TABLE 3.
Common genes involved in the biological processes affected by long-term biocide exposurea
| Process | Gene(s) | Description (reference) | Regulation | Condition(s) |
|---|---|---|---|---|
| Motility | fli series | Related to flagellum | Down | BENZ, ETOH, GLUTA, ISOP, PERA, PHE, POV, SOD, XID |
| flg series | Related to flagellum | Down | BENZ, ETOH, ISOP, PERA, PHE, POV, SOD, XID | |
| cheY, cheZ | Chemotaxis/motility | Down | BENZ, ETOH, ISOP, PERA, PHE, POV, SOD, XID | |
| motA, motB | Motility protein | Down | BENZ, ETOH, ISOP, PERA, PHE, POV, SOD, XID | |
| Biofilm | bssR | Regulator of biofilm formation | Up | PERA, PHE, POV, SOD |
| csgD | Transcriptional regulator | Up | GLUTA, ISOP, PHE, XID | |
| csrB | Regulatory RNA | Up | ETOH, ISOP, PERA, PHE, XID | |
| Aerobic/anaerobic growth | sdhB, sdhC, sdhA | Succinate dehydrogenase; part of the TCA cycle | Down | ETOH, H2O2, PERA, PHE, POV, SOD, XID |
| gltA | Citrate synthase; part of the TCA cycle | Down | ETOH, PERA, PHE, POV, SOD, XID | |
| cyA, cyB | Cytochrome components; induced under oxygen limitation conditions (58) | Up | POV, PERA, XID, SOD, PHE, ISOP, ETOH, GLUTA | |
| ompW | Outer membrane protein; upregulated during the transition from the aerobic to the anaerobic state (59) | Up | PERA, PHE, POV, SOD | |
| glpABC | Glycerol-3-phosphate dehydrogenase; functional under anaerobic conditions | Up | PERA, PHE, POV, SOD | |
| nrdD | DNA synthesis and repair; functional under anaerobic conditions (60) | Up | GLUTA, PHE, SOD, POV, PERA | |
| katE | Response to oxidative stress; upregulated in the aerobic state compared to its regulation during anaerobiosis (61) | Down | ETOH | |
| puuA | Putrescine utilization pathway; upregulated during the transition from the anaerobic to the aerobic state and downregulated in the absence of oxygen (62) | Down | ETOH, ISOP, SOD, XID PERA, PHE, POV | |
| acnA | Citric acid and glyoxylate cycles; repressed during anaerobiosis (63) | Down | ETOH, SOD | |
| Acid stress | hdeA, hdeB | Chaperone | Up | POV, XID, PHE, PERA, SOD, GLUTA |
| gadB, gadC | Glutamate decarboxylase | Up | XID, PHE, GLUTA | |
| asr | Acid shock protein | Up | ETOH, ISOP | |
| DNA damage | hisA | Isomerase | Up | PERA, PHE, POV, SOD, XID |
| feoA, feoB | Iron transport proteins | Up | ETOH, PERA, PHE, POV, SOD, XID | |
| deoABC | Thymidine phosphorylase | Up | ETOH, PERA, PHE, POV, SOD, XID | |
| Stress response | osmC | Has peroxidase activity and accumulates under some other stress conditions, such as osmotic stress (64) | Up | XID |
| uspGF | General stress factors with increased expression under several stress conditions (65) | Up | PERA, PHE | |
| gpmM | Role in oxidative stress response (66) | Up | PERA, POV | |
| wrbA | Unclear physiological functions in the cell | Up | PERA, PHE, POV, XID | |
| zinT | Protein that binds cadmium and zinc; was proposed to be a general stress factor with an unknown mechanism and a possible interaction role with ABC transporters (67) | Up | SOD | |
| Response to antibiotics | acrA | Multidrug efflux protein | Up | PHE, PHE30, BENZ30 |
| ybjG | Phosphatase | Up | BENZ30 | |
| phoU | Phosphate signaling protein | Up | BENZ30, POV30, ISOP, ETOH | |
| ybhG | Role in drug resistance (34) | Up | PHE, PHE30 | |
| sseA | 3-Mercaptopyruvate sulfurtransferase | Up | XID, ISOP |
a
A summary of the genes up- or downregulated after long-term exposure to biocides is shown. The complete list with the respective log2 fold change in expression and P values can be found in Table S1 in the supplemental material. When the reference is not explicit, the gene function was obtained from the EcoCyc database (55).