Supporting information for Xu et al. (2003) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0337479100

 

Table 2. Three hundred highly expressed genes in LB as determined by RNA versus gDNA method

Gene description

Gene ID

Density of genespring

Protein synthesis

ribosomal protein L34 (rpmH) {Haemophilus influenzae}

VC0007

4.3

ribosomal protein L28 (rpmB) {Haemophilus influenzae}

VC0218

5.5

ribosomal protein L33 (rpmG) {Escherichia coli}

VC0219

3.6

ribosomal protein L11 (rplK) {Escherichia coli}

VC0324

37.2

ribosomal protein L1 (rplA) {Escherichia coli}

VC0325

45.5

ribosomal protein L10 (rplJ) {Haemophilus influenzae}

VC0326

98.3

ribosomal protein L7/L12 (rplL) {Haemophilus influenzae}

VC0327

18.8

ribosomal protein S12 (rpsL) {Haemophilus influenzae}

VC0359

28.8

ribosomal protein S7 (rpsG)

VC0360

11.1

ribosomal protein S6 (rpsF) {Haemophilus influenzae}

VC0366

11.4

ribosomal protein S18 (rpsR) {Escherichia coli}

VC0368

9.5

ribosomal protein L9 (rplI) {Escherichia coli}

VC0369

5.3

ribosomal protein L21 (rplU) {Haemophilus influenzae}

VC0435

24.6

ribosomal protein L27 (rpmA) {Escherichia coli}

VC0436

6.7

ribosomal protein S21 (rpsU) {Escherichia coli}

VC0520

3.2

ribosomal protein S16 (rpsP) {Escherichia coli}

VC0561

17.6

ribosomal protein L19 (rplS) {{Escherichia coli}

VC0564

6.1

ribosomal protein L13 FRAMESHIFT (rplM)

VC0570

20.6

ribosomal protein S9 (rpsI) {Escherichia coli}

VC0571

6.7

ribosomal protein S15 (rpsO) {Escherichia coli}

VC0646

6.0

ribosomal protein S20 (rpsT) {Vibrio cholerae}

VC0679

5.1

ribosomal protein L25 (rplY) {Escherichia coli}

VC1640

13.9

ribosomal protein S1 (rpsA) {Escherichia coli}

VC1915

34.8

ribosomal protein L32 (rpmF) {Haemophilus influenzae}

VC2025

5.9

ribosomal protein S2 (rpsB) {Escherichia coli}

VC2260

28.9

ribosomal protein L17 (rplQ) {Escherichia coli}

VC2570

29.6

ribosomal protein S4 (rpsD) {Escherichia coli}

VC2572

29.9

ribosomal protein S11 FRAMESHIFT (rpsK)

VC2573

28.3

ribosomal protein S13 (rpsM) {Escherichia coli}

VC2574

69.9

ribosomal protein L36 (rpmJ) {Vibrio cholerae}

VC2575

11.8

ribosomal protein L15 (rplO) {Haemophilus influenzae}

VC2577

27.0

ribosomal protein L30 (rpmD) {Haemophilu

VC2578

21.2

ribosomal protein S5 (rpsE) {Haemophilus influenzae}

VC2579

21.6

ribosomal protein L18 (rplR)

VC2580

29.7

ribosomal protein L6 (rplF)

VC2581

29.4

ribosomal protein S8 (rpsH) {Escherichia coli}

VC2582

25.2

ribosomal protein S14 (rpsN) {Escherichia coli}

VC2583

34.6

ribosomal protein L5 (rplE)

VC2584

32.3

ribosomal protein L24 (rplX) {Escherichia coli}

VC2585

31.1

ribosomal protein L14 (rplN) {Haemophilus influenzae}

VC2586

32.6

ribosomal protein S17 (rpsQ) {Escherichia coli}

VC2587

23.6

ribosomal protein L29 (rpmC) {Escherichia coli}

VC2588

44.2

ribosomal protein L16 (rplP) {Escherichia coli}

VC2589

35.5

ribosomal protein S3 (rpsC) {Escherichia coli}

VC2590

32.4

ribosomal protein L22 (rplV) {Haemophilus influenzae}

VC2591

22.2

ribosomal protein S19 (rpsS) {Haemophilus influenzae}

VC2592

20.8

ribosomal protein L2 (rplB)

