1
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Hayashi S. Variation of tRNA modifications with and without intron dependency. Front Genet 2024; 15:1460902. [PMID: 39296543 PMCID: PMC11408192 DOI: 10.3389/fgene.2024.1460902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 08/26/2024] [Indexed: 09/21/2024] Open
Abstract
tRNAs have recently gained attention for their novel regulatory roles in translation and for their diverse functions beyond translation. One of the most remarkable aspects of tRNA biogenesis is the incorporation of various chemical modifications, ranging from simple base or ribose methylation to more complex hypermodifications such as formation of queuosine and wybutosine. Some tRNAs are transcribed as intron-containing pre-tRNAs. While the majority of these modifications occur independently of introns, some are catalyzed in an intron-inhibitory manner, and in certain cases, they occur in an intron-dependent manner. This review focuses on pre-tRNA modification, including intron-containing pre-tRNA, in both intron-inhibitory and intron-dependent fashions. Any perturbations in the modification and processing of tRNAs may lead to a range of diseases and disorders, highlighting the importance of understanding these mechanisms in molecular biology and medicine.
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Affiliation(s)
- Sachiko Hayashi
- Graduate School of Science, University of Hyogo, Ako-gun, Japan
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2
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Valentin-Alvarado LE, Appler KE, De Anda V, Schoelmerich MC, West-Roberts J, Kivenson V, Crits-Christoph A, Ly L, Sachdeva R, Greening C, Savage DF, Baker BJ, Banfield JF. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nat Commun 2024; 15:6384. [PMID: 39085194 PMCID: PMC11291895 DOI: 10.1038/s41467-024-49872-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kathryn E Appler
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Environmental Systems Sciences; ETH Zürich, Zürich, Switzerland
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexander Crits-Christoph
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Cultivarium, Watertown, MA, USA
| | - Lynn Ly
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
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3
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Yuan L, Han Y, Zhao J, Zhang Y, Sun Y. Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex. Nat Commun 2023; 14:6071. [PMID: 37770519 PMCID: PMC10539383 DOI: 10.1038/s41467-023-41845-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Removal of introns from transfer RNA precursors (pre-tRNAs) occurs in all living organisms. This is a vital phase in the maturation and functionality of tRNA. Here we present a 3.2 Å-resolution cryo-EM structure of an active human tRNA splicing endonuclease complex bound to an intron-containing pre-tRNA. TSEN54, along with the unique regions of TSEN34 and TSEN2, cooperatively recognizes the mature body of pre-tRNA and guides the anticodon-intron stem to the correct position for splicing. We capture the moment when the endonucleases are poised for cleavage, illuminating the molecular mechanism for both 3' and 5' cleavage reactions. Two insertion loops from TSEN54 and TSEN2 cover the 3' and 5' splice sites, respectively, trapping the scissile phosphate in the center of the catalytic triad of residues. Our findings reveal the molecular mechanism for eukaryotic pre-tRNA recognition and cleavage, as well as the evolutionary relationship between archaeal and eukaryotic TSENs.
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Affiliation(s)
- Ling Yuan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yaoyao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jiazheng Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yixiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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4
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Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. New insights into RNA processing by the eukaryotic tRNA splicing endonuclease. J Biol Chem 2023; 299:105138. [PMID: 37544645 PMCID: PMC10485636 DOI: 10.1016/j.jbc.2023.105138] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
Through its role in intron cleavage, tRNA splicing endonuclease (TSEN) plays a critical function in the maturation of intron-containing pre-tRNAs. The catalytic mechanism and core requirement for this process is conserved between archaea and eukaryotes, but for decades, it has been known that eukaryotic TSENs have evolved additional modes of RNA recognition, which have remained poorly understood. Recent research identified new roles for eukaryotic TSEN, including processing or degradation of additional RNA substrates, and determined the first structures of pre-tRNA-bound human TSEN complexes. These recent discoveries have changed our understanding of how the eukaryotic TSEN targets and recognizes substrates. Here, we review these recent discoveries, their implications, and the new questions raised by these findings.
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Affiliation(s)
- Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
| | - Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National, Institutes of Health, Research Triangle Park, North Carolina, USA.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA.
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5
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Nagato Y, Tomikawa C, Yamaji H, Soma A, Takai K. Intron-Dependent or Independent Pseudouridylation of Precursor tRNA Containing Atypical Introns in Cyanidioschyzon merolae. Int J Mol Sci 2022; 23:ijms232012058. [PMID: 36292915 PMCID: PMC9602550 DOI: 10.3390/ijms232012058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic precursor tRNAs (pre-tRNAs) often have an intron between positions 37 and 38 of the anticodon loop. However, atypical introns are found in some eukaryotes and archaea. In an early-diverged red alga Cyanidioschyzon merolae, the tRNAIle(UAU) gene contains three intron coding regions, located in the D-, anticodon, and T-arms. In this study, we focused on the relationship between the intron removal and formation of pseudouridine (Ψ), one of the most universally modified nucleosides. It had been reported that yeast Pus1 is a multiple-site-specific enzyme that synthesizes Ψ34 and Ψ36 in tRNAIle(UAU) in an intron-dependent manner. Unexpectedly, our biochemical experiments showed that the C. merolae ortholog of Pus1 pseudouridylated an intronless tRNAIle(UAU) and that the modification position was determined to be 55 which is the target of Pus4 but not Pus1 in yeast. Furthermore, unlike yeast Pus1, cmPus1 mediates Ψ modification at positions 34, 36, and/or 55 only in some specific intron-containing pre-tRNAIle(UAU) variants. cmPus4 was confirmed to be a single-site-specific enzyme that only converts U55 to Ψ, in a similar manner to yeast Pus4. cmPus4 did not catalyze the pseudouridine formation in pre-tRNAs containing an intron in the T-arm.
