Table 2.
Microarray comparisons of RNA abundances in T. kodakarensis LC124 versus T. kodakarensis TS517 and in T. kodakarensis LC125 versus TS517a
| Comparison and gene | Predicted or known function | Fold difference |
|---|---|---|
| LC124 vs TS517 | ||
| Upregulated by deletion of TK1413 (histone A) | ||
| TK2195 | Aspartate carbamoyltransferase, regulatory subunit | 3.5 |
| TK2196 | Aspartate carbamoyltransferase, catalytic subunit | 3.1 |
| TK1927 | Hypothetical membrane protein | 3.4 |
| TK0190 | GMP synthase, glutamine amidotransferase component | 2.2 |
| TK0191 | Predicted nucleic acid-binding protein | 1.1 |
| TK0192 | Hypothetical protein | 2.1 |
| TK0193 | GMP synthase, PP-loop-ATPase component | 3.3 |
| TK0194 | Inosine-5′-monophosphate dehydrogenase | 2.9 |
| TK0157 | Xanthine/uracil permease | 3.1 |
| TK0475 | d-Arabino 3-hexulose-6-phosphate formaldehyde lyase, fused to phosphohexuloisomerase | 2.9 |
| TK0268 | 2-Dehydro-3-deoxyphosphoheptonate aldolase | 2.8 |
| TK0269 | Transketolase, C-terminal section | 1.3 |
| TK0270 | Transketolase, N-terminal section | 2.6 |
| TK0271 | Hypothetical protein | 2.0 |
| TK1893 | Glycerate kinase-related protein | 2.7 |
| TK0835 | Phosphoribosylaminoimidazole carboxylase, ATPase subunit | 2.6 |
| TK0204 | Phosphoribosylamine-glycine ligase | 2.5 |
| TK0203 | Hypothetical protein | 2.2 |
| TK1895 | Purine-nucleoside phosphorylase | 2.4 |
| TK0010 | Hypothetical protein | 2.4 |
| TK2147 | Methyl-accepting chemotaxis protein | 2.2 |
| TK1002 | Adenylosuccinate synthase | 2.2 |
| TK1287 | Uracil phosphoribosyltransferase | 2.2 |
| TK2138 | Orotate phosphoribosyltransferase | 2.1 |
| TK1737 | Xanthine/guanine phosphoribosyltransferase | 2.1 |
| TK0766 | Hypothetical membrane protein | 2.1 |
| TK1605 | Hydrolase, metallo-beta-lactamase superfamily | 2.1 |
| TK1961 | Replication factor A complex, RPA41 subunit | 2.1 |
| TK1459 | Hypothetical protein | 2.0 |
| TK0252 | Indole-3-glycerol phosphate synthase | 2.0 |
| Downregulated by deletion of TK1413 (histone A) | ||
| TK0161 | ABC-type multidrug transport system, ATPase component | 3.0 |
| TK0162 | Hypothetical membrane protein | 2.0 |
| TK0163 | Hypothetical membrane protein | 2.3 |
| TK0164 | S-layer-like array protein | 3.8 |
| TK0165 | Hypothetical protein | 2.0 |
| TK0166 | Hypothetical protein | 5.3 |
| TK1413 | Archaeal histone A | 3.6 |
| TK0982 | Hypothetical membrane protein | 3.5 |
| TK0465 | Acetyl-CoA synthetase I, beta subunit | 2.3 |
| TK0466 | Hypothetical protein, conserved | 1.2 |
| TK0467 | Hypothetical protein | 3.4 |
| TK0468 | Hypothetical protein | 2.1 |
| TK1025 | Hypothetical protein | 3.4 |
| TK2114 | Hypothetical protein | 3.3 |
| TK1463 | Hypothetical protein | 3.0 |
| TK0589 | Hypothetical protein | 2.8 |
| TK1229 | Hypothetical protein | 2.8 |
| TK1316 | Predicted membrane protease subunit, stomatin/prohibitin homologue | 2.7 |
| TK0773 | Predicted ATP-dependent endonuclease | 2.7 |
| TK0751 | Hypothetical protein | 2.7 |
| TK1405 | Phosphoenolpyruvate carboxykinase | 2.6 |