VC2593

35.8

ribosomal protein L23 (rplW) {Escherichia coli}

VC2594

16.5

ribosomal protein L4 (rplD) {Yersinia pestis}

VC2595

40.0

ribosomal protein L3 (rplC) {Escherichia coli}

VC2596

38.0

ribosomal protein S10 (rpsJ) {Escherichia coli}

VC2597

30.7

ribosomal protein L31 (rpmE) {Haemophilus influenzae}

VC2679

7.2

ribosomal protein L35 (rpmI) {Vibrio cholerae}

VCA0289

13.0

ribosomal protein L20 (rplT) {Vibrio cholerae}

VCA0290

6.5

initiation factor IF-1 (infA) {Escherichia coli}

VC1737

5.4

initiation factor IF-2 (infB) {Escherichia coli}

VC0643

4.1

initiation factor IF-3, POINTMUTATION (infC)

VCA0288

17.2

elongation factor G (fusA)

VC0361

11.0

elongation factor G (fusA) {Synechocystis sp.}

VC2342

14.0

elongation factor Ts (tsf) {Escherichia coli}

VC2259

5.2

elongation factor TU (tufA) {Salmonella typhimurium}

VC0362

33.0

elongation factor Tu (tufB) {Haemophilus influenzae}

VC0321

33.2

peptide chain release factor 2, FRAMESHIT

VC0663

4.0

ribosomal-protein-alanine acetyltransferase

VC0657

3.6

glutaminyl-tRNA synthetase (glnS) {Escherichia coli}

VC0997

3.4

glycyl-tRNA synthetase, alpha chain

VC0021

3.3

lysyl-tRNA synthetase, heat inducible (lysU)

VC0664

4.2

tyrosyl-tRNA synthetase (tyrS) {Haemophilus influenzae}

VC0631

3.2

threonyl-tRNA synthetase (thrS) {Escherichia coli}

VCA0287

4.5

tRNA (5-methylaminomethyl-2-thiouridylate) methyltransferase (trmU)

VC1128

3.5

tRNA (guanine-N1)-methyltransferase (trmD)

VC0563

17.3

Protein fate

preprotein translocase, SecE subunit (secE)

VC0322

5.8

preprotein translocase, SecG subunit (secG)

VC0640

11.7

preprotein translocase, SecY subunit (secY)

VC2576

51.6

protein-transport protein SecB (secB) {Escherichia coli}

VC2653

4.0

dnaK protein (dnaK) {Vibrio cholerae}

VC0855

12.9

trigger factor (tig) {Escherichia coli}

VC1923

12.1

heat shock protein HtpG (htpG) {Haemophilus influenzae}

VC0985

7.1

16 kDa heat shock protein A (ibpA) {Escherichia coli}

VC0018

3.4

chaperonin, 10 Kd subunit (groES) {Escherichia coli}

VCA0819

4.1

chaperonin, 60 Kd subunit (groEL) {Escherichia coli}

VCA0820

3.8

chaperonin, 10 Kd subunit (groES) {Pasteurella multocida}

VC2665

31.8

chaperonin, 60 Kd subunit (groEL) {Salmonella typhimurium}

VC2664

14.9

peptidyl-prolyl cis-trans isomerase, FKBP-type (fkpA)

VC0354

6.9

polypeptide deformylase (def)

VC0046

3.2

ATP-dependent Clp protease, proteolytic subunit (clpP)

VC1922

4.1

trypsin, putative {Mus musculus}

VC1649

5.9

protease HslVU, subunit HslV (hslV)

VC2675

3.8

protease DO (htrA) {Escherichia coli}

VC0566

3.7

protease HslVU, ATPase subunit HslU (hslU)

VC2674

3.2

clpB protein (clpB) {Escherichia coli}

VC0711

4.1

O-sialoglycoprotein endopeptidase, FRAMESHIFT

VC0521

4.7

Transporter and binding protein

ABC transporter, ATP-binding protein

VC1499

5.8

ABC transporter, ATP-binding protein

VC0698

4.6

PTS system, glucose-specific IIBC component (ptsG)

VC2013

4.1

maltoporin (ompS) {Vibrio cholerae}

VCA1028

3.2

long-chain fatty acid transport protein (fadL-2)

VC1043

5.9

lipopolysaccharide/O-antigen transport protein (rfbH)

VC0246

5.1

lipopolysaccharide/O-antigen transport protein (rfbI)

VC0247

7.8

peptide ABC transporter, permease protein

VC0172

8.9

spermidine/putrescine ABC transporter (potB)

VC1427

3.3

spermidine/putrescine ABC transporter (potA)

VC1428

3.5

spermidine/putrescine ABC transporter (potD)

VC1425

3.7

oligopeptide ABC transporter, periplasmi (oppA)

VC1091

3.3

serine transporter (sdaC) {Escherichia coli}

VC1301

4.0

iron(III) ABC transporter, periplasmic

VC0608

8.9

ferric vibriobactin-binding protein (irgA)

