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Pavelich IJ, Maehigashi T, Hoffer ED, Ruangprasert A, Miles SJ, Dunham CM. Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability. Nucleic Acids Res 2019; 47:10400-10413. [PMID: 31501867 PMCID: PMC6821326 DOI: 10.1093/nar/gkz760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 11/30/2022] Open
Abstract
Chromosomally-encoded toxin-antitoxin complexes are ubiquitous in bacteria and regulate growth through the release of the toxin component typically in a stress-dependent manner. Type II ribosome-dependent toxins adopt a RelE-family RNase fold and inhibit translation by degrading mRNAs while bound to the ribosome. Here, we present biochemical and structural studies of the Escherichia coli YoeB toxin interacting with both a UAA stop and an AAU sense codon in pre- and post-mRNA cleavage states to provide insights into possible mRNA substrate selection. Both mRNAs undergo minimal changes during the cleavage event in contrast to type II ribosome-dependent RelE toxin. Further, the 16S rRNA decoding site nucleotides that monitor the mRNA in the aminoacyl(A) site adopt different orientations depending upon which toxin is present. Although YoeB is a RelE family member, it is the sole ribosome-dependent toxin that is dimeric. We show that engineered monomeric YoeB is active against mRNAs bound to both the small and large subunit. However, the stability of monomeric YoeB is reduced ∼20°C, consistent with potential YoeB activation during heat shock in E. coli as previously demonstrated. These data provide a molecular basis for the ability of YoeB to function in response to thermal stress.
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Affiliation(s)
- Ian J Pavelich
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric D Hoffer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Stacey J Miles
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
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Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Nucleic Acids Res 2019; 47:1557-1563. [PMID: 30476222 PMCID: PMC6379664 DOI: 10.1093/nar/gky1178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 01/18/2023] Open
Abstract
Decoding is thought to be governed by a conformational transition in the ribosome—open (off) to closed (on)—that occurs upon codon–anticodon pairing in the A site. Ribosomal ambiguity (ram) mutations increase miscoding and map to disparate regions, consistent with a role for ribosome dynamics in decoding, yet precisely how these mutations act has been unclear. Here, we solved crystal structures of 70S ribosomes harboring 16S ram mutations G299A and G347U in the absence A-site tRNA (A-tRNA) and in the presence of a near-cognate anticodon stem-loop (ASL). In the absence of an A-tRNA, each of the mutant ribosomes exhibits a partially closed (on) state. In the 70S-G347U structure, the 30S shoulder is rotated inward and intersubunit bridge B8 is disrupted. In the 70S-G299A structure, the 30S shoulder is rotated inward and decoding nucleotide G530 flips into the anti conformation. Both of these mutant ribosomes adopt the fully closed (on) conformation in the presence of near-cognate A-tRNA, just as they do with cognate A-tRNA. Thus, these ram mutations act by promoting the open (off) to closed (on) transition, albeit in somewhat distinct ways. This work reveals the functional importance of 30S shoulder rotation for productive aminoacylated-tRNA incorporation.
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Affiliation(s)
- Eric D Hoffer
- Department of Biochemistry and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tatsuya Maehigashi
- Department of Biochemistry and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Correspondence may also be addressed to Kurt Fredrick. Tel: +1 614 292 6679; Fax: +1 614 292 8120;
| | - Christine M Dunham
- Department of Biochemistry and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- To whom correspondence should be addressed. Tel: +1 404 712 1756; Fax: +1 404 727 2738; E-mail:
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Rodnina MV, Fischer N, Maracci C, Stark H. Ribosome dynamics during decoding. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0182. [PMID: 28138068 PMCID: PMC5311926 DOI: 10.1098/rstb.2016.0182] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 11/24/2022] Open
Abstract
Elongation factors Tu (EF-Tu) and SelB are translational GTPases that deliver aminoacyl-tRNAs (aa-tRNAs) to the ribosome. In each canonical round of translation elongation, aa-tRNAs, assisted by EF-Tu, decode mRNA codons and insert the respective amino acid into the growing peptide chain. Stop codons usually lead to translation termination; however, in special cases UGA codons are recoded to selenocysteine (Sec) with the help of SelB. Recruitment of EF-Tu and SelB together with their respective aa-tRNAs to the ribosome is a multistep process. In this review, we summarize recent progress in understanding the role of ribosome dynamics in aa-tRNA selection. We describe the path to correct codon recognition by canonical elongator aa-tRNA and Sec-tRNASec and discuss the local and global rearrangements of the ribosome in response to correct and incorrect aa-tRNAs. We present the mechanisms of GTPase activation and GTP hydrolysis of EF-Tu and SelB and summarize what is known about the accommodation of aa-tRNA on the ribosome after its release from the elongation factor. We show how ribosome dynamics ensures high selectivity for the cognate aa-tRNA and suggest that conformational fluctuations, induced fit and kinetic discrimination play major roles in maintaining the speed and fidelity of translation. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
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