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A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq.

Pandey SP, Minesinger BK, Kumar J, Walker GC - Nucleic Acids Res. (2011)

Bottom Line: Similar to hfq, smc01113 regulates the accumulation of sRNAs as well as the target mRNAs.Our study provides the first line of evidence for such conceptual parallels.Furthermore, our investigation gives insights into the sRNA-mediated regulation of stress adaptation in S. meliloti.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.

ABSTRACT
The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share structural similarities with the MID domain of the Argonaute (AGO) proteins, and might similarly bind to a small-RNA (sRNA) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial sRNA pathway. Indeed, eliminating SMc01113/YbeY expression in Sinorhizobium meliloti produces symbiotic and physiological phenotypes strikingly similar to those of the hfq mutant. Hfq, an RNA chaperone, is central to bacterial sRNA-pathway. We evaluated the expression of 13 target genes in the smc01113 and hfq mutants. Further, we predicted the sRNAs that may potentially target these genes, and evaluated the accumulation of nine sRNAs in WT and smc01113 and hfq mutants. Similar to hfq, smc01113 regulates the accumulation of sRNAs as well as the target mRNAs. AGOs are central components of the eukaryotic sRNA machinery and conceptual parallels between the prokaryotic and eukaryotic sRNA pathways have long been drawn. Our study provides the first line of evidence for such conceptual parallels. Furthermore, our investigation gives insights into the sRNA-mediated regulation of stress adaptation in S. meliloti.

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Loss of hfq or SMc01113 similarly deregulates sRNA accumulation. The WT, smc01113 and hfq mutants, were grown in the RMM till exponential (sras03, 11, 16, 45, 47, 51 and 65) or stationary phase (sra35 and sra63), RNA was extracted and qPCR was performed. Transcript accumulation in the WT strain was fixed to 1 and relative transcript abundance to WT in the two mutants were evaluated as in Figures 3 and 4. ‘Single’ and ‘double asterisk’ shows significant difference at P ≤ 0.05 and P ≤ 0.01, respectively.
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Figure 5: Loss of hfq or SMc01113 similarly deregulates sRNA accumulation. The WT, smc01113 and hfq mutants, were grown in the RMM till exponential (sras03, 11, 16, 45, 47, 51 and 65) or stationary phase (sra35 and sra63), RNA was extracted and qPCR was performed. Transcript accumulation in the WT strain was fixed to 1 and relative transcript abundance to WT in the two mutants were evaluated as in Figures 3 and 4. ‘Single’ and ‘double asterisk’ shows significant difference at P ≤ 0.05 and P ≤ 0.01, respectively.

Mentions: Using qPCR analyses, we next investigated the relationship between changes in sRNA accumulation in smc01113 and hfq mutants, and the changes in the various potential mRNA targets. Of the nine sRNAs tested, the accumulation of eight sRNAs (sras 03, 11, 16, 45, 47, 51, 63 and 65) was similarly reduced in both the hfq and smc01113 mutants compared to the WT Rm1021 (Figure 5). In contrast, sra35 was strongly up-regulated in both hfq and smc01113 mutants relative to the WT Rm1021 strain (Figure 5). The pattern of the variation of sRNAs relative to particular mRNA target indicated both, inverse correlations (up-regulation of target corresponding to down-regulation of the sRNAs and vice versa) as well as direct correlations (change of target and the targeting sRNAs in the same direction; Figure 6A).Figure 5.


A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq.

Pandey SP, Minesinger BK, Kumar J, Walker GC - Nucleic Acids Res. (2011)

Loss of hfq or SMc01113 similarly deregulates sRNA accumulation. The WT, smc01113 and hfq mutants, were grown in the RMM till exponential (sras03, 11, 16, 45, 47, 51 and 65) or stationary phase (sra35 and sra63), RNA was extracted and qPCR was performed. Transcript accumulation in the WT strain was fixed to 1 and relative transcript abundance to WT in the two mutants were evaluated as in Figures 3 and 4. ‘Single’ and ‘double asterisk’ shows significant difference at P ≤ 0.05 and P ≤ 0.01, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113577&req=5

Figure 5: Loss of hfq or SMc01113 similarly deregulates sRNA accumulation. The WT, smc01113 and hfq mutants, were grown in the RMM till exponential (sras03, 11, 16, 45, 47, 51 and 65) or stationary phase (sra35 and sra63), RNA was extracted and qPCR was performed. Transcript accumulation in the WT strain was fixed to 1 and relative transcript abundance to WT in the two mutants were evaluated as in Figures 3 and 4. ‘Single’ and ‘double asterisk’ shows significant difference at P ≤ 0.05 and P ≤ 0.01, respectively.
Mentions: Using qPCR analyses, we next investigated the relationship between changes in sRNA accumulation in smc01113 and hfq mutants, and the changes in the various potential mRNA targets. Of the nine sRNAs tested, the accumulation of eight sRNAs (sras 03, 11, 16, 45, 47, 51, 63 and 65) was similarly reduced in both the hfq and smc01113 mutants compared to the WT Rm1021 (Figure 5). In contrast, sra35 was strongly up-regulated in both hfq and smc01113 mutants relative to the WT Rm1021 strain (Figure 5). The pattern of the variation of sRNAs relative to particular mRNA target indicated both, inverse correlations (up-regulation of target corresponding to down-regulation of the sRNAs and vice versa) as well as direct correlations (change of target and the targeting sRNAs in the same direction; Figure 6A).Figure 5.

Bottom Line: Similar to hfq, smc01113 regulates the accumulation of sRNAs as well as the target mRNAs.Our study provides the first line of evidence for such conceptual parallels.Furthermore, our investigation gives insights into the sRNA-mediated regulation of stress adaptation in S. meliloti.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.

ABSTRACT
The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share structural similarities with the MID domain of the Argonaute (AGO) proteins, and might similarly bind to a small-RNA (sRNA) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial sRNA pathway. Indeed, eliminating SMc01113/YbeY expression in Sinorhizobium meliloti produces symbiotic and physiological phenotypes strikingly similar to those of the hfq mutant. Hfq, an RNA chaperone, is central to bacterial sRNA-pathway. We evaluated the expression of 13 target genes in the smc01113 and hfq mutants. Further, we predicted the sRNAs that may potentially target these genes, and evaluated the accumulation of nine sRNAs in WT and smc01113 and hfq mutants. Similar to hfq, smc01113 regulates the accumulation of sRNAs as well as the target mRNAs. AGOs are central components of the eukaryotic sRNA machinery and conceptual parallels between the prokaryotic and eukaryotic sRNA pathways have long been drawn. Our study provides the first line of evidence for such conceptual parallels. Furthermore, our investigation gives insights into the sRNA-mediated regulation of stress adaptation in S. meliloti.

Show MeSH
Related in: MedlinePlus