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Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe G. H3K4me1 recruits DNA repair proteins in plants. THE PLANT CELL 2024; 36:2410-2426. [PMID: 38531669 PMCID: PMC11132887 DOI: 10.1093/plcell/koae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
Abstract
DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined 2 proteins which, in plants, contain Tudor histone reader domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved in homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch repair protein. The MSH6 Tudor domain of Arabidopsis (Arabidopsis thaliana) binds to H3K4me1 as previously demonstrated for PDS5C, which localizes to H3K4me1-rich gene bodies and essential genes. Mutations revealed by ultradeep sequencing of wild-type and msh6 knockout lines in Arabidopsis show that functional MSH6 is critical for the reduced rate of single-base substitution (SBS) mutations in gene bodies and H3K4me1-rich regions. We explored the breadth of these mechanisms among plants by examining a large rice (Oryza sativa) mutation data set. H3K4me1-associated hypomutation is conserved in rice as are the H3K4me1-binding residues of MSH6 and PDS5C Tudor domains. Recruitment of DNA repair proteins by H3K4me1 in plants reveals convergent, but distinct, epigenome-recruited DNA repair mechanisms from those well described in humans. The emergent model of H3K4me1-recruited repair in plants is consistent with evolutionary theory regarding mutation modifier systems and offers mechanistic insight into intragenomic mutation rate variation in plants.
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Affiliation(s)
- Daniela Quiroz
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
| | - Satoyo Oya
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Diego Lopez-Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Kehan Zhao
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Lissandro Ortega
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Alissza Ali
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
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2
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Bullinaria JA. Simulating the Effect of Environmental Change on Evolving Populations. ARTIFICIAL LIFE 2024; 30:147-170. [PMID: 38478879 DOI: 10.1162/artl_a_00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
This study uses evolutionary simulations to explore the strategies that emerge to enable populations to cope with random environmental changes in situations where lifetime learning approaches are not available to accommodate them. In particular, it investigates how the average magnitude of change per unit time and the persistence of the changes (and hence the resulting autocorrelation of the environmental time series) affect the change tolerances, population diversities, and extinction timescales that emerge. Although it is the change persistence (often discussed in terms of environmental noise color) that has received most attention in the recent literature, other factors, particularly the average change magnitude, interact with this and can be more important drivers of the adaptive strategies that emerge. Moreover, when running simulations, the choice of change representation and normalization can also affect the outcomes. Detailed simulations are presented that are designed to explore all these issues. They also reveal significant dependences on the associated mutation rates and the extent to which they can evolve, and they clarify how evolution often leads populations into strategies with higher risks of extinction. Overall, this study shows how modeling the effect of environmental change requires more care than may have previously been realized.
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3
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO Rep 2024; 25:2306-2322. [PMID: 38528170 PMCID: PMC11093987 DOI: 10.1038/s44319-024-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low-variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen-recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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4
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Livnat A, Love AC. Mutation and evolution: Conceptual possibilities. Bioessays 2024; 46:e2300025. [PMID: 38254311 DOI: 10.1002/bies.202300025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024]
Abstract
Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate detecting mutation rates within specific loci at an ultra-high, individual base pair resolution.
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Affiliation(s)
- Adi Livnat
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Alan C Love
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota (Twin Cities), Minneapolis, Minnesota, USA
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5
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [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: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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6
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Calamari ZT, Song A, Cohen E, Akter M, Roy RD, Hallikas O, Christensen MM, Li P, Marangoni P, Jernvall J, Klein OD. Conserved and derived expression patterns and positive selection on dental genes reveal complex evolutionary context of ever-growing rodent molars. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572015. [PMID: 38187646 PMCID: PMC10769287 DOI: 10.1101/2023.12.18.572015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Background Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells are lost at the onset of tooth root formation, but this loss of continuous crown growth is difficult to study in the mouse because regulatory signaling overlaps with signals that pattern tooth size and shape. Within the voles (Cricetidae, Rodentia, Glires), species have evolved both rooted and unrooted molars that have similar size and shape. We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. Results Our de novo genome recovered 91% of single-copy orthologs for Euarchontoglires and had a total length of 2.44 Gigabases, enabling genomic and transcriptomic analyses. We identified six dental genes undergoing positive selection across Glires and two genes undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Transcriptomics analyses demonstrated conserved patterns of dental gene expression with species-specific variation likely related to developmental timing and morphological differences between mouse and vole molars. Conclusions Our results support ongoing dental gene evolution in rodents with unrooted molars. We identify candidate genes for further functional analyses, particularly Dspp, which plays an important role in mineralizing tissues. Our expression results support conservation of dental genes between voles and model species like mice, while revealing significant effects of overall tooth morphology on gene expression.
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Affiliation(s)
- Zachary T. Calamari
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- The Graduate Center, City University of New York, 365 Fifth Ave, New York, NY 10016, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Division of Paleontology, American Museum of Natural History, Central Park West at 79 Street, New York, NY, 10024, USA
| | - Andrew Song
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- Cornell University, 616 Thurston Ave, Ithaca, NY 14853, USA
| | - Emily Cohen
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- New York University College of Dentistry, 345 E 34 St, New York, NY 10010
| | - Muspika Akter
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Outi Hallikas
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mona M. Christensen
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pengyang Li
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
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7
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Kenchanmane Raju SK, Lensink M, Kliebenstein DJ, Niederhuth C, Monroe G. Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs. THE NEW PHYTOLOGIST 2023; 240:1292-1304. [PMID: 37614211 DOI: 10.1111/nph.19227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM accumulate more variation, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may facilitate the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.
