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Tower J. Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging. FRONTIERS IN AGING 2024; 5:1376060. [PMID: 38818026 PMCID: PMC11137231 DOI: 10.3389/fragi.2024.1376060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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2
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Girard C. The tri-flow adaptiveness of codes in major evolutionary transitions. Biosystems 2024; 237:105133. [PMID: 38336225 DOI: 10.1016/j.biosystems.2024.105133] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.
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Affiliation(s)
- Chris Girard
- Department of Global and Sociocultural Studies, Florida International University, Miami, FL 33199, United States.
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3
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Gospodaryov DV, Ballard JWO, Camus MF, DeSalle R, Garvin MR, Richter U. Editorial: Energy-producing organelles and the nucleus: a phenomenal genomic friendship. Front Genet 2023; 14:1230032. [PMID: 37424728 PMCID: PMC10328751 DOI: 10.3389/fgene.2023.1230032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
- Dmytro V. Gospodaryov
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - J. William O. Ballard
- School of Biosciences, University of Melbourne, Parkville, VIC, Australia
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - M. Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, United States
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - Michael R. Garvin
- Computational Predictive Biology, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Uwe Richter
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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4
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García Pascual B, Nordbotten JM, Johnston IG. Cellular and environmental dynamics influence species-specific extents of organelle gene retention. Proc Biol Sci 2023; 290:20222140. [PMID: 36883279 PMCID: PMC9993063 DOI: 10.1098/rspb.2022.2140] [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] [Indexed: 03/09/2023] Open
Abstract
Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the reasons for these differences are not completely understood. Here, we use a mathematical model to explore the hypothesis that the energetic demands imposed by an organism's changing environment influence how many oDNA genes it retains. The model couples the physical biology of cell processes of gene expression and transport to a supply-and-demand model for the environmental dynamics to which an organism is exposed. The trade-off between fulfilling metabolic and bioenergetic environmental demands, and retaining genetic integrity, is quantified for a generic gene encoded either in oDNA or in nuclear DNA. Species in environments with high-amplitude, intermediate-frequency oscillations are predicted to retain the most organelle genes, whereas those in less dynamic or noisy environments the fewest. We discuss support for, and insight from, these predictions with oDNA data across eukaryotic taxa, including high oDNA gene counts in sessile organisms exposed to day-night and intertidal oscillations (including plants and algae) and low counts in parasites and fungi.
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Affiliation(s)
| | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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5
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Shimpi GG, Bentlage B. Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes. Bioessays 2023; 45:e2200190. [PMID: 36412071 DOI: 10.1002/bies.202200190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
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6
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Systems Biology of Ageing. Subcell Biochem 2023; 102:415-424. [PMID: 36600142 DOI: 10.1007/978-3-031-21410-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ageing process is highly complex involving multiple processes operating at different biological levels. Systems Biology presents an approach using integrative computational and laboratory study that allows us to address such complexity. The approach relies on the computational analysis of knowledge and data to generate predictive models that may be validated with further laboratory experimentation. Our understanding of ageing is such that translational opportunities are within reach and systems biology offers a means to ensure that optimal decisions are made. We present an overview of the methods employed from bioinformatics and computational modelling and describe some of the insights into ageing that have been gained.
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7
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Beck EA, Bassham S, Cresko WA. Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions. Front Genet 2022; 13:925786. [PMID: 36159975 PMCID: PMC9499175 DOI: 10.3389/fgene.2022.925786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA is primarily maternally inherited in most animals and evolves about 10 times faster than biparentally inherited nuclear DNA. Mitochondrial dysfunction (mt-dys) arises when interactions between the co-evolving mitochondrial and nuclear genomes are perturbed in essential processes like oxidative phosphorylation (OXPHOS). Over time mt-dys can lead to mitochondrial diseases (mt-diseases), which are surprisingly prevalent and include common diseases such as Alzheimer’s, Parkinson’s, and diabetes. Unfortunately, the strong impact that intraspecific mitochondrial and nuclear genetic variation has on mt-disease complicates its study and the development of effective treatments. Animal models have advanced our understanding of mt-disease but their relevance to human conditions is often limited by their relatively low nuclear genetic diversity. Many traditional laboratory models also typically have a single mitochondrial haplotype (mitotype), in stark contrast to over 5,000 mitotypes in humans worldwide. The threespine stickleback fish has an evolutionary history that has made it a favorable evolutionary mutant model (EMM) for studying mito-nuclear interactions and possibly mt-diseases. EMMs are species with naturally evolved states that mimic maladaptive human diseases. In threespine stickleback, a period of isolation followed by introgression of the mitochondrial genome from a sister species resulted in the maintenance of two distinct mitochondrial haplotypes which continue to segregate within many populations of wild stickleback. The existence of two mitogenomes segregating in numerous genetically diverse populations provides a unique system for exploring complex mito-nuclear dynamics. Here we provide the first complete coding region analysis of the two threespine stickleback mitotypes, whose mitogenomic divergence exceeds that of other mammalian models for mitochondrial disease and even that between ancient and modern humans. We find that divergence is not uniform across the mitogenome, but primarily impacts protein coding genes, and significantly impacts proteins in Complex I of OXPHOS. The full characterization of these highly divergent intraspecific mitotypes provides a foundation for the development of threespine stickleback as an EMM for mito-nuclear interactions.
