Table 2.
Genes differentially expressed as a result of various stress conditions.
| Locus tags | Gene: description | Upregulation or downregulation | ||||||
|---|---|---|---|---|---|---|---|---|
| NCDO712 | MG1363 | Cold | Heat | Acid | Osmotic | Oxidative | Starvation | |
| AMINO ACID TRANSPORT AND METABOLISM | ||||||||
| NCDO_0301 | llmg_0335 | plpA/metQ: Methionine ABC transporter | 6.7 | 3.0 | ||||
| NCDO_1706 | llmg_1776 | metC: Cystathionine gamma-lyase | 3.1 | 2.7 | 13.2 | 2.8 | 5.6 | |
| NCDO_1707 | llmg_1775 | cysK: Cysteine synthase | 4.1 | 2.5 | 10.9 | 2.2 | 7.2 | |
| NCDO_2243/7 | llmg_2309/13 | arcABD1C1C2: arginine deiminase pathway | 10.9 ± 2.1 | −2.8 ± 0.7 | 2.2 ± 0.6 | |||
| NCDO_2384 | llmg_2477 | lysP: Lysine-specific permease | −8.0 | −2.1 | −4.9 | |||
| TRANSPORTERS, ABC/PTC/PORIN | ||||||||
| NCDO_0184 | llmg_0454 | bglP: PTS system. trehalose-specific IIB component | −17.4 | −2.4 | 3.2 | |||
| NCDO_0191 | llmg_0446 | msmK: Multiple sugar ABC transporter. ATP-binding protein | 3.0 | −4.4 | −3.8 | 15.4 | ||
| NCDO_0199 | llmg_0438 | ptcA: PTS system. cellobiose-specific IIA component | −2.4 | −14.6 | ||||
| NCDO_0381 | llmg_1097 | glpF2: glycerol uptake facilitator | −10.3 | 2.1 | ||||
| NCDO_0584 | llmg_1210 | emrB: Drug resistance transporter EmrB/QacA subfamily | 6.1 | |||||
| NCDO_0687 | llmg_0697 | oppD: Oligopeptide transport ATP-binding protein | 4.6 | 3.0 | 2.6 | 14.6 | ||
| NCDO_0938 | llmg_0910 | amtB: Ammonium transporter | −6.7 | 2.2 | ||||
| NCDO_1110 | llmg_1195 | ribU: Substrate-specific component of riboflavin transporter | 11.8 | 2.4 | 4.4 | |||
| NCDO_2331/3 | llmg_2398/400 | zitoperon: Zinc ABC transporter | 13.4 ± 5.4 | 5.0 ± 3.5 | ||||
| CARBON METABOLISM | ||||||||
| NCDO_0183 | llmg_0455 | trePP: Trehalose 6-phosphate phosphorylase | 6.8 | 2.4 | −2.4 | −2.5 | 9.8 | |
| NCDO_1543/5 | llmg_1568/70 | fruAKR: fructose operon | −17.6 ± 2.2 | −28.4 ± 10 | −11.1 ± 6.0 | −11.9 ± 2.7 | ||
| FATTY ACID BIOSYNTHESIS | ||||||||
| accABCD | Acetyl-CoA carboxylases | 3.9 ± 1.0 | 6.5 ± 1.7 | 3.4 ± 0.4 | 8.0 ± 2.8 | |||
| fabIZ1THDGFZ2 | Fatty acid biosynthesis | 2.0 ± 0.9 | −2.1 ± 0.9 | 3.7 ± 1.6 | −3.2 ± 1.5 | 3.7 ± 0.7 | 1.9 ± 3.0 | |
| NUCLEOTIDE TRANSPORT AND METABOLISM | ||||||||
| purFLQSCHD | de novo biosynthesis of purines | 2.7 ± 0.5 | 2.0 ± 0.4 | 7.9 ± 5.2 | 6.5 ± 2.4 | |||
| pyrRPBKDBFEC-carAB | de novo biosynthesis of pyrimidines | 4.3 ± 0.9 | 16.9 ± 1.7 | 12.5 ± 3.5 | ||||
| STRESS RESPONSE | ||||||||
| NCDO_0206 | llmg_0430 | cstA: Carbon starvation protein A | −2.3 | 2.5 | ||||
| NCDO_0207 | llmg_0429 | sodA: Manganese superoxide dismutase | −1.9 | −2.1 | ||||
| NCDO_0225 | llmg_0411 | groEL: Heat shock protein 60 family chaperone | 17.4 | 7.3 | −2.1 | |||
| NCDO_0226 | llmg_0410 | groES: Heat shock protein 60 family co-chaperone | −2.0 | 17.3 | 7.5 | −2.4 | ||
| NCDO_0463 | llmg_0180 | cspE: cold shock protein E | −2.2 | −3.1 | −9.1 | |||
| NCDO_0514 | llmg_0132 | sugE: Quaternary ammonium compound-resistance protein | 18.2 | −2.3 | ||||
