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Chrisanfova G, Mozharovskaya L, Zhukova T, Nefedova D, Semyenova S. Non-coding Regions of Mitochondrial DNA and the cox1 Gene Reveal Genetic Variability Among Local Belarusian Populations of the Causative Agent of Cercarial Dermatitis, Bird Schistosome Trichobilharzia szidati (Digenea: Schistosomatidae). Acta Parasitol 2021; 66:1193-1203. [PMID: 33860433 DOI: 10.1007/s11686-021-00371-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION The cercariae of avian blood flukes Trichobilharzia szidati (Digenea, Schistosomatidae) are known to cause cercarial allergic dermatitis ("swimmer's itch") in humans. Global epidemics can have significant impacts on local tourism-related economies in recreational areas. Little is known about the genetic polymorphism of the parasite population, or about the variability of the non-coding regions of mitochondrial DNA (mtDNA) and the possibility of using this as a genetic marker. MATERIALS AND METHODS The T. szidati cercariae were collected over 7 years from 33 naturally infected Lymnaea stagnalis snails from five sites at two neighboring lakes in Belarus. We investigated the variability of the short (SNR) and long (LNR) non-coding regions of mt DNA and the genetic diversity within the 1125-bp sequences of the gene for subunit 1 of cytochrome c oxidase (cox1). RESULTS In the SNR sequences, we found only length variability caused by changes in the number of bases in the mononucleotide tracts T6-T8. LNR demonstrates high variability in nucleotide sequence length (182-260 bp) depending on the presence of two long deletions of 59 and 78 nucleotides. Both mitochondrial loci (LNR and cox1) are characterized by high haplotype diversity (H = 0.922 and H = 1.0, respectively); the nucleotide diversity is significantly higher for LNR (π = 1.926 ± 0.443) compared to cox1 (π = 0.704 ± 0.059). Phylogenetic reconstructions based on the variability of each of the loci (LNR and cox1) and their concatenated sequences revealed their shallow structure and the absence of a correlation between the distribution of single-nucleotide polymorphisms and the geographic origin of parasites from two Belarusian lakes. We identified at last four weakly sublineages in the phylogenetic pattern of T. szidati. The carriers of each deletion have specific patterns for each of the two loci and form their own phylogeographic sublineages. An association between two fixed LNR substitutions and a fixed non-synonymous substitution in cox1 was found in four representatives of one lineage that had a short deletion in the LNR. CONCLUSIONS This study clarified the phylogeographic structure of the Belarusian population of T. szidati. Our data provide the basis for the use two mt markers in large-scale population studies of the parasite, as well as for studying the molecular evolution of coding and non-coding mtDNA in trematodes.
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Affiliation(s)
- Galina Chrisanfova
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Lyudmila Mozharovskaya
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatyana Zhukova
- Naroch Biological Station Named After G. G. Vinberg, Belarusian State University, Myadel District, Minsk Region, Belarus
| | - Darya Nefedova
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Seraphima Semyenova
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.
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Lin JP, Tsai MH, Kroh A, Trautman A, Machado DJ, Chang LY, Reid R, Lin KT, Bronstein O, Lee SJ, Janies D. The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida). Genomics 2020; 112:1686-1693. [PMID: 31629878 PMCID: PMC7032948 DOI: 10.1016/j.ygeno.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/18/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well resolved. Complete mitochondrial genomes are currently available for 29 echinoid species, but no clypeasteroid had been sequenced to date. DNA extracted from a single live individual of Sinaechinocyamus mai was sequenced with 10× Genomics technology. This first complete mitochondrial genome (mitogenome) for the order Clypeasteroida is 15,756 base pairs in length. Phylogenomic analysis based on 34 ingroup taxa belonging to nine orders of the class Echinoidea show congruence between our new genetic inference and published trees based on morphologic characters, but also includes some intriguing differences that imply the need for additional investigation.
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Affiliation(s)
- Jih-Pai Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan.
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Aaron Trautman
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA; Bioinformatics Graduate Program, University of São Paulo, Brazil
| | - Lo-Yu Chang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Robert Reid
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Kuan-Ting Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel; Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Shyh-Jye Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
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Zhao W, Li Z, Huang X, Zhang Y, Ding J, Chang Y. The complete mitochondrial genome of Salmacis sphaeroides variegate(Mortensen, 1942). Mitochondrial DNA B Resour 2019; 4:3829-3830. [PMID: 33366207 PMCID: PMC7707404 DOI: 10.1080/23802359.2019.1684215] [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: 11/16/2022] Open
Abstract
In this study, the complete mitochondrial genome of Salmacis sphaeroides variegate was determined on Illumina HiSeq platform. The genome was 15,770 bp in size and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 1 control region (180 bp). The composition of A + T in S. sphaeroides mtDNA was 61.90%. Except ND6 and 6 tRNAs, the others are on the H-strand. The phylogenetic relationships of 11 species of sea urchins were analyzed using the neighbor-joining method using software MEGA 7.0. S. sphaeroides was most closely related to Temnopleurus hardwickii.
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Affiliation(s)
- Wenfei Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
| | - Zhe Li
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
| | - Xiaofang Huang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
| | - Yang Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University, Dalian, Liaoning, P. R. China
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Mu W, Liu J, Zhang H. The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida. Ecol Evol 2018; 8:10673-10686. [PMID: 30519397 PMCID: PMC6262923 DOI: 10.1002/ece3.4427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023] Open
Abstract
Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world's oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep-sea member of the order Brisingida. Similar to other starfish, it contained 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty-two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep-sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila's adaptation to deep-sea environment.
