Table 1.
CodY-binding sites within the 15 highest enriched CodY-binding regions of the L. monocytogenes genomea.
| Region ranking and putative target gene(s) | Alternative gene name(s) | Distanceb (nt) from: |
Site length (nt) | Site locationc with respect to the target gene(s) | Maximal enrichment factor of the binding region | Site detection by ChIP-Seqd | |
|---|---|---|---|---|---|---|---|
| first gene | second gene | ||||||
| 1. LMRG_RS01035 | mfd | −24 | 8 | UPSTREAM | 554.0 | yes | |
| 2. LMRG_RS00580 | lmaA | 282 | 7 | INTERNAL | 335.1 | yes | |
| 3. LMRG_RS07545,LMRG_RS07550 | amtB,glnK | 1110 | −104 | 6 | INTERNAL,UPSTREAM | 302.1 | no |
| 4. LMRG_RS04970,LMRG_RS04975 | 797 | −99 | 9 | INTERNAL,UPSTREAM | 288.0 | yes | |
| 5. LMRG_RS01845,LMRG_RS01850 | 377 | −63 | NDe | INTERNAL,UPSTREAM | 274.6 | yes | |
| 5. LMRG_RS01845,LMRG_RS01850 | 399 | −41 | ND | INTERNAL,UPSTREAM | 274.6 | yes | |
| 6. LMRG_RS13490 | 136 | 6 | INTERNAL | 257.1 | yes | ||
| 7. LMRG_RS11140/LMRG_RS11145 | oppA | −11 | −593 | ND | UPSTREAM/UPSTREAM | 250.1 | no |
| 7. LMRG_RS11140/LMRG_RS11145 | oppA | −149 | −460 | 16 | UPSTREAM/UPSTREAM | 250.1 | no |
| 7. LMRG_RS11140/LMRG_RS11145 | oppA | −179 | −425 | ND | UPSTREAM/UPSTREAM | 250.1 | no |
| 8. LMRG_RS00110,LMRG_RS00115 | 179 | −323 | 10 | INTERNAL,UPSTREAM | 217.5 | no | |
| 8. LMRG_RS00110,LMRG_RS00115 | 390 | −114 | 8 | INTERNAL,UPSTREAM | 217.5 | yes | |
| 9. LMRG_RS10840,LMRG_RS10835 | 1331 | −138 | 7 | INTERNAL,UPSTREAM | 211.0 | yes | |
| 10. LMRG_RS09960 | 796 | ND | INTERNAL | 168.2 | no | ||
| 10. LMRG_RS09960 | 751 | ND | INTERNAL | 168.2 | yes | ||
| 11. LMRG_RS00240 | agrB | −124 | 3 | UPSTREAM | 156.7 | yes | |
| 12. LMRG_RS08950,LMRG_RS08945 | purC,purS | 647 | −78 | 8 | INTERNAL,UPSTREAM | 140.0 | yes |
| 13. LMRG_RS00135 | 110 | 6 | INTERNAL | 116.8 | yes | ||
| 14. LMRG_RS02565/LMRG_RS02570 | −176 | −186 | ND | UPSTREAM/UPSTREAM | 115.1 | no | |
| 14. LMRG_RS02565/LMRG_RS02570 | −276 | −91 | 16 | UPSTREAM/UPSTREAM | 115.1 | yes | |
| 14. LMRG_RS02570 | 86 | 17 | INTERNAL | 115.1 | no | ||
| 15. LMRG_RS02730 | 462 | 3 | INTERNAL | 111.2 | yes | ||
See Dataset S2 for additional information.
Distances from the translation start of putative target genes.
“upstream” indicates the location of a CodY-binding site in the regulatory region of a gene; “upstream/upstream” indicates the location of a CodY-binding site in the regulatory region between two divergent genes; “internal” indicates the location of a CodY-binding site within the coding region of a gene; for some internal sites, nearby adjacent genes are shown as candidate targets for regulation (the gene names are separated by a comma).
Only the strongest IDAP-Seq site was detected for some regions.
ND (not determinable) indicates that the site boundary and the site length could not be determined because of the presence of a second, nearby CodY-binding site.