TABLE 2.
Selected DEGs for V. vulnificus grown at infective temperatures (25, 28, and 37°C) vs. non-infective temperature (20°C).
| Gene(s)a | 25°Cb | 28°Cc | 37°Cd | Putative function/processe |
| Metabolic and nutrient transport and utilization genes (including iron) | ||||
| fadH | 11.3 | – | 2.3 | Unsatturated fatty acids metabolism |
| Peptide ABC transporters# | 10.4-2.4 | – | 3.9 | Peptide transport |
| ilvE, ilvG, ilvI | 7.8-2.5 | – | 2.1 | Amino acid biosynthesis |
| trpCD | 6.1-4 | – | 2.8 | Amino acid biosynthesis (tryptophan) |
| C4-dicarboxylate transporters# | 6-2.4 | – | 20.7-2.9 | Dicarboxilate transport |
| argG, argI | 5-2.1 | 2.1 | – | Amino acid metabolism |
| Ferric iron ABC transporter*# | 3.7 | 3.4-2.3 | 2.6 | Ferric iron transport |
| Long-chain fatty acid transport protein | 3.3 | – | – | Fatty acids transport |
| Vulnibactin biosynthetic genes*# | 3-2.3 | 2.9-2.5 | 2.3 | Vulnibactin biosynthesis and transport |
| hisBD | 2.7 | −2.1 | – | Amino acid biosynthesis |
| fabGH | 2.4 | – | 2.4 | Fatty acids metabolism |
| Amino acid ABC transporter* | 2.3 | 5.5-2.8 | 13.8-6.2 | Amino acid transport |
| metB, metK, metL | 2.3-2.1 | 8.5 | 2.8 | Amino acid biosynthesis |
| L-serine dehydratase | 2.3 | – | – | Amino acid metabolism |
| potB, potD*# | 2.2 | 2 | – | Polyamine transport |
| PTS system, N-acetylglucosamine-specific IIB, IID components*# | 2.1 | – | 3.5 | Aminosugar transport |
| Nitrate ABC transporter | 2.1 | – | – | Nitrogen metabolism |
| ftbp*# | 2 | 2 | 2.8 | Fish transferrin binding protein |
| rbsABCD# | −2.6 | −(3.4-3.7) | 6.6-3.4 | Ribose ABC transport system |
| Short chain fatty acids transporter | −2.7 | −2.4 | – | Fatty acids transport |
| malG | −2.9 | −3.1 | – | Maltose/maltodextrin ABC transporter |
| prsA | −3.1 | −2.6 | – | Ribose metabolism |
| Chitinase proteins | – | 22.3-2.5 | 8.8 | Chitinase activity |
| serB | – | 10.6 | 9.8 | Amino acid biosynthesis |
| pflA | – | 8.4 | – | Glucose metabolism |
| Succinate-semialdehyde dehydrogenase [NADP+] | – | 8.4 | – | Amino acid degradation |
| nupC*# | – | 6.7 | 8.1 | Permease for nucleoside uptake |
| dns*# | – | 5.7 | – | Degradation of DNA for nutrient uptake (competence related) |
| Zinc ABC transporter | – | 4.5-3.5 | – | Zinc transport |
| Lipase-related proteins | – | 4.2-2.7 | 8-5.3 | Extracellular lipid utilization |
| Phosphate ABC transporter# | – | 3.8-2.6 | 6.6 | Phosphate transport |
| trkA, trkH | – | 3.1 | 3.9-2.4 | Potassium uptake |
| oppBCD, oppF | – | 3-2.7 | 7.9-2.1 | Oligopeptide transport system permease |
| ktrA# | – | 2.8 | 3.4 | Potassium uptake |
| thrC | – | 2.7 | – | Amino acid iosynthesis |
| dctQ# | – | 2.3 | 6.5 | TRAP dicarboxylate transporters |
| proA | – | 2.3 | – | Amino acid biosynthesis |
| Ferrous iron transporter B | – | 2 | – | Ferrous iron transport |
| acp12 | – | −(2.6-3.7) | – | Fatty acids biosynthesis |
| glgX# | – | – | 12.8 | Glycogen debranching enzyme |
| hmgA | – | – | 10-4 | Amino acid degradation |
| citAB | – | – | 8.3-2.8 | Citrate metabolism |
| Anaerobic respiration | ||||
