1
|
Wilhelm CA, Kaitany K, Kelly A, Yacoub M, Koutmos M. The protein-only RNase Ps, endonucleases that cleave pre-tRNA: Biological relevance, molecular architectures, substrate recognition and specificity, and protein interactomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1836. [PMID: 38453211 DOI: 10.1002/wrna.1836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/27/2024] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Protein-only RNase P (PRORP) is an essential enzyme responsible for the 5' maturation of precursor tRNAs (pre-tRNAs). PRORPs are classified into three categories with unique molecular architectures, although all three classes of PRORPs share a mechanism and have similar active sites. Single subunit PRORPs, like those found in plants, have multiple isoforms with different localizations, substrate specificities, and temperature sensitivities. Most recently, Arabidopsis thaliana PRORP2 was shown to interact with TRM1A and B, highlighting a new potential role between these enzymes. Work with At PRORPs led to the development of a ribonuclease that is being used to protect against plant viruses. The mitochondrial RNase P complex, found in metazoans, consists of PRORP, TRMT10C, and SDR5C1, and has also been shown to have substrate specificity, although the cause is unknown. Mutations in mitochondrial tRNA and mitochondrial RNase P have been linked to human disease, highlighting the need to continue understanding this complex. The last class of PRORPs, homologs of Aquifex RNase P (HARPs), is found in thermophilic archaea and bacteria. This most recently discovered type of PRORP forms a large homo-oligomer complex. Although numerous structures of HARPs have been published, it is still unclear how HARPs bind pre-tRNAs and in what ratio. There is also little investigation into the substrate specificity and ideal conditions for HARPs. Moving forward, further work is required to fully characterize each of the three classes of PRORP, the pre-tRNA binding recognition mechanism, the rules of substrate specificity, and how these three distinct classes of PRORP evolved. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
| | - Kipchumba Kaitany
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Abigail Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Yacoub
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
2
|
Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
3
|
Jin X, Huang Z, Xie L, Liu L, Han D, Cheng L. Photo‐Facilitated Detection and Sequencing of 5‐Formylcytidine RNA. Angew Chem Int Ed Engl 2022; 61:e202210652. [DOI: 10.1002/anie.202210652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Zu‐Rui Huang
- China National Center for Bioinformation Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Li‐Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Da‐Li Han
- China National Center for Bioinformation Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou 310024 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
4
|
Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021; 49:9077-9096. [PMID: 34417604 PMCID: PMC8450103 DOI: 10.1093/nar/gkab688] [Citation(s) in RCA: 443] [Impact Index Per Article: 147.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE’s ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the program's ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits.
Collapse
Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Brian Y Lin
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Allysia J Mak
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| |
Collapse
|
5
|
Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA. Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. EMBO J 2021; 40:e105496. [PMID: 33283887 PMCID: PMC7957426 DOI: 10.15252/embj.2020105496] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5 C-methyltransferases have been studied, the impact of the global cytosine-5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5 C in RNA, demonstrating that this modification is non-essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5 C sites in the RNome in vivo. We find that NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5 C34-modified tRNA. This leads to reduced translation efficiency of UUG-rich transcripts and impaired fertility, suggesting a role of m5 C tRNA wobble methylation in the adaptation to higher temperatures.
Collapse
Affiliation(s)
- Isabela Cunha Navarro
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Francesca Tuorto
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
- Division of BiochemistryMannheim Institute for Innate Immunoscience (MI3)Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
| | - David Jordan
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Carine Legrand
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
| | - Jonathan Price
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Fabian Braukmann
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Alan G Hendrick
- STORM Therapeutics LimitedBabraham Research CampusCambridgeUK
| | - Alper Akay
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg‐University MainzMainzGermany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg‐University MainzMainzGermany
| | - Frank Lyko
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
| | - Eric A Miska
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Wellcome Sanger InstituteWellcome Genome CampusCambridgeUK
| |
Collapse
|
6
|
Hennig O, Philipp S, Bonin S, Rollet K, Kolberg T, Jühling T, Betat H, Sauter C, Mörl M. Adaptation of the Romanomermis culicivorax CCA-Adding Enzyme to Miniaturized Armless tRNA Substrates. Int J Mol Sci 2020; 21:E9047. [PMID: 33260740 PMCID: PMC7730189 DOI: 10.3390/ijms21239047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial genome of the nematode Romanomermis culicivorax encodes for miniaturized hairpin-like tRNA molecules that lack D- as well as T-arms, strongly deviating from the consensus cloverleaf. The single tRNA nucleotidyltransferase of this organism is fully active on armless tRNAs, while the human counterpart is not able to add a complete CCA-end. Transplanting single regions of the Romanomermis enzyme into the human counterpart, we identified a beta-turn element of the catalytic core that-when inserted into the human enzyme-confers full CCA-adding activity on armless tRNAs. This region, originally identified to position the 3'-end of the tRNA primer in the catalytic core, dramatically increases the enzyme's substrate affinity. While conventional tRNA substrates bind to the enzyme by interactions with the T-arm, this is not possible in the case of armless tRNAs, and the strong contribution of the beta-turn compensates for an otherwise too weak interaction required for the addition of a complete CCA-terminus. This compensation demonstrates the remarkable evolutionary plasticity of the catalytic core elements of this enzyme to adapt to unconventional tRNA substrates.
Collapse
Affiliation(s)
- Oliver Hennig
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Susanne Philipp
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Sonja Bonin
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Kévin Rollet
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Tim Kolberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Tina Jühling
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| |
Collapse
|
7
|
Krahn N, Fischer JT, Söll D. Naturally Occurring tRNAs With Non-canonical Structures. Front Microbiol 2020; 11:596914. [PMID: 33193279 PMCID: PMC7609411 DOI: 10.3389/fmicb.2020.596914] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Transfer RNA (tRNA) is the central molecule in genetically encoded protein synthesis. Most tRNA species were found to be very similar in structure: the well-known cloverleaf secondary structure and L-shaped tertiary structure. Furthermore, the length of the acceptor arm, T-arm, and anticodon arm were found to be closely conserved. Later research discovered naturally occurring, active tRNAs that did not fit the established 'canonical' tRNA structure. This review discusses the non-canonical structures of some well-characterized natural tRNA species and describes how these structures relate to their role in translation. Additionally, we highlight some newly discovered tRNAs in which the structure-function relationship is not yet fully understood.
