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The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109kb in size and contains a stable integrated plasmid. ACTA ACUST UNITED AC 2008; 112:1136-52. [DOI: 10.1016/j.mycres.2008.04.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 03/19/2008] [Accepted: 04/24/2008] [Indexed: 11/17/2022]
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52
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Voigt O, Erpenbeck D, Wörheide G. A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata. BMC Genomics 2008; 9:350. [PMID: 18655725 PMCID: PMC2518934 DOI: 10.1186/1471-2164-9-350] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 07/26/2008] [Indexed: 01/30/2023] Open
Abstract
Background Animal mitochondrial (mt) genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2). Results The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp). Conclusion ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.
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Affiliation(s)
- Oliver Voigt
- Courant Research Center Geobiology, Georg-August-Universität Göttingen, Goldschmidtstr, 3, 37077 Göttingen, Germany.
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53
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Kim E, Lane CE, Curtis BA, Kozera C, Bowman S, Archibald JM. Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics 2008; 9:215. [PMID: 18474103 PMCID: PMC2397417 DOI: 10.1186/1471-2164-9-215] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 05/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. RESULTS The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a approximately 20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22-336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages. CONCLUSION Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.
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Affiliation(s)
- Eunsoo Kim
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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54
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Warda M, Han J. Retracted: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. Proteomics 2008. [DOI: 10.1002/pmic.200700695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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55
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Kayal E, Lavrov DV. The mitochondrial genome of Hydra oligactis (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny. Gene 2007; 410:177-86. [PMID: 18222615 DOI: 10.1016/j.gene.2007.12.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 11/15/2007] [Accepted: 12/04/2007] [Indexed: 10/22/2022]
Abstract
The 16,314-nuceotide sequence of the linear mitochondrial DNA (mtDNA) molecule of Hydra oligactis (Cnidaria, Hydrozoa)--the first from the class Hydrozoa--has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs, as is typical for cnidarians. All genes have the same transcriptional orientation and their arrangement in the genome is similar to that of the jellyfish Aurelia aurita. In addition, a partial copy of cox1 is present at one end of the molecule in a transcriptional orientation opposite to the rest of the genes, forming a part of inverted terminal repeat characteristic of linear mtDNA and linear mitochondrial plasmids. The sequence close to at least one end of the molecule contains several homonucleotide runs as well as small inverted repeats that are able to form strong secondary structures and may be involved in mtDNA maintenance and expression. Phylogenetic analysis of mitochondrial genes of H. oligactis and other cnidarians supports the Medusozoa hypothesis but also suggests that Anthozoa may be paraphyletic, with octocorallians more closely related to the Medusozoa than to the Hexacorallia. The latter inference implies that Anthozoa is paraphyletic and that the polyp (rather than a medusa) is the ancestral body type in Cnidaria.
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Affiliation(s)
- Ehsan Kayal
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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56
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Marcadé I, Cordaux R, Doublet V, Debenest C, Bouchon D, Raimond R. Structure and Evolution of the Atypical Mitochondrial Genome of Armadillidium vulgare (Isopoda, Crustacea). J Mol Evol 2007; 65:651-9. [PMID: 17906827 DOI: 10.1007/s00239-007-9037-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 08/02/2007] [Accepted: 08/17/2007] [Indexed: 10/22/2022]
Abstract
The crustacean isopod Armadillidium vulgare is characterized by an unusual approximately 42-kb-long mitochondrial genome consisting of two molecules co-occurring in mitochondria: a circular approximately 28-kb dimer formed by two approximately 14-kb monomers fused in opposite polarities and a linear approximately 14-kb monomer. Here we determined the nucleotide sequence of the fundamental monomeric unit of A. vulgare mitochondrial genome, to gain new insight into its structure and evolution. Our results suggest that the junction zone between monomers of the dimer structure is located in or near the control region. Direct sequencing indicated that the nucleotide sequences of the different monomer units are virtually identical. This suggests that gene conversion and/or replication processes play an important role in shaping nucleotide sequence variation in this mitochondrial genome. The only heteroplasmic site we identified predicts an alloacceptor tRNA change from tRNA(Ala) to tRNA(Val). Therefore, in A. vulgare, tRNA(Ala) and tRNA(Val) are found at the same locus in different monomers, ensuring that both tRNAs are present in mitochondria. The presence of this heteroplasmic site in all sequenced individuals suggests that the polymorphism is selectively maintained, probably because of the necessity of both tRNAs for maintaining proper mitochondrial functions. Thus, our results provide empirical evidence for the tRNA gene recruitment model of tRNA evolution. Moreover, interspecific comparisons showed that the A. vulgare mitochondrial gene order is highly derived compared to the putative ancestral arthropod type. By contrast, an overall high conservation of mitochondrial gene order is observed within crustacean isopods.
