User:Rcrzarg/Small non-coding RNAs in the legume Sinorhizobium meliloti

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Genomic regions of the identified S. meliloti sRNA genes. The schematics (drawn to scale) summarize the bioinformatic predictions and the results of the experimental mapping. The smr genes are represented by grey arrows and the flanking ORFs by the dotted black arrows. Numbers indicate co-ordinates in the S. meliloti 1021 genome database. Experimentally determined 5'- and 3'-ends of the Smr transcripts are boxed. 3'-ends of the differentially expressed sRNAs were assigned to the last U in the consecutive stretch after extended stem-loops of Rho-independent terminators, which are denoted by black dots above the horizontal lines. The white arrowhead indicates the processing site for SmrC7. Putative σ70 promoters are indicated by single arrowheads, and putative transcription factors binding sites by double arrowheads.


Post-genomic research has rendered bacterial small non-coding RNAs (sRNAs) as major players in post-transcriptional regulation of gene expression in response to environmental stimuli[1]. The α-subdivision of the Proteobacteria includes Gram-negative microorganisms with diverse life styles; frequently involving long-term interactions with higher eukaryotes[2].

Sinorhizobium meliloti[edit]

Sinorhizobium meliloti is a α-proteobacteria representative able to induce the formation of new specialized organs, the so-called nodules, in the roots of its cognate legume hosts. Within the nodule cells bacteria undergo a morphological differentiation to bacteroid, their endosymbiotic nitrogen-fixing competent form[3]. S. meliloti is an agronomically relevant microorganism that establishes a nitrogen-fixing endosymbiosis with various forage legumes, including alfalfa (Medicago sativa L). In the proximity of the root hairs, the plant flavone luteolin specifically induces the synthesis and secretion of lipo-quitooligosaccharide signal molecules (Nod factors) in S. meliloti upon the transcriptional activation of the nodulation (Nod) genes by the NodD1/NodD2 proteins [4][5]. Subsequently, bacterial Nod factors trigger infection and organogenesis of new specialized organs in the plant, the so-called root nodules, where the microsymbiont differentiates into its nitrogen-fixing competent form, the bacteroid, within the plant cell. Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate.


Two complementary strategies, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the IGRs of S. meliloti. Verification of eQRNA/RNAz predictions by Northern hybridization and RACE mapping led to the identification of eight previously unknown loci expressing small transcripts and organized in independent transcription units. Seven of the identified sRNAs are differentially regulated in free-living and symbiotic bacteria, which predicts novel regulatory functions for bacterial sRNAs in the α-proteobacteria–eukaryotes interactions[6].

Oligonuclotide probes used in Northern hybridizations
Candidate# Alternative names Accession number Start End Predicted length (nt) Flanking genes Sequence[7] Target strand[8]
SmrC7 Sra03/Sm13 AM939557 201639 201834 148-150[9]/106[10] polA/SMc02851 5'-ACCAGATGAGGACAAAGGCCTCATC-3' <
SmrC9 Sra32/Sm10 AM939558 1398397 1398274 149 SMc01933/proS 5'-CGCGTGATCTTTAATCCGTTTCCGG-3' <
SmrC14 Sm7 AM939559 1667641 1667484 123 SMc02051/tig 5'-TGCTTGATCTGATTGGCAACCGGGA-3' <
SmrC15 Sra41/Sm3 AM939560 1698744 1698610 115 SMc01226/SMc01225 5'-GAGGAGAAAGCCGCTAGATGCACCA-3' <
SmrC16 Sra41/Sm3’ AM939561 1699021 1698812 121 SMc01226/SMc01225 5'-ACTGGGAGGAGAAGCCACCAAAGAT-3' <
SmrC22 SmB6 AM939564 2972265 2972118 139 SMc03975/SMc03976 5'-TACTAGGTAGGTGGGCACCGTATGC-3' <
SmrB35 - AM939563 577732 577875 181 SMb20551/SMb20552 5'-TGGTAAGCGATGATGAGGAAGGTCG-3' <
SmrC45 6S/Sra56/Sm1 AM939562 3105374 3105169 161[11] SMc02983/SMc02984 5'-CCGCACCGTCGTTGCTTCAAGATGT-3' <


  1. ^ Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit Rev Biochem Mol Biol. 40: 93–113. doi:10.1080/10409230590918702. PMID 15814430. 
  2. ^ Batut J, Andersson SGE, O’Callaghan D (2004). "The evolution of chronic infection strategies in the α-proteobacteria". Nat Rev. 2: 933–945. doi:10.1038/nrmicro1044. PMID 15550939. 
  3. ^ Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC (2007). "How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model". Nat Rev. 5: 619–633. doi:10.1038/nrmicro1705. PMID 17632573. 
  4. ^ Göttfert M (1993). "Regulation and function of rhizobial nodulation genes". FEMS Microbiol Rev. 10 (1-2): 39–63. PMID 8431309. 
  5. ^ Patriarca EJ, Tatè R, Ferraioli S, Iaccarino M (2004). "Organogenesis of legume root nodules". Int Rev Cytol. 234: 201–261. doi:10.1016/S0074-7696(04)34005-2. PMID 15066376. 
  6. ^ del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI (2007). "Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics". Mol Microbiol. 66 (5): 1080–1091. doi:10.1111/j.1365-2958.2007.05978.x. PMID 17971083. 
  7. ^ Probes giving hybridization signals are in boldface.
  8. ^ >, strand given in the S. meliloti 1021 genome database; <, complementary strand.
  9. ^ Primary transcript
  10. ^ Processed transcript
  11. ^ 5’- and 3’-end experimentally mapped