51
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Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase. PLoS Biol 2016; 14:e1002465. [PMID: 27224426 PMCID: PMC4880308 DOI: 10.1371/journal.pbio.1002465] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/19/2016] [Indexed: 01/07/2023] Open
Abstract
D-aminoacyl-tRNA deacylase (DTD) removes D-amino acids mischarged on tRNAs and is thus implicated in enforcing homochirality in proteins. Previously, we proposed that selective capture of D-aminoacyl-tRNA by DTD's invariant, cross-subunit Gly-cisPro motif forms the mechanistic basis for its enantioselectivity. We now show, using nuclear magnetic resonance (NMR) spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that DTD effectively misedits Gly-tRNAGly. High-resolution crystal structure reveals that the architecture of DTD's chiral proofreading site is completely porous to achiral glycine. Hence, L-chiral rejection is the only design principle on which DTD functions, unlike other chiral-specific enzymes such as D-amino acid oxidases, which are specific for D-enantiomers. Competition assays with elongation factor thermo unstable (EF-Tu) and DTD demonstrate that EF-Tu precludes Gly-tRNAGly misediting at normal cellular concentrations. However, even slightly higher DTD levels overcome this protection conferred by EF-Tu, thus resulting in significant depletion of Gly-tRNAGly. Our in vitro observations are substantiated by cell-based studies in Escherichia coli that show that overexpression of DTD causes cellular toxicity, which is largely rescued upon glycine supplementation. Furthermore, we provide direct evidence that DTD is an RNA-based catalyst, since it uses only the terminal 2'-OH of tRNA for catalysis without the involvement of protein side chains. The study therefore provides a unique paradigm of enzyme action for substrate selection/specificity by DTD, and thus explains the underlying cause of DTD's activity on Gly-tRNAGly. It also gives a molecular and functional basis for the necessity and the observed tight regulation of DTD levels, thereby preventing cellular toxicity due to misediting.
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52
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Richardson CJ, First EA. Hyperactive Editing Domain Variants Switch the Stereospecificity of Tyrosyl-tRNA Synthetase. Biochemistry 2016; 55:2526-37. [DOI: 10.1021/acs.biochem.6b00157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charles J. Richardson
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
| | - Eric A. First
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
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53
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Melo Czekster C, Robertson WE, Walker AS, Söll D, Schepartz A. In Vivo Biosynthesis of a β-Amino Acid-Containing Protein. J Am Chem Soc 2016; 138:5194-7. [PMID: 27086674 DOI: 10.1021/jacs.6b01023] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
It has recently been reported that ribosomes from erythromycin-resistant Escherichia coli strains, when isolated in S30 extracts and incubated with chemically mis-acylated tRNA, can incorporate certain β-amino acids into full length DHFR in vitro. Here we report that wild-type E. coli EF-Tu and phenylalanyl-tRNA synthetase collaborate with these mutant ribosomes and others to incorporate β(3)-Phe analogs into full length DHFR in vivo. E. coli harboring the most active mutant ribosomes are robust, with a doubling time only 14% longer than wild-type. These results reveal the unexpected tolerance of E. coli and its translation machinery to the β(3)-amino acid backbone and should embolden in vivo selections for orthogonal translational machinery components that incorporate diverse β-amino acids into proteins and peptides. E. coli harboring mutant ribosomes may possess the capacity to incorporate many non-natural, non-α-amino acids into proteins and other sequence-programmed polymeric materials.
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Affiliation(s)
- Clarissa Melo Czekster
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Wesley E Robertson
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Allison S Walker
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Dieter Söll
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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54
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Richardson CJ, First EA. Altering the Enantioselectivity of Tyrosyl-tRNA Synthetase by Insertion of a Stereospecific Editing Domain. Biochemistry 2016; 55:1541-53. [DOI: 10.1021/acs.biochem.5b01167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charles J. Richardson
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
| | - Eric A. First
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
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55
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Wang J, Kwiatkowski M, Forster AC. Kinetics of tRNAPyl-mediated amber suppression inEscherichia colitranslation reveals unexpected limiting steps and competing reactions. Biotechnol Bioeng 2016; 113:1552-9. [DOI: 10.1002/bit.25917] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular Biology; Uppsala University; Husargatan 3, Box 596 Uppsala 75124 Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular Biology; Uppsala University; Husargatan 3, Box 596 Uppsala 75124 Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular Biology; Uppsala University; Husargatan 3, Box 596 Uppsala 75124 Sweden
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56
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Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Nat Chem Biol 2016; 12:153-8. [PMID: 26727240 PMCID: PMC5726394 DOI: 10.1038/nchembio.1998] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/10/2015] [Indexed: 11/26/2022]
Abstract
Regulation of gene expression in response to the changing environment is critical for cell survival. For instance, binding of macrolide antibiotics to the ribosome promote the translation arrest at the leader ORFs ermCL and ermBL necessary for inducing antibiotic resistance genes ermC and ermB. Cladinose-containing macrolides, like erythromycin (ERY), but not ketolides e.g., telithromycin (TEL), arrest translation of ermCL, while either ERY or TEL stall ermBL translation. How the ribosome distinguishes between chemically similar small molecules is unknown. We show that single amino acid changes in the leader peptide switch the specificity of recognition of distinct molecules, triggering gene activation in response to only ERY, only TEL, to both antibiotics, or preventing stalling altogether. Thus, the ribosomal response to chemical signals can be modulated by minute changes in the nascent peptide, suggesting that protein sequences could have been optimized for rendering translation sensitive to environmental cues.
