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Wesp V, Theißen G, Schuster S. Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content. Sci Rep 2023; 13:22996. [PMID: 38151539 PMCID: PMC10752896 DOI: 10.1038/s41598-023-49626-9] [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: 06/13/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
Knowledge of the frequencies of synonymous triplets in protein-coding and non-coding DNA stretches can be used in gene finding. These frequencies depend on the GC content of the genome or parts of it. An example of interest is provided by stop codons. This is relevant for the definition of Open Reading Frames. A generic case is provided by pseudo-random sequences, especially when they code for complex proteins or when they are non-coding and not subject to selection pressure. Here, we calculate, for such sequences and for all 25 known genetic codes, the frequency of each amino acid and stop codon based on their set of codons and as a function of GC content. The amino acids can be classified into five groups according to the GC content where their expected frequency reaches its maximum. We determine the overall Shannon information based on groups of synonymous codons and show that it becomes maximum at a percent GC of 43.3% (for the standard code). This is in line with the observation that in most fungi, plants, and animals, this genomic parameter is in the range from 35 to 50%. By analysing natural sequences, we show that there is a clear bias for triplets corresponding to stop codons near the 5'- and 3'-splice sites in the introns of various clades.
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Affiliation(s)
- Valentin Wesp
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
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2
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Corrêa de Barros R, Moreira da Rocha R. Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.
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3
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Žihala D, Eliáš M. Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae. Genome Biol Evol 2020; 11:2992-3007. [PMID: 31617565 PMCID: PMC6821328 DOI: 10.1093/gbe/evz210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/15/2022] Open
Abstract
Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.
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Affiliation(s)
- David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
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Abstract
Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.
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Affiliation(s)
- Julien Pichon
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.,Université de Paris, Paris, France
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.,The Francis Crick Institute, London, NW1 1AT, UK.,Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
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5
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Gonzalez DL, Giannerini S, Rosa R. On the origin of degeneracy in the genetic code. Interface Focus 2019; 9:20190038. [PMID: 31641429 PMCID: PMC6802134 DOI: 10.1098/rsfs.2019.0038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023] Open
Abstract
The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.
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Affiliation(s)
- D L Gonzalez
- CNR-IMM, UOS di Bologna, Via Gobetti 101, 40129 Bologna, Italy.,Dipartimento di Scienze Statistiche, Università di Bologna, via delle Belle Arti 41, 40126 Bologna, Italy
| | - S Giannerini
- Dipartimento di Scienze Statistiche, Università di Bologna, via delle Belle Arti 41, 40126 Bologna, Italy
| | - R Rosa
- CNR-IMM, UOS di Bologna, Via Gobetti 101, 40129 Bologna, Italy
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6
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Perseke M, Golombek A, Schlegel M, Struck TH. The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Mol Phylogenet Evol 2013; 66:898-905. [DOI: 10.1016/j.ympev.2012.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 11/09/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
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7
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Görlich D, Dittrich P. Molecular codes in biological and chemical reaction networks. PLoS One 2013; 8:e54694. [PMID: 23372756 PMCID: PMC3553058 DOI: 10.1371/journal.pone.0054694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 12/17/2012] [Indexed: 01/15/2023] Open
Abstract
Shannon’s theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process “meaningful” information from those that do not. Here, we present a formal method to assess a system’s semantic capacity by analyzing a reaction network’s capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems posses different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.
