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Mukai T, Reynolds NM, Crnković A, Söll D. Bioinformatic Analysis Reveals Archaeal tRNA Tyr and tRNA Trp Identities in Bacteria. Life (Basel) 2017; 7:life7010008. [PMID: 28230768 PMCID: PMC5370408 DOI: 10.3390/life7010008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 12/01/2022] Open
Abstract
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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Moutiez M, Schmitt E, Seguin J, Thai R, Favry E, Belin P, Mechulam Y, Gondry M. Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases. Nat Commun 2014; 5:5141. [DOI: 10.1038/ncomms6141] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/02/2014] [Indexed: 11/09/2022] Open
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Moutiez M, Seguin J, Fonvielle M, Belin P, Jacques IB, Favry E, Arthur M, Gondry M. Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei. Nucleic Acids Res 2014; 42:7247-58. [PMID: 24782519 PMCID: PMC4066775 DOI: 10.1093/nar/gku348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNA substrates in a sequential ping-pong mechanism to form a cyclodipeptide. The crystal structures of three CDPSs have been determined and all show a Rossmann-fold domain similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs). Structural features and mutational analyses however suggest that CDPSs and aaRSs interact differently with their tRNA substrates. We used AlbC from Streptomyces noursei that mainly produces cyclo(l-Phe-l-Leu) to investigate the interaction of a CDPS with its substrates. We demonstrate that Phe-tRNAPhe is the first substrate accommodated by AlbC. Its binding to AlbC is dependent on basic residues located in the helix α4 that form a basic patch at the surface of the protein. AlbC does not use all of the Leu-tRNALeu isoacceptors as a second substrate. We show that the G1-C72 pair of the acceptor stem is essential for the recognition of the second substrate. Substitution of D163 located in the loop α6–α7 or D205 located in the loop β6–α8 affected Leu-tRNALeu isoacceptors specificity, suggesting the involvement of these residues in the binding of the second substrate. This is the first demonstration that the two substrates of CDPSs are accommodated in different binding sites.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Binding Sites
- Peptide Synthases/chemistry
- Peptide Synthases/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Streptomyces/enzymology
- Substrate Specificity
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Affiliation(s)
- Mireille Moutiez
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Seguin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Matthieu Fonvielle
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Pascal Belin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Isabelle Béatrice Jacques
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Emmanuel Favry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Michel Arthur
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Muriel Gondry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
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4
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Guo LT, Chen XL, Zhao BT, Shi Y, Li W, Xue H, Jin YX. Human tryptophanyl-tRNA synthetase is switched to a tRNA-dependent mode for tryptophan activation by mutations at V85 and I311. Nucleic Acids Res 2007; 35:5934-43. [PMID: 17726052 PMCID: PMC2034488 DOI: 10.1093/nar/gkm633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
For most aminoacyl-tRNA synthetases (aaRS), their cognate tRNA is not obligatory to catalyze amino acid activation, with the exception of four class I (aaRS): arginyl-tRNA synthetase, glutamyl-tRNA synthetase, glutaminyl-tRNA synthetase and class I lysyl-tRNA synthetase. Furthermore, for arginyl-, glutamyl- and glutaminyl-tRNA synthetase, the integrated 3' end of the tRNA is necessary to activate the ATP-PPi exchange reaction. Tryptophanyl-tRNA synthetase is a class I aaRS that catalyzes tryptophan activation in the absence of its cognate tRNA. Here we describe mutations located at the appended β1–β2 hairpin and the AIDQ sequence of human tryptophanyl-tRNA synthetase that switch this enzyme to a tRNA-dependent mode in the tryptophan activation step. For some mutant enzymes, ATP-PPi exchange activity was completely lacking in the absence of tRNATrp, which could be partially rescued by adding tRNATrp, even if it had been oxidized by sodium periodate. Therefore, these mutant enzymes have strong similarity to arginyl-tRNA synthetase, glutaminyl-tRNA synthetase and glutamyl-tRNA synthetase in their mode of amino acid activation. The results suggest that an aaRS that does not normally require tRNA for amino acid activation can be switched to a tRNA-dependent mode.