Collapse
Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
| |
Collapse
|
8
|
Arakawa S, Kamizaki K, Kuwana Y, Kataoka N, Naoe C, Takemoto C, Yokogawa T, Hori H. Application of solid-phase DNA probe method with cleavage by deoxyribozyme for analysis of long non-coding RNAs. J Biochem 2020; 168:273-283. [PMID: 32289169 DOI: 10.1093/jb/mvaa048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/02/2020] [Indexed: 11/12/2022] Open
Abstract
The solid-phase DNA probe method is a well-established technique for tRNA purification. We have applied this method for purification and analysis of other non-coding RNAs. Three columns for purification of tRNAPhe, transfer-messenger RNA (tmRNA) and 16S rRNA from Thermus thermophilus were connected in tandem and purifications were performed. From each column, tRNAPhe, tmRNA and 16S rRNA could be purified in a single step. This is the first report of purification of native tmRNA from T. thermophilus and the purification demonstrates that the solid-phase DNA probe method is applicable to non-coding RNA, which is present in lower amounts than tRNA. Furthermore, if a long non-coding RNA is cleaved site-specifically and the fragment can be purified by the solid-phase DNA probe method, modified nucleosides in the long non-coding RNA can be analysed. Therefore, we designed a deoxyribozyme (DNAzyme) to perform site-specific cleavage of 16S rRNA, examined optimum conditions and purified the resulting RNA fragment. Sequencing of complimentary DNA and mass spectrometric analysis revealed that the purified RNA corresponded to the targeted fragment of 16S rRNA. Thus, the combination of DNAzyme cleavage and purification using solid-phase DNA probe methodology can be a useful technique for analysis of modified nucleosides in long non-coding RNAs.
Collapse
Affiliation(s)
- Shizuka Arakawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kohsuke Kamizaki
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yusuke Kuwana
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Naruki Kataoka
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Chieko Naoe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chie Takemoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Yokogawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
9
|
Wang R, Jin X, Kong D, Chen Z, Liu J, Liu L, Cheng L. Visible‐Light Facilitated Fluorescence “Switch‐On” Labelling of 5‐Formylpyrimidine RNA. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui‐Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - De‐Long Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Zhi‐Gang Chen
- BNLMS, State Key Laboratory of Polymer Physics and Chemistry, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Ji Liu
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- Key Lab of Functional Molecular Engineering of Guangdong ProvinceSouth China University of Technology Guangzhou 510640 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
10
|
Jin X, Wang R, Xie L, Kong D, Liu L, Cheng L. A Chemical Photo‐Oxidation of 5‐Methyl Cytidines. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900811] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Rui‐Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Li‐Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - De‐Long Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| |
Collapse
|
11
|
Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M. Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res 2019; 46:9170-9180. [PMID: 29986062 PMCID: PMC6158502 DOI: 10.1093/nar/gky593] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/20/2018] [Indexed: 12/19/2022] Open
Abstract
As adapter molecules to convert the nucleic acid information into the amino acid sequence, tRNAs play a central role in protein synthesis. To fulfill this function in a reliable way, tRNAs exhibit highly conserved structural features common in all organisms and in all cellular compartments active in translation. However, in mitochondria of metazoans, certain dramatic deviations from the consensus tRNA structure are described, where some tRNAs lack the D- or T-arm without losing their function. In Enoplea, this miniaturization comes to an extreme, and functional mitochondrial tRNAs can lack both arms, leading to a considerable size reduction. Here, we investigate the secondary and tertiary structure of two such armless tRNAs from Romanomermis culicivorax. Despite their high AU content, the transcripts fold into a single and surprisingly stable hairpin structure, deviating from standard tRNAs. The three-dimensional form is boomerang-like and diverges from the standard L-shape. These results indicate that such unconventional miniaturized tRNAs can still fold into a tRNA-like shape, although their length and secondary structure are very unusual. They highlight the remarkable flexibility of the protein synthesis apparatus and suggest that the translational machinery of Enoplea mitochondria may show compensatory adaptations to accommodate these armless tRNAs for efficient translation.
Collapse
Affiliation(s)
- Tina Jühling
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany.,Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Joern Pütz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Catherine Florentz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Claude Sauter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| |
Collapse
|
12
|
Wellner K, Mörl M. Post-Transcriptional Regulation of tRNA Pools To Govern the Central Dogma: A Perspective. Biochemistry 2019; 58:299-304. [PMID: 30192518 DOI: 10.1021/acs.biochem.8b00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their initial discovery, tRNAs have risen from sole adapter molecules during protein synthesis to pivotal modulators of gene expression. Through their many interactions with tRNA-associated protein factors, they play a central role in maintaining cell homeostasis, especially regarding the fine-tuning in response to a rapidly changing cellular environment. Here, we provide a perspective on current tRNA topics with a spotlight on the regulation of post-transcriptional shaping of tRNA molecules. First, we give an update on aberrant structural features that a yet functional fraction of mitochondrial tRNAs can exhibit. Then, we outline several aspects of the regulatory contribution of ribonucleases with a focus on tRNA processing versus tRNA elimination. We close with a comment on the possible consequences for the intracellular examination of nascent tRNA precursors regarding respective processing factors that have been shown to associate with the tRNA transcription machinery in alternative moonlighting functions.
Collapse
Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
| | - Mario Mörl
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
| |
Collapse
|
13
|
Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
|
14
|
Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Mol Cell Biol 2017; 37:e00214-17. [PMID: 28784718 PMCID: PMC5640816 DOI: 10.1128/mcb.00214-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/17/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mutations in the tRNA methyltransferase 1 (TRMT1) gene have been identified as the cause of certain forms of autosomal-recessive intellectual disability (ID). However, the molecular pathology underlying ID-associated TRMT1 mutations is unknown, since the biological role of the encoded TRMT1 protein remains to be determined. Here, we have elucidated the molecular targets and function of TRMT1 to uncover the cellular effects of ID-causing TRMT1 mutations. Using human cells that have been rendered deficient in TRMT1, we show that TRMT1 is responsible for catalyzing the dimethylguanosine (m2,2G) base modification in both nucleus- and mitochondrion-encoded tRNAs. TRMT1-deficient cells exhibit decreased proliferation rates, alterations in global protein synthesis, and perturbations in redox homeostasis, including increased endogenous ROS levels and hypersensitivity to oxidizing agents. Notably, ID-causing TRMT1 variants are unable to catalyze the formation of m2,2G due to defects in RNA binding and cannot rescue oxidative stress sensitivity. Our results uncover a biological role for TRMT1-catalyzed tRNA modification in redox metabolism and show that individuals with TRMT1-associated ID are likely to have major perturbations in cellular homeostasis due to the lack of m2,2G modifications.