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Affiliation(s)
- Yasuha Nagato
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Ehime, Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Ehime, Japan
- Correspondence: ; Tel.: +81-89-927-9947
| | - Hideyuki Yamaji
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Ehime, Japan
| | - Akiko Soma
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Chiba, Japan
| | - Kazuyuki Takai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Ehime, Japan
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6
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Sekulovski S, Trowitzsch S. Transfer RNA processing - from a structural and disease perspective. Biol Chem 2022; 403:749-763. [PMID: 35728022 DOI: 10.1515/hsz-2021-0406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/24/2022] [Indexed: 01/05/2023]
Abstract
Transfer RNAs (tRNAs) are highly structured non-coding RNAs which play key roles in translation and cellular homeostasis. tRNAs are initially transcribed as precursor molecules and mature by tightly controlled, multistep processes that involve the removal of flanking and intervening sequences, over 100 base modifications, addition of non-templated nucleotides and aminoacylation. These molecular events are intertwined with the nucleocytoplasmic shuttling of tRNAs to make them available at translating ribosomes. Defects in tRNA processing are linked to the development of neurodegenerative disorders. Here, we summarize structural aspects of tRNA processing steps with a special emphasis on intron-containing tRNA splicing involving tRNA splicing endonuclease and ligase. Their role in neurological pathologies will be discussed. Identification of novel RNA substrates of the tRNA splicing machinery has uncovered functions unrelated to tRNA processing. Future structural and biochemical studies will unravel their mechanistic underpinnings and deepen our understanding of neurological diseases.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
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7
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Gerber JL, Köhler S, Peschek J. Eukaryotic tRNA splicing - one goal, two strategies, many players. Biol Chem 2022; 403:765-778. [PMID: 35621519 DOI: 10.1515/hsz-2021-0402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/10/2022] [Indexed: 12/28/2022]
Abstract
Transfer RNAs (tRNAs) are transcribed as precursor molecules that undergo several maturation steps before becoming functional for protein synthesis. One such processing mechanism is the enzyme-catalysed splicing of intron-containing pre-tRNAs. Eukaryotic tRNA splicing is an essential process since intron-containing tRNAs cannot fulfil their canonical function at the ribosome. Splicing of pre-tRNAs occurs in two steps: The introns are first excised by a tRNA-splicing endonuclease and the exons are subsequently sealed by an RNA ligase. An intriguing complexity has emerged from newly identified tRNA splicing factors and their interplay with other RNA processing pathways during the past few years. This review summarises our current understanding of eukaryotic tRNA splicing and the underlying enzyme machinery. We highlight recent structural advances and how they have shaped our mechanistic understanding of tRNA splicing in eukaryotic cells. A special focus lies on biochemically distinct strategies for exon-exon ligation in fungi versus metazoans.
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Affiliation(s)
- Janina L Gerber
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Sandra Köhler
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Jirka Peschek
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
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8
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Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova K, Koonin E, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Res 2022; 50:4601-4615. [PMID: 35466371 PMCID: PMC9071458 DOI: 10.1093/nar/gkac271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
Site-specific incorporation of distinct non-canonical amino acids into proteins via genetic code expansion requires mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. Pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs are ideal for genetic code expansion and have been extensively engineered for developing mutually orthogonal pairs. Here, we identify two novel wild-type PylRS/tRNAPyl pairs simultaneously present in the deep-rooted extremely halophilic euryarchaeal methanogen Candidatus Methanohalarchaeum thermophilum HMET1, and show that both pairs are functional in the model halophilic archaeon Haloferax volcanii. These pairs consist of two different PylRS enzymes and two distinct tRNAs with dissimilar discriminator bases. Surprisingly, these two PylRS/tRNAPyl pairs display mutual orthogonality enabled by two unique features, the A73 discriminator base of tRNAPyl2 and a shorter motif 2 loop in PylRS2. In vivo translation experiments show that tRNAPyl2 charging by PylRS2 is defined by the enzyme's shortened motif 2 loop. Finally, we demonstrate that the two HMET1 PylRS/tRNAPyl pairs can simultaneously decode UAG and UAA codons for incorporation of two distinct noncanonical amino acids into protein. This example of a single base change in a tRNA leading to additional coding capacity suggests that the growth of the genetic code is not yet limited by the number of identity elements fitting into the tRNA structure.
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Affiliation(s)
| | | | | | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Huiming Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuxing Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,Sino-Danish College, University of the Chinese Academy of Sciences, Beijing, China
| | - Paul Wassel
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yue Shen
- Correspondence may also be addressed to Yue Shen.
| | - Dieter Söll
- To whom correspondence should be addressed. Tel: +1 203 4326200;
| | - Xian Fu
- Correspondence may also be addressed to Xian Fu.
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9
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Tocchini-Valentini GD, Tocchini-Valentini GP. Archaeal tRNA-Splicing Endonuclease as an Effector for RNA Recombination and Novel Trans-Splicing Pathways in Eukaryotes. J Fungi (Basel) 2021; 7:jof7121069. [PMID: 34947051 PMCID: PMC8707768 DOI: 10.3390/jof7121069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
We have characterized a homodimeric tRNA endonuclease from the euryarchaeota Ferroplasma acidarmanus (FERAC), a facultative anaerobe which can grow at temperatures ranging from 35 to 42 °C. This enzyme, contrary to the eukaryal tRNA endonucleases and the homotetrameric Methanocaldococcus jannaschii (METJA) homologs, is able to cleave minimal BHB (bulge–helix–bulge) substrates at 30 °C. The expression of this enzyme in Schizosaccharomyces pombe (SCHPO) enables the use of its properties as effectors by inserting BHB motif introns into hairpin loops normally seen in mRNA transcripts. In addition, the FERAC endonuclease can create proteins with new functionalities through the recombination of protein domains.
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Affiliation(s)
- Giuseppe D. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
- Correspondence:
| | - Glauco P. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
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10
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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: 787] [Impact Index Per Article: 196.8] [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.
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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
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11
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Schwarz TS, Berkemer SJ, Bernhart SH, Weiß M, Ferreira-Cerca S, Stadler PF, Marchfelder A. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. Front Microbiol 2020; 11:594838. [PMID: 33329479 PMCID: PMC7714728 DOI: 10.3389/fmicb.2020.594838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.