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Affiliation(s)
- Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
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8
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Epigenetic Alterations under Oxidative Stress in Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6439097. [PMID: 36071870 PMCID: PMC9444469 DOI: 10.1155/2022/6439097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022]
Abstract
Epigenetic regulation of gene expression, including DNA methylation and histone modifications, provides finely tuned responses for cells that undergo cellular environment changes. Abundant evidences have demonstrated the detrimental role of oxidative stress in various human pathogenesis since oxidative stress results from the imbalance between reactive oxygen species (ROS) accumulation and antioxidant defense system. Stem cells can self-renew themselves and meanwhile have the potential to differentiate into many other cell types. As some studies have described the effects of oxidative stress on homeostasis and cell fate decision of stem cells, epigenetic alterations have emerged crucial for mediating the stem cell behaviours under oxidative stress. Here, we review recent findings on the oxidative effects on DNA and histone modifications in stem cells. We propose that epigenetic alterations and oxidative stress may influence each other in stem cells.
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9
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Broz AK, Keene A, Fernandes Gyorfy M, Hodous M, Johnston IG, Sloan DB. Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity. Proc Natl Acad Sci U S A 2022; 119:e2206973119. [PMID: 35969753 PMCID: PMC9407294 DOI: 10.1073/pnas.2206973119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of MutS Homolog 1 (MSH1), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in Arabidopsis. We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In msh1 mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes (N) for plastids and mitochondria were N ∼ 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria (N ∼ 1.3), potentially because of its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.
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Affiliation(s)
- Amanda K. Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Alexandra Keene
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | | | - Mychaela Hodous
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, 5007, Norway
- Computational Biology Unit, University of Bergen, Bergen, 5007, Norway
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
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10
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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11
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Morganti C, Ito K. Mitochondrial Contributions to Hematopoietic Stem Cell Aging. Int J Mol Sci 2021; 22:11117. [PMID: 34681777 PMCID: PMC8537916 DOI: 10.3390/ijms222011117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial dysfunction and stem cell exhaustion are two hallmarks of aging. In the hematopoietic system, aging is linked to imbalanced immune response and reduced regenerative capacity in hematopoietic stem cells (HSCs), as well as an increased predisposition to a spectrum of diseases, including myelodysplastic syndrome and acute myeloid leukemia. Myeloid-biased differentiation and loss of polarity are distinct features of aged HSCs, which generally exhibit enhanced mitochondrial oxidative phosphorylation and increased production of reactive oxygen species (ROS), suggesting a direct role for mitochondria in the degenerative process. Here, we provide an overview of current knowledge of the mitochondrial mechanisms that contribute to age-related phenotypes in HSCs. These include mitochondrial ROS production, alteration/activation of mitochondrial metabolism, the quality control pathway of mitochondria, and inflammation. Greater understanding of the key machineries of HSC aging will allow us to identify new therapeutic targets for preventing, delaying, or even reversing aspects of this process.
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Affiliation(s)
- Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Departments of Cell Biology and Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Departments of Cell Biology and Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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12
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Abstract
How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. The acquisition of the mitochondrial predecessor by an archaeal host cell fundamentally altered the topology of genes in relation to bioenergetic membranes. Mitochondria internalised not only the bioenergetic membranes but also the genetic machinery needed for local control of oxidative phosphorylation. Gene loss from mitochondria enabled expansion of the nuclear genome, giving rise to an extreme genomic asymmetry that is ancestral to all extant eukaryotes. This genomic restructuring gave eukaryotes thousands of fold more energy availability per gene. In principle, that difference can support more and larger genes, far more non-coding DNA, greater regulatory complexity, and thousands of fold more protein synthesis per gene. These changes released eukaryotes from the bioenergetic constraints on prokaryotes, facilitating the evolution of morphological complexity.
