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Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 PMCID: PMC11346449 DOI: 10.1042/bcj20230415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.
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Affiliation(s)
| | - Maria Johansen
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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2
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Rodríguez-Valdez G, Martínez-Cerda ME, Mejía-Reyes JG, Tapia-Juárez M, Olmos-Orizaba E, Cortés-Rojo C, Cortés-García CJ, Contreras-Celedón CA, Solorio-Alvarado CR, Chacón-García L. A Metastable Semiquinone Molecular Switch Modulated by Ascorbate/O 2: A Study from a System Far-From-Equilibrium to Biological Assays in Mitochondria. Chembiochem 2024:e202400401. [PMID: 38981854 DOI: 10.1002/cbic.202400401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/11/2024]
Abstract
A molecular switch based on the metastable radical anion derived from a substituted heteroaryl quinone is described. Pyrrolyl quinone thiocyanate (PQ 9) showed an interaction with the fluoride anion that was visible to the naked eye and quantified by UV/vis and 1H and 13 C NMR. The metastable quinoid species formed by the interaction with F- ("ON" state) showed a molecular switching effect autocontrolled by the presence of ascorbate ("OFF" state) and back to the "ON" state by an autooxidation process, measured by visible and UV/vis spectroscopy. Due to its out-of-equilibrium properties and the exchange of matter and energy, a dissipative structural behaviour is proposed. Considering its similarity to the mechanism of coenzyme Q in oxidative phosphophorylation, PQ 9 was evaluated on Saccharomyces cerevisiae mitochondrial function for inhibition of complexes II, III and IV, reactive oxygen species (ROS) production, catalase activity and lipid peroxidation. The results showed that PQ 9 inhibited complex III activity as well as the activity of all electron transport chain (ETC) complexes. In addition, PQ 9 reduced ROS production and catalase activity in yeast. The results suggest that PQ 9 may have potential applications as a new microbicidal compound by inducing ETC dysfunction.
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Affiliation(s)
- Gabriela Rodríguez-Valdez
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Marlen E Martínez-Cerda
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Jisell G Mejía-Reyes
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Melissa Tapia-Juárez
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Eridani Olmos-Orizaba
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Christian Cortés-Rojo
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Carlos J Cortés-García
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Claudia A Contreras-Celedón
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
| | - Cesar R Solorio-Alvarado
- División de Ciencias Naturales y Exactas, Departamento de Química, Universidad de Guanajuato, Campus Guanajuato, Noria Alta S/N, 36050, Guanajuato, Mexico
| | - Luis Chacón-García
- Laboratorio de Diseño Molecular, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, Francisco J. Múgica S/N, 58030, Morelia, Mexico
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3
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Phua CZJ, Zhao X, Turcios-Hernandez L, McKernan M, Abyadeh M, Ma S, Promislow D, Kaeberlein M, Kaya A. Genetic perturbation of mitochondrial function reveals functional role for specific mitonuclear genes, metabolites, and pathways that regulate lifespan. GeroScience 2023; 45:2161-2178. [PMID: 37086368 PMCID: PMC10651825 DOI: 10.1007/s11357-023-00796-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023] Open
Abstract
Altered mitochondrial function is tightly linked to lifespan regulation, but underlying mechanisms remain unclear. Here, we report the chronological and replicative lifespan variation across 167 yeast knock-out strains, each lacking a single nuclear-coded mitochondrial gene, including 144 genes with human homologs, many associated with diseases. We dissected the signatures of observed lifespan differences by analyzing profiles of each strain's proteome, lipidome, and metabolome under fermentative and respiratory culture conditions, which correspond to the metabolic states of replicative and chronologically aging cells, respectively. Examination of the relationships among extended longevity phenotypes, protein, and metabolite levels revealed that although many of these nuclear-encoded mitochondrial genes carry out different functions, their inhibition attenuates a common mechanism that controls cytosolic ribosomal protein abundance, actin dynamics, and proteasome function to regulate lifespan. The principles of lifespan control learned through this work may be applicable to the regulation of lifespan in more complex organisms, since many aspects of mitochondrial function are highly conserved among eukaryotes.
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Affiliation(s)
- Cheryl Zi Jin Phua
- Genome Institute of Singapore, Agency for Science, Technology, and Research (A* STAR), Singapore, Singapore
| | - Xiaqing Zhao
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Lesly Turcios-Hernandez
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Morrigan McKernan
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology, and Research (A* STAR), Singapore, Singapore
| | - Daniel Promislow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA.
