TABLE 1.
Relative expression of common up-regulated genes in response to UVC, UVB, and UVA radiationa
| Gene | Cluster groupb | Product(s) | Functionc | UVR ratios (± SD) (by min)
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UVC
|
UVB
|
UVA
|
||||||||||
| 5 | 20 | 60 | 5 | 20 | 60 | 5 | 20 | 60 | ||||
| SOA0013 | I | UmuD protein | DNA metabolism | 5.1 ± 1.1 | 15.2 ± 1.7 | 16.1 ± 2.9 | 4.0 ± 1.0 | 11.0 ± 3.0 | 19.8 ± 3.5 | 5.0 ± 2.3 | 4.3 ± 1.3 | 4.3 ± 2.0 |
| SO0089 | I | Hypothetical protein | Unknown function | 3.1 ± 0.7 | 6.7 ± 1.7 | 6.9 ± 0.9 | 2.3 ± 0.4 | 5.1 ± 2.1 | 7.0 ± 2.5 | 2.3 ± 1.0 | 2.3 ± 1.1 | 1.6 ± 0.4 |
| SOA0012 | I | UmuC protein | DNA metabolism | 3.6 ± 1.3 | 8.4 ± 1.7 | 8.1 ± 0.7 | 2.6 ± 0.5 | 6.3 ± 1.9 | 8.0 ± 2.0 | 2.6 ± 0.5 | 3.3 ± 0.9 | 2.1 ± 0.5 |
| SO3061 | I | DNA topoisomerase III | DNA metabolism | 4.1 ± 0.8 | 8.0 ± 0.9 | 9.9 ± 3.3 | 2.9 ± 0.3 | 6.9 ± 0.5 | 9.8 ± 1.2 | 3.5 ± 0.2 | 3.4 ± 0.5 | 2.1 ± 0.4 |
| SO2603 | I | Conserved hypothetical proteins | Unknown function | 3.2 ± 0.2 | 5.2 ± 0.3 | 5.7 ± 0.6 | 2.6 ± 0.3 | 4.8 ± 0.3 | 5.7 ± 0.5 | 2.7 ± 0.2 | 2.4 ± 0.4 | 1.6 ± 0.3 |
| SO2604 | I | Conserved hypothetical proteins | Unknown function | 3.7 ± 0.5 | 6.1 ± 0.8 | 6.7 ± 0.9 | 3.0 ± 0.8 | 5.5 ± 1.6 | 7.3 ± 0.9 | 3.5 ± 0.6 | 3.1 ± 0.4 | 2.1 ± 0.4 |
| SO1114 | I | DNA-damage-inducible protein P | Unknown function | 3.6 ± 0.3 | 6.8 ± 0.7 | 6.2 ± 0.8 | 3.6 ± 0.6 | 5.8 ± 1.6 | 12.3 ± 1.8 | 4.2 ± 0.9 | 4.7 ± 1.3 | 2.9 ± 0.5 |
| SO3462 | I | DNA repair protein RecN | DNA metabolism | 7.9 ± 1.6 | 16.0 ± 3.7 | 15.0 ± 1.4 | 7.4 ± 1.2 | 11.5 ± 1.8 | 20.3 ± 1.0 | 6.8 ± 0.7 | 6.3 ± 1.0 | 3.7 ± 0.9 |
| SO3429 | I | Regulatory protein RecX | DNA metabolism | 4.8 ± 1.3 | 7.8 ± 0.3 | 7.4 ± 1.4 | 4.1 ± 0.7 | 6.3 ± 1.2 | 9.6 ± 1.2 | 3.5 ± 0.3 | 3.3 ± 0.2 | 2.1 ± 0.2 |
| SO4603 | I | LexA repressor | Regulatory function | 6.7 ± 0.6 | 12.2 ± 1.2 | 11.8 ± 2.1 | 8.0 ± 1.1 | 9.9 ± 2.0 | 17.6 ± 1.8 | 5.6 ± 1.8 | 6.1 ± 2.0 | 3.4 ± 0.8 |