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Affiliation(s)
| | - Sarah J Berkemer
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions, Leipzig University, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Matthias Weiß
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Peter F Stadler
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Santa Fe Institute, Santa Fe, NM, United States
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12
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Qi L, Li J, Jia J, Yue L, Dong X. Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea. RNA Biol 2020; 17:1427-1441. [PMID: 32449429 DOI: 10.1080/15476286.2020.1771946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNAAla-23S-tRNACys-5S) in Methanolobus psychrophilus, one representative of methanoarchaea. Enzymatic assay demonstrated that EndA, a tRNA splicing endoribonuclease, cleaved bulge-helix-bulge (BHB) motifs buried in the processing stems of pre-16S and pre-23S rRNAs. Northern blot and quantitative PCR detected splicing-coupled circularization of pre-16S and pre-23S rRNAs, which accounted for 2% and 12% of the corresponding rRNAs, respectively. Importantly, endoribonuclease Nob1 was determined to linearize circular pre-16S rRNA at the mature 3' end so to expose the anti-Shine-Dalgarno sequence, while circular pre-23S rRNA was linearized at the mature 5' end by an unknown endoribonuclease. The resultant 5' and 3' extension in linearized pre-16S and pre-23S rRNAs were finally matured through 5'-3' and 3'-5' exoribonucleolytic trimming, respectively. Additionally, a novel processing pathway of endoribonucleolysis coupled with exoribonucleolysis was identified for the pre-5S rRNA maturation in this methanogen, which could be also conserved in most methanogenic euryarchaea. Based on evaluating the phylogenetic conservation of the key elements that are involved in circularization and linearization of pre-rRNA maturation, we predict that the rRNA maturation mode revealed here could be prevalent among archaea.
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Affiliation(s)
- Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Jia Jia
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
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13
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Yang S, Qu G, Fu B, Yang F, Zeng W, Cai Y, Ye T, Yang Y, Deng X, Xiang W, Peng D, Zhou B. The function of KptA/Tpt1 gene - a minor review. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:577-591. [PMID: 32438974 DOI: 10.1071/fp19159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/06/2020] [Indexed: 06/11/2023]
Abstract
Rapid response of uni- and multicellular organisms to environmental changes and their own growth is achieved through a series of molecular mechanisms, often involving modification of macromolecules, including nucleic acids, proteins and lipids. The ADP-ribosylation process has ability to modify these different macromolecules in cells, and is closely related to the biological processes, such as DNA replication, transcription, signal transduction, cell division, stress, microbial aging and pathogenesis. In addition, tRNA plays an essential role in the regulation of gene expression, as effector molecules, no-load tRNA affects the overall gene expression level of cells under some nutritional stress. KptA/Tpt1 is an essential phosphotransferase in the process of pre-tRNA splicing, releasing mature tRNA and participating in ADP-ribose. The objective of this review is concluding the gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms. At the same time, the results of promoter elements analysis were also shown in the present study. Moreover, the problems in the function of KptA/Tpt1 that have not been clarified at the present time are summarised, and some suggestions to solve those problems are given. This review presents no only a summary of clear function of KptA/Tpt1 in the process of tRNA splicing and ADP-ribosylation of organisms, but also gives some proposals to clarify unclear problems of it in the future.
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Affiliation(s)
- Shiquan Yang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Gaoyi Qu
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Bixia Fu
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Feng Yang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Weixian Zeng
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Yunzhang Cai
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Tao Ye
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | | | - Xiangwen Deng
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China
| | - Wenhua Xiang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China
| | - Dan Peng
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and Forestry Biotechnology Hunan Key Laboratories, Changsha, Hunan, 410004, China
| | - Bo Zhou
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China; and Forestry Biotechnology Hunan Key Laboratories, Changsha, Hunan, 410004, China; and Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; and Corresponding author.
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14
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Schmidt CA, Giusto JD, Bao A, Hopper AK, Matera AG. Molecular determinants of metazoan tricRNA biogenesis. Nucleic Acids Res 2020; 47:6452-6465. [PMID: 31032518 PMCID: PMC6614914 DOI: 10.1093/nar/gkz311] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Mature tRNAs are generated by multiple post-transcriptional processing steps, which can include intron removal. Recently, we discovered a new class of circular non-coding RNAs in metazoans, called tRNA intronic circular (tric)RNAs. To investigate the mechanism of tricRNA biogenesis, we generated constructs that replace native introns of human and fruit fly tRNA genes with the Broccoli fluorescent RNA aptamer. Using these reporters, we identified cis-acting elements required for tricRNA formation in vivo. Disrupting a conserved base pair in the anticodon-intron helix dramatically reduces tricRNA levels. Although the integrity of this base pair is necessary for proper splicing, it is not sufficient. In contrast, strengthening weak bases in the helix also interferes with splicing and tricRNA production. Furthermore, we identified trans-acting factors important for tricRNA biogenesis, including several known tRNA processing enzymes such as the RtcB ligase and components of the TSEN endonuclease complex. Depletion of these factors inhibits Drosophila tRNA intron circularization. Notably, RtcB is missing from fungal genomes and these organisms normally produce linear tRNA introns. Here, we show that in the presence of ectopic RtcB, yeast lacking the tRNA ligase Rlg1/Trl1 are converted into producing tricRNAs. In summary, our work characterizes the major players in eukaryotic tricRNA biogenesis.
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Affiliation(s)
- Casey A Schmidt
- Curriculum in Genetics & Molecular Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph D Giusto
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alicia Bao
- Center for RNA Biology and Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Anita K Hopper
- Center for RNA Biology and Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - A Gregory Matera
- Curriculum in Genetics & Molecular Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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15
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Payea MJ, Hauke AC, De Zoysa T, Phizicky EM. Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast. RNA (NEW YORK, N.Y.) 2020; 26:29-43. [PMID: 31619505 PMCID: PMC6913130 DOI: 10.1261/rna.073155.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/11/2019] [Indexed: 05/20/2023]
Abstract
During tRNA maturation in yeast, aberrant pre-tRNAs are targeted for 3'-5' degradation by the nuclear surveillance pathway, and aberrant mature tRNAs are targeted for 5'-3' degradation by the rapid tRNA decay (RTD) pathway. RTD is catalyzed by the 5'-3' exonucleases Xrn1 and Rat1, which act on tRNAs with an exposed 5' end due to the lack of certain body modifications or the presence of destabilizing mutations in the acceptor stem, T-stem, or tRNA fold. RTD is inhibited by mutation of MET22, likely due to accumulation of the Met22 substrate adenosine 3',5' bis-phosphate, which inhibits 5'-3' exonucleases. Here we provide evidence for a new tRNA quality control pathway in which intron-containing pre-tRNAs with destabilizing mutations in the anticodon stem are targeted for Met22-dependent pre-tRNA decay (MPD). Multiple SUP4οc anticodon stem variants that are subject to MPD each perturb the bulge-helix-bulge structure formed by the anticodon stem-loop and intron, which is important for splicing, resulting in substantial accumulation of end-matured unspliced pre-tRNA as well as pre-tRNA decay. Mutations that restore exon-intron structure commensurately reduce pre-tRNA accumulation and MPD. The MPD pathway can contribute substantially to decay of anticodon stem variants, since pre-tRNA decay is largely suppressed by removal of the intron or by restoration of exon-intron structure, each also resulting in increased tRNA levels. The MPD pathway is general as it extends to variants of tRNATyr(GUA) and tRNASer(CGA) These results demonstrate that the integrity of the anticodon stem-loop and the efficiency of tRNA splicing are monitored by a quality control pathway.