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Affiliation(s)
- Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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Colnaghi M, Pomiankowski A, Lane N. The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development. eLife 2021; 10:69344. [PMID: 34279226 PMCID: PMC8337077 DOI: 10.7554/elife.69344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/16/2021] [Indexed: 12/16/2022] Open
Abstract
Selection against deleterious mitochondrial mutations is facilitated by germline processes, lowering the risk of genetic diseases. How selection works is disputed: experimental data are conflicting and previous modeling work has not clarified the issues; here, we develop computational and evolutionary models that compare the outcome of selection at the level of individuals, cells and mitochondria. Using realistic de novo mutation rates and germline development parameters from mouse and humans, the evolutionary model predicts the observed prevalence of mitochondrial mutations and diseases in human populations. We show the importance of organelle-level selection, seen in the selective pooling of mitochondria into the Balbiani body, in achieving high-quality mitochondria at extreme ploidy in mature oocytes. Alternative mechanisms debated in the literature, bottlenecks and follicular atresia, are unlikely to account for the clinical data, because neither process effectively eliminates mitochondrial mutations under realistic conditions. Our findings explain the major features of female germline architecture, notably the longstanding paradox of over-proliferation of primordial germ cells followed by massive loss. The near-universality of these processes across animal taxa makes sense in light of the need to maintain mitochondrial quality at extreme ploidy in mature oocytes, in the absence of sex and recombination.
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Affiliation(s)
- Marco Colnaghi
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrew Pomiankowski
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Nick Lane
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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14
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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15
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Friedrich VK, Rubel MA, Schurr TG. Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease. Am J Hum Biol 2021; 34:e23629. [PMID: 34146380 DOI: 10.1002/ajhb.23629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood. METHODS To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease. RESULTS The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs. CONCLUSIONS Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.
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Affiliation(s)
- Volney K Friedrich
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Translational Imaging and Precision Medicine, University of California - San Diego, La Jolla, California, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [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] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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17
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Pen I, Flatt T. Asymmetry, division of labour and the evolution of ageing in multicellular organisms. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190729. [PMID: 33678014 PMCID: PMC7938170 DOI: 10.1098/rstb.2019.0729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2020] [Indexed: 01/14/2023] Open
Abstract
Between the 1930s and 1960s, evolutionary geneticists worked out the basic principles of why organisms age. Despite much progress in the evolutionary biology of ageing since that time, however, many puzzles remain. The perhaps most fundamental of these is the question of which organisms should exhibit senescence and which should not (or which should age rapidly and which should not). The evolutionary origin of ageing from a non-senescent state has been conceptually framed, for example, in terms of the separation between germ-line and soma, the distinction between parents and their offspring, and-in unicellular organisms-the unequal distribution of cellular damage at cell division. These ideas seem to be closely related to the concept of 'division of labour' between reproduction and somatic maintenance. Here, we review these concepts and develop a toy model to explore the importance of such asymmetries for the evolution of senescence. We apply our model to the simplest case of a multicellular system: an organism consisting of two totipotent cells. Notably, we find that in organisms which reproduce symmetrically and partition damage equally, senescence is still able to evolve, contrary to previous claims. Our results might have some bearing on understanding the origin of the germ-line-soma separation and the evolution of senescence in multicellular organisms and in colonial species consisting of multiple types of individuals, such as, for example, eusocial insects with their different castes. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'
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Affiliation(s)
- Ido Pen
- Theoretical Research in Evolutionary Life Sciences, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
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18
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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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19
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Radzvilavicius A. Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution. Bioessays 2021; 43:e2100009. [PMID: 33729620 DOI: 10.1002/bies.202100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/08/2022]
Abstract
"Selfish" gene theories have offered invaluable insight into eukaryotic genome evolution, but they can also be misleading. The "selfish mitochondrion" hypothesis, developed in the 90s explained uniparental organelle inheritance as a mechanism of conflict resolution, improving cooperation between genetically distinct compartments of the cell. But modern population genetic models provided a more general explanation for uniparental inheritance based on mutational variance redistribution, modulating the efficiency of both purifying and adaptive selection. Nevertheless, as reviewed here, "selfish" conflict theories still dominate the literature. While these hypotheses are rich in metaphor and highly intuitive, selective focus on only one type of mitochondrial mutation limits the generality of our understanding and hinders progress in mito-nuclear evolution theory. Recognizing that uniparental inheritance may have evolved-and is maintained across the eukaryotic tree of life-because of its influence on mutational variance and improved selection will only increase the generality of our evolutionary reasoning, retaining "selfish" conflict explanations as a special case of a much broader theory.
