1
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Tsuru S, Hatanaka N, Furusawa C. Promoters Constrain Evolution of Expression Levels of Essential Genes in Escherichia coli. Mol Biol Evol 2024; 41:msae185. [PMID: 39219319 PMCID: PMC11406756 DOI: 10.1093/molbev/msae185] [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: 05/22/2024] [Revised: 07/31/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024] Open
Abstract
Variability in expression levels in response to random genomic mutations varies among genes, influencing both the facilitation and constraint of phenotypic evolution in organisms. Despite its importance, both the underlying mechanisms and evolutionary origins of this variability remain largely unknown due to the mixed contributions of cis- and trans-acting elements. To address this issue, we focused on the mutational variability of cis-acting elements, that is, promoter regions, in Escherichia coli. Random mutations were introduced into the natural and synthetic promoters to generate mutant promoter libraries. By comparing the variance in promoter activity of these mutant libraries, we found no significant difference in mutational variability in promoter activity between promoter groups, suggesting the absence of a signature of natural selection for mutational robustness. In contrast, the promoters controlling essential genes exhibited a remarkable bias in mutational variability, with mutants displaying higher activities than the wild types being relatively rare compared to those with lower activities. Our evolutionary simulation on a rugged fitness landscape provided a rationale for this vulnerability. These findings suggest that past selection created nonuniform mutational variability in promoters biased toward lower activities of random mutants, which now constrains the future evolution of downstream essential genes toward higher expression levels.
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Affiliation(s)
- Saburo Tsuru
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naoki Hatanaka
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chikara Furusawa
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka 565-0874, Japan
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2
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Patel D, Amiji H, Shropshire W, Condic N, Lermi NO, Sabha Y, John B, Hanson B, Karras GI. Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.547572. [PMID: 37745611 PMCID: PMC10516021 DOI: 10.1101/2023.07.21.547572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.
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3
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Posadas-García YS, Espinosa-Soto C. Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. BMC Bioinformatics 2022; 23:509. [DOI: 10.1186/s12859-022-05067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consensus is still lacking regarding evolutionary mechanisms involved in evolution through gene duplication as well as the conditions that affect them. We argue that a better understanding of evolution through gene duplication requires considering explicitly that genes do not act in isolation. It demands studying how the perturbation that gene duplication implies percolates through the web of gene interactions. Due to evolution’s contingent nature, the paths that lead to the final fate of duplicates must depend strongly on the early stages of gene duplication, before gene copies have accumulated distinctive changes.
Methods
Here we use a widely-known model of gene regulatory networks to study how gene duplication affects network behavior in early stages. Such networks comprise sets of genes that cross-regulate. They organize gene activity creating the gene expression patterns that give cells their phenotypic properties. We focus on how duplication affects two evolutionarily relevant properties of gene regulatory networks: mitigation of the effect of new mutations and access to new phenotypic variants through mutation.
Results
Among other observations, we find that those networks that are better at maintaining the original phenotype after duplication are usually also better at buffering the effect of single interaction mutations and that duplication tends to enhance further this ability. Moreover, the effect of mutations after duplication depends on both the kind of mutation and genes involved in it. We also found that those phenotypes that had easier access through mutation before duplication had higher chances of remaining accessible through new mutations after duplication.
Conclusion
Our results support that gene duplication often mitigates the impact of new mutations and that this effect is not merely due to changes in the number of genes. The work that we put forward helps to identify conditions under which gene duplication may enhance evolvability and robustness to mutations.
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4
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Martin NS, Ahnert SE. Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map. J R Soc Interface 2022; 19:20220072. [PMID: 35702868 PMCID: PMC9198509 DOI: 10.1098/rsif.2022.0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
The genotype-phenotype (GP) map of RNA secondary structure links each RNA sequence to its corresponding secondary structure. Previous research has shown that the large-scale structural properties of GP maps, such as the size of neutral sets in genotype space, can influence evolutionary outcomes. In order to use neutral set sizes, efficient and accurate computational methods are needed to compute them. Here, we propose a new method, which is based on free energy estimates and is much faster than existing sample-based methods. Moreover, this approach can give insight into the reasons behind neutral set size variations, for example, why structures with fewer stacks tend to have larger neutral set sizes. In addition, we generalize neutral set size calculations from the previously studied many-to-one framework, where each sequence folds into a single energetically preferred structure, to a fuller many-to-many framework, where several low-energy structures are included. We find that structures with high neutral sets in one framework also tend to have large neutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.