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Affiliation(s)
- Matthew J Payea
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Thareendra De Zoysa
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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16
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Schmidt CA, Matera AG. tRNA introns: Presence, processing, and purpose. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1583. [DOI: 10.1002/wrna.1583] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Casey A. Schmidt
- Curriculum in Genetics and Molecular Biology Integrative Program for Biological and Genome Sciences, University of North Carolina Chapel Hill North Carolina
| | - A. Gregory Matera
- Curriculum in Genetics and Molecular Biology Integrative Program for Biological and Genome Sciences, University of North Carolina Chapel Hill North Carolina
- Department of Biology, Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina
- Department of Genetics, Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina
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17
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Wang Y, Zeng Z, Liu TL, Sun L, Yao Q, Chen KP. TA, GT and AC are significantly under-represented in open reading frames of prokaryotic and eukaryotic protein-coding genes. Mol Genet Genomics 2019; 294:637-647. [PMID: 30758669 DOI: 10.1007/s00438-019-01535-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/31/2019] [Indexed: 01/01/2023]
Abstract
Genomes can be considered a combination of 16 dinucleotides. Analysing the relative abundance of different dinucleotides may reveal important features of genome evolution. In present study, we conducted extensive surveys on the relative abundances of dinucleotides in various genomic components of 28 bacterial, 20 archaean, 19 fungal, 24 plant and 29 animal species. We found that TA, GT and AC are significantly under-represented in open reading frames of all organisms and in intergenic regions and introns of most organisms. Specific dinucleotides are of greatly varied usage at different codon positions. The significantly low representations of TA, GT and AC are considered the evolutionary consequences of preventing formation of pre-mature stop codons and of reducing intron-splicing options in candidate primary mRNA sequences. These data suggest that a reduction of TA and GT occurred on both strands of the DNA sequence at an early stage of de novo gene birth. Interestingly, GT and AC are also significantly under-represented in current prokaryotic genomes, suggesting that ancient prokaryotic protein-coding genes might have contained introns. The greatly varied usages of specific dinucleotides at different codon positions are considered evolutionary accommodations to compensate the unavailability of specific codons and to avoid formation of pre-mature stop codons. This is the first report presenting data of dinucleotide relative abundance to indicate the possible existence of spliceosomal introns in ancient prokaryotic genes and to hypothesize early steps of de novo gene birth.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Zhen Zeng
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Tian-Lei Liu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Ling Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Ke-Ping Chen
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
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18
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Hirata A. Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases. Front Genet 2019; 10:103. [PMID: 30809252 PMCID: PMC6379350 DOI: 10.3389/fgene.2019.00103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
RNA-splicing endonuclease (EndA) cleaves out introns from archaeal and eukaryotic precursor (pre)-tRNA and is essential for tRNA maturation. In archaeal EndA, the molecular mechanisms underlying complex assembly, substrate recognition, and catalysis have been well understood. Recently, certain studies have reported novel findings including the identification of new subunit types in archaeal EndA structures, providing insights into the mechanism underlying broad substrate specificity. Further, metagenomics analyses have enabled the acquisition of numerous DNA sequences of EndAs and intron-containing pre-tRNAs from various species, providing information regarding the co-evolution of substrate specificity of archaeal EndAs and tRNA genetic diversity, and the evolutionary pathway of archaeal and eukaryotic EndAs. Although the complex structure of the heterothermic form of eukaryotic EndAs is unknown, previous reports regarding their functions indicated that mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly, and yeast EndA significantly cleaves mitochondria-localized mRNA encoding cytochrome b mRNA processing 1 (Cpb1) for mRNA maturation. This mini-review summarizes the aforementioned results, discusses their implications, and offers my personal opinion regarding future directions for the analysis of the structure and function of EndAs.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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19
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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20
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Wu Y, Wu P, Wang B, Shao ZQ. Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea. Front Microbiol 2018; 9:1245. [PMID: 29930548 PMCID: PMC6000648 DOI: 10.3389/fmicb.2018.01245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 05/23/2018] [Indexed: 12/02/2022] Open
Abstract
Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Ping Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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21
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Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A. The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res 2018; 46:1958-1972. [PMID: 29346615 PMCID: PMC5829648 DOI: 10.1093/nar/gky003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/25/2017] [Accepted: 01/03/2018] [Indexed: 11/14/2022] Open
Abstract
Four different types (α4, α'2, (αβ)2 and ϵ2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αβ)2 and ϵ2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αβ)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and β subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (αβ)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (αβ)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.
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Affiliation(s)
- Ayano Kaneta
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Wataru Morikazu
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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22
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23
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Wang Y, Tao XF, Su ZX, Liu AK, Liu TL, Sun L, Yao Q, Chen KP, Gu X. Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization. Evol Bioinform Online 2016; 12:303-312. [PMID: 27980385 PMCID: PMC5154736 DOI: 10.4137/ebo.s40703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/18/2016] [Accepted: 09/22/2016] [Indexed: 12/04/2022] Open
Abstract
Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5′-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5′-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xia-Fang Tao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Zhi-Xi Su
- School of Life Sciences, Fudan University, Shanghai, China
| | - A-Ke Liu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Tian-Lei Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ling Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-Ping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gu
- School of Life Sciences, Fudan University, Shanghai, China.; Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life. Life (Basel) 2016; 6:life6010012. [PMID: 26999216 PMCID: PMC4810243 DOI: 10.3390/life6010012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.