Collapse
Affiliation(s)
- Joshua M Dewe
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Benjamin L Fuller
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | | | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| |
Collapse
|
15
|
Nagao A, Ohara M, Miyauchi K, Yokobori SI, Yamagishi A, Watanabe K, Suzuki T. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Nat Struct Mol Biol 2017; 24:778-782. [PMID: 28783151 DOI: 10.1038/nsmb.3449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
The genetic code is not frozen but still evolving, which can result in the acquisition of 'dialectal' codons that deviate from the universal genetic code. RNA modifications in the anticodon region of tRNAs play a critical role in establishing such non-universal genetic codes. In echinoderm mitochondria, the AAA codon specifies asparagine instead of lysine. By analyzing mitochondrial (mt-) tRNALys isolated from the sea urchin (Mesocentrotus nudus), we discovered a novel modified nucleoside, hydroxy-N6-threonylcarbamoyladenosine (ht6A), 3' adjacent to the anticodon (position 37). Biochemical analysis revealed that ht6A37 has the ability to prevent mt-tRNALys from misreading AAA as lysine, thereby indicating that hydroxylation of N6-threonylcarbamoyladenosine (t6A) contributes to the establishment of the non-universal genetic code in echinoderm mitochondria.
Collapse
Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Ohara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Yokobori
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kimitsuna Watanabe
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| |
Collapse
|
16
|
Kawarada L, Suzuki T, Ohira T, Hirata S, Miyauchi K, Suzuki T. ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. Nucleic Acids Res 2017; 45:7401-7415. [PMID: 28472312 PMCID: PMC5499545 DOI: 10.1093/nar/gkx354] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/17/2017] [Accepted: 04/22/2017] [Indexed: 11/13/2022] Open
Abstract
ALKBH1 is a 2-oxoglutarate- and Fe2+-dependent dioxygenase responsible for multiple cellular functions. Here, we show that ALKBH1 is involved in biogenesis of 5-hydroxymethyl-2΄-O-methylcytidine (hm5Cm) and 5-formyl-2΄-O-methylcytidine (f5Cm) at the first position (position 34) of anticodon in cytoplasmic tRNALeu, as well as f5C at the same position in mitochondrial tRNAMet. Because f5C34 of mitochondrial tRNAMet is essential for translation of AUA, a non-universal codon in mammalian mitochondria, ALKBH1-knockout cells exhibited a strong reduction in mitochondrial translation and reduced respiratory complex activities, indicating that f5C34 formation mediated by ALKBH1 is required for efficient mitochondrial functions. We reconstituted formation of f5C34 on mitochondrial tRNAMetin vitro, and found that ALKBH1 first hydroxylated m5C34 to form hm5C34, and then oxidized hm5C34 to form f5C34. Moreover, we found that the frequency of 1-methyladenosine (m1A) in two mitochondrial tRNAs increased in ALKBH1-knockout cells, indicating that ALKBH1 also has demethylation activity toward m1A in mt-tRNAs. Based on these results, we conclude that nuclear and mitochondrial ALKBH1 play distinct roles in tRNA modification.
Collapse
Affiliation(s)
- Layla Kawarada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shoji Hirata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
17
|
Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
Collapse
Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
| |
Collapse
|
18
|
Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues. Biochem J 2017; 474:957-969. [PMID: 28130490 DOI: 10.1042/bcj20160929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 11/17/2022]
Abstract
Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aa-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively, recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegansC. elegans EF-Tu2 specifically recognizes the seryl moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans) EF-Tu species. We report here that two EF-Tu species also participate in Drosophila melanogaster mitochondria. Both D. melanogaster EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. D. melanogaster EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in D. melanogaster mitochondria, but do exist in related arthropod species. In addition, D. melanogaster EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mt translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems.
Collapse
|
19
|
Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5-Formylcytosine Modification in Mitochondrial tRNA Met. Biomolecules 2017; 7:biom7010024. [PMID: 28257121 PMCID: PMC5372736 DOI: 10.3390/biom7010024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/24/2017] [Indexed: 01/13/2023] Open
Abstract
Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt-tRNAMet) also recognises AUA during translation initiation and elongation. Post-transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5-formylcytosine (f5C) modification of position 34 in mt-tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease.
Collapse
|
20
|
NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). Nat Chem Biol 2016; 12:546-51. [PMID: 27214402 DOI: 10.1038/nchembio.2099] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/15/2016] [Indexed: 12/18/2022]
Abstract
In human mitochondria, the AUA codon encodes methionine via a mitochondrial transfer RNA for methionine (mt-tRNA(Met)) that contains 5-formylcytidine (f(5)C) at the first position of the anticodon (position 34). f(5)C34 is required for deciphering the AUA codon during protein synthesis. Until now, the biogenesis and physiological role of f(5)C34 were unknown. We demonstrate that biogenesis of f(5)C34 is initiated by S-adenosylmethionine (AdoMet)-dependent methylation catalyzed by NSUN3, a putative methyltransferase in mitochondria. NSUN3-knockout cells showed strong reduction in mitochondrial protein synthesis and reduced oxygen consumption, leading to deficient mitochondrial activity. We reconstituted formation of 5-methylcytidine (m(5)C) at position 34 (m(5)C34) on mt-tRNA(Met) with recombinant NSUN3 in the presence of AdoMet, demonstrating that NSUN3-mediated m(5)C34 formation initiates f(5)C34 biogenesis. We also found two disease-associated point mutations in mt-tRNA(Met) that impaired m(5)C34 formation by NSUN3, indicating that a lack of f(5)C34 has pathological consequences.
Collapse
|
21
|
Wang R, Luo Z, He K, Delaney MO, Chen D, Sheng J. Base pairing and structural insights into the 5-formylcytosine in RNA duplex. Nucleic Acids Res 2016; 44:4968-77. [PMID: 27079978 PMCID: PMC4889945 DOI: 10.1093/nar/gkw235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022] Open
Abstract
5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex.
Collapse
Affiliation(s)
- Rui Wang
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Zhipu Luo
- Synchrotron Radiation Research Section, MCL National Cancer Institute, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Kaizhang He
- Dharmacon, GE Healthcare, Lafayette, CO 80026, USA
| | | | - Doris Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| |
Collapse
|
22
|
Bezerra AR, Guimarães AR, Santos MAS. Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) 2015; 5:1610-28. [PMID: 26569314 PMCID: PMC4695839 DOI: 10.3390/life5041610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
Collapse
Affiliation(s)
- Ana R Bezerra
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Ana R Guimarães
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Manuel A S Santos
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| |
Collapse
|
23
|
Salinas-Giegé T, Giegé R, Giegé P. tRNA biology in mitochondria. Int J Mol Sci 2015; 16:4518-59. [PMID: 25734984 PMCID: PMC4394434 DOI: 10.3390/ijms16034518] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.