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4
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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5
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Galeota-Sprung B, Fernandez A, Sniegowski P. Changes to the mtDNA copy number during yeast culture growth. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211842. [PMID: 35814911 PMCID: PMC9257595 DOI: 10.1098/rsos.211842] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
We show that the mitochondrial DNA (mtDNA) copy number in growing cultures of the yeast Saccharomyces cerevisiae increases by a factor of up to 4, being lowest (approx. 10 per haploid genome) and stable during rapid fermentative growth, and highest at the end of the respiratory phase. When yeast are grown on glucose, the onset of the mtDNA copy number increase coincides with the early stages of the diauxic shift, and the increase continues through respiration. A lesser yet still substantial copy number increase occurs when yeast are grown on a nonfermentable carbon source, i.e. when there is no diauxic shift. The mtDNA copy number increase during and for some time after the diauxic shift is not driven by an increase in cell size. The copy number increase occurs in both haploid and diploid strains but is markedly attenuated in a diploid wild isolate that is a ready sporulator. Strain-to-strain differences in mtDNA copy number are least apparent in fermentation and most apparent in late respiration or stationary phase. While changes in mitochondrial morphology and function were previously known to accompany changes in physiological state, it had not been previously shown that the mtDNA copy number changes substantially over time in a clonal growing culture. The mtDNA copy number in yeast is therefore a highly dynamic phenotype.
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Affiliation(s)
- Ben Galeota-Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy Fernandez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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6
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Christinaki AC, Kanellopoulos SG, Kortsinoglou AM, Andrikopoulos MΑ, Theelen B, Boekhout T, Kouvelis VN. Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts. Genome Biol Evol 2022; 14:6586520. [PMID: 35576568 PMCID: PMC9154068 DOI: 10.1093/gbe/evac073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events.
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Affiliation(s)
- Anastasia C Christinaki
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Spyros G Kanellopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Alexandra M Kortsinoglou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Marios Α Andrikopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
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7
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Deng S, Ma X, Chen Y, Feng H, Zhou D, Wang X, Zhang Y, Zhao M, Zhang J, Daly P, Wei L. LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus ( Nelumbo nucifera) Rhizomes. PLANT DISEASE 2022; 106:231-246. [PMID: 34494867 DOI: 10.1094/pdis-06-21-1223-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yields of edible rhizome from cultivation of the perennial hydrophyte lotus (Nelumbo nucifera) can be severely reduced by rhizome rot disease caused by Fusarium species. There is a lack of rapid field-applicable methods for detection of these pathogens on lotus plants displaying symptoms of rhizome rot. Fusarium commune (91%) and Fusarium oxysporum (9%) were identified at different frequencies from lotus samples showing symptoms of rhizome rot. Because these two species can cause different severity of disease and their morphology is similar, molecular diagnostic-based methods to detect these two species were developed. Based on the comparison of the mitochondrial genome of the two species, three specific DNA loci targets were found. The designed primer sets for conventional PCR, quantitative PCR, and loop-mediated isothermal amplification (LAMP) precisely distinguished the above two species when isolated from lotus and other plants. The LAMP detection limits were 10 pg/μl and 1 pg/μl of total DNA for F. commune and F. oxysporum, respectively. We also carried out field-mimicked experiments on lotus seedlings and rhizomes (including inoculated samples and field-diseased samples), and the results indicated that the LAMP primer sets and the supporting portable methods are suitable for rapid diagnosis of the lotus disease in the field. The LAMP-based detection method will aid in the rapid identification of whether F. oxysporum or F. commune is infecting lotus plants with symptoms of rhizome rot and can facilitate efficient pesticide use and prevent disease spread through vegetative propagation of Fusarium-infected lotus rhizomes.
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Affiliation(s)
- Sheng Deng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xin Ma
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yifan Chen
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
| | - Hui Feng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Dongmei Zhou
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xiaoyu Wang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Yong Zhang
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, U.S.A
| | - Min Zhao
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Jinfeng Zhang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Paul Daly
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Lihui Wei
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
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8
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Fonseca PLC, De-Paula RB, Araújo DS, Tomé LMR, Mendes-Pereira T, Rodrigues WFC, Del-Bem LE, Aguiar ERGR, Góes-Neto A. Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements. Front Microbiol 2021; 12:787283. [PMID: 34925295 PMCID: PMC8672057 DOI: 10.3389/fmicb.2021.787283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023] Open
Abstract
Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.
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Affiliation(s)
- Paula L C Fonseca
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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9
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Abstract
Mitochondria are complex organelles with two membranes. Their architecture is determined by characteristic folds of the inner membrane, termed cristae. Recent studies in yeast and other organisms led to the identification of four major pathways that cooperate to shape cristae membranes. These include dimer formation of the mitochondrial ATP synthase, assembly of the mitochondrial contact site and cristae organizing system (MICOS), inner membrane remodelling by a dynamin-related GTPase (Mgm1/OPA1), and modulation of the mitochondrial lipid composition. In this review, we describe the function of the evolutionarily conserved machineries involved in mitochondrial cristae biogenesis with a focus on yeast and present current models to explain how their coordinated activities establish mitochondrial membrane architecture.