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Affiliation(s)
- Nora S. Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sebastian E. Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
- The Alan Turing Institute, British Library, Euston Road, London NW1 2DB, UK
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5
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Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021; 38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
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Affiliation(s)
- Susanna Manrubia
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, Spain; UC3M-Santander Big Data Institute (IBiDat), Getafe, Madrid, Spain
| | - Jacobo Aguirre
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Centro de Astrobiología, CSIC-INTA, ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, I(2)SysBio (CSIC-UV), València, Spain; The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics Group, Utrecht University, the Netherlands
| | - Bhavin S Khatri
- The Francis Crick Institute, London, UK; Department of Life Sciences, Imperial College London, London, UK
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Marcel Weiß
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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6
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Mitteroecker P, Stansfield E. A model of developmental canalization, applied to human cranial form. PLoS Comput Biol 2021; 17:e1008381. [PMID: 33591964 PMCID: PMC7909690 DOI: 10.1371/journal.pcbi.1008381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/26/2021] [Accepted: 01/14/2021] [Indexed: 11/26/2022] Open
Abstract
Developmental mechanisms that canalize or compensate perturbations of organismal development (targeted or compensatory growth) are widely considered a prerequisite of individual health and the evolution of complex life, but little is known about the nature of these mechanisms. It is even unclear if and how a “target trajectory” of individual development is encoded in the organism’s genetic-developmental system or, instead, emerges as an epiphenomenon. Here we develop a statistical model of developmental canalization based on an extended autoregressive model. We show that under certain assumptions the strength of canalization and the amount of canalized variance in a population can be estimated, or at least approximated, from longitudinal phenotypic measurements, even if the target trajectories are unobserved. We extend this model to multivariate measures and discuss reifications of the ensuing parameter matrix. We apply these approaches to longitudinal geometric morphometric data on human postnatal craniofacial size and shape as well as to the size of the frontal sinuses. Craniofacial size showed strong developmental canalization during the first 5 years of life, leading to a 50% reduction of cross-sectional size variance, followed by a continual increase in variance during puberty. Frontal sinus size, by contrast, did not show any signs of canalization. Total variance of craniofacial shape decreased slightly until about 5 years of age and increased thereafter. However, different features of craniofacial shape showed very different developmental dynamics. Whereas the relative dimensions of the nasopharynx showed strong canalization and a reduction of variance throughout postnatal development, facial orientation continually increased in variance. Some of the signals of canalization may owe to independent variation in developmental timing of cranial components, but our results indicate evolved, partly mechanically induced mechanisms of canalization that ensure properly sized upper airways and facial dimensions. Developmental mechanisms that canalize or compensate perturbations of organismal development are a prerequisite of individual health and the evolution of complex life. However, surprisingly little is known about these mechanisms, partly because the “target trajectories” of individual development cannot be directly observed. Here we develop a statistical model of developmental canalization that allows one to estimate the strength of canalization and the amount of canalized variance in a population even if the target trajectories are unobserved. We applied these approaches to data on human postnatal craniofacial growth. Whereas overall craniofacial size was strongly canalized during the first 5 years of age, frontal sinus size did not show any signs of canalization. The relative dimensions of the nasopharynx showed strong canalization and a reduction of variance throughout postnatal development, whereas other shape features, such as facial orientation, continually increased in variance. Our results indicate evolved, partly mechanically induced mechanisms of canalization that ensure properly sized upper airways and facial dimensions.
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Affiliation(s)
- Philipp Mitteroecker
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- * E-mail:
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7
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Pesevski M, Dworkin I. Genetic and environmental canalization are not associated among altitudinally varying populations of Drosophila melanogaster. Evolution 2020; 74:1755-1771. [PMID: 32562566 DOI: 10.1111/evo.14039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 05/19/2020] [Accepted: 05/30/2020] [Indexed: 01/23/2023]
Abstract
Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves are limited despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as a correlated response to environmental canalization (congruence model). Yet, empirical evidence has not consistently supported predictions of a correlation between genetic and environmental canalization. In a recent study, a population of Drosophila adapted to high altitude showed evidence of genetic decanalization relative to those from low altitudes. Using strains derived from these populations, we tested if they varied for multiple aspects of environmental canalization We observed the expected differences in wing size, shape, cell (trichome) density and mutational defects between high- and low-altitude populations. However, we observed little evidence for a relationship between measures of environmental canalization with population or with defect frequency. Our results do not support the predicted association between genetic and environmental canalization.
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Affiliation(s)
- Maria Pesevski
- Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Ian Dworkin
- Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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8
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Abstract
Evolvability is the ability of a biological system to produce phenotypic variation that is both heritable and adaptive. It has long been the subject of anecdotal observations and theoretical work. In recent years, however, the molecular causes of evolvability have been an increasing focus of experimental work. Here, we review recent experimental progress in areas as different as the evolution of drug resistance in cancer cells and the rewiring of transcriptional regulation circuits in vertebrates. This research reveals the importance of three major themes: multiple genetic and non-genetic mechanisms to generate phenotypic diversity, robustness in genetic systems, and adaptive landscape topography. We also discuss the mounting evidence that evolvability can evolve and the question of whether it evolves adaptively.
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9
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Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy. PLoS Genet 2017; 13:e1006768. [PMID: 28493864 PMCID: PMC5444853 DOI: 10.1371/journal.pgen.1006768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/25/2017] [Accepted: 04/19/2017] [Indexed: 11/19/2022] Open
Abstract
The functional basis of genetic robustness, the ability of organisms to suppress the effects of mutations, remains incompletely understood. We exposed a set of 15 strains of Saccharomyces cerevisiae form diverse environments to increasing doses of the chemical mutagen EMS. The number of the resulting random mutations was similar for all tested strains. However, there were differences in immediate mortality after the mutagenic treatment and in defective growth of survivors. An analysis of gene expression revealed that immediate mortality was lowest in strains with lowest expression of transmembrane proteins, which are rich in thiol groups and thus vulnerable to EMS. A signal of genuine genetic robustness was detected for the other trait, the ability to grow well despite bearing non-lethal mutations. Increased tolerance of such mutations correlated with high expression of genes responsible for the oxidative energy metabolism, suggesting that the negative effect of mutations can be buffered if enough energy is available. We confirmed this finding in three additional tests of the ability to grow on (i) fermentable or non-fermentable sources of carbon, (ii) under chemical inhibition of the electron transport chain and (iii) during overexpression of its key component, cytochrome c. Our results add the capacity to generate energy as a general mechanism of genetic robustness. The ability to suppress phenotypic effects of mutations is termed genetic robustness. Its functional basis and evolutionary origin remain insufficiently understood despite decades of research. In fact, it is still largely untested whether genetic robustness is a trait of substantial, within-species variation. We used a model organism, Saccharomyces cerevisiae, to study both phenotypic signs and functional underpinnings of genetic robustness. We introduced random mutations into a set of well-characterized yeast strain. There was considerable variation in the growth rate among clones recovered after mutagenesis, which is an indication of genetic robustness. Using available data on gene expression for our strains, we found that genetic robustness was strongest among strains with enhanced expression of genes related to the energy metabolism. We reasoned that, regardless of the specific mutations, the capacity to generate metabolic energy may be a general underlying mechanism for buffering the effects of random mutations across the genome. We confirmed this hypothesis in further experiments in which we showed that genetic robustness decreases when the energy metabolism is compromised and increases when it is boosted.
