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Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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Gu XH, Guo N, Chen HX, Sitko J, Li LW, Guo BQ, Li L. Mitogenomic phylogenies suggest the resurrection of the subfamily Porrocaecinae and provide insights into the systematics of the superfamily Ascaridoidea (Nematoda: Ascaridomorpha), with the description of a new species of Porrocaecum. Parasit Vectors 2023; 16:275. [PMID: 37563590 PMCID: PMC10416420 DOI: 10.1186/s13071-023-05889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND The family Toxocaridae is a group of zooparasitic nematodes of veterinary, medical and economic significance. However, the evolutionary relationship of Porrocaecum and Toxocara, both genera currently classified in Toxocaridae, and the monophyly of the Toxocaridae remain under debate. Moreover, the validity of the subgenus Laymanicaecum in the genus Porrocaecum is open to question. Due to the scarcity of an available genetic database, molecular identification of Porrocaecum nematodes is still in its infancy. METHODS A number of Porrocaecum nematodes collected from the Eurasian marsh harrier Circus aeruginosus (Linnaeus) (Falconiformes: Accipitridae) in the Czech Republic were identified using integrated morphological methods (light and scanning electron microscopy) and molecular techniques (sequencing and analyzing the nuclear 18S, 28S and ITS regions). The complete mitochondrial genomes of the collected nematode specimens and of Porrocaecum (Laymanicaecum) reticulatum (Linstow, 1899) were sequenced and annotated for the first time. Phylogenetic analyses of ascaridoid nematodes based on the amino acid sequences of 12 protein-coding genes of mitochondrial genomes were performed using maximum likelihood and Bayesian inference. RESULTS A new species of Porrocaecum, named P. moraveci n. sp., is described based on the morphological and genetic evidence. The mitogenomes of P. moraveci n. sp. and P. reticulatum both contain 36 genes and are 14,517 and 14,210 bp in length, respectively. Comparative mitogenomics revealed that P. moraveci n. sp. represents the first known species with three non-coding regions and that P. reticulatum has the lowest overall A + T content in the mitogenomes of ascaridoid nematodes tested to date. Phylogenetic analyses showed the representatives of Toxocara clustered together with species of the family Ascarididae rather than with Porrocaecum and that P. moraveci n. sp. is a sister to P. reticulatum. CONCLUSIONS The characterization of the complete mitochondrial genomes of P. moraveci n. sp. and P. reticulatum is reported for the first time. Mitogenomic phylogeny analyses indicated that the family Toxocaridae is non-monophyletic and that the genera Porrocaecum and Toxocara do not have an affinity. The validity of the subgenus Laymanicaecum in Porrocaecum was also rejected. Our results suggest that: (i) Toxocaridae should be degraded to a subfamily of the Ascarididae that includes only the genus Toxocara; and (ii) the subfamily Porrocaecinae should be resurrected to include only the genus Porrocaecum. The present study enriches the database of ascaridoid mitogenomes and provides a new insight into the systematics of the superfamily Ascaridoidea.
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Affiliation(s)
- Xiao-Hong Gu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei Province, People's Republic of China
| | - Ning Guo
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei Province, People's Republic of China
| | - Hui-Xia Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei Province, People's Republic of China
| | - Jiljí Sitko
- Muzeum Komenského V Přerově, 750 02, Přerově, Czech Republic
| | - Lin-Wei Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China
| | - Bing-Qian Guo
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China
| | - Liang Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, People's Republic of China.
- Hebei Research Center of the Basic Discipline Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei Province, People's Republic of China.
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Deng YP, Suleman, Zhang XL, Li R, Li LY, Fu YT, Liu GH, Yao C. Aonchotheca (Nematoda: Capillariidae) is validated as a separated genus from Capillaria by both mitochondrial and nuclear ribosomal DNA. Parasit Vectors 2022; 15:493. [PMID: 36585724 PMCID: PMC9805247 DOI: 10.1186/s13071-022-05609-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca's systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. RESULTS We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69-67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61-34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. CONCLUSIONS Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae.
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Affiliation(s)
- Yuan-Ping Deng
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Suleman
- grid.502337.00000 0004 4657 4747Department of Zoology, University of Swabi, Swabi, 23561 Khyber Pakhtunkhwa Pakistan
| | - Xue-Ling Zhang
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Rong Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Le-Yan Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Yi-Tian Fu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Chaoqun Yao
- grid.412247.60000 0004 1776 0209Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae. Animals (Basel) 2022; 12:ani12243546. [PMID: 36552470 PMCID: PMC9774135 DOI: 10.3390/ani12243546] [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: 10/11/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode.
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Han L, Yang Y, Li H, Zhou X, Zhou M, Liu T, Lu Y, Wang Q, Yang S, Shi M, Li X, Du S, Guan C, Zhang Y, Guo W, Wang J, Chai H, Lan T, Liu H, Liu Q, Sun H, Hou Z. Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families. Int J Biol Macromol 2022; 221:1394-1403. [PMID: 36116597 DOI: 10.1016/j.ijbiomac.2022.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/05/2022]
Abstract
The Ascaridoidea family and Heterakoidea family are the most common and typical representative of large parasites. Although our understanding of these parasites' diversity has expanded by analyses of some mitochondrial genes, there is limited information on these species' evolutionary rates. Here we determined ten complete mitogenome sequences of five subfamilies of Ascaridoidea and one subfamily of Heterakoidea. The phylogenetic tree divided the Ascaridoidea into six monophyletic major clades, and the divergence time of Heterakoidea family and Ascaridoidea family can be placed during the early Carboniferous Period (300-360 Mya). The reconstruction of the ancestral state showed that the gene orders of all species in Ascaridoidea were conserved, and the Heterakoidea had obvious genome rearrangement. The conserved blocks between them were divided into five and the main types are tandem-duplication/random loss (TDRL). These results will help to better understand the gene rearrangements and evolutionary position of ascaris species.
