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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)
[26, 27, 62, 67]
2 OT SMc04042< SMc04043< > NN – s70 y Sm Rl Re At ~80 nt duplet < 100 nt - sm8 = suhB [65, 67], this work
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 [26, 27]
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 [26, 27]
13 SP polA< SMc02851> > NN – s70 y Sm Rl Re At ~150 nt duplet, ~140 & ~90 nt - smrC7 = sra03 [26, 27]
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
  1. 1 Rfam, RNA families database [33, 67]; OT, IgR with annotated orphan terminator; tR, IgR flanking tRNAs; SP, sRNAPredictHT.
  2. 2 The transcribed strand is indicated (>, forward; <, reverse)
  3. 3 Putative promoter sequence detected by conservation in sequence alignment, search of consensus sequences or neural network promoter prediction. s70, sequence highly similar to the S. meliloti constitutive promoter consensus sequence [49]; NN, neural network promoter prediction [47]; PhoB, sequence detected with homology to the PhoB transcriptional regulator binding consensus [51].
  4. 4 Sm, Sinorhizobium medicae WSM419; Rl, Rhizobium leguminosarum biovar viciae 3841; Re, Rhizobium etli CFN42; At, Agrobacterium tumefaciens C58; Ml, Mesorhizobium loti MAFF303099; Oa, Ochrobactrum anthropi ATCC49188; Msp, Mesorhizobium sp. BNC1; Bo, Brucella ovis ATCC25840.
  5. 5 Approximate length of sRNA based on putative 5' and 3' ends.
  6. 6 PCR failed to amplify the IgR.
  7. 7 Detection on the oligonucleotide microarray Sm14kOLI. > and < denote the orientation of the detected signal (absolute M-value ≥ 2.5 represents an enrichment of small RNA transcripts). A, B, C, H, O and S denote the stress condition under which the signal was detected (A, acidic; B, basic; C, cold shock; H, heat shock; O, oxidative, S, saline). The coordinates of the oligonucleotide probes that gave positive signals are indicated in brackets. -, not detected under the conditions studied. (*), M-value ≥ 2.
  8. 8 Gene name as designated in the literature (smrC#, sra#) [26, 27]or according to our predictive scheme (sm#).