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Espinosa-Soto C. Selection for distinct gene expression properties favours the evolution of mutational robustness in gene regulatory networks. J Evol Biol 2016; 29:2321-2333. [DOI: 10.1111/jeb.12959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/26/2016] [Indexed: 11/27/2022]
Affiliation(s)
- C. Espinosa-Soto
- Instituto de Física; Universidad Autónoma de San Luis Potosí; San Luis Potosí Mexico
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11
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Presloid JB, Mohammad TF, Lauring AS, Novella IS. Antigenic diversification is correlated with increased thermostability in a mammalian virus. Virology 2016; 496:203-214. [PMID: 27344137 DOI: 10.1016/j.virol.2016.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
Abstract
The theory of plastogenetic congruence posits that ultimately, the pressure to maintain function in the face of biomolecular destabilization produces robustness. As temperature goes up so does destabilization. Thus, genetic robustness, defined as phenotypic constancy despite mutation, should correlate with survival during thermal challenge. We tested this hypothesis using vesicular stomatitis virus (VSV). We produced two sets of evolved strains after selection for higher thermostability by either preincubation at 37°C or by incubation at 40°C during infection. These VSV populations became more thermostable and also more fit in the absence of thermal selection, demonstrating an absence of tradeoffs. Eleven out of 12 evolved populations had a fixed, nonsynonymous substitution in the nucleocapsid (N) open reading frame. There was a partial correlation between thermostability and mutational robustness that was observed when the former was measured at 42°C, but not at 37°C. These results are consistent with our earlier work and suggest that the relationship between robustness and thermostability is complex. Surprisingly, many of the thermostable strains also showed increased resistance to monoclonal antibody and polyclonal sera, including sera from natural hosts. These data suggest that evolved thermostability may lead to antigenic diversification and an increased ability to escape immune surveillance in febrile hosts, and potentially to an improved robustness. These relationships have important implications not only in terms of viral pathogenesis, but also for the development of vaccine vectors and oncolytic agents.
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Affiliation(s)
- John B Presloid
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA
| | - Tasneem F Mohammad
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA
| | - Adam S Lauring
- Department of Internal Medicine, Division of Infectious Diseases and Department of Microbiology & Immunology. University of Michigan, Ann Arbor, MI 41809, USA.
| | - Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA.
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12
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Manrubia S, Cuesta JA. Evolution on neutral networks accelerates the ticking rate of the molecular clock. J R Soc Interface 2015; 12:20141010. [PMID: 25392402 DOI: 10.1098/rsif.2014.1010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Large sets of genotypes give rise to the same phenotype, because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as the genotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NNs). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NNs with arbitrary topology, we analyse the effect of assortativity, of NN (phenotype) fitness and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive 'phenotypic entrapment' entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.
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Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain Systems Biology Programme, National Centre for Biotechnology (CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain Department of Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Madrid, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
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13
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Simon TP. Trait canalization analysis of water quality, temperature, and developmental associations with early life stages of two fish species. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 94:688-694. [PMID: 25863479 DOI: 10.1007/s00128-015-1540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Evaluation of trait robustness based on environmental fluctuation in ontogenetic life stages are needed to evaluate stability and trait response during critical developmental events. Hardness, alkalinity, acidity, light intensity, and thermal differences were studied for trait canalization variation in morphometric, meristic, ontogenetic processes, and pigment characteristics. Trait canalization was observed with no statistical differences (p > 0.05) in mixed random two-way ANOVA comparisons between various block and treatment effects for hardness, alkalinity or acidity. Thermal block variation differences in six measures, including mandible length, yolk sac length, midpostanal depth, and head width, incubation, and hatching length, varied significantly (p ≤ 0.05) with declining temperatures. Water quality and thermal attributes exhibited trait canalization and did not increase character state variation in the early life stage morphological expression, which result in stable phenotypic inheritance rather than variable environmental conditions during embryonic and larval development.