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Affiliation(s)
- Isabelle Marcadé
- Laboratoire de Génétique et Biologie des Populations de Crustacés, UMR CNRS 6556, Université de Poitiers, 40 Avenue du Recteur Pineau, F-86022 Poitiers, France.
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57
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Cannino G, Di Liegro CM, Rinaldi AM. Nuclear-mitochondrial interaction. Mitochondrion 2007; 7:359-66. [PMID: 17822963 DOI: 10.1016/j.mito.2007.07.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 07/24/2007] [Accepted: 07/24/2007] [Indexed: 12/16/2022]
Abstract
The biogenesis of mitochondria depends on the coordinated expression of nuclear and mitochondrial genomes. Consequently, the control of mitochondrial biogenesis and function depends on extremely complex processes requiring a variety of well orchestrated regulatory mechanisms. It is clear that the interplay of transcription factors and coactivators contributes to the expression of both nuclear and mitochondrial respiratory genes. In addition, the regulation of mitochondria biogenesis depends on proteins that, interacting with messenger RNAs for mitochondrial proteins, influence their metabolism and expression. Moreover, a tight regulation of the import and final assembly of mitochondrial protein is essential to endow mitochondria with functional complexes. These studies represent the basis for understanding the mechanisms involved in the nucleus-mitochondrion communication, a cross-talk essential for the cell.
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Affiliation(s)
- G Cannino
- Dipartimento di Biologia Cellulare e dello Sviluppo A.Monroy, University of Palermo, Italy
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58
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Roy J, Faktorová D, Lukes J, Burger G. Unusual Mitochondrial Genome Structures throughout the Euglenozoa. Protist 2007; 158:385-96. [PMID: 17499547 DOI: 10.1016/j.protis.2007.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Accepted: 03/18/2007] [Indexed: 11/28/2022]
Abstract
Mitochondrial DNA of Kinetoplastea is composed of different chromosomes, the maxicircle (bearing 'regular' genes) and numerous minicircles (specifying guide RNAs involved in RNA editing). In trypanosomes [Kinetoplastea], DNA circles are compacted into a single dense body, the kinetoplast. This report addresses the question whether multi-chromosome mitochondrial genomes and compacted chromosome organization are restricted to Kinetoplastea or rather occur throughout Euglenozoa, i.e., Kinetoplastea, Euglenida and Diplonemea. To this end, we investigated the diplonemid Rhynchopus euleeides and the euglenids Petalomonas cantuscygni, Peranema trichophorum and Entosiphon sulcatum, using light and electron microscopy and molecular techniques. Our findings together with previously published data show that multi-chromosome mitochondrial genomes prevail across Euglenozoa, while kinetoplast-like mtDNA packaging is confined to trypanosomes.