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Affiliation(s)
- Arunas Radzvilavicius
- Department of Philosophy and Charles Perkins Centre, University of Sydney, New South Wales, Australia
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20
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Iannello M, Bettinazzi S, Breton S, Ghiselli F, Milani L. A Naturally Heteroplasmic Clam Provides Clues about the Effects of Genetic Bottleneck on Paternal mtDNA. Genome Biol Evol 2021; 13:6130822. [PMID: 33555290 PMCID: PMC7936021 DOI: 10.1093/gbe/evab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies within an organism. Since these copies are not identical, a single individual carries a heterogeneous population of mtDNAs, a condition known as heteroplasmy. Several factors play a role in the dynamics of the within-organism mtDNA population: among them, genetic bottlenecks, selection, and strictly maternal inheritance are known to shape the levels of heteroplasmy across mtDNAs. In Metazoa, the only evolutionarily stable exception to the strictly maternal inheritance of mitochondria is the doubly uniparental inheritance (DUI), reported in 100+ bivalve species. In DUI species, there are two highly divergent mtDNA lineages, one inherited through oocyte mitochondria (F-type) and the other through sperm mitochondria (M-type). Having both parents contributing to the mtDNA pool of the progeny makes DUI a unique system to study the dynamics of mtDNA populations. Since, in bivalves, the spermatozoon has few mitochondria (4–5), M-type mtDNA faces a tight bottleneck during embryo segregation, one of the narrowest mitochondrial bottlenecks investigated so far. Here, we analyzed the F- and M-type mtDNA variability within individuals of the DUI species Ruditapes philippinarum and investigated for the first time the effects of such a narrow bottleneck affecting mtDNA populations. As a potential consequence of this narrow bottleneck, the M-type mtDNA shows a large variability in different tissues, a condition so pronounced that it leads to genotypes from different tissues of the same individual not to cluster together. We believe that such results may help understanding the effect of low population size on mtDNA bottleneck.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Stefano Bettinazzi
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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21
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Qu T, Calabrese P, Singhavi P, Tower J. Incorporating antagonistic pleiotropy into models for molecular replicators. Biosystems 2020; 201:104333. [PMID: 33359635 DOI: 10.1016/j.biosystems.2020.104333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
In modern cells, chromosomal genes composed of DNA encode multi-subunit protein/RNA complexes that catalyze the replication of the chromosome and cell. One prevailing theory for the origin of life posits an early stage involving self-replicating macromolecules called replicators, which can be considered genes capable of self-replication. One prevailing theory for the genetics of aging in humans and other organisms is antagonistic pleiotropy, which posits that a gene can be beneficial in one context, and detrimental in another context. We previously reported that the conceptual simplicity of molecular replicators facilitates the generation of two simple models involving antagonistic pleiotropy. Here a third model is proposed, and each of the three models is presented with improved definition of the time variable. Computer simulations were used to calculate the proliferation of a hypothetical two-subunit replicator (AB), when one of the two subunits (B) exhibits antagonistic pleiotropy, leading to an advantage for B to be unstable. In model 1, instability of B yields free A subunits, which in turn stimulate the activity of other AB replicators. In model 2, B is lost and sometimes replaced by a more active mutant form, B'. In model 3, B becomes damaged and loses activity, and its instability allows it to be replaced by a new B. For each model, conditions were identified where instability of B was detrimental, and where instability of B was beneficial. The results are consistent with the hypothesis that antagonistic pleiotropy can promote molecular instability and system complexity, and provide further support for a model linking aging and evolution.
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Affiliation(s)
- Tianjiao Qu
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pratik Singhavi
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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22
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Webb M, Sideris DP. Intimate Relations-Mitochondria and Ageing. Int J Mol Sci 2020; 21:ijms21207580. [PMID: 33066461 PMCID: PMC7589147 DOI: 10.3390/ijms21207580] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction is associated with ageing, but the detailed causal relationship between the two is still unclear. We review the major phenomenological manifestations of mitochondrial age-related dysfunction including biochemical, regulatory and energetic features. We conclude that the complexity of these processes and their inter-relationships are still not fully understood and at this point it seems unlikely that a single linear cause and effect relationship between any specific aspect of mitochondrial biology and ageing can be established in either direction.
