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User:Rcrzarg/Small non-coding RNAs in the endosymbiotic diazotroph alfa-proteobacterium Sinorhizobium meliloti

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Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti

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SmrC7
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.

Introduction

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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

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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 morphological 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 α-proteobacteria, accumulated differentially in free-living and endosymbiotic bacteria. These findings anticipate a function for these sRNAs as trans-acting antisense riboregulators of α-proteobacteria-eukaryote interactions.[5].

Oligonuclotide probes used in Northern hybridizations
Candidate# Family name Alternative names Accession number Start End Predicted length (nt) Flanking genes Sequence[6] Target strand[7]
Smr7C αr7 Sra03/Sm13 AM939557 201639 201834 148-150[8]/106[9] polA/SMc02851 5'-ACCAGATGAGGACAAAGGCCTCATC-3' <
5'-GATGAGGCCTTTGTCCTCATCTGGT-3' >
Smr9C αr9 Sra32/Sm10 AM939558 1398397 1398274 149 SMc01933/proS 5'-CGCGTGATCTTTAATCCGTTTCCGG-3' <
5'-CCGGAAACGGATTAAAGATCACGCG-3' >
Smr14C αr14 Sm7 AM939559 1667641 1667484 123 SMc02051/tig 5'-TGCTTGATCTGATTGGCAACCGGGA-3' <
5'-TCCCGGTTGCCAATCAGATCAAGCA-3' >
Smr15C αr15-16 Sra41/Sm3 AM939560 1698744 1698610 115 SMc01226/SMc01225 5'-GAGGAGAAAGCCGCTAGATGCACCA-3' <
5'-TGGTGCATCTAGCGGCTTTCTCCTC-3' >
Smr16C αr15-16 Sra41/Sm3’ AM939561 1699021 1698812 121 SMc01226/SMc01225 5'-ACTGGGAGGAGAAGCCACCAAAGAT-3' <
5'-ATCTTTGGTGGCTTCTCCTCCCAGT-3' >
Smr22C αr22 SmB6 AM939564 2972265 2972118 139 SMc03975/SMc03976 5'-TACTAGGTAGGTGGGCACCGTATGC-3' <
5'-GCATACGGTGCCCACCTACCTAGTA-3' >
Smr35B αr35 SmelB053 AM939563 577732 577875 181 SMb20551/SMb20552 5'-TGGTAAGCGATGATGAGGAAGGTCG-3' <
5'-CGACCTTCCTCATCATCGCTTACCA-3' >
Smr45C αr45 6S/Sra56/Sm1 AM939562 3105374 3105169 161[10] 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: 93–113. doi:10.1080/10409230590918702. PMID 15814430.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 17971083.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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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