VC0475

5.0

tolB protein (tolB) {Escherichia coli}

VC1836

4.1

NupC family protein {Haemophilus influenzae}

VC2352

5.5

LysE/YggA family protein {Escherichia coli}

VC0481

4.1

Cellular process

antioxidant, AhpC/Tsa family

VC0731

7.4

stringent starvation protein A (sspA)

VC0576

7.5

stringent starvation protein B (sspB)

VC0577

3.8

bolA protein (bolA)

VC2296

5.8

cell division protein FtsZ (ftsz)

VC2397

3.5

cell division protein FtsQ (ftsQ)

VC2399

3.2

cell division protein FtsJ (ftsJ)

VC0636

3.4

superoxide dismutase, Fe (sodB)

VC2045

9.3

Cellular process (chemotaxis and motility)

chemotaxis protein CheY (cheY)

VC2065

5.9

chemotaxis protein CheZ (cheZ)

VC2064

5.9

chemotaxis protein CheA (cheA)

VC2063

4.0

methyl-accepting chemotaxis protein

VC1643

3.8

basal-body rod modification protein FlgD

VC2198

3.2

flagellar basal-body rod protein FlgB

VC2200

3.4

flagellin FlaD (flaD) {Vibrio cholerae}

VC2143

5.6

Energy metabolism

ATP synthase F1, beta subunit (atpD)

VC2764

7.8

ATP synthase F1, gamma subunit (atpG)

VC2765

4.2

ATP synthase F1, alpha subunit (atpA)

VC2766

10.3

ATP synthase F1, delta subunit (atpH)

VC2767

12.8

ATP synthase F0, B subunit (atpF)

VC2768

9.8

ATP synthase F0, C subunit (atpE)

VC2769

6.6

ATP synthase F0, A subunit (atpB)

VC2770

4.4

ATP synthase protein I (atpI)

VC2771

7.3

NADH:ubiquinone oxidoreductase, Na trans (nqrA)

VC2295

14.7

NADH:ubiquinone oxidoreductase, Na trans (nqrD)

VC2292

11.1

NADH:ubiquinone oxidoreductase, Na trans (nqrB)

VC2294

8.0

NADH:ubiquinone oxidoreductase, Na trans (nqrC)

VC2293

8.2

NADH:ubiquinone oxidoreductase, Na trans (nqrE)

VC2291

6.3

NADH:ubiquinone oxidoreductase, Na trans (nqrF)

VC2290

6.6

ubiquinol–cytochrome c reductase, iron-sulfur subunit

VC0573

3.4

ubiquinol–cytochrome c reductase, cytochrome B (petB)

VC0574

3.5

ubiquinol–cytochrome c reductase, cytochrome C (petC)

VC0575

9.3

cytochrome c oxidase, subunit CcoN

VC1442

4.4

cytochrome d ubiquinol oxidase, subunit I (cydA)

VC1844

3.6

Flavodoxin 1 (fldA) {Escherichia coli}

VC2099

4.8

thioredoxin (trxA) {Escherichia coli}

VC0306

3.8

pyruvate dehydrogenase, E3 component (lpdA)

VC2412

9.1

pyruvate dehydrogenase, E2 component (aceF)

VC2413

13.7

pyruvate dehydrogenase, E1 component (aceE)

VC2414

19.5

pyruvate kinase I (pykF) {Escherichia coli}

VC0485

3.7

2,3-bisphosphoglycerate-independent phosphoglycerate mutase (yibO)

VC0336

4.8

fructose-bisphosphate aldolase, class II (fbaA)

VC0478

3.7

Glyceraldehyde 3-phosphate dehydrogenase (gapA)

VC2000

13.7

enolase (eno) {Escherichia coli}

VC2447

5.9

2-oxoglutarate dehydrogenase, E2 component, Dihydrolipoaminde succinyltransferase (sucB)

VC2086

4.4

2-oxoglutarate dehydrogenase, E1 component (sucA)

VC2087

3.6

transaldolase B (talB) {Haemophilus influenzae}

VCA0623

8.4

Transketolase 1 (tktA) {Escherichia coli}

VCA0624

3.9

phosphomannomutase (rfbB) {Vibrio cholerae}

VC0242

8.54

phosphoglucomutase and phosphomannomutas (glmM)

VC0639

5.0

iron-containing alcohol dehydrogenase family protein RfbM

VC0250

9.4

formate acetyltransferase (pflB)

VC1866

3.5

phosphate acetyltransferase (pta)

