Table 5 Common and specific biological processes enriched during exponential growth of wild-type P. veronii^a

UP

ATP synthesis

nuoEG, atpAFGH

nuoEGKMNL, atpAFGH

nuoEGKLMN, atpABCFGH

Aerobic respiration

cyoABC

cyoABC

cyoABC

Toluene catabolic process

dmpBCDFH, nahHIJKLMNOT

dmpBCDGH

Regulation of transcription

tuf, lepA, efp, arnF, nusA, mfd

nusABG, rho, rpoD, rstA, gntR

Tricarboxylic acid cycle

sucABC, sdhAB, acnB, icd

sucABC, sdhAB, acnB, icd

sucABC, sdhAB

Urea catabolism and transport

ureABC, urea ABC transporter

urea ABC transporter

Translation-ribosome biosynthesis

rpl, rps, prfABC

rpl, rps

rpl, rps, prfABC, GTPase Der, GTPase Era

Translation-elongation factor

tsf, tuf, fusA, efp

tsf, tuf, fusA, efp

tsf, tuf, fusA, efp

Glutamate biosynthesis

gltB, gltI

arnF, gltD, gltI

Sulfate and taurine transport

cysADW

cysADW, tauABC

cysADW

Protein folding

surA, cyp18,

htpG, surA, groL,dnaJ, arnF, hscA, cyp18, ppiA

Fatty acid biosynthesis

Malonyl-CoA - accABCD, fabDF

Malonyl-CoA - accABCD, fabADFGZ

Water-soluble vitamin metabolic process

Inosine-purADHLMTU

Riboflavin - ribDFH2; thiamine - thiIL; cobalamine – cobNPS; folate - folDE2KD; inosine - purADEHKLMTU

Bacterial membrane organization

Peptidoglycan/LPS – rfaCG; cell shape determination – minE, minD; Lipid A – lpxAB; Isoprenoids - ispEFG; cell division zapE

Flagellum assembly – fliDKM, flgBCDE, flaG

Peptidoglycan/LPS - uppSP, lptD, rfaPCG

Cell shape determination - minE, mrdB, mreB, minD; Lipid A – lpxABDH; Isoprenoids – ispEFG; cell division zapE; ferripyoverdine receptor – fpvA

Transcriptional regulators:

AraC; ArsR

AraC; ArsR; MerR; LysR; TetR; LuxR; ttgVW

AraC; ArsR, ttgRVW; qseB; norR; copG;

DOWN

Organic substance metabolism

branched-chain amino acid - bkdA1A2B

branched-chain amino acid - bkdA1A2B;

arginine - arcABCD; malonate - mdcBCG; biopolymer - phbCB; phenylalanine - hmgA, maiA; molybdenum - moaAA1B

branched-chain amino acid - bkdA1A2BIpdV; vanillate - vanAB; biopolymer -phhAB; arginine - dauAB;, molybdenum -moaAA1B; putrescine - putA, puuABC

Nitrate respiration

narIJ, nirQS, nosZ

narGIJLY, nirQS, norRR2

narGJKL, nirQS, nosZ

Transposition

integrase, transposases, base plate protein

transposases, insertion element

Aerobic respiration

cytochrome B559-B561-CBB3; cydB

cytochrome B559-B561-CBB3; cydB

cytochrome B559-B561-CBB3; cydAB, ctaD; hem biosynthesis - cpo, hemN, hemH; ferrodoxin, cytochrome c oxidase

Response to stress

flavohemoprotein – hmp;

heat shock protein,

universal stress protein A

flavohemoprotein – hmp;

heat shock protein;

Universal stress protein A;

cold shock protein

flavohemoprotein - hmp; osmotic stress – cysG;

heat shock protein; virulence sensor bvgAS; universal stress protein A; Catalase –katE;

cold shock protein

Transport

putrescine – potAGHI; glycine betaine -opuAA-AB; magnesium - mgtAB; mercury – merATP; RND transporter; sulfate transporter; citrate transporter, MFS transporter