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

From: Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils

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
  1. aEnrichment defined in comparison to the 1 h transition phase transcriptome signatures