| SO4604 | I | Conserved hypothetical protein | Unknown function | 6.9 ± 0.8 | 11.8 ± 1.9 | 12.5 ± 1.3 | 7.6 ± 1.9 | 9.5 ± 2.7 | 20.1 ± 1.7 | 7.0 ± 1.0 | 7.1 ± 2.1 | 3.8 ± 0.8 |
| SO3430 | I | RecA protein | DNA metabolism | 5.0 ± 1.2 | 8.0 ± 1.2 | 9.4 ± 2.1 | 4.0 ± 0.6 | 6.8 ± 0.9 | 10.2 ± 2.6 | 3.5 ± 0.5 | 3.6 ± 0.6 | 2.3 ± 0.2 |
| SO4605 | I | Hypothetical protein | Unknown function | 5.7 ± 1.6 | 8.3 ± 2.9 | 6.4 ± 2.0 | 5.1 ± 2.3 | 9.5 ± 4.2 | 8.7 ± 3.3 | 3.0 ± 1.7 | 3.2 ± 0.4 | 2.3 ± 0.4 |
| SO1757 | I | Conserved hypothetical protein | Unknown function | 13.6 ± 2.8 | 22.6 ± 2.9 | 16.7 ± 3.0 | 20.7 ± 8.9 | 17.2 ± 7.8 | 32.7 ± 3.9 | 23.2 ± 7.7 | 33.0 ± 18.8 | 14.5 ± 5.7 |
| SO3327 | I | Hypothetical protein | Unknown function | 2.0 ± 1.0 | 5.0 ± 1.1 | 4.5 ± 0.8 | 2.5 ± 0.6 | 2.0 ± 1.3 | 5.4 ± 3.1 | 3.8 ± 1.4 | 1.5 ± 0.5 | 1.8 ± 0.7 |
| SO2037 | I | Site-specific recombinase, phage integrase family | DNA metabolism | 1.7 ± 0.7 | 1.9 ± 0.6 | 2.4 ± 0.4 | 1.2 ± 0.4 | 1.6 ± 0.4 | 2.2 ± 0.6 | 1.8 ± 0.6 | 2.3 ± 1.0 | 1.5 ± 0.5 |
| SO2998 | II | Hypothetical protein | Unknown function | 0.9 ± 0.1 | 2.2 ± 0.5 | 15.2 ± 4.2 | 0.9 ± 0.2 | 1.3 ± 0.3 | 14.7 ± 4.6 | 0.8 ± 0.2 | 1.4 ± 0.1 | 2.2 ± 0.4 |
| SO3000 | II | Conserved hypothetical protein | Unknown function | 1.0 ± 0.4 | 3.1 ± 1.2 | 25.3 ± 5.9 | 0.9 ± 0.2 | 1.8 ± 0.5 | 37.5 ± 5.4 | 1.0 ± 0.1 | 1.5 ± 0.3 | 3.1 ± 0.8 |
| SO2993 | II | Prophage lambdaSo, type II DNA modification methyltransferase | DNA metabolism | 0.9 ± 0.3 | 3.0 ± 1.1 | 26.2 ± 4.9 | 1.0 ± 0.1 | 1.7 ± 0.1 | 35.6 ± 5.4 | 1.6 ± 0.2 | 1.5 ± 0.3 | 2.9 ± 0.9 |
| SO2997 | II | Hypothetical protein | Unknown function | 0.9 ± 0.2 | 2.6 ± 0.6 | 17.3 ± 3.7 | 0.9 ± 0.2 | 1.5 ± 0.5 | 19.5 ± 5.7 | 1.0 | 1.2 ± 0.2 | 2.5 ± 0.5 |
| SO2988 | II | Conserved hypothetical protein | Unknown function | 1.1 ± 0.2 | 2.5 ± 0.5 | 21.0 ± 3.7 | 0.9 ± 0.1 | 1.3 ± 0.2 | 21.6 ± 3.9 | 1.2 ± 0.4 | 1.4 ± 0.4 | 2.1 ± 0.6 |
| SO3001 | II | Hypothetical protein | Unknown function | 1.0 ± 0.1 | 2.3 ± 0.6 | 23.1 ± 10.7 | 0.8 ± 0.1 | 1.3 ± 0.2 | 19.1 ± 8.7 | 0.8 ± 0.3 | 1.3 ± 0.1 | 2.2 ± 0.7 |
