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. The Alphaproteobacteria includes Gram-negative microorganisms with diverse life styles; frequently involving long-term interactions with higher eukaryotes.
Sinorhizobium meliloti 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). Within the nodule cells bacteria undergo a morphology differentiation to bacteroid, their endosymbiotic nitrogen-fixing competent form. Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate.
Discovery 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.
+ sRNA families summary sRNA Family name Alternative names Accession number 5’-end 3’-end Predicted length (nt) Flanking genes SequenceProbes giving hybridization signals are in boldface. Target strand, strand given in the S. meliloti 1021 genome database; <, complementary strand. Smr7C αr7 Sra03/Sm13/SmelC023 AM939557 201679 201828 150Primary transcript/106Processed transcript 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' > Sra56/Sm1/SmelC667/6S AM939564 2972251 2972091 161 5’- and 3’-end experimentally mapped 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' >
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