Collapse
Affiliation(s)
- Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| |
Collapse
|
24
|
Kazayama A, Yamagami R, Yokogawa T, Hori H. Improved solid-phase DNA probe method for tRNA purification: large-scale preparation and alteration of DNA fixation. J Biochem 2015; 157:411-8. [DOI: 10.1093/jb/mvu089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/02/2014] [Indexed: 11/12/2022] Open
|
25
|
Watanabe YI, Suematsu T, Ohtsuki T. Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet 2014; 5:109. [PMID: 24822055 PMCID: PMC4013460 DOI: 10.3389/fgene.2014.00109] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/12/2014] [Indexed: 11/16/2022] Open
Abstract
Conventional tRNAs have highly conserved sequences, four-armed cloverleaf secondary structures, and L-shaped tertiary structures. However, metazoan mitochondrial tRNAs contain several exceptional structures. Almost all tRNAsSer for AGY/N codons lack the D-arm. Furthermore, in some nematodes, no four-armed cloverleaf-type tRNAs are present: two tRNAsSer without the D-arm and 20 tRNAs without the T-arm are found. Previously, we showed that in nematode mitochondria, an extra elongation factor Tu (EF-Tu) has evolved to support interaction with tRNAs lacking the T-arm, which interact with C-terminal domain 3 in conventional EF-Tu. Recent mitochondrial genome analyses have suggested that in metazoan lineages other than nematodes, tRNAs without the T-arm are present. Furthermore, even more simplified tRNAs are predicted in some lineages. In this review, we discuss mitochondrial tRNAs with divergent structures, as well as protein factors, including EF-Tu, that support the function of truncated metazoan mitochondrial tRNAs.
Collapse
Affiliation(s)
- Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo Tokyo, Japan
| | - Takuma Suematsu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo Tokyo, Japan
| | - Takashi Ohtsuki
- Department of Biotechnology, Okayama University Okayama, Japan
| |
Collapse
|
26
|
Ohira T, Suzuki T, Miyauchi K, Suzuki T, Yokobori SI, Yamagishi A, Watanabe K. Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria. J Biol Chem 2013; 288:7645-7652. [PMID: 23362261 DOI: 10.1074/jbc.m112.439554] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-universal genetic codes are frequently found in animal mitochondrial decoding systems. In squid mitochondria, four codons deviate from the universal genetic code, namely AUA, UGA, and AGA/AGG (AGR) for Met, Trp, and Ser, respectively. To understand the molecular basis for establishing the non-universal genetic code, we isolated and analyzed five mitochondrial tRNAs from a squid, Loligo bleekeri. Primary structures of the isolated tRNAs, including their post-transcriptional modifications, were analyzed by mass spectrometry. tRNA(Met)(AUR) possessed an unmodified cytidine at the first position of the anticodon, suggesting that the AUA codon is deciphered by CAU anticodon via non-canonical A-C pairing. We identified 5-taurinomethyluridine (τm(5)U) at the first position of the anticodon in tRNA(Trp)(UGR). τm(5)U enables tRNA(Trp) to decipher UGR codons as Trp. In addition, 5-taurinomethyl-2-thiouridine (τm(5)s(2)U) was found in mitochondrial tRNAs for Leu(UUR) and Lys in L. bleekeri. This is the first discovery of τm(5)U and τm(5)s(2)U in molluscan mitochondrial tRNAs.
Collapse
Affiliation(s)
- Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shin-Ichi Yokobori
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Hyogo 679-5148, Japan.
| |
Collapse
|
27
|
Watanabe K, Yokobori SI. tRNA Modification and Genetic Code Variations in Animal Mitochondria. J Nucleic Acids 2011; 2011:623095. [PMID: 22007289 PMCID: PMC3191813 DOI: 10.4061/2011/623095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/04/2011] [Indexed: 12/03/2022] Open
Abstract
In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNATrp for UGA, tRNAMet for AUA, tRNAAsn for AAA, and tRNASer and tRNAGly for AGA/AGG) are all modified; tRNATrp has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNAMet has 5-formylcytidine or 5-taurinomethyluridine, tRNASer has 7-methylguanosine and tRNAGly has 5-taurinomethyluridine in their anticodon wobble position, and tRNAAsn has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
Collapse
Affiliation(s)
- Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | | |
Collapse
|
28
|
Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
29
|
Matsumoto T, Ishikawa SA, Hashimoto T, Inagaki Y. A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Mol Phylogenet Evol 2011; 60:68-72. [PMID: 21530665 DOI: 10.1016/j.ympev.2011.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 10/18/2022]
Abstract
We here report a deviant genetic code, in which AUA is read as methionine (Met) instead of isoleucine (Ile), in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Although L. chlorophorum cDNA sequences of 11 plastid-encoded genes were deposited in the GenBank database, the non-canonical usage of AUA in this dinoflagellate plastid has been overlooked prior to this study. We compared 11 plastid-encoded genes of L. chlorophorum with the corresponding genes of 17 green algal plastids. Intriguingly, AUA often occurred in the L. chlorophorum sequences at codon positions that are predominantly occupied by Met amongst the green algal sequences. Coincidentally, the L. chlorophorum sequences utilized few AUA codons at the positions predominantly occupied by Ile amongst the green algal sequences. These observations clearly indicated that both AUA and AUG encode Met, while AUU and AUC encode Ile, in the L. chlorophorum plastid. Despite the rapidly-evolving nature of L. chlorophorum plastid-encoded genes, our statistical tests incorporating the deviant code suggest no significant difference in amino acid composition among the L. chlorophorum plastid and the green algal plastids considered in this study. Finally, the possible evolutionary events required for the reassignment of AUA from Ile to Met in Lepitodinium plastids were discussed.
Collapse
Affiliation(s)
- Takuya Matsumoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | | | | | | |
Collapse
|
30
|
Yu H, Li Q. Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS One 2011; 6:e16147. [PMID: 21267462 PMCID: PMC3022732 DOI: 10.1371/journal.pone.0016147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 12/07/2010] [Indexed: 11/19/2022] Open
Abstract
Background Animal mitochondrial genomes typically encode one tRNA for each synonymous codon family, so that each tRNA anticodon essentially has to wobble to recognize two or four synonymous codons. Several factors have been hypothesized to determine the nucleotide at the wobble site of a tRNA anticodon in mitochondrial genomes, such as the codon-anticodon adaptation hypothesis, the wobble versatility hypothesis, the translation initiation and elongation conflict hypothesis, and the wobble cost hypothesis. Principal Findings In this study, we analyzed codon usage and tRNA anticodon wobble sites of 29 marine bivalve mitochondrial genomes to evaluate features of the wobble nucleotides in tRNA anticodons. The strand-specific mutation bias favors G and T on the H strand in all the 29 marine bivalve mitochondrial genomes. A bias favoring G and T is also visible in the third codon positions of protein-coding genes and the wobble sites of anticodons, rejecting that codon usage bias drives the wobble sites of tRNA anticodons or tRNA anticodon bias drives the evolution of codon usage. Almost all codon families (98.9%) from marine bivalve mitogenomes support the wobble versatility hypothesis. There are a few interesting exceptions involving tRNATrp with an anticodon CCA fixed in Pectinoida species, tRNASer with a GCU anticodon fixed in Mytiloida mitogenomes, and the uniform anticodon CAU of tRNAMet translating the AUR codon family. Conclusions/Significance These results demonstrate that most of the nucleotides at the wobble sites of tRNA anticodons in marine bivalve mitogenomes are determined by wobble versatility. Other factors such as the translation initiation and elongation conflict, and the cost of wobble translation may contribute to the determination of the wobble nucleotide in tRNA anticodons. The finding presented here provides valuable insights into the previous hypotheses of the wobble nucleotide in tRNA anticodons by adding some new evidence.