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Affiliation(s)
- Michael Webb
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
| | - Dionisia P Sideris
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
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23
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Pull CD, McMahon DP. Superorganism Immunity: A Major Transition in Immune System Evolution. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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24
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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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25
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Kuhle B, Chihade J, Schimmel P. Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs. Nat Commun 2020; 11:969. [PMID: 32080176 PMCID: PMC7033119 DOI: 10.1038/s41467-020-14725-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/30/2020] [Indexed: 01/05/2023] Open
Abstract
Metazoan complexity and life-style depend on the bioenergetic potential of mitochondria. However, higher aerobic activity and genetic drift impose strong mutation pressure and risk of irreversible fitness decline in mitochondrial (mt)DNA-encoded genes. Bilaterian mitochondria-encoded tRNA genes, key players in mitochondrial activity, have accumulated mutations at significantly higher rates than their cytoplasmic counterparts, resulting in foreshortened and fragile structures. Here we show that fragility of mt tRNAs coincided with the evolution of bilaterian animals. We demonstrate that bilaterians compensated for this reduced structural complexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoacyl-tRNA synthetase (aaRS). Structural readout by nuclear-encoded aaRS partners relaxed the sequence constraints on mt tRNAs and facilitated accommodation of functionally disruptive mutational insults by cis-acting epistatic compensations. Our results thus suggest that mutational freedom in mt tRNA genes is an adaptation to increased mutation pressure that was associated with the evolution of animal complexity. Bilaterian mitochondria-encoded tRNA genes accumulate mutations at higher rates than their cytoplasmic tRNA counterparts, resulting in idiosyncratic structures. Here the authors suggest an evolutionary basis for the observed mutational freedom of mitochondrial (mt) tRNAs and reveal the associated co-adaptive structural and functional changes in mt aminoacyl-tRNA synthetases.
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Affiliation(s)
- Bernhard Kuhle
- The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Joseph Chihade
- Department of Chemistry, Carleton College, 1 North College St., Northfield, MN, 55057, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Florida Research Institute, Jupiter, FL, 33458, USA.
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26
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DuBuc TQ, Schnitzler CE, Chrysostomou E, McMahon ET, Febrimarsa, Gahan JM, Buggie T, Gornik SG, Hanley S, Barreira SN, Gonzalez P, Baxevanis AD, Frank U. Transcription factor AP2 controls cnidarian germ cell induction. Science 2020; 367:757-762. [PMID: 32054756 PMCID: PMC7025884 DOI: 10.1126/science.aay6782] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022]
Abstract
Clonal animals do not sequester a germ line during embryogenesis. Instead, they have adult stem cells that contribute to somatic tissues or gametes. How germ fate is induced in these animals, and whether this process is related to bilaterian embryonic germline induction, is unknown. We show that transcription factor AP2 (Tfap2), a regulator of mammalian germ lines, acts to commit adult stem cells, known as i-cells, to the germ cell fate in the clonal cnidarian Hydractinia symbiolongicarpus Tfap2 mutants lacked germ cells and gonads. Transplanted wild-type cells rescued gonad development but not germ cell induction in Tfap2 mutants. Forced expression of Tfap2 in i-cells converted them to germ cells. Therefore, Tfap2 is a regulator of germ cell commitment across germ line-sequestering and germ line-nonsequestering animals.