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Affiliation(s)
- Wendan Mu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jun Liu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Haibin Zhang
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
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Bronstein O, Kroh A, Haring E. Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids. BMC Evol Biol 2018; 18:80. [PMID: 29848319 PMCID: PMC5977486 DOI: 10.1186/s12862-018-1198-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region. RESULTS Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids. CONCLUSIONS Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.
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Affiliation(s)
- Omri Bronstein
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
| | - Andreas Kroh
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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Abstract
Single data sets, whether derived from morphological or molecular evidence, provide one-off estimates of the correct phylogeny. Their reliability can only be gauged by statistical approaches such as bootstrapping or clade decay, but these test only whether there are sufficient characters in the data matrix to justify the groupings identified. They do not test whether the characters themselves are reliable. Consequently, confidence in the correctness of phylogenetic interpretations comes primarily from discovering the same (or statistically indistinguishable) patterns from independent data sets.Congruence studies are most advanced for echinoids, where four independent data sets (two morphological and two molecular) provide strong corroboration for a single phylogenetic scheme. Analysis of all four data sets combined generates a highly robust hypothesis of relationships. The situation is very different for asteroids. Two analyses based on morphological data have reached very different conclusions. Three independent molecular data sets also have been compiled, but none has a statistically reliable signal concerning higher taxon relationships. Even combining all three molecular data sets fails to generate a statistically robust solution, implying that the major lines of asteroids diverged rapidly from one another. For ophiuroids, both morphological and molecular data generate topologies that for the most part lack statistical robustness. There is currently no cladistic analysis of holothurian relationships based on morphological data, and only a few taxa have been sequenced. The molecular data is, however, congruent and does permit an initial assessment of relationships. Nothing definite can be deduced about crinoid relationships since even fewer molecular sequences are known and morphological analysis remains sketchy.Class-level relationships derived from two morphological and two molecular data sets also show considerable congruence, though a single definitive solution has yet to emerge.
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Láruson ÁJ. Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora. Ecol Evol 2017; 7:4543-4551. [PMID: 28690785 PMCID: PMC5496550 DOI: 10.1002/ece3.3042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 11/11/2022] Open
Abstract
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular‐clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene. Major global oceanographic changes have been inferred during this time frame, potentially driving species diversification through environmental selection pressures. To test for signatures of selection acting on the mitochondria, the historical rate of gene evolution of individual MT genes was assessed through a branch‐site comparison of nonsynonymous to synonymous substitution ratios (ω). Models of positive selection and neutral evolution, as compared via a likelihood ratio test, show no evidence of strong historical positive selection on mitochondrial genes at the genesis of the Odontophora. However, while pairwise ω comparison revealed signatures of strong negative selection, relatively elevated ω values were observed within the Strongylocentrotus genus.
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Affiliation(s)
- Áki Jarl Láruson
- Department of Biology University of Hawai'i at Mānoa Honolulu HI USA
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8
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Dilly GF, Gaitán-Espitia JD, Hofmann GE. Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology. Mol Ecol Resour 2014; 15:425-36. [DOI: 10.1111/1755-0998.12316] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 06/24/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
Affiliation(s)
- G. F. Dilly
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
| | - J. D. Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - G. E. Hofmann
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
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9
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Brauer A, Kurz A, Stockwell T, Baden-Tillson H, Heidler J, Wittig I, Kauferstein S, Mebs D, Stöcklin R, Remm M. The mitochondrial genome of the venomous cone snail Conus consors. PLoS One 2012; 7:e51528. [PMID: 23236512 PMCID: PMC3517553 DOI: 10.1371/journal.pone.0051528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 11/05/2012] [Indexed: 11/18/2022] Open
Abstract
Cone snails are venomous predatory marine neogastropods that belong to the species-rich superfamily of the Conoidea. So far, the mitochondrial genomes of two cone snail species (Conus textile and Conus borgesi) have been described, and these feed on snails and worms, respectively. Here, we report the mitochondrial genome sequence of the fish-hunting cone snail Conus consors and describe a novel putative control region (CR) which seems to be absent in the mitochondrial DNA (mtDNA) of other cone snail species. This possible CR spans about 700 base pairs (bp) and is located between the genes encoding the transfer RNA for phenylalanine (tRNA-Phe, trnF) and cytochrome c oxidase subunit III (cox3). The novel putative CR contains several sequence motifs that suggest a role in mitochondrial replication and transcription.
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Shao YJ, Hu XQ, Peng GD, Wang RX, Gao RN, Lin C, Shen WD, Li R, Li B. Structure and evolution of the mitochondrial genome of Exorista sorbillans: the Tachinidae (Diptera: Calyptratae) perspective. Mol Biol Rep 2012; 39:11023-30. [PMID: 23053992 DOI: 10.1007/s11033-012-2005-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
Abstract
The first complete mitochondrial genome (mitogenome) of Tachinidae Exorista sorbillans (Diptera) is sequenced by PCR-based approach. The circular mitogenome is 14,960 bp long and has the representative mitochondrial gene (mt gene) organization and order of Diptera. All protein-coding sequences are initiated with ATN codon; however, the only exception is Cox I gene, which has a 4-bp ATCG putative start codon. Ten of the thirteen protein-coding genes have a complete termination codon (TAA), but the rest are seated on the H strand with incomplete codons. The mitogenome of E. sorbillans is biased toward A+T content at 78.4 %, and the strand-specific bias is in reflection of the third codon positions of mt genes, and their T/C ratios as strand indictor are higher on the H strand more than those on the L strand pointing at any strain of seven Diptera flies. The length of the A+T-rich region of E. sorbillans is 106 bp, including a tandem triple copies of a13-bp fragment. Compared to Haematobia irritans, E. sorbillans holds distant relationship with Drosophila. Phylogenetic topologies based on the amino acid sequences, supporting that E. sorbillans (Tachinidae) is clustered with strains of Calliphoridae and Oestridae, and superfamily Oestroidea are polyphyletic groups with Muscidae in a clade.
