.1 |
NADH:ubiquinone oxidoreductase, Na translocating (nqrD) | VC2292 | 3.1 |
NADH:ubiquinone oxidoreductase, Na translocating, subunit (nqrC) | VC2293 | 3.6 |
NADH:ubiquinone oxidoreductase, Na translocating (nqrB) | VC2294 | 4.8 |
NADH:ubiquinone oxidoreductase, Na translocating, subunit (nqrA) | VC2295 | 6.5 |
thiol:disulfide interchange protein DsbE (dsbE) | VC2051 | 3.1 |
cytochrome c-type protein YecK (yecK) | VC1951 | 5.5 |
Pathogenesis | ||
MSHA pilin protein MshB (mshB) {Vibrio cholerae} | VC0408 | 3.0 |
MSHA pilin protein MshA (mshA) | VC0409 | 5.9 |
MSHA pilin protein MshC, FRAMESHIFT (mshC) | VC0410 | 5.4 |
MSHA pilin protein MshD (mshD) {Vibrio cholerae} | VC0411 | 8 |
hemagglutinin/protease (hap) | VCA0865 | 17.6 |
hemolysin, putative | VC0578 | 3.0 |
haemolysin (hlyA) | VCA0219 | 7.1 |
agglutination protein | VC1621 | 3.5 |
toxin co-regulated pilus biosynthesis protein (tcpH) | VC0827 | 2.8 |
toxin co-regulated pilus biosynthesis protein (tcpP) | VC0826 | 3.4 |
cholera toxin transcriptional activator (toxR) | VC0984 | 4.0 |
DNA-binding protein VicH (vicH) {Escherichia coli} | VC1130 | 3.5 |
Regulatory function | ||
sigma-54 modulation protein, putative | VC0706 | 8.1 |
sigma-54 modulation protein, putative | VC2530 | 4.0 |
flagellar regulatory protein A (flrA) | VC2137 | 3.0 |
sigma-E factor negative regulatory protein | VC2466 | 3.5 |
sigma-E factor regulatory protein RseB | VC2465 | 2.8 |
transcriptional regulator, LuxR family | VCA1078 | 3.3 |
transcriptional regulator, MerR family | VC0974 | 3.4 |
transcriptional regulator, LysR family | VC1049 | 3.6 |
transcriptional regulator | VCA0566 | 3.3 |
transcriptional regulator, TetR family | VCA0917 | 3.3 |
transcriptional regulator, ROK family | VC2007 | 6.8 |
transcriptional repressor, LacI family | VC2677 | 4.9 |
zinc uptake regulation protein, putative | VC0378 | 3.3 |
sensor histidine kinase | VC1315 | 4.0 |
cold shock domain family protein | VCA0933 | 29.6 |
cold shock transcriptional regulator CspA | VCA0166 | 9.8 |
cyclic AMP receptor protein | VC2614 | 4.5 |
aerobic respiration control protein ArcA | VC2368 | 23.4 |
host factor-I, putative | VC0347 | 6.3 |
DNA-binding response regulator | VC1320 | 3.9 |
adenylate cyclase (cyaA) | VC0122 | 3.1 |
negative regulator of flagellin synthesis (flgM) | VC2204 | 4.1 |
hemagglutinin/protease regulatory protein | VC0583 | 3.0 |
Transcription | ||
DNA-directed RNA polymerase, alpha subunit (rpoA) | VC2571 | 4.5 |
RNA polymerase sigma-54 factor (rpoN) | VC2529 | 2.9 |
RNA polymerase sigma-70 factor, ECF subfamily | VC2302 | 4.6 |
RNA polymerase sigma-E factor (rpoE) | VC2467 | 4.4 |
transcription termination factor Rho (rho) | VC0307 | 5.8 |
ATP-dependent RNA helicase RhlB (rhlB) | VC0305 | 3.8 |
RNA-binding protein | VC0159 | 12.9 |
16S rRNA processing protein RimM (rimM) | VC0562 | 3.5 |
ribonuclease E (rne) {Escherichia coli} | VC2030 | 3.5 |
ribonuclease R (vacB) {Escherichia coli} | VC2599 | 3.1 |
RNA polymerase sigma factor for flagellar operon (fliA) | VC2066 | 6.9 |
DNA metabolism | ||
DNA-binding protein HU-beta (hupB) | VC1919 | 6.7 |
endonuclease IV (nfo) | VC2360 | 4.3 |
excinuclease ABC, subunit C (uvrC) | VC1214 | 3.2 |
Purine, pyrimidines, nucleosides | ||
CTP synthase (pyrG) | VC2448 | 8.8 |
uridine phosphorylase (udp-1) | VC1034 | 8.0 |
cytidine deaminase (cdd) | VC1231 | 3.2 |
adenylosuccinate synthetase (purA) {Vibrio cholerae} | VC2602 | 4.6 |
dihydroorotate dehydrogenase (pyrD) | VC1491 | 3.2 |
2`,3`-cyclic-nucleotide 2`-phosphodiesterase (cpdB) | VC2562 | 3.3 |
Fat acid metabolism | ||
acyl carrier protein (acp) | VC2020 | 3.2 |
acyl protein synthase/acyl-CoA reductase (rfbN) | VC0251 | 4.1 |
long-chain-fatty-acid–CoA ligase | VC2484 | 2.9 |
fatty oxidation complex, alpha subunit | VC1047 | 3.6 |
Cell envelope | ||
outer membrane protein OmpV (ompV) | VC1318 | 22.2 |
outer membrane protein OmpW (ompW) | VCA0867 | 4.9 |
outer membrane protein OmpU (ompU) | VC0633 | 35.4 |
rare lipoprotein B (rlpB) | VC0954 | 3.2 |
major outer membrane lipoprotein (lpp) | VCA0059 | 7.8 |
D-alanyl-D-alanine endopeptidase (pbpG) | VCA0870 | 3.2 |