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Affiliation(s)
| | - Mariele Lensink
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Grey Monroe
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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8
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with distinct genomic and epigenomic features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523861. [PMID: 36711945 PMCID: PMC9882162 DOI: 10.1101/2023.01.12.523861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 94720
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 94720
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 94720
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9
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Gitschlag BL, Cano AV, Payne JL, McCandlish DM, Stoltzfus A. Mutation and Selection Induce Correlations between Selection Coefficients and Mutation Rates. Am Nat 2023; 202:534-557. [PMID: 37792926 DOI: 10.1086/726014] [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] [Indexed: 10/06/2023]
Abstract
AbstractThe joint distribution of selection coefficients and mutation rates is a key determinant of the genetic architecture of molecular adaptation. Three different distributions are of immediate interest: (1) the "nominal" distribution of possible changes, prior to mutation or selection; (2) the "de novo" distribution of realized mutations; and (3) the "fixed" distribution of selectively established mutations. Here, we formally characterize the relationships between these joint distributions under the strong-selection/weak-mutation (SSWM) regime. The de novo distribution is enriched relative to the nominal distribution for the highest rate mutations, and the fixed distribution is further enriched for the most highly beneficial mutations. Whereas mutation rates and selection coefficients are often assumed to be uncorrelated, we show that even with no correlation in the nominal distribution, the resulting de novo and fixed distributions can have correlations with any combination of signs. Nonetheless, we suggest that natural systems with a finite number of beneficial mutations will frequently have the kind of nominal distribution that induces negative correlations in the fixed distribution. We apply our mathematical framework, along with population simulations, to explore joint distributions of selection coefficients and mutation rates from deep mutational scanning and cancer informatics. Finally, we consider the evolutionary implications of these joint distributions together with two additional joint distributions relevant to parallelism and the rate of adaptation.
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10
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Tuffaha MZ, Varakunan S, Castellano D, Gutenkunst RN, Wahl LM. Shifts in Mutation Bias Promote Mutators by Altering the Distribution of Fitness Effects. Am Nat 2023; 202:503-518. [PMID: 37792927 DOI: 10.1086/726010] [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: 10/06/2023]
Abstract
AbstractRecent experimental evidence demonstrates that shifts in mutational biases-for example, increases in transversion frequency-can change the distribution of fitness effects of mutations (DFE). In particular, reducing or reversing a prevailing bias can increase the probability that a de novo mutation is beneficial. It has also been shown that mutator bacteria are more likely to emerge if the beneficial mutations they generate have a larger effect size than observed in the wild type. Here, we connect these two results, demonstrating that mutator strains that reduce or reverse a prevailing bias have a positively shifted DFE, which in turn can dramatically increase their emergence probability. Since changes in mutation rate and bias are often coupled through the gain and loss of DNA repair enzymes, our results predict that the invasion of mutator strains will be facilitated by shifts in mutation bias that offer improved access to previously undersampled beneficial mutations.
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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12
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Garte S. Targeted Hypermutation as a Survival Strategy: A Theoretical Approach. Acta Biotheor 2023; 71:20. [PMID: 37668864 DOI: 10.1007/s10441-023-09471-9] [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: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.
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Affiliation(s)
- Seymour Garte
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA.
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13
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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14
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Monroe JG. Potential and limits of (mal)adaptive mutation rate plasticity in plants. THE NEW PHYTOLOGIST 2023; 237:2020-2026. [PMID: 36444532 DOI: 10.1111/nph.18640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Genetic mutations provide the heritable material for plant adaptation to their environments. At the same time, the environment can affect the mutation rate across plant genomes. However, the extent to which environmental plasticity in mutation rates can facilitate or hinder adaptation remains a longstanding and unresolved question. Emerging discoveries of mechanisms affecting mutation rate variability provide opportunities to consider this question in a new light. Links between chromatin states, transposable elements, and DNA repair suggest cases of adaptive mutation rate plasticity could occur. Yet, numerous evolutionary and biological forces are expected to limit the impact of any such mutation rate plasticity on adaptive evolution. Persistent uncertainty about the significance of mutation rate plasticity on adaptation motivates new experimental and theoretical research relevant to understanding plant responses in changing environments.
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Affiliation(s)
- J Grey Monroe
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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15
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Melde RH, Bao K, Sharp NP. Recent insights into the evolution of mutation rates in yeast. Curr Opin Genet Dev 2022; 76:101953. [PMID: 35834945 PMCID: PMC9491374 DOI: 10.1016/j.gde.2022.101953] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/08/2023]
Abstract
Mutation is the origin of all genetic variation, good and bad. The mutation process can evolve in response to mutations, positive or negative selection, and genetic drift, but how these forces contribute to mutation-rate variation is an unsolved problem at the heart of genetics research. Mutations can be challenging to measure, but genome sequencing and other tools have allowed for the collection of larger and more detailed datasets, particularly in the yeast-model system. We review key hypotheses for the evolution of mutation rates and describe recent advances in understanding variation in mutational properties within and among yeast species. The multidimensional spectrum of mutations is increasingly recognized as holding valuable clues about how this important process evolves.
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Affiliation(s)
- Robert H Melde
- Department of Genetics, University of Wisconsin-Madison, USA.
| | - Kevin Bao
- Department of Genetics, University of Wisconsin-Madison, USA
| | - Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, USA. https://twitter.com/@sharpnath
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16
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Paul BG, Eren AM. Eco-evolutionary significance of domesticated retroelements in microbial genomes. Mob DNA 2022; 13:6. [PMID: 35197094 PMCID: PMC8867640 DOI: 10.1186/s13100-022-00262-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 01/03/2023] Open
Abstract
Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA—a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature’s instructions in various RNA templates. Beneficial retroelements—those that can provide a fitness advantage to their host—evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.
