Table 1 First compilation of S. meliloti chromosomal IgRs predicted to encode sRNAs.
From: Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011
IgR# | Found by1 | Adjacent genes2 | sRNA strand2 | Prom.?3 | Term.?3 | Blast hits in4 | Expected size5 | Band size in Northern blot | Microarray detection7 | Gene8 | Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Rfam | SMc03975> SMc03976< | < | s70 | n | eubacteria | ~160 nt | ~155 nt | <, H, C, S, A, B, O (2972187–2972236) | 6S RNA (smrC22 = sra56) | |
2 | OT | SMc04042< SMc04043< | > | NN – s70 | y | Sm Rl Re At | ~80 nt | duplet < 100 nt | - | sm8 = suhB | |
3 | SP | SMc01933< proS> | < | NN – s70 | y | Sm Re Rl At Ml | ~150 nt | ~165 nt | <, A, C, H, S (1398340–1398389 1398389–1398340) | smrC9 = sra32 | |
4 | tR | Gln-tRNA< SMc00810> | < | - | y | Sm Re Rl | ? | multiple ~150 $~& 80 nt mainly | - | sm137 | this work |
5 | tR | SMc02151< Thr-tRNA< | > | NN – s70 | y | - | ~240 nt | no bands detected | >, S (*) (560802–560753) | sra12 | [27] |
6 | OT | gltB< SMc04029> | > | NN | y | Sm Re Rl | ~100–200 nt | not done 6 | >, A, C (3031662–3031711) | - | this work |
7 | OT | SMc04453< SMc01885> | < | NN | y | Sm Re Rl | ~390 nt | duplet, ~135 & ~200 nt | <, A, C, O, S (2321429–2321478) | sm26 | this work |
8 | OT | SMc01257< sda> | > | NN – s70 – PhoB | y | Sm At Oa Msp | ~170 nt | not done 6 | - | sm30 | this work |
9 | OT | thdF< rho< | > | s70 | y | Sm | ~180 nt | not done | - | sm130 | this work |
10 | SP | SMc00034> SMc00096< | > | s70 | y | Sm Re Rl | ~190 nt | ~175 nt | - | sra25 | [27] |
11 | SP | SMc00108< SMc00109< | < | s70 | y | Sm Rl Re At | ~100–120 nt | duplet, ~120 $~& 110 nt | - | sm145 | this work |
12 | SP | celR2> rpmG< | > | s70 | y | Sm Rl Re At Ml Msp Ac | ~150 nt | not done 6 | >, A, B, C, H, O, S (1411684–1411733 1411738–1411689) | smrC10 = sra33 | |
13 | SP | polA< SMc02851> | > | NN – s70 | y | Sm Rl Re At | ~150 nt | duplet, ~140 & ~90 nt | - | smrC7 = sra03 | |
14 | SP | SMc02910< SMc02911> | > | s70 | y | Sm Re Rl At Ml Bo Oa | ~60–150 nt | multiple, ~90–100 & ~180–210 | >, B, C, O, (267010–267059 267059–267010) | sm76 | this work |
15 | SP | SMc03988> SMc03989> | > | s70 | y | Sm Rl Re At | ~110 nt | ~80 nt | >, A, B, C, H, O, S (2986452–2986501 2986508–2986459) | sm84 | this work |
16 | SP | atpH< SMc02497< | > | s70 | y | Sm Rl Re At | ~110 nt | ~100 nt | - | sm270 | this work |
17 | SP | dapF< ffh> | > | s70 | y | Sm Rl Re At | ~120 nt | not done | >, A, B, O, S (3522279–3522328) | sm5 | this work |
18 | OT | SMc00821> SMc00822> | > | - | y | Sm Re Rl | ~80 nt | not done | >, A, C, H, O, S (843459–843508 843508–843459) | sm190 | this work |