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Affiliation(s)
- Thomas P Simon
- School of Public and Environmental Affairs, Indiana University, 1315 E. Tenth Street, Bloomington, IN, 47405, USA,
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14
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Derényi I, Szöllősi GJ. Effective temperature of mutations. PHYSICAL REVIEW LETTERS 2015; 114:058101. [PMID: 25699467 DOI: 10.1103/physrevlett.114.058101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Indexed: 06/04/2023]
Abstract
Biological macromolecules experience two seemingly very different types of noise acting on different time scales: (i) point mutations corresponding to changes in molecular sequence and (ii) thermal fluctuations. Examining the secondary structures of a large number of microRNA precursor sequences and model lattice proteins, we show that the effects of single point mutations are statistically indistinguishable from those of an increase in temperature by a few tens of kelvins. The existence of such an effective mutational temperature establishes a quantitative connection between robustness to genetic (mutational) and environmental (thermal) perturbations.
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Affiliation(s)
- Imre Derényi
- ELTE-MTA "Lendulet" Biophysics Research Group, Department of Biological Physics, Eötvös University, Pázmány Peter Setany 1A, H-1117 Budapest, Hungary
| | - Gergely J Szöllősi
- ELTE-MTA "Lendulet" Biophysics Research Group, Department of Biological Physics, Eötvös University, Pázmány Peter Setany 1A, H-1117 Budapest, Hungary
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15
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Pei S, Anthony JS, Meyer MM. Sampled ensemble neutrality as a feature to classify potential structured RNAs. BMC Genomics 2015; 16:35. [PMID: 25649229 PMCID: PMC4333902 DOI: 10.1186/s12864-014-1203-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 12/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structured RNAs have many biological functions ranging from catalysis of chemical reactions to gene regulation. Yet, many homologous structured RNAs display most of their conservation at the secondary or tertiary structure level. As a result, strategies for structured RNA discovery rely heavily on identification of sequences sharing a common stable secondary structure. However, correctly distinguishing structured RNAs from surrounding genomic sequence remains challenging, especially during de novo discovery. RNA also has a long history as a computational model for evolution due to the direct link between genotype (sequence) and phenotype (structure). From these studies it is clear that evolved RNA structures, like protein structures, can be considered robust to point mutations. In this context, an RNA sequence is considered robust if its neutrality (extent to which single mutant neighbors maintain the same secondary structure) is greater than that expected for an artificial sequence with the same minimum free energy structure. RESULTS In this work, we bring concepts from evolutionary biology to bear on the structured RNA de novo discovery process. We hypothesize that alignments corresponding to structured RNAs should consist of neutral sequences. We evaluate several measures of neutrality for their ability to distinguish between alignments of structured RNA sequences drawn from Rfam and various decoy alignments. We also introduce a new measure of RNA structural neutrality, the structure ensemble neutrality (SEN). SEN seeks to increase the biological relevance of existing neutrality measures in two ways. First, it uses information from an alignment of homologous sequences to identify a conserved biologically relevant structure for comparison. Second, it only counts base-pairs of the original structure that are absent in the comparison structure and does not penalize the formation of additional base-pairs. CONCLUSION We find that several measures of neutrality are effective at separating structured RNAs from decoy sequences, including both shuffled alignments and flanking genomic sequence. Furthermore, as an independent feature classifier to identify structured RNAs, SEN yields comparable performance to current approaches that consider a variety of features including stability and sequence identity. Finally, SEN outperforms other measures of neutrality at detecting mutational robustness in bacterial regulatory RNA structures.
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Affiliation(s)
- Shermin Pei
- Boston College, 140 Commonwealth Ave., Chestnut Hill, 02467, MA, USA.
| | - Jon S Anthony
- Boston College, 140 Commonwealth Ave., Chestnut Hill, 02467, MA, USA.
| | - Michelle M Meyer
- Boston College, 140 Commonwealth Ave., Chestnut Hill, 02467, MA, USA.
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16
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Siegal ML, Leu JY. On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2014; 45:496-517. [PMID: 26034410 PMCID: PMC4448758 DOI: 10.1146/annurev-ecolsys-120213-091705] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.
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Affiliation(s)
- Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003;
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 11529;
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17
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Gombar S, MacCarthy T, Bergman A. Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity? PLoS Comput Biol 2014; 10:e1003450. [PMID: 24604070 PMCID: PMC3945085 DOI: 10.1371/journal.pcbi.1003450] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/10/2013] [Indexed: 01/08/2023] Open
Abstract
The evolution of ever increasing complex life forms has required innovations at the molecular level in order to overcome existing barriers. For example, evolving processes for cell differentiation, such as epigenetic mechanisms, facilitated the transition to multicellularity. At the same time, studies using gene regulatory network models, and corroborated in single-celled model organisms, have shown that mutational robustness and environmental robustness are correlated. Such correlation may constitute a barrier to the evolution of multicellularity since cell differentiation requires sensitivity to cues in the internal environment during development. To investigate how this barrier might be overcome, we used a gene regulatory network model which includes epigenetic control based on the mechanism of histone modification via Polycomb Group Proteins, which evolved in tandem with the transition to multicellularity. Incorporating the Polycomb mechanism allowed decoupling of mutational and environmental robustness, thus allowing the system to be simultaneously robust to mutations while increasing sensitivity to the environment. In turn, this decoupling facilitated cell differentiation which we tested by evaluating the capacity of the system for producing novel output states in response to altered initial conditions. In the absence of the Polycomb mechanism, the system was frequently incapable of adding new states, whereas with the Polycomb mechanism successful addition of new states was nearly certain. The Polycomb mechanism, which dynamically reshapes the network structure during development as a function of expression dynamics, decouples mutational and environmental robustness, thus providing a necessary step in the evolution of multicellularity.