Collapse
Affiliation(s)
- Hong Yu
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Qi Li
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
- * E-mail:
| |
Collapse
|
31
|
The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons. J Mol Biol 2010; 406:257-74. [PMID: 21168417 DOI: 10.1016/j.jmb.2010.11.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 11/21/2022]
Abstract
Human mitochondrial mRNAs utilize the universal AUG and the unconventional isoleucine AUA codons for methionine. In contrast to translation in the cytoplasm, human mitochondria use one tRNA, hmtRNA(Met)(CAU), to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl- (A-) sites of the ribosome. The hmtRNA(Met)(CAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f(5)C(34)), and a cytidine substituting for the invariant uridine at position 33 of the canonical U-turn in tRNAs. The structure of the tRNA anticodon stem and loop domain (hmtASL(Met)(CAU)), determined by NMR restrained molecular modeling, revealed how the f(5)C(34) modification facilitates the decoding of AUA at the P- and the A-sites. The f(5)C(34) defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASL(Met)(CAU). The hmtASL(Met)(CAU) exhibited a C-turn conformation that has some characteristics of the U-turn motif. Codon binding studies with both Escherichia coli and bovine mitochondrial ribosomes revealed that the f(5)C(34) facilitates AUA binding in the A-site and suggested that the modification favorably alters the ASL binding kinetics. Mitochondrial translation by many organisms, including humans, sometimes initiates with the universal isoleucine codons AUU and AUC. The f(5)C(34) enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f(5)C(34), expand codon recognition from the traditional AUG to the non-traditional, synonymous codons AUU and AUC as well as AUA, in the reassignment of universal codons in the mitochondria.
Collapse
|
32
|
Watanabe K. Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:11-39. [PMID: 20075606 PMCID: PMC3417567 DOI: 10.2183/pjab.86.11] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 11/17/2009] [Indexed: 05/17/2023]
Abstract
In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.
Collapse
Affiliation(s)
- Kimitsuna Watanabe
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
| |
Collapse
|
33
|
Takemoto C, Spremulli LL, Benkowski LA, Ueda T, Yokogawa T, Watanabe K. Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Res 2009; 37:1616-27. [PMID: 19151083 PMCID: PMC2655697 DOI: 10.1093/nar/gkp001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial (mt) tRNAMet has the unusual modified nucleotide 5-formylcytidine (f5C) in the first position of the anticodon. This tRNA must translate both AUG and AUA as methionine. By constructing an in vitro translation system from bovine liver mitochondria, we examined the decoding properties of the native mt tRNAMet carrying f5C in the anticodon compared to a transcript that lacks the modification. The native mt Met-tRNA could recognize both AUA and AUG codons as Met, but the corresponding synthetic tRNAMet lacking f5C (anticodon CAU), recognized only the AUG codon in both the codon-dependent ribosomal binding and in vitro translation assays. Furthermore, the Escherichia coli elongator tRNAMetm with the anticodon ac4CAU (ac4C = 4-acetylcytidine) and the bovine cytoplasmic initiator tRNAMet (anticodon CAU) translated only the AUG codon for Met on mt ribosome. The codon recognition patterns of these tRNAs were the same on E. coli ribosomes. These results demonstrate that the f5C modification in mt tRNAMet plays a crucial role in decoding the nonuniversal AUA codon as Met, and that the genetic code variation is compensated by a change in the tRNA anticodon, not by a change in the ribosome. Base pairing models of f5C-G and f5C-A based on the chemical properties of f5C are presented.
Collapse
Affiliation(s)
- Chie Takemoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | | | | | | | | | | |
Collapse
|
34
|
Lusic H, Gustilo EM, Vendeix FAP, Kaiser R, Delaney MO, Graham WD, Moye VA, Cantara WA, Agris PF, Deiters A. Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet. Nucleic Acids Res 2008; 36:6548-57. [PMID: 18927116 PMCID: PMC2582600 DOI: 10.1093/nar/gkn703] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human mitochondrial methionine transfer RNA (hmtRNA(Met)(CAU)) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position-34 (f(5)C(34)). The role of this modification in (hmtRNA(Met)(CAU)) for the decoding of AUA, as well as AUG, in both the peptidyl- and aminoacyl-sites of the ribosome in either chain initiation or chain elongation is still unknown. We report the first synthesis and analyses of the tRNA's anticodon stem and loop domain containing the 5-formylcytidine modification. The modification contributes to the tRNA's anticodon domain structure, thermodynamic properties and its ability to bind codons AUA and AUG in translational initiation and elongation.
Collapse
Affiliation(s)
- Hrvoje Lusic
- Department of Chemistry, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 and Dharmacon, 2650 Crescent Drive #100, Lafayette, CO 80026, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Masta SE, Boore JL. Parallel Evolution of Truncated Transfer RNA Genes in Arachnid Mitochondrial Genomes. Mol Biol Evol 2008; 25:949-59. [DOI: 10.1093/molbev/msn051] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
36
|
Armstrong MR, Husmeier D, Phillips MS, Blok VC. Segregation and Recombination of a Multipartite Mitochondrial DNA in Populations of the Potato Cyst Nematode Globodera pallida. J Mol Evol 2007; 64:689-701. [PMID: 17541676 DOI: 10.1007/s00239-007-0023-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 02/28/2007] [Indexed: 10/23/2022]
Abstract
The discovery that the potato cyst nematode Globodera pallida has a multipartite mitochondrial DNA (mtDNA) composed, at least in part, of six small circular mtDNAs (scmtDNAs) raised a number of questions concerning the population-level processes that might act on such a complex genome. Here we report our observations on the distribution of some scmtDNAs among a sample of European and South American G. pallida populations. The occurrence of sequence variants of scmtDNA IV in population P4A from South America, and that particular sequence variants are common to the individuals within a single cyst, is described. Evidence for recombination of sequence variants of scmtDNA IV in P4A is also reported. The mosaic structure of P4A scmtDNA IV sequences was revealed using several detection methods and recombination breakpoints were independently detected by maximum likelihood and Bayesian MCMC methods.