D-alanine–D-alanine ligase (ddlA) {Trep | VCA0572 | 3.1 |
mannose-1-phosphate guanylyltransferase (rfbA) | VC0241 | 4.8 |
GDP-mannose 4,6-dehydratase (rfbD) | VC0243 | 6.4 |
perosamine synthase (rfbE) | VC0244 | 5.6 |
peptidoglycan-associated lipoprotein (pal) | VC1835 | 3.7 |
Biosynthesis of cofactor | ||
thiamin biosynthesis lipoprotein ApbE (apbE) | VC2289 | 4.4 |
biotin synthesis protein BioC (bioC) | VC1114 | 3.7 |
dethiobiotin synthetase (bioD) | VC1115 | 5.9 |
biotin sulfoxide reductase (bisZ) | VC1950 | 3.8 |
naphthoate synthase (menB) | VC1973 | 4.0 |
uroporphyrin-III C-methyltransferase (cysG) | VC2561 | 3.3 |
Central intermediary metabolism | ||
N-acetyltransferase, GNAT family | VC2332 | 4.2 |
Unknown, hypothetical and conserved hypothetical | ||
rfbT protein (rfbT) {Vibrio cholerae} | VC0258 | 3.1 |
rfbT protein {Vibrio cholera} | VC0255 | 2.9 |
rfbL protein (rfbL) {Vibrio cholerae} | VC0249 | 5.7 |
rfbG protein (rfbG) {Vibrio cholerae} | VC0245 | 5.6 |
histidine triad family protein, | VC2075 | 5.1 |
c-di-GMP phosphodiesterase A-related proein | VC0653 | 3.6 |
enterobactin synthetase component F-related protein | VC1579 | 3.5 |
GGDEF family protein | VC0900 | 4.1 |
O-methyltransferase-related protein | VC0091 | 4.6 |
hypothetical protein | VC0314 | 48.0 |
hypothetical protein | VC0388 | 20.5 |
hypothetical protein | VC0572 | 3.5 |
hypothetical protein | VC0600 | 3.6 |
hypothetical protein | VC0713 | 57.0 |
hypothetical protein | VC0967 | 7.4 |
selenoprotein W-related protein | VC0982 | 4.5 |
hypothetical protein | VC1100 | 5.0 |
hypothetical protein | VC1865 | 7.5 |
hypothetical protein | VC1909 | 4.0 |
hypothetical protein | VC1999 | 3.9 |
hypothetical protein | VC2005 | 3.8 |
hypothetical protein | VC2034 | 4.4 |
hypothetical protein | VC2038 | 3.4 |
hypothetical protein | VC2076 | 7.5 |
hypothetical protein | VC2155 | 32.6 |
hypothetical protein | VC2221 | 5.6 |
hypothetical protein | VC2304 | 8.2 |
hypothetical protein | VC2306 | 7.4 |
hypothetical protein | VC2313 | 4.1 |
hypothetical protein | VC2315 | 5.3 |
hypothetical protein | VC2317 | 5.7 |
hypothetical protein | VC2318 | 5.1 |
hypothetical protein | VC2321 | 3.3 |
hypothetical protein | VC2325 | 3.5 |
hypothetical protein | VC2328 | 4.2 |
hypothetical protein | VC2331 | 3.3 |
hypothetical protein | VC2354 | 4.3 |
hypothetical protein | VC2372 | 3.2 |
hypothetical protein | VC2375 | 3.6 |
hypothetical protein | VC2495 | 15.2 |
hypothetical protein | VC2752 | 5.8 |
hypothetical protein | VCA0065 | 3.2 |
hypothetical protein | VCA0379 | 4.1 |
hypothetical protein | VCA0535 | 3.7 |
hypothetical protein | VCA0561 | 2.9 |
hypothetical protein | VCA0571 | 3.8 |
hypothetical protein | VCA0869 | 4.4 |
hypothetical protein | VCA0892 | 3.4 |
hypothetical protein | VCA0935 | 3.6 |
hypothetical protein | VCA0976 | 3.4 |
hypothetical protein | VCA1030 | 3.1 |
conserved hypothetical protein | VC0005 | 3.9 |
conserved hypothetical protein | VC0567 | 3.3 |
conserved hypothetical protein | VC0580 | 3.8 |
conserved hypothetical protein | VC0641 | 3.1 |
conserved hypothetical protein | VC0651 | 3.3 |
conserved hypothetical protein | VC0981 | 3.8 |
conserved hypothetical protein | VC1249 | 3.5 |
conserved hypothetical protein | VC1317 | 7.4 |
conserved hypothetical protein | VC1433 | 3.9 |
conserved hypothetical protein | VC1497 | 3.5 |
conserved hypothetical protein | VC1871 | 4.3 |
conserved hypothetical protein | VC2001 | 4.0 |
conserved hypothetical protein | VC2009 | 3.3 |
conserved hypothetical protein | VC2026 | 3.8 |
conserved hypothetical protein | VC2041 | 3.0 |
conserved hypothetical protein | VC2060 | 5.7 |
conserved hypothetical protein | VC2378 | 3.2 |
conserved hypothetical protein | VC2647 | 5.2 |
conserved hypothetical protein | VCA0243 | 3.3 |
conserved hypothetical protein | VCA0248 | 3.3 |
conserved hypothetical protein | VCA0536 | 3.6 |
conserved hypothetical protein | VCA0907 | 2.7 |
conserved hypothetical protein | VCA0908 | 9.7 |
conserved hypothetical protein | VCA1065 | 4.6 |
conserved hypothetical protein FRAMESHIFT | VCF2526 | 7.1 |