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Affiliation(s)
- Saurabh Gombar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Thomas MacCarthy
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Applied Mathematics and Statistics, State University of New York, Stony Brook, New York, United States of America
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
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18
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Abstract
Robustness is considered a ubiquitous property of living systems at all levels of organization, and small noncoding RNA (sncRNA) is a genuine model for its study at the molecular level. In this communication, we question whether microRNA precursors (pre-miRNAs) are actually structurally robust, as previously suggested. We found that natural pre-miRNAs are not more robust than expected under an appropriate null model. On the contrary, we found that eukaryotic pre-miRNAs show a significant enrichment in conformational flexibility at the thermal equilibrium of the molecule, that is, in their plasticity. Our results further support the selection for functional diversification and evolvability in sncRNAs.
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Affiliation(s)
- Guillermo Rodrigo
- Institute of Systems and Synthetic Biology, CNRS, UEVE, Genopole, Évry, France
- *Corresponding author: E-mail:
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC, UPV, València, Spain
- Santa Fe Institute, Santa Fe, New Mexico
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19
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Congruent evolution of fitness and genetic robustness in vesicular stomatitis virus. J Virol 2013; 87:4923-8. [PMID: 23408631 DOI: 10.1128/jvi.02796-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Quasispecies theory is a case of mutation-selection balance for evolution at high mutation rates, such as those observed in RNA viruses. One of the main predictions of this model is the selection for robustness, defined as the ability of an organism to remain phenotypically unchanged in the face of mutation. We have used a collection of vesicular stomatitis virus strains that had been evolving either under positive selection or under random drift. We had previously shown that the former increase in fitness while the latter have overall fitness decreases (I. S. Novella, J. B. Presloid, T. Zhou, S. D. Smith-Tsurkan, B. E. Ebendick-Corpus, R. N. Dutta, K. L. Lust, and C. O. Wilke, J. Virol. 84:4960-4968, 2010). Here, we determined the robustness of these strains and demonstrated that strains under positive selection not only increase in fitness but also increase in robustness. In contrast, strains under drift not only decreased in fitness but also decreased in robustness. There was a good overall correlation between fitness and robustness. We also tested whether there was a correlation between fitness and thermostability, and we observed that the correlation was imperfect, indicating that the fitness effects of mutations are exerted in part at a level other than changing the resistance of the protein to temperature.
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20
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Abstract
It is known that the conservation of protein-coding genes is associated with their sequences both various species, such as animals and plants. However, the association between microRNA (miRNA) conservation and their sequences in various species remains unexplored. Here we report the association of miRNA conservation with its sequence features, such as base content and cleavage sites, suggesting that miRNA sequences contain the fingerprints for miRNA conservation. More interestingly, different species show different and even opposite patterns between miRNA conservation and sequence features. For example, mammalian miRNAs show a positive/negative correlation between conservation and AU/GC content, whereas plant miRNAs show a negative/positive correlation between conservation and AU/GC content. Further analysis puts forward the hypothesis that the introns of protein-coding genes may be a main driving force for the origin and evolution of mammalian miRNAs. At the 5′ end, conserved miRNAs have a preference for base U, while less-conserved miRNAs have a preference for a non-U base in mammals. This difference does not exist in insects and plants, in which both conserved miRNAs and less-conserved miRNAs have a preference for base U at the 5′ end. We further revealed that the non-U preference at the 5′ end of less-conserved mammalian miRNAs is associated with miRNA function diversity, which may have evolved from the pressure of a highly sophisticated environmental stimulus the mammals encountered during evolution. These results indicated that miRNA sequences contain the fingerprints for conservation, and these fingerprints vary according to species. More importantly, the results suggest that although species share common mechanisms by which miRNAs originate and evolve, mammals may develop a novel mechanism for miRNA origin and evolution. In addition, the fingerprint found in this study can be predictor of miRNA conservation, and the findings are helpful in achieving a clearer understanding of miRNA function and evolution.
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Affiliation(s)
- Bing Shi
- Department of Cardiology, Peking University Third Hospital, Beijing, China
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China
- * E-mail: (BS); (JW)
| | - Wei Gao
- Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Juan Wang
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China
- * E-mail: (BS); (JW)
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21
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Hayden EJ, Weikert C, Wagner A. Directional selection causes decanalization in a group I ribozyme. PLoS One 2012; 7:e45351. [PMID: 23028955 PMCID: PMC3445466 DOI: 10.1371/journal.pone.0045351] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/14/2012] [Indexed: 11/19/2022] Open
Abstract
A canalized genotype is robust to environmental or genetic perturbations. Canalization is expected to result from stabilizing selection on a well-adapted phenotype. Decanalization, the loss of robustness, might follow periods of directional selection toward a new optimum. The evolutionary forces causing decanalization are still unknown, in part because it is difficult to determine the fitness effects of mutations in populations of organisms with complex genotypes and phenotypes. Here, we report direct experimental measurements of robustness in a system with a simple genotype and phenotype, the catalytic activity of an RNA enzyme. We find that the robustness of a population of RNA enzymes decreases during a period of directional selection in the laboratory. The decrease in robustness is primarily caused by the selective sweep of a genotype that is decanalized relative to the wild-type, both in terms of mutational robustness and environmental robustness (thermodynamic stability). Our results experimentally demonstrate that directional selection can cause decanalization on short time scales, and demonstrate co-evolution of mutational and environmental robustness.