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Affiliation(s)
- Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Laboratory of Vector-Borne Diseases and Pathogens Ecology, Northeast Forestry University, Harbin 150040, China
| | - Yuling Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Tianlu Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangcheng Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuyun Li
- Harbin Northern Forest Zoo, Harbin 150040, China
| | - Shan Du
- Inner Mongolia Agriculture University, Hohhot 010000, China
| | - Chunyu Guan
- Harbin Northern Forest Zoo, Harbin 150040, China
| | - Yong Zhang
- Center for Animal Disease Control and Prevention of Ordos, Inner Mongolia, Ordos 017000, China
| | - Wei Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongliang Chai
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin 150040, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; BGI Life Science Joint Research Center, Northeast Forestry University, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; BGI Life Science Joint Research Center, Northeast Forestry University, China
| | - Quan Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
| | - Heting Sun
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang, China.
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin 150040, China.
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Carreno RA, Nadler SA. PHYLOGENETIC ANALYSIS OF THE LUNGWORMS (NEMATODA: METASTRONGYLOIDEA) INFERRED USING NUCLEAR RIBOSOMAL AND MITOCHONDRIAL DNA SEQUENCES. J Parasitol 2022; 108:441-452. [PMID: 36197732 DOI: 10.1645/21-124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Phylogenetic relationships among the mammal-parasitic lungworms (Metastrongyloidea) were inferred using small- and large-subunit ribosomal DNA sequences together with 12S ribosomal mtDNA sequences. Maximum parsimony and Bayesian inference methods were used from optimal alignments and those filtered for alignment ambiguity. Analysis of 30 ingroup sequences using ribosomal DNA sequences yielded a single most parsimonious tree. Monophyly of the Metastrongyloidea was supported, but there was no support for monophyly of any of the 7 families as they have been traditionally defined. Parafilaroides decorus, an abursate lungworm of pinnipeds currently classified in the Filaroididae, was nested within a clade containing members of the Pseudaliidae, parasites of cetaceans. The tree also shows clades somewhat resembling the traditional familial divisions of the Metastrongyloidea, but in all groups, paraphyletic relationships were recovered. In a combined analysis of nuclear rDNA and 12S mtDNA, maximum parsimony and Bayesian analyses showed similar patterns to those observed with only nuclear rDNA sequences. Based on the phylogeny, the respiratory tract was inferred to be the ancestral predilection site for Metastrongyloidea, with multiple evolutionary invasions of extrapulmonary sites such as sinuses, circulatory system, and meninges. Similarly, the ancestral host was inferred to be a carnivore with subsequent colonization events into marsupial, rodent, artiodactyl, pinniped, and cetacean hosts.
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Affiliation(s)
- Ramon A Carreno
- Department of Zoology, Ohio Wesleyan University, Delaware, Ohio 43015
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, California 95616
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Liu Y, Jingjing Z, Li C. Characterization of the complete mitochondrial genome of a nematode species, Caenorhabditis tribulationis (Nematoda, Rhabditidae). Mitochondrial DNA B Resour 2022; 7:930-932. [PMID: 35692637 PMCID: PMC9176374 DOI: 10.1080/23802359.2022.2079103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
In the present study, we reported the complete mitogenome sequence of Caenorhabditis tribulationis Stevens & Félix 2019. The whole mitogenome of C. tribulationis is 14006 bp in length with an extreme bias of high AT content (75.26%) (GenBank accession no. OL362111). The mitochondrial genome contains 12 protein-coding genes (PCGs), 22 transfer RNA (tRNAs) genes, 2 ribosomal RNA (12S rRNA and 16S rRNA) genes, and a control region. All genes were unidirectionally transcribed on the same strand, typical for other nematode mitogenomes. 9 PCGs were initiated by typical ATN codons, except for NAD2, CYTB and NAD4, which were start with TTG codons. All the PCGs were predicted to use the typical TAN as the stop codons. The phylogenetic analysis showed that the relationship of C. tribulationis is very close to other species in the family Rhabditidae and separated form species of the families Ascarididae, Toxocaridae, Anisakidae and Ascaridiidae with high bootstrap value support.
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Affiliation(s)
- Yuheng Liu
- Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, P. R. China
| | - Zhang Jingjing
- School of Pharmacy, Lanzhou University, Lanzhou, P. R. China
| | - Chao Li
- Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, P. R. China
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Comparative mitogenomics of Spirocerca lupi from South Africa and China: Variation and possible heteroplasmy. Vet Parasitol 2021; 300:109595. [PMID: 34678674 DOI: 10.1016/j.vetpar.2021.109595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/21/2022]
Abstract
The complete mitochondrial genome of Spirocerca lupi isolated from a dog in South Africa was sequenced using next generation sequencing (NGS) technology and the 12 protein coding genes along with the two rRNA genes were compared to 18 other nematode species as well as S. lupi from China. The mitochondrial genome of S. lupi South Africa had a mean genetic diversity of 6.1 % compared to S. lupi China with some variation in nucleotide composition, gene positioning and size. Pairwise distance results indicated slightly higher variation when compared to the pairwise distances of other closely related species, however, this variation was not high enough for it to be considered a cryptic species. Phylogenetic analysis indicated that S. lupi from the two continents are very similar. In addition, single nucleotide polymorphisms were detected in the nad2 gene with ten sequence variants identified from 10 clones from a single nematode, suggesting possible heteroplasmy. The origin of the heteroplasmy is currently unknown but it is speculated to have arisen from accumulated mutations in the mitochondria during somatic replication.
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Palevich N, Maclean PH, Choi YJ, Mitreva M. Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta. Front Genet 2020; 11:573395. [PMID: 33133162 PMCID: PMC7578395 DOI: 10.3389/fgene.2020.573395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.