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Affiliation(s)
- Blair G Paul
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA.
| | - A Murat Eren
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA. .,Department of Medicine, University of Chicago, Chicago, IL, USA.
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17
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Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022; 602:101-105. [PMID: 35022609 PMCID: PMC8810380 DOI: 10.1038/s41586-021-04269-6] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, USA.
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | | | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Faculty of Biology, Ludwig Maximilian University, Martinsried, Germany
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marie Klein
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Julia Hildebrandt
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Daniel Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Eric Imbert
- ISEM, University of Montpellier, Montpellier, France
| | - Jon Ågren
- Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Charles B Fenster
- Oak Lake Field Station, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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18
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Melamed D, Nov Y, Malik A, Yakass MB, Bolotin E, Shemer R, Hiadzi EK, Skorecki KL, Livnat A. De novo mutation rates at the single-mutation resolution in a human HBB gene-region associated with adaptation and genetic disease. Genome Res 2022; 32:488-498. [PMID: 35031571 PMCID: PMC8896469 DOI: 10.1101/gr.276103.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022]
Abstract
Although it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here, we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa, and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the “HbS mutation” when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.
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19
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Love A, Wagner GP. Co-option of stress mechanisms in the origin of evolutionary novelties. Evolution 2021; 76:394-413. [PMID: 34962651 PMCID: PMC9303342 DOI: 10.1111/evo.14421] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022]
Abstract
It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation.
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Affiliation(s)
- Alan Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT-06520.,Yale Systems Biology Institute, West Haven, CT-06516.,Department of Evolutionary Biology, University of Vienna, Austria
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20
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Yoder AD, Tiley GP. The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals. Mol Ecol 2021; 30:6087-6100. [PMID: 34062029 DOI: 10.1111/mec.16007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/22/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would stagnate. Yet, it is a double-edged sword. An excess of mutations can have devastating effects on fitness and population viability. It is therefore one of the great challenges of molecular ecology to determine the rate and mechanisms by which these mutations accrue across the tree of life. Advances in high-throughput sequencing technologies are providing new opportunities for characterizing the rates and mutational spectra within species and populations thus informing essential evolutionary parameters such as the timing of speciation events, the intricacies of historical demography, and the degree to which lineages are subject to the burdens of mutational load. Here, we will focus on both the challenge and promise of whole-genome comparisons among parents and their offspring from known pedigrees for the detection of germline mutations as they arise in a single generation. The potential of these studies is high, but the field is still in its infancy and much uncertainty remains. Namely, the technical challenges are daunting given that pedigree-based genome comparisons are essentially searching for needles in a haystack given the very low signal to noise ratio. Despite the challenges, we predict that rapidly developing methods for whole-genome comparisons hold great promise for integrating empirically derived estimates of de novo mutation rates and mutation spectra across many molecular ecological applications.
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Affiliation(s)
- Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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21
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Swiatczak B. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism. Bioessays 2020; 42:e2000032. [PMID: 32767393 DOI: 10.1002/bies.202000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/03/2020] [Indexed: 12/15/2022]
Abstract
Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China
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22
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A Comprehensive View of Translesion Synthesis in Escherichia coli. Microbiol Mol Biol Rev 2020; 84:84/3/e00002-20. [PMID: 32554755 DOI: 10.1128/mmbr.00002-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The lesion bypass pathway, translesion synthesis (TLS), exists in essentially all organisms and is considered a pathway for postreplicative gap repair and, at the same time, for lesion tolerance. As with the saying "a trip is not over until you get back home," studying TLS only at the site of the lesion is not enough to understand the whole process of TLS. Recently, a genetic study uncovered that polymerase V (Pol V), a poorly expressed Escherichia coli TLS polymerase, is not only involved in the TLS step per se but also participates in the gap-filling reaction over several hundred nucleotides. The same study revealed that in contrast, Pol IV, another highly expressed TLS polymerase, essentially stays away from the gap-filling reaction. These observations imply fundamentally different ways these polymerases are recruited to DNA in cells. While access of Pol IV appears to be governed by mass action, efficient recruitment of Pol V involves a chaperone-like action of the RecA filament. We present a model of Pol V activation: the 3' tip of the RecA filament initially stabilizes Pol V to allow stable complex formation with a sliding β-clamp, followed by the capture of the terminal RecA monomer by Pol V, thus forming a functional Pol V complex. This activation process likely determines higher accessibility of Pol V than of Pol IV to normal DNA. Finally, we discuss the biological significance of TLS polymerases during gap-filling reactions: error-prone gap-filling synthesis may contribute as a driving force for genetic diversity, adaptive mutation, and evolution.
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23
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Romero-Mujalli D, Jeltsch F, Tiedemann R. Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change. BMC Evol Biol 2019; 19:175. [PMID: 31462290 PMCID: PMC6714099 DOI: 10.1186/s12862-019-1494-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats. RESULTS The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats. CONCLUSIONS Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become - at least locally - extinct.
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Affiliation(s)
- Daniel Romero-Mujalli
- University of Potsdam, Evolutionary Biology/Systematic Zoology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany. .,Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.