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Affiliation(s)
- Yuan-jun Shao
- School of Basic Medicine and Biological Sciences, Soochow University, Jiangsu, 215123, People's Republic of China.
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Wangensteen OS, Turon X, Pérez-Portela R, Palacín C. Natural or naturalized? Phylogeography suggests that the abundant sea urchin Arbacia lixula is a recent colonizer of the Mediterranean. PLoS One 2012; 7:e45067. [PMID: 23028765 PMCID: PMC3444468 DOI: 10.1371/journal.pone.0045067] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 08/14/2012] [Indexed: 11/18/2022] Open
Abstract
We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94-205 kya in the Mediterranean, and 31-67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.
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Affiliation(s)
- Owen S Wangensteen
- Department of Animal Biology, University of Barcelona, Barcelona, Spain.
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Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0087-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kroh A, Madeira P, Haring E. Species distributions: virtual or real – the case of
Arbaciella elegans
(Echinoidea: Arbaciidae). J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00636.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Andreas Kroh
- Naturhistorisches Museum Wien, Geologisch‐Paläontologische Abteilung, Wien, Austria
| | - Patrícia Madeira
- MPB – Marine PalaeoBiogeography Working Group, Departamento de Biologia, Universidade dos Açores, Ponta Delgada, Azores
- Centro do IMAR da Universidade dos Açores, Horta, Azores, Portugal
| | - Elisabeth Haring
- Naturhistorisches Museum Wien, I. Zoologische Abteilung, Wien, Austria
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Passamonti M, Ricci A, Milani L, Ghiselli F. Mitochondrial genomes and Doubly Uniparental Inheritance: new insights from Musculista senhousia sex-linked mitochondrial DNAs (Bivalvia Mytilidae). BMC Genomics 2011; 12:442. [PMID: 21896183 PMCID: PMC3176263 DOI: 10.1186/1471-2164-12-442] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 09/06/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Doubly Uniparental Inheritance (DUI) is a fascinating exception to matrilinear inheritance of mitochondrial DNA (mtDNA). Species with DUI are characterized by two distinct mtDNAs that are inherited either through females (F-mtDNA) or through males (M-mtDNA). DUI sex-linked mitochondrial genomes share several unusual features, such as additional protein coding genes and unusual gene duplications/structures, which have been related to the functionality of DUI. Recently, new evidence for DUI was found in the mytilid bivalve Musculista senhousia. This paper describes the complete sex-linked mitochondrial genomes of this species. RESULTS Our analysis highlights that both M and F mtDNAs share roughly the same gene content and order, but with some remarkable differences. The Musculista sex-linked mtDNAs have differently organized putative control regions (CR), which include repeats and palindromic motifs, thought to provide sites for DNA-binding proteins involved in the transcriptional machinery. Moreover, in male mtDNA, two cox2 genes were found, one (M-cox2b) 123bp longer. CONCLUSIONS The complete mtDNA genome characterization of DUI bivalves is the first step to unravel the complex genetic signals allowing Doubly Uniparental Inheritance, and the evolutionary implications of such an unusual transmission route in mitochondrial genome evolution in Bivalvia. The observed redundancy of the palindromic motifs in Musculista M-mtDNA may have a role on the process by which sperm mtDNA becomes dominant or exclusive of the male germline of DUI species. Moreover, the duplicated M-COX2b gene may have a different, still unknown, function related to DUI, in accordance to what has been already proposed for other DUI species in which a similar cox2 extension has been hypothesized to be a tag for male mitochondria.
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Affiliation(s)
- Marco Passamonti
- Department of Biologia Evoluzionistica Sperimentale, University of Bologna, Bologna, Italy.
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He CB, Wang J, Gao XG, Song WT, Li HJ, Li YF, Liu WD, Su H. The complete mitochondrial genome of the hard clam Meretrix meretrix. Mol Biol Rep 2010; 38:3401-9. [PMID: 21086173 DOI: 10.1007/s11033-010-0449-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 11/08/2010] [Indexed: 11/26/2022]
Abstract
Veneridae is a diverse, commercially important, and cosmopolitan family. Here we present the complete mitochondrial genome of the hard clam Meretrix meretrix (Bivalvia: Veneridae). The entire mitochondrial genome (mitogenome) sequence of M. meretrix is 19,826 bp in length, and contains 37 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 23 tRNAs. All genes are encoded on the heavy strand. In contrast to the typical animal mitochondrial genome, it lacks the protein-coding gene ATP8, and has only one copy of the tRNA(Ser) gene, but three duplications of the tRNA(Gln), which is the first report among the present molluscan mtDNAs. We observed that the gene arrangement between M. meretrix and M. petechialis is same except one more tRNAGln gene in M. meretrix., and the sequence similarity is as high as 99%, indicating that M. petechialis and M. meretrix could be treated as a junior synonym of M. meretrix. Maximum Likelihood and Bayeslan analysis of 12 concatenated protein-coding amino acid sequences place the Unionidae as a sister group to other bivalves, which reflects the general opinion that the Unionidae deverged very early in Bivalvia evolution.
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Affiliation(s)
- Chong-Bo He
- The Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Dalian 116023, China.