Collapse
Affiliation(s)
- Miles R Armstrong
- Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
| | | | | | | |
Collapse
|
37
|
Arita M, Suematsu T, Osanai A, Inaba T, Kamiya H, Kita K, Sisido M, Watanabe YI, Ohtsuki T. An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu. Nucleic Acids Res 2006; 34:5291-9. [PMID: 17012285 PMCID: PMC1636415 DOI: 10.1093/nar/gkl526] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 07/05/2006] [Accepted: 07/08/2006] [Indexed: 11/20/2022] Open
Abstract
EF-Tu delivers aminoacyl-tRNAs to ribosomes in the translation system. However, unusual truncations found in some animal mitochondrial tRNAs seem to prevent recognition by a canonical EF-Tu. We showed previously that the chromadorean nematode has two distinct EF-Tus, one of which (EF-Tu1) binds only to T-armless aminoacyl-tRNAs and the other (EF-Tu2) binds to D-armless Ser-tRNAs. Neither of the EF-Tus can bind to canonical cloverleaf tRNAs. In this study, by analyzing the translation system of enoplean nematode Trichinella species, we address how EF-Tus and tRNAs have evolved from the canonical structures toward those of the chromadorean translation system. Trichinella mitochondria possess three types of tRNAs: cloverleaf tRNAs, which do not exist in chromadorean nematode mitochondria; T-armless tRNAs; and D-armless tRNAs. We found two mitochondrial EF-Tu species, EF-Tu1 and EF-Tu2, in Trichinella britovi. T.britovi EF-Tu2 could bind to only D-armless Ser-tRNA, as Caenorhabditis elegans EF-Tu2 does. In contrast to the case of C.elegans EF-Tu1, however, T.britovi EF-Tu1 bound to all three types of tRNA present in Trichinella mitochondria. These results suggest that Trichinella mitochondrial translation system, and particularly the tRNA-binding specificity of EF-Tu1, could be an intermediate state between the canonical system and the chromadorean nematode mitochondrial system.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Caenorhabditis elegans Proteins/chemistry
- Evolution, Molecular
- Helminth Proteins/chemistry
- Helminth Proteins/metabolism
- Mitochondria/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/metabolism
- Protein Biosynthesis
- RNA/chemistry
- RNA/metabolism
- RNA, Helminth/chemistry
- RNA, Helminth/metabolism
- RNA, Mitochondrial
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Trp/chemistry
- RNA, Transfer, Trp/metabolism
- Sequence Alignment
- Trichinella/genetics
Collapse
Affiliation(s)
- Masashi Arita
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Takuma Suematsu
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
- Department of Biomedical Chemistry, The University of Tokyo7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Arihiro Osanai
- Department of Parasitology, Hirosaki University School of Medicine5, Zafu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Takashi Inaba
- Department of Parasitology, Hirosaki University School of Medicine5, Zafu-cho, Hirosaki, Aomori 036-8562, Japan
- Department of Medical Technology, Hirosaki UniversityHriosaki, Aomori 036-8564, Japan
| | - Haruo Kamiya
- Department of Parasitology, Hirosaki University School of Medicine5, Zafu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, The University of Tokyo7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Masahiko Sisido
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Yoh-ichi Watanabe
- Department of Biomedical Chemistry, The University of Tokyo7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Takashi Ohtsuki
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| |
Collapse
|
38
|
He Y, Jones J, Armstrong M, Lamberti F, Moens M. The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes. J Mol Evol 2005; 61:819-33. [PMID: 16315110 DOI: 10.1007/s00239-005-0102-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present.
Collapse
Affiliation(s)
- Y He
- Gewasbescherming-CLO, Burg. Van Gansberghelaan 96,, Merelbeke, 9820, Belgium
| | | | | | | | | |
Collapse
|
39
|
Maynard BT, Kerr LJ, McKiernan JM, Jansen ES, Hanna PJ. Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:645-58. [PMID: 16206015 DOI: 10.1007/s10126-005-0013-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2005] [Accepted: 04/07/2005] [Indexed: 05/04/2023]
Abstract
The complete mitochondrial DNA of the blacklip abalone Haliotis rubra (Gastropoda: Mollusca) was cloned and 16,907 base pairs were sequenced. The sequence represents an estimated 99.85% of the mitochondrial genome, and contains 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes found in other metazoan mtDNA. An AT tandem repeat and a possible C-rich domain within the putative control region could not be fully sequenced. The H. rubra mtDNA gene order is novel for mollusks, separated from the black chiton Katharina tunicata by the individual translocations of 3 tRNAs. Compared with other mtDNA regions, sequences from the ATP8, NAD2, NAD4L, NAD6, and 12S rRNA genes, as well as the control region, are the most variable among representatives from Mollusca, Arthropoda, and Rhynchonelliformea, with similar mtDNA arrangements to H. rubra. These sequences are being evaluated as genetic markers within commercially important Haliotis species, and some applications and considerations for their use are discussed.
Collapse
Affiliation(s)
- Ben T Maynard
- School of Biological & Chemical Sciences, Deakin University, Geelong, VIC 3217, Australia
| | | | | | | | | |
Collapse
|
40
|
Suematsu T, Sato A, Sakurai M, Watanabe K, Ohtsuki T. A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2. Nucleic Acids Res 2005; 33:4683-91. [PMID: 16113240 PMCID: PMC1188084 DOI: 10.1093/nar/gki784] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 08/04/2005] [Accepted: 08/04/2005] [Indexed: 12/03/2022] Open
Abstract
Nematode mitochondria expresses two types of extremely truncated tRNAs that are specifically recognized by two distinct elongation factor Tu (EF-Tu) species named EF-Tu1 and EF-Tu2. This is unlike the canonical EF-Tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes all elongator tRNAs. EF-Tu2 specifically recognizes Ser-tRNA(Ser) that lacks a D arm but has a short T arm. Our previous study led us to speculate the lack of the D arm may be essential for the tRNA recognition of EF-Tu2. However, here, we showed that the EF-Tu2 can bind to D arm-bearing Ser-tRNAs, in which the D-T arm interaction was weakened by the mutations. The ethylnitrosourea-modification interference assay showed that EF-Tu2 is unique, in that it interacts with the phosphate groups on the T stem on the side that is opposite to where canonical EF-Tu binds. The hydrolysis protection assay using several EF-Tu2 mutants then strongly suggests that seven C-terminal amino acid residues of EF-Tu2 are essential for its aminoacyl-tRNA-binding activity. Our results indicate that the formation of the nematode mitochondrial (mt) EF-Tu2/GTP/aminoacyl-tRNA ternary complex is probably supported by a unique interaction between the C-terminal extension of EF-Tu2 and the tRNA.