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Affiliation(s)
- Till Klecker
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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10
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Jiang PH, Hou CY, Teng SC. An HSP90 cochaperone Ids2 maintains the stability of mitochondrial DNA and ATP synthase. BMC Biol 2021; 19:242. [PMID: 34763695 PMCID: PMC8582188 DOI: 10.1186/s12915-021-01179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteostasis unbalance and mitochondrial dysfunction are two hallmarks of aging. While the chaperone folds and activates its clients, it is the cochaperone that determines the specificity of the clients. Ids2 is an HSP90's cochaperone controlling mitochondrial functions, but no in vivo clients of Ids2 have been reported yet. RESULTS We performed a screen of the databases of HSP90 physical interactors, mitochondrial components, and mutants with respiratory defect, and identified Atp3, a subunit of the complex V ATP synthase, as a client of Ids2. Deletion of IDS2 destabilizes Atp3, and an α-helix at the middle region of Ids2 recruits Atp3 to the folding system. Shortage of Ids2 or Atp3 leads to the loss of mitochondrial DNA. The intermembrane space protease Yme1 is critical to maintaining the Atp3 protein level. Moreover, Ids2 is highly induced when cells carry out oxidative respiration. CONCLUSIONS These findings discover a cochaperone essentially for maintaining the stability of mitochondrial DNA and the proteostasis of the electron transport chain-crosstalk between two hallmarks of aging.
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Affiliation(s)
- Pei-Heng Jiang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chen-Yan Hou
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, Taiwan.
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11
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Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence. Life (Basel) 2021; 11:life11070663. [PMID: 34357035 PMCID: PMC8303319 DOI: 10.3390/life11070663] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/11/2022] Open
Abstract
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 present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
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12
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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Plazzi F, Puccio G, Passamonti M. HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades. Mitochondrion 2021; 58:285-295. [PMID: 33639269 DOI: 10.1016/j.mito.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
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Ravoitytė B, Lukša J, Yurchenko V, Serva S, Servienė E. Saccharomyces paradoxus Transcriptional Alterations in Cells of Distinct Phenotype and Viral dsRNA Content. Microorganisms 2020; 8:microorganisms8121902. [PMID: 33266158 PMCID: PMC7761358 DOI: 10.3390/microorganisms8121902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 11/28/2020] [Accepted: 11/29/2020] [Indexed: 01/23/2023] Open
Abstract
Killer yeasts are attractive antifungal agents with great potential applications in the food industry. Natural Saccharomyces paradoxus isolates provide new dsRNA-based killer systems available for investigation. The presence of viral dsRNA may alter transcriptional profile of S. paradoxus. To test this possibility, a high-throughput RNA sequencing was employed to compare the transcriptomes of S. paradoxus AML 15-66 K66 killer strains after curing them of either M-66 alone or both M-66 and L-A-66 dsRNA viruses. The S. paradoxus cells cured of viral dsRNA(s) showed respiration deficient or altered sporulation patterns. We have identified numerous changes in the transcription profile of genes including those linked to ribosomes and amino acid biosynthesis, as well as mitochondrial function. Our work advance studies of transcriptional adaptations of Saccharomyces spp. induced by changes in phenotype and set of dsRNA viruses, reported for the first time.
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Affiliation(s)
- Bazilė Ravoitytė
- Laboratory of Genetics, Institute of Botany, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania;
- Correspondence: (B.R.); (E.S.)
| | - Juliana Lukša
- Laboratory of Genetics, Institute of Botany, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania;
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Malaya Pirogovskaya str. 20, 119435 Moscow, Russia
| | - Saulius Serva
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Vilnius University, Saulėtekio al. 7, 10257 Vilnius, Lithuania;
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Saulėtekio al. 11, 10223 Vilnius, Lithuania
| | - Elena Servienė
- Laboratory of Genetics, Institute of Botany, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania;
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Saulėtekio al. 11, 10223 Vilnius, Lithuania
- Correspondence: (B.R.); (E.S.)
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15
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Dixon TA, Pretorius IS. Drawing on the Past to Shape the Future of Synthetic Yeast Research. Int J Mol Sci 2020; 21:E7156. [PMID: 32998303 PMCID: PMC7583028 DOI: 10.3390/ijms21197156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Some years inspire more hindsight reflection and future-gazing than others. This is even more so in 2020 with its evocation of perfect vision and the landmark ring to it. However, no futurist can reliably predict what the world will look like the next time that a year's first two digits will match the second two digits-a numerical pattern that only occurs once in a century. As we leap into a new decade, amid uncertainties triggered by unforeseen global events-such as the outbreak of a worldwide pandemic, the accompanying economic hardship, and intensifying geopolitical tensions-it is important to note the blistering pace of 21st century technological developments indicate that while hindsight might be 20/20, foresight is 50/50. The history of science shows us that imaginative ideas, research excellence, and collaborative innovation can, for example, significantly contribute to the economic, cultural, social, and environmental recovery of a post-COVID-19 world. This article reflects on a history of yeast research to indicate the potential that arises from advances in science, and how this can contribute to the ongoing recovery and development of human society. Future breakthroughs in synthetic genomics are likely to unlock new avenues of impactful discoveries and solutions to some of the world's greatest challenges.
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Affiliation(s)
- Thomas A. Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW 2109, Australia;
| | - Isak S. Pretorius
- Chancellery and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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16
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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17
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Fu Y, Tigano M, Sfeir A. Safeguarding mitochondrial genomes in higher eukaryotes. Nat Struct Mol Biol 2020; 27:687-695. [PMID: 32764737 DOI: 10.1038/s41594-020-0474-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Mitochondria respond to DNA damage and preserve their own genetic material in a manner distinct from that of the nucleus but that requires organized mito-nuclear communication. Failure to resolve mtDNA breaks leads to mitochondrial dysfunction and affects host cells and tissues. Here, we review the pathways that safeguard mitochondrial genomes and examine the insights gained from studies of cellular and tissue-wide responses to mtDNA damage and mito-nuclear genome incompatibility.