VC1097

8.4

acetate kinase (ackA) {Escherichia coli}

VC1098

10.9

aspartate ammonia-lyase (aspA) {Haemophilus influenzae}

VC2698

10.3

trehalose-6-phosphate hydrolase (treC)

VC0911

3.4

deoxyribose-phosphate aldolase (deoC)

VC2350

4.2

malate oxidoreductase, putative

VC2681

3.3

Pathogenesis

DNA-binding protein VicH (vicH)

VC1130

3.9

Regulatory function

pyruvate dehydrogenase complex repressor (pdhR)

VC2415

10.6

factor-for-inversion stimulation protein (fis)

VC0290

7.4

aerobic respiration control protein ArcA (fexA)

VC2368

6.5

host factor-I, putative {Haemophilus influenzae}

VC0347

4.6

cold shock transcriptional regulator CspA (cspA)

VCA0166

4.8

ferric uptake regulation protein (fur)

VC2106

4.9

transcriptional reguator, TetR family

VC0333

3.5

Fatty acid metabolism

acyl carrier protein (acp)

VC2020

7.9

3-oxoacyl-(acyl-carrier-protein) reductase (fabG)

VC2021

6.5

malonyl Coa-acyl carrier protein transac (fabD)

VC2022

5.6

3-oxoacyl-(acyl-carrier-protein) synthase (fabH)

VC2023

4.4

fatty acid/phospholipid synthesis protein (plsX)

VC2024

3.6

3-oxoacyl-(acyl-carrier-protein) synthase (fabB)

VC2109

6.5

acetyl-CoA carboxylase, biotin carboxyla (accC)

VC0295

5.9

acetyl-CoA carboxylase, biotin carboxyl (accB)

VC0296

9.0

acetyl-CoA carboxylase, carboxyl transferase (accD)

VC1000

3.8

acyl carrier protein, putative

VC0248

4.9

acyl protein synthase/acyl-CoA reductase RfbN

VC0251

10.4

myo-inositol-monophosphatase

VC0745

3.8

Cell envelope

outer membrane protein OmpU (ompU)

VC0633

92.4

outer membrane protein OmpV (ompV)

VC1318

11.1

inner membrane protein, 60 kDa (yidC)

VC0004

4.3

outer membrane protein OmpA (ompA)

VC2213

3.7

outer membrane protein OmpH (ompH)

VC2251

3.4

peptidoglycan-associated lipoprotein (pal)

VC1835

6.6

lipoprotein, putative {Haemophilus influenzae}

VC2298

5.1

mannose-1-phosphate guanylyltransferase (rfbA)

VC0241

7.3

GDP-mannose 4,6-dehydratase (rfbD)

VC0243

13.3

perosamine synthase (rfbE) {Vibrio cholerae}

VC0244

9.6

phosphoheptose isomerase, putative

VC0579

3.6

major outer membrane lipoprotein (lpp)

VCA0059

4.5

Transcription

DNA-directed RNA polymerase, alpha subunit (rpoA)

VC2571

19.2

DNA-directed RNA polymerase, beta' subunit (rpoC)

VC0329

8.8

DNA-directed RNA polymerase, beta subunit (rpoB)

VC0328

9.4

DNA-directed RNA polymerase, omega subunit (rpoZ)

VC2709

6.9

RNA polymerase sigma factor RpoD (rpoD)

VC0517

3.6

RNA polymerase sigma factor for flagella (fliA)

VC2066

4.7

transcription elongation factor GreA (greA)

VC0634

6.0

transcription termination factor Rho (rho)

VC0307

4.8

transcription antitermination protein NusG (nusG)

VC0323

7.4

16S rRNA processing protein RimM (rimM)

VC0562

15.6

ribosome-binding factor A (rbfA)

VC0644

3.9

N utilization substance protein A (nusA)

VC0642

4.5

RNA-binding protein {Helicobacter pylori}

VC0159

21.3

ribonuclease E (rne) {Escherichia coli}

VC2030

3.9

ribonuclease P protein component (rnpA)

VC0006

3.7

ATP-dependent RNA helicase SrmB (srmB)

VC0660

4.0

ATP-dependent RNA helicase RhlB (rhlB)

VC0305

3.5

DNA metabolism

DNA gyrase, subunit A, FRAMESHIFT (gyrA)

VC1258

4.0

primosomal replication protein N (priB)

