Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti
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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
[edit]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
[edit]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 | 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
[edit]- ^ 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.
- ^ 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.
- ^ Patriarca EJ, Tatè R, Ferraioli S, Iaccarino M (2004). "Organogenesis of legume root nodules". Int Rev Cytol. International Review of Cytology. 234: 201–261. doi:10.1016/S0074-7696(04)34005-2. ISBN 9780123646385. PMID 15066376.
- ^ 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.
- ^ 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.
- ^ Probes giving hybridization signals are in boldface.
- ^ , strand given in the S. meliloti 1021 genome database; <, complementary strand.
- ^ Primary transcript
- ^ Processed transcript
- ^ 5’- and 3’-end experimentally mapped