| | - Florian Jeltsch
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Ralph Tiedemann
- University of Potsdam, Evolutionary Biology/Systematic Zoology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
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24
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Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, Mansour Y, Baror-Sebban S, Masika H, Farago M, Berger M, Carmi S, Buganim Y, Koren A, Simon I. Germline DNA replication timing shapes mammalian genome composition. Nucleic Acids Res 2019; 46:8299-8310. [PMID: 29986092 PMCID: PMC6144785 DOI: 10.1093/nar/gky610] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
Mammalian DNA replication is a highly organized and regulated process. Large, Mb-sized regions are replicated at defined times along S-phase. Replication Timing (RT) is thought to play a role in shaping the mammalian genome by affecting mutation rates. Previous analyses relied on somatic RT profiles. However, only germline mutations are passed on to offspring and affect genomic composition. Therefore, germ cell RT information is necessary to evaluate the influences of RT on the mammalian genome. We adapted the RT mapping technique for limited amounts of cells, and measured RT from two stages in the mouse germline - primordial germ cells (PGCs) and spermatogonial stem cells (SSCs). RT in germline cells exhibited stronger correlations to both mutation rate and recombination hotspots density than those of RT in somatic tissues, emphasizing the importance of using correct tissues-of-origin for RT profiling. Germline RT maps exhibited stronger correlations to additional genetic features including GC-content, transposable elements (SINEs and LINEs), and gene density. GC content stratification and multiple regression analysis revealed independent contributions of RT to SINE, gene, mutation, and recombination hotspot densities. Together, our results establish a central role for RT in shaping multiple levels of mammalian genome composition.
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Affiliation(s)
- Yishai Yehuda
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel
| | - Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nina Mayorek
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Kirill Makedonski
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oriya Vardi
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Leonor Cohen-Daniel
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yousef Mansour
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shulamit Baror-Sebban
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hagit Masika
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marganit Farago
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Berger
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Koren
- Deptartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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25
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Vigué L, Eyre-Walker A. The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae. PeerJ 2019; 7:e7216. [PMID: 31293838 PMCID: PMC6599670 DOI: 10.7717/peerj.7216] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/30/2019] [Indexed: 12/31/2022] Open
Abstract
Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.
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26
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Poetsch AR, Boulton SJ, Luscombe NM. Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis. Genome Biol 2018; 19:215. [PMID: 30526646 PMCID: PMC6284305 DOI: 10.1186/s13059-018-1582-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/08/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined. RESULTS To bridge the gap between our understanding of DNA repair and mutation distributions, we developed a novel method, AP-seq, capable of mapping apurinic sites and 8-oxo-7,8-dihydroguanine bases at approximately 250-bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of apurinic sites varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike single nucleotide variants (SNVs) in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Apurinic sites and oxidative damage are also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe a reduction at chromatin loop anchors with increased damage load towards inactive compartments. Less damage is found at promoters, exons, and termination sites, but not introns, in a seemingly transcription-independent but GC content-dependent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, coding sequence, and other functional elements. CONCLUSIONS Our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safeguards the regulatory and coding regions of genes from mutations.
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Affiliation(s)
- Anna R Poetsch
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan.
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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27
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Adam L, San Lucas FA, Fowler R, Yu Y, Wu W, Liu Y, Wang H, Menter D, Tetzlaff MT, Ensor J, Manyam G, Arold ST, Huff C, Kopetz S, Scheet P, Overman MJ. DNA Sequencing of Small Bowel Adenocarcinomas Identifies Targetable Recurrent Mutations in the ERBB2 Signaling Pathway. Clin Cancer Res 2018; 25:641-651. [PMID: 30352910 DOI: 10.1158/1078-0432.ccr-18-1480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/13/2018] [Accepted: 10/18/2018] [Indexed: 01/07/2023]
Abstract
PURPOSE Little is known about the genetic alterations characteristic of small bowel adenocarcinoma (SBA). Our purpose was to identify targetable alterations and develop experimental models of this disease.Experimental Design: Whole-exome sequencing (WES) was completed on 17 SBA patient samples and targeted-exome sequencing (TES) on 27 samples to confirm relevant driver mutations. Two SBA models with ERBB2 kinase activating mutations were tested for sensitivity to anti-ERBB2 agents in vivo and in vitro. Biochemical changes were measured by reverse-phase protein arrays. RESULTS WES identified somatic mutations in 4 canonical pathways (WNT, ERBB2, STAT3, and chromatin remodeling), which were validated in the TES cohort. Although APC mutations were present in only 23% of samples, additional WNT-related alterations were seen in 12%. ERBB2 mutations and amplifications were present in 23% of samples. Patients with alterations in the ERBB2 signaling cascade (64%) demonstrated worse clinical outcomes (median survival 70.3 months vs. 109 months; log-rank HR = 2.4, P = 0.03). Two ERBB2-mutated (V842I and Y803H) cell lines were generated from SBA patient samples. Both demonstrated high sensitivity to ERBB2 inhibitor dacomitinib (IC50 < 2.5 nmol/L). In xenografts derived from these samples, treatment with dacomitinib reduced tumor growth by 39% and 59%, respectively, whereas it had no effect in an SBA wild-type ERBB2 model. CONCLUSIONS The in vitro and in vivo models of SBA developed here provide a valuable resource for understanding targetable mutations in this disease. Our findings support clinical efforts to target activating ERBB2 mutations in patients with SBA that harbor these alterations.
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Affiliation(s)
- Liana Adam
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yao Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenhui Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yulun Liu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Huamin Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joe Ensor
- Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - Ganiraju Manyam
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - Chad Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Baker KT, Salk JJ, Brentnall TA, Risques RA. Precancer in ulcerative colitis: the role of the field effect and its clinical implications. Carcinogenesis 2018; 39:11-20. [PMID: 29087436 PMCID: PMC6248676 DOI: 10.1093/carcin/bgx117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/22/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
Cumulative evidence indicates that a significant proportion of cancer evolution may occur before the development of histological abnormalities. While recent improvements in DNA sequencing technology have begun to reveal the presence of these early preneoplastic clones, the concept of 'premalignant field' was already introduced by Slaughter more than half a century ago. Also referred to as 'field effect', 'field defect' or 'field cancerization', these terms describe the phenomenon by which molecular alterations develop in normal-appearing tissue and expand to form premalignant patches with the potential to progress to dysplasia and cancer. Field effects have been well-characterized in ulcerative colitis, an inflammatory bowel disease that increases the risk of colorectal cancer. The study of the molecular alterations that define these fields is informative of mechanisms of tumor initiation and progression and has provided potential targets for early cancer detection. Herein, we summarize the current knowledge about the molecular alterations that comprise the field effect in ulcerative colitis and the clinical utility of these fields for cancer screening and prevention.