Collapse
Affiliation(s)
- Takuma Suematsu
- Department of Integrated Bioscience, Graduate School of Frontier Science, The University of Tokyo5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Aya Sato
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Masayuki Sakurai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Kimitsuna Watanabe
- Department of Integrated Bioscience, Graduate School of Frontier Science, The University of Tokyo5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Takashi Ohtsuki
- Department of Bioscience and Biotechnology, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| |
Collapse
|
41
|
Shao R, Mitani H, Barker SC, Takahashi M, Fukunaga M. Novel Mitochondrial Gene Content and Gene Arrangement Indicate Illegitimate Inter-mtDNA Recombination in the Chigger Mite, Leptotrombidium pallidum. J Mol Evol 2005; 60:764-73. [PMID: 15931495 DOI: 10.1007/s00239-004-0226-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Accepted: 12/30/2004] [Indexed: 11/24/2022]
Abstract
To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.
Collapse
Affiliation(s)
- Renfu Shao
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan.
| | | | | | | | | |
Collapse
|
42
|
Qiu Y, Song D, Zhou K, Sun H. The mitochondrial sequences of Heptathela hangzhouensis and Ornithoctonus huwena reveal unique gene arrangements and atypical tRNAs. J Mol Evol 2005; 60:57-71. [PMID: 15696368 DOI: 10.1007/s00239-004-0010-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Accepted: 07/29/2004] [Indexed: 10/25/2022]
Abstract
We have sequenced the complete mitochondrial genomes of the spiders Heptathela hangzhouensis and Ornithoctonus huwena. Both genomes encode 13 protein-coding genes, 22 tRNA genes, and 2 ribosomal RNA genes. H. hangzhouensis, a species of the suborder Mesothelae and a representative of the most basal clade of Araneae, possesses a gene order identical to that of Limulus polyphemus of Xiphosura. On the other hand, O. huwena, a representative of suborder Opisthothelae, infraorder Mygalomorphae, was found to have seven tRNA genes positioned differently from those of Limulus. The rrnL-trnL1-nad1 arrangement shared by the araneomorph families Salticidae, Nesticidae, and Linyphiidae and the mygalomorph family Theraphosidae is a putative synapomorphy joining the mygalomorph with the araneomorph. Between the two species examined, base compositions also differ significantly. The lengths of most protein-coding genes in H. hangzhouensis and O. huwena mtDNA are either identical to or slightly shorter than their Limulus counterparts. Usage of initiation and termination codons in these protein-coding genes seems to follow patterns conserved among most arthropod and some other metazoan mitochondrial genomes. The sequences of the 3' ends of rrnS and rrnL in the two species are similar to those reported for Limulus, and the entire genes are shortened by about 100-250 nucleotides with respect to Limulus. The lengths of most tRNA genes from the two species are distinctly shorter than those of Limulus and the sequences reveal unusual inferred tRNA secondary structures. Our finding provides new molecular evidence supporting that the suborder Mesothelae is basal to opisthothelids.
Collapse
Affiliation(s)
- Yang Qiu
- Jiangsu Key Lab for Bioresource Technology, College of Life Sciences, Nanjing Normal University, Nanjing 210097, PR China
| | | | | | | |
Collapse
|
43
|
Sakurai M, Ohtsuki T, Suzuki T, Watanabe K. Unusual usage of wobble modifications in mitochondrial tRNAs of the nematode Ascaris suum. FEBS Lett 2005; 579:2767-72. [PMID: 15907479 DOI: 10.1016/j.febslet.2005.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 04/05/2005] [Accepted: 04/07/2005] [Indexed: 10/25/2022]
Abstract
To understand the decoding property of nematode mitochondrial tRNAs with unusual secondary structures, post-transcriptional modifications at wobble positions of Ascaris suum mitochondrial tRNAs corresponding to two-codon families ending with a purine were analyzed. 5-Carboxymethylaminomethyluridine (cmnm(5)U) was identified at the wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln), while 5-carboxymethylaminomethyl-2-thiouridine (cmnm(5)s(2)U) was present in tRNA(UAA)(Leu)andtRNA(Trp). In most bacterial and mitochondrial tRNAs, the 2-thiouridine derivative is present in tRNAs for Lys, Glu and Gln. These is no report that cmnm(5)s(2)U is used in tRNA(UAA)(Leu)andtRNA(Trp). The unusual usage of wobble modifications might assist decoding of nematode mitochondrial mRNAs.
Collapse
Affiliation(s)
- Masayuki Sakurai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | | |
Collapse
|
44
|
Okamoto H, Watanabe K, Ikeuchi Y, Suzuki T, Endo Y, Hori H. Substrate tRNA Recognition Mechanism of tRNA (m7G46) Methyltransferase from Aquifex aeolicus. J Biol Chem 2004; 279:49151-9. [PMID: 15358762 DOI: 10.1074/jbc.m408209200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA (m7G46) methyltransferase catalyzes the methyl transfer from S-adenosylmethionine to N7 atom of the guanine 46 residue in tRNA. Analysis of the Aquifex aeolicus genome revealed one candidate open reading frame, aq065, encoding this gene. The aq065 protein was expressed in Escherichia coli and purified to homogeneity on 15% SDS-polyacrylamide gel electrophoresis. Although the overall amino acid sequence of the aq065 protein differs considerably from that of E. coli YggH, the purified aq065 protein possessed a tRNA (m7G46) methyltransferase activity. The modified nucleoside and its location were determined by liquid chromatography-mass spectroscopy. To clarify the RNA recognition mechanism of the enzyme, we investigated the methyl transfer activity to 28 variants of yeast tRNAPhe and E. coli tRNAThr. It was confirmed that 5'-leader and 3'-trailer RNAs of tRNA precursor are not required for the methyl transfer. We found that the enzyme specificity was critically dependent on the size of the variable loop. Experiments using truncated variants showed that the variable loop sequence inserted between two stems is recognized as a substrate, and the most important recognition site is contained within the T stem. These results indicate that the L-shaped tRNA structure is not required for methyl acceptance activity. It was also found that nucleotide substitutions around G46 in three-dimensional core decrease the activity.