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Affiliation(s)
- Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Young-Jun Choi
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
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10
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Xie Y, Li Y, Gu X, Liu Y, Zhou X, Wang L, He R, Peng X, Yang G. Molecular characterization of ascaridoid parasites from captive wild carnivores in China using ribosomal and mitochondrial sequences. Parasit Vectors 2020; 13:382. [PMID: 32727607 PMCID: PMC7391581 DOI: 10.1186/s13071-020-04254-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the public health importance of toxocariasis/toxascariasis, only a few species of these ascaridoid parasites from wild canine and feline carnivores have been studied at the molecular level so far. Poor understanding of diversity, host distribution and the potential (zoonotic) transmission of the ascaridoid species among wild animals negatively affects their surveillance and control in natural settings. In this study, we updated previous knowledge by profiling the genetic diversity and phylogenetic relationships of ascaridoid species among eleven wild canine and feline animals on the basis of a combined analysis of the ribosomal internal transcribed spacer region (ITS) gene and the partial mitochondrial cytochrome c oxidase subunit 2 (cox2) and NADH dehydrogenase subunit 1 (nad1) genes. RESULTS In total, three genetically distinct ascaridoid lineages were determined to be present among these wild carnivores sampled, including Toxocara canis in Alopex lagopus and Vulpes vulpes, Toxocara cati in Felis chaus, Prionailurus bengalensis and Catopuma temmincki and Toxascaris leonina in Canis lupus, Panthera tigris altaica, Panthera tigris amoyensis, Panthera tigris tigris, Panthera leo and Lynx lynx. Furthermore, it was evident that T. leonina lineage split into three well-supported subclades depending on their host species, i.e. wild felids, dogs and wolves and foxes, based on integrated genetic and phylogenetic evidence, supporting that a complex of T. leonina other than one species infecting these hosts. CONCLUSIONS These results provide new molecular insights into classification, phylogenetic relationships and epidemiological importance of ascaridoids from wild canids and felids and also highlight the complex of the taxonomy and genetics of Toxascaris in their wild and domestic carnivorous hosts.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yingxin Li
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunjian Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuan Zhou
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
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Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M. Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res 2019; 46:9170-9180. [PMID: 29986062 PMCID: PMC6158502 DOI: 10.1093/nar/gky593] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/20/2018] [Indexed: 12/19/2022] Open
Abstract
As adapter molecules to convert the nucleic acid information into the amino acid sequence, tRNAs play a central role in protein synthesis. To fulfill this function in a reliable way, tRNAs exhibit highly conserved structural features common in all organisms and in all cellular compartments active in translation. However, in mitochondria of metazoans, certain dramatic deviations from the consensus tRNA structure are described, where some tRNAs lack the D- or T-arm without losing their function. In Enoplea, this miniaturization comes to an extreme, and functional mitochondrial tRNAs can lack both arms, leading to a considerable size reduction. Here, we investigate the secondary and tertiary structure of two such armless tRNAs from Romanomermis culicivorax. Despite their high AU content, the transcripts fold into a single and surprisingly stable hairpin structure, deviating from standard tRNAs. The three-dimensional form is boomerang-like and diverges from the standard L-shape. These results indicate that such unconventional miniaturized tRNAs can still fold into a tRNA-like shape, although their length and secondary structure are very unusual. They highlight the remarkable flexibility of the protein synthesis apparatus and suggest that the translational machinery of Enoplea mitochondria may show compensatory adaptations to accommodate these armless tRNAs for efficient translation.
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Affiliation(s)
- Tina Jühling
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany.,Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Joern Pütz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Catherine Florentz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Claude Sauter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
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12
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Carapelli A, Bu Y, Chen WJ, Nardi F, Leo C, Frati F, Luan YX. Going Deeper into High and Low Phylogenetic Relationships of Protura. Genes (Basel) 2019; 10:E292. [PMID: 30974866 PMCID: PMC6523364 DOI: 10.3390/genes10040292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022] Open
Abstract
Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification. Mitochondrial and nuclear markers have been applied herein to investigate and summarize proturan systematics at different hierarchical levels. Two new mitochondrial genomes are described and included in a phylum-level phylogenetic analysis, but the position of Protura could not be resolved with confidence due to an accelerated rate of substitution and extensive gene rearrangements. Mitochondrial and nuclear loci were also applied in order to revise the intra-class systematics, recovering three proturan orders and most of the families/subfamilies included as monophyletic, with the exception of the subfamily Acerentominae. At the species level, most morphologically described species were confirmed using molecular markers, with some exceptions, and the advantages of including nuclear, as well as mitochondrial, markers and morphology are discussed. At all levels, an enlarged taxon sampling and the integration of data from different sources may be of significant help in solving open questions that still persist on the evolutionary history of Protura.
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Affiliation(s)
- Antonio Carapelli
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai 200041, China.
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Wan-Jun Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Chiara Leo
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Francesco Frati
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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13
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Wellner K, Mörl M. Post-Transcriptional Regulation of tRNA Pools To Govern the Central Dogma: A Perspective. Biochemistry 2019; 58:299-304. [PMID: 30192518 DOI: 10.1021/acs.biochem.8b00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their initial discovery, tRNAs have risen from sole adapter molecules during protein synthesis to pivotal modulators of gene expression. Through their many interactions with tRNA-associated protein factors, they play a central role in maintaining cell homeostasis, especially regarding the fine-tuning in response to a rapidly changing cellular environment. Here, we provide a perspective on current tRNA topics with a spotlight on the regulation of post-transcriptional shaping of tRNA molecules. First, we give an update on aberrant structural features that a yet functional fraction of mitochondrial tRNAs can exhibit. Then, we outline several aspects of the regulatory contribution of ribonucleases with a focus on tRNA processing versus tRNA elimination. We close with a comment on the possible consequences for the intracellular examination of nascent tRNA precursors regarding respective processing factors that have been shown to associate with the tRNA transcription machinery in alternative moonlighting functions.