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25
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Jay ZJ, Inskeep WP. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. Biol Direct 2015; 10:35. [PMID: 26156036 PMCID: PMC4496867 DOI: 10.1186/s13062-015-0065-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022] Open
Abstract
Background Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Results Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. Conclusions The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis. Reviewers This article was reviewed by Dr. Eugene Koonin and Dr. W. Ford Doolittle. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0065-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
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26
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Lopes RRS, Kessler AC, Polycarpo C, Alfonzo JD. Cutting, dicing, healing and sealing: the molecular surgery of tRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:337-49. [PMID: 25755220 DOI: 10.1002/wrna.1279] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 11/09/2022]
Abstract
All organisms encode transfer RNAs (tRNAs) that are synthesized as precursor molecules bearing extra sequences at their 5' and 3' ends; some tRNAs also contain introns, which are removed by splicing. Despite commonality in what the ultimate goal is (i.e., producing a mature tRNA), mechanistically, tRNA splicing differs between Bacteria and Archaea or Eukarya. The number and position of tRNA introns varies between organisms and even between different tRNAs within the same organism, suggesting a degree of plasticity in both the evolution and persistence of modern tRNA splicing systems. Here we will review recent findings that not only highlight nuances in splicing pathways but also provide potential reasons for the maintenance of introns in tRNA. Recently, connections between defects in the components of the tRNA splicing machinery and medically relevant phenotypes in humans have been reported. These differences will be discussed in terms of the importance of splicing for tRNA function and in a broader context on how tRNA splicing defects can often have unpredictable consequences.
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Affiliation(s)
- Raphael R S Lopes
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biotecnologia e Biologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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27
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Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution. Life (Basel) 2015; 5:321-31. [PMID: 25629271 PMCID: PMC4390854 DOI: 10.3390/life5010321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/14/2015] [Accepted: 01/21/2015] [Indexed: 01/17/2023] Open
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70-100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. Thus, study of the evolution of tRNA molecules may reveal the processes that led to the establishment of the central dogma: genetic information flows from DNA to RNA to protein. Thanks to the development of DNA sequencers in this century, we have determined a huge number of nucleotide sequences from complete genomes as well as from transcriptomes in many species. Recent analyses of these large data sets have shown that particular tRNA genes, especially in Archaea, are disrupted in unique ways: some tRNA genes contain multiple introns and some are split genes. Even tRNA molecules themselves are fragmented post-transcriptionally in many species. These fragmented small RNAs are known as tRNA-derived fragments (tRFs). In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves.
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28
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Experimental confirmation of a whole set of tRNA molecules in two archaeal species. Int J Mol Sci 2015; 16:2187-203. [PMID: 25608653 PMCID: PMC4307357 DOI: 10.3390/ijms16012187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/17/2022] Open
Abstract
Based on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Creanarchaeota, Aeropyrum pernix and Sulfolobus tokodaii, were determined approximately 15 years ago. In these genome datasets, 47 and 46 tRNA genes were detected, respectively. Among them, 14 and 24 genes, respectively, were predicted to be interrupted tRNA genes. To confirm the actual transcription of these predicted tRNA genes and identify the actual splicing patterns of the predicted interrupted tRNA molecules, RNA samples were prepared from each archaeal species and used to synthesize cDNA molecules with tRNA sequence-specific primers. Comparison of the nucleotide sequences of cDNA clones representing unspliced and spliced forms of interrupted tRNA molecules indicated that some introns were located at positions other than one base 3' from anticodon region and that bulge-helix-bulge structures were detected around the actual splicing sites in each interrupted tRNA molecule. Whole-set analyses of tRNA molecules revealed that the archaeal tRNA splicing mechanism may be essential for efficient splicing of all tRNAs produced from interrupted tRNA genes in these archaea.
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29
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Mitra S, Das P, Samadder A, Das S, Betai R, Chakrabarti J. Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates. J Biomol Struct Dyn 2015; 33:2104-20. [PMID: 25581620 DOI: 10.1080/07391102.2014.990925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promoter sequences, namely, A-Box and B-Box, were investigated and evidence gathered that the intervention of optional nucleotides at 17a and 17b correlated with the optimal length of the A-Box. The presence of canonical transcription terminator sequences at the immediate vicinity of tRNA genes was ventured. Even though non-canonical introns had been reported in red alga, green alga, and nucleomorph so far, fairly motivating evidence of their existence emerged in tRNA genes of other eukaryotes. Non-canonical introns were seen to interfere with the internal promoters in two cases, questioning their transcription fidelity. In a first of its kind, phylogenetic constructs based on tRNA molecules delineated and built the trees of the vast and diverse invertebrates and vertebrates. Finally, two tRNA models representing the invertebrates and the vertebrates were drawn, by isolating the dominant consensus in the positional fluctuations of nucleotide compositions.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Kolkata 700032 , India
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30
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Yoshihisa T. Handling tRNA introns, archaeal way and eukaryotic way. Front Genet 2014; 5:213. [PMID: 25071838 PMCID: PMC4090602 DOI: 10.3389/fgene.2014.00213] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/20/2014] [Indexed: 11/25/2022] Open
Abstract
Introns are found in various tRNA genes in all the three kingdoms of life. Especially, archaeal and eukaryotic genomes are good sources of tRNA introns that are removed by proteinaceous splicing machinery. Most intron-containing tRNA genes both in archaea and eukaryotes possess an intron at a so-called canonical position, one nucleotide 3′ to their anticodon, while recent bioinformatics have revealed unusual types of tRNA introns and their derivatives especially in archaeal genomes. Gain and loss of tRNA introns during various stages of evolution are obvious both in archaea and eukaryotes from analyses of comparative genomics. The splicing of tRNA molecules has been studied extensively from biochemical and cell biological points of view, and such analyses of eukaryotic systems provided interesting findings in the past years. Here, I summarize recent progresses in the analyses of tRNA introns and the splicing process, and try to clarify new and old questions to be solved in the next stages.
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Affiliation(s)
- Tohru Yoshihisa
- Graduate School of Life Science, University of Hyogo Ako-gun, Hyogo, Japan
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31
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Abstract
In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Scott William Roy
- Department of Biology, San Francisco State University, San Francisco, California 94132
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32
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Fujishima K, Kanai A. tRNA gene diversity in the three domains of life. Front Genet 2014; 5:142. [PMID: 24904642 PMCID: PMC4033280 DOI: 10.3389/fgene.2014.00142] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022] Open
Abstract
Transfer RNA (tRNA) is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs) are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs) possess long variable arms that are specific to eukaryotic class II tRNASer and tRNALeu but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus, this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.