VC0367

8.2

endonuclease IV (nfo) {Escherichia coli}

VC2360

8.8

seqA protein (seqA) {Escherichia coli}

VC2096

3.5

Purine, pyrimidines, nucleosides, and nucleotides

UTP–glucose-1-phosphate uridylyltransferase

VC0395

3.6

adenylosuccinate synthetase (purA) {Vibrio cholerae}

VC2602

6.3

adenylate kinase (adk) {Escherichia coli}

VC0986

3.6

uridine phosphorylase (udp) {Escherichia coli}

VC1034

4.7

purine nucleoside phosphorylase (deoD)

VC2347

4.6

phosphopentomutase (deoB) {Escherichia coli}

VC2348

3.2

CTP synthase (pyrG)

VC2448

5.7

purine nucleoside phosphorylase (deoD)

VCA0053

3.3

Amino acid biosynthesis

glutamate–ammonia ligase (glnA)

VC2746

4.9

3-dehydroquinate dehydratase (aroQ)

VC0297

4.1

diaminopimelate decarboxylase (lysA)

VC0125

5.0

N-acetylglutamate synthase (argA)

VC2316

4.0

Biosynthesis of cofactor

riboflavin synthase, beta subunit (ribH)

VC2268

4.7

lipoic acid synthetase (lipA) {Escherich

VC0943

3.6

lipoate-protein ligase B (lipB) (lipB)

VC0944

3.5

uroporphyrin-III C-methyltransferase (cysG)

VC2561

5.9

D-erythrose 4-phosphate dehydrogenase (epd)

VC0476

3.4

undecaprenyl diphosphate synthase (uppS)

VC2256

3.3

pantoate–beta-alanine ligase (panC)

VC0591

4.0

3-methyl-2-oxobutanoate hydroxymethyltransferase (panB)

VC0592

3.4

2-amino-4-hydroxy-6-hydroxymethyldihydro (folK-2)

VC0593

3.8

Central intermediary metabolism

sulfate adenylate transferase, subunit 2 (cysD)

VC2560

5.6

biosynthetic arginine decarboxylase (speA)

VCA0815

3.2

inorganic pyrophosphatase (ppa)

VC2545

3.6

Unknown, Hypothetical, and Conserved Hypothetical Proteins

GTP-binding protein LepA (lepA)

VC2463

3.8

NifR3/Smm1 family protein {Escherichia coli}

VC0291

4.7

glucose inhibited division protein A

VC2775

4.2

enterobactin synthetase component F-relaated protein

VC1579

5.3

rfbL protein (rfbL) {Vibrio cholerae}

VC0249

9.8

rfbG protein (rfbG) {Vibrio cholerae}

VC0245

11.6

hesB family protein

VC0627

3.4

hypothetical protein

VC0160

17.6

hypothetical protein

VC0179

4

hypothetical protein

VC0314

204.5

hypothetical protein

VC0388

39.6

hypothetical protein

VC0567

5.3

hypothetical protein

VC0569

6.9

hypothetical protein

VC0598

7.1

hypothetical protein

VC0599

7

hypothetical protein

VC0600

9.2

hypothetical protein

VC0713

185.5

hypothetical protein

VC0714

3.6

hypothetical protein

VC0740

4

hypothetical protein

VC1201

4.4

hypothetical protein

VC1485

4

hypothetical protein

VC1924

3.6

hypothetical protein

VC2098

4

hypothetical protein

VC2170

7.8

hypothetical protein

VC2155

51.1

hypothetical protein

VC2304

16.4

hypothetical protein

VC2306

9.8

hypothetical protein

VC2313

8.2

hypothetical protein

VC2317

11.5

hypothetical protein

VC2318

7.5

hypothetical protein

VC2321

7.5

hypothetical protein

VC2325

7

hypothetical protein

VC2328

9.7

hypothetical protein

VC2331

9.3

hypothetical protein

VC2351

6.7

hypothetical protein

VC2375

8.1

hypothetical protein

VC2495

27.6

hypothetical protein

VC2752

28.6

hypothetical protein

VC2753

12.6

hypothetical protein

VCA0005

5.3

conserved hypothetical protein

VC0005

5

conserved hypothetical protein

VC0355

4.2

conserved hypothetical protein

VC0519

5.6

conserved hypothetical protein

VC0641

6.5

conserved hypothetical protein

VC0742

3.4

conserved hypothetical protein

VC0770

5.1

conserved hypothetical protein

VC0962

4.5

conserved hypothetical protein

VC1055

4.2

conserved hypothetical protein

VC1143

3.2

conserved hypothetical protein

VC1497

5.1

conserved hypothetical protein

VC1834

3.7

conserved hypothetical protein

VC2026

8.7

conserved hypothetical protein

VC2478

5.6

conserved hypothetical protein

VC2654

4.4

conserved hypothetical protein

VCA1021

4.7