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Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
| | - Mario Mörl
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
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14
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Characterization of the complete mitochondrial genome of Ortleppascaris sinensis (Nematoda: Heterocheilidae) and comparative mitogenomic analysis of eighteen Ascaridida nematodes. J Helminthol 2017. [PMID: 28637530 DOI: 10.1017/s0022149x17000542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ortleppascaris sinensis (Nematoda: Ascaridida) is a dominant intestinal nematode of the captive Chinese alligator. However, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. In this study, the complete mitochondrial (mt) genome sequence of O. sinensis was first determined using a polymerase chain reaction (PCR)-based primer-walking strategy, and this is also the first sequencing of the complete mitochondrial genome of a member of the genus Ortleppascaris. The circular mitochondrial genome (13,828 bp) of O. sinensis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes, but lacked the ATP synthetase subunit 8 gene. Finally, phylogenetic analysis of mtDNAs indicated that the genus Ortleppascaris should be attributed to the family Heterocheilidae. It is necessary to sequence more mtNDAs of Ortleppascaris nematodes in the future to test and confirm our conclusion. The complete mitochondrial genome sequence of O. sinensis reported here should contribute to molecular diagnosis, epidemiological investigations and ecological studies of O. sinensis and other related Ascaridida nematodes.
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15
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Zou Y, Wu F, Guo YX, Wang HB, Fang YQ, Kang M, Lin Q. Determining geographical variations in Ascaris suum isolated from different regions in northwest China through sequences of three mitochondrial genes. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:411-415. [PMID: 26730765 DOI: 10.3109/19401736.2015.1129404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sequence diversities in three mitochondrial DNA (mtDNA) regions, namely portions of NADH dehydrogenase subunit 1 (pnad1), cytochrome c oxidase subunit 1 (pcox1), and NADH dehydrogenase subunit 4 (pnad4), were investigated in all Ascaris suum samples isolated from four regions in northwestern China. Those genes were amplified by PCR method and the lengths of pnad1, pcox1, and pnad4 were 419 bp, 711 bp, and 723 bp, respectively. The intraspecific sequence variations within A. suum samples were 0-2.9% for pnad1, 0-2.1% for pcox1, and 0-3.1% for pnad4. Phylogenetic analysis combined with three sequences of mtDNA fragments showed that all A. suum samples were monophyletic groups, but samples from the same geographical origin did not always cluster together. The results suggested that the three mtDNA fragments could not be used as molecular markers to identify the A. suum isolates from four regions, and have important implications for studying molecular epidemiology and population genetics of A. suum.
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Affiliation(s)
- Yong Zou
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
| | - Fei Wu
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
| | - Ya-Xu Guo
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
| | - Hui-Bao Wang
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
| | - Yan-Qin Fang
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
| | - Ming Kang
- b College of Agriculture and Animal Husbandry, Qinghai University , Xining , Qinghai Province , People's Republic of China
| | - Qing Lin
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi Province , People's Republic of China
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16
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Wei-Ye L, Fang SH, Wang YQ. Complete mitochondrial genome of Epigonichthys cultellus (Cephalochordata: Branchiostomatidae). Zoolog Sci 2015; 31:766-72. [PMID: 25366160 DOI: 10.2108/zs130213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The systematic position of the amphioxus species with dextral gonads distributed in the southeast Pacific and Indian Oceans has remained to be clarified due to the adoption of different names by different researchers. Mitochondrial (mt) DNA is generally considered to be a powerful molecular marker in taxonomic studies. For a reliable systematics of the amphioxi collected from the South China Sea, we sequenced the complete mtDNA from a single specimen and compared it with those of the other eight amphioxus species. The present mtDNA genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, with the same gene order as those in Branchiostoma and Epigonichthys, which, however, is different from that in Asymmetron. Based on our morphological data (including measurements of some characters) and the features of the mt genome, together with the distribution records of the dextral-gonad amphioxi, we conclude that the present mtDNA sequence most likely represents that of E. cultellus.
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Affiliation(s)
- Li Wei-Ye
- 1 School of Life Sciences, Xiamen University, Xiamen 361102, China
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17
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Watanabe YI, Suematsu T, Ohtsuki T. Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet 2014; 5:109. [PMID: 24822055 PMCID: PMC4013460 DOI: 10.3389/fgene.2014.00109] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/12/2014] [Indexed: 11/16/2022] Open
Abstract
Conventional tRNAs have highly conserved sequences, four-armed cloverleaf secondary structures, and L-shaped tertiary structures. However, metazoan mitochondrial tRNAs contain several exceptional structures. Almost all tRNAsSer for AGY/N codons lack the D-arm. Furthermore, in some nematodes, no four-armed cloverleaf-type tRNAs are present: two tRNAsSer without the D-arm and 20 tRNAs without the T-arm are found. Previously, we showed that in nematode mitochondria, an extra elongation factor Tu (EF-Tu) has evolved to support interaction with tRNAs lacking the T-arm, which interact with C-terminal domain 3 in conventional EF-Tu. Recent mitochondrial genome analyses have suggested that in metazoan lineages other than nematodes, tRNAs without the T-arm are present. Furthermore, even more simplified tRNAs are predicted in some lineages. In this review, we discuss mitochondrial tRNAs with divergent structures, as well as protein factors, including EF-Tu, that support the function of truncated metazoan mitochondrial tRNAs.
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Affiliation(s)
- Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo Tokyo, Japan
| | - Takuma Suematsu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo Tokyo, Japan
| | - Takashi Ohtsuki
- Department of Biotechnology, Okayama University Okayama, Japan
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18
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Ma YG, Huang Y, Lei FM. Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2014; 35:81-91. [PMID: 24668650 DOI: 10.11813/j.issn.0254-5853.2014.2.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.