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Affiliation(s)
- Kosuke Fujishima
- NASA Ames Research Center Moffett Field, CA, USA ; Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
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33
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34
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Soma A. Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development. Front Genet 2014; 5:63. [PMID: 24744771 PMCID: PMC3978253 DOI: 10.3389/fgene.2014.00063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/12/2014] [Indexed: 12/02/2022] Open
Abstract
A number of genome analyses and searches using programs that focus on the RNA-specific bulge-helix-bulge (BHB) motif have uncovered a wide variety of disrupted tRNA genes. The results of these analyses have shown that genetic information encoding functional RNAs is described in the genome cryptically and is retrieved using various strategies. One such strategy is represented by circularly permuted tRNA genes, in which the sequences encoding the 5′-half and 3′-half of the specific tRNA are separated and inverted on the genome. Biochemical analyses have defined a processing pathway in which the termini of tRNA precursors (pre-tRNAs) are ligated to form a characteristic circular RNA intermediate, which is then cleaved at the acceptor-stem to generate the typical cloverleaf structure with functional termini. The sequences adjacent to the processing site located between the 3′-half and the 5′-half of pre-tRNAs potentially form a BHB motif, which is the dominant recognition site for the tRNA-intron splicing endonuclease, suggesting that circularization of pre-tRNAs depends on the splicing machinery. Some permuted tRNAs contain a BHB-mediated intron in their 5′- or 3′-half, meaning that removal of an intron, as well as swapping of the 5′- and 3′-halves, are required during maturation of their pre-tRNAs. To date, 34 permuted tRNA genes have been identified from six species of unicellular algae and one archaeon. Although their physiological significance and mechanism of development remain unclear, the splicing system of BHB motifs seems to have played a key role in the formation of permuted tRNA genes. In this review, current knowledge of circularly permuted tRNA genes is presented and some unanswered questions regarding these species are discussed.
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Affiliation(s)
- Akiko Soma
- Graduate School of Horticulture, Chiba University Matsudo, Japan
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35
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Soma A, Sugahara J, Onodera A, Yachie N, Kanai A, Watanabe S, Yoshikawa H, Ohnuma M, Kuroiwa H, Kuroiwa T, Sekine Y. Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep 2014; 3:2321. [PMID: 23900518 PMCID: PMC3728597 DOI: 10.1038/srep02321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/10/2013] [Indexed: 12/03/2022] Open
Abstract
The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 3′-half of the tRNA coding sequence lies upstream of the 5′-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.
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Affiliation(s)
- Akiko Soma
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
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36
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Su AAH, Tripp V, Randau L. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 2013; 41:6250-8. [PMID: 23620296 PMCID: PMC3695527 DOI: 10.1093/nar/gkt317] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/03/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022] Open
Abstract
The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.
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MESH Headings
- Euryarchaeota/genetics
- Euryarchaeota/metabolism
- High-Throughput Nucleotide Sequencing
- Hot Temperature
- Inverted Repeat Sequences
- RNA Editing
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- Andreas A. H. Su
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
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37
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Zuo Z, Peng D, Yin X, Zhou X, Cheng H, Zhou R. Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves. Mol Biol Evol 2013; 30:2087-98. [PMID: 23744908 DOI: 10.1093/molbev/mst107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transfer RNAs (tRNAs) play an important role linking mitochondrial RNA and amino acids during protein biogenesis. Four types of tRNA genes have been identified in living organisms. However, the evolutionary origin of tRNAs remains largely unknown. In this article, we conduct a deep sequence analysis of diverse genomes that cover all three domains of life to unveil the evolutionary history of tRNA genes from tRNA halves. tRNA half homologs were detected in diverse organisms, and some of them were expressed in mouse tissues. Continuous tRNA genes have a conserved pattern similar to indels, which is, more closely flanking regions have higher single nucleotide substitution rates, whereas tRNA half homologs do not have this pattern. In addition, tRNAs tend to break into tRNA halves when tissues are incubated in vitro, the tendency of tRNA to break into tRNA halves may be a "side-effect" of tRNA genes evolving from tRNA halves. These results suggest that modern tRNAs originated from tRNA halves through a repeat element-mediated mechanism. These findings provide insight into the evolutionary origin of tRNA genes.
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Affiliation(s)
- Zhixiang Zuo
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
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38
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Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol 2013; 10:1204-10. [PMID: 23702463 DOI: 10.4161/rna.24972] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Prokaryotic transcripts constitute almost always uninterrupted intervals when mapped back to the genome. Split reads, i.e., RNA-seq reads consisting of parts that only map to discontiguous loci, are thus disregarded in most analysis pipelines. There are, however, some well-known exceptions, in particular, tRNA splicing and circularized small RNAs in Archaea as well as self-splicing introns. Here, we reanalyze a series of published RNA-seq data sets, screening them specifically for non-contiguously mapping reads. We recover most of the known cases together with several novel archaeal ncRNAs associated with circularized products. In Eubacteria, only a handful of interesting candidates were obtained beyond a few previously described group I and group II introns. Most of the atypically mapping reads do not appear to correspond to well-defined, specifically processed products. Whether this diffuse background is, at least in part, an incidental by-product of prokaryotic RNA processing or whether it consists entirely of technical artifacts of reverse transcription or amplification remains unknown.
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Affiliation(s)
- Gero Doose
- Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Leipzig, Germany; Transcriptome Bioinformatics; LIFE - Leipzig Research Center for Civilization Diseases; University of Leipzig; Leipzig, Germany
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39
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Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes. Proc Natl Acad Sci U S A 2012; 109:21325-9. [PMID: 23236183 DOI: 10.1073/pnas.1219336110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unusual tRNA genes, found in some algae, have their mature terminal 3' portion in front of their 5' portion in the genome. The transcripts from such genes must be cleaved by a pre-tRNA endonuclease to form a functional tRNA. We present a mechanism for the generation of "corrected" tRNAs from such a "permuted" pre-tRNA configuration. We used two avatar (av) or model pre-tRNAs and two splicing endonucleases with distinct mechanisms of recognition of the pre-tRNA. The splicing results are compatible with an evolutionary route in which permuted genes result from a duplication event followed by DNA rearrangement. The model pre-tRNAs permit description of the features that a transcript, derived from a rearranged duplicated gene, must have to give rise to functional tRNA. The two tRNA endonucleases are a eukaryal enzyme that normally acts in a mature domain-dependent mode and an archaeal enzyme that acts in a mature domain-independent mode. Both av pre-tRNAs are able to fold into two conformations: 1 and 2. We find that only conformation 2 can yield a corrected functional tRNA. This result is consistent with contemporary algae representing snapshots of different evolutionary stages, with duplicated genes preceding recombinatorial events generating a permutated gene. In a scenario elucidated by the use of the av pre-tRNAs, algal permuted tRNA genes could have further lost one of two mature domains, eliminating steric problems for the algal tRNA endonuclease, which remains a typical eukaryal enzyme capable of correcting the permuted transcript to a functional tRNA.