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MESH Headings
- Animals
- DNA, Circular/genetics
- DNA, Circular/isolation & purification
- DNA, Circular/ultrastructure
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/isolation & purification
- DNA, Kinetoplast/ultrastructure
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/ultrastructure
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Protozoan/ultrastructure
- Euglenida/genetics
- Euglenida/ultrastructure
- Microscopy, Electron, Transmission
- Microscopy, Fluorescence
- Mitochondria/diagnostic imaging
- Mitochondria/genetics
- Ultrasonography
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Affiliation(s)
- Joannie Roy
- Centre Robert Cedergren, Bioinformatics & Genomics, Département de biochimie, Université de Montréal, Montréal, QC, Canada, H3 T 1J4
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59
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Abstract
When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a "roll and spread" mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.
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60
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Shao Z, Graf S, Chaga OY, Lavrov DV. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene 2006; 381:92-101. [PMID: 16945488 DOI: 10.1016/j.gene.2006.06.021] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Revised: 06/20/2006] [Accepted: 06/23/2006] [Indexed: 11/17/2022]
Abstract
The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.
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Affiliation(s)
- Zhiyong Shao
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa 50011, USA
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61
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Kosa P, Valach M, Tomaska L, Wolfe KH, Nosek J. Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants. Nucleic Acids Res 2006; 34:2472-81. [PMID: 16684995 PMCID: PMC1459067 DOI: 10.1093/nar/gkl327] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.
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Affiliation(s)
- Peter Kosa
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University Mlynska dolina, CH-1 and B-1, 842 15, Bratislava, Slovak Republic
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62
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Abstract
Chromosomes may be either circular or linear, the latter being prone to erosion caused by incomplete replication, degradation and inappropriate repair. Despite these problems, the linear form of DNA is frequently found in viruses, bacteria, eukaryotic nuclei and organelles. The high incidence of linear chromosomes and/or genomes evokes why and how they emerged in evolution. Here we suggest that the primordial terminal structures (telomeres) of linear chromosomes in eukaryotic nuclei were derived from selfish element(s), which caused the linearization of ancestral circular genome. The telomeres were then essential in solving the emerged problems. Molecular fossils of such elements were recently identified in phylogenetically distant genomes and were shown to generate terminal arrays of tandem repeats. These arrays might mediate the formation of higher order structures at chromosomal termini that stabilize the linear chromosomal form by fulfilling essential telomeric functions.
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Affiliation(s)
- Jozef Nosek
- Department of Biochemistry, Comenius University, Bratislava, Slovakia.
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63
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Mallet MA, Lee RW. Identification of Three Distinct Polytomella Lineages Based on Mitochondrial DNA Features. J Eukaryot Microbiol 2006; 53:79-84. [PMID: 16579809 DOI: 10.1111/j.1550-7408.2005.00079.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Polytomella is composed of colorless green algae closely related to Chlamydomonas reinhardtii. Species in the genus have been used in diverse fields of biological research, most recently to study mitochondrial function and mitochondrial genome evolution in the Chlorophyceae, but the phylogenetic relationship between the various available taxa has not yet been clarified and it is not known whether they also possess fragmented mitochondrial genomes, as reported for Polytomella parva. We therefore examined cox1 sequence from seven Polytomella taxa with the goal of establishing their phylogenetic relationships and relating this information to their mitochondrial DNA (mtDNA) fragmentation pattern. We found that the Polytomella isolates examined fall into three distinct lineages, two of which possess fragmented mitochondrial genomes. The third and earliest branching lineage, represented by Polytomella capuana, appears to possess an intact mtDNA. In addition, there is evidence for variation in both size and number of mtDNA fragments between various Polytomella isolates, even within the same lineage. The considerable amount of sequence divergence between lineages seems to correlate with the geographic origin of the strains, leading us to believe that greater amounts of sequence divergence could be uncovered by a broader sampling of Polytomella.