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Affiliation(s)
- Eric J Hayden
- Department of Bioengineering, Stanford University, Stanford, California, United States of America.
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22
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Abstract
Histone modification is an important mechanism of gene regulation in eukaryotes. Why many histone modifications can be stably maintained in the midst of genetic and environmental changes is a fundamental question in evolutionary biology. We obtained genome-wide profiles of three histone marks, H3 lysine 4 tri-methylation (H3K4me3), H3 lysine 4 mono-methylation (H3K4me1), and H3 lysine 27 acetylation (H3K27ac), for several cell types from human and mouse. We identified histone modifications that were stable among different cell types in human and histone modifications that were evolutionarily conserved between mouse and human in the same cell type. We found that histone modifications that were stable among cell types were also likely to be conserved between species. This trend was consistently observed in promoter, intronic, and intergenic regions for all of the histone marks tested. Importantly, the trend was observed regardless of the expression breadth of the nearby gene, indicating that slow evolution of housekeeping genes was not the major reason for the correlation. These regions showed distinct genetic and epigenetic properties, such as clustered transcription factor binding sites (TFBSs), high GC content, and CTCF binding at flanking sides. Based on our observations, we proposed that TFBS clustering in or near a histone modification plays a significant role in stabilizing and conserving the histone modification because TFBS clustering promotes TFBS conservation, which in turn promotes histone modification conservation. In summary, the results of this study support the view that in mammalian genomes a common mechanism maintains histone modifications against both genetic and environmental (cellular) changes.
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Affiliation(s)
- Yong H. Woo
- Department of Ecology and Evolution, The University of Chicago
| | - Wen-Hsiung Li
- Department of Ecology and Evolution, The University of Chicago
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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23
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Whitacre JM. Biological robustness: paradigms, mechanisms, and systems principles. Front Genet 2012; 3:67. [PMID: 22593762 PMCID: PMC3350086 DOI: 10.3389/fgene.2012.00067] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/05/2012] [Indexed: 12/31/2022] Open
Abstract
Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g., mutational, environmental) are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior.
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24
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Rodrigo G, Fares MA. Describing the structural robustness landscape of bacterial small RNAs. BMC Evol Biol 2012; 12:52. [PMID: 22500888 PMCID: PMC3368786 DOI: 10.1186/1471-2148-12-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes. RESULTS Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs) encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity. CONCLUSION Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
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25
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Abstract
Phenotypes that vary in response to DNA mutations are essential for evolutionary adaptation and innovation. Therefore, it seems that robustness, a lack of phenotypic variability, must hinder adaptation. The main purpose of this review is to show why this is not necessarily correct. There are two reasons. The first is that robustness causes the existence of genotype networks--large connected sets of genotypes with the same phenotype. I discuss why genotype networks facilitate phenotypic variability. The second reason emerges from the evolutionary dynamics of evolving populations on genotype networks. I discuss how these dynamics can render highly robust phenotypes more variable, using examples from protein and RNA macromolecules. In addition, robustness can help avoid an important evolutionary conflict between the interests of individuals and populations-a conflict that can impede evolutionary adaptation.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Y27-J-54 Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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26
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Chen BS, Lin YP. On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach. Evol Bioinform Online 2011; 7:201-33. [PMID: 22084563 PMCID: PMC3210637 DOI: 10.4137/ebo.s8123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network's evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective.
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Affiliation(s)
- Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan 30013
| | - Ying-Po Lin
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan 30013
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27
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Wagner A. Genotype networks shed light on evolutionary constraints. Trends Ecol Evol 2011; 26:577-84. [DOI: 10.1016/j.tree.2011.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/01/2011] [Accepted: 07/04/2011] [Indexed: 10/17/2022]
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28
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The molecular origins of evolutionary innovations. Trends Genet 2011; 27:397-410. [PMID: 21872964 DOI: 10.1016/j.tig.2011.06.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/10/2011] [Accepted: 06/13/2011] [Indexed: 11/22/2022]
Abstract
The history of life is a history of evolutionary innovations, qualitatively new phenotypic traits that endow their bearers with new, often game-changing abilities. We know many individual examples of innovations and their natural history, but we know little about the fundamental principles of phenotypic variability that permit new phenotypes to arise. Most phenotypic innovations result from changes in three classes of systems: metabolic networks, regulatory circuits, and macromolecules. I here highlight two important features that these classes of systems share. The first is the ubiquity of vast genotype networks - connected sets of genotypes with the same phenotype. The second is the great phenotypic diversity of small neighborhoods around different genotypes in genotype space. I here explain that both features are essential for the phenotypic variability that can bring forth qualitatively new phenotypes. Both features emerge from a common cause, the robustness of phenotypes to perturbations, whose origins are linked to life in changing environments.
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29
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Barrière A, Gordon KL, Ruvinsky I. Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet 2011; 7:e1002095. [PMID: 21655084 PMCID: PMC3107193 DOI: 10.1371/journal.pgen.1002095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 04/07/2011] [Indexed: 11/25/2022] Open
Abstract
Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter. Comparison between genome sequences of different species is a powerful tool in modern biology because important features are maintained by natural selection and are therefore conserved. However, some important sequences within genomes evolve considerably faster than others. One possible explanation is that they encode little or no function. Alternatively, they may evolve under different constraints that permit sequence turnover while maintaining function. Here we report that the promoter of the unc-47 gene of C. elegans contains two discrete elements. One has a highly conserved sequence that determines the spatial expression pattern. Another shows no sequence conservation, but it makes expression of the gene robust, that is, consistent between individuals and resilient to environmental challenges. Remarkably, multiple unrelated sequences are capable of promoting robust expression. Nucleotide composition of these sequences suggests that open chromatin may play a role in conferring robustness of gene expression. Because general sequence composition and therefore expression robustness can be maintained despite sequence turnover, our results offer an explanation of how rapidly diverging promoter elements can nevertheless remain functionally conserved.