| TK2053 | ABC-type multidrug transport system, ATPase component | 2.2 |
| TK2079 | Probable formate transporter | 2.2 |
| TK0443 | Hypothetical membrane protein | 2.2 |
| TK0719 | ABC-type molybdate transport system, ATPase component | 2.2 |
| TK0878 | Translation initiation factor eIF-5A | 2.1 |
| TK0844 | Tungsten-containing oxidoreductase | 2.1 |
| TK1481 | NADH:polysulfide oxidoreductase | 2.0 |
| TK1335 | Hypothetical protein | 2.0 |
| TK1780 | Hypothetical protein | 2.0 |
| TK0675 | Hypothetical protein | 2.0 |
| TK1949 | Hypothetical protein | 2.0 |
| TK1123 | 2-Oxoacid:ferredoxin oxidoreductases, gamma subunit | 2.0 |
| TK1334 | Dephospho-CoA kinase | 2.0 |
| TK1060 | Hypothetical protein | 2.0 |
| LC125 vs TS517 | ||
| Upregulated by deletion of TK2289 (histone B) | ||
| TK0264 | Archaeal shikimate kinase | 7.8 |
| TK2195 | Aspartate carbamoyltransferase, regulatory subunit | 6.5 |
| TK2196 | Aspartate carbamoyltransferase, catalytic subunit | 4.3 |
| TK0766 | Hypothetical membrane protein | 5.4 |
| TK0157 | Xanthine/uracil permease | 4.7 |
| TK0202 | Phosphoribosylformylglycinamidine synthase, PurS component | 2.6 |
| TK0203 | Hypothetical protein | 3.6 |
| TK0204 | Phosphoribosylamine-glycine ligase | 4.0 |
| TK0190 | GMP synthase, glutamine amidotransferase component | 2.5 |
| TK0191 | Predicted nucleic acid-binding protein | 1.6 |
| TK0192 | Hypothetical protein | 2.4 |
| TK0193 | GMP synthase, PP-loop-ATPase component | 4.0 |
| TK0194 | Inosine-5′-monophosphate dehydrogenase | 3.1 |
| TK0835 | Phosphoribosylaminoimidazole carboxylase, ATPase subunit | 3.4 |
| TK0207 | Formate-dependent phosphoribosylglycinamide formyltransferase | 2.9 |
| TK0603 | Hypothetical protein | 2.9 |
| TK0604 | Hypothetical protein | 2.8 |
| TK1090 | Hypothetical membrane protein | 2.7 |
| TK0561 | Adenylosuccinate lyase | 2.7 |
| TK1352 | Hypothetical protein | 2.6 |
| TK1583 | Hypothetical protein | 2.6 |
| TK0418 | Hypothetical protein | 2.5 |
| TK1287 | Uracil phosphoribosyltransferase | 2.5 |
| TK0260 | Probable aromatic aminotransferase | 2.4 |
| TK1895 | Purine-nucleoside phosphorylase | 2.4 |
| TK0084 | Hypothetical protein | 2.3 |
| TK0612 | Hypothetical protein | 2.3 |
| TK1923 | Hypothetical membrane protein | 2.3 |
| TK2180 | Hypothetical protein | 2.3 |
| TK1002 | Adenylosuccinate synthase | 2.3 |
| TK0199 | Predicted permease | 2.2 |
| TK0475 | d-Arabino 3-hexulose-6-phosphate formaldehyde lyase, fused to phosphohexuloisomerase | 2.2 |
| TK0838 | Thioredoxin | 2.2 |
| TK0983 | Hypothetical protein | 2.2 |
| TK1822 | Predicted ATPase | 2.2 |
| TK0762 | Glycosyltransferase | 2.2 |
| TK2138 | Orotate phosphoribosyltransferase | 2.2 |
| TK0531 | Hypothetical protein | 2.2 |
| TK1841 | Predicted site-specific integrase-resolvase | 2.2 |
| TK0836 | Phosphoribosylaminoimidazole carboxylase, catalytic subunit | 2.2 |
| TK0407 | Hypothetical protein | 2.2 |
| TK2182 | Hypothetical protein | 2.2 |
| TK0737 | Hypothetical protein | 2.2 |
| TK0210 | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 2.1 |
| TK1557 | Predicted dehydrogenase | 2.1 |