| SO3002 | II | Conserved hypothetical protein | Unknown function | 1.1 ± 0.3 | 2.2 ± 0.7 | 21.5 ± 3.8 | 0.9 ± 0.1 | 1.4 ± 0.3 | 24.8 ± 8.4 | 0.9 ± 0.2 | 1.4 ± 0.2 | 2.1 ± 0.3 |
| SO2984 | II | Conserved hypothetical protein | Unknown function | 1.0 ± 0.2 | 1.8 ± 0.3 | 14.3 ± 1.9 | 1.0 ± 0.2 | 1.3 ± 0.2 | 14.8 ± 1.0 | 1.0 ± 0.2 | 1.0 | 2.2 ± 0.5 |
| SO2985 | II | Prophage lambdaSo, replication protein O | Other categories | 1.1 ± 0.4 | 2.0 ± 0.6 | 15.8 ± 2.8 | 1.0 ± 0.1 | 1.3 ± 0.2 | 15.9 ± 2.8 | 1.2 ± 0.2 | 1.4 ± 0.5 | 2.2 ± 0.4 |
| SO2983 | II | Hypothetical protein | Unknown function | 1.1 ± 0.1 | 1.8 ± 0.4 | 16.0 ± 3.7 | 0.8 ± 0.2 | 1.3 ± 0.2 | 17.3 ± 1.0 | 1.3 ± 0.1 | 1.1 ± 0.2 | 2.1 ± 0.3 |
| SO0644 | II | Prophage MuSol, DNA transpo- sition protein, putative | Other categories | 1.0 ± 0.1 | 2.2 ± 0.6 | 13.3 ± 1.2 | 1.0 ± 0.4 | 1.4 ± 0.4 | 19.0 ± 2.0 | 2.3 ± 0.7 | 1.2 ± 0.5 | 1.3 ± 0.1 |
| SO1759 | III | Conserved hypothetical proteins | Unknown function | 10.0 ± 4.6 | 10.7 ± 1.1 | 6.7 ± 1.0 | 13.3 ± 3.5 | 11.3 ± 4.2 | 11.3 ± 2.5 | 11.1 ± 3.7 | 8.3 ± 3.2 | 4.4 ± 2.4 |
| SO3849 | III | Conserved hypothetical proteins | Unknown function | 9.7 ± 3.9 | 9.8 ± 1.2 | 5.2 ± 0.5 | 11.1 ± 3.8 | 11.9 ± 8.5 | 9.3 ± 1.4 | 7.2 ± 1.9 | 5.5 ± 3.1 | 1.7 ± 0.3 |
| SO1761d | III | Conserved hypothetical proteins | Unknown function | 2.8 ± 1.4 | 3.4 ± 2.4 | 2.2 ± 0.7 | 5.3 ± 3.4 | 4.0 ± 2.2 | 2.8 ± 1.1 | 4.3 ± 2.3 | 3.9 ± 2.1 | 3.9 ± 0.8 |
| SO3854 | III | ISSo12, transposase | Other categories | 8.0 ± 3.5 | 8.0 ± 3.6 | 3.8 ± 1.0 | 3.0 ± 1.0 | 5.7 ± 2.0 | 4.3 ± 2.0 | 2.5 ± 1.2 | 1.5 ± 0.6 | 1.1 ± 0.2 |
a
The data presented here are the ratios of UVR-irradiated samples to the controls.
b
Cluster analysis was performed using either standard correlation or distance to calculate the similarities.
c
The functional groups are based on the published genome annotation (14).
d
The only gene that showed different clusters (cluster I or cluster III), by use of two methods.