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Affiliation(s)
- Timothy Q DuBuc
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eleni Chrysostomou
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Emma T McMahon
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Febrimarsa
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - James M Gahan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Tara Buggie
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Shirley Hanley
- National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Gonzalez
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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27
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Valuchova S, Mikulkova P, Pecinkova J, Klimova J, Krumnikl M, Bainar P, Heckmann S, Tomancak P, Riha K. Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy. eLife 2020; 9:52546. [PMID: 32041682 DOI: 10.7554/elife.52546.sa2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/04/2020] [Indexed: 05/27/2023] Open
Abstract
In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavlina Mikulkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Pecinkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Klimova
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Michal Krumnikl
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
- Department of Computer Science, FEECS VSB - Technical University of Ostrava, Ostrava, Czech Republic
| | - Petr Bainar
- IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karel Riha
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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28
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Valuchova S, Mikulkova P, Pecinkova J, Klimova J, Krumnikl M, Bainar P, Heckmann S, Tomancak P, Riha K. Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy. eLife 2020; 9:e52546. [PMID: 32041682 PMCID: PMC7012603 DOI: 10.7554/elife.52546] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/04/2020] [Indexed: 12/21/2022] Open
Abstract
In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Pavlina Mikulkova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jana Pecinkova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jana Klimova
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
| | - Michal Krumnikl
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
- Department of Computer ScienceFEECS VSB – Technical University of OstravaOstravaCzech Republic
| | - Petr Bainar
- IT4InnovationsVSB–Technical University of OstravaOstravaCzech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Karel Riha
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
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29
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Schaack S, Ho EKH, Macrae F. Disentangling the intertwined roles of mutation, selection and drift in the mitochondrial genome. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190173. [PMID: 31787045 PMCID: PMC6939366 DOI: 10.1098/rstb.2019.0173] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding and quantifying the rates of change in the mitochondrial genome is a major component of many areas of biological inquiry, from phylogenetics to human health. A critical parameter in understanding rates of change is estimating the mitochondrial mutation rate (mtDNA MR). Although the first direct estimates of mtDNA MRs were reported almost 20 years ago, the number of estimates has not grown markedly since that time. This is largely owing to the challenges associated with time- and labour-intensive mutation accumulation (MA) experiments. But even MA experiments do not solve a major problem with estimating mtDNA MRs-the challenge of disentangling the role of mutation from other evolutionary forces acting within the cell. Now that it is widely understood that any newly generated mutant allele in the mitochondria will initially be at very low frequency (1/N, where N is the number of mtDNA molecules in the cell), the importance of understanding the effective population size (Ne) of the mtDNA and the size of genetic bottlenecks during gametogenesis and development has come into the spotlight. In addition to these factors regulating the role of genetic drift, advances in our understanding of mitochondrial replication and turnover allow us to more easily envision how natural selection within the cell might favour or purge mutations in multi-copy organellar genomes. Here, we review the unique features of the mitochondrial genome that pose a challenge for accurate MR estimation and discuss ways to overcome those challenges. Estimates of mtDNA MRs remain one of the most widely used parameters in biology, thus accurate quantification and a deeper understanding of how and why they may vary within and between individuals, populations and species is an important goal. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Sarah Schaack
- Department of Biology, Reed College, Portland, OR 97202, USA
| | - Eddie K H Ho
- Department of Biology, Reed College, Portland, OR 97202, USA
| | - Fenner Macrae
- Department of Biology, Reed College, Portland, OR 97202, USA
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30
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Matkarimov BT, Saparbaev MK. DNA Repair and Mutagenesis in Vertebrate Mitochondria: Evidence for Asymmetric DNA Strand Inheritance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:77-100. [DOI: 10.1007/978-3-030-41283-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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López EH, Palumbi SR. Somatic Mutations and Genome Stability Maintenance in Clonal Coral Colonies. Mol Biol Evol 2019; 37:828-838. [DOI: 10.1093/molbev/msz270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractOne challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17 to 22 branches from each of four Acropora hyacinthus colonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide in A. hyacinthus is on the same order of magnitude (10−7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Loss of heterozygosity variants outnumber gain of heterozygosity mutations ∼2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.
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Affiliation(s)
- Elora H López
- Biology Department, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - Stephen R Palumbi
- Biology Department, Hopkins Marine Station, Stanford University, Pacific Grove, CA
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32
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Abstract
Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.
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Affiliation(s)
- Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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33
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Schoen DJ, Schultz ST. Somatic Mutation and Evolution in Plants. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024955] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.
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Affiliation(s)
- Daniel J. Schoen
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Stewart T. Schultz
- Department of Ecology, Agronomy, and Aquaculture, University of Zadar, 23000 Zadar, Croatia
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34
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Affiliation(s)
- Matthias Galipaud
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
| | - Hanna Kokko
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
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35
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Mitochondrial Genome (mtDNA) Mutations that Generate Reactive Oxygen Species. Antioxidants (Basel) 2019; 8:antiox8090392. [PMID: 31514455 PMCID: PMC6769445 DOI: 10.3390/antiox8090392] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondria are critical for the energetic demands of virtually every cellular process within nucleated eukaryotic cells. They harbour multiple copies of their own genome (mtDNA), as well as the protein-synthesing systems required for the translation of vital subunits of the oxidative phosphorylation machinery used to generate adenosine triphosphate (ATP). Molecular lesions to the mtDNA cause severe metabolic diseases and have been proposed to contribute to the progressive nature of common age-related diseases such as cancer, cardiomyopathy, diabetes, and neurodegenerative disorders. As a consequence of playing a central role in cellular energy metabolism, mitochondria produce reactive oxygen species (ROS) as a by-product of respiration. Here we review the evidence that mutations in the mtDNA exacerbate ROS production, contributing to disease.