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Affiliation(s)
- Yi Fu
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA.
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18
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Stenger M, Le DT, Klecker T, Westermann B. Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae. MICROBIAL CELL 2020; 7:234-249. [PMID: 32904421 PMCID: PMC7453639 DOI: 10.15698/mic2020.09.729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8m, we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.
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Affiliation(s)
- Maria Stenger
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Duc Tung Le
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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19
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Abstract
Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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20
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Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
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Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLoS One 2020; 15:e0224007. [PMID: 31978166 PMCID: PMC6980612 DOI: 10.1371/journal.pone.0224007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
The root rot causing oomycete, Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14–20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection of P. agathidicida that targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of other Phytophthora isolates and detected as little as 1 fg of total P. agathidicida DNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended soil bioassay and LAMP testing of DNA extracted from baits. In these comparisons, P. agathidicida was detected more frequently using the LAMP test. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the extended soil bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions about P. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid LAMP bioassay also has the potential to empower local communities to evaluate the pathogen status of local kauri stands, providing information for disease management and conservation initiatives.
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Affiliation(s)
- Richard C. Winkworth
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail:
| | - Briana C. W. Nelson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | | | | | - Peter J. Lockhart
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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22
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Yoo BC, Yadav NS, Orozco EM, Sakai H. Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PeerJ 2020; 8:e8362. [PMID: 31934513 PMCID: PMC6951285 DOI: 10.7717/peerj.8362] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2019] [Indexed: 11/20/2022] Open
Abstract
We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated "Edit Plasmids," were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion.
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Bernal M, Yang X, Lisby M, Mazón G. The FANCM family Mph1 helicase localizes to the mitochondria and contributes to mtDNA stability. DNA Repair (Amst) 2019; 82:102684. [DOI: 10.1016/j.dnarep.2019.102684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/24/2022]
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24
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Gonçalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol 2019; 138:219-232. [PMID: 31146023 DOI: 10.1016/j.ympev.2019.05.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.
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Affiliation(s)
- Deise J P Gonçalves
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA.
| | - Beryl B Simpson
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA
| | - Edgardo M Ortiz
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Department of Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Emil-Ramann Strasse 2, Freising D-85354, Germany
| | - Gustavo H Shimizu
- Department of Plant Biology, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Genomics and Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Twist and Turn-Topoisomerase Functions in Mitochondrial DNA Maintenance. Int J Mol Sci 2019; 20:ijms20082041. [PMID: 31027213 PMCID: PMC6514783 DOI: 10.3390/ijms20082041] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
Like any genome, mitochondrial DNA (mtDNA) also requires the action of topoisomerases to resolve topological problems in its maintenance, but for a long time, little was known about mitochondrial topoisomerases. The last years have brought a closer insight into the function of these fascinating enzymes in mtDNA topology regulation, replication, transcription, and segregation. Here, we summarize the current knowledge about mitochondrial topoisomerases, paying special attention to mammalian mitochondrial genome maintenance. We also discuss the open gaps in the existing knowledge of mtDNA topology control and the potential involvement of mitochondrial topoisomerases in human pathologies. While Top1mt, the only exclusively mitochondrial topoisomerase in mammals, has been studied intensively for nearly a decade, only recent studies have shed some light onto the mitochondrial function of Top2β and Top3α, enzymes that are shared between nucleus and mitochondria. Top3α mediates the segregation of freshly replicated mtDNA molecules, and its dysfunction leads to mtDNA aggregation and copy number depletion in patients. Top2β, in contrast, regulates mitochondrial DNA replication and transcription through the alteration of mtDNA topology, a fact that should be acknowledged due to the frequent use of Topoisomerase 2 inhibitors in medical therapy.
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26
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Malina C, Larsson C, Nielsen J. Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res 2019; 18:4969682. [PMID: 29788060 DOI: 10.1093/femsyr/foy040] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
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Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
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27
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The DNA damage response is developmentally regulated in the African trypanosome. DNA Repair (Amst) 2018; 73:78-90. [PMID: 30470509 PMCID: PMC6329875 DOI: 10.1016/j.dnarep.2018.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/12/2018] [Accepted: 11/12/2018] [Indexed: 01/19/2023]
Abstract
Genomes are affected by a wide range of damage, which has resulted in the evolution of a number of widely conserved DNA repair pathways. Most of these repair reactions have been described in the African trypanosome Trypanosoma brucei, which is a genetically tractable eukaryotic microbe and important human and animal parasite, but little work has considered how the DNA damage response operates throughout the T. brucei life cycle. Using quantitative PCR we have assessed damage induction and repair in both the nuclear and mitochondrial genomes of the parasite. We show differing kinetics of repair for three forms of DNA damage, and dramatic differences in repair between replicative life cycle forms found in the testse fly midgut and the mammal. We find that mammal-infective T. brucei cells repair oxidative and crosslink-induced DNA damage more efficiently than tsetse-infective cells and, moreover, very distinct patterns of induction and repair of DNA alkylating damage in the two life cycle forms. We also reveal robust repair of DNA lesions in the highly unusual T. brucei mitochondrial genome (the kinetoplast). By examining mutants we show that nuclear alkylation damage is repaired by the concerted action of two repair pathways, and that Rad51 acts in kinetoplast repair. Finally, we correlate repair with cell cycle arrest and cell growth, revealing that induced DNA damage has strikingly differing effects on the two life cycle stages, with distinct timing of alkylation-induced cell cycle arrest and higher levels of damage induced death in mammal-infective cells. Our data reveal that T. brucei regulates the DNA damage response during its life cycle, a capacity that may be shared by many microbial pathogens that exist in variant environments during growth and transmission.