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Affiliation(s)
- Dennis Görlich
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Jena, Germany
- Institute of Biostatistics and Clinical Research, University of Muenster, Muenster, Germany
| | - Peter Dittrich
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Jena, Germany
- * E-mail:
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8
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Abascal F, Posada D, Zardoya R. The evolution of the mitochondrial genetic code in arthropods revisited. ACTA ACUST UNITED AC 2012; 23:84-91. [PMID: 22397376 DOI: 10.3109/19401736.2011.653801] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A variant of the invertebrate mitochondrial genetic code was previously identified in arthropods (Abascal et al. 2006a, PLoS Biol 4:e127) in which, instead of translating the AGG codon as serine, as in other invertebrates, some arthropods translate AGG as lysine. Here, we revisit the evolution of the genetic code in arthropods taking into account that (1) the number of arthropod mitochondrial genomes sequenced has triplicated since the original findings were published; (2) the phylogeny of arthropods has been recently resolved with confidence for many groups; and (3) sophisticated probabilistic methods can be applied to analyze the evolution of the genetic code in arthropod mitochondria. According to our analyses, evolutionary shifts in the genetic code have been more common than previously inferred, with many taxonomic groups displaying two alternative codes. Ancestral character-state reconstruction using probabilistic methods confirmed that the arthropod ancestor most likely translated AGG as lysine. Point mutations at tRNA-Lys and tRNA-Ser correlated with the meaning of the AGG codon. In addition, we identified three variables (GC content, number of AGG codons, and taxonomic information) that best explain the use of each of the two alternative genetic codes.
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Affiliation(s)
- Federico Abascal
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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9
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Faure E, Delaye L, Tribolo S, Levasseur A, Seligmann H, Barthélémy RM. Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene. Biol Direct 2011; 6:56. [PMID: 22024028 PMCID: PMC3214167 DOI: 10.1186/1745-6150-6-56] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 10/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as mitochondrial DNA (mtDNA). Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1). PRESENTATION OF THE HYPOTHESIS A positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. This putative gene has been named gau for gene antisense ubiquitous in mtDNAs. The length of the deduced protein is approximately 100 amino acids. In vertebrates, several stop codons have been found in the mt gau region, and potentially functional gau regions have been found in nuclear genomes. However, a recent bioinformatics study showed that several hypothetical overlapping mt genes could be predicted, including gau; this involves the possible import of the cytosolic AGR tRNA into the mitochondria and/or the expression of mt antisense tRNAs with anticodons recognizing AGR codons according to an alternative genetic code that is induced by the presence of suppressor tRNAs. Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. Moreover, BLAST analysis identified rare, sense-oriented ESTs with poly(A) tails that include the entire gau region. Immunohistochemical analyses using an anti-Gau monoclonal antibody revealed strict co-localization of Gau proteins and a mitochondrial marker. TESTING THE HYPOTHESIS This hypothesis could be tested by purifying the gau gene product and determining its sequence. Cell biological experiments are needed to determine the physiological role of this protein. IMPLICATIONS OF THE HYPOTHESIS Studies of the gau ORF will shed light on the origin of novel genes and their functions in organelles and could also have medical implications for human diseases that are caused by mitochondrial dysfunction. Moreover, this strengthens evidence for mitochondrial genes coded according to an overlapping genetic code.
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Affiliation(s)
- Eric Faure
- Université de Provence, Marseille cedex 3, France.
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10
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Suzuki T, Miyauchi K, Suzuki T, Yokobori SI, Shigi N, Kondow A, Takeuchi N, Yamagishi A, Watanabe K. Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria. J Biol Chem 2011; 286:35494-35498. [PMID: 21873425 PMCID: PMC3195572 DOI: 10.1074/jbc.m111.279810] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/09/2011] [Indexed: 11/06/2022] Open
Abstract
Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm(5)U) at the anticodon wobble positions of tRNA(Met)(AUR), tRNA(Trp)(UGR), and tRNA(Gly)(AGR), suggesting that τm(5)U plays a critical role in the accurate deciphering of all four non-universal codes by preventing the misreading of pyrimidine-ending near-cognate codons (NNY) in their respective family boxes. Acquisition of the wobble modification appears to be a prerequisite for the genetic code alteration.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shin-Ichi Yokobori
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Naoki Shigi
- Biomedicinal Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Akiko Kondow
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Nono Takeuchi
- Department of Medical Genome, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwa, Chiba 277-8652, Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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11
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Watanabe K, Yokobori SI. tRNA Modification and Genetic Code Variations in Animal Mitochondria. J Nucleic Acids 2011; 2011:623095. [PMID: 22007289 PMCID: PMC3191813 DOI: 10.4061/2011/623095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/04/2011] [Indexed: 12/03/2022] Open
Abstract
In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNATrp for UGA, tRNAMet for AUA, tRNAAsn for AAA, and tRNASer and tRNAGly for AGA/AGG) are all modified; tRNATrp has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNAMet has 5-formylcytidine or 5-taurinomethyluridine, tRNASer has 7-methylguanosine and tRNAGly has 5-taurinomethyluridine in their anticodon wobble position, and tRNAAsn has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
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Affiliation(s)
- Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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12
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The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol 2011; 11:134. [PMID: 21599892 PMCID: PMC3121625 DOI: 10.1186/1471-2148-11-134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/20/2011] [Indexed: 11/30/2022] Open
Abstract
Background The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution. Results The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys. Conclusion A strong reversed asymmetrical mutational constraint in the mitochondrial genome of Rhabdopleura compacta may have arisen by an inversion of the replication direction and adaptation to this bias in the protein sequences leading to an enigmatic mitochondrial genome. Although, phylogenetic analyses of protein coding sequences are hampered, features of the tRNA system of R. compacta support the monophyly of Ambulacraria. The identical reassignment of AGG to Lysine in two distinct groups may have occurred by convergent evolution in the anticodon sequence of the tRNALys.
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13
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Yu H, Li Q. Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS One 2011; 6:e16147. [PMID: 21267462 PMCID: PMC3022732 DOI: 10.1371/journal.pone.0016147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 12/07/2010] [Indexed: 11/19/2022] Open
Abstract
Background Animal mitochondrial genomes typically encode one tRNA for each synonymous codon family, so that each tRNA anticodon essentially has to wobble to recognize two or four synonymous codons. Several factors have been hypothesized to determine the nucleotide at the wobble site of a tRNA anticodon in mitochondrial genomes, such as the codon-anticodon adaptation hypothesis, the wobble versatility hypothesis, the translation initiation and elongation conflict hypothesis, and the wobble cost hypothesis. Principal Findings In this study, we analyzed codon usage and tRNA anticodon wobble sites of 29 marine bivalve mitochondrial genomes to evaluate features of the wobble nucleotides in tRNA anticodons. The strand-specific mutation bias favors G and T on the H strand in all the 29 marine bivalve mitochondrial genomes. A bias favoring G and T is also visible in the third codon positions of protein-coding genes and the wobble sites of anticodons, rejecting that codon usage bias drives the wobble sites of tRNA anticodons or tRNA anticodon bias drives the evolution of codon usage. Almost all codon families (98.9%) from marine bivalve mitogenomes support the wobble versatility hypothesis. There are a few interesting exceptions involving tRNATrp with an anticodon CCA fixed in Pectinoida species, tRNASer with a GCU anticodon fixed in Mytiloida mitogenomes, and the uniform anticodon CAU of tRNAMet translating the AUR codon family. Conclusions/Significance These results demonstrate that most of the nucleotides at the wobble sites of tRNA anticodons in marine bivalve mitogenomes are determined by wobble versatility. Other factors such as the translation initiation and elongation conflict, and the cost of wobble translation may contribute to the determination of the wobble nucleotide in tRNA anticodons. The finding presented here provides valuable insights into the previous hypotheses of the wobble nucleotide in tRNA anticodons by adding some new evidence.