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Affiliation(s)
- Antoine Barrière
- Department of Ecology and Evolution and Institute for Genomics and Systems Biology, Chicago, Illinois, United States of America
| | - Kacy L. Gordon
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Department of Ecology and Evolution and Institute for Genomics and Systems Biology, Chicago, Illinois, United States of America
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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30
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Churkin A, Cohen M, Shemer-Avni Y, Barash D. Bioinformatic analysis of the neutrality of RNA secondary structure elements across genotypes reveals evidence for direct evolution of genetic robustness in HCV. J Bioinform Comput Biol 2011; 8:1013-26. [PMID: 21121024 DOI: 10.1142/s0219720010005087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 08/18/2010] [Accepted: 08/18/2010] [Indexed: 01/11/2023]
Abstract
The properties and origin of genetic robustness have recently been investigated in several works that examined microRNA stem-loop structures, and a variety of conclusions have been reached without agreement. Considering that this is a universal phenomenon that is not restricted to miRNAs, we recall the original work on this topic that began from looking at viral RNAs of several types. We provide a link to this work by examining the neutrality of HCV structural elements, performing a detailed bioinformatic analysis using RNA secondary structure predictions across genotypes. This study provides supporting evidence for direct evolution of genetic robustness that is not limited to noncoding RNAs participating in gene regulation, but includes functionally important structural elements of the hepatitis C virus (HCV) that show excess of robustness beyond the intrinsic robustness of their stem-loop structure. These findings further support the adaptive behavior of genetic robustness in functional RNAs of various types that seem to have evolved with selection pressure towards increased robustness.
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Affiliation(s)
- Alexander Churkin
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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31
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Genetic and environment-induced pathways to innovation: on the possibility of a universal relationship between robustness and adaptation in complex biological systems. Evol Ecol 2011. [DOI: 10.1007/s10682-011-9464-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Price N, Cartwright RA, Sabath N, Graur D, Azevedo RBR. Neutral evolution of robustness in Drosophila microRNA precursors. Mol Biol Evol 2011; 28:2115-23. [PMID: 21285032 DOI: 10.1093/molbev/msr029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mutational robustness describes the extent to which a phenotype remains unchanged in the face of mutations. Theory predicts that the strength of direct selection for mutational robustness is at most the magnitude of the rate of deleterious mutation. As far as nucleic acid sequences are concerned, only long sequences in organisms with high deleterious mutation rates and large population sizes are expected to evolve mutational robustness. Surprisingly, recent studies have concluded that molecules that meet none of these conditions--the microRNA precursors (pre-miRNAs) of multicellular eukaryotes--show signs of selection for mutational and/or environmental robustness. To resolve the apparent disagreement between theory and these studies, we have reconstructed the evolutionary history of Drosophila pre-miRNAs and compared the robustness of each sequence to that of its reconstructed ancestor. In addition, we "replayed the tape" of pre-miRNA evolution via simulation under different evolutionary assumptions and compared these alternative histories with the actual one. We found that Drosophila pre-miRNAs have evolved under strong purifying selection against changes in secondary structure. Contrary to earlier claims, there is no evidence that these RNAs have been shaped by either direct or congruent selection for any kind of robustness. Instead, the high robustness of Drosophila pre-miRNAs appears to be mostly intrinsic and likely a consequence of selection for functional structures.
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Affiliation(s)
- Nicholas Price
- Department of Biology and Biochemistry, University of Houston, USA.
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33
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Domingo-Calap P, Pereira-Gómez M, Sanjuán R. Selection for thermostability can lead to the emergence of mutational robustness in an RNA virus. J Evol Biol 2010; 23:2453-60. [PMID: 20831733 DOI: 10.1111/j.1420-9101.2010.02107.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mutational robustness has important evolutionary implications, yet the mechanisms leading to its emergence remain poorly understood. One possibility is selection acting on a correlated trait, as for instance thermostability (plastogenetic congruence). Here, we examine the correlation between mutational robustness and thermostability in experimental populations of the RNA bacteriophage Qβ. Thermostable viruses evolved after only six serial passages in the presence of heat shocks, and genome sequencing suggested that thermostability can be conferred by several alternative mutations. To test whether thermostable viruses have increased mutational robustness, we performed additional passages in the presence of nitrous acid. Whereas in control lines this treatment produced the expected reduction in growth rate caused by the accumulation of deleterious mutations, thermostable viruses showed no such reduction, indicating that they are more resistant to mutagenesis. Our results suggest that selection for thermostability can lead to the emergence of mutational robustness driven by plastogenetic congruence. As temperature is a widespread selective pressure in nature, the mechanism described here may be relevant to the evolution of mutational robustness.