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40
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Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res 2012; 40:10554-66. [PMID: 22941657 PMCID: PMC3488258 DOI: 10.1093/nar/gks826] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cleavage of introns from precursor transfer RNAs (tRNAs) by tRNA splicing endonuclease (EndA) is essential for tRNA maturation in Archaea and Eukarya. In the past, archaeal EndAs were classified into three types (α′2, α4 and α2β2) according to subunit composition. Recently, we have identified a fourth type of archaeal EndA from an uncultivated archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2, which is deeply branched within Euryarchaea. The ARMAN-2 EndA forms an ε2 homodimer and has broad substrate specificity like the α2β2 type EndAs found in Crenarchaea and Nanoarchaea. However, the precise architecture of ARMAN-2 EndA was unknown. Here, we report the crystal structure of the ε2 homodimer of ARMAN-2 EndA. The structure reveals that the ε protomer is separated into three novel units (αN, α and βC) fused by two distinct linkers, although the overall structure of ARMAN-2 EndA is similar to those of the other three types of archaeal EndAs. Structural comparison and mutational analyses reveal that an ARMAN-2 type-specific loop (ASL) is involved in the broad substrate specificity and that K161 in the ASL functions as the RNA recognition site. These findings suggest that the broad substrate specificities of ε2 and α2β2 EndAs were separately acquired through different evolutionary processes.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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41
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Popow J, Schleiffer A, Martinez J. Diversity and roles of (t)RNA ligases. Cell Mol Life Sci 2012; 69:2657-70. [PMID: 22426497 PMCID: PMC3400036 DOI: 10.1007/s00018-012-0944-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 12/29/2022]
Abstract
The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.
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Affiliation(s)
- Johannes Popow
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
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Sugahara J, Fujishima K, Nunoura T, Takaki Y, Takami H, Takai K, Tomita M, Kanai A. Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One 2012; 7:e32504. [PMID: 22403667 PMCID: PMC3293823 DOI: 10.1371/journal.pone.0032504] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/31/2012] [Indexed: 11/27/2022] Open
Abstract
Understanding the mechanistic basis of the disruption of tRNA genes, as manifested in the intron-containing and split tRNAs found in Archaea, will provide considerable insight into the evolution of the tRNA molecule. However, the evolutionary processes underlying these disruptions have not yet been identified. Previously, a composite genome of the deep-branching archaeon Caldiarchaeum subterraneum was reconstructed from a community genomic library prepared from a C. subterraneum–dominated microbial mat. Here, exploration of tRNA genes from the library reveals that there are at least three types of heterogeneity at the tRNAThr(GGU) gene locus in the Caldiarchaeum population. All three involve intronic gain and splitting of the tRNA gene. Of two fosmid clones found that encode tRNAThr(GGU), one (tRNAThr-I) contains a single intron, whereas another (tRNAThr-II) contains two introns. Notably, in the clone possessing tRNAThr-II, a 5′ fragment of the tRNAThr-I (tRNAThr-F) gene was observed 1.8-kb upstream of tRNAThr-II. The composite genome contains both tRNAThr-II and tRNAThr-F, although the loci are >500 kb apart. Given that the 1.8-kb sequence flanked by tRNAThr-F and tRNAThr-II is predicted to encode a DNA recombinase and occurs in six regions of the composite genome, it may be a transposable element. Furthermore, its dinucleotide composition is most similar to that of the pNOB8-type plasmid, which is known to integrate into archaeal tRNA genes. Based on these results, we propose that the gain of the tRNA intron and the scattering of the tRNA fragment occurred within a short time frame via the integration and recombination of a mobile genetic element.
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Affiliation(s)
- Junichi Sugahara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Kosuke Fujishima
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Takuro Nunoura
- Subsurface Geobiology & Advanced Research Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Ken Takai
- Subsurface Geobiology & Advanced Research Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail:
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Chen WY, Singh D, Lai LB, Stiffler MA, Lai HD, Foster MP, Gopalan V. Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors. Nucleic Acids Res 2012; 40:4666-80. [PMID: 22298511 PMCID: PMC3378863 DOI: 10.1093/nar/gks013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
RNase P, which catalyzes tRNA 5′-maturation, typically comprises a catalytic RNase P RNA (RPR) and a varying number of RNase P proteins (RPPs): 1 in bacteria, at least 4 in archaea and 9 in eukarya. The four archaeal RPPs have eukaryotic homologs and function as heterodimers (POP5•RPP30 and RPP21•RPP29). By studying the archaeal Methanocaldococcus jannaschii RPR's cis cleavage of precursor tRNAGln (pre-tRNAGln), which lacks certain consensus structures/sequences needed for substrate recognition, we demonstrate that RPP21•RPP29 and POP5•RPP30 can rescue the RPR's mis-cleavage tendency independently by 4-fold and together by 25-fold, suggesting that they operate by distinct mechanisms. This synergistic and preferential shift toward correct cleavage results from the ability of archaeal RPPs to selectively increase the RPR's apparent rate of correct cleavage by 11 140-fold, compared to only 480-fold for mis-cleavage. Moreover, POP5•RPP30, like the bacterial RPP, helps normalize the RPR's rates of cleavage of non-consensus and consensus pre-tRNAs. We also show that archaeal and eukaryal RNase P, compared to their bacterial relatives, exhibit higher fidelity of 5′-maturation of pre-tRNAGln and some of its mutant derivatives. Our results suggest that protein-rich RNase P variants might have evolved to support flexibility in substrate recognition while catalyzing efficient, high-fidelity 5′-processing.
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Affiliation(s)
- Wen-Yi Chen
- Department of Biochemistry, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Moreira S, Breton S, Burger G. Unscrambling genetic information at the RNA level. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:213-28. [PMID: 22275292 DOI: 10.1002/wrna.1106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genomics aims at unraveling the blueprint of life; however, DNA sequence alone does not always reveal the proteins and structural RNAs encoded by the genome. The reason is that genetic information is often encrypted. Recognizing the logic of encryption, and understanding how living cells decode hidden information--at the level of DNA, RNA or protein--is challenging. RNA-level decryption includes topical RNA editing and more 'macroscopic' transcript rearrangements. The latter events involve the four types of introns recognized to date, notably spliceosomal, group I, group II, and archaeal/tRNA splicing. Intricate variants, such as alternative splicing and trans-splicing, have been reported for each intron type, but the biological significance has not always been confirmed. Novel RNA-level unscrambling processes were recently discovered in mitochondria of dinoflagellates and diplonemids, and potentially euglenids. These processes seem not to rely on known introns, and the corresponding molecular mechanisms remain to be elucidated.