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Affiliation(s)
- Yong-Gui Ma
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huang
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Fu-Min Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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19
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Beagley CT, Wolstenholme DR. Characterization and localization of mitochondrial DNA-encoded tRNAs and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile. Curr Genet 2013; 59:139-52. [PMID: 23801360 DOI: 10.1007/s00294-013-0395-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/12/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
The mitochondrial (mt) genome of the sea anemone Metridium senile contains genes for only two transfer RNAs (tRNAs), tRNAf-Met and tRNATrp. Experiments were conducted to seek evidence for the occurrence of functional tRNAs corresponding to these genes and for the participation of nuclear DNA-encoded tRNAs in mt-protein synthesis. RNA sequences corresponding to the two mt-tRNA genes were located in mitochondria and it was shown that 3'-CC (and possibly A, but no other nucleotide) is added post-transcriptionally to the 3' end of at least 50 % of mt-tRNAf-Met molecules and to a small fraction of the mt-tRNATrp molecules. Using specific oligonucleotide primers based on expected nuclear DNA-encoded tRNAs in a series of RACE experiments, we located the nuclear genes for tRNAGln, tRNAIle, tRNAi-Met, tRNAVal and tRNAThr. Data from Northern blot analyses indicated that mtDNA-encoded tRNAf-Met is limited to mitochondria but that nuclear DNA-encoded tRNAVal and tRNAi-Met are present in the cytoplasm and in mitochondria. These data provide direct evidence that in M. senile, mature, functional tRNAs are transcribed from the mtDNA-encoded tRNAf-Met and tRNATrp genes, and are consistent with the interpretation that both nuclear DNA-encoded tRNAVal and tRNAi-Met are utilized in mitochondrial and cytosolic protein synthesis.
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Affiliation(s)
- C Timothy Beagley
- Department of Biology, University of Utah, Salt Lake City, UT 84121, USA.
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20
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Analysis of the complete mitochondrial genome sequence of Larus brunnicephalus (Aves, Laridae). YI CHUAN = HEREDITAS 2012. [DOI: 10.3724/sp.j.1005.2012.01434] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Bernt M, Braband A, Schierwater B, Stadler PF. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol 2012; 69:328-38. [PMID: 23142697 DOI: 10.1016/j.ympev.2012.10.020] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 10/20/2012] [Accepted: 10/22/2012] [Indexed: 11/30/2022]
Abstract
Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
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22
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Advances in the study of helminth mitochondrial genomes and their associated applications. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-011-4748-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res 2011; 40:2833-45. [PMID: 22139921 PMCID: PMC3326299 DOI: 10.1093/nar/gkr1131] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.
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Affiliation(s)
- Frank Jühling
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
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Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites. BMC Genomics 2009; 10:598. [PMID: 20003349 PMCID: PMC2797822 DOI: 10.1186/1471-2164-10-598] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 12/11/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Atypical tRNAs are functional minimal tRNAs, lacking either the D- or T-arm. They are significantly shorter than typical cloverleaf tRNAs. Widespread occurrence of atypical tRNAs was first demonstrated for secernentean nematodes and later in various arachnids. Evidence started to accumulate that tRNAs of certain acariform mites are even shorter than the minimal tRNAs of nematodes, raising the possibility that tRNAs lacking both D- and T-arms might exist in these organisms. The presence of cloverleaf tRNAs in acariform mites, particularly in the house dust mite genus Dermatophagoides, is still disputed. RESULTS Mitochondrial tRNAs of Dermatophagoides farinae are minimal, atypical tRNAs lacking either the T- or D-arm. The size (49-62, 54.4 +/- 2.86 nt) is significantly (p = 0.019) smaller than in Caenorhabditis elegans (53-63, 56.3 +/- 2.30 nt), a model minimal tRNA taxon. The shortest tRNA (49 nt) in Dermatophagoides is approaching the length of the shortest known tRNAs (45-49 nt) described in other acariform mites. The D-arm is absent in these tRNAs, and the inferred T-stem is small (2-3 bp) and thermodynamically unstable, suggesting that it may not exist in reality. The discriminator nucleotide is probably not encoded and is added postranscriptionally in many Dermatophagoides tRNAs. CONCLUSIONS Mitochondrial tRNAs of acariform mites are largely atypical, non-cloverleaf tRNAs. Among them, the shortest known tRNAs with no D-arm and a short and unstable T-arm can be inferred. While our study confirmed seven tRNAs in Dermatophagoides by limited EST data, further experimental evidence is needed to demonstrate extremely small and unusual tRNAs in acariform mites.
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Jang KH, Hwang UW. Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa. BMC Genomics 2009; 10:167. [PMID: 19379522 PMCID: PMC2678162 DOI: 10.1186/1471-2164-10-167] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/21/2009] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata) was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny. RESULTS The complete mitochondrial genome (15,433 bp) of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata), one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of F. hispida (Bryozoa, Gymnolaemata, Ctenostomata), which has only 36 components with loss of tRNAser(ucn) genes. The B. neritina mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida) and a chiton Katharina tunicate than to that of F. hispida. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (B. neritina and F. hispida) was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta. CONCLUSION This study presents the complete mitochondrial genome of a cheliostome bryozoan, B. neritina. The phylogenetic analyses suggest a close relationship between Bryozoa and Brachiopoda within the Lophotrochozoa. However, the sister group of Bryozoa + Brachiopoda is still ambiguous, although it has some attractions with Annelida-Echiura or Phoronida + Entoprocta. If the latter is a true phylogeny, lophophorate monophyly including Entoprocta is supported. Consequently, the present results imply that Brachiozoa (= Brachiopoda + Phoronida) and the recently-resurrected Bryozoa concept comprising Ectoprocta and Entoprocta may be refuted.
