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Small non-coding RNAs in Sinorhizobium meliloti

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Smr7CSmr9CSmr14C2Smr15C1 & Smr15C2Smr22CSmr35BSmr45C
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 red arrows and the flanking ORFs by blue arrows. Numbers indicate co-ordinates in the S. meliloti 1021 genome database. Experimentally determined 5'- and 3'-ends of the Smr transcripts are indicated with numbers. 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 green dots above the horizontal lines. The grey arrowhead indicates the processing site for Smr7C.

Within genetics, 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 Alphaproteobacteria includes Gram-negative microorganisms with diverse life styles; frequently involving long-term interactions with higher eukaryotes.[2]

Sinorhizobium meliloti

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Sinorhizobium meliloti is an agronomically relevant α-proteobacterium able to induce the formation of new specialized organs, the so-called nodules, in the roots of its cognate legume hosts (i.e. some Medicago species).[3] Within the nodule cells bacteria undergo a morphology differentiation to bacteroid, their endosymbiotic nitrogen-fixing competent form.[4] Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate.

Discovery

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Two complementary computational screens, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the intergenic regions IGRs of S. meliloti. Verification of eQRNA/RNAz predictions by Northern hybridization and RACE mapping led to the identification of eight previously unknown genes, with recognizable promoter and termination signatures, expressing small transcripts. These new genomic loci were referred to as smr, for S. meliloti RNA. Seven of the Smr transcripts, which conservation is restricted to phylogenetically related Alphaproteobacteria, accumulated differentially in free-living and endosymbiotic bacteria. These findings anticipate a function for these sRNAs as trans-acting antisense riboregulators of Alphaproteobacteria-eukaryote interactions.[5]

sRNA families summary
sRNA Family name Alternative names Accession number 5’-end 3’-end Predicted length (nt) Flanking genes Sequence[6] Target strand[7]
Smr7C αr7 Sra03/Sm13/SmelC023 AM939557 201679 201828 150[8]/106[9] polA/SMc02851 5'-ACCAGATGAGGACAAAGGCCTCATC-3' <
5'-GATGAGGCCTTTGTCCTCATCTGGT-3' >
Smr9C αr9 Sra32/Sm10/SmelC289 AM939558 1398425 1398277 149 SMc01933/proS 5'-CGCGTGATCTTTAATCCGTTTCCGG-3' <
5'-CCGGAAACGGATTAAAGATCACGCG-3' >
Smr14C2 αr14 Sm7/SmelC397 AM939559 1667613 1667491 123 SMc02051/tig 5'-TGCTTGATCTGATTGGCAACCGGGA-3' <
5'-TCCCGGTTGCCAATCAGATCAAGCA-3' >
Smr15C1 αr15 Sra41/Sm3/SmelC411 AM939560 1698731 1698617 115 SMc01226/SMc01225 5'-GAGGAGAAAGCCGCTAGATGCACCA-3' <
5'-TGGTGCATCTAGCGGCTTTCTCCTC-3' >
Smr15C2 αr15 Sra41/Sm3’/SmelC412 AM939561 1698817 1698937 121 SMc01226/SMc01225 5'-ACTGGGAGGAGAAGCCACCAAAGAT-3' <
5'-ATCTTTGGTGGCTTCTCCTCCCAGT-3' >
Smr22C αr22 Sra56/Sm1/SmelC667/6S AM939564 2972251 2972091 161 [10] SMc03975/SMc03976 5'-TACTAGGTAGGTGGGCACCGTATGC-3' <
5'-GCATACGGTGCCCACCTACCTAGTA-3' >
Smr35B αr35 SmB6/SmelC053 AM939563 577730 577868 139 SMb20551/SMb20552 5'-TGGTAAGCGATGATGAGGAAGGTCG-3' <
5'-CGACCTTCCTCATCATCGCTTACCA-3' >
Smr45C αr45 SmelC706 AM939562 3105445 3105265 181 SMc02983/SMc02984 5'-CCGCACCGTCGTTGCTTCAAGATGT-3' <
5'-ACATCTTGAAGCAACGACGGTGCGG-3' >

References

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  1. ^ Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit Rev Biochem Mol Biol. 40 (2): 93–113. doi:10.1080/10409230590918702. PMID 15814430. S2CID 22677443.
  2. ^ Batut J; Andersson SGE; O’Callaghan D (2004). "The evolution of chronic infection strategies in the α-proteobacteria". Nat Rev Microbiol. 2 (12): 933–945. doi:10.1038/nrmicro1044. PMID 15550939. S2CID 6135682.
  3. ^ Patriarca EJ, Tatè R, Ferraioli S, Iaccarino M (2004). "Organogenesis of Legume Root Nodules". International Review of Cytology Volume 234. Vol. 234. pp. 201–261. doi:10.1016/S0074-7696(04)34005-2. ISBN 9780123646385. PMID 15066376. {{cite book}}: |journal= ignored (help)
  4. ^ Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC (2007). "How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model". Nat Rev Microbiol. 5 (8): 619–633. doi:10.1038/nrmicro1705. PMC 2766523. PMID 17632573.
  5. ^ 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. PMC 2780559. PMID 17971083.
  6. ^ Probes giving hybridization signals are in boldface.
  7. ^ , strand given in the S. meliloti 1021 genome database; <, complementary strand.
  8. ^ Primary transcript
  9. ^ Processed transcript
  10. ^ 5’- and 3’-end experimentally mapped
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