Table 1.
Genes downregulated upon a temperature shift from 37°C to 25°C.
| Gene ID | Gene annotation | Fold Change (exp1, exp2, exp3) |
| Energy production and conversion | ||
| RT0261 | Complex III (mitochondrial electron transport). [Rickettsia typhi str. Wilmington] | 0.5 (0.2, 0.6, 0.9) |
| RT0345 | NADH dehydrogenase beta subunit [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.6, 0.7) |
| RT0171 | 2-oxoglutarate dehydrogenase (lipoamide) E1 component [Rickettsia typhi str. Wilmington] | 0.7 (0.5, 0.7, 0.6) |
| Cell cycle control, mitosis and meiosis | ||
| RT0380 | putative intracellular septation protein [Rickettsia typhi str. Wilmington] | 0.6 (0.4, 0.9, 0.6) |
| Amino acid transport and metabolism | ||
| RT0297 | AtrC1-like cationic amino acid transporter protein [Rickettsia typhi str. Wilmington] | 0.6 (0.3, 0.6, 1.8) |
| RT0473 | cysteine desulfurase [Rickettsia typhi str. Wilmington] | 0.6 (0.7, 0.7, 0.5) |
| RT0118 | glutamine transport system permease protein GlnP [Rickettsia typhi str. Wilmington] | 0.6 (0.3, 0.9, 0.4) |
| RT0474 | cysteine desulfurase protein IscS/NifS [Rickettsia typhi str. Wilmington] | 0.6 (0.4, 0.9, 0.6) |
| Nucleotide transport and metabolism | ||
| RT0498 | ribonucleotide-diphosphate reductase alpha subunit [Rickettsia typhi str. Wilmington] | 0.4 (0.4, 0.4, 0.5) |
| Carbohydrate transport and metabolism | ||
| RT0479 | hypothetical protein RT0479 [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 0.5, 0.6) |
| RT0290 | ribose-5-phosphate isomerase B [Rickettsia typhi str. Wilmington] | 0.6 (1.1, 0.6, 0.3) |
| Coenzyme transport and metabolism | ||
| RT0829 | 5-aminolevulinate synthase [Rickettsia typhi str. Wilmington] | 0.5 (0.2, 0.5, 0.8) |
| RT0501 | methylenetetrahydrofolate dehydrogenase (NADP+) [Rickettsia typhi str. Wilmington] | 0.7 (0.6, 0.7, 0.6) |
| Translation | ||
| RT0638 | 30S ribosomal protein S14 [Rickettsia typhi str. Wilmington] | 0.5 (0.7, 0.6, 0.3) |
| RT0812 | methionine aminopeptidase [Rickettsia typhi str. Wilmington] | 0.5 (0.6, 0.5, 0.4) |
| RT0645 | 30S ribosomal protein S3 [Rickettsia typhi str. Wilmington] | 0.5 (0.5, 0.6, 0.4) |
| RT0653 | elongation factor Tu [Rickettsia typhi str. Wilmington] | 0.5 (0.3, 0.6, 0.6) |
| RT0644 | 50S ribosomal protein L16 [Rickettsia typhi str. Wilmington] | 0.5 (0.6, 0.5, 0.5) |
| RT0140 | aspartyl/glutamyl-tRNA amidotransferase subunit B [Rickettsia typhi str. Wilmington] | 0.5 (1.4, 0.4, 0.4) |
| RT0642 | 30S ribosomal protein S17 [Rickettsia typhi str. Wilmington] | 0.6 (0.8, 0.6, 0.4) |
| RT0648 | 50S ribosomal protein L2 [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 0.7, 0.6) |
| RT0316 | glutamyl-tRNA synthetase [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.8, 0.6) |
| RT0372 | prolyl-tRNA synthetase [Rickettsia typhi str. Wilmington] | 0.7 (0.4, 0.7, 0.9) |
| RT0606 | isoleucyl-tRNA synthetase [Rickettsia typhi str. Wilmington] | 0.7 (0.4, 0.8, 0.7) |
| Transcription | ||
| RT0129 | DNA-directed RNA polymerase beta subunit [Rickettsia typhi str. Wilmington] | 0.5 (0.3, 0.5, 0.8) |
| RT0130 | DNA-directed RNA polymerase beta' subunit [Rickettsia typhi str. Wilmington] | 0.7 (0.6, 0.6, 0.9) |
| RT0152 | transcription antitermination protein NusB [Rickettsia typhi str. Wilmington] | 0.7 (0.6, 0.7, 0.6) |
| RT0061 | transcriptional activator protein CzcR [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.7, 0.6) |
| Replication, recombination and repair | ||
| RT0706 | DNA ligase [Rickettsia typhi str. Wilmington] | 0.4 (0.3, 0.3, 0.6) |
| RT0228* | dinucleoside polyphosphate hydrolase [Rickettsia typhi str. Wilmington] | 0.5 (0.5, 0.5, 0.4) |
