TABLE 7.
Comparison of differentially expressed genes with known or predicted function that are common between the physiological versus environmental and 37°C upshift gene lists
| Response to temp change and ORF | Gene | COG categorya | Description of gene product | Differential expression atb:
|
||
|---|---|---|---|---|---|---|
| 37°C + 39°C vs 20°C + 30°C | 37°C upshift vs 30°C | 37°C upshift vs 37°C | ||||
| No change upon temp adaptation | ||||||
| LA2453 | C | 4Fe-4S binding protein | + | + | 0 | |
| LA3011 | D | Cell division protein with ATPase domain | − | − | 0 | |
| LA0693 | lysC | E | Aspartate kinase | − | − | 0 |
| LB123 | aroK | E | Shikimate kinase | − | − | 0 |
| LA1372 | G | Permease | + | + | 0 | |
| LB102 | G | Sugar phosphatase | + | + | 0 | |
| LA0786 | G | Glycosyltransferase | − | − | 0 | |
| LA0970 | G | Permease component of an ABC transporter complex | − | − | 0 | |
| LA1392 | G | Sugar kinase | − | − | 0 | |
| LA2958 | I | Hydrolase, acyltransferase | + | + | 0 | |
| LA3928 | caiA | I | Acyl-CoA dehydrogenase | + | + | 0 |
| LA0438 | I | Acyl-CoA dehydrogenase | − | − | 0 | |
| LA1970 | J | poly(A) polymerase family of proteins | + | + | 0 | |
| LA1282 | K | Transcriptional regulator, AcrR family | + | + | 0 | |
| LA1816 | K | Transcriptional regulator | + | + | 0 | |
| LA2728 | K | Transcriptional regulator | + | + | 0 | |
| LA3652 | K | RNA polymerase sigma subunit | + | + | 0 | |
| LA4298 | K | Transcriptional regulator, MarR family | + | + | 0 | |
| LB104 | K | AcrR family transcriptional regulator | + | + | 0 | |
| LA0984 | L | ATP-dependent DNA ligase | + | + | 0 | |
| LA1456 | radC | L | DNA repair protein | + | + | 0 |
| LA0281 | alkA | L | DNA-3-methyladenine glycosylase II | − | − | 0 |
| LA2347 | xerC | L | Tyrosine site-specific recombinase XerC | − | − | 0 |
| LA4049 | srmB | L | ATP-dependent RNA helicase (superfamily II) | − | − | 0 |
| LA1284 | lolE | M | Lipoprotein releasing system, LolE permease component | + | + | 0 |
| LA2058 | ddlA | M | d-alanined-alanine ligase | − | − | 0 |
| LB323 | M | Transglycosylase | − | − | 0 | |
| LA3489 | flgC | N | Endoflagellar proximal basal body rod protein | + | + | 0 |
| LA2666 | flgA | N | Endoflagellar basal body P-ring biosynthesis protein | − | − | 0 |
| LA1563 | O | Small heat shock protein (molecular chaperone) | + | + | 0 | |
| LA1879 | clpA | O | Endopeptidase Clp, ATP-dependent proteolytic subunit | + | + | 0 |
| LA4299 | btuE | O | Glutathione peroxidase | + | + | 0 |
| LB174 | htpX | O | Zn-dependent protease with chaperone function | + | + | 0 |
| LA2949 | O | Trypsin-like serine protease | − | − | 0 | |
| LA0593 | copZ | P | Copper chaperone | + | + | 0 |
| LA0594 | P | Cation transport ATPase, possibly copper | + | + | 0 | |
| LA1859 | katE | P | Catalase | + | + | 0 |
| LA3110 | kdpC | P | Potassium-transporting ATPase C chain | + | + | 0 |
| LA4245 | P | Monooxygenase | − | − | 0 | |
| LA4246 | phoD | P | Phosphodiesterase I | − | − | 0 |
| LA0816 | T | Receiver component of a two-component response regulator | + | + | 0 | |
| LA1743 | T | Chemotaxis protein, methyltransferase | + | + | 0 | |
| LA1744 | T | Chemotaxis protein, methylesterase | + | + | 0 | |
| LA1746 | T | Sensor and regulator protein of a two-component response regulator | + | + | 0 | |
| LA1860 | T | Sensor protein of a two-component response regulator | + | + | 0 | |
| LA2117 | T | Anti-sigma factor antagonist | + | + | 0 | |
| LA2223 | T | Sensor histidine kinase of a two-component response regulator | + | + | 0 | |
| LA3858 | T | Sensor histidine kinase and response regulator of a two-component complex, part (C terminus) | + | + | 0 | |
| LA0049 | T | Methyl-accepting chemotaxis protein | − | − | 0 | |
| LA0565 | T | adenylate cyclase | − | − | 0 | |
| LA0802 | U | Pilus assembly protein | + | + | 0 | |
| LA1285 | V | Lipoprotein releasing system, LolD ATPase component | + | + | 0 | |
| LA2014 | V | CreD-like protein | − | − | 0 | |
| LA3871 | V | Cation, multidrug efflux pump | − | − | 0 | |
| Transiently expressed | ||||||
| LA2598 | gmk | F | Guanylate kinase | 0 | + | + |
| LA0980 | thiC | H | Thiamine biosynthesis protein ThiC | 0 | − | − |
| LA2335 | ubiX | H | 3-polyprenyl-4-hydroxybenzoate decarboxylase | 0 | + | + |
| LA0001 | dnaA | L | Chromosomal replication initiator protein | 0 | + | + |
| LA1964 | M | AcrA-related membrane protein, part (N terminus) | 0 | + | + | |
| LA2417 | flgL | N | Endoflagellar hook-filament protein | 0 | + | + |
| LA3778 | ligB | N | LigB lipoprotein | − | + | + |
| LA0666 | mauG | P | Cytochrome c peroxidase | 0 | + | + |
| LA0280 | T | Cyclic AMP-binding protein | 0 | − | − | |
| LA2427 | cheW | T | Chemotaxis signal transduction protein | 0 | + | + |
| LA2473 | T | Cyclic AMP-binding protein, regulatory protein | 0 | + | + | |
| LA3699 | T | Protein-tyrosine-phosphatase | 0 | + | + | |
| LA1142 | secD | U | Preprotein translocase, SecD subunit | 0 | − | − |
| LA1457 | G | DNA repair protein | + | 0 | − | |
| Up-regulated across all 3 comparisons | ||||||
| LA0145 | D | ATPase of the PP-loop superfamily | + | + | + | |
| LA1212 | uspA | T | Universal stress protein UspA | + | + | + |
| LA1504 | M | Metallopeptidase | + | + | + | |
a
COG categories are as described for Fig. 3.
b
+, up-regulated genes; −, down-regulated genes; 0, genes which were not significantly differentially expressed.