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Affiliation(s)
- P Domingo-Calap
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
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Qiu C, Wang J, Yao P, Wang E, Cui Q. microRNA evolution in a human transcription factor and microRNA regulatory network. BMC SYSTEMS BIOLOGY 2010; 4:90. [PMID: 20584335 PMCID: PMC2914650 DOI: 10.1186/1752-0509-4-90] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 06/29/2010] [Indexed: 02/08/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are important cellular components. The understanding of their evolution is of critical importance for the understanding of their function. Although some specific evolutionary rules of miRNAs have been revealed, the rules of miRNA evolution in cellular networks remain largely unexplored. According to knowledge from protein-coding genes, the investigations of gene evolution in the context of biological networks often generate valuable observations that cannot be obtained by traditional approaches. RESULTS Here, we conducted the first systems-level analysis of miRNA evolution in a human transcription factor (TF)-miRNA regulatory network that describes the regulatory relations among TFs, miRNAs, and target genes. We found that the architectural structure of the network provides constraints and functional innovations for miRNA evolution and that miRNAs showed different and even opposite evolutionary patterns from TFs and other protein-coding genes. For example, miRNAs preferentially coevolved with their activators but not with their inhibitors. During transcription, rapidly evolving TFs frequently activated but rarely repressed miRNAs. In addition, conserved miRNAs tended to regulate rapidly evolving targets, and upstream miRNAs evolved more rapidly than downstream miRNAs. CONCLUSIONS In this study, we performed the first systems level analysis of miRNA evolution. The findings suggest that miRNAs have a unique evolution process and thus may have unique functions and roles in various biological processes and diseases. Additionally, the network presented here is the first TF-miRNA regulatory network, which will be a valuable platform of systems biology.
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Affiliation(s)
- Chengxiang Qiu
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China
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Whitacre JM, Bender A. Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems. Theor Biol Med Model 2010; 7:20. [PMID: 20550663 PMCID: PMC2901314 DOI: 10.1186/1742-4682-7-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 06/15/2010] [Indexed: 10/26/2022] Open
Abstract
A generic mechanism--networked buffering--is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems.
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Affiliation(s)
- James M Whitacre
- School of Computer Science, University of Birmingham, Edgbaston, UK.
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Szejka A, Drossel B. Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021908. [PMID: 20365596 DOI: 10.1103/physreve.81.021908] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Indexed: 05/29/2023]
Abstract
We study the evolution of Boolean networks as model systems for gene regulation. Inspired by biological networks, we select simultaneously for robust attractors and for the ability to respond to external inputs by changing the attractor. Mutations change the connections between the nodes and the update functions. In order to investigate the influence of the type of update functions, we perform our simulations with canalizing as well as with threshold functions. We compare the properties of the fitness landscapes that result for different versions of the selection criterion and the update functions. We find that for all studied cases the fitness landscape has a plateau with maximum fitness resulting in the fact that structurally very different networks are able to fulfill the same task and are connected by neutral paths in network ("genotype") space. We find furthermore a connection between the attractor length and the mutational robustness, and an extremely long memory of the initial evolutionary stage.
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Affiliation(s)
- Agnes Szejka
- Institut für Festkörperphysik, TU Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany
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Masel J, Siegal ML. Robustness: mechanisms and consequences. Trends Genet 2009; 25:395-403. [PMID: 19717203 DOI: 10.1016/j.tig.2009.07.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/11/2009] [Accepted: 07/13/2009] [Indexed: 01/09/2023]
Abstract
Biological systems are robust to perturbation by mutations and environmental fluctuations. New data are shedding light on the biochemical and network-level mechanisms responsible for robustness. Robustness to mutation might have evolved as an adaptation to reduce the effect of mutations, as a congruent byproduct of adaptive robustness to environmental variation, or as an intrinsic property of biological systems selected for their primary functions. Whatever its mechanism or origin, robustness to mutation results in the accumulation of phenotypically cryptic genetic variation. Partial robustness can lead to pre-adaptation, and thereby might contribute to evolvability. The identification and characterization of phenotypic capacitors - which act as switches of the degree of robustness - are critical to understanding the mechanisms and consequences of robustness.
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Affiliation(s)
- Joanna Masel
- Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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Gros PA, Tenaillon O. Selection for chaperone-like mediated genetic robustness at low mutation rate: impact of drift, epistasis and complexity. Genetics 2009; 182:555-64. [PMID: 19307609 PMCID: PMC2691763 DOI: 10.1534/genetics.108.099366] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 03/11/2009] [Indexed: 01/19/2023] Open
Abstract
Genetic robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Overexpression of chaperones, to assist the folding of proteins carrying deleterious mutations, is so far one of the most accepted molecular mechanisms enhancing genetic robustness. Most theories on the evolution of robustness have focused on the implications of high mutation rate. Here we show that genetic drift, which is modulated by population size, organism complexity, and epistasis, can be a sufficient force to select for chaperone-mediated genetic robustness. Using an exact analytical solution, we also show that selection for costly genetic robustness leads to a paradox: the decrease of population fitness on long timescales and the long-term dependency on robustness mechanisms. We suggest that selection for genetic robustness could be universal and not restricted to high mutation rate organisms such as RNA viruses. The evolution of the endosymbiont Buchnera illustrates this selection mechanism and its paradox: the increased dependency on chaperones mediating genetic robustness. Our model explains why most chaperones might have become essential even in optimal growth conditions.
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Affiliation(s)
- Pierre-Alexis Gros
- Université Paris 7 Denis Diderot, Faculté de Médecine Xavier Bichat, 75018 Paris, France.
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