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Affiliation(s)
- Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jesse J Salk
- Division of Hematology and Oncology, Department of Medicine, University of
Washington, Seattle, WA, USA
- TwinStrand Biosciences Seattle, WA, USA
| | - Teresa A Brentnall
- Division of Gasteroenterology, Department of Medicine, University of
Washington, Seattle, WA, USA
| | - Rosa Ana Risques
- To whom correspondence should be addressed. Tel: +206-616-4976; Fax:
+206-543-1140;
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29
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Was the Watchmaker Blind? Or Was She One-Eyed? BIOLOGY 2017; 6:biology6040047. [PMID: 29261138 PMCID: PMC5745452 DOI: 10.3390/biology6040047] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/04/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022]
Abstract
The question whether evolution is blind is usually presented as a choice between no goals at all ('the blind watchmaker') and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are short-term goals within rather than external to organisms. Organisms and their interacting populations have evolved mechanisms by which they can harness blind stochasticity and so generate rapid functional responses to environmental challenges. They can achieve this by re-organising their genomes and/or their regulatory networks. Epigenetic as well as DNA changes are involved. Evolution may have no foresight, but it is at least partially directed by organisms themselves and by the populations of which they form part. Similar arguments support partial direction in the evolution of behavior.
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30
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Chernomas R, Hudson I, Chernomas G. Can Neoliberal Capitalism Affect Human Evolution? INTERNATIONAL JOURNAL OF HEALTH SERVICES 2017; 48:166-188. [PMID: 29233063 DOI: 10.1177/0020731417742258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The connection between genes and health outcomes is significantly moderated by social factors. Health inequalities result from the differential accumulation of exposures and resource access rooted in class-based circumstances. In the neoliberal era in the United States, changed physical and socioeconomic conditions facing the poorer members of society have been characterized as traumatogenic (capable of producing a wound or injury). This paper will argue that research that points to the transgenerational influence of environmental impacts on health suggests 2 important reconsiderations of the link between the economy and health. First, an understanding of the health of any society requires an understanding not only of current but also past environmental conditions and the economy that produces those conditions. Second, it suggests that the way in which economic policy is analyzed needs to be reconsidered to incorporate the transgenerational impacts of environmental conditions produced by those policies.
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Affiliation(s)
- Robert Chernomas
- 1 Department of Economics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ian Hudson
- 1 Department of Economics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gregory Chernomas
- 2 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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31
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Cabrera-Becerril A, Vargas-De-León C, Hernández S, Miramontes P, Peralta R. Modeling the dynamics of chromosomal alteration progression in cervical cancer: A computational model. PLoS One 2017; 12:e0180882. [PMID: 28723940 PMCID: PMC5516994 DOI: 10.1371/journal.pone.0180882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 12/16/2022] Open
Abstract
Computational modeling has been applied to simulate the heterogeneity of cancer behavior. The development of Cervical Cancer (CC) is a process in which the cell acquires dynamic behavior from non-deleterious and deleterious mutations, exhibiting chromosomal alterations as a manifestation of this dynamic. To further determine the progression of chromosomal alterations in precursor lesions and CC, we introduce a computational model to study the dynamics of deleterious and non-deleterious mutations as an outcome of tumor progression. The analysis of chromosomal alterations mediated by our model reveals that multiple deleterious mutations are more frequent in precursor lesions than in CC. Cells with lethal deleterious mutations would be eliminated, which would mitigate cancer progression; on the other hand, cells with non-deleterious mutations would become dominant, which could predispose them to cancer progression. The study of somatic alterations through computer simulations of cancer progression provides a feasible pathway for insights into the transformation of cell mechanisms in humans. During cancer progression, tumors may acquire new phenotype traits, such as the ability to invade and metastasize or to become clinically important when they develop drug resistance. Non-deleterious chromosomal alterations contribute to this progression.
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Affiliation(s)
- Augusto Cabrera-Becerril
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cruz Vargas-De-León
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Sergio Hernández
- Programa de Dinámica Nolineal, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Pedro Miramontes
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
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32
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Sahakyan AB, Balasubramanian S. Single genome retrieval of context-dependent variability in mutation rates for human germline. BMC Genomics 2017; 18:81. [PMID: 28086752 PMCID: PMC5237266 DOI: 10.1186/s12864-016-3440-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. CONCLUSIONS The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.
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Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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33
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Welch JJ. What's wrong with evolutionary biology? BIOLOGY & PHILOSOPHY 2016; 32:263-279. [PMID: 28298744 PMCID: PMC5329086 DOI: 10.1007/s10539-016-9557-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.
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Affiliation(s)
- John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, CB23EH UK
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34
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Gjuvsland AB, Zörgö E, Samy JK, Stenberg S, Demirsoy IH, Roque F, Maciaszczyk-Dziubinska E, Migocka M, Alonso-Perez E, Zackrisson M, Wysocki R, Tamás MJ, Jonassen I, Omholt SW, Warringer J. Disentangling genetic and epigenetic determinants of ultrafast adaptation. Mol Syst Biol 2016; 12:892. [PMID: 27979908 PMCID: PMC5199126 DOI: 10.15252/msb.20166951] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical-experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation-accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic-adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data-driven individual-based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation-speeding mechanisms in general.
