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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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sRNA-target relation in S. meliloti and conservation of motifs in sRNAs and their possible targets in other related rhizobium species. (A) Correlation between the direction of accumulation of the sRNAs and their target in the S. meliloti strains mutated for hfq and SMc01113, as derived from Figures 3–5. Red and green shows inverse correlation, and yellow shows that the sRNAs and their predicted targets show accumulation in the similar direction. (B) Schematic representation of the three sra16 binding sites in the dppA1 gene. Sra16 was down-regulated whereas dppA1 was up-regulated in the hfq and smc01113 mutants. (C) Conservation of the target-sRNA motif sequences in the three related rhizobium species. Weblogos were generated as described in the text.
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Figure 6: sRNA-target relation in S. meliloti and conservation of motifs in sRNAs and their possible targets in other related rhizobium species. (A) Correlation between the direction of accumulation of the sRNAs and their target in the S. meliloti strains mutated for hfq and SMc01113, as derived from Figures 3–5. Red and green shows inverse correlation, and yellow shows that the sRNAs and their predicted targets show accumulation in the similar direction. (B) Schematic representation of the three sra16 binding sites in the dppA1 gene. Sra16 was down-regulated whereas dppA1 was up-regulated in the hfq and smc01113 mutants. (C) Conservation of the target-sRNA motif sequences in the three related rhizobium species. Weblogos were generated as described in the text.

Mentions: Informed by these considerations, we performed a bioinformatic analysis to identify S. meliloti sRNAs (17) that could potentially bind to the genes differentially regulated in the hfq and smc01113 mutants. Our analysis revealed that these genes have a large number of potential sRNA binding sites (Supplementary Table S1). Genes with multiple sRNA-binding sites of >10 nt, for specific sRNAs were identified; e.g. dppA1 had three different complementary sites for the sRNA, sra16 (Figure 6B). It was strikingly apparent that a single sRNA has the potential to target more than one gene, and that a single gene can be targeted by several sRNAs (Supplementary Table S1; Figure 6A). For instance, sodC had a 13-nt sRNA complementary site for one sRNA, 12-nt seeds for five sRNAs, and 11-nt seeds for eight sRNAs (Supplementary Table S1). The potential for single sRNA to target multiple mRNAs is also striking. For example, our analysis indicated that sra35 potentially targets three genes, sra03 may target six genes and sra16 may target 10 genes (Supplementary Table S1, Figure 6A). Similar observations of ‘one-to-many’ sRNA–mRNA interactions, common in eukaryotes [e.g. (39)], have been previously reported in some other bacterial species, and would have profound effects on cellular physiology and stress adaptation (43,65,68–70). Using a combination of such criteria of longest seed length and potential to target several genes, we selected 9 sRNAs for their expression analysis in WT, a smc01113 mutant and an hfq mutant.


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)

sRNA-target relation in S. meliloti and conservation of motifs in sRNAs and their possible targets in other related rhizobium species. (A) Correlation between the direction of accumulation of the sRNAs and their target in the S. meliloti strains mutated for hfq and SMc01113, as derived from Figures 3–5. Red and green shows inverse correlation, and yellow shows that the sRNAs and their predicted targets show accumulation in the similar direction. (B) Schematic representation of the three sra16 binding sites in the dppA1 gene. Sra16 was down-regulated whereas dppA1 was up-regulated in the hfq and smc01113 mutants. (C) Conservation of the target-sRNA motif sequences in the three related rhizobium species. Weblogos were generated as described in the text.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
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Figure 6: sRNA-target relation in S. meliloti and conservation of motifs in sRNAs and their possible targets in other related rhizobium species. (A) Correlation between the direction of accumulation of the sRNAs and their target in the S. meliloti strains mutated for hfq and SMc01113, as derived from Figures 3–5. Red and green shows inverse correlation, and yellow shows that the sRNAs and their predicted targets show accumulation in the similar direction. (B) Schematic representation of the three sra16 binding sites in the dppA1 gene. Sra16 was down-regulated whereas dppA1 was up-regulated in the hfq and smc01113 mutants. (C) Conservation of the target-sRNA motif sequences in the three related rhizobium species. Weblogos were generated as described in the text.
Mentions: Informed by these considerations, we performed a bioinformatic analysis to identify S. meliloti sRNAs (17) that could potentially bind to the genes differentially regulated in the hfq and smc01113 mutants. Our analysis revealed that these genes have a large number of potential sRNA binding sites (Supplementary Table S1). Genes with multiple sRNA-binding sites of >10 nt, for specific sRNAs were identified; e.g. dppA1 had three different complementary sites for the sRNA, sra16 (Figure 6B). It was strikingly apparent that a single sRNA has the potential to target more than one gene, and that a single gene can be targeted by several sRNAs (Supplementary Table S1; Figure 6A). For instance, sodC had a 13-nt sRNA complementary site for one sRNA, 12-nt seeds for five sRNAs, and 11-nt seeds for eight sRNAs (Supplementary Table S1). The potential for single sRNA to target multiple mRNAs is also striking. For example, our analysis indicated that sra35 potentially targets three genes, sra03 may target six genes and sra16 may target 10 genes (Supplementary Table S1, Figure 6A). Similar observations of ‘one-to-many’ sRNA–mRNA interactions, common in eukaryotes [e.g. (39)], have been previously reported in some other bacterial species, and would have profound effects on cellular physiology and stress adaptation (43,65,68–70). Using a combination of such criteria of longest seed length and potential to target several genes, we selected 9 sRNAs for their expression analysis in WT, a smc01113 mutant and an hfq mutant.

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