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36
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Hood WR, Williams AS, Hill GE. An Ecologist’s Guide to Mitochondrial DNA Mutations and Senescence. Integr Comp Biol 2019; 59:970-982. [DOI: 10.1093/icb/icz097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual’s age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.
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Affiliation(s)
- Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ashley S Williams
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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37
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Johnston IG. Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells. MOLECULAR PLANT 2019; 12:764-783. [PMID: 30445187 DOI: 10.1016/j.molp.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
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Affiliation(s)
- Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK; Birmingham Institute for Forest Research, University of Birmingham, Birmingham, UK.
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38
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Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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39
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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40
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Abstract
Microbial symbioses exhibit astounding adaptations, yet all symbionts face the problem of how to reliably associate with host offspring every generation. A common strategy is vertical transmission, in which symbionts are directly transmitted from the female to her offspring. The diversity of symbionts and vertical transmission mechanisms is as expansive as the diversity of eukaryotic host taxa that house them. However, there are several common themes among these mechanisms based on the degree to which symbionts associate with the host germline during transmission. In this review, we detail three distinct vertical transmission strategies, starting with associations that are transmitted from host somatic cells to offspring somatic cells, either due to lacking a germline or avoiding it. A second strategy involves somatically-localized symbionts that migrate into the germline during host development. The third strategy we discuss is one in which the symbiont maintains continuous association with the germline throughout development. Unexpectedly, the vast majority of documented vertically inherited symbionts rely on the second strategy: soma-to-germline migration. Given that not all eukaryotes contain a sequestered germline and instead produce offspring from somatic stem cell lineages, this soma-to-germline migration is discussed in the context of multicellular evolution. Lastly, as recent genomics data have revealed an abundance of horizontal gene transfer events from symbiotic and non-symbiotic bacteria to host genomes, we discuss their impact on eukaryotic host evolution.
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Affiliation(s)
- Shelbi L Russell
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States.
| | - Laura Chappell
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - William Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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41
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Richardson LA, Schmid SL, Bhandoola A, Harly C, Hedenström A, Laub MT, Mace GM, Sengupta P, Stock AM, Read AF, Malik HS, Estelle M, Lowell S, Kimmelman J. The PLOS Biology XV Collection: 15 Years of Exceptional Science Highlighted across 12 Months. PLoS Biol 2019; 17:e3000180. [PMID: 30811478 PMCID: PMC6411196 DOI: 10.1371/journal.pbio.3000180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/11/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Lauren A. Richardson
- Public Library of Science, San Francisco, California, United States of America
- * E-mail:
| | - Sandra L. Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Avinash Bhandoola
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Christelle Harly
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | - Michael T. Laub
- Department of Biology Howard Hughes Medical Institute Graduate Program in Microbiology Graduate Program in Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Georgina M. Mace
- Department of Genetics, Evolution and Environment, Center for Biodiversity and Environment Research, University College London, London, United Kingdom
| | - Piali Sengupta
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Ann M. Stock
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Kimmelman
- Studies of Translation, Ethics, and Medicine, Biomedical Ethics Unit, McGill University, Montreal, Quebec, Canada
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42
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Hahn A, Zuryn S. The Cellular Mitochondrial Genome Landscape in Disease. Trends Cell Biol 2018; 29:227-240. [PMID: 30509558 DOI: 10.1016/j.tcb.2018.11.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022]
Abstract
Mitochondrial genome (mitochondrial DNA, mtDNA) lesions that unbalance bioenergetic and oxidative outputs are an important cause of human disease. A major impediment in our understanding of the pathophysiology of mitochondrial disorders is the complexity with which mtDNA mutations are spatiotemporally distributed and managed within individual cells, tissues, and organs. Unlike the comparatively static nuclear genome, accumulating evidence highlights the variability, dynamism, and modifiability of the mtDNA nucleotide sequence between individual cells over time. In this review, we summarize and discuss the impact of mtDNA defects on disease within the context of a mosaic and shifting mutational landscape.
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Affiliation(s)
- Anne Hahn
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Australia
| | - Steven Zuryn
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Australia.