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Affiliation(s)
- Hong Yu
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Qi Li
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
- * E-mail:
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14
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Yu H, Li Q. Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS One 2011; 6:e16147. [PMID: 21267462 DOI: 10.1371/journal.pone0016147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 12/07/2010] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Animal mitochondrial genomes typically encode one tRNA for each synonymous codon family, so that each tRNA anticodon essentially has to wobble to recognize two or four synonymous codons. Several factors have been hypothesized to determine the nucleotide at the wobble site of a tRNA anticodon in mitochondrial genomes, such as the codon-anticodon adaptation hypothesis, the wobble versatility hypothesis, the translation initiation and elongation conflict hypothesis, and the wobble cost hypothesis. PRINCIPAL FINDINGS In this study, we analyzed codon usage and tRNA anticodon wobble sites of 29 marine bivalve mitochondrial genomes to evaluate features of the wobble nucleotides in tRNA anticodons. The strand-specific mutation bias favors G and T on the H strand in all the 29 marine bivalve mitochondrial genomes. A bias favoring G and T is also visible in the third codon positions of protein-coding genes and the wobble sites of anticodons, rejecting that codon usage bias drives the wobble sites of tRNA anticodons or tRNA anticodon bias drives the evolution of codon usage. Almost all codon families (98.9%) from marine bivalve mitogenomes support the wobble versatility hypothesis. There are a few interesting exceptions involving tRNA(Trp) with an anticodon CCA fixed in Pectinoida species, tRNA(Ser) with a GCU anticodon fixed in Mytiloida mitogenomes, and the uniform anticodon CAU of tRNA(Met) translating the AUR codon family. CONCLUSIONS/SIGNIFICANCE These results demonstrate that most of the nucleotides at the wobble sites of tRNA anticodons in marine bivalve mitogenomes are determined by wobble versatility. Other factors such as the translation initiation and elongation conflict, and the cost of wobble translation may contribute to the determination of the wobble nucleotide in tRNA anticodons. The finding presented here provides valuable insights into the previous hypotheses of the wobble nucleotide in tRNA anticodons by adding some new evidence.
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Affiliation(s)
- Hong Yu
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
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15
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Masuda I, Matsuzaki M, Kita K. Extensive frameshift at all AGG and CCC codons in the mitochondrial cytochrome c oxidase subunit 1 gene of Perkinsus marinus (Alveolata; Dinoflagellata). Nucleic Acids Res 2010; 38:6186-94. [PMID: 20507907 PMCID: PMC2952869 DOI: 10.1093/nar/gkq449] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Diverse mitochondrial (mt) genetic systems have evolved independently of the more uniform nuclear system and often employ modified genetic codes. The organization and genetic system of dinoflagellate mt genomes are particularly unusual and remain an evolutionary enigma. We determined the sequence of full-length cytochrome c oxidase subunit 1 (cox1) mRNA of the earliest diverging dinoflagellate Perkinsus and show that this gene resides in the mt genome. Apparently, this mRNA is not translated in a single reading frame with standard codon usage. Our examination of the nucleotide sequence and three-frame translation of the mRNA suggest that the reading frame must be shifted 10 times, at every AGG and CCC codon, to yield a consensus COX1 protein. We suggest two possible mechanisms for these translational frameshifts: a ribosomal frameshift in which stalled ribosomes skip the first bases of these codons or specialized tRNAs recognizing non-triplet codons, AGGY and CCCCU. Regardless of the mechanism, active and efficient machinery would be required to tolerate the frameshifts predicted in Perkinsus mitochondria. To our knowledge, this is the first evidence of translational frameshifts in protist mitochondria and, by far, is the most extensive case in mitochondria.
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Affiliation(s)
- Isao Masuda
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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16
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Watanabe K. Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:11-39. [PMID: 20075606 PMCID: PMC3417567 DOI: 10.2183/pjab.86.11] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 11/17/2009] [Indexed: 05/17/2023]
Abstract
In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.
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Affiliation(s)
- Kimitsuna Watanabe
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
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17
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Massey SE, Garey JR. A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs. J Mol Evol 2007; 64:399-410. [PMID: 17390094 DOI: 10.1007/s00239-005-0260-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.
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Affiliation(s)
- Steven E Massey
- Department of Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
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18
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Abascal F, Posada D, Knight RD, Zardoya R. Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol 2006; 4:e127. [PMID: 16620150 PMCID: PMC1440934 DOI: 10.1371/journal.pbio.0040127] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 02/17/2006] [Indexed: 11/18/2022] Open
Abstract
The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.