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Affiliation(s)
- Arne B Gjuvsland
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Enikö Zörgö
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jeevan Ka Samy
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Simon Stenberg
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ibrahim H Demirsoy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Francisco Roque
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | | | - Magdalena Migocka
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Elisa Alonso-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Inge Jonassen
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Stig W Omholt
- Centre for Biodiversity Dynamics, Department of Biology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Jonas Warringer
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway .,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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35
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A Magic Spot in Genome Maintenance. Trends Genet 2016; 33:58-67. [PMID: 27931778 DOI: 10.1016/j.tig.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/02/2023]
Abstract
Nucleotide excision repair (NER) is the key DNA repair system that eliminates the majority of DNA helix-distorting lesions. RNA polymerase (RNAP) expedites the recognition of DNA damage by NER components via transcription-coupled DNA repair (TCR). In bacteria, a modified nucleotide ppGpp ('magic spot') is a pleiotropic second messenger that mediates the response to nutrient deficiencies by altering the initiation properties of RNAP. In this review, we discuss newly elucidated roles of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in transcription elongation that couple this alarmone to DNA damage repair and maintenance.
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36
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DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA. Heredity (Edinb) 2016; 118:88-95. [PMID: 27827387 DOI: 10.1038/hdy.2016.108] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/07/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022] Open
Abstract
Selection is expected to be more efficient in species that are more diverse because both the efficiency of natural selection and DNA sequence diversity are expected to depend upon the effective population size. We explore this relationship across a data set of 751 mammal species for which we have mitochondrial polymorphism data. We introduce a method by which we can examine the relationship between our measure of the efficiency of natural selection, the nonsynonymous relative to the synonymous nucleotide site diversity (πN/πS), and synonymous nucleotide diversity (πS), avoiding the statistical non-independence between the two quantities. We show that these two variables are strongly negatively and linearly correlated on a log scale. The slope is such that as πS doubles, πN/πS is reduced by 34%. We show that the slope of this relationship differs between the two phylogenetic groups for which we have the most data, rodents and bats, and that it also differs between species with high and low body mass, and between those with high and low mass-specific metabolic rate.
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37
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Roy SW. Is Mutation Random or Targeted?: No Evidence for Hypermutability in Snail Toxin Genes. Mol Biol Evol 2016; 33:2642-7. [PMID: 27486220 DOI: 10.1093/molbev/msw140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene family that undergoes rapid diversification of their protein-coding sequences by positive selection. Previous reconstructions of the sequence evolution of conotoxin genes claimed striking patterns: (1) elevated synonymous change, interpreted as being due to targeted "hypermutation" in this region; (2) elevated transversion-to-transition ratios, interpreted as reflective of the particular mechanism of hypermutation; and (3) much lower rates of synonymous change in the codons encoding several highly conserved cysteine residues, interpreted as strong position-specific codon bias. This work has spawned a variety of studies on the potential mechanisms of hypermutation and on causes for cysteine codon bias, and has inspired hypermutation hypotheses for various other fast-evolving genes. Here, I show that all three findings are likely to be artifacts of statistical reconstruction. First, by simulating nonsynonymous change I show that high rates of dN can lead to overestimation of dS. Second, I show that there is no evidence for any of these three patterns in comparisons of closely related conotoxin sequences, suggesting that the reported findings are due to breakdown of statistical methods at high levels of sequence divergence. The current findings suggest that mutation and codon bias in conotoxin genes may not be atypical, and that random mutation and selection can explain the evolution of even these exceptional loci.
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Affiliation(s)
- Scott W Roy
- Department of Biology, San Francisco State University
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38
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Vos M, Hesselman MC, Te Beek TA, van Passel MWJ, Eyre-Walker A. Rates of Lateral Gene Transfer in Prokaryotes: High but Why? Trends Microbiol 2016; 23:598-605. [PMID: 26433693 DOI: 10.1016/j.tim.2015.07.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/01/2015] [Accepted: 07/20/2015] [Indexed: 12/12/2022]
Abstract
Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, University of Exeter, Penryn, UK.
| | | | - Tim A Te Beek
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Centre for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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39
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Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes. Sci Rep 2015; 5:16972. [PMID: 26593880 PMCID: PMC4655331 DOI: 10.1038/srep16972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
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40
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Hara Y. Tempo and mode of genomic mutations unveil human evolutionary history. Genes Genet Syst 2015; 90:123-31. [PMID: 26510567 DOI: 10.1266/ggs.90.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mutations that have occurred in human genomes provide insight into various aspects of evolutionary history such as speciation events and degrees of natural selection. Comparing genome sequences between human and great apes or among humans is a feasible approach for inferring human evolutionary history. Recent advances in high-throughput or so-called 'next-generation' DNA sequencing technologies have enabled the sequencing of thousands of individual human genomes, as well as a variety of reference genomes of hominids, many of which are publicly available. These sequence data can help to unveil the detailed demographic history of the lineage leading to humans as well as the explosion of modern human population size in the last several thousand years. In addition, high-throughput sequencing illustrates the tempo and mode of de novo mutations, which are producing human genetic variation at this moment. Pedigree-based human genome sequencing has shown that mutation rates vary significantly across the human genome. These studies have also provided an improved timescale of human evolution, because the mutation rate estimated from pedigree analysis is half that estimated from traditional analyses based on molecular phylogeny. Because of the dramatic reduction in sequencing cost, sequencing on-demand samples designed for specific studies is now also becoming popular. To produce data of sufficient quality to meet the requirements of the study, it is necessary to set an explicit sequencing plan that includes the choice of sample collection methods, sequencing platforms, and number of sequence reads.