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Affiliation(s)
- Sandrine Moreira
- Robert-Cedergren Centre for Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada
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Chan PP, Holmes AD, Smith AM, Tran D, Lowe TM. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res 2011; 40:D646-52. [PMID: 22080555 PMCID: PMC3245099 DOI: 10.1093/nar/gkr990] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.
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Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA
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Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res 2011; 39:9695-704. [PMID: 21880595 PMCID: PMC3239211 DOI: 10.1093/nar/gkr692] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
tRNA splicing endonucleases, essential enzymes found in Archaea and Eukaryotes, are involved in the processing of pre-tRNA molecules. In Archaea, three types of splicing endonuclease [homotetrameric: α4, homodimeric: α2, and heterotetrameric: (αβ)2] have been identified, each representing different substrate specificity during the tRNA intron cleavage. Here, we discovered a fourth type of archaeal tRNA splicing endonuclease (ε2) in the genome of the acidophilic archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2 and its closely related species, ARMAN-1. The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a novel three-unit architecture. Homodimeric formation was confirmed by cross-linking assay, and site-directed mutagenesis determined that the conserved L10-pocket interaction between catalytic and structural unit is necessary for the assembly. A tRNA splicing assay reveal that ε2 endonuclease cleaves both canonical and non-canonical bulge–helix–bulge motifs, similar to that of (αβ)2 endonuclease. Unlike other ARMAN and Euryarchaeota, tRNAs found in ARMAN-2 are highly disrupted by introns at various positions, which again resemble the properties of archaeal species with (αβ)2 endonuclease. Thus, the discovery of ε2 endonuclease in an archaeon deeply branched within Euryarchaeota represents a new example of the coevolution of tRNA and their processing enzymes.
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Affiliation(s)
- Kosuke Fujishima
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
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Yamazaki S, Yoshinari S, Kita K, Watanabe YI, Kawarabayasi Y. Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7. Gene 2011; 489:103-10. [PMID: 21872648 DOI: 10.1016/j.gene.2011.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 11/25/2022]
Abstract
The acidothermophilic crenarchaeon, Sulfolobus tokodaii strain7, was isolated from a hot spring in Beppu, Kyushu, Japan. Whole genomic data of this microorganism indicated that among 46 putative tRNA genes identified, 24 were interrupted tRNA genes containing an intron. A sequence comparison between the cDNA sequences for unspliced and spliced tRNAs indicated that all predicted tRNAs were expressed and all intron portions were spliced in this microorganism. However, the actual cleavage site in the splicing process was not determined for 13 interrupted tRNAs because of the presence of the same nucleotides at both 5' and 3' border regions of each intron. The cleavage sites for all the introns, which were determined by an in vitro cleavage experiment with recombinant splicing endonuclease as well as cDNA sequencing of the spliced tRNAs, indicated that non-canonical BHB structure motifs were also recognized and processed by the splicing machinery in this organism. This is the first report to empirically determine the actual cleavage and splice sites of introns in the whole set of archaeal tRNA genes, and reassigns the exon-intron borders with a novel and more plausible non-canonical BHB structure.
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Affiliation(s)
- Syuji Yamazaki
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo, Japan
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Hirata A, Kitajima T, Hori H. Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop. Nucleic Acids Res 2011; 39:9376-89. [PMID: 21846775 PMCID: PMC3241643 DOI: 10.1093/nar/gkr615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In Crenarchaea, several tRNA genes are predicted to express precursor-tRNAs (pre-tRNAs) with canonical or non-canonical introns at various positions. We initially focused on the tRNA(Thr) species of hyperthermophilic crenarchaeon, Aeropyrum pernix (APE) and found that in the living APE cells three tRNA(Thr) species were transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them were cleaved from standard and non-standard positions. Biochemical studies revealed that the APE splicing endonuclease (APE-EndA) removed both types of introns, including the non-canonical introns, without any nucleotide modification. To clarify the underlying reasons for broad substrate specificity of APE-EndA, we determined the crystal structure of wild-type APE-EndA and subsequently compared its structure with that of Archaeaoglobus fulgidus (AFU)-EndA, which has narrow substrate specificity. Remarkably, structural comparison revealed that APE-EndA possesses a Crenarchaea specific loop (CSL). Introduction of CSL into AFU-EndA enhanced its intron-cleaving activity irrespective of the position or motif of the intron. Thus, our biochemical and crystallographic analyses of the chimera-EndA demonstrated that the CSL is responsible for the broad substrate specificity of APE-EndA. Furthermore, mutagenesis studies revealed that Lys44 in CSL functions as the RNA recognition site.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering and Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan
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Chan PP, Cozen AE, Lowe TM. Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol 2011; 12:R38. [PMID: 21489296 PMCID: PMC3218864 DOI: 10.1186/gb-2011-12-4-r38] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/30/2011] [Accepted: 04/13/2011] [Indexed: 01/19/2023] Open
Abstract
Background As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional. Results Using an improved version of the gene-finding program tRNAscan-SE, comparative analyses and experimental verifications, we have now identified four novel trans-spliced tRNA genes, each in a different species of the Desulfurococcales branch of the Archaea: tRNAAsp(GUC) in Aeropyrum pernix and Thermosphaera aggregans, and tRNALys(CUU) in Staphylothermus hellenicus and Staphylothermus marinus. Each of these includes features surprisingly similar to previously studied split tRNAs, yet comparative genomic context analysis and phylogenetic distribution suggest several independent, relatively recent splitting events. Additionally, we identified the first examples of permuted tRNA genes in Archaea: tRNAiMet(CAU) and tRNATyr(GUA) in Thermofilum pendens, which appear to be permuted in the same arrangement seen previously in red alga. Conclusions Our findings illustrate that split tRNAs are sporadically spread across a major branch of the Archaea, and that permuted tRNAs are a new shared characteristic between archaeal and eukaryotic species. The split tRNA discoveries also provide new clues to their evolutionary history, supporting hypotheses for recent acquisition via viral or other mobile elements.
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Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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50
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Das S, Mitra S, Sahoo S, Chakrabarti J. Novel Hybrid Encodes both Continuous and Split tRNA Genes? J Biomol Struct Dyn 2011; 28:827-31. [DOI: 10.1080/07391102.2011.10508610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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