Table 3.
Noncoding DNA bound by Rgg in the exponential phase of growth
| Category and Spy49 no.a | Geneb | Description | ChIP-chip fold enrichmentc | Transcript fold change (rgg mutant/WT)d |
|---|---|---|---|---|
| Virulence associated | ||||
| 1671 | emm49 | Antiphagocytic M protein | 8.4 | 2 |
| 1334-1335 | – | Esterase | 3.0 | – |
| 1683 | sfbX49 | Fibronectin-binding protein | 2.1 | 5 |
| 1684 | sof | Serum opacity factor | 2.1 | 7 |
| 830 | sclB | Streptococcal collagen-like surface protein | 2.2 | 3 |
| 1651 | – | Fibronectin-binding protein | 2.0 | −3 |
| Synthesis | ||||
| 1557c | asp | Alkaline shock protein | 3.6 | 2 |
| 1183c | – | Peroxide resistance protein | 3.6 | – |
| 1428c | rpsF | 30S ribosomal protein S6 | 3.5 | −2 |
| 127 | – | Translation initiation inhibitor | 3.4 | – |
| 1163c | – | Cytoplasmic protein | 5.0 | 3 |
| Transcriptional regulators | ||||
| 1113c | – | Transcription factor | 5.6 | −2 |
| 862-863 | – | Two-component sensor histidine kinase | 3.2 | – |
| 1334-1335 | copY | Negative transcriptional regulator | 3.0 | – |
| 1533 | – | MerR family transcriptional regulator | 2.5 | – |
| 725-726 | – | LysR family transcriptional regulator | 2.2 | −3 |
| 1142 | – | Biotin repressor family transcriptional regulator | 2.1 | – |
| 380-381 | mtsR | Metal-dependent transcriptional regulator | 12.2 | 2 |
| 380-381 | mtsA | Metal ABC transporter substrate-binding lipoprotein precursor | 12.2 | – |
| Prophage related | ||||
| 790 | – | Cell wall hydrolase | 5.1 | ND |
| 1518 | – | Cro protein | 3.0 | ND |
| 1529 | – | Phage transcriptional repressor protein | 2.2 | ND |
| 792 | speH | Streptococcal pyrogenic exotoxin H | 2.3 | ND |
| Insertion element related | ||||
| 677c | – | Transposase | 6.5 | ND |
| 1032 | – | Transposase | 4.7 | ND |
| 166 | – | M protein trans-acting positive-regulator-like protein | 4.8 | ND |
| 1819c | – | Transposase | 4.6 | ND |
| Metabolism | ||||
| 1616c | – | Oxidoreductase | 5.0 | 7 |
| 457 | – | Glycosyl transferase | 3.7 | 4 |
| 201 | – | Carbonic anhydrase | 3.0 | −2 |
| 876-877 | – | GTP pyrophosphokinase | 2.8 | 3 |
| 1697 | pflD | Pyruvate formate lyase 3 | 2.3 | −2 |
| 725-726 | – | Rhodanese super family protein | 2.2 | – |
| Transport | ||||
| 548 | pepD | Dipeptidase A | 16.1 | 2 |
| 1661 | dppB | Dipeptide transport system permease protein DppB | 8.0 | – |
| 862-863 | – | l-Malate permease | 3.2 | 2 |
| 1140 | fdhC | Formate transporter | 2.6 | – |
| 876-877 | – | Chloride channel protein | 2.8 | 3 |
| Repair | ||||
| 1160c | phr | Deoxyribodipyrimidine photolyase | 5.9 | 3 |
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 (43). Contiguous genes 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 indicates that the gene is not named.
c
ChIP-chip fold enrichment was calculated as a ratio of signal intensity between the SA5 and rgg mutant strains.
d
Fold changes in the transcript levels are from the previous study (26). A dash indicates that no change in the transcript level was observed. WT, wild type; ND, not determined.