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Perseke M, Bernhard D, Fritzsch G, Brümmer F, Stadler PF, Schlegel M. Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata. Mol Phylogenet Evol 2010; 56:201-11. [DOI: 10.1016/j.ympev.2010.01.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 01/27/2010] [Accepted: 01/30/2010] [Indexed: 10/19/2022]
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17
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Wen J, Hu C, Zhang L, Luo P, Zhao Z, Fan S, Su T. The application of PCR–RFLP and FINS for species identification used in sea cucumbers (Aspidochirotida: Stichopodidae) products from the market. Food Control 2010. [DOI: 10.1016/j.foodcont.2009.06.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Shen X, Tian M, Liu Z, Cheng H, Tan J, Meng X, Ren J. Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 2009; 439:79-86. [DOI: 10.1016/j.gene.2009.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/07/2009] [Accepted: 03/13/2009] [Indexed: 11/30/2022]
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19
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Scouras A, Smith MJ. The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: Signature nucleotide bias and unique nad4L gene rearrangement within crinoids. Mol Phylogenet Evol 2006; 39:323-34. [PMID: 16359875 DOI: 10.1016/j.ympev.2005.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 10/26/2005] [Accepted: 11/01/2005] [Indexed: 10/25/2022]
Abstract
Complete DNA sequences have been determined for the mitochondrial genomes of the crinoids Phanogenia gracilis (15892 bp) and Gymnocrinus richeri (15966 bp). The mitochondrial genetic map of the stalkless feather star P. gracilis is identical to that of the comatulid feather star Florometra serratissima (Scouras, A., Smith, M.J., 2001. Mol. Biol. Evol. 18, 61-73). The mitochondrial gene order of the stalked crinoid G. richeri differs from that of F. serratissima and P. gracilis by the transposition of the nad4L protein gene. The G. richeri nad4L mitochondrial map position is unique among metazoa and is likely a derived feature in this stalked crinoid. Nucleotide compositional analyses of protein genes encoded on the major sense strand confirm earlier conclusions regarding a crinoid-distinctive T over C bias. All three crinoids exhibit high T levels in third codon positions, whereas other echinoderm classes favor A or C in the third codon position. The nucleotide bias is reflected in the relative synonymous codon usage patterns of crinoids versus other echinoderms. We suggest that the nucleotide bias of crinoids, in comparison to other echinoderms, indicates that a physical inversion of the origin of replication has occurred in the crinoid lineage. Evolutionary rate tests support the use of the cytochrome b (cob) gene in molecular phylogenetic analyses of echinoderms. A consensus echinoderm tree was generated based on cytochrome b nucleotide alignments that placed the asteroids as a sister group to a clade containing the ophiuroids and the (echinoids+holothuroids) with the crinoids basal to the rest of the echinoderm classes: [Crinoid,(Asteroid,(Ophiuroid,(Echinoid,Holothuroid)))].
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Affiliation(s)
- Andrea Scouras
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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20
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Yasuda N, Hamaguchi M, Sasaki M, Nagai S, Saba M, Nadaoka K. Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus. BMC Genomics 2006; 7:17. [PMID: 16438737 PMCID: PMC1382216 DOI: 10.1186/1471-2164-7-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 01/27/2006] [Indexed: 11/18/2022] Open
Abstract
Background The crown-of-thorns starfish, Acanthaster planci (L.), has been blamed for coral mortality in a large number of coral reef systems situated in the Indo-Pacific region. Because of its high fecundity and the long duration of the pelagic larval stage, the mechanism of outbreaks may be related to its meta-population dynamics, which should be examined by larval sampling and population genetic analysis. However, A. planci larvae have undistinguished morphological features compared with other asteroid larvae, hence it has been difficult to discriminate A. planci larvae in plankton samples without species-specific markers. Also, no tools are available to reveal the dispersal pathway of A. planci larvae. Therefore the development of highly polymorphic genetic markers has the potential to overcome these difficulties. To obtain genomic information for these purposes, the complete nucleotide sequences of the mitochondrial genome of A. planci and its putative sibling species, A. brevispinus were determined and their characteristics discussed. Results The complete mtDNA of A. planci and A. brevispinus are 16,234 bp and 16,254 bp in size, respectively. These values fall within the length variation range reported for other metazoan mitochondrial genomes. They contain 13 proteins, 2 rRNA, and 22 tRNA genes and the putative control region in the same order as the asteroid, Asterina pectinifera. The A + T contents of A. planci and A. brevispinus on their L strands that encode the majority of protein-coding genes are 56.3% and 56.4% respectively and are lower than that of A. pectinifera (61.2%). The percent similarity of nucleotide sequences between A. planci and A. brevispinus is found to be highest in the CO2 and CO3 regions (both 90.6%) and lowest in ND2 gene (84.2%) among the 13 protein-coding genes. In the deduced putative amino acid sequences, CO1 is highly conserved (99.2%), and ATP8 apparently evolves faster any of the other protein-coding gene (85.2%). Conclusion The gene arrangement, base composition, codon usage and tRNA structure of A. planci are similar to those of A. brevispinus. However, there are significant variations between A. planci and A. brevispinus. Complete mtDNA sequences are useful for the study of phylogeny, larval detection and population genetics.