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57
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Wang J, Kwiatkowski M, Forster AC. Kinetics of Ribosome-Catalyzed Polymerization Using Artificial Aminoacyl-tRNA Substrates Clarifies Inefficiencies and Improvements. ACS Chem Biol 2015; 10:2187-92. [PMID: 26191973 DOI: 10.1021/acschembio.5b00335] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomal synthesis of polymers of unnatural amino acids (AAs) is limited by low incorporation efficiencies using the artificial AA-tRNAs, but the kinetics have yet to be studied. Here, kinetics were performed on five consecutive incorporations using various artificial AA-tRNAs with all intermediate products being analyzed. Yields within a few seconds displayed similar trends to our prior yields after 30 min without preincubation, demonstrating the relevance of fast kinetics to traditional long-incubation translations. Interestingly, the two anticodon swaps were much less inhibitory in the present optimized system, which should allow more flexibility in the engineering of artificial AA-tRNAs. The biggest kinetic defect was caused by the penultimate dC introduced from the standard, chemoenzymatic, charging method. This prompted peptidyl-tRNA drop-off, decreasing processivities during five consecutive AA incorporations. Indeed, two tRNA charging methods that circumvented the dC dramatically improved efficiencies of ribosomal, consecutive, unnatural AA incorporations to give near wild-type kinetics.
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Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
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58
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Maini R, Chowdhury SR, Dedkova LM, Roy B, Daskalova SM, Paul R, Chen S, Hecht SM. Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids. Biochemistry 2015; 54:3694-706. [PMID: 25982410 PMCID: PMC4472090 DOI: 10.1021/acs.biochem.5b00389] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/16/2015] [Indexed: 02/04/2023]
Abstract
In an earlier study, β³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different β-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate β-amino acids into DHFR, in spite of the use of a single puromycin for the selection of the individual clones. In this study, we examine the extent to which the structure of the β³-puromycin employed for ribosome selection influences the regio- and stereochemical preferences of the modified ribosomes during protein synthesis; the mechanistic probe was a single suppressor tRNA(CUA) activated with each of four methyl-β-alanine isomers (1-4). The modified ribosomes were found to incorporate each of the four isomeric methyl-β-alanines into DHFR but exhibited a preference for incorporation of 3(S)-methyl-β-alanine (β-mAla; 4), i.e., the isomer having the same regio- and stereochemistry as the O-methylated β-tyrosine moiety of β³-puromycin. Also conducted were a selection of clones that are responsive to β²-puromycin and a demonstration of reversal of the regio- and stereochemical preferences of these clones during protein synthesis. These results were incorporated into a structural model of the modified regions of 23S rRNA, which included in silico prediction of a H-bonding network. Finally, it was demonstrated that incorporation of 3(S)-methyl-β-alanine (β-mAla; 4) into a short α-helical region of the nucleic acid binding domain of hnRNP LL significantly stabilized the helix without affecting its DNA binding properties.
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MESH Headings
- Alanine/analogs & derivatives
- Alanine/chemistry
- Alanine/metabolism
- Escherichia coli/enzymology
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/biosynthesis
- Heterogeneous-Nuclear Ribonucleoprotein L/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/genetics
- Humans
- Hydrogen Bonding
- Models, Molecular
- Molecular Dynamics Simulation
- Mutant Proteins/biosynthesis
- Mutant Proteins/chemistry
- Mutant Proteins/genetics
- Nucleotide Motifs
- Peptidyl Transferases/genetics
- Peptidyl Transferases/metabolism
- Protein Conformation
- Protein Stability
- Puromycin/analogs & derivatives
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Ribosomes/metabolism
- Stereoisomerism
- Substrate Specificity
- Tetrahydrofolate Dehydrogenase/biosynthesis
- Tetrahydrofolate Dehydrogenase/chemistry
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sasha M. Daskalova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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