| Nitrate reductase cytochrome c550-type subunit* | 2.7 | – | 3 | Nitrite reductase complex subunit |
| napC, napE, napGH*# | – | 22.5-6.7 | 3.9-2.2 | Subunit of the periplasmic nitrite reductase complex |
| Nitrite reductase subunits | – | 3.5-2.8 | – | Nitrite reductase complex |
| nrfF | – | – | 23.3 | Formate-dependent nitrite reductase complex |
| Stress response and defense mechanisms | ||||
| Anaerobic glycerol-3-phosphate dehydrogenase subunits (B, C)# | 4.6-2.2 | – | 4.4-3.7 | Phospholipid biosynthesis/membrane regeneration |
| S-(hydroxymethyl)glutathione dehydrogenase# | 3 | 2.3 | – | Resistance to oxidative stress |
| aphF | 2.8 | – | – | Alkyl hydroperoxide reductase protein F. Resistance to oxidative stress |
| Glutathione S-transferase# | 2.7 | 4.5 | – | Resistance to oxidative stress |
| uspA | 2.7 | – | – | Universal stress protein A, involved in DA-damage resistance |
| mutS* | 2.5 | – | – | DNA mismatch repair protein |
| Superoxide dismutase [Cu–Zn] precursor | 2.3 | – | – | Resistance to oxidative stress |
| plsXY# | 2.2 | 4.9 | 3.3 | Phospholipid biosynthesis/membrane regeneration |
| Phosphoglycerol transferase I*# | 2.2 | 4.2 | – | Phospholipid biosynthesis/membrane regeneration |
| YfgC precursor* | 2.1 | – | – | Outer membrane integrity |
| cydD | 2.1 | – | – | Glutathione transport |
| Permease of the drug/metabolite transporters (DMT)# | 2 | 4.8-2.1 | 11.5-2.3 | Resistance to microcidal compounds |
| Glycerophosphoryl diester phosphodiesterase# | 2 | – | 3.1 | Phospholipid biosynthesis/membrane regeneration |
| sspAB | −(2-2.3) | −2.1 | – | Stringent starvation proteins |
| rseABC*# | – | 9.5-6.2 | – | Negative regulatory proteins for RpoE, a sigma factor for envelope stress response |
| nsrR*# | – | 8.2 | – | Repressor for resistance to nitrosative stress |
| cmeB | – | 7.2 | – | Drug efflux system |
| clpB*# | – | 5.7 | – | Stress-induced chaperone |
| Formate efflux transporter*# | – | 4.8 | – | Resistance to microcidal peptides |
| cspD* | – | 3.7 | – | Cold shock proteins, involved in stress caused by membrane damage |
| Manganese superoxide dismutase | – | 3.5 | 11 | Resistance to oxidative stress |
| norR* | – | 3.4 | – | Anaerobic nitric oxide reductase transcription regulator |
| uvrC*# | – | 3.2 | 4.5 | Excinuclease ABC subunit C for DNA repair |
| marR | – | 3 | 6.6 | Multiple antibiotic resistance protein |
| htpG | – | 3 | – | Chaperone protein |
| msrAB# | – | 2.7 | 2.3 | Peptide methionine sulfoxide reductase involved in reparation of oxidized proteins |
| ohr* | – | −2.6 | -3.65 | Repressor for organic hydroperoxidase resistance |
| degQ# | – | – | 2.1 | Outer membrane integrity |
| Flagellum, pili and chemotaxis | ||||
| Methyl-accepting chemotaxis protein*# | 8.5-2.4 | 12.8-2.5 | 15.5-2 | Chemotaxis |
| mshH, mshJK, mshOP*# | 2.7 | 3.2-2.1 | 4.2-2.1 | Pili MSHA biosynthesis |
| fleQ, fleS | 2.4-2.2 | 2 | 4.1-3.1 | Flagellar regulatory protein |
| flgA, flgHI, flgL, flgT*# | 2.2-2.1 | 4.1 | 11.9-3.2 | Flagellar basal-body rod proteins |
| tadBCD, tadZ* | 2.2-2 | 14.1-3.2 | 10 | Flp pili assembly |