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Burger G, Valach M. Perfection of eccentricity: Mitochondrial genomes of diplonemids. IUBMB Life 2018; 70:1197-1206. [PMID: 30304578 DOI: 10.1002/iub.1927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/14/2023]
Abstract
Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 70(12):1197-1206, 2018.
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Affiliation(s)
- Gertraud Burger
- Département de Biochimie, Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Québec, Canada
| | - Matus Valach
- Département de Biochimie, Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Québec, Canada
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29
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Yan Z, Li Z, Yan L, Yu Y, Cheng Y, Chen J, Liu Y, Gao C, Zeng L, Sun X, Guo L, Xu J. Deletion of the sex-determining gene SXI1α enhances the spread of mitochondrial introns in Cryptococcus neoformans. Mob DNA 2018; 9:24. [PMID: 30026817 PMCID: PMC6048814 DOI: 10.1186/s13100-018-0129-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Background Homing endonuclease genes (HEGs) are widely distributed genetic elements in the mitochondrial genomes of a diversity of eukaryotes. Due to their ability to self-propagate within and between genomes, these elements can spread rapidly in populations. Whether and how such elements are controlled in genomes remains largely unknown. Results Here we report that the HEG-containing introns in the mitochondrial COX1 gene in Cryptococcus neoformans are mobile and that their spread in sexual crosses is influenced by mating type (MAT) α-specific homeodomain gene SXI1α. C. neoformans has two mating types, MATa and MATα. In typical crosses between strains of the two mating types, only a small portion (< 7%) of diploid fusants inherited the HEGs from the MATα parent. However, disruption of the SXI1α gene resulted in the majority (> 95%) of the diploid fusants inheriting the HEG-containing introns from the MATα parent, a frequency significantly higher than those of intronless mitochondrial genes. Conclusions Our results suggest that SXI1α not only determines uniparental mitochondrial inheritance but also inhibits the spread of HEG-containing introns in the mitochondrial genome in C. neoformans.
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Affiliation(s)
- Zhun Yan
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Zhimin Li
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Li Yan
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Yongting Yu
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Yi Cheng
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Jia Chen
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Yunyun Liu
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Chunsheng Gao
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Liangbin Zeng
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Xiangping Sun
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Litao Guo
- 1Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan China
| | - Jianping Xu
- 2Department of Biology, McMaster University, Hamilton, ON L8S 4K1 Canada
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30
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Verspohl A, Pignedoli S, Giudici P. The inheritance of mitochondrial DNA in interspecific Saccharomyces hybrids and their properties in winemaking. Yeast 2017; 35:173-187. [PMID: 29048749 DOI: 10.1002/yea.3288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
The inheritance of mitochondrial DNA (mtDNA) in yeast hybrids is heteroplasmic, turning into homoplasmic after few cell cycles. Mitotype restoration is reported to be biparental and random. This study shows that mitotype restoration follows fixed schemata. We created isogenic, interspecific Saccharomyces cerevisiae × Saccharomyces uvarum hybrids through direct mating and analysed their mating frequency and mitotype. The mating frequency increased for most crosses in staggered mating. Mitotyping revealed that breeding lines with the same parental strain of S. cerevisiae and different parental strains of S. uvarum give rise to the same mitotype. According to our results, we postulate that the inheritance of mtDNA is dominated by one parental strain and that the superior mitotype is specific to each breeding line. Technological tests showed typical hybrid heterosis. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alexandra Verspohl
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
| | - Samuele Pignedoli
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
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31
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Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. PLoS Genet 2017; 13:e1007041. [PMID: 29036220 PMCID: PMC5658192 DOI: 10.1371/journal.pgen.1007041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/26/2017] [Accepted: 09/21/2017] [Indexed: 01/23/2023] Open
Abstract
A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.