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Affiliation(s)
- Kuem Hee Jang
- Department of Biology, Graduate School & Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea
- Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, Korea
| | - Ui Wook Hwang
- Department of Biology, Graduate School & Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea
- Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, Korea
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Masta SE, Boore JL. Parallel Evolution of Truncated Transfer RNA Genes in Arachnid Mitochondrial Genomes. Mol Biol Evol 2008; 25:949-59. [DOI: 10.1093/molbev/msn051] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Bandyopadhyay PK, Stevenson BJ, Cady MT, Olivera BM, Wolstenholme DR. Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: gene order and gastropod phylogeny. Toxicon 2006; 48:29-43. [PMID: 16806344 DOI: 10.1016/j.toxicon.2006.04.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 04/13/2006] [Indexed: 11/22/2022]
Abstract
We have determined the first complete nucleotide sequence of the mitochondrial genome of a venomous mollusc, the Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis. It is 15,380 nucleotide pairs (ntp) and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion's own protein synthesizing system. The protein mRNAs, ribosomal RNAs and 13 of the tRNAs are transcribed from the same strand, the remaining tRNAs from the other strand. The longest segment of unassigned sequence is 139 ntp and includes a 82 ntp segment that is a perfect inverted repeat sequence of 37 ntp separated by 8 nt. The gene arrangement of L. cerithiformis mtDNA shows remarkable similarity to the gene arrangements of mtDNAs of the vetigastropod Haliotis rubra, the polyplacophoran Katharina tunicata and the cephalopod Octopus vulgaris, but differs dramatically from the gene arrangements found in the mtDNAs of pulmonate and opisthobranch gastropods, as well as mtDNAs of bivalves and scaphopods. A single sixteen gene inversion that distinguishes L. cerithiformis mtDNA from mtDNAs of H. rubra, K. tunicata and O. vulgaris is shared by mtDNA of a littorinomorph gastropod Littorina saxitalis, suggesting a close relationship of conoidean and littorinomorph gastropods.
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Affiliation(s)
- Pradip K Bandyopadhyay
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
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29
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He Y, Jones J, Armstrong M, Lamberti F, Moens M. The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes. J Mol Evol 2005; 61:819-33. [PMID: 16315110 DOI: 10.1007/s00239-005-0102-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present.
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Affiliation(s)
- Y He
- Gewasbescherming-CLO, Burg. Van Gansberghelaan 96,, Merelbeke, 9820, Belgium
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30
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Hu M, Chilton NB, Gasser RB. The mitochondrial genome of Strongyloides stercoralis (Nematoda) – idiosyncratic gene order and evolutionary implications. Int J Parasitol 2003; 33:1393-408. [PMID: 14527522 DOI: 10.1016/s0020-7519(03)00130-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete mitochondrial genome sequence of the parasitic nematode Strongyloides stercoralis was determined, and its organisation and structure compared with other nematodes for which complete mitochondrial sequence data were available. The mitochondrial genome of S. stercoralis is 13,758 bp in size and contains 36 genes (all transcribed in the clockwise direction) but lacks the atp8 gene. This genome has a high T content (55.9%) and a low C content (8.3%). Corresponding to this T content, there are 16 (poly-T) tracts of >/=12 Ts distributed across the genome. In protein-coding genes, the T bias is greatest (76.4%) at the third codon position compared with the first and second codon positions. Also, the C content is higher at the first (9.3%) and second (13.4%) codon positions than at the third (2%) position. These nucleotide biases have a significant effect on predicted codon usage patterns and, hence, on amino acid compositions of the mitochondrial proteins. Interestingly, six of the 12 protein-coding genes are predicted to employ a unique initiation codon (TTT), which has not yet been reported for any other animal mitochondrial genome. The secondary structures predicted for the 22 transfer RNA (trn) genes and the two ribosomal RNA (rrn) genes are similar to those of other nematodes. In contrast, the gene arrangement in the mitochondrial genome of S. stercoralis is different from all other nematodes studied to date, revealing only a limited number of shared gene boundaries (atp6-nad2 and cox2-rrnL). Evolutionary analyses of mitochondrial nucleotide and amino acid sequence data sets for S. stercoralis and seven other nematodes demonstrate that the mitochondrial genome provides a rich source of phylogenetically informative characters. In conclusion, the S. stercoralis mitochondrial genome, with its unique gene order and characteristics, should provide a resource for comparative mitochondrial genomics and systematics studies of parasitic nematodes.
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Affiliation(s)
- Min Hu
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
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31
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Ohtsuki T, Kawai G, Watanabe K. The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) having a short T arm and lacking the entire D arm. FEBS Lett 2002; 514:37-43. [PMID: 11904178 DOI: 10.1016/s0014-5793(02)02328-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The tertiary structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) was examined by nuclear magnetic resonance analysis using its transcript, since tRNA(Ser)(UCU), lacking the D arm and possessing a truncated T arm, is the shortest of all the known tRNAs. Most basepairs in the proposed secondary structure of tRNA(Ser)(UCU) were shown to exist, but the connector region comprising the truncated D loop and the extra loop was flexible. This flexibility, would enable adjustment of the mutual distance between the 3'-terminus and the anticodon consistent with that of usual tRNAs. Thus, tRNA(Ser)UCU appears to function in a similar way to that of usual tRNAs in the ribosome.
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Affiliation(s)
- Takashi Ohtsuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan
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32
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Hu M, Chilton NB, Gasser RB. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Int J Parasitol 2002; 32:145-58. [PMID: 11812491 DOI: 10.1016/s0020-7519(01)00316-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complete mitochondrial genome sequences were determined for two species of human hookworms, Ancylostoma duodenale (13,721 bp) and Necator americanus (13,604 bp). The circular hookworm genomes are amongst the smallest reported to date for any metazoan organism. Their relatively small size relates mainly to a reduced length in the AT-rich region. Both hookworm genomes encode 12 protein, two ribosomal RNA and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with three other species of Secernentea studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T, but low in G and C. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. For both hookworm species, genes were arranged in the same order as for Caenorhabditis elegans, except for the presence of a non-coding region between genes nad3 and nad5. In A. duodenale, this non-coding region is predicted to form a stem-and-loop structure which is not present in N. americanus. The mitochondrial genome structure for both hookworms differs from Ascaris suum only in the location of the AT-rich region, whereas there are substantial differences when compared with Onchocerca volvulus, including four gene or gene-block translocations and the positions of some transfer RNA genes and the AT-rich region. Based on genome organisation and amino acid sequence identity, A. duodenale and N. americanus were more closely related to C. elegans than to A. suum or O. volvulus (all secernentean nematodes), consistent with a previous phylogenetic study using ribosomal DNA sequence data. Determination of the complete mitochondrial genome sequences for two human hookworms (the first members of the order Strongylida ever sequenced) provides a foundation for studying the systematics, population genetics and ecology of these and other nematodes of socio-economic importance.
