TABLE 2 .
List of genes downregulated in response to NaHS stress (≥3-fold) or by Angeli’s salt (≥5-fold)
| Locus tag (Newman) |
Locus tag (N315) |
Gene name |
Fold repression (S2−) |
Fold repression (Angeli’s salt)a |
Function | CymR regulon?b |
ΔcstR regulation? |
|---|---|---|---|---|---|---|---|
| NWMN_0115 | SA0165 | 16.9 | 4.2 | Hypothetical | + | ||
| NWMN_0116 | SA0166 | 34.0 | 5.7 | ABC transporter: putative TauB (sulfonate) | + | ||
| NWMN_0117 | SA0167 | 11.5 | 5.1 | ABC transporter: putative TauA | + | ||
| NWMN_0118 | SA0168 | 13.0 | 6.6 | ABC transporter: putative TauC | + | ||
| NWMN_0119 | SA0169 | 13.7 | 3.6 | Putative CiaA: NAD-dependent formate dehydrogenase | + | ||
| NWMN_0143 | SA0198 | 11.9 | 3.1 | ABC transporter: peptide (ATPase)c | + | −/+ downd | |
| NWMN_0144 | SA0199 | 9.4 | 11.1 | ABC transporter: peptide (permease)c | − | ||
| NWMN_0145 | SA0200 | 11.8 | 9.4 | ABC transporter: peptide (permease)c | − | −/+ downd | |
| NWMN_0146 | SA0201 | rlp | 6.0 | 4.3 | Putative RGD-containing lipoprotein | − | |
| NWMN_0374 | SA0368 | tcyP | 7.5 | 4.4 | Putative cystine transporter homolog | + | |
| NWMN_0391 | SA0385 | ssl4nm | 5.1 | Superantigen-like protein 4 | − | Down | |
| NWMN_0400 | ssl11nm | 3.3 | 5.4 | Superantigen-like protein 11 | − | −/+ downd | |
| NWMN_0401 | 3.4 | 7.1 | Hypothetical | − | −/+ downd | ||
| NWMN_0423 | SA0417 | 2.3e | 5.4 | Sodium-dependent symporter | − | −/+ upd | |
| NWMN_0424 | SA0418 | cysM | 5.7 | Cystathionine-β-synthase (CBS) | + | ||
| NWMN_0425 | SA0419 | metB | 8.5 | Cystathionine-γ-lyase (CSE) | + | ||
| NWMN_0426 | SA0420 | 13.0 | 11.6 | ABC transporter: peptide (ATPase) | − | −/+ downd | |
| NWMN_0427 | SA0421 | 13.9 | 11.9 | ABC transporter: peptide (permease) | − | −/+ downd | |
| NWMN_0428 | SA0422 | 9.9 | 4.1 | ABC transporter: peptide (substrate binding) | − | −/+ downd | |
| NWMN_0475 | SA0471 | cysK | 10.4 | Cysteine synthase (OAS + H2S → acetate + Cys) | + | ||
| NWMN_0557 | SA0551 | 7.5 | Up 4.6 | Putative pyridine nucleotide disulfide oxidoreductase | − | ||
| NWMN_0558 | SA0552 | 16.6 | Rrf2 family repressor (related to B. subtilis SaiR) | − | |||
| NWMN_0655 | SA0641 | mgrA | 5.1 | MarR family repressor MgrA | − | ||
| NWMN_0757 | 2.3e | 28.8 | Secreted von Willebrand factor-binding protein | − | −/+ downd | ||
| NWMN_0759 | 3.0 | Hypothetical | − | −/+ downd | |||
| NWMN_0766 | SA0751 | 4.2 | Hypothetical | − | |||
| NWMN_0813 | SA0804 | 5.8 | Sodium/proton antiporter family protein | − | |||
| NWMN_0831 | SA0821 | argH | 3.0 | Argininosuccinate lyase (Arg biosynthesis) | − | −/+ downd | |
| NWMN_0832 | SA0822 | argG | 6.2 | Argininosuccinate synthase (Arg biosynthesis) | − | −/+ downd | |
| NWMN_0907 | SA0890 | 6.5 | Hypothetical | − | |||
| NWMN_1047 | SA0983 | isdG | 3.1f | Heme-degrading monooxygenase | − | ||
| NWMN_1066 | SA1000 | 5.1 | Hypothetical (fibrinogen binding) | − | |||