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Affiliation(s)
- Li-Tao Guo
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - Xiang-Long Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - Bo-Tao Zhao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - Yi Shi
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - Wei Li
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - Hong Xue
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
| | - You-Xin Jin
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031 and Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kwoloon, Hong Kong, China
- *To whom correspondence should be addressed. 0086 21 549212220086 21 5492 1011
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Vasil'eva IA, Moor NA. Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. BIOCHEMISTRY (MOSCOW) 2007; 72:247-63. [PMID: 17447878 DOI: 10.1134/s0006297907030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.
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Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Shen N, Guo L, Yang B, Jin Y, Ding J. Structure of human tryptophanyl-tRNA synthetase in complex with tRNATrp reveals the molecular basis of tRNA recognition and specificity. Nucleic Acids Res 2006; 34:3246-58. [PMID: 16798914 PMCID: PMC1538984 DOI: 10.1093/nar/gkl441] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are a family of enzymes responsible for the covalent link of amino acids to their cognate tRNAs. The selectivity and species-specificity in the recognitions of both amino acid and tRNA by aaRSs play a vital role in maintaining the fidelity of protein synthesis. We report here the first crystal structure of human tryptophanyl-tRNA synthetase (hTrpRS) in complex with tRNATrp and Trp which, together with biochemical data, reveals the molecular basis of a novel tRNA binding and recognition mechanism. hTrpRS recognizes the tRNA acceptor arm from the major groove; however, the 3′ end CCA of the tRNA makes a sharp turn to bind at the active site with a deformed conformation. The discriminator base A73 is specifically recognized by an α-helix of the unique N-terminal domain and the anticodon loop by an α-helix insertion of the C-terminal domain. The N-terminal domain appears to be involved in Trp activation, but not essential for tRNA binding and acylation. Structural and sequence comparisons suggest that this novel tRNA binding and recognition mechanism is very likely shared by other archaeal and eukaryotic TrpRSs, but not by bacterial TrpRSs. Our findings provide insights into the molecular basis of tRNA specificity and species-specificity.
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Affiliation(s)
- Ning Shen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
- Graduate School of Chinese Academy of Sciences320 Yue-Yang Road, Shanghai 200031, China
| | - Litao Guo
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
- Graduate School of Chinese Academy of Sciences320 Yue-Yang Road, Shanghai 200031, China
| | - Bei Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
- Graduate School of Chinese Academy of Sciences320 Yue-Yang Road, Shanghai 200031, China
| | - Youxin Jin
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
- To whom correspondence should be addressed. Tel: 86 21 54921619; Fax: 86 21 54921116;
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Yang XL, Otero FJ, Ewalt KL, Liu J, Swairjo MA, Köhrer C, RajBhandary UL, Skene RJ, McRee DE, Schimmel P. Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J 2006; 25:2919-29. [PMID: 16724112 PMCID: PMC1500858 DOI: 10.1038/sj.emboj.7601154] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 04/27/2006] [Indexed: 11/09/2022] Open
Abstract
Aminoacylation of tRNA is the first step of protein synthesis. Here, we report the co-crystal structure of human tryptophanyl-tRNA synthetase and tRNATrp. This enzyme is reported to interact directly with elongation factor 1alpha, which carries charged tRNA to the ribosome. Crystals were generated from a 50/50% mixture of charged and uncharged tRNATrp. These crystals captured two conformations of the complex, which are nearly identical with respect to the protein and a bound tryptophan. They are distinguished by the way tRNA is bound. In one, uncharged tRNA is bound across the dimer, with anticodon and acceptor stem interacting with separate subunits. In this cross-dimer tRNA complex, the class I enzyme has a class II-like tRNA binding mode. This structure accounts for biochemical investigations of human TrpRS, including species-specific charging. In the other conformation, presumptive aminoacylated tRNA is bound only by the anticodon, the acceptor stem being free and having space to interact precisely with EF-1alpha, suggesting that the product of aminoacylation can be directly handed off to EF-1alpha for the next step of protein synthesis.
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Affiliation(s)
- Xiang-Lei Yang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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