Table 2. Stabilised and degradosome ORFs with an associated RNase Y cleavage site.
| ORF | Starta | End a | Length | Strand | Number of RNase Y sites inside the ORF | Distance to the nearest RNase Y site b | Half-life change (fold) | Steady-state change (fold) |
|---|---|---|---|---|---|---|---|---|
| Stabilised ORFs with an associated RNase Y cleavage site | ||||||||
| dnaX | 502594 | 504291 | 1698 | + | 0 | 22 | 2.3 | 1.9 |
| rplY | 529681 | 530334 | 654 | + | 1 | 0 | 8.5 | 5.5 |
| rplA | 576747 | 577439 | 693 | + | 0 | 12 | 4.2 | 2.2 |
| SA0502 | 587068 | 587322 | 255 | + | 1 | 0 | 3.9 | 1 |
| SA0641 | 735417 | 735860 | 444 | - | 0 | -144 | 2.0 | 1 |
| gapR | 831619 | 832632 | 1014 | + | 0 | 1 | 3.5 | 1 |
| Gap | 832685 | 833695 | 1011 | + | 1 | 0 | 2.1 | 1.1 |
| fabD | 1213830 | 1214756 | 927 | + | 1 | 0 | 2.1 | 2.9 |
| rpsB | 1245199 | 1245966 | 768 | + | 1 | 0 | 9.9 | 21.1 |
| Tsf | 1246148 | 1247029 | 882 | + | 0 | -106 | 8.1 | 9.5 |
| rpsO | 1265805 | 1266074 | 270 | + | 0 | 74 | 3.1 | 2.0 |
| glnR | 1306778 | 1307146 | 369 | + | 1 | 0 | 2.9 | 1.2 |
| glyS | 1600376 | 1601767 | 1392 | + | 0 | -115 | 3.3 | 2.0 |
| rpsU | 1608721 | 1608897 | 177 | - | 0 | -35 | 9.2 | 9.8 |
| dnaK | 1613514 | 1615346 | 1833 | - | 0 | -18 | 5.0 | 4.1 |
| grpE | 1615415 | 1616041 | 627 | - | 1 | 0 | 9.6 | 6.2 |
| hrcA | 1616073 | 1617050 | 978 | - | 1 | 0 | 14.4 | 7.6 |
| valS | 1693943 | 1696573 | 2631 | - | 0 | -181 | 2.4 | 1.8 |
| SA1734 | 1986743 | 1987303 | 561 | + | 3 | 0 | 2.2 | 2.5 |
| SA1735 | 1987356 | 1988285 | 930 | + | 0 | -168 | 2.2 | 1.7 |
| RNase Y cleavage sites associated with degradosome ORFs | ||||||||
| SA0941 | 1068429 | 1068599 | 171 | - | 0 | -129, -141, -144 | 1 c | 1.5 c |
| rnjA | 1066732 | 1068429 | 1698 | - | 0 | -347, -359, -362 | 1.2 | 1 |
| rnjB | 1268775 | 1270448 | 1674 | + | 1 | 0 | 1.3 c | 1.1 c |
| pfkA | 1736036 | 1736959 | 924 | - | 2 | 0 | 0 | 0 |
| cvfA | 1281967 | 1283526 | 1560 | + | 0 | -54 | ND d | ND d |
a) Genome positions from S. aureus N315 (NC_002745.2) are used throughout the manuscript.
b) On the same strand and shown by RT-PCR or RNA-seq to be potentially on the same RNA molecule, 0 = Cleavage is inside the ORF, negative numbers indicate upstream cleavage.
c) Did not pass the quality criteria.
d) Not determined.