Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content>
ABSTRACT YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2016-12-01
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| Series: | mBio |
| Online Access: | https://journals.asm.org/doi/10.1128/mBio.01785-16 |
| _version_ | 1819199709454008320 |
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| author | Maarten Vercruysse Caroline Köhrer Yang Shen Sandra Proulx Anubrata Ghosal Bryan W. Davies Uttam L. RajBhandary Graham C. Walker |
| author_facet | Maarten Vercruysse Caroline Köhrer Yang Shen Sandra Proulx Anubrata Ghosal Bryan W. Davies Uttam L. RajBhandary Graham C. Walker |
| author_sort | Maarten Vercruysse |
| collection | DOAJ |
| description | ABSTRACT YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY’s involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3′ end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY—and not amino acids known to be important for YbeY’s RNase activity—functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results. IMPORTANCE Ribosomes are ribonucleoprotein complexes responsible for a key cellular function, protein synthesis. Their assembly is a highly coordinated process of RNA cleavage, RNA posttranscriptional modification, RNA conformational changes, and protein-binding events. Many open questions remain after almost 5 decades of study, including which RNase is responsible for final processing of the 16S rRNA 3′ end. The highly conserved RNase YbeY, belonging to a core set of RNases essential in many bacteria, was previously shown to participate in 16S rRNA processing and ribosome quality control. However, detailed mechanistic insight into YbeY’s ribosome-associated function has remained elusive. This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era). In addition, we identified key residues of YbeY involved in the interaction with S11 and propose a possible binding mode of YbeY to the ribosome using in silico docking. |
| first_indexed | 2024-12-23T03:20:39Z |
| format | Article |
| id | doaj.art-17b5a820c273493788ed9a01f2254ec3 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-12-23T03:20:39Z |
| publishDate | 2016-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-17b5a820c273493788ed9a01f2254ec32022-12-21T18:02:00ZengAmerican Society for MicrobiologymBio2150-75112016-12-017610.1128/mBio.01785-16Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content>Maarten Vercruysse0Caroline Köhrer1Yang Shen2Sandra Proulx3Anubrata Ghosal4Bryan W. Davies5Uttam L. RajBhandary6Graham C. Walker7Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USADepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USADepartment of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas, USADepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USADepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USADepartment of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USADepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USADepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USAABSTRACT YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY’s involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3′ end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY—and not amino acids known to be important for YbeY’s RNase activity—functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results. IMPORTANCE Ribosomes are ribonucleoprotein complexes responsible for a key cellular function, protein synthesis. Their assembly is a highly coordinated process of RNA cleavage, RNA posttranscriptional modification, RNA conformational changes, and protein-binding events. Many open questions remain after almost 5 decades of study, including which RNase is responsible for final processing of the 16S rRNA 3′ end. The highly conserved RNase YbeY, belonging to a core set of RNases essential in many bacteria, was previously shown to participate in 16S rRNA processing and ribosome quality control. However, detailed mechanistic insight into YbeY’s ribosome-associated function has remained elusive. This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era). In addition, we identified key residues of YbeY involved in the interaction with S11 and propose a possible binding mode of YbeY to the ribosome using in silico docking.https://journals.asm.org/doi/10.1128/mBio.01785-16 |
| spellingShingle | Maarten Vercruysse Caroline Köhrer Yang Shen Sandra Proulx Anubrata Ghosal Bryan W. Davies Uttam L. RajBhandary Graham C. Walker Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> mBio |
| title | Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> |
| title_full | Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> |
| title_fullStr | Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> |
| title_full_unstemmed | Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> |
| title_short | Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in <named-content content-type="genus-species">Escherichia coli</named-content> |
| title_sort | identification of ybey protein interactions involved in 16s rrna maturation and stress regulation in named content content type genus species escherichia coli named content |
| url | https://journals.asm.org/doi/10.1128/mBio.01785-16 |
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