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Affiliation(s)
- Min Hu
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Victoria 3030, Werribee, Australia
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33
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Ohtsuki T, Takemoto C, Kawai G, Ueda T, Kita K, Kojima S, Kaziro Y, Nyborg J, Watanabe K. An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria. J Biol Chem 2001; 276:21571-7. [PMID: 11262399 DOI: 10.1074/jbc.m011118200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have found the gene for a translation elongation factor Tu (EF-Tu) homologue in the genome of the nematode Caenorhabditis elegans. Because the corresponding protein was detected immunologically in a nematode mitochondrial (mt) extract, it could be regarded as a nematode mt EF-Tu. The protein possesses an extension of about 57 amino acids (we call this domain 3') at the C terminus, which is not found in any other known EF-Tu. Because most nematode mt tRNAs lack a T stem, domain 3' may be related to this feature. The nematode EF-Tu bound to nematode T stem-lacking tRNA, but bacterial EF-Tu was unable to do so. A series of domain exchange experiments strongly suggested that domains 3 and 3' are essential for binding to T stem-lacking tRNAs. This finding may constitute a novel example of the co-evolution of a structurally simplified RNA and the cognate RNA-binding protein, the latter having apparently acquired an additional domain to compensate for the lack of a binding site(s) on the RNA.
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Affiliation(s)
- T Ohtsuki
- Department of Chemistry, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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34
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Lavrov DV, Brown WM. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. Genetics 2001; 157:621-37. [PMID: 11156984 PMCID: PMC1461501 DOI: 10.1093/genetics/157.2.621] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The complete mitochondrial DNA (mtDNA) of the nematode Trichinella spiralis has been amplified in four overlapping fragments and 16,656 bp of its sequence has been determined. This sequence contains the 37 genes typical of metazoan mtDNAs, including a putative atp8, which is absent from all other nematode mtDNAs examined. The genes are transcribed from both mtDNA strands and have an arrangement relatable to those of coelomate metazoans, but not to those of secernentean nematodes. All protein genes appear to initiate with ATN codons, typical for metazoans. Neither TTG nor GTT start codons, inferred for several genes of other nematodes, were found. The 22 T. spiralis tRNA genes fall into three categories: (i) those with the potential to form conventional "cloverleaf" secondary structures, (ii) those with TPsiC arm + variable arm replacement loops, and (iii) those with DHU-arm replacement loops. Mt-tRNA(R) has a 5'-UCG-3' anticodon, as in most other metazoans, instead of the very unusual 5'-ACG-3' present in the secernentean nematodes. The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level.
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Affiliation(s)
- D V Lavrov
- Department of Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA.
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35
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Helm M, Brulé H, Friede D, Giegé R, Pütz D, Florentz C. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA (NEW YORK, N.Y.) 2000; 6:1356-79. [PMID: 11073213 PMCID: PMC1370008 DOI: 10.1017/s1355838200001047] [Citation(s) in RCA: 221] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A number of mitochondrial (mt) tRNAs have strong structural deviations from the classical tRNA cloverleaf secondary structure and from the conventional L-shaped tertiary structure. As a consequence, there is a general trend to consider all mitochondrial tRNAs as "bizarre" tRNAs. Here, a large sequence comparison of the 22 tRNA genes within 31 fully sequenced mammalian mt genomes has been performed to define the structural characteristics of this specific group of tRNAs. Vertical alignments define the degree of conservation/variability of primary sequences and secondary structures and search for potential tertiary interactions within each of the 22 families. Further horizontal alignments ascertain that, with the exception of serine-specific tRNAs, mammalian mt tRNAs do fold into cloverleaf structures with mostly classical features. However, deviations exist and concern large variations in size of the D- and T-loops. The predominant absence of the conserved nucleotides G18G19 and T54T55C56, respectively in these loops, suggests that classical tertiary interactions between both domains do not take place. Classification of the tRNA sequences according to their genomic origin (G-rich or G-poor DNA strand) highlight specific features such as richness/poorness in mismatches or G-T pairs in stems and extremely low G-content or C-content in the D- and T-loops. The resulting 22 "typical" mammalian mitochondrial sequences built up a phylogenetic basis for experimental structural and functional investigations. Moreover, they are expected to help in the evaluation of the possible impacts of those point mutations detected in human mitochondrial tRNA genes and correlated with pathologies.