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Affiliation(s)
- Joseph C. Sanchez
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Thomas J. Pohl
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Haley M. Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail:
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32
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Prasai K, Robinson LC, Scott RS, Tatchell K, Harrison L. Evidence for double-strand break mediated mitochondrial DNA replication in Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:7760-7773. [PMID: 28549155 PMCID: PMC5569933 DOI: 10.1093/nar/gkx443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/04/2017] [Indexed: 01/30/2023] Open
Abstract
The mechanism of mitochondrial DNA (mtDNA) replication in Saccharomyces cerevisiae is controversial. Evidence exists for double-strand break (DSB) mediated recombination-dependent replication at mitochondrial replication origin ori5 in hypersuppressive ρ− cells. However, it is not clear if this replication mode operates in ρ+ cells. To understand this, we targeted bacterial Ku (bKu), a DSB binding protein, to the mitochondria of ρ+ cells with the hypothesis that bKu would bind persistently to mtDNA DSBs, thereby preventing mtDNA replication or repair. Here, we show that mitochondrial-targeted bKu binds to ori5 and that inducible expression of bKu triggers petite formation preferentially in daughter cells. bKu expression also induces mtDNA depletion that eventually results in the formation of ρ0 cells. This data supports the idea that yeast mtDNA replication is initiated by a DSB and bKu inhibits mtDNA replication by binding to a DSB at ori5, preventing mtDNA segregation to daughter cells. Interestingly, we find that mitochondrial-targeted bKu does not decrease mtDNA content in human MCF7 cells. This finding is in agreement with the fact that human mtDNA replication, typically, is not initiated by a DSB. Therefore, this study provides evidence that DSB-mediated replication is the predominant form of mtDNA replication in ρ+ yeast cells.
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Affiliation(s)
- Kanchanjunga Prasai
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Lucy C Robinson
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Rona S Scott
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Kelly Tatchell
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Lynn Harrison
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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33
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Chen XJ, Clark-Walker GD. Unveiling the mystery of mitochondrial DNA replication in yeasts. Mitochondrion 2017; 38:17-22. [PMID: 28778567 DOI: 10.1016/j.mito.2017.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/12/2017] [Accepted: 07/28/2017] [Indexed: 11/27/2022]
Abstract
Conventional DNA replication is initiated from specific origins and requires the synthesis of RNA primers for both the leading and lagging strands. In contrast, the replication of yeast mitochondrial DNA is origin-independent. The replication of the leading strand is likely primed by recombinational structures and proceeded by a rolling circle mechanism. The coexistent linear and circular DNA conformers facilitate the recombination-based initiation. The replication of the lagging strand is poorly understood. Re-evaluation of published data suggests that the rolling circle may also provide structures for the synthesis of the lagging-strand by mechanisms such as template switching. Thus, the coupling of recombination with rolling circle replication and possibly, template switching, may have been selected as an economic replication mode to accommodate the reductive evolution of mitochondria. Such a replication mode spares the need for conventional replicative components, including those required for origin recognition/remodelling, RNA primer synthesis and lagging-strand processing.
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Affiliation(s)
- Xin Jie Chen
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.
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Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. ACTA ACUST UNITED AC 2017; 24:2. [PMID: 28164041 PMCID: PMC5282644 DOI: 10.1186/s40709-017-0060-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 12/17/2022]
Abstract
Mitochondrial DNA (mtDNA) has been studied intensely for “its own” merit. Its role for the function of the cell and the organism remains a fertile field, its origin and evolution is an indispensable part of the evolution of life and its interaction with the nuclear DNA is among the most important cases of genome synergism and co-evolution. Also, mtDNA was proven one of the most useful tools in population genetics and molecular phylogenetics. In this article we focus on animal mtDNA and discuss briefly how our views about its structure, function and transmission have changed, how these changes affect the information we have accumulated through its use in the fields of phylogeny and population structure and what are the most important questions that remain open for future research.
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35
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Ravoitytė B, Wellinger RE. Non-Canonical Replication Initiation: You're Fired! Genes (Basel) 2017; 8:genes8020054. [PMID: 28134821 PMCID: PMC5333043 DOI: 10.3390/genes8020054] [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: 11/10/2016] [Accepted: 01/19/2017] [Indexed: 12/25/2022] Open
Abstract
The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis-acting DNA sequences, the so-called origins of replication (ori), with trans-acting factors involved in the onset of DNA synthesis. The interplay of cis-acting elements and trans-acting factors ensures that cells initiate replication at sequence-specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause break-induced (BIR) or transcription-initiated replication (TIR), respectively. These non-canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non-canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.
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Affiliation(s)
- Bazilė Ravoitytė
- Nature Research Centre, Akademijos g. 2, LT-08412 Vilnius, Lithuania.
| | - Ralf Erik Wellinger
- CABIMER-Universidad de Sevilla, Avd Americo Vespucio sn, 41092 Sevilla, Spain.
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Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Solà M. DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. Nucleic Acids Res 2017; 45:951-967. [PMID: 27899643 PMCID: PMC5314765 DOI: 10.1093/nar/gkw1147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/16/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022] Open
Abstract
The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction.