| TK0197 | Phosphoribosylformylglycinamidine synthase II | 2.1 |
| TK1591 | Predicted transcription regulator | 2.1 |
| TK1869 | Probable phosphate transport system regulator | 2.1 |
| TK0120 | Proline dehydrogenase, gamma subunit (4Fe-4S cluster-binding component) | 2.1 |
| TK0625 | Multisubunit sodium/hydrogen antiporter, MnhD subunit | 2.1 |
| TK0906 | Endonuclease V (deoxyinosine 3′-endonuclease) | 2.1 |
| TK0396 | Hypothetical protein | 2.1 |
| TK0091 | Hypothetical protein | 2.1 |
| TK1838 | Hypothetical membrane protein | 2.0 |
| TK1444 | Homoserine kinase | 2.0 |
| TK1289 | Sodium-driven multidrug efflux pump protein | 2.0 |
| Downregulated by deletion of TK2289 (histone B) | ||
| TK2289 | Archaeal histone B | 9.8 |
| TK0179 | Hypothetical protein | 2.3 |
| TK0180 | Acetyl-CoA acetyltransferase | 3.6 |
| TK0181 | 3-Hydroxy-3-methylglutaryl-CoA synthase | 3.4 |
| TK2076 | Formate:ferredoxin oxidoreductase, alpha subunit | 3.2 |
| TK2077 | Formate:ferredoxin oxidoreductase, 4Fe-4S cluster-binding beta subunit | 2.9 |
| TK2078 | Formate:ferredoxin oxidoreductase, 4Fe-4S cluster-binding gamma subunit | 2.8 |
| TK2079 | Probable formate transporter | 3.1 |
| TK1830 | Probable alpha-amylase | 3.2 |
| TK1413 | Archaeal histone A | 2.7 |
| TK1405 | Phosphoenolpyruvate carboxykinase | 2.6 |
| TK1431 | Glutamate dehydrogenase | 2.6 |
| TK1046 | Hypothetical protein | 2.4 |
| TK1624 | Methylmalonyl-CoA decarboxylase, gamma subunit | 2.3 |
| TK0560 | Archaeal chromatin protein, Alba | 2.2 |
| TK1245 | Hypothetical protein | 2.2 |
| TK2048 | Hypothetical protein | 2.2 |
| TK0136 | Indolepyruvate:ferredoxin oxidoreductase, alpha subunit | 2.1 |
| TK0307 | SSU ribosomal protein S10P | 2.1 |
| TK2268 | Aspartate aminotransferase | 2.1 |
| TK0352 | Thymidine phosphorylase | 2.1 |
| TK2035 | Glycine cleavage system protein T (aminomethyltransferase) | 2.1 |
| TK1539 | LSU ribosomal protein L2P | 2.1 |
| TK0878 | Translation initiation factor eIF-5A | 2.1 |
| TK1500 | SSU ribosomal protein S9P | 2.1 |
| TK0465 | Acetyl-CoA synthetase I, beta subunit | 2.0 |
| TK1534 | Protein translation factor SUI1 homologue | 2.0 |
| TK1295 | Predicted thiol protease | 2.0 |
| TK0308 | Translation elongation factor EF-1, alpha subunit | 2.0 |
| TK1469 | Hydrolase, metallo-beta-lactamase superfamily | 2.0 |
| TK1174 | Predicted acetyltransferase, isoleucine patch superfamily | 2.0 |
a
Shown are average values from two independent experiments for all transcripts for which expression levels increased or decreased by at least 2-fold in T. kodakarensis LC124 or LC125 compared with their abundances in T. kodakarensis TS517. The microarrays had amplicons from all 2,306 T. kodakarensis ORFs (6) spotted twice at different locations. Genes in operons that exhibited significant changes in expression levels are listed even when the expression levels of some genes did not change by 2-fold. Shading highlights operons and genes with the same transcription responses to the absence of HTkA or HTkB. CoA, coenzyme A; SSU, small subunit; LSU, large subunit.