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Affiliation(s)
- Nina Yasuda
- Mechanical and Environmental Informatics, Graduate school of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552. Japan
| | - Masami Hamaguchi
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Miho Sasaki
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Masaki Saba
- 581-60 Sakura-cho, Matsuzaka, Mie 515-0071, Japan
| | - Kazuo Nadaoka
- Mechanical and Environmental Informatics, Graduate school of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552. Japan
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Mizi A, Zouros E, Moschonas N, Rodakis GC. The Complete Maternal and Paternal Mitochondrial Genomes of the Mediterranean Mussel Mytilus galloprovincialis: Implications for the Doubly Uniparental Inheritance Mode of mtDNA. Mol Biol Evol 2005; 22:952-67. [PMID: 15647523 DOI: 10.1093/molbev/msi079] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The maternal (F) and paternal (M) mitochondrial genomes of the mussel Mytilus galloprovincialis have diverged by about 20% in nucleotide sequence but retained identical gene content and gene arrangement and similar nucleotide composition and codon usage bias. Both lack the ATPase8 subunit gene, have two tRNAs for methionine and a longer open-reading frame for cox3 than seen in other mollusks. Between the F and M genomes, tRNAs are most conserved followed by rRNAs and protein-coding genes, even though the degree of divergence varies considerably among the latter. Divergence at nad3 is exceptionally low most likely because this gene includes the origin of transcription of the lagging strand (O(L)). Noncoding regions are the least conserved with the notable exception of the central domain of the main control region and a segment of another noncoding region immediately following nad3. The amino acid divergence (14%) of the two genomes is smaller than in two other pairs of conspecific genomes that are available in GenBank, that of the clam Venerupis philippinarum (34%) and of the fresh water mussel Inversidens japanensis (50%), suggesting that doubly uniparental inheritance of mtDNA emerged at different times in the three species or that there has been a relatively recent replacement of the male genome by the female in the Mytilus line. The latter hypothesis is supported from phylogenetic and population studies of Mytilidae. That the M genome contains a full complement of genes with no premature termination codons argues against it being a selfish element that rides with the sperm. It is shorter than the F by 118 bp, which apparently cannot account for the postulated replicative advantage of this genome over the F in male gonads. The high similarity of the two genomes explains why the F genome may assume the role of the M genome, but it does not exclude the possibility that for this to happen some M-specific sequences must be transferred on to the F genome by means of recombination. If such sequences exist they would most likely be located in noncoding regions.
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Affiliation(s)
- Athanasia Mizi
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, Greece
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22
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Scouras A, Beckenbach K, Arndt A, Smith MJ. Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny. Mol Phylogenet Evol 2004; 31:50-65. [PMID: 15019608 DOI: 10.1016/j.ympev.2003.07.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2002] [Revised: 07/09/2003] [Indexed: 11/30/2022]
Abstract
The complete mitochondrial genome sequences have been determined for the holothuroid Cucumaria miniata and two ophiuroid species Ophiopholis aculeata and Ophiura lütkeni. In addition, the nucleotide sequence of the mitochondrial protein-coding genes for the asteroid Pisaster ochraceus has been completed. Maximum-likelihood and LogDet distance analyses of concatenated protein-coding sequences produced a series of trees that did not conclusively support generally accepted models of echinoderm phylogeny. The ophiuroid data consistently demonstrated accelerated nucleotide divergence rates and lack of stationarity. This confounds the phylogenetic analyses. Molecular investigations using individual protein-coding gene alignments demonstrated that the cytochrome b gene exhibits the least deviation in rate and stationarity and generated some trees consistent with proposed echinoderm phylogenies. Phylogenies based on echinoderm mitochondrial gene rearrangements also proved problematic because of extensive variation in gene order between and within classes. A comparison of the two distinctive ophiuroid mitochondrial gene orders supports the hypothesis that O. lütkeni has a more derived mitochondrial gene order versus O. aculeata. The variation in the echinoderm mitochondrial gene maps reinforces the limitations of the application of mitochondrial gene rearrangements as a global phylogenetic tool.
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Affiliation(s)
- Andrea Scouras
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Boulevard, Burnaby, BC, Canada V5A 1S6
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23
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Shearer TL, Van Oppen MJH, Romano SL, Wörheide G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 2002; 11:2475-87. [PMID: 12453233 DOI: 10.1046/j.1365-294x.2002.01652.x] [Citation(s) in RCA: 425] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein-coding sequences. Hence, mtDNA markers are of limited use for population-level studies in these organisms. Mitochondrial gene sequence divergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.
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Affiliation(s)
- T L Shearer
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
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24
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Fernandez-Silva P, Polosa PL, Roberti M, Di Ponzio B, Gadaleta MN, Montoya J, Cantatore P. Sea urchin mtDBP is a two-faced transcription termination factor with a biased polarity depending on the RNA polymerase. Nucleic Acids Res 2001; 29:4736-43. [PMID: 11713324 PMCID: PMC92518 DOI: 10.1093/nar/29.22.4736] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The sea urchin mitochondrial displacement (D)-loop binding protein mtDBP has been previously identified and cloned. The polypeptide (348 amino acids) displays a significant homology with the human mitochondrial transcription termination factor mTERF. This similarity, and the observation that the 3' ends of mitochondrial RNAs coded by opposite strands mapped in correspondence of mtDBP-binding sites, suggested that mtDBP could function as transcription termination factor in sea urchin mitochondria. To investigate such a role we tested the capability of mtDBP bound to its target sequence in the main non-coding region to affect RNA elongation by mitochondrial and bacteriophage T3 and T7 RNA polymerases. We show that mtDBP was able to terminate transcription bidirectionally when initiated by human mitochondrial RNA polymerase but only unidirectionally when initiated by T3 or T7 RNA polymerases. Time-course experiments indicated that mtDBP promotes true transcription termination rather than transcription pausing. These results indicate that mtDBP is able to function as a bipolar transcription termination factor in sea urchin mitochondria. The functional significance of such an activity could be linked to the previously proposed dual role of the protein in modulating mitochondrial DNA transcription and replication.