| NCDO_0544 | llmg_0528 | clpE: ATP-dependent Clp protease. ATP-binding subunit | 12.4 | 6.0 | 2.1 | |||
| NCDO_0641 | llmg_0638 | clpP: ATP-dependent Clp protease. proteolytic subunit | 2.0 | 3.7 | 4.4 | |||
| NCDO_0951 | llmg_0986 | clpB: Chaparonin. ClpB protein | 3.0 | 6.0 | 3.0 | 2.8 | ||
| NCDO_1029 | llmg_1049 | busAB: ABC-type glycine betaine transport system | −2.2 | 6.7 | −2.6 | |||
| NCDO_1030 | llmg_1048 | busAA: Glycine betaine ABC transport system. ATP-binding | −2.7 | 7.7 | −4.7 | |||
| NCDO_1062 | llmg_1104 | lmrB: Multidrug resistance protein B | 2.7 | −4.1 | −2.3 | −6.3 | −2.7 | |
| NCDO_1185 | llmg_1256 | cspD: cold shock protein D | 4.2 | −5.2 | ||||
| NCDO_1186 | llmg_1255 | cspC: cold shock protein C | 7.4 | 2.5 | −7.7 | |||
| NCDO_1206 | llmg_1256 | cspD: cold shock protein D | −2.3 | −3.3 | −27.0 | |||
| NCDO_1537 | llmg_1576 | hrcA: Heat-inducible transcription repressor | 10.8 | 3.1 | 11.8 | 8.8 | ||
| NCDO_1538 | llmg_1575 | grpE: Heat shock protein | 15.2 | 12.4 | 6.7 | |||
| NCDO_1539 | llmg_1574 | dnaK: chaperone protein | 14.6 | 10.2 | 2.3 | |||
| NCDO_1794 | llmg_1847 | cspA: cold shock protein A | 21.2 | 3.1 | −14.1 | |||
| NCDO_1795 | llmg_1846 | cspB: cold shock protein B | 7.7 | −33.1 | ||||
| NCDO_2408 | llmg_2502 | dnaJ: Chaperone protein | −3.5 | 5.3 | 4.9 | |||
| TRANSCRIPTION FACTORS | ||||||||
| NCDO_0643 | llmg_0640 | spxA: transcriptional regulator Spx/MgsR | −3.2 | −3.6 | −18.8 | |||
| NCDO_0937 | llmg_0911 | glnB: Nitrogen regulatory protein P-II | −2.8 | 2.1 | −10.8 | 3.5 | ||
| NCDO_1088 | llmg_1130 | spxA: Transcriptional regulator Spx/MgsR | 2.4 | 3.0 | 52.9 | |||
| NCDO_1129 | llmg_1177 | gadR: positive regulator | −6.7 | −4.0 | ||||
| NCDO_1636 | llmg_1703 | spxA: transcriptional regulator Spx | −4.7 | 3.0 | 12.5 | |||
| NCDO_1781 | llmg_1860 | rmaB: Transcriptional regulator. MarR family | −2.0 | 7.5 | ||||
| NCDO_2330 | llmg_2401 | zitR: Transcriptional repressor AdcR for Zn(2+) | 36.6 | 2.6 | 15.7 | |||
| UNKNOWN FUNCTION OR POORLY CHARACTERIZED | ||||||||
| NCDO_0342 | llmg_0294 | Hypothetical protein | −3.1 | −4.0 | −3.3 | −2.0 | −12.2 | |
| NCDO_1187 | llmg_1254 | Hypothetical protein directly upstream of cspC | 8.5 | −3.3 | ||||
| NCDO_1519 | llmg_1594 | yjgB: P54 ENTFC NLPP60 family protein | 5.0 | −3.2 | -3.4 | 11.2 | −5.5 | |
| NCDO_1793 | llmg_1848 | Hypothetical protein directly downstream of cspA | 9.7 | -2.8 | −4.4 | |||
| NCDO_2075/7 | llmg_2163/4 | ythoperon: hypothetical proteins | 10.4 ± 1.6 | 3.3 ± 0.3 | ||||
| NCDO_2419 | llmg_2513 | ywoG: Major facilitator family transporter | 3.0 | −4.5 | 9.1 | −6.6 | −3.4 | 11.2 |
| NCDO_2420 | llmg_2514 | SH1215: Universal stress protein family | −18.3 | 6.8 | −3.2 | |||
| NCDO_2421 | llmg_2515 | Hypothetical protein | −21.7 | 4.2 | −3.2 | |||
Genes are shown in this table when they are differentially expressed ≥10-fold, with a p ≤ 0.05 and logCPM ≤ 1 in at least one of the stress conditions, or previously reported in the literature during the relevant stress condition. sRNA and tRNA genes are excluded from this table as they are reported separately.