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Affiliation(s)
- Arka Chakraborty
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Giorgio Medici
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
| | - Josep Vilardell
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain
- Molecular Genomics Department, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, 08028, Spain
| | - Maria Solà
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
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37
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Ellenberger S, Burmester A, Wöstemeyer J. The fate of mitochondria after infection of the Mucoralean fungus Absidia glauca by the fusion parasite Parasitella parasitica: comparison of mitochondrial genomes in zygomycetes. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:113-120. [PMID: 28034347 DOI: 10.1080/24701394.2016.1248432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Absidia glauca and Parasitella parasitica constitute a versatile experimental system for studying horizontal gene transfer between a mucoralean host and its fusion parasite. The A. glauca chondriome has a length of approximately 63 kb and a GC content of 28%. The chondriome of P. parasitica is larger, 83 kb, and contains 31% GC base pairs. These mtDNAs contain the standard fungal mitochondrial gene set, small and large subunit rRNAs, plus ribonuclease P RNA. Comparing zygomycete chondriomes reveals an unusually high number of homing endonuclease genes in P. parasitica, substantiating the mobility of intron elements independent of host-parasite interactions.
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Affiliation(s)
- Sabrina Ellenberger
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
| | - Anke Burmester
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
| | - Johannes Wöstemeyer
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
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Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab 2016; 24:91-103. [PMID: 27411011 PMCID: PMC5287496 DOI: 10.1016/j.cmet.2016.06.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023]
Abstract
Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious metabolic consequences. We sought to study regulation of selfish mtDNA dynamics. We establish that the large 3.1-kb deletion-bearing mtDNA variant uaDf5 is a selfish genome in Caenorhabditis elegans. Next, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wild-type mtDNA. These data suggest the existence of a homeostatic copy-number control that is exploited by uaDf5 to "hitchhike" to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPR(mt)) in uaDf5 animals. Loss of UPR(mt) causes a decrease in uaDf5 frequency, whereas its constitutive activation increases uaDf5 levels. UPR(mt) activation protects uaDf5 from mitophagy. Taken together, we propose that mtDNA copy-number control and UPR(mt) represent two homeostatic response mechanisms that play important roles in regulating selfish mitochondrial genome dynamics.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Biological Sciences Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama D Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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Oldenburg DJ, Bendich AJ. DNA maintenance in plastids and mitochondria of plants. FRONTIERS IN PLANT SCIENCE 2015; 6:883. [PMID: 26579143 PMCID: PMC4624840 DOI: 10.3389/fpls.2015.00883] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/05/2015] [Indexed: 05/02/2023]
Abstract
The DNA molecules in plastids and mitochondria of plants have been studied for over 40 years. Here, we review the data on the circular or linear form, replication, repair, and persistence of the organellar DNA (orgDNA) in plants. The bacterial origin of orgDNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of orgDNA. In cells active in orgDNA replication, most orgDNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism. In contrast to the stable chromosomal DNA molecules in bacteria and the plant nucleus, the molecular integrity of orgDNA declines during leaf development at a rate that varies among plant species. This decline is attributed to degradation of damaged-but-not-repaired molecules, with a proposed repair cost-saving benefit most evident in grasses. All orgDNA maintenance activities are proposed to occur on the nucleoid tethered to organellar membranes by developmentally-regulated proteins.
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Abstract
Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.
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Affiliation(s)
- Stephan Greiner
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Johanna Sobanski
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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Gerhold JM, Sedman T, Visacka K, Slezakova J, Tomaska L, Nosek J, Sedman J. Replication intermediates of the linear mitochondrial DNA of Candida parapsilosis suggest a common recombination based mechanism for yeast mitochondria. J Biol Chem 2014; 289:22659-22670. [PMID: 24951592 DOI: 10.1074/jbc.m114.552828] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Variation in the topology of mitochondrial DNA (mtDNA) in eukaryotes evokes the question if differently structured DNAs are replicated by a common mechanism. RNA-primed DNA synthesis has been established as a mechanism for replicating the circular animal/mammalian mtDNA. In yeasts, circular mtDNA molecules were assumed to be templates for rolling circle DNA-replication. We recently showed that in Candida albicans, which has circular mapping mtDNA, recombination driven replication is a major mechanism for replicating a complex branched mtDNA network. Careful analyses of C. albicans-mtDNA did not reveal detectable amounts of circular DNA molecules. In the present study we addressed the question of how the unit sized linear mtDNA of Candida parapsilosis terminating at both ends with arrays of tandem repeats (mitochondrial telomeres) is replicated. Originally, we expected to find replication intermediates diagnostic of canonical bi-directional replication initiation at the centrally located bi-directional promoter region. However, we found that the linear mtDNA of Candida parapsilosis also employs recombination for replication initiation. The most striking findings were that the mitochondrial telomeres appear to be hot spots for recombination driven replication, and that stable RNA:DNA hybrids, with a potential role in mtDNA replication, are also present in the mtDNA preparations.
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Affiliation(s)
- Joachim M Gerhold
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and.
| | - Tiina Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and
| | - Katarina Visacka
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Judita Slezakova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Juhan Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and
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Dokianakis E, Ladoukakis ED. Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses. Ecol Evol 2014; 4:2633-41. [PMID: 25077015 PMCID: PMC4113288 DOI: 10.1002/ece3.1069] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 12/17/2022] Open
Abstract
Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter- than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter- and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex-specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error-prone mechanism, but rather, it may be under complex genetic control.
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Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA. Microbiol Mol Biol Rev 2014; 77:476-96. [PMID: 24006472 DOI: 10.1128/mmbr.00007-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.