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Affiliation(s)
- Federico Abascal
- Departamento de Bioquímica, Genética, e Inmunología, Universidad de Vigo, Vigo, Spain.
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19
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Sakurai M, Ohtsuki T, Suzuki T, Watanabe K. Unusual usage of wobble modifications in mitochondrial tRNAs of the nematode Ascaris suum. FEBS Lett 2005; 579:2767-72. [PMID: 15907479 DOI: 10.1016/j.febslet.2005.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 04/05/2005] [Accepted: 04/07/2005] [Indexed: 10/25/2022]
Abstract
To understand the decoding property of nematode mitochondrial tRNAs with unusual secondary structures, post-transcriptional modifications at wobble positions of Ascaris suum mitochondrial tRNAs corresponding to two-codon families ending with a purine were analyzed. 5-Carboxymethylaminomethyluridine (cmnm(5)U) was identified at the wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln), while 5-carboxymethylaminomethyl-2-thiouridine (cmnm(5)s(2)U) was present in tRNA(UAA)(Leu)andtRNA(Trp). In most bacterial and mitochondrial tRNAs, the 2-thiouridine derivative is present in tRNAs for Lys, Glu and Gln. These is no report that cmnm(5)s(2)U is used in tRNA(UAA)(Leu)andtRNA(Trp). The unusual usage of wobble modifications might assist decoding of nematode mitochondrial mRNAs.
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Affiliation(s)
- Masayuki Sakurai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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20
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Nohara M, Nishida M, Miya M, Nishikawa T. Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species. J Mol Evol 2005; 60:526-37. [PMID: 15883887 DOI: 10.1007/s00239-004-0238-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 11/07/2004] [Indexed: 11/26/2022]
Abstract
Complete mitochondrial (mt) DNA sequences of two lancelets, Epigonichthys maldivensis and E. lucayanus, were compared with those of two Branchiostoma lancelets and several deuterostomes previously surveyed. The mt-gene order of E. lucayanus was quite different from that of E. maldivensis, the latter being identical to the two Branchiostoma species. A remarkable genomic change in E. lucayanus mtDNA was an inversion, indicating the possibility of recombination of the mt-genome. Gene rearrangements, probably attributable to tandem genome duplications and subsequent random deletions, were observed in two parts. Short major unassignable sequences of the examined lancelets were regarded as a part of putative regulative elements, judging from some sequence similarity to the conserved sequence block (CSB) in mammalian mtDNA. The considerable mt-genome reorganization in E. lucayanus seemed to have affected the nucleotide substitution pattern, suggested by base composition analyses. The present analysis also suggested that AGR codons in lancelet mtDNA were likely to correspond to serine residue, rather than glycine. Furthermore, the AGG codon, so far reputed to be unassignable in lancelet mtDNA, was found twice in E. maldivensis, indicating the availability of all four AGN codons in some lancelets. This finding lends support to an alternative hypothesis regarding the evolutionary history of AGR-codon assignment in extant chordates, rather than that previously proposed. A molecular phylogenetic tree of the Epigonichthys and Branchiostoma species based on DNA sequences of the 13 mt-protein genes doubted the monophyly of the former genus, unlike the prevailing classification based on their different gonadal arrangements.
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Affiliation(s)
- Masahiro Nohara
- Yokohama R&D Center, HITEC Co., Ltd., 3-55-1 Hagoromo-cho, Naka-ku, Yokohama, Kanagawa, 231-0047, Japan
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21
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Abstract
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a new framework for codon reassignment that incorporates two previously proposed mechanisms (codon disappearance and ambiguous intermediate) and introduces two further mechanisms (unassigned codon and compensatory change). Our theory is based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA or the gain of function of an existing tRNA due to mutation or base modification. The four mechanisms are distinguished by whether the codon disappears from the genome during the reassignment and by the order of the gain and loss events. We present simulations of the gain-loss model showing that all four mechanisms can occur within the same framework as the parameters are varied. We investigate the way the frequencies of the mechanisms are influenced by selection strengths, the number of codons undergoing reassignment, directional mutation pressure, and selection for reduced genome size.