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Affiliation(s)
- P Fernandez-Silva
- Departamento de Bioquimica y Biologia Molecular y Celular, Universidad de Zaragoza, Miguel Servet 177, E-50013 Zaragoza, Spain
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25
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Abstract
The complete nucleotide sequence of the mitochondrial genome of the crinoid Florometra serratissima has been determined. It is a circular DNA molecule, 16,005 bp in length, containing the genes for 13 proteins, small and large ribosomal RNAs, and 22 transfer RNAs (tRNAs). Three regions of unassigned sequence (UAS) greater than 73 bp have been located. The largest, UAS I, is 432 bp long and exhibits sequence similarity to the putative mitochondrial control regions seen in other animals. UAS II (77 bp) and UAS III (73 bp) are located between the 5' ends of coding sequences and may play roles as bidirectional promoters. Analyses of nucleotide composition revealed that the major peptide-encoding strand is high in T and low in C. This bias is reflected in a specific pattern of codon usage. Molecular phylogenetic analyses based on cytochrome c oxidase (COI, COII, and COIII) amino acid and nucleotide sequences did not resolve all the relationships between echinoderm classes. The overall animal mitochondrial gene content has been maintained in the crinoid, but there is extensive rearrangement with respect to both the echinoid and the asteroid mtDNA gene maps. Florometra serratissima has a novel genome organization in a segment containing most of the tRNA genes, large and small rRNA genes, and the NADH dehydrogenase subunit 1 and 2 genes. Potential pathways and mechanisms for gene rearrangements between mitochondrial gene maps of echinoderm classes and vertebrates are discussed as indicators of early deuterostome phylogeny.
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Affiliation(s)
- A Scouras
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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26
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Sumida M, Kaneda H, Kato Y, Kanamori Y, Yonekawa H, Nishioka M. Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs. Genes Genet Syst 2000; 75:79-92. [PMID: 10925786 DOI: 10.1266/ggs.75.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The nucleotide sequences of the D-loop region and its flanking genes of the mitochondrial DNA (mtDNA) from Japanese pond frogs were determined by the methods of PCR, cloning, and sequencing. The frogs belonged to two species, one subspecies, and one local race. The gene arrangements adjacent to the D-loop region were analyzed. The frogs shared a unique mitochondrial gene order that was found in Rana catesbeiana; i.e., cyt b--D-loop region--tRNA(Leu(CUN))--tRNA(Thr)--tRNA(Pro)--tRNA(Phe)--12S rRNA. The arrangements of the three tRNA genes of these frogs were different from those of X. laevis, a species which has the same overall structure as in mammals. Highly repetitive sequences with repeat units (16-bp or 17-bp sequence specific for each taxon) were found in the D-loop region. The length of repetitive sequences varied from 0.6 kbp to 1.2 kbp, and caused the extensive size variation in mtDNA. Several short sequence elements such as putative TAS, OH, CSB-1, and CSB-2 were found in the D-loop region of these frogs. The sequences of these short regulatory elements were conserved in R. catesbeiana, X. laevis, and also in human. The comparison of sequence divergences of the D-loop region and its adjacent genes among various taxa revealed that the rates of nucleotide substitutions depend on genes. The nucleotide sequences of the 3'-side segment of the D-loop region were the most variable among taxa, whereas those of the tRNA and 12S rRNA genes were the most conservative.
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Affiliation(s)
- M Sumida
- Laboratory for Amphibian Biology, Graduate School of Science, Hiroshima University, Japan.
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27
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Yokobori SI, Ueda T, Feldmaier-Fuchs G, Pääbo S, Ueshima R, Kondow A, Nishikawa K, Watanabe K. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 1999; 153:1851-62. [PMID: 10581290 PMCID: PMC1460873 DOI: 10.1093/genetics/153.4.1851] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.
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Affiliation(s)
- S i Yokobori
- Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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28
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Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 1999; 238:195-209. [PMID: 10570997 DOI: 10.1016/s0378-1119(99)00270-x] [Citation(s) in RCA: 317] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
One of the most important aspects of mitochondrial (mt) genome evolution in Metazoa is constancy of size and gene content of mtDNA, whose plasticity is maintained through a great variety of gene rearrangements probably mediated by tRNA genes. The trend of mtDNA to maintain the same genetic structure within a phylum (e.g., Chordata) is generally accepted, although more recent reports show that a considerable number of transpositions are observed also between closely related organisms. Base composition of mtDNA is extremely variable. Genome GC content is often low and, when it increases, the two complementary bases distribute asymmetrically, creating, particularly in vertebrates, a negative GC-skew. In mammals, we have found coding strand base composition and average degree of gene conservation to be related to the asymmetric replication mechanism of mtDNA. A quantitative measurement of mtDNA evolutionary rate has revealed that each of the various components has a different evolutionary rate. Non-synonymous rates are gene specific and fall in a range comparable to that of nuclear genes, whereas synonymous rates are about 22-fold higher in mt than in nuclear genes. tRNA genes are among the most conserved but, when compared to their nuclear counterparts, they evolve 100 times faster. Finally, we describe some molecular phylogenetic reconstructions which have produced unexpected outcomes, and might change our vision of the classification of living organisms.
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Affiliation(s)
- C Saccone
- Centro di Studio sui Mitocondri e Metabolismo Energetico, CNR, Bari, Italy.