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Affiliation(s)
- Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies
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41
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Delihas N. Complexity of a small non-protein coding sequence in chromosomal region 22q11.2: presence of specialized DNA secondary structures and RNA exon/intron motifs. BMC Genomics 2015; 16:785. [PMID: 26467088 PMCID: PMC4607176 DOI: 10.1186/s12864-015-1958-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DiGeorge Syndrome is a genetic abnormality involving ~3 Mb deletion in human chromosome 22, termed 22q.11.2. To better understand the non-coding regions of 22q.11.2, a small 10,000 bp non-protein-coding sequence close to the DiGeorge Critical Region 6 gene (DGCR6) was chosen for analysis and functional entities as the homologous sequence in the chimpanzee genome could be aligned and used for comparisons. METHODS The GenBank database provided genomic sequences. In silico computer programs were used to find homologous DNA sequences in human and chimpanzee genomes, generate random sequences, determine DNA sequence alignments, sequence comparisons and nucleotide repeat copies, and to predicted DNA secondary structures. RESULTS At its 5' half, the 10,000 bp sequence has three distinct sections that represent phylogenetically variable sequences. These Variable Regions contain biased mutations with a very high A + T content, multiple copies of the motif TATAATATA and sequences that fold into long A:T-base-paired stem loops. The 3' half of the 10,000 bp unit, highly conserved between human and chimpanzee, has sequences representing exons of lncRNA genes and segments of introns of protein genes. Central to the 10,000 bp unit are the multiple copies of a sequence that originates from the flanking 5' end of the translocation breakpoint Type A sequence. This breakpoint flanking sequence carries the exon and intron motifs. The breakpoint Type A sequence seems to be a major player in the proliferation of these RNA motifs, as well as the proliferation of Variable Regions in the 10,000 bp segment and other regions within 22q.11.2. CONCLUSIONS The data indicate that a non-coding region of the chromosome may be reserved for highly biased mutations that lead to formation of specialized sequences and DNA secondary structures. On the other hand, the highly conserved nucleotide sequence of the non-coding region may form storage sites for RNA motifs.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony, Brook University, Stony Brook, NY, 11794, USA.
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42
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Abstract
Spontaneously occurring mutations accumulate in somatic cells throughout a person’s lifetime. The majority of these mutations do not have a noticeable effect, but some can alter key cellular functions. Early somatic mutations can cause developmental disorders, whereas the progressive accumulation of mutations throughout life can lead to cancer and contribute to aging. Genome sequencing has revolutionized our understanding of somatic mutation in cancer, providing a detailed view of the mutational processes and genes that drive cancer. Yet, fundamental gaps remain in our knowledge of how normal cells evolve into cancer cells. We briefly summarize a number of the lessons learned over 5 years of cancer genome sequencing and discuss their implications for our understanding of cancer progression and aging.
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Affiliation(s)
| | - Peter J. Campbell
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
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43
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Hershberg R. Mutation--The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria. Cold Spring Harb Perspect Biol 2015; 7:a018077. [PMID: 26330518 DOI: 10.1101/cshperspect.a018077] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mutation is the engine of evolution in that it generates the genetic variation on which the evolutionary process depends. To understand the evolutionary process we must therefore characterize the rates and patterns of mutation. Starting with the seminal Luria and Delbruck fluctuation experiments in 1943, studies utilizing a variety of approaches have revealed much about mutation rates and patterns and about how these may vary between different bacterial strains and species along the chromosome and between different growth conditions. This work provides a critical overview of the results and conclusions drawn from these studies, of the debate surrounding some of these conclusions, and of the challenges faced when studying mutation and its role in bacterial evolution.
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Affiliation(s)
- Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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44
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Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 2015; 348:880-6. [PMID: 25999502 PMCID: PMC4471149 DOI: 10.1126/science.aaa6806] [Citation(s) in RCA: 1135] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
How somatic mutations accumulate in normal cells is central to understanding cancer development but is poorly understood. We performed ultradeep sequencing of 74 cancer genes in small (0.8 to 4.7 square millimeters) biopsies of normal skin. Across 234 biopsies of sun-exposed eyelid epidermis from four individuals, the burden of somatic mutations averaged two to six mutations per megabase per cell, similar to that seen in many cancers, and exhibited characteristic signatures of exposure to ultraviolet light. Remarkably, multiple cancer genes are under strong positive selection even in physiologically normal skin, including most of the key drivers of cutaneous squamous cell carcinomas. Positively selected mutations were found in 18 to 32% of normal skin cells at a density of ~140 driver mutations per square centimeter. We observed variability in the driver landscape among individuals and variability in the sizes of clonal expansions across genes. Thus, aged sun-exposed skin is a patchwork of thousands of evolving clones with over a quarter of cells carrying cancer-causing mutations while maintaining the physiological functions of epidermis.
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Affiliation(s)
| | - Amit Roshan
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Peter Ellis
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK. Francis Crick Institute, London, UK. Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stuart McLaren
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Anthony Fullam
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | | | - Jose M Tubio
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Sara Widaa
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | | | - Philip H Jones
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK.
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK. Department of Haematology, University of Cambridge, Cambridge, UK.