| fliF, fliM*# | 2 | 2.2-2.1 | 3.6-2.6 | Flagellar motor activity |
| Probable type IV pilus assembly FimV-related | −2.4 | −2.4 | – | Pili MSHA |
| rpoN*# | – | 27.1 | 3.8 | RNA polymerase sigma factor |
| flgN | – | 8.7 | 2.1 | Flagellar biosynthesis protein |
| flgK, flgM*# | – | 8.5 | 16 | Hook associated protein |
| motAB*# | – | 7.5-2.8 | 3.6 | Flagellar motor rotation protein |
| fleN*# | – | 5.8 | 2.1 | Flagellar synthesis regulator |
| RNA polymerase sigma factor for flagellar operon | – | 5.4 | – | Flagellar biosynthesis |
| acfD | – | 4 | – | Accessory colonization factor, putatively involved in motility |
| fliL | – | 3.7 | – | Controls rotational direction of flagella during chemotaxis |
| flaD. flaFG*# | – | 3.6-2.3 | 6.5-4 | Flagellin protein |
| cheD | – | 3.3 | – | Chemotaxis protein |
| Chemotaxis regulator# | – | 3.1 | 5.8 | Transmits chemoreceptor signals to flagellar motor |
| LPS and capsule | ||||
| cpsABC# | 2 | 5.5-3.3 | – | Capsule biosynthesis |
| sypAB, sypR | – | 5.1-2.3 | 15.8-5.2 | Capsule biosynthesis |
| wza# | – | −2.8 | – | LPS biosynthesis |
| galE | – | – | 4.7 | O-antigen biosynthesis |
| lptA | – | – | 2.3 | LPS biosynthesis |
| Transcriptional regulators | ||||
| Nitrogen regulation protein NR(I)* | 3.1 | −2.7 | – | Nitrogen starvation |
| tetR*# | 2.6 | 7.9 | – | Involved in transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity |
| rpoS | 2.5 | – | – | Stress and metabolism management |
| arcA# | −2.4 | −2.6 | – | Repressor for aerobic metabolism |
| uxuR*# | – | 9 | – | Repressor for oligogalacturonide metabolism |
| mall*# | – | 4.3 | – | Maltose regulon repressor protein |
| deoR | – | 4 | – | Repressor of deoxyribose operon |
| vpsT*# | – | 3.7 | 5.1 | Repressor of biofilm and biofilm related polysaccharide formation |
| luxO*# | – | 3.6 | – | Involved in quorum sensing pathways |
| phoR*# | – | 2.9 | – | Histidine kinase for PhoB, involved in phosphate metabolism |
| luxU*# | – | 2.9 | – | Phosphorelay protein involved in quorum sensing |
| CRP* | – | 2.9 | 5 | cAMP receptor protein, regulatory protein |
| argR | – | 2.5 | – | Repressor of arginine metabolism |
| luxQ*# | – | −2.6 | – | Autoinducer 2 sensor kinase/phosphatase, involved in quorum sensing |
| smcR# | – | – | 2.2 | Involved in quorum sensing pathways |
| fabR*# | – | – | −2.7 | Repressor for unsaturated fatty acid biosynthesis |
The value of fold change per gene at each infective temperature (25, 28, and 37°C vs. non-infective temperature [20°C]) is shown. Only genes with values of fold change −2 ≤ X ≤ 2 with a p-value cut-off of 0.05 were considered. aIdentified DEGs are indicated. b–dFold change value or range of values for each identified gene or group of related genes at 25°Cb, 28°Cc, and 37°Cd. See Supplementary Tables S2–S4 for specific gene and fold change value. ePutative function for selected genes and related process. *Differentially expressed in iron stimulon (Pajuelo et al., 2016). #Differentially expressed in eel or iron-overloaded human serum (Hernández-Cabanyero et al., 2019). –, not detected as differentially expressed.