Table 3.
Noncoding DNA bound by Rgg
| Category and Spy49 no.a | Geneb | Description | ChIP-chip fold enrichmentc | Transcript fold change (rgg mutant/wt)d |
|---|---|---|---|---|
| Virulence associated | ||||
| 1626 | pulA | Pullulanase | 6.0 | 2 |
| 1692-1693 | mf1 | Streptodornase B/mitogenic factor 1 | 4.90 | 5 |
| 1455 | spd-3 | Streptodornase | 3.6 | 5 |
| 1690-1691 | speB | Streptococcal pyrogenic exotoxin B | 2.7 | −59 |
| Transcriptional regulator | ||||
| 1690-1691 | rgg | Rgg | 2.7 | 3 |
| 710-711 | cpsY | Putative transcriptional regulator | 2.8 | — |
| 1761-1762 | (—) | Putative arginine repressor | 2.7 | 5 |
| 1113 | (—) | Putative transcription factor | 2.4 | −2 |
| Prophage related | ||||
| 1720-1721 | (—) | Transposase | 8.1 | — |
| 355 | (—) | Hypothetical protein | 7.0 | ND |
| 396 | (—) | Surface antigen | 5.7 | 6 |
| 746 | (—) | Integrase | 5.6 | 11 |
| 565 | (—) | Transposase | 5.1 | 5 |
| 1499c | (—) | Phage endodeoxyribonuclease | 2.1 | — |
| Metabolism | ||||
| 612 | rgpAc | Rhamnosyltransferase | 8.7 | — |
| 1720-1721 | ahpC | Alkyl hydroperoxide reductase protein C | 8.1 | — |
| 1632c | relA | (p)ppGpp synthetase | 5.7 | — |
| 1429-1430 | mutY | A/G-specific adenine glycosylase | 3.4 | 2 |
| 1793-1794 | sdhB | l-Serine dehydratase, beta subunit | 2.5 | −3 |
| 850-851 | (—) | Polysaccharide deacetylase family protein | 2.2 | — |
| 850-851 | folC1 | Folylpolyglutamate synthase | 2.2 | −3 |
| Synthesis | ||||
| 967 | dpfB | Phosphopantothenate-cysteine ligase | 5.0 | — |
| 1436-1437 | (—) | RNase HIII | 4.6 | — |
| 143 | nusG | Transcription antitermination protein | 2.9 | — |
| 1047 | (—) | BigG family transcription antiterminator | 2.9 | 2 |
| 1761-1762 | argS | Arginyl-tRNA synthetase | 2.7 | 2 |
| 1793-1794 | mnmA | tRNA-specific 2-thiouridylase | 2.5 | — |
| 1091 | deaD2 | Putative RNA helicase | 2.3 | — |
| 1506 | dnaC | DNA replication protein C | 2.1 | — |
| Repair | ||||
| 1160 | phr | Deoxyribodipyrimidine photolyase | 9.8 | — |
| 603 | rexB | ATP-dependent exonuclease, subunit B | 6.0 | — |
| Hypothetical | ||||
| 1692-1693 | (—) | Hypothetical protein | 4.9 | — |
| 1436-1437 | (—) | Hypothetical protein | 4.6 | — |
| 1429-1430 | (—) | Hypothetical protein | 3.4 | — |
| 710-711 | (—) | Hypothetical protein | 2.8 | — |
a
Genes are categorized based on KEGG genome annotations. Spy49 numbers are the open reading frames based on the S. pyogenes strain NZ131 genome annotation (37). Contiguous genes that are likely to be cotranscribed are separated by a hyphen. Where a Spy49 number is underlined, the description is specific to the underlined Spy49 gene designation.
b
A dash within parentheses indicates that the gene is not named.
c
Calculated as a ratio of signal intensity between the SA5 and rgg mutant strains.
d
Determined previously (16). A dash indicates no change in the transcript level. ND, not determined.