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Affiliation(s)
- Martin A Mallet
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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64
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Nosek J, Tomaska L, Bolotin-Fukuhara M, Miyakawa I. Mitochondrial chromosome structure: an insight from analysis of complete yeast genomes. FEMS Yeast Res 2005. [DOI: 10.1111/j.1574-1364.2005.00016.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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65
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Filée J, Forterre P. Viral proteins functioning in organelles: a cryptic origin? Trends Microbiol 2005; 13:510-3. [PMID: 16157484 DOI: 10.1016/j.tim.2005.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 08/04/2005] [Accepted: 08/31/2005] [Indexed: 10/25/2022]
Abstract
Although mitochondria derive from alpha-proteobacteria, many proteins acting in this organelle did not originate from bacteria. In particular, phylogenetic evidence indicates that RNA polymerase, DNA polymerase and DNA primase--with homologues encoded by T3/T7-like bacteriophages--have replaced the ancestral proteins of bacterial origin. To date, there was no clear explanation for this puzzling observation. Bacterial genomics has now revealed the presence of cryptic prophages that are related to T3/T7 in several genomes of proteobacteria. We propose that such a prophage was present in the ancestral alpha-proteobacterium at the origin of mitochondria and that RNA polymerase, DNA polymerase and DNA primase encoded by this prophage replaced the original bacterial enzymes to function in mitochondria. Another T3/T7 viral-like RNA polymerase is functional in the chloroplast, indicating that a strong selection pressure has favored replacement of some cellular proteins by viral proteins in organelle evolution.
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Affiliation(s)
- Jonathan Filée
- Laboratoire de Microbiologie et Génétique Moléculaire, CNRS UMR-5100, 118 Route de Narbonne, 31062 Toulouse Cedex 04, France.
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66
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Marande W, Lukes J, Burger G. Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids. EUKARYOTIC CELL 2005; 4:1137-46. [PMID: 15947205 PMCID: PMC1151984 DOI: 10.1128/ec.4.6.1137-1146.2005] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2005] [Accepted: 04/19/2005] [Indexed: 11/20/2022]
Abstract
Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of Diplonema papillatum, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the cox1 gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous cox1 mRNA requires trans-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of Diplonema is not only different from that of kinetoplastids but unique among eukaryotes as a whole.
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MESH Headings
- Animals
- Base Sequence
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/ultrastructure
- Electrophoresis, Agar Gel
- Euglenida/genetics
- Euglenida/ultrastructure
- Evolution, Molecular
- Genes, rRNA
- Genome, Protozoan
- Kinetoplastida/classification
- Kinetoplastida/genetics
- Kinetoplastida/ultrastructure
- Microscopy, Electron
- Microscopy, Fluorescence
- Mitochondria/genetics
- Mitochondria/ultrastructure
- Phylogeny
- RNA Editing
- RNA Splicing
- RNA, Guide, Kinetoplastida/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
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Affiliation(s)
- William Marande
- Université de Montréal, Robert-Cedergren Centre for Bioinformatics and Genomics, Department of Biochemistry, 2900 Boulevard Edouard-Montpetit, Montreal, Quebec H3T 1J4, Canada
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67
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Gabaldón T, Huynen MA. Shaping the mitochondrial proteome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1659:212-20. [PMID: 15576054 DOI: 10.1016/j.bbabio.2004.07.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 07/15/2004] [Accepted: 07/28/2004] [Indexed: 10/26/2022]
Abstract
Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14-16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome.
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Affiliation(s)
- Toni Gabaldón
- NCMLS, Nijmegen Center for Molecular Life Sciences, P/O: CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
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68
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Nosek J, Rycovska A, Makhov AM, Griffith JD, Tomaska L. Amplification of telomeric arrays via rolling-circle mechanism. J Biol Chem 2005; 280:10840-5. [PMID: 15657051 DOI: 10.1074/jbc.m409295200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative (telomerase-independent) lengthening of telomeres mediated through homologous recombination is often accompanied by a generation of extrachromosomal telomeric circles (t-circles), whose role in direct promotion of recombinational telomere elongation has been recently demonstrated. Here we present evidence that t-circles in a natural telomerase-deficient system of mitochondria of the yeast Candida parapsilosis replicate independently of the linear chromosome via a rolling-circle mechanism. This is supported by an observation of (i) single-stranded DNA consisting of concatameric arrays of telomeric sequence, (ii) lasso-shaped molecules representing rolling-circle intermediates, and (iii) preferential incorporation of deoxyribonucleotides into telomeric fragments and t-circles. Analysis of naturally occurring variant t-circles revealed conserved motifs with potential function in driving the rolling-circle replication. These data indicate that extrachromosomal t-circles observed in a wide variety of organisms, including yeasts, plants, Xenopus laevis, and certain human cell lines, may represent independent replicons generating telomeric sequences and, thus, actively participating in telomere dynamics. Moreover, because of the promiscuous occurrence of t-circles across phyla, the results from yeast mitochondria have implications related to the primordial system of telomere maintenance, providing a paradigm for evolution of telomeres in nuclei of early eukaryotes.
