201
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Harms MJ, Thornton JW. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet 2013; 14:559-71. [PMID: 23864121 DOI: 10.1038/nrg3540] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality - the purviews of evolutionary biology and biochemistry, respectively - are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do.
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Affiliation(s)
- Michael J Harms
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
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202
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Wilkins AD, Venner E, Marciano DC, Erdin S, Atri B, Lua RC, Lichtarge O. Accounting for epistatic interactions improves the functional analysis of protein structures. Bioinformatics 2013; 29:2714-21. [PMID: 24021383 PMCID: PMC3799481 DOI: 10.1093/bioinformatics/btt489] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Motivation: The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure. Methods and Results: We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions. Conclusions: Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction. Contact:lichtarge@bcm.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Angela D Wilkins
- Department of Molecular and Human Genetics, CIBR Center for Computational and Integrative Biomedical Research and Program in Structural and Computational Biology & Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030 and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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203
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Ingles-Prieto A, Ibarra-Molero B, Delgado-Delgado A, Perez-Jimenez R, Fernandez JM, Gaucher EA, Sanchez-Ruiz JM, Gavira JA. Conservation of protein structure over four billion years. Structure 2013; 21:1690-7. [PMID: 23932589 PMCID: PMC3774310 DOI: 10.1016/j.str.2013.06.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/07/2013] [Accepted: 06/26/2013] [Indexed: 01/07/2023]
Abstract
Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis.
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Affiliation(s)
- Alvaro Ingles-Prieto
- Facultad de Ciencias, Departamento de Química Física, Universidad de Granada, Granada, 18071, Spain
| | - Beatriz Ibarra-Molero
- Facultad de Ciencias, Departamento de Química Física, Universidad de Granada, Granada, 18071, Spain
| | - Asuncion Delgado-Delgado
- Facultad de Ciencias, Departamento de Química Física, Universidad de Granada, Granada, 18071, Spain
| | - Raul Perez-Jimenez
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Julio M. Fernandez
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Eric A. Gaucher
- Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, and Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia, 30332, USA
| | - Jose M. Sanchez-Ruiz
- Facultad de Ciencias, Departamento de Química Física, Universidad de Granada, Granada, 18071, Spain,To whom correspondence should be addressed: CONTACT: Jose M. Sanchez-Ruiz., , TEL: 34-958243189, FAX: 34-958272879
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas – Universidad de Granada), Avenida de las Palmeras 4, Armilla, Granada, 18100, Spain,To whom correspondence should be addressed: CONTACT: Jose M. Sanchez-Ruiz., , TEL: 34-958243189, FAX: 34-958272879
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204
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Colucci JK, Ortlund EA. Expression, purification and crystallization of the ancestral androgen receptor-DHT complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:994-6. [PMID: 23989146 DOI: 10.1107/s1744309113018745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/05/2013] [Indexed: 11/10/2022]
Abstract
Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).
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Affiliation(s)
- Jennifer K Colucci
- Department of Biochemistry and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30033, USA
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205
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Podgornaia AI, Casino P, Marina A, Laub MT. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. Structure 2013; 21:1636-47. [PMID: 23954504 DOI: 10.1016/j.str.2013.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 06/25/2013] [Accepted: 07/03/2013] [Indexed: 02/01/2023]
Abstract
Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, Escherichia coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes and a systematic mutagenesis study reveal how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions and protein evolution and for the design of novel protein interfaces.
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Affiliation(s)
- Anna I Podgornaia
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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206
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Abstract
For over the last 2 decades, positively selected amino acid sites have been inferred almost exclusively by showing that the number of nonsynonymous substitutions per nonsynonymous site (dn) is greater than that of synonymous substitutions per synonymous site (ds). However, virtually none of these statistical results have been experimentally tested and remain as hypotheses. To perform such experimental tests, we must connect genotype and phenotype and relate the phenotypic changes to the environmental and behavioral changes of the organism. The genotype-phenotype relationship can be established only by synthesizing and manipulating "proper" ancestral phenotypes, whereas the actual functions of adaptive mutations can be learned by studying their chemical roles in phenotypic changes.
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207
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Natarajan C, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF. Epistasis among adaptive mutations in deer mouse hemoglobin. Science 2013; 340:1324-7. [PMID: 23766324 DOI: 10.1126/science.1236862] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epistatic interactions between mutant sites in the same protein can exert a strong influence on pathways of molecular evolution. We performed protein engineering experiments that revealed pervasive epistasis among segregating amino acid variants that contribute to adaptive functional variation in deer mouse hemoglobin (Hb). Amino acid mutations increased or decreased Hb-O2 affinity depending on the allelic state of other sites. Structural analysis revealed that epistasis for Hb-O2 affinity and allosteric regulatory control is attributable to indirect interactions between structurally remote sites. The prevalence of sign epistasis for fitness-related biochemical phenotypes has important implications for the evolutionary dynamics of protein polymorphism in natural populations.
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208
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Abstract
Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.
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209
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Kulikov AM, Mel’nikov AI, Gornostaev NG, Lazebny OE. Dominance status of shape of male genitalia in interspecific crosses of some Drosophila virilis group species. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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210
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Musille PM, Pathak M, Lauer JL, Griffin PR, Ortlund EA. Divergent sequence tunes ligand sensitivity in phospholipid-regulated hormone receptors. J Biol Chem 2013; 288:20702-12. [PMID: 23737522 DOI: 10.1074/jbc.m113.472837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The members of the NR5A subfamily of nuclear receptors (NRs) are important regulators of pluripotency, lipid and glucose homeostasis, and