TABLE 2 .
Roles of the genes of the core SigX regulon in transformation
| Function and locus taga |
Gene | Role or activity (reference[s]) | Transformation of mutants (reference[s])b |
||||
|---|---|---|---|---|---|---|---|
| SMU no. | SP no. | SSA no. | SMU | SP | SSA (45) | ||
| Recombination | |||||||
| 327 | 0023 | 2157 | radA | DNA repair protein RadA (71) | ↓ (71) | ||
| 644 | 0978 | 0749 | coiA | Recombination | ↓ (72) | ↓ | |
| 1001 | 1266 | 1185 | dprA | DNA-processing protein, mediates RecA (72, 73) loading onto internalized single-stranded DNA, competence shutoff (74–76) | ↓ (77) | ↓ (13, 74) | |
| 1967 | 1908 | 0214 | ssbB | Single-stranded DNA binding, DNA protection (78) | ↓ (77) | ↓ (79–81) | ↓ |
| 2085 | 1940 | 2245 | recA | Recombinase A, strand exchange (74, 82) | ↓ (77, 83) | ↓ (84) | ↓ (85) |
| Recombination (core in DpnII group) | |||||||
| 505 | 1734 | 1717 | dpnA | Single-strand methylase (56) | ↓ (56)g | ||
| 506 | 1733 | 1716 | dpnB | DpnII restrictase targeting unmethylated double-stranded DNA (56) | Yes (77) | ||
| Uptake | |||||||
| 498 | 2208 | 1836 | coMFA | ATP-dependent DNA/RNA helicase, translocase involved in single-stranded DNA uptake (86) | ↓ (87) | ↓ | |
| 499 | 2207 | 1835 | comFC | Late competence protein (59) | ↓ (59, 87) | ↓ | |
| 539 | 1808 | 0642 | cilC, pilD | Signal peptidase type IV, pilin cleavage (13, 88) | ↓ (39) | ↓ (13) | ↓ |
| 625 | 0954 | 0715 | comEA | Membrane protein with DNA-binding motif (double-stranded DNA receptor) (89) | ↓ (90) | ↓ | |
| 626 | 0955 | 0716 | comEC | Membrane channel (59, 91) | ↓c | ↓ (90) | ↓ |
| 1979 | 2045 | 0191 | Adenine-specific DNA methylase (13) | ↓ (50) | Yesd (13) | ||
| 1980 | 2047 | 0190 | comGG | Minor pilin (92–94) | ↓ (50) | ↓ (13, 93) | ↓ |
| 1981 | 2048 | 0189 | comGF | Minor pilin (92–94) | ↓ (50) | ↓ (93) | |
| 1982 | 2049 | 0188 | comGE | Minor pilin (92–94) | ↓ (50) | ↓ (93) | ↓ |
| 1983 | 2050 | 0187 | comGD | Minor pilin (92–94) | ↓ (50) | ↓ (93) | ↓ |
| 1984 | 2051 | 0186 | comGC | Major pilin (92, 94) | ↓ (50) | ↓ (59, 92, 93) | ↓ |
| 1985 | 2052 | 0185 | comGB | Competence protein, ABC transporter subunit (94) | ↓ (50) | ↓ (59, 93) | ↓ |
| 1987 | 2053 | 0184 | comGA | Pilus assembly ATPase (94) | ↓ (50) | ↓ (59, 92, 93) | ↓ |
| Lysis (CHAP domain conserved) | |||||||
| 836 | 0036 | lytF | Murein hydrolase (39, 61, 77, 95) | ↓ (39, 77) | |||
| 2201 | cbpD | Murein hydrolase (96) | Yes (96) | ||||
| Unknown functions in competenceh | |||||||
| 325 | 0021 | 2160 | dut | Deoxyuridine 5′-triphosphate nucleotidohydrolase | Yes (13) | ||
| 354 | 1981 | 2117 | rmuC, ccs50 | DNA recombination protein RmuC | Yes (13) | ||
| 355 | 1980 | 2116 | yhaM, cbf1 | CMP-binding factor 1, 23S RNA maturation | Yes (13) | ||
| 500 | 2206 | 1834 | yfiA | Ribosome hibernation-promoting factor (Hpf), sigma factor (σ54) modulation | Yes (13) | ||
| 645 | 0979 | 0751 | pepB | Oligopeptidase | Yes (13) | ||
| 769 | 0782 | 1537 | pilC | Membrane protein of pilus assembly | Yese (32, 39, 77) | Yes (13) | |
| 1055 | 1088 | 1218 | radC | DNA repair protein RadC | ↓ (39) | Yes (45) | |
| 1978 | 2044 | 0192 | ackA | Bifunctional acetaldehyde-coenzyme A/alcohol dehydrogenase (13, 97) | Yes (97) | Yes (93) | |
| 2086 | 1941 | 2246 | cinA | Competence damage-inducible protein A (98) | ↓f (98) | Yes (85) | |
a
Gene locus tag as in GenBank (SMU, S. mutans UA159, accession no. AE014133; SP, S. pneumoniae, TIGR4 accession no. AE005672; in bold, S. pneumoniae G54, accession no. CP001015; SSA, S. sanguinis SK36, accession no. CP000387.1).
b
Yes, deletion mutants not affected in transformation; ↓, >2-fold reduction.
c
Unpublished data.
d
70% of WT.
e
Results with CSP showed a <2-fold reduction, but in one of the studies without CSP, there were no transformants (32).
f
Deletion of cinA affected the expression of the downstream gene recA, which was not fully restored by cinA complementation from a plasmid.
g
Transformation with unmethylated DNA was reduced in the deletion mutant.
h
Annotation at KEGG (99).