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Affiliation(s)
- Jozef Nosek
- Department of Biochemistry, Mlynska dolina CH-1, Comenius University, 842 15 Bratislava, Slovakia
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69
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Rothermund K, Wentura D. Underlying processes in the implicit association test: dissociating salience from associations. J Exp Psychol Gen 2004; 133:139-65. [PMID: 15149248 DOI: 10.1037/0096-3445.133.2.139] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The authors investigated whether effects of the Implicit Association Test (IAT) are influenced by salience asymmetries, independent of associations. Two series of experiments analyzed unique effects of salience by using nonassociated, neutral categories that differed in salience. In a 3rd series, salience asymmetries were manipulated experimentally while holding associations between categories constant. In a 4th series, valent associations of the target categories were manipulated experimentally while holding salience asymmetries constant. Throughout, IAT effects were found to depend on salience asymmetries. Additionally, salience asymmetries between categories were assessed directly with a visual search task to provide an independent criterion of salience asymmetries. Salience asymmetries corresponded to IAT effects and also accounted for common variance in IAT effects and explicit measures of attitudes or the self-concept.
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70
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Thao ML, Baumann L, Baumann P. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 2004; 4:25. [PMID: 15291971 PMCID: PMC512530 DOI: 10.1186/1471-2148-4-25] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 08/03/2004] [Indexed: 11/21/2022] Open
Abstract
Background With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. Results We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII)-tRNAgly-NADH dehydrogenase subunit 3(ND3)-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. Conclusions In whiteflies, the region of the mitochondrial genome consisting of genes encoding for COIII-tRNAgly-ND3-tRNAala-tRNAarg-tRNAasn can be transposed from its ancestral position to four different locations on the mitochondrial genome. Related species within clusters established by phylogenetic analysis of host and endosymbiont genes have the same mitochondrial gene arrangement indicating a transposition in the ancestor of these clusters.
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MESH Headings
- Animals
- Anticodon/genetics
- Aphids/genetics
- Chromosome Deletion
- DNA, Mitochondrial/genetics
- Electron Transport Complex IV/genetics
- Evolution, Molecular
- Gene Order/genetics
- Genes, Insect/genetics
- Genome
- Hemiptera/genetics
- Mitochondria/genetics
- NADH Dehydrogenase/genetics
- Polymerase Chain Reaction/methods
- Protein Subunits/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Asn/genetics
- RNA, Transfer, Gly/genetics
- RNA, Untranslated/genetics
- Recombination, Genetic/genetics
- Sequence Analysis, DNA/methods
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Affiliation(s)
- MyLo L Thao
- Microbiology Section, University of California, One Shields Ave., Davis, California, USA, 95616-8665
| | - Linda Baumann
- Microbiology Section, University of California, One Shields Ave., Davis, California, USA, 95616-8665
| | - Paul Baumann
- Microbiology Section, University of California, One Shields Ave., Davis, California, USA, 95616-8665
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71
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Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J, Tomaska L. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis. Mol Genet Genomics 2004; 272:173-80. [PMID: 15449175 DOI: 10.1007/s00438-004-1046-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Accepted: 07/12/2004] [Indexed: 01/27/2023]
Abstract
The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population of linear DNA molecules that are heterogeneous in size. The length of the shortest molecules is 30,922 bp, whereas the longer molecules have expanded terminal tandem arrays (nx738 bp). The mitochondrial genome is highly compact, with less than 8% of the sequence corresponding to non-coding intergenic spacers. In silico analysis predicted genes encoding fourteen protein subunits of complexes of the respiratory chain and ATP synthase, rRNAs of the large and small subunits of the mitochondrial ribosome, and twenty-four transfer RNAs. These genes are organized into two transcription units. In addition, six intronic ORFs coding for homologues of RNA maturase, reverse transcriptase and DNA endonucleases were identified. In contrast to its overall molecular architecture, the coding sequences of the linear mitochondrial DNA of C. parapsilosis are highly similar to their counterparts in the circular mitochondrial genome of its close relative C. albicans. The complete sequence has implications for both mitochondrial DNA replication and the evolution of linear DNA genomes.