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Affiliation(s)
- M Helm
- Unité Propre de Recherche 9002 du Centre National de la Recherche Scientifique, Département Mécanismes et Macromolécules de la Synthèse Protéique, et Cristallogenèse, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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36
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Beagley CT, Okimoto R, Wolstenholme DR. Mytilus mitochondrial DNA contains a functional gene for a tRNASer(UCN) with a dihydrouridine arm-replacement loop and a pseudo-tRNASer(UCN) gene. Genetics 1999; 152:641-52. [PMID: 10353906 PMCID: PMC1460622 DOI: 10.1093/genetics/152.2.641] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 2500-nucleotide pair (ntp) sequence of F-type mitochondrial (mt) DNA of the Pacific Rim mussel Mytilus californianus (class Bivalvia, phylum Mollusca) that contains two complete (ND2 and ND3) and two partial (COI and COIII) protein genes and nine tRNA genes is presented. Seven of the encoded tRNAs (Ala, Arg, His, Met(AUA), Pro, Ser(UCN), and Trp) have the potential to fold into the orthodox four-armed tRNA secondary structure, while two [tRNASer(AGN) and a second tRNASer(UCN)] will fold only into tRNAs with a dihydrouridine (DHU) arm-replacement loop. Comparison of these mt-tRNA gene sequences with previously published, corresponding M. edulis F-type mtDNA indicates that similarity between the four-armed tRNASer(UCN) genes is only 63.8% compared with an average of 92.1% (range 86.2-98. 5%) for the remaining eight tRNA genes. Northern blot analysis indicated that mature tRNAs encoded by the DHU arm-replacement loop-containing tRNASer(UCN), tRNASer(AGN), tRNAMet(AUA), tRNATrp, and tRNAPro genes occur in M. californianus mitochondria, strengthening the view that all of these genes are functional. However, Northern blot and 5' RACE (rapid amplification of cDNA ends) analyses indicated that the four-armed tRNASer(UCN) gene is transcribed into a stable RNA that includes the downstream COI sequence and is not processed into a mature tRNA. On the basis of these observations the M. californianus and M. edulis four-armed tRNASer(UCN) sequences are interpreted as pseudo-tRNASer(UCN) genes.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Bivalvia/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Electron Transport Complex I
- Electron Transport Complex IV/genetics
- Molecular Sequence Data
- NADH Dehydrogenase/genetics
- Nucleic Acid Conformation
- Proteins/genetics
- Pseudogenes
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Uridine/analogs & derivatives
- Uridine/chemistry
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Affiliation(s)
- C T Beagley
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
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37
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Beagley CT, Okimoto R, Wolstenholme DR. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 1998; 148:1091-108. [PMID: 9539427 PMCID: PMC1460033 DOI: 10.1093/genetics/148.3.1091] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The circular, 17,443 nucleotide-pair mitochondrial (mt) DNA molecule of the sea anemone, Metridium senile (class Anthozoa, phylum Cnidaria) is presented. This molecule contains genes for 13 energy pathway proteins and two ribosomal (r) RNAs but, relative to other metazoan mtDNAs, has two unique features: only two transfer RNAs (tRNA(f-Met) and tRNA(Trp)) are encoded, and the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 5 (ND5) genes each include a group I intron. The COI intron encodes a putative homing endonuclease, and the ND5 intron contains the molecule's ND1 and ND3 genes. Most of the unusual characteristics of other metazoan mtDNAs are not found in M. senile mtDNA: unorthodox translation initiation codons and partial translation termination codons are absent, the use of TGA to specify tryptophan is the only genetic code modification, and both encoded tRNAs have primary and secondary structures closely resembling those of standard tRNAs. Also, with regard to size and secondary structure potential, the mt-s-rRNA and mt-1-rRNA have the least deviation from Escherichia coli 16S and 23S rRNAs of all known metazoan mt-rRNAs. These observations indicate that most of the genetic variations previously reported in metazoan mtDNAs developed after Cnidaria diverged from the common ancestral line of all other Metazoa.
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Affiliation(s)
- C T Beagley
- Department of Biology, University of Utah, Salt Lake City 84112, USA
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38
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Watanabe Y, Tsurui H, Ueda T, Furusihima-Shimogawara R, Takamiya S, Kita K, Nishikawa K, Watanabe K. Primary sequence of mitochondrial tRNA(Arg) of a nematode Ascaris suum: occurrence of unmodified adenosine at the first position of the anticodon. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1350:119-22. [PMID: 9048878 DOI: 10.1016/s0167-4781(96)00211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondrial tRNA(Arg) from a nematode, Ascaris suum, was purified and sequenced at the RNA level. An unmodified adenosine was found to exist at the anticodon first position, suggesting that, contrary to the conventional wobble rule, the anticodon ACG of the tRNA can translate all the CGN codons.
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Affiliation(s)
- Y Watanabe
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Japan
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39
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Szymański M, Opioła T, Barciszewska MZ, Barciszewski J. The nucleotide sequence of 5S ribosomal RNA from the parasitic nematode Ascaris suum. Evolutionary relationships in nematodes. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1308:251-255. [PMID: 8809117 DOI: 10.1016/0167-4781(96)00115-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have determined the nucleotide sequence of 5S ribosomal RNA from the parasitic nematode Ascaris suum. The analysis of all Nematoda 5S rRNAs and their genes shows that this group must have diverged from other Metazoa at early stages of evolution. This conclusion is supported by the sequence variability in single-stranded regions which are strongly conserved in animal 5S rRNAs.
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Affiliation(s)
- M Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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40
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Ohtsuki T, Kawai G, Watanabe Y, Kita K, Nishikawa K, Watanabe K. Preparation of biologically active Ascaris suum mitochondrial tRNAMet with a TV-replacement loop by ligation of chemically synthesized RNA fragments. Nucleic Acids Res 1996; 24:662-7. [PMID: 8604307 PMCID: PMC145695 DOI: 10.1093/nar/24.4.662] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ascaris suum mitochondrial tRNA Met lacking the entire T stem was prepared by enzymatic ligation of two chemically synthesized RNA fragments. The synthetic tRNA could be charged with methionine by A.suum mitochondrial extract, although the charging activity was considerably low compared with that of the native tRNA, probably due to lack of modification. Enzymatic probing of the synthetic tRNA showed a very similar digestion pattern to that of the native tRNA Met, which has already been concluded to take an L-shape-like structure [Watanabe et al. (1994) J. Biol. Chem., 269, 22902-22906]. These results suggest that the synthetic tRNA possesses almost the same conformation as the native one, irrespective of the presence or absence of modified residues. The method of preparing the bizarre tRNA used here will provide a useful tool for elucidating the tertiary structure of such tRNAs, because they can be obtained without too much difficulty in the amounts necessary for physicochemical studies such as NMR spectroscopy.
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Affiliation(s)
- T Ohtsuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Japan
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41
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Okimoto R, Macfarlane JL, Wolstenholme DR. The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis. J Mol Evol 1994; 39:598-613. [PMID: 7528811 DOI: 10.1007/bf00160405] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.
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Affiliation(s)
- R Okimoto
- Department of Biology, University of Utah, Salt Lake City 84112
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