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Affiliation(s)
- Supratim Sengupta
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
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22
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Yokobori SI, Oshima T, Wada H. Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates. Mol Phylogenet Evol 2004; 34:273-83. [PMID: 15619441 DOI: 10.1016/j.ympev.2004.10.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2004] [Revised: 09/28/2004] [Accepted: 10/01/2004] [Indexed: 10/26/2022]
Abstract
The evolutionary history of the diverse lifestyles adopted by urochordates has attracted intense interest because it may effect the evolutionary history of vertebrates. Here, we report the complete mitochondrial (mt) DNA sequence of the pelagic thaliacean doliolid Doliolum nationalis. The doliolid mt genome shares the unusual tRNAs of trnM(uau) and trnG(ucu) with other ascidians, such as Halocynthia and Ciona. On the other hand, the gene order of the doliolid mt genome is significantly different from that of any ascidian species or vertebrate reported to date. Phylogenetic analyses of the amino acid sequences of 12 protein-coding genes strongly support the sister-grouping of doliolids and the Phlebobranch ascidian Ciona, with the Stolidobranch ascidian alocynthia as the outgroup, thereby providing strong support for the paraphyly of ascidians, as has been suggested by 18S rDNA studies. Given the paraphyletic nature of ascidians, it seems likely that the common ancestor of ascidians and thaliaceans was sessile, as are the present-day ascidians, and that the thaliaceans subsequently evolved a pelagic lifestyle.
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Affiliation(s)
- Shin-ichi Yokobori
- Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan.
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23
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Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K. Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J 2002; 21:6581-9. [PMID: 12456664 PMCID: PMC136959 DOI: 10.1093/emboj/cdf656] [Citation(s) in RCA: 273] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Taurine (2-aminoethanesulphonic acid), a naturally occurring, sulfur-containing amino acid, is found at high concentrations in mammalian plasma and tissues. Although taurine is involved in a variety of processes in humans, it has never been found as a component of a protein or a nucleic acid, and its precise biochemical functions are not fully understood. Here, we report the identification of two novel taurine-containing modified uridines (5-taurinomethyluridine and 5-taurinomethyl-2-thiouridine) in human and bovine mitochondrial tRNAs. Our work further revealed that these nucleosides are synthesized by the direct incorporation of taurine supplied to the medium. This is the first reported evidence that taurine is a constituent of biological macromolecules, unveiling the prospect of obtaining new insights into the functions and subcellular localization of this abundant amino acid. Since modification of these taurine-containing uridines has been found to be lacking in mutant mitochondrial tRNAs for Leu(UUR) and Lys from pathogenic cells of the mitochondrial encephalomyopathies MELAS and MERRF, respectively, our findings will considerably deepen our understanding of the molecular pathogenesis of mitochondrial encephalomyopathic diseases.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering and Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-301, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan Corresponding authors e-mail: or T.Suzuki and T.Suzuki contributed equally to this work
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering and Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-301, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan Corresponding authors e-mail: or T.Suzuki and T.Suzuki contributed equally to this work
| | - Takeshi Wada
- Department of Chemistry and Biotechnology, Graduate School of Engineering and Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-301, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan Corresponding authors e-mail: or T.Suzuki and T.Suzuki contributed equally to this work
| | - Kazuhiko Saigo
- Department of Chemistry and Biotechnology, Graduate School of Engineering and Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-301, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan Corresponding authors e-mail: or T.Suzuki and T.Suzuki contributed equally to this work
| | - Kimitsuna Watanabe
- Department of Chemistry and Biotechnology, Graduate School of Engineering and Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-301, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan Corresponding authors e-mail: or T.Suzuki and T.Suzuki contributed equally to this work