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Affiliation(s)
- J Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH-1, 842 15, Bratislava, Slovak Republic
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Rycovska A, Valach M, Tomaska L, Bolotin-Fukuhara M, Nosek J. Linear versus circular mitochondrial genomes: intraspecies variability of mitochondrial genome architecture in Candida parapsilosis. MICROBIOLOGY-SGM 2004; 150:1571-1580. [PMID: 15133118 DOI: 10.1099/mic.0.26988-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The yeast species Candida parapsilosis, an opportunistic pathogen, exhibits genetic and genomic heterogeneity. To assess the polymorphism at the level of mitochondrial DNA (mtDNA), the organization of the mitochondrial genome in strains belonging to the three variant groups of this species was investigated. Although these analyses revealed a group-specific restriction fragment pattern of mtDNA, strains belonging to different groups appear to have similar genes in the same gene order. An extensive survey of C. parapsilosis isolates uncovered surprising alterations in the molecular architecture of their mitochondrial genome. A screening strategy for strains harbouring mtDNA with rearranged architecture showed that nearly all strains from groups I and III possess linear mtDNA molecules terminating with arrays of tandem repeat units, while most of the group II strains have a circular mitochondrial genome. In addition, it was found that linear genophores in mitochondria of strains from different groups differ in the sequence of the mitochondrial telomeric repeat unit. The occurrence of altered forms of mtDNA among C. parapsilosis strains opens up the unique possibility to address questions concerning the evolutionary origin and replication strategy of linear and circular genomes in mitochondria.
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Affiliation(s)
- Adriana Rycovska
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Matus Valach
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
| | | | - Jozef Nosek
- Institute of Genetics and Microbiology, University of Paris XI, 91 405 Orsay, France
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
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73
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Tomaska L, McEachern MJ, Nosek J. Alternatives to telomerase: keeping linear chromosomes via telomeric circles. FEBS Lett 2004; 567:142-6. [PMID: 15165907 DOI: 10.1016/j.febslet.2004.04.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 04/15/2004] [Accepted: 04/19/2004] [Indexed: 11/16/2022]
Abstract
Recombination is often capable of lengthening telomeres in situations where telomerase is absent. This recombinational telomere maintenance is often accompanied by telomeric instability including the accumulation of extrachromosomal telomeric circles (t-circles). Recent results of in vivo and in vitro experiments have suggested that t-circles can lead to the production of extended stretches of telomeric DNA by serving as templates for rolling-circle synthesis. This implies that t-circles can provide an efficient means of telomere elongation. The existence of t-circles in both nuclear and mitochondrial compartments of distantly related species suggests that they may be important contributors to an evolutionary conserved telomerase-independent mechanism of maintenance of telomeric tandem arrays.
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Affiliation(s)
- Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-1, 84215 Bratislava, Slovakia.
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Affiliation(s)
- Gertraud Burger
- Canadian Institute for Advanced Research, Programme in Evolutionary Biology, Départment de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4.
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