| NWMN_1068 | SA1002 | 5.6 | Hypothetical | − | |||
| NWMN_1069 | SA1003 | 3.4 | Hypothetical (fibrinogen binding) | − | |||
| NWMN_1070 | SA1004 | 6.9 | Hypothetical (fibrinogen binding) | − | |||
| NWMN_1352 | SA1275 | 5.0 | Hypothetical | − | |||
| NWMN_1749 | SA1674 | tcyC | 1.8e | 7.1 | ABC transporter: cystine (ATPase)e | + | Down |
| NWMN_1750 | SA1675 | tycB | 1.6e | 6.7 | ABC transporter: cystine (permease)e | + | Down |
| NWMN_1751 | SA1676 | tycA | 1.2e | 4.8 | ABC transporter: cystine (cystine binding)e | + | |
| NWMN_1877 | SA1755 | chp | 32.7 | Chemotaxis-inhibiting protein | − | ||
| NWMN_1951 | SA1849 | 9.8 | 4.4 | TusA-like (SirA/YedF/YeeD) protein | + | ||
| NWMN_1952 | SA1850 | 14.2 | 5.0 | Putative thiosulfate (TS) importer | + | ||
| NWMN_2049 | SA1949 | czrA | 15.9 | Zinc-specific repressor (ArsR family) | − | ||
| NWMN_2050 | SA1950 | czrB | 14.0 | Zinc cation diffusion facilitator (CDF) transporter | − | ||
| NWMN_2075 | SA1976 | 11.8 | Hypothetical | − | |||
| NWMN_2186 | SA2080 | ydbM | 9.3 | Putative CiaA; acyl (butyryl)-CoA dehydrogenase | + | ||
| NWMN_2199 | SA2093 | 2.1e | 4.2 | Secretory antigen precursor SsaA | − | ||
| NWMN_2200 | SA2094 | nhaC | 8.4 | Sodium/proton antiporter family, NhaC | − | ||
| NWMN_2201 | SA2095 | 2.1e | 9.5 | Dehydrogenase family protein | − | ||
| NWMN_2203 | 6.5 | Secretory antigen precursor SsaA | − | ||||
| NWMN_2265 | SA2153 | 5.5 | Hypothetical | − | |||
| NWMN_2311 | SA2200 | 6.1 | ABC transporter: amino acid (ATPase) | − | |||
| NWMN_2312 | SA2201 | 5.3 | ABC transporter: amino acid (permease) | − | |||
| NWMN_2313 | SA2202 | 10.1 | ABC transporter: amino acid (substrate binding) | − | |||
| NWMN_2317 | SA2206 | sbi | 5.0 | Immunoglobulin G-binding protein | − | ||
| NWMN_2470 | SA2357 | 5.2 | Hypothetical (regulatory protein) | − | |||
| NWMN_2472 | SA2359 | 7.0 | Hypothetical (just upstream of dtr) | − | |||
| NWMN_2473 | SA2360 | 5.4 | Hypothetical (just upstream of dtr) | − | −/+ downd | ||
| NWMN_2577 | SA2471 | hisG | 7.9 | ATP phosphoribosyltransferase C subunit (His biosynthesis) | − | ||
| NWMN_2578 | SA2472 | hisZ | 6.0 | ATP phosphoribosyltransferase R subunit (His biosynthesis) | − |
a
Fold induction shown if S2− induction is ≥3.0-fold.
b
CymR regulon as determined previously on TSB plus 2.0 mM cysteine (3).
c
Proposed to be involved in glutathione (GSH) assimilation and degradation (3).
d
Approximately 2-fold repressed (downregulated [down]) or activated (upregulated [up]) in the ΔcstR strain (see Tables 3 and 4 for a list of genes differentially expressed in the ΔcstR strain), with adjusted P value of ≤0.05.
e
At least 2-fold induction with NaHS (see Table S1A; adjusted P value of ≤0.05) in HNO induction is significant.
f
The entire isd operon is modestly (≥2-fold) repressed (see Table S1A for a complete listing of these genes).