Collapse
Affiliation(s)
- Hironori Okamoto
- Department of Applied Chemistry, Faculty of Engineering, Ehime University, Bunkyo 3, Matsuyama, 790-8577, Japan
| | | | | | | | | | | |
Collapse
|
45
|
Ohtsuki T, Kawai G, Watanabe K. The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) having a short T arm and lacking the entire D arm. FEBS Lett 2002; 514:37-43. [PMID: 11904178 DOI: 10.1016/s0014-5793(02)02328-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The tertiary structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) was examined by nuclear magnetic resonance analysis using its transcript, since tRNA(Ser)(UCU), lacking the D arm and possessing a truncated T arm, is the shortest of all the known tRNAs. Most basepairs in the proposed secondary structure of tRNA(Ser)(UCU) were shown to exist, but the connector region comprising the truncated D loop and the extra loop was flexible. This flexibility, would enable adjustment of the mutual distance between the 3'-terminus and the anticodon consistent with that of usual tRNAs. Thus, tRNA(Ser)UCU appears to function in a similar way to that of usual tRNAs in the ribosome.
Collapse
Affiliation(s)
- Takashi Ohtsuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan
| | | | | |
Collapse
|
46
|
Dörner M, Altmann M, Pääbo S, Mörl M. Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 2001; 12:2688-98. [PMID: 11553708 PMCID: PMC59704 DOI: 10.1091/mbc.12.9.2688] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The mitochondrial tRNA gene for lysine was analyzed in 11 different marsupial mammals. Whereas its location is conserved when compared with other vertebrate mitochondrial genomes, its primary sequence and inferred secondary structure are highly unusual and variable. For example, eight species lack the expected anticodon. Because the corresponding transcripts are not altered by any RNA-editing mechanism, the lysyl-tRNA gene seems to represent a mitochondrial pseudogene. Purification of marsupial mitochondria and in vitro aminoacylation of isolated tRNAs with lysine, followed by analysis of aminoacylated tRNAs, show that a nuclear-encoded tRNA(Lys) is associated with marsupial mitochondria. We conclude that a functional tRNA(Lys) encoded in the nuclear genome is imported into mitochondria in marsupials. Thus, tRNA import is not restricted to plant, yeast, and protozoan mitochondria but also occurs also in mammals.
Collapse
Affiliation(s)
- M Dörner
- Max-Planck-Institute for Evolutionary Anthropology, D-04105 Leipzig, Germany
| | | | | | | |
Collapse
|
47
|
Ohtsuki T, Takemoto C, Kawai G, Ueda T, Kita K, Kojima S, Kaziro Y, Nyborg J, Watanabe K. An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria. J Biol Chem 2001; 276:21571-7. [PMID: 11262399 DOI: 10.1074/jbc.m011118200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have found the gene for a translation elongation factor Tu (EF-Tu) homologue in the genome of the nematode Caenorhabditis elegans. Because the corresponding protein was detected immunologically in a nematode mitochondrial (mt) extract, it could be regarded as a nematode mt EF-Tu. The protein possesses an extension of about 57 amino acids (we call this domain 3') at the C terminus, which is not found in any other known EF-Tu. Because most nematode mt tRNAs lack a T stem, domain 3' may be related to this feature. The nematode EF-Tu bound to nematode T stem-lacking tRNA, but bacterial EF-Tu was unable to do so. A series of domain exchange experiments strongly suggested that domains 3 and 3' are essential for binding to T stem-lacking tRNAs. This finding may constitute a novel example of the co-evolution of a structurally simplified RNA and the cognate RNA-binding protein, the latter having apparently acquired an additional domain to compensate for the lack of a binding site(s) on the RNA.
Collapse
Affiliation(s)
- T Ohtsuki
- Department of Chemistry, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Lavrov DV, Brown WM. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. Genetics 2001; 157:621-37. [PMID: 11156984 PMCID: PMC1461501 DOI: 10.1093/genetics/157.2.621] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The complete mitochondrial DNA (mtDNA) of the nematode Trichinella spiralis has been amplified in four overlapping fragments and 16,656 bp of its sequence has been determined. This sequence contains the 37 genes typical of metazoan mtDNAs, including a putative atp8, which is absent from all other nematode mtDNAs examined. The genes are transcribed from both mtDNA strands and have an arrangement relatable to those of coelomate metazoans, but not to those of secernentean nematodes. All protein genes appear to initiate with ATN codons, typical for metazoans. Neither TTG nor GTT start codons, inferred for several genes of other nematodes, were found. The 22 T. spiralis tRNA genes fall into three categories: (i) those with the potential to form conventional "cloverleaf" secondary structures, (ii) those with TPsiC arm + variable arm replacement loops, and (iii) those with DHU-arm replacement loops. Mt-tRNA(R) has a 5'-UCG-3' anticodon, as in most other metazoans, instead of the very unusual 5'-ACG-3' present in the secernentean nematodes. The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level.
Collapse
Affiliation(s)
- D V Lavrov
- Department of Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA.
| | | |
Collapse
|
49
|
Abstract
With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.
Collapse
|
50
|
Masta SE. Mitochondrial sequence evolution in spiders: intraspecific variation in tRNAs lacking the TPsiC Arm. Mol Biol Evol 2000; 17:1091-100. [PMID: 10889222 DOI: 10.1093/oxfordjournals.molbev.a026390] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Analyses of mitochondrial DNA sequences from three species of Habronattus jumping spiders (Chelicerata: Arachnida: Araneae) reveal unusual inferred tRNA secondary structures and gene arrangements, providing new information on tRNA evolution within chelicerate arthropods. Sequences from the protein-coding genes NADH dehydrogenase subunit 1 (ND1), cytochrome oxidase subunit I (COI), and subunit II (COII) were obtained, along with tRNA, tRNA, and large-subunit ribosomal RNA (16S) sequences; these revealed several peculiar features. First, inferred secondary structures of tRNA and, likely, tRNA, lack the TPsiC arm and the variable arm and therefore do not form standard cloverleaf structures. In place of these arms is a 5-6-nt T arm-variable loop (TV) replacement loop such as that originally described from nematode mitochondrial tRNAs. Intraspecific variation occurs in the acceptor stem sequences in both tRNAs. Second, while the proposed secondary structure of the 3' end of 16S is similar to that reported for insects, the sequence at the 5' end is extremely divergent, and the entire gene is truncated about 300 nt with respect to Drosophila yakuba. Third, initiation codons appear to consist of ATY (ATT and ATC) and TTG for ND1 and COII, respectively. Finally, Habronattus shares the same ND1-tRNA-16S gene arrangement as insects and crustaceans, thus illustrating variation in a tRNA gene arrangement previously proposed as a character distinguishing chelicerates from insects and crustaceans.
Collapse
Affiliation(s)
- S E Masta
- Department of Ecology and Evolutionary Biology, University of Arizona, Arizona, USA.
| |
Collapse
|