| RT0805 | tyrosine recombinase [Rickettsia typhi str. Wilmington] | 0.6 (0.7, 0.6, 0.6) |
| Cell wall/membrane biogenesis | ||
| RT0393* | hypothetical protein RT0393 [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 0.6, 0.6) |
| RT0326 | probable glycosyltransferase [Rickettsia typhi str. Wilmington] | 0.7 (0.6, 0.8, 0.4) |
| Posttranslational modification, protein turnover, chaperones | ||
| RT0319* | hypothetical protein RT0319 [Rickettsia typhi str. Wilmington] | 0.5 (0.3, 0.6, 0.3) |
| RT0617 | chaperonin GroEL [Rickettsia typhi str. Wilmington] | 0.5 (0.4, 0.4, 1.0) |
| RT0191 | co-chaperone HscB [Rickettsia typhi str. Wilmington] | 0.5 (0.7, 0.7, 0.2) |
| RT0828* | heat shock protein 90 [Rickettsia typhi str. Wilmington] | 0.5 (0.3, 0.6, 0.5) |
| RT0318 | thioredoxin peroxidase I [Rickettsia typhi str. Wilmington] | 0.5 (0.6, 0.8, 0.4) |
| RT0111 | protease activity modulator protein HflK [Rickettsia typhi str. Wilmington] | 0.6 (0.8, 0.4, 0.6) |
| RT0476 | Glutathione S-alkyltransferase. [Rickettsia typhi str. Wilmington] | 0.6 (0.2, 0.7, 1.1) |
| RT0618* | co-chaperonin GroES [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.5, 0.7) |
| RT0176 | molecular chaperone DnaK [Rickettsia typhi str. Wilmington] | 0.6 (0.4, 0.6, 1.1) |
| Inorganic ion transport and metabolism | ||
| RT0612 | zinc/manganese ABC transporter permease protein [Rickettsia typhi str. Wilmington] | 0.6 (0.3, 1.1, 0.6) |
| RT0258 | hypothetical protein RT0258 [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.9, 0.6) |
| General function prediction only | ||
| RT0320* | hypothetical protein RT0320 [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.5, 0.6) |
| RT0431 | hypothetical protein RT0431 [Rickettsia typhi str. Wilmington] | 0.6 (0.4, 0.6, 1.2) |
| RT0035 | GTP-binding protein [Rickettsia typhi str. Wilmington] | 0.6 (0.3, 0.9, 1.2) |
| Function unknown | ||
| RT0471 | iron-binding protein IscA/HesB [Rickettsia typhi str. Wilmington] | 0.5 (0.4, 0.7, 0.6) |
| RT0519* | rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington] | 0.6 (0.7, 0.7, 0.4) |
| Signal transduction mechanism | ||
| RT0550 | nitrogen assimilation regulatory protein NtrX [Rickettsia typhi str. Wilmington] | 0.6 (0.5, 0.7, 0.6) |
| not in COG database | ||
| RT0259 | heme exporter protein B [Rickettsia typhi str. Wilmington] | 0.5 (0.6, 0.8, 0.3) |
| RT0077* | nucleoside diphosphate kinase [Rickettsia typhi str. Wilmington] | 0.5 (0.6, 0.5, 0.5) |
| RT0874 | coproporphyrinogen III oxidase [Rickettsia typhi str. Wilmington] | 0.5 (0.7, 0.7, 0.3) |
| RT0325* | rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 0.8, 0.4) |
| RT0426 | rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington] | 0.6 (0.2, 0.6, 1.5) |
| RT0485 | cell surface antigen [Rickettsia typhi str. Wilmington] | 0.6 (1.1, 0.7, 0.2) |
| RT0686 | rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington] | 0.6 (0.7, 0.6, 0.5) |
| RT0126 | 50S ribosomal protein L1 [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 1.0, 0.6) |
| RT0102 | hypothetical protein RT0102 [Rickettsia typhi str. Wilmington] | 0.6 (0.6, 0.8, 0.5) |
| RT0701 | possible beta-glucosidase [Rickettsia typhi str. Wilmington] | 0.6 (0.8, 0.6, 0.5) |
Genes are grouped by functional categories. Gene IDs with asterisks and/or bold are statistically significant (see Methods). Fold change values in bold were obtained by comparing the normalized mean signal intensities of all three independent experiments using the Spotfire analysis program. Immediately following these values are the fold change values for each individual experiment (experiment 1, experiment 2 and experiment 3, respectively).