Table 2.
Transcriptomic changes of genes during varied environmental selections.
| Environments | Groups | DEGs and their involved metabolic pathways or biological functions* |
References | Strain IDs | |||
|---|---|---|---|---|---|---|---|
| Up-regulation | Down-regulation | ||||||
| Carbon starvation | P1-P2 | 367 | Fermentation and response to starvation | 1542 | Glucose transport | Morin et al. (2020) | K-12 MG1655 |
| P2-P3 | 15 | Acetate metabolism | 855 | Sugar and amino acid transport; Cell motility | |||
| P3-P4 | 107 | Stress response; Motility regulation | 178 | Amino acid/sugar and acid transport; Catabolism | |||
| pathway; Cell motility | |||||||
| Heat stress | Early | 20 (e.g., clpB, dnaKJ, groSL, grpE, hslVU, hspQ, htpG, ibpA) | Response to heat | 18 (e.g., purB, purD, purE, purL, purT) | Purine biosynthesis | Kim et al. (2020) | BL21 |
| Middle | 12 | Not detected | 8 | Not detected | |||
| Late | 47 (e.g., entCEB, entD, fes-entF) | Enterobactin metabolic process | 19 | Not detected | |||
| Exposure to Cr (VI) | MDR strain | 194 | 320 | Zeng et al. (2023) | LM13, ATCC25922 | ||
| arnA, mdtG, mdtL | Antibiotic resistance | mdtE, mdtF, mdfA | Antibiotic resistance | ||||
| rsmB, rlmJ, rsmJ | DNA and RNA methyltransferase | rlmI, rlmG, rlmF | DNA and RNA methyltransferase | ||||
| cybB, cysC, cysH, cysN | Oxidative stress response | ||||||
| Susceptible strain | 304 | 461 | |||||
| arnA, bcr, mdtE, mdtG, mdtO | Antibiotic resistance genes | rlmN, rlmI, rlmG, rlmF | DNA and RNA methyltransferase | ||||
| ssuB, ssuC | Sulfur transport | sodB, katG | Oxidative stress response | ||||
| cybB, sodA, cysC, cysH, cysJ, cysM | Oxidative stress response | ||||||
| Bovine digestive content | Rumen | 59 | 8 (e.g., argI, arnA, arnD/pmrJ, arnT) | Drug export | Segura et al. (2021) | EDL933 | |
| emrD, glpD, nemA | Drug export | ||||||
| ychH, yhcN | Multiple stress response | ||||||
| Small intestine | 59 | 8 (e.g., argI, arnA, arnC, arnT, arnD/pmrJ) | Drug export | ||||
| emrD, glpD, glpT, tnaB | Drug export | ||||||
| adiA, cadB, caiF | Acid resistance response | ||||||
| clpB, dnaK | Temperature-change response | ||||||
| Rectum | 32 (e.g., ahpC, ahpF, grxA, katG, sodB, trxC, yaaA, yhaK) | Oxidative stress response | 27 | ||||
| argI, arnA, arnC, arnT, arnD/pmrJ | Drug export | ||||||
| gadA, gadE/yhiE | Acid resistance response | ||||||
| slp, yhiM, yhiO | Multiple stress response | ||||||
| Guanylhydr-azone treatment | Pathogenic strain | 383 | 366 | Wang et al. (2022) | RM8082, ATCC25922 | ||
| marA, gadX | Multidrug efflux system | eptA, arnC | Multidrug efflux system | ||||
| cma, cba, clpF, eaeH | Virulence genes | rpl/rpm, rps | Ribosome assembly pathway | ||||
| flgB, flgC, motA, motB | Flagellar assembly pathway | ||||||
| Nonpathogenic strain | 787 | 1169 | |||||
| mdtM, gadX, mdtG, evgA, mdtH | Multidrug efflux system | eptA, yojI, msbA, arnC, mdfA, emrB, emrA, bacA | Multidrug efflux system | ||||
| rpl/rpm, rps | Ribosome assembly pathway | ||||||
| clbR, clbD, clbE, clbA, clbF, clbC, clbI, clbB, clbG, clbQ | Virulence genes | flgB, flgC | Flagellar assembly pathway | ||||
| murA, mrcA | peptidoglycan biosynthesis | ||||||
*Genes showing the expression levels of ≥ 2- or ≤ 0.5-fold were considered DEGs.