Limits...
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.

Show MeSH

Related in: MedlinePlus

Sinorhizobium meliloti ORF, SMc01113/ybey, shares similarities with Ago protein. (A) Alignment of the protein sequences of the S. meliloti and E. coli homologs, SMc01113 and YbeY. (B) Alignment of protein sequences of the YbeY and Ago-Mid domain. Structural alignment of Ago-Mid domain (red) and YbeY (green) from N. crassa (C) and A. aeolicus AGO (2NUB) proteins (D). Manually docked PO4 shows potential interactions with the Arg59, K61 residues (E) in the positively charged cavity (F). (G) The lowest energy docked 4mer RNA (Cluspro 2.0 web server) onto YbeY surface fits nicely into the protein cavity, with negatively charged RNA backbone aligned towards the positively charged protein surface.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3113577&req=5

Figure 1: Sinorhizobium meliloti ORF, SMc01113/ybey, shares similarities with Ago protein. (A) Alignment of the protein sequences of the S. meliloti and E. coli homologs, SMc01113 and YbeY. (B) Alignment of protein sequences of the YbeY and Ago-Mid domain. Structural alignment of Ago-Mid domain (red) and YbeY (green) from N. crassa (C) and A. aeolicus AGO (2NUB) proteins (D). Manually docked PO4 shows potential interactions with the Arg59, K61 residues (E) in the positively charged cavity (F). (G) The lowest energy docked 4mer RNA (Cluspro 2.0 web server) onto YbeY surface fits nicely into the protein cavity, with negatively charged RNA backbone aligned towards the positively charged protein surface.

Mentions: SMc01113 homologs are found in nearly every bacterium including symbiotic and pathogenic bacteria [Supplementary Figure S1; (24,27)]. SMc01113 and its E. coli homolog, YbeY, show amino acid similarity of >70% (Figure 1A). Expression of the E. coli homolog complements the symbiotic defects of the smc01113 mutant of S. meliloti (24,51). Sequence and structural similarities of the YbeY to AGO protein were readily apparent when we performed homology studies with the YbeY. Sequence alignment of SMc01113/YbeY showed similarities with AGO protein sequences from Neurospora crassa, A. Aeolicus and other species. In particular, SMc01113/YbeY showed sequence similarity with the MID domain of the AGO protein (Figure 1). The MID domain contains the binding site for the 5′-end of the eukaryotic sRNAs, by binding to the PO4 group of a nucleic acid. The structure of E. coli YbeY (27) has been solved, as have the structures of AGO proteins from A. aeolicus and the Thermus thermophilus (32,33). Recently, the crystal structure of a eukaryotic MID-domain, recognizing the 5′-terminal phosphate of a guide RNA, has also been solved, and it highly resembles the previous structures of MID domains from other species (52).Figure 1.


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)

Sinorhizobium meliloti ORF, SMc01113/ybey, shares similarities with Ago protein. (A) Alignment of the protein sequences of the S. meliloti and E. coli homologs, SMc01113 and YbeY. (B) Alignment of protein sequences of the YbeY and Ago-Mid domain. Structural alignment of Ago-Mid domain (red) and YbeY (green) from N. crassa (C) and A. aeolicus AGO (2NUB) proteins (D). Manually docked PO4 shows potential interactions with the Arg59, K61 residues (E) in the positively charged cavity (F). (G) The lowest energy docked 4mer RNA (Cluspro 2.0 web server) onto YbeY surface fits nicely into the protein cavity, with negatively charged RNA backbone aligned towards the positively charged protein surface.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Sinorhizobium meliloti ORF, SMc01113/ybey, shares similarities with Ago protein. (A) Alignment of the protein sequences of the S. meliloti and E. coli homologs, SMc01113 and YbeY. (B) Alignment of protein sequences of the YbeY and Ago-Mid domain. Structural alignment of Ago-Mid domain (red) and YbeY (green) from N. crassa (C) and A. aeolicus AGO (2NUB) proteins (D). Manually docked PO4 shows potential interactions with the Arg59, K61 residues (E) in the positively charged cavity (F). (G) The lowest energy docked 4mer RNA (Cluspro 2.0 web server) onto YbeY surface fits nicely into the protein cavity, with negatively charged RNA backbone aligned towards the positively charged protein surface.
Mentions: SMc01113 homologs are found in nearly every bacterium including symbiotic and pathogenic bacteria [Supplementary Figure S1; (24,27)]. SMc01113 and its E. coli homolog, YbeY, show amino acid similarity of >70% (Figure 1A). Expression of the E. coli homolog complements the symbiotic defects of the smc01113 mutant of S. meliloti (24,51). Sequence and structural similarities of the YbeY to AGO protein were readily apparent when we performed homology studies with the YbeY. Sequence alignment of SMc01113/YbeY showed similarities with AGO protein sequences from Neurospora crassa, A. Aeolicus and other species. In particular, SMc01113/YbeY showed sequence similarity with the MID domain of the AGO protein (Figure 1). The MID domain contains the binding site for the 5′-end of the eukaryotic sRNAs, by binding to the PO4 group of a nucleic acid. The structure of E. coli YbeY (27) has been solved, as have the structures of AGO proteins from A. aeolicus and the Thermus thermophilus (32,33). Recently, the crystal structure of a eukaryotic MID-domain, recognizing the 5′-terminal phosphate of a guide RNA, has also been solved, and it highly resembles the previous structures of MID domains from other species (52).Figure 1.

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