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Dubie JJ, Katju V, Bergthorsson U. Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans. Heredity (Edinb) 2024:10.1038/s41437-024-00704-2. [PMID: 38969772 DOI: 10.1038/s41437-024-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/07/2024] Open
Abstract
Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.
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Affiliation(s)
- Joseph J Dubie
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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Estes S, Dietz ZP, Katju V, Bergthorsson U. Evolutionary codependency: insights into the mitonuclear interaction landscape from experimental and wild Caenorhabditis nematodes. Curr Opin Genet Dev 2023; 81:102081. [PMID: 37421904 DOI: 10.1016/j.gde.2023.102081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these areas. We review recent discoveries with relevance to mitonuclear coevolution and conflict and offer several fertile areas for future work.
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Affiliation(s)
- Suzanne Estes
- Portland State University, Department of Biology, Portland, OR, USA.
| | - Zachary P Dietz
- Portland State University, Department of Biology, Portland, OR, USA
| | - Vaishali Katju
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
| | - Ulfar Bergthorsson
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
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Jeedigunta SP, Minenkova AV, Palozzi JM, Hurd TR. Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline. Annu Rev Genomics Hum Genet 2021; 22:55-80. [PMID: 34038145 DOI: 10.1146/annurev-genom-121420-081805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates.
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Affiliation(s)
- Swathi P Jeedigunta
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Anastasia V Minenkova
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Jonathan M Palozzi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
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Havird JC, Weaver RJ, Milani L, Ghiselli F, Greenway R, Ramsey AJ, Jimenez AG, Dowling DK, Hood WR, Montooth KL, Estes S, Schulte PM, Sokolova IM, Hill GE. Beyond the Powerhouse: Integrating Mitonuclear Evolution, Physiology, and Theory in Comparative Biology. Integr Comp Biol 2020; 59:856-863. [PMID: 31504533 DOI: 10.1093/icb/icz132] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this symposium volume, scientists working in diverse organismal systems spanning vast biological scales address emerging topics in integrative, comparative biology in light of mitonuclear interactions.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Ryan J Weaver
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.,Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, 40126, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, 40126, Italy
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Adam J Ramsey
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Ana G Jimenez
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68502, USA
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Inna M Sokolova
- Department of Marine Biology, Institute of Biological Sciences, University of Rostock, Rostock, Germany.,Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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Wagner JT, Howe DK, Estes S, Denver DR. Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates. Genes (Basel) 2020; 11:genes11010077. [PMID: 31936803 PMCID: PMC7016712 DOI: 10.3390/genes11010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the nduo-5 deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of C. briggsae with different nduo-5 deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between C. briggsae isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support C. briggsae as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.
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Affiliation(s)
- Josiah T. Wagner
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
- Correspondence:
| | - Dana K. Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.K.H.); (D.R.D.)
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA;
| | - Dee R. Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.K.H.); (D.R.D.)
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