Table 5 Common and specific biological processes enriched during exponential growth of wild-type P. veroniia
| Regulation | Biological process | Liquid | Silt | Jonction |
|---|---|---|---|---|
| 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 |