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43
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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44
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Abstract
For the last 100 years, it has been uncontroversial to state that the plant germline is set aside late in development, but there is surprisingly little evidence to support this view. In contrast, much evolutionary theory and several recent empirical studies seem to suggest the opposite-that the germlines of some and perhaps most plants may be set aside early in development. But is this really the case? How much does it matter? How can we reconcile the new evidence with existing knowledge of plant development? And is there a way to reliably establish the timing of germline segregation in both model and nonmodel plants? Answering these questions is vital to understanding one of the most fundamental aspects of plant development and evolution.
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Affiliation(s)
- Robert Lanfear
- Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
- Biological Sciences, Macquarie University, Sydney, Australia
- * E-mail:
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45
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Radzvilavicius AL, Blackstone NW. The evolution of individuality revisited. Biol Rev Camb Philos Soc 2018; 93:1620-1633. [DOI: 10.1111/brv.12412] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 02/21/2018] [Accepted: 02/28/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Neil W. Blackstone
- Department of Biological Sciences; Northern Illinois University; DeKalb IL 60115 U.S.A
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46
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Radzvilavicius AL, Lane N, Pomiankowski A. Sexual conflict explains the extraordinary diversity of mechanisms regulating mitochondrial inheritance. BMC Biol 2017; 15:94. [PMID: 29073898 PMCID: PMC5658935 DOI: 10.1186/s12915-017-0437-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mitochondria are predominantly inherited from the maternal gamete, even in unicellular organisms. Yet an extraordinary array of mechanisms enforce uniparental inheritance, which implies shifting selection pressures and multiple origins. RESULTS We consider how this high turnover in mechanisms controlling uniparental inheritance arises using a novel evolutionary model in which control of mitochondrial transmission occurs either during spermatogenesis (by paternal nuclear genes) or at/after fertilization (by maternal nuclear genes). The model treats paternal leakage as an evolvable trait. Our evolutionary analysis shows that maternal control consistently favours strict uniparental inheritance with complete exclusion of sperm mitochondria, whereas some degree of paternal leakage of mitochondria is an expected outcome under paternal control. This difference arises because mito-nuclear linkage builds up with maternal control, allowing the greater variance created by asymmetric inheritance to boost the efficiency of purifying selection and bring benefits in the long term. In contrast, under paternal control, mito-nuclear linkage tends to be much weaker, giving greater advantage to the mixing of cytotypes, which improves mean fitness in the short term, even though it imposes a fitness cost to both mating types in the long term. CONCLUSIONS Sexual conflict is an inevitable outcome when there is competition between maternal and paternal control of mitochondrial inheritance. If evolution has led to complete uniparental inheritance through maternal control, it creates selective pressure on the paternal nucleus in favour of subversion through paternal leakage, and vice versa. This selective divergence provides a reason for the repeated evolution of novel mechanisms that regulate the transmission of paternal mitochondria, both in the fertilized egg and spermatogenesis. Our analysis suggests that the widespread occurrence of paternal leakage and prevalence of heteroplasmy are natural outcomes of this sexual conflict.
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Affiliation(s)
- Arunas L Radzvilavicius
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nick Lane
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Andrew Pomiankowski
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
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47
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Mitigating Mitochondrial Genome Erosion Without Recombination. Genetics 2017; 207:1079-1088. [PMID: 28893855 DOI: 10.1534/genetics.117.300273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023] Open
Abstract
Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed.
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48
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Pozzi A, Plazzi F, Milani L, Ghiselli F, Passamonti M. SmithRNAs: Could Mitochondria "Bend" Nuclear Regulation? Mol Biol Evol 2017; 34:1960-1973. [PMID: 28444389 PMCID: PMC5850712 DOI: 10.1093/molbev/msx140] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria, and identified several putative sncRNAs of mitochondrial origin. Some sncRNAs are transcribed by intergenic regions that form stable stem-hairpin structures, which makes them good miRNA-like candidates. We decided to name them small mitochondrial highly-transcribed RNAs (smithRNAs). Many concurrent data support that we have recovered sncRNAs of mitochondrial origin that might be involved in gonad formation and able to affect nuclear gene expression. This possibility has been never suggested before. If mtDNA can affect nuclear gene expression through RNA interference, this opens a plethora of new possibilities for it to interact with the nucleus, and makes metazoan mtDNA a much more complex genome than previously thought.
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Affiliation(s)
- Andrea Pozzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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49
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50
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Abstract
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.
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Affiliation(s)
- Robin A Weiss
- Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT, UK.
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