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Zubko EI, Zubko MK. Deficiencies in mitochondrial DNA compromise the survival of yeast cells at critically high temperatures. Microbiol Res 2014; 169:185-95. [DOI: 10.1016/j.micres.2013.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 06/25/2013] [Accepted: 06/29/2013] [Indexed: 11/25/2022]
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O'Brien MA, Misner I, Lane CE. Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J Eukaryot Microbiol 2013; 61:146-54. [PMID: 24252096 DOI: 10.1111/jeu.12092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/12/2013] [Accepted: 10/17/2013] [Indexed: 01/08/2023]
Abstract
As a lineage, oomycetes have adapted to a wide range of lifestyles. Although the common ancestor of the group was likely a marine pathogen, extant members inhabit a spectrum from free-living saprobes to obligate biotrophs. The mitochondrial genomes of Achlya hypogyna and Thraustotheca clavata were sequenced to directly compare a facultative parasitic species (A. hypogyna) to a closely related free living saprobe (T. clavata). Both sequenced mitochondrial genomes are circular, with sizes of 46,869 bp for A. hypogyna and 47,381 bp for T. clavata. They share 63 common genes, indicating little influence of lifestyle on gene content, but small differences in total number and order of genes. Achlya hypogyna has a single copy of nad2, whereas T. clavata has one pseudogene (rps7) and two duplicated genes (nad5 and nad2), each with one full and one truncated copy. The genomes encode a total of 29 or 30 tRNAs (A. hypogyna and T. clavata, respectively) for 19 amino acids. Three unidentified open reading frames are conserved, and one is unique to T. clavata. Comparisons of these genomes with published sequences of the closely related Saprolegnia ferax mitochondrial genome, and four other more distantly related oomycetes, reveals no correlation in genome content or architecture with lifestyle.
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Affiliation(s)
- Megan A O'Brien
- Department of Biology, The University of Rhode Island, Kingston, RI, 02881
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Westermann B. Mitochondrial inheritance in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:1039-46. [PMID: 24183694 DOI: 10.1016/j.bbabio.2013.10.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/08/2013] [Accepted: 10/22/2013] [Indexed: 11/25/2022]
Abstract
Mitochondria are the site of oxidative phosphorylation, play a key role in cellular energy metabolism, and are critical for cell survival and proliferation. The propagation of mitochondria during cell division depends on replication and partitioning of mitochondrial DNA, cytoskeleton-dependent mitochondrial transport, intracellular positioning of the organelle, and activities coordinating these processes. Budding yeast Saccharomyces cerevisiae has proven to be a valuable model organism to study the mechanisms that drive segregation of the mitochondrial genome and determine mitochondrial partitioning and behavior in an asymmetrically dividing cell. Here, I review past and recent advances that identified key components and cellular pathways contributing to mitochondrial inheritance in yeast. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference. Guest Editors: Manuela Pereira and Miguel Teixeira.
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47
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Jasmin JN, Zeyl C. RAPID EVOLUTION OF CHEATING MITOCHONDRIAL GENOMES IN SMALL YEAST POPULATIONS. Evolution 2013; 68:269-75. [DOI: 10.1111/evo.12228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/30/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Jean-Nicolas Jasmin
- Department of Biology; Wake Forest University; Winston-Salem North Carolina 27109
| | - Clifford Zeyl
- Department of Biology; Wake Forest University; Winston-Salem North Carolina 27109
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48
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Kukat C, Larsson NG. mtDNA makes a U-turn for the mitochondrial nucleoid. Trends Cell Biol 2013; 23:457-63. [PMID: 23721879 DOI: 10.1016/j.tcb.2013.04.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
Abstract
Mitochondria contain mtDNA derived from the ancestral endosymbiont genome. Important subunits of the oxidative phosphorylation system, which supplies cells with the energy currency ATP, are encoded by mtDNA. A naked mtDNA molecule is longer than a typical mitochondrion and is therefore compacted in vivo to form a nucleoprotein complex, denoted the mitochondrial nucleoid. Mitochondrial transcription factor A (TFAM) is the main factor packaging mtDNA into nucleoids and is also essential for mtDNA transcription initiation. The crystal structure of TFAM shows that it bends mtDNA in a sharp U-turn, which likely provides the structural basis for its dual functions. Super-resolution imaging studies have revealed that the nucleoid has an average diameter of ∼100nm and frequently contains a single copy of mtDNA. In this review the structure of the mitochondrial nucleoid and its possible regulatory roles in mtDNA expression will be discussed.
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Affiliation(s)
- Christian Kukat
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
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49
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Friedrich A, Jung PP, Hou J, Neuvéglise C, Schacherer J. Comparative mitochondrial genomics within and among yeast species of the Lachancea genus. PLoS One 2012; 7:e47834. [PMID: 23112855 PMCID: PMC3480396 DOI: 10.1371/journal.pone.0047834] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 09/21/2012] [Indexed: 12/18/2022] Open
Abstract
Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.
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Affiliation(s)
- Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
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Yamauchi A, Telschow A. Bistability of endosymbiont evolution of genome size and host sex control. J Theor Biol 2012; 309:58-66. [DOI: 10.1016/j.jtbi.2012.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 05/16/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
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