TABLE 1 .
Known RNase III cleavage sites and top putative RNase III cleavage sites as identified by RNA-seq coverage differences between the WT strain and rnc deletion mutanta
| Location | Annotation | Ratio 1 | Ratio 2 | WT reads Rep. A (no.) | WT reads Rep. B (no.) | ΔRNase III reads (no.) | Gene(s) affected | Reference or result of in vitro cleavage assay |
|---|---|---|---|---|---|---|---|---|
| Known cleavage sites identified in this study | ||||||||
| 4166537 | Intergenic (muri-rrsB) | 415 | 587 | 41 | 29 | 17,025 | rRNA (rrsB) | 10 |
| 4035410 | Intergenic (hemG-rrsA) | 314 | 925 | 53 | 18 | 16,647 | rRNA (rrsA) | 10 |
| 3311286 | psrO | 3,782 | 3,782 | 3 | 3 | 11,347 | pnp | 15 |
| 2731278 | Intergenic (rrsG-clpB) | 487 | 534 | 23 | 21 | 11,206 | rRNA (rrsG) | 10 |
| 223653 | Intergenic (gmhB-rrsH) | 271 | 491 | 29 | 16 | 7,853 | rRNA (rrsH) | 10 |
| 3428875 | Intergenic (rrsD-yrdA) | 340 | 234 | 20 | 29 | 6,791 | rRNA (rrsD) | 10 |
| 3943398 | Intergenic (rrsC-gltU) | 1,309 | 2,619 | 4 | 2 | 5,237 | rRNA (rrsC) | 10 |
| 4209733 | Intergenic (rrsE-gltV) | 4,959 | 2,480 | 1 | 2 | 4,959 | rRNA (rrsE) | 10 |
| 4168221 | Intergenic (rrsB-gltT) | 123,700 | 123,700 | 0.01 | 0.01 | 1,237 | rRNA (rrsB) | 10 |
| 4168637 | Intergenic (gltT-rrlB) | 120 | 419 | 7 | 2 | 837 | rRNA (rrlB) | 9 |
| 3427176 | Intergenic (Ileu-rrsD) | 77,500 | 775 | 0.01 | 1 | 775 | rRNA (rrsD) | 10 |
| 3397879 | yhdE | 114 | 98 | 6 | 7 | 684 | rng | 63 |
| 225355 | Intergenic (rrsH-ileV) | 64,300 | 643 | 0.01 | 1 | 643 | rRNA (rrsH) | 10 |
| 4037115 | Intergenic (rrsA-ileT) | 62,600 | 62,600 | 0.01 | 0.01 | 626 | rRNA (rrsA) | 10 |
| 3318176 | Intergenic (rimP-metY) | 102 | 609 | 6 | 1 | 609 | metY | 46 |
| 4037523 | rrlA | 149 | 223 | 3 | 2 | 446 | rRNA (rrlA) | 9 |
| 758515 | P67/sucA | 30,500 | 305 | 0.01 | 1 | 305 | sucA | 64 |
| 4207874 | Intergenic (purH-rrsE) | 29,000 | 290 | 0.01 | 1 | 290 | rRNA (rrsE) | 10 |
| 3946623 | Intergenic (rrlC-rrfC) | 22,700 | 227 | 0.01 | 1 | 227 | rRNA (rrlC) | 9 |
| 2729186 | Intergenic (rrlG-gltW) | 55 | 221 | 4 | 1 | 221 | rRNA (rrlG) | 9 |
| 4040443 | Intergenic (rrlA-rrfA) | 20,300 | 203 | 0.01 | 1 | 203 | rRNA (rrlA) | 9 |
| 4212954 | Intergenic (rrlE-rrfE) | 19,500 | 65 | 0.01 | 3 | 195 | rRNA (rrlE) | 9 |
| 3941526 | Intergenic (yieP-rrsC) | 16,200 | 41 | 0.01 | 4 | 162 | rRNA (rrsC) | 10 |
| 4171559 | Intergenic (rrlB-rrfB) | 12,100 | 12,100 | 0.01 | 0.01 | 121 | rRNA (rrlB) | 9 |
| 3423873 | Intergenic (rrfD-rrlD) | 11,700 | 117 | 0.01 | 1 | 117 | rRNA (rrlD) | 9 |
| 2726273 | Intergenic (rrfG-rrlG) | 11,500 | 58 | 0.01 | 2 | 115 | rRNA (rrlG) | 9 |
| Putative cleavage sites identified in this study | ||||||||
| 122961 | Intergenic (pdhR-aceE) | 6,977 | 1,550 | 2 | 9 | 13,954 | aceE, aceF, lpdA | Y |
| 639695 | Intergenic (ahpC-ahpF) | 900 | 900 | 4 | 4 | 3,598 | ahpC | Y |
| 1799278 | Intergenic (pheM-rplT) | 639 | 799 | 5 | 4 | 3,196 | pheM, pheS, pheT | Y |
| 4330944 | proP | 66 | 83 | 15 | 12 | 992 | prop | Y |
| 3889207 | tnaA* | 301 | 129 | 3 | 7 | 903 | tnaC, tnaA, tnaB | Y |
| 755579 | sdhD* | 545 | 42 | 1 | 13 | 545 | sdhC, sdhD | Y |
| 3683389 | dctA | 74 | 74 | 7 | 7 | 518 | dctA | Y |
| 2171807 | Intergenic (gatR-gatD) | 213 | 47 | 2 | 9 | 426 | gatR, gatD | N |
| 3609652 | yhhQ | 58 | 77 | 4 | 3 | 231 | yhhQ | N |
| 951147 | Intergenic (pflA-pflB) | 15,800 | 15,800 | 0.01 | 0.01 | 158 | pflB | Y |
| 2351931 | glpT | 14,300 | 143 | 0.01 | 1 | 143 | glpT | N |
| 2237178 | mglC* | 133 | 13,300 | 1 | 0.01 | 133 | mglC, mglA, mglB | N |
| 4307817 | alsE* | 126 | 63 | 1 | 2 | 126 | alsB, Alsa, alsE, alsC, alsK | N |
| 2090031 | hisL | 11,900 | 60 | 0.01 | 2 | 119 | hisL | Y |
| 1166043 | Intergenic (ycfP-ndh) | 10,800 | 10,800 | 0.01 | 0.01 | 108 | ndh | Y |
| 159578 | gluQ* | 10,400 | 52 | 0.01 | 2 | 104 | gluQ | N |
| 444573 | Intergenic (panE-yajQ) | 48 | 32 | 2 | 3 | 96 | yajQ, panE | Y |
| 1622816 | Intergenic (yneM-mgrR) | 9,100 | 91 | 0.01 | 1 | 91 | yneM, mgrR | N |
Positions with zero reads were given a pseudocount of 0.01 reads. Asterisks (*) indicate that multiple cleavage sites were identified within a region and combined into one entry in the table. “Y” indicates there was observed cleavage of an in vitro transcribed transcript when incubated with purified enzyme, while “N” indicates a lack of observed cleavage. Ratio 1, number of reads in ΔRNase III divided by number of reads in WT replicate A; Ratio 2, number of reads in ΔRNase III divided by number of reads in WT replicate B; Rep. A, number of reads in WT replicate A; Rep. B, number of reads in WT replicate B.