Table 3.
The top twenty PHX genes in one radiation-sensitive and the four radiation-resistant species.a
| Gene |
E(g)
|
||||
|---|---|---|---|---|---|
| D. geo | D. rad | K. rad | R. xyl | E. coli | |
| RPs | |||||
| L2 (rplB) | 1.20 | 1.37 | 1.27 | 1.08 | 1.17 |
| L3 (rplC) | 1.18 | 1.37 | 1.36 | 1.03 | 1.16 |
| L15(rplO) | (1.03) | 1.31 | 1.58 | (1.00) | 1.13 |
| L19 (rplS) | 1.18 | 1.40 | 1.32 | (1.01) | 1.12 |
| L22 (rplV) | 1.19 | 1.38 | (1.03) | 1.05 | (1.09) |
| L24 (rplX) | 1.16 | 1.28 | 1.56 | (1.00) | 1.13 |
| S1 (rpsA) | 1.31 | 1.45 | 1.54 | 1.11 | 1.13 |
| S2 (rpsB) | 1.11 | 1.47 | 1.38 | (1.00) | 1.15 |
| S3 (rpsC) | 1.20 | 1.37 | 1.36 | 1.04 | 1.15 |
| S4(rpsD) | 1.21 | 1.39 | 1.43 | 1.17 | 1.12 |
| S13 (rpsM) | 1.05 | 1.18 | 1.43 | 1.04 | 1.05 |
| TFs | |||||
| Translation elongation factor G (fusA) | 1.18 | 1.45 | 1.41 | (1.00) | 1.15 |
| Elongation factor Tu | 1.07 | 1.44 | 1.43 | (0.97) | 1.15 |
| 1.08 | 1.44 | – | (0.97) | 1.14 | |
| Elongation factor Ts | (1.02) | 1.52 | 1.22 | 1.03 | 1.15 |
| Transcriptional regulator, Crp/Fnr family | 1.18 | 1.11 | (0.96) | 1.03 | – |
| RNA polymerase beta subunit (rpoB) | 1.11 | 1.41 | 1.53 | (0.87) | 1.19 |
| DNA-directed RNA polymerase subunit beta’ | 1.06 | 1.47 | 1.80 | 1.11 | – |
| Chaperones | |||||
| DnaK protein (dnaK) | 1.29 | 1.50 | 1.53 | (0.98) | 1.17 |
| Chaperone DnaJ (dnaJ) |
1.13 1.04 |
(0.93) | 1.28 | 1.09 | 1.13 |
| 60 kDa chaperonin (groEL) | 1.30 | 1.66 | 1.54 | 1.05 | 1.15 |
| Co-chaperonin GroES | 1.06 | 1.15 | 1.29 | 1.04 | 1.08 |
| Information storage and processing | |||||
| Translation-associated GTPase | (0.91) | 1.30 | (0.84) | 1.10 | (0.96) |
| Recombinase A (recA) | 1.17 | 1.46 | 1.30 | (0.95) | 1.08 |
| GCN5-related N-acetyltransferase | (0.81) | 1.08 | 1.10 | – | |
| DeaD/Deah box helicase domain-containing protein | 1.17 | – | 1.50 | (0.90) | – |
| Cellular processes and signaling | |||||
| Glycosyl transferase family protein | (0.86) | (0.76) | 1.25 | 1.10 | (0.88) |
| (0.90) | 1.24 | 1.07 | (0.89) | ||
| 1.24 | 1.05 | (0.81) | |||
| 1.09 | (0.85) | ||||
| (0.80) | |||||
| (1.02) | |||||
| (1.02) | |||||
| ATP-dependent protease | 1.21 | 1.31 | 1.13 | – | 1.06 |
| Peptidase s8 and s53, subtilisin, kexin, sedolisin | 1.26 | – | 1.05 | (0.92) | – |
| Flagellar motor switch protein FliG | – | – | 1.53 | – | (0.93) |
| S-layer-like protein region | 1.18 |
1.49 1.45 |
– | – | – |
| Mandelate racemase/muconate lactonizing enzyme-like protein | (0.89) | 1.07 | 1.10 | – | |
| UTP-glucose-1-phosphate uridylyltransferase | – | – | 1.43 | – | 1.05 |
| Histidine kinase | (0.93) | – | 1.43 | (0.91) | |
| Metabolism | |||||
| Energy production and conversion | |||||
| Aconitate hydratase (acnA) | (1.00) | 1.56 | 1.38 | 1.06 | (0.68) |
| Aldo/keto reductase | 1.18 | (0.98) | (0.67) | (1.00) | (0.82) |
| Thioredoxin | (1.01) | 1.11 | 1.10 | 1.09 | 1.09 |
| 1.07 | 1.02 | (0.93) | |||
| Isocitrate lyase (aceA) | 1.09 | 1.55 | – | (0.98) | (0.98) |
| F0F1 ATP synthase subunit beta | 1.05 | 1.10 | 1.54 | 1.12 | |
| F0F1 ATP synthase subunit alpha | – | 1.51 | 1.07 | 1.17 | |
| FAD-dependent pyridine nucleotide-disulphide oxidoreductase | (1.03) | (0.80) | 1.54 | 1.00 | (0.73) |
| Light-independent protochlorophyllide reductase subunit B | – | – | 1.12 | ||
| Oxidoreductase-like protein | 1.03 | 1.09 | 1.13 | 1.10 | |
| Lipid metabolism | |||||
| Acyl-CoA dehydrogenase-like protein | 1.16 | 1.54 | (0.82) | 1.06 | (0.87) |
| 1.06 | |||||
| 1.05 | |||||
| Amino acid transport and metabolism | |||||
| Extracellular solute binding protein, family 5 | 1.16 | 1.47 | – | – | – |
| 1.12 | 1.47 | ||||
| 1.06 | 1.02 | ||||
| 1.01 | |||||
| Histidinol phosphate aminotransferase | – | – | – | 1.11 | (0.92) |
| Glycine hydroxymethyltransferase | (1.00) | – | 1.42 | – | |
| Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein | – |
1.50 1.46 |
– | 1.08 | – |
| ABC transporter related inner-membrane translocator |
1.13 1.05 |
1.48 |
1.53 1.47 |
1.05 1.05 |
– |
| (0.87) | – | 1.43 | 1.01 | – | |
| Binding-protein-dependent transport systems inner membrane component | 1.08 | – | 1.23 | 1.11 | – |
| 1.02 | 1.08 | 1.10 | |||
| Nucleotide transport and metabolism | |||||
| Nucleoside-diphosphate kinase (ndk) | 1.19 | 1.05 | 1.18 | (0.96) | 1.11 |
| Bifunctional 2′,3′-cyclic nucleotide 2′-phosphodiesterase/3′-nucleotidase periplasmic precursor protein | 1.18 | (0.85) | 1.22 | – | – |
| Others | |||||
| Membrane lipoprotein | 1.17 | 1.43 | 1.22 | (0.83) | 1.22 |
| Hypothetical protein | 1.18 | 1.44 | 1.52 | 1.12 | |
| 1.17 | 1.44 | 1.10 | |||
| 1.10 | |||||
| 1.10 | |||||
| 1.09 | |||||
a
The numbers underlined indicate the top 20 PHX genes; numbers in parentheses indicate the corresponding genes are not PHX, ‘–’ denotes the gene is absent in the corresponding species.