A Genomics Approach to Mitochondrial Evolution (original) (raw)
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Genome structure and gene content in protist mitochondrial DNAs
Nucleic Acids Research, 1998
Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly unicellular eukaryotes) become available. This review surveys the 23 complete protist mtDNA sequences that have been determined to date, commenting on such aspects as mitochondrial genome structure, gene content, ribosomal RNA, introns, transfer RNAs and the genetic code and phylogenetic implications. We also illustrate the utility of a comparative genomics approach to gene identification by providing evidence that orfB in plant and protist mtDNAs is the homolog of atp8, the gene in animal and fungal mtDNA that encodes subunit 8 of the F 0 portion of mitochondrial ATP synthase. Although several protist mtDNAs, like those of animals and most fungi, are seen to be highly derived, others appear to be have retained a number of features of the ancestral, proto-mitochondrial genome. Some of these ancestral features are also shared with plant mtDNA, although the latter have evidently expanded considerably in size, if not in gene content, in the course of evolution. Comparative analysis of protist mtDNAs is providing a new perspective on mtDNA evolution: how the original mitochondrial genome was organized, what genes it contained, and in what ways it must have changed in different eukaryotic phyla.
Mitochondrial Genome Evolution
2013
Mitochondria are membrane-enclosed organelles present in most eukaryotic cells that generate the majority of the cells ATP supply. Derived from a proteobacterial ancestor, mitochondria harbor their own, drastically reduced genome. Starting from a prokaryote-like ancestral state encoding a complete rRNA operon, a complete set of tRNAs required for translation, and key enzymes of the respiratory chain as well as some ribosomal proteins, the mitogenome has been dramatically restructured and further reduced in many of the eukaryote lineages.
Evolution of the mitochondrial genetic system: an overview
Gene, 2000
Mitochondria, semi-autonomous organelles possessing their own genetic system, are commonly accepted to descend from free-living eubacteria, namely hydrogen-producing alpha-proteobacteria. The progressive loss of genes from the primitive eubacterium to the nucleus of the eukaryotic cell is strongly justi®ed by the Muller rachet principle, which postulates that asexual genomes, like mitochondrial ones, accumulate deleterious and sublethal mutations faster than sexual genomes, like the nucleus. According to this principle, the mitochondrial genome would be doomed to death; instead, we observe that the mitochondrial genome has a variable size and structure in the different organisms, though it contains more or less the same set of genes. This is an example of genetic conservation versus structural diversity. From an evolutionary point of view the genetic system of organelles is clearly under strong selective pressure and for its survival it needs to utilize strategies to slow down or halt the ratchet. Anyway, the mitochondrial genome changes with time, and the rate of evolution is different for both diverse regions of the mtDNA and between lineages, as demonstrated in the case of mammalian mt genomes. We report here our data on the evolution of the mitochondrial DNA in mammals which demonstrate the suitability of mtDNA as a molecular tool for evolutionary analyses. q
Genetic aspects of mitochondrial genome evolution
Molecular Phylogenetics and Evolution, 2013
Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
Life, 2021
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the...
A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
Current biology : CB, 2017
The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids an...
The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the oppositeonly the head enters the eggbecame fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra-and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.
ZARAMIT: A System for the Evolutionary Study of Human Mitochondrial DNA
Lecture Notes in Computer Science, 2009
ZARAMIT is an information system capable of fully automated phylogeny reconstruction. Methods have been tailored to mitochondrial DNA sequences, with focus on subproblem partitioning. We have built exhaustive human mitochondrial phylogenies (approximately 5500 sequences) and detected problems in existing haplogroup hierarchies through data-driven classification. Information on the project can be found on zaramit.org. 1 The case for mitochondrial DNA Mitochondria, organelles present in most eukaryotic cells, are responsible for the generation of most of the cell's chemical energy. They are also remarkable for possessing their own, separate genome, which coexists with nuclear DNA and is inherited independently. Further, mitochondrial DNA (mtDNA) has several features which make it an ideal candidate for conducting evolutionary studies. Firstly, it is small in mammals (15000 to 17000 base pairs) and encodes a homogeneous set of genes with little variation between species. Secondly, it exists within a very reactive environment where ROS are common: this provokes high mutation rates, approximately an order of magnitude above those of nuclear DNA. Thirdly, it displays matrilineal inheritance, which coupled with the virtual absence of recombination results in a pure evolutionary marker. These properties make mtDNA suitable for studying evolutionary relations between closely related organisms due to its comparatively high resolution. Despite the high proportion of changes between individuals, their absolute number is small, owing to the short length of these sequences. This, in turn, permits a compact expression of mtDNA sequences as differences from a canonical reference sequence [1]. We are especially interested in the reconstruction of exhaustive human mitochondrial phylogenies which may let us spot potentially deleterious mutations. These are among the most common causes of rare genetic diseases, such as LHON This research was supported in part by Projects PM063/2007 of the Government of Aragon and TIN2008-06582-C03-02 of the Spanish Government's MICINN View publication stats View publication stats