Table 1.
Identification, conservation and functional data of S. meliloti sRNAs.
| Symbionts | Pathogens | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name/s in S. meliloti 1021 and (S. meliloti 2011) a | Genome Copies | Coordinates in S. meliloti 1021 Genome | Strand | Predicted Promoter Motifs [27] | Hfq Co-IP RNA [32] | Expression in Nodules b [34] | S. meliloti | S. fredii | S. medicae | R. leguminosarum | R. etli | M. loti | B. japonicum | Agrobacterium sp. | Brucella sp. | Others | |
| Housekeeping | SMc04478/tmRNA/ssrA | 1 | 2291143–2291463 | + | RpoD | ||||||||||||
| SmelC035/sra05/4.5S/SRP–RNA/ffs (SMc06075) | 1 | 259927–260032 | + | RpoD RpoN | ZII/IZ/ZIII | ||||||||||||
| SmelC667/sra56/Smr22C/6S RNA/ssrs (SMc06867) | 1 | 2972090–2972252 | - | RpoD | IZ/ZIII | ||||||||||||
| SmelC809/sra50/SmrC19/RNase P/rnpB (SMc06867) | 1 | 2356793–2357134 | - | RpoD | IZ/ZIII | ||||||||||||
| trans-sRNAs | SmelC411/sm3/sra41/smrC15/AbcR2 (SMc06510) | 3 | 1698731–1698617 | - | RpoD RpoH1/2 | IZ/ZIII | |||||||||||
| SmelC412/sm3’/sra41/smrC16/AbcR1 (SMc06511) | 3 | 1698937–1698817 | - | RpoD | ZII/IZ/ZIII | ||||||||||||
| SmelC397/smrC14/NfeR1 (SMc06496) | 6 | 1667613–1667492 | - | RpoD | IZ/ZIII | ||||||||||||
| SmelC689/MmgR (SMc06891) | 3 | 3046712–3046789 | + | RpoD RpoN | IZ/ZIII | ||||||||||||
| SmelC706/smrC45/SpeF (SMc06909) | 1 | 3105298–3105445 | - | RpoH1/2 | ZIII | ||||||||||||
| SmelA075/smA8 (SMa6506) | 5 | 1220693–1220808 | + | RpoD | ZII/IZ | ||||||||||||
| SmelC023/sra03/smrC7 (SMc06056) | 1 | 201679–201825 | + | RpoD RpoH1/2 | ZII/ZIII | ||||||||||||
| SmelC289/sra32/smrC9 (SMc06412) | 1 | 1398278–1398426 | - | RpoD | ZII | ||||||||||||
| SmelC291/sra33/smrC10/EcpR1 (SMc06416+SMc06418) | 1 | 1411678–1411848 | + | ZII/IZ | |||||||||||||
| SmelC671/sm84 (SMc06875) | 1 | 2986421–2986520 | + | ZII | |||||||||||||
| SmelA099/smrA6 (SMa6570) | 1 | 1328175–1328334 | - | ZII/IZ/ZIII | |||||||||||||
| SmelB053/smrB35 (SMb23147) | 3 | 577730–577873 | + | RpoD RpoH1/2 | ZII | ||||||||||||
| SmelC151 (SMc06261) | 1 | 843451–843524 | + | IZ/ZIII | |||||||||||||
| SmelC587/sm104/RcsR1 (rnTrpL?) | 1 | 2575832–2575947 | - | ||||||||||||||
| SmelC165 | 1 | 910182–910297 | + | RpoN | |||||||||||||
| SmelC416/sm138 (SMc06519+) | 1 | 1718814–1718919 | - | ||||||||||||||
| SmelC500 (SMc06663) | 1 | 2180099–2180274 | - | ZII | |||||||||||||
| SmelC507 (SMc06677) | 1 | 2206348–2206579 | + | RpoD RpoH1/2 | ZII | ||||||||||||
| SmelC549/sm4 (SMc06721) | 1 | 2371597–2371855 | + | RpoD RpoH1/2 | ZII/IZ(ZIII | ||||||||||||
| SmelC601 (SMc06778) | 1 | 2625313–2625439 | - | RpoE2 | ZII/IZ/ZIII | ||||||||||||
| SmelC775/GspR1 (SMc07200) | 1 | 3509658–3509803 | + | ZII | |||||||||||||
| SmelA003 | 4 | 15179–15268 | + | ||||||||||||||
| SmelA033/smA3a/smrA2 | 1 | 512140–512221 | - | RpoD | |||||||||||||
| SmelB003 (SMb23003) | 1 | 30240–30345 | + | RpoH1 | IZ/ZIII | ||||||||||||
| SmelB008 | 1 | 65071–65147 | + | RpoE2 | |||||||||||||
| SmelB009 | 1 | 65186–65266 | - | RpoH1/2 | |||||||||||||
| SmelB033 (SMb23075) | 1 | 379319–379391 | - | RpoN | IZ | ||||||||||||
| SmelB044/smrB3b (SMb23116) | 2 | 541771–541909 | - | ZII/IZ | |||||||||||||
| SmelB075 (SMb23231) | 1 | 800730–800793 | - | RpoH1/2 | ZII | ||||||||||||
| SmelB126/smB9 (SMb23362) | 4 | 1325476–1325586 | + | RpoE2 | ZII/ZIII | ||||||||||||
| SmelC434/sm118 (SMc06565) | 1 | 1821211–1821366 | + | ZII | |||||||||||||
| SmelA001 (SMa6000) | 1 | 1002–1054 | + | RpoE2 | IZ/ZIII | ||||||||||||
| SmelA014 (SMa6078) | 1 | 206669–206772 | + | RpoH1/2 | ZII | ||||||||||||
| SmelA018 (SMa6091) | 1 | 234850–234930 | - | RpoE2 | ZIII | ||||||||||||
| SmelA019 | 1 | 235259–235355 | + | RpoH1/2 | ZII/IZ/ZIII | ||||||||||||
| SmelA020 (SMa6094) | 1 | 235393–235497 | - | RpoH1/2 | ZII/IZ/ZIII | ||||||||||||
| SmelA054 (SMa6367) | 1 | 911299–911374 | + | ZII | |||||||||||||
| SmelA056 (SMa6389) | 1 | 954480–954620 | - | ZII | |||||||||||||
| SmelC032 | 1 | 241172–241247 | + | ||||||||||||||
| SmelC749 (SMc07132) | 1 | 3383055–3383121 | - | ZIII | |||||||||||||
a sRNAs identified in the chromosome (SmelC) and megaplasmids pSymA (SmelA) and pSymB (SmelB). In bold, sRNAs with assigned functions as described in the text. b Nodule zones: ZII, invasion zone; IZ, bacteroid differentiation zone; ZIII, N fixation zone. Shadowed boxes stand for the presence/conservation of a given sRNA, +, positive/-, negative DNA strand.