TABLE 5.
Differentially regulated genes sustaining regulated functional categories in the five strains (compared to strain LD61, as shown in Table 4)a
| Functional category or subcategory | Differentially regulated gene(s)b in strain: |
||||
|---|---|---|---|---|---|
| UCMA5713 | LD55 | LL08 | LL52 | S86 | |
| Amino acid biosynthesis | |||||
| Aromatic amino acid | trpA B | aroH | trpAB | aroCDH | aroH |
| Branched chain | ilvCD, leuC | ilvD, leuC | ilvBCD, leuBD | ilvBD, leuBC | ilvBCDN, leuBC |
| Histidine | hisZ | hisCZ | hisACDGHIKZ | hisDHIZ | hisCZ |
| Transport and energy metabolism | |||||
| Sugars | galKMT, glk, lacCZ, thgA | galM, glk, gntZ, lacCZ | bglA, galKMT, gntZ, lacCZ, scrK, thgA, uxaC, ypdBD, yrcA | galEKMT, lacZ, thgA yidC | galKM, thgA, uxaC |
| Glutamate/GABA | gadC, gadB | ||||
| Glutamate/ornithine | gltQS, argBCDEJ | ||||
| Arginine deiminase pathway | arcD2, arcBC1 | arcABC1 | arcBC1 | ||
| Biogenic amine synthesis | potAD | ||||
| Citrate metabolism | citCDEF, icd | ||||
| Glycolysis | ldh | yjhF, pgmB | |||
| Fermentation | als | ackA1A2, frdC, butB | |||
| Alternative sugar metabolism | scrK, yrcA ypdBD | ||||
| ATP-PMF conversion | atpDEH | ||||
| PTS and carbohydrate transport | celB, ptcABC, rgpC, ypdA, yngFypcGH | ||||
| Biosynthesis of cofactors, prosthetic groups, and carrier | |||||
| Thioredoxin, glutaredoxin, and glutathione | gshR, trxB1 | ||||
| Cell envelope | |||||
| Adaptations and atypical conditions | tpx | ||||
| Polysaccharide | rgpBEF, ycbBDFHIJ | ||||
| Peptidoglycan | murA1BC | ||||
| Translation | |||||
| Ribosomal proteins and translation factors | rplBCNT, rpsCDGQS,rpmI, rnpA, infC | ||||
| Regulatory functions | |||||
| AraC family regulators | xylR | ||||
| DeoR family regulators | lacR | ||||
| General | purR | birA2, rmeD, ydcG, yjaJ, ypfD,yrtfA ysfD | argR, birA1, copR, tenA,yabA, ybeD, ydcGyecA, ykhIyliA | glnR, rmeBymiA, ynaB, | |
| GntR family regulators | rgrB | ||||
| GTP-binding proteins | yphL,yyaL | ylqL, yyaL | |||
| LacI family regulators | rliB | rliC | |||
| LysR family regulators | fhuR | ||||
| MarR family regulators | rmaG | rmaA,zitR | rmaC, rmaIJ | ||
| Two-component systems | llrG | ||||
a
The expression ratios are listed in Table S1 in the supplemental material. Genes that are underlined exhibited increased expression compared to that in strain LD61, while genes that are not underlined showed expression lower than that in LD61.
b
Student test; FDR ≤ 7% for significance.