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29
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Loguercio Polosa P, Roberti M, Musicco C, Gadaleta MN, Quagliariello E, Cantatore P. Cloning and characterisation of mtDBP, a DNA-binding protein which binds two distinct regions of sea urchin mitochondrial DNA. Nucleic Acids Res 1999; 27:1890-9. [PMID: 10101198 PMCID: PMC148398 DOI: 10.1093/nar/27.8.1890] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The cDNA for the sea urchin mitochondrial D-loop-binding protein (mtDBP), a 40 kDa protein which binds two homologous regions of mitochondrial DNA (the D-loop region and the boundary between the oppositely transcribed ND5 and ND6 genes), has been cloned. Four different 3'-untranslated regions have been detected that are related to each other in pairs and do not contain the canonical polyadenylation signal. The in vitro synthesised mature protein (348 amino acids), deprived of the putative signal sequence, binds specifically to its DNA target sequence and produces a DNase I footprint identical to that given by the natural protein. mtDBP contains two leucine zippers, one of which is bipartite, and two small N- and C-terminal basic domains. A deletion mutation analysis of the recombinant protein has shown that the N-terminal region and the two leucine zippers are necessary for the binding. Furthermore, evidence was provided that mtDBP binds DNA as a monomer. This rules out a dimerization role for the leucine zippers and rather suggests that intramolecular interactions between leucine zippers take place. A database search has revealed as the most significative homology a match with the human mitochondrial transcription termination factor (mTERF), a protein that also binds DNA as a monomer and contains three leucine zippers forming intramolecular interactions. These similarities, and the observation that mtDBP-binding sites contain the 3'-ends of mtRNAs coded by opposite strands and the 3'-end of the D-loop structure, point to a dual function of the protein in modulating sea urchin mitochondrial DNA transcription and replication.
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Affiliation(s)
- P Loguercio Polosa
- Dipartimento di Biochimica e Biologia Molecolare, Università di Bari and the Centro Studi sui Mitocondri e Metabolismo Energetico, CNR, Via Orabona 4, 70125 Bari, Italy
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30
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Abstract
Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems-'mitochondrial genomics'-serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.
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Affiliation(s)
- J L Boore
- Department of Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA.
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31
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Rasmussen AS, Arnason U. Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree. Proc Natl Acad Sci U S A 1999; 96:2177-82. [PMID: 10051614 PMCID: PMC26756 DOI: 10.1073/pnas.96.5.2177] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Chondrichthyes (cartilaginous fishes) are commonly accepted as being sister group to the other extant Gnathostomata (jawed vertebrates). To clarify gnathostome relationships and to aid in resolving and dating the major piscine divergences, we have sequenced the complete mtDNA of the starry skate and have included it in phylogenetic analysis along with three squalomorph chondrichthyans-the common dogfish, the spiny dogfish, and the star spotted dogfish-and a number of bony fishes and amniotes. The direction of evolution within the gnathostome tree was established by rooting it with the most closely related non-gnathostome outgroup, the sea lamprey, as well as with some more distantly related taxa. The analyses placed the chondrichthyans in a terminal position in the piscine tree. These findings, which also suggest that the origin of the amniote lineage is older than the age of the oldest extant bony fishes (the lungfishes), challenge the evolutionary direction of several morphological characters that have been used in reconstructing gnathostome relationships. Applying as a calibration point the age of the oldest lungfish fossils, 400 million years, the molecular estimate placed the squalomorph/batomorph divergence at approximately 190 million years before present. This dating is consistent with the occurrence of the earliest batomorph (skates and rays) fossils in the paleontological record. The split between gnathostome fishes and the amniote lineage was dated at approximately 420 million years before present.
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Affiliation(s)
- A S Rasmussen
- Department of Genetics, Division of Evolutionary Molecular Systematics, University of Lund, Sölvegatan 29, S-223 62 Lund, Sweden
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32
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Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 1998; 8:668-74. [PMID: 9914213 DOI: 10.1016/s0959-437x(98)80035-x] [Citation(s) in RCA: 404] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Gene arrangement comparisons are a powerful tool for phylogenetic studies, especially those focused on ancient relationships. Recent reports using metazoan mitochondrial genomes address evolutionary relationships as well as rates and mechanisms of rearrangement. Mitochondrial systems serve as a model for larger-scale comparisons of whole organismal genomes and a stimulus for developing methods for reconstructing the patterns of rearrangement.
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Affiliation(s)
- J L Boore
- Department of Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA.
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Castresana J, Feldmaier-Fuchs G, Yokobori S, Satoh N, Pääbo S. The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 1998; 150:1115-23. [PMID: 9799263 PMCID: PMC1460392 DOI: 10.1093/genetics/150.3.1115] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The complete nucleotide sequence of the mitochondrial genome of the hemichordate Balanoglossus carnosus (acorn worm) was determined. The arrangement of the genes encoding 13 protein, 22 tRNA, and 2 rRNA genes is essentially the same as in vertebrates, indicating that the vertebrate and hemichordate mitochondrial gene arrangement is close to that of their common ancestor, and, thus, that it has been conserved for more than 600 million years, whereas that of echinoderms has been rearranged extensively. The genetic code of hemichordate mitochondria is similar to that of echinoderms in that ATA encodes isoleucine and AGA serine, whereas the codons AAA and AGG, whose amino acid assignments also differ between echinoderms and vertebrates, are absent from the B. carnosus mitochondrial genome. There are three noncoding regions of length 277, 41, and 32 bp: the larger one is likely to be equivalent to the control region of other deuterostomes, while the two others may contain transcriptional promoters for genes encoded on the minor coding strand. Phylogenetic trees estimated from the inferred protein sequences indicate that hemichordates are a sister group of echinoderms.