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24
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Hanada T, Suzuki T, Yokogawa T, Takemoto-Hori C, Sprinzl M, Watanabe K. Translation ability of mitochondrial tRNAsSer with unusual secondary structures in an in vitro translation system of bovine mitochondria. Genes Cells 2001; 6:1019-30. [PMID: 11737263 DOI: 10.1046/j.1365-2443.2001.00491.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Metazoan mitochondrial (mt) tRNAs are structurally quite different from the canonical cloverleaf secondary structure. The mammalian mt tRNASerGCU for AGY codons (Y = C or U) lacks the entire D arm, whereas tRNASerUGA for UCN codons (N = A, G, C or U) has an extended anti-codon stem. It has been a long-standing problem to prove experimentally how these tRNAsSer work in the mt translation system. RESULTS To solve the above-mentioned problem, we examined their translational abilities in an in vitro bovine mitochondrial translation system using transcripts of altered tRNASer analogues derived from bovine mitochondria. Both tRNASer analogues had almost the same ability to form ternary complexes with mt EF-Tu and GTP. The D-arm-lacking tRNASer GCU analogue had considerably lower translational activity than the tRNASerUGA analogue and produced mostly short oligopeptides, up to a tetramer. In addition, tRNASerGCU analogue was disfavoured by the ribosome when other tRNAs capable of decoding the cognate codon were available. CONCLUSION Both mt tRNASerGCU and tRNASerUGA analogues with unusual secondary structure were found to be capable of translation on the ribosome. However, the tRNASerGCU analogue has some molecular disadvantage on the ribosome, which probably derives from the lack of a D arm.
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Affiliation(s)
- T Hanada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Yokobori SI, Ueda T, Feldmaier-Fuchs G, Pääbo S, Ueshima R, Kondow A, Nishikawa K, Watanabe K. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 1999; 153:1851-62. [PMID: 10581290 PMCID: PMC1460873 DOI: 10.1093/genetics/153.4.1851] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.
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Affiliation(s)
- S i Yokobori
- Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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26
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Tomita K, Ueda T, Ishiwa S, Crain PF, McCloskey JA, Watanabe K. Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria. Nucleic Acids Res 1999; 27:4291-7. [PMID: 10518623 PMCID: PMC148706 DOI: 10.1093/nar/27.21.4291] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial (mt) tRNA(Trp), tRNA(Ile), tRNA(Met), tRNA(Ser)GCU, tRNA(Asn)and tRNA(Lys)were purified from Drosophila melanogaster (fruit fly) and their nucleotide sequences were determined. tRNA(Lys)corresponding to both AAA and AAG lysine codons was found to contain the anticodon CUU, C34 at the wobble position being unmodified. tRNA(Met)corresponding to both AUA and AUG methionine codons was found to contain 5-formylcytidine (f(5)C) at the wobble position, although the extent of modification is partial. These results suggest that both C and f(5)C as the wobble bases at the anticodon first position (position 34) can recognize A at the codon third position (position 3) in the fruit fly mt translation system. tRNA(Ser)GCU corresponding to AGU, AGC and AGA serine codons was found to contain unmodified G at the anticodon wobble position, suggesting the utilization of an unconventional G34-A3 base pair during translation. When these tRNA anticodon sequences are compared with those of other animal counterparts, it is concluded that either unmodified C or G at the wobble position can recognize A at the codon third position and that modification from A to t(6)A at position 37, 3'-adjacent to the anticodon, seems to be important for tRNA possessing C34 to recognize A3 in the mRNA in the fruit fly mt translation system.
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MESH Headings
- Animals
- Anticodon/genetics
- Base Pairing/genetics
- Base Sequence
- Chromatography, High Pressure Liquid
- Chromatography, Thin Layer
- Codon/genetics
- Drosophila melanogaster/classification
- Drosophila melanogaster/cytology
- Drosophila melanogaster/genetics
- Genetic Code
- Mass Spectrometry
- Mitochondria/genetics
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Protein Biosynthesis/genetics
- RNA/chemistry
- RNA/genetics
- RNA/isolation & purification
- RNA, Mitochondrial
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/isolation & purification
- Ribonuclease H/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- K Tomita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113, Japan
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