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45
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Braun E. The unforeseen challenge: from genotype-to-phenotype in cell populations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:036602. [PMID: 25719211 DOI: 10.1088/0034-4885/78/3/036602] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological cells present a paradox, in that they show simultaneous stability and flexibility, allowing them to adapt to new environments and to evolve over time. The emergence of stable cell states depends on genotype-to-phenotype associations, which essentially reflect the organization of gene regulatory modes. The view taken here is that cell-state organization is a dynamical process in which the molecular disorder manifests itself in a macroscopic order. The genome does not determine the ordered cell state; rather, it participates in this process by providing a set of constraints on the spectrum of regulatory modes, analogous to boundary conditions in physical dynamical systems. We have developed an experimental framework, in which cell populations are exposed to unforeseen challenges; novel perturbations they had not encountered before along their evolutionary history. This approach allows an unbiased view of cell dynamics, uncovering the potential of cells to evolve and develop adapted stable states. In the last decade, our experiments have revealed a coherent set of observations within this framework, painting a picture of the living cell that in many ways is not aligned with the conventional one. Of particular importance here, is our finding that adaptation of cell-state organization is essentially an efficient exploratory dynamical process rather than one founded on random mutations. Based on our framework, a set of concepts underlying cell-state organization-exploration evolving by global, non-specific, dynamics of gene activity-is presented here. These concepts have significant consequences for our understanding of the emergence and stabilization of a cell phenotype in diverse biological contexts. Their implications are discussed for three major areas of biological inquiry: evolution, cell differentiation and cancer. There is currently no unified theoretical framework encompassing the emergence of order, a stable state, in the living cell. Hopefully, the integrated picture described here will provide a modest contribution towards a physics theory of the cell.
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Affiliation(s)
- Erez Braun
- Department of Physics and Network Biology Research Laboratories, Technion, Haifa 32000, Israel
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46
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Evolution in changing environments: modifiers of mutation, recombination, and migration. Proc Natl Acad Sci U S A 2014; 111:17935-40. [PMID: 25427794 DOI: 10.1073/pnas.1417664111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental changes in the patterns of this variation have been important areas of focus in population genetics. On one hand, periods of constant selection pull the genetic makeup of populations toward local fitness optima. On the other, to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced--such as the rates of recombination, mutation, or migration--populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation, and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that the shape, size, variance, and asymmetry of environmental fluctuation have different but predictable effects on evolutionary dynamics.
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47
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Koren A, Handsaker RE, Kamitaki N, Karlić R, Ghosh S, Polak P, Eggan K, McCarroll SA. Genetic variation in human DNA replication timing. Cell 2014; 159:1015-1026. [PMID: 25416942 PMCID: PMC4359889 DOI: 10.1016/j.cell.2014.10.025] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
Abstract
Genomic DNA replicates in a choreographed temporal order that impacts the distribution of mutations along the genome. We show here that DNA replication timing is shaped by genetic polymorphisms that act in cis upon megabase-scale DNA segments. In genome sequences from proliferating cells, read depth along chromosomes reflected DNA replication activity in those cells. We used this relationship to analyze variation in replication timing among 161 individuals sequenced by the 1000 Genomes Project. Genome-wide association of replication timing with genetic variation identified 16 loci at which inherited alleles associate with replication timing. We call these "replication timing quantitative trait loci" (rtQTLs). rtQTLs involved the differential use of replication origins, exhibited allele-specific effects on replication timing, and associated with gene expression variation at megabase scales. Our results show replication timing to be shaped by genetic polymorphism and identify a means by which inherited polymorphism regulates the mutability of nearby sequences.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosa Karlić
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, 10000 Zagreb, Croatia
| | - Sulagna Ghosh
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paz Polak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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48
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Induced mutations in yeast cell populations adapting to an unforeseen challenge. PLoS One 2014; 9:e111133. [PMID: 25340744 PMCID: PMC4207790 DOI: 10.1371/journal.pone.0111133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/22/2014] [Indexed: 12/24/2022] Open
Abstract
The modern evolutionary synthesis assumes that mutations occur at random, independently of the environment in which they confer an advantage. However, there are indications that cells facing challenging conditions can adapt rapidly, utilizing processes beyond selection of pre-existing genetic variation. Here, we show that a strong regulatory challenge can induce mutations in many independent yeast cells, in the absence of general mutagenesis. Whole genome sequencing of cell lineages reveals a repertoire of independent mutations within a single lineage that arose only after the cells were exposed to the challenging environment, while other cells in the same lineage adapted without any mutation in their genomes. Thus, our experiments uncovered multiple alternative routes for heritable adaptation that were all induced in the same lineage during a short time period. Our results demonstrate the existence of adaptation mechanisms beyond random mutation, suggesting a tight connection between physiological and genetic processes.
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49
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Stalled transcription complexes promote DNA repair at a distance. Proc Natl Acad Sci U S A 2014; 111:4037-42. [PMID: 24554077 DOI: 10.1073/pnas.1322350111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcription-coupled nucleotide excision repair (TCR) accelerates the removal of noncoding lesions from the template strand of active genes, and hence contributes to genome-wide variations in mutation frequency. Current models for TCR suppose that a lesion must cause RNA polymerase (RNAP) to stall if it is to be a substrate for accelerated repair. We have examined the substrate requirements for TCR using a system in which transcription stalling and damage location can be uncoupled. We show that Mfd-dependent TCR in bacteria involves the formation of a damage search complex that can detect lesions downstream of a stalled RNAP, and that the strand specificity of the accelerated repair pathway is independent of the requirement for a lesion to stall RNAP. We also show that an ops (operon polarity suppressor) transcription pause site, which causes backtracking of RNAP, can promote the repair of downstream lesions when those lesions do not themselves cause the polymerase to stall. Our findings indicate that the transcription-repair coupling factor Mfd, which is an ATP-dependent superfamily 2 helicase that binds to RNAP, continues to translocate along DNA after RNAP has been displaced until a lesion in the template strand is located. The discovery that pause sites can promote the repair of nonstalling lesions suggests that TCR pathways may play a wider role in modulating mutation frequencies in different parts of the genome than has previously been suspected.
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50
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de Lorenzo V. From theselfish genetoselfish metabolism: Revisiting the central dogma. Bioessays 2014; 36:226-35. [DOI: 10.1002/bies.201300153] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Víctor de Lorenzo
- Systems & Synthetic Biology Program; Centro Nacional de Biotecnología CSIC Cantoblanco; Madrid Spain
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