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Affiliation(s)
- J Castresana
- Institute of Zoology, University of Munich, D-80333 Munich, Germany.
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Spruyt N, Delarbre C, Gachelin G, Laudet V. Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates. Nucleic Acids Res 1998; 26:3279-85. [PMID: 9628930 PMCID: PMC147690 DOI: 10.1093/nar/26.13.3279] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no sequence reminiscent of a control region. The organisation of the coding genes, as well as of the two rRNA genes, is identical to that of the sea lamprey. Some differences in the repartition of the tRNA genes occur when compared to the lamprey. The mitochondrial codon usage of the amphioxus is reminiscent of that of urochordates since the AGA codon is read as a glycine and not as a stop codon as in vertebrates. Moreover, the base composition at the wobble positions of the codon is strongly biased toward guanine. Altogether, these data clearly emphasise the close relationships between amphioxus and vertebrates, and reinforce the notion that prochordates may be viewed as the brother group of vertebrates.
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Affiliation(s)
- N Spruyt
- CNRS UMR 319, Mécanismes du Développement et de la Cancérisation, Institut de Biologie de Lille, Institut Pasteur, 1 rue Calmette, 59021 Lille, France
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Rasmussen AS, Janke A, Arnason U. The mitochondrial DNA molecule of the hagfish (Myxine glutinosa) and vertebrate phylogeny. J Mol Evol 1998; 46:382-8. [PMID: 9541532 DOI: 10.1007/pl00006317] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vertebrates are traditionally classified into two distinct groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed vertebrates). Extant agnathans are represented by hagfishes (Myxiniformes) and lampreys (Petromyzontiformes), frequently grouped together within the Cyclostomata. Whereas the recognition of the Gnathostomata as a clade is commonly acknowledged, a consensus has not been reached regarding whether or not Cyclostomata represents a clade. In the present study we have used newly established sequences of the protein-coding genes of the mitochondrial DNA molecule of the hagfish to explore agnathan and gnathostome relationships. The phylogenetic analysis of Pisces, using echinoderms as outgroup, placed the hagfish as a sister group of Vertebrata sensu stricto, i.e., the lamprey and the gnathostomes. The phylogenetic analysis of the Gnathostomata identified a basal divergence between gnathostome fishes and a branch leading to birds and mammals, i.e., between "Anamnia" and Amniota. The lungfish has a basal position among gnathostome fishes with the teleosts as the most recently evolving lineage. The findings portray a hitherto unrecognized polarity in the evolution of bony fishes. The presently established relationships are incompatible with previous molecular studies.
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Affiliation(s)
- Andrew B. Smith
- Department of Palaeontology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; e-mail:
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Roberti M, Musicco C, Loguercio Polosa P, Gadaleta MN, Quagliariello E, Cantatore P. Purification and characterization of a mitochondrial, single-stranded-DNA-binding protein from Paracentrotus lividus eggs. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:52-8. [PMID: 9249008 DOI: 10.1111/j.1432-1033.1997.00052.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A binding protein for single-stranded DNA was purified from Paracentrotus lividus egg mitochondria to near homogeneity by chromatography on DEAE-Sephacel and single-stranded-DNA-cellulose. The protein consists of a single polypeptide of about 15 kDa. Glycerol gradient sedimentation analysis suggested that P. lividus mitochondrial single-stranded-DNA-binding protein exists as a homo-oligomer, possibly a tetramer, in solution. The protein shows a stronger preference for poly(dT) with respect to single-stranded M13, poly(dI) and poly(dC). Binding to poly(dA) takes place with much lower affinity. The binding-site size, determined by gel mobility-shift experiments with oligonucleotides of different length, is approximately 45 nucleotides. The binding to single-stranded DNA occurs with low or no cooperativity and is not influenced by ionic strength. The protein has a very high affinity for the DNA: its apparent macroscopic association constant is 2x10(9) M(-1), a value which is the highest among the mitochondrial single-stranded-DNA-binding proteins characterized to date. The lack of cooperativity and the high association constant represent distinctive features of this protein and might be related to the peculiar mechanism of sea urchin mitochondrial DNA replication.
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Affiliation(s)
- M Roberti
- Department of Biochemistry and Molecular Biology, University of Bari and Centro Studi sui Mitocondri e Metabolismo Energetico, CNR, Italy
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De Giorgi C, Martiradonna A, Pesole G, Saccone C. Lineage-specific evolution of echinoderm mitochondrial ATP synthase subunit 8. J Bioenerg Biomembr 1997; 29:233-9. [PMID: 9298708 DOI: 10.1023/a:1022406026196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Peculiar evolutionary properties of the subunit 8 of mitochondrial ATP synthase (ATPase8) are revealed by comparative analyses carried out between both closely and distantly related species of echinoderms. The analysis of nucleotide substitution in the three echinoids demonstrated a relaxation of amino acid functional constraints. The deduced protein sequences display a well conserved domain at the N-terminus, while the central part is very variable. At the C-terminus, the broad distribution of positively charged amino acids, which is typical of other organisms, is not conserved in the two different echinoderm classes of the sea urchins and of the sea stars. Instead, a motif of three amino acids, so far not described elsewhere, is conserved in sea urchins and is found to be very similar to the motif present in the sea stars. Our results indicate that the N-terminal region seems to follow the same evolutionary pattern in different organisms, while the maintenance of the C-terminal part in a phylum-specific manner may reflect the co-evolution of mitochondrial and nuclear genes.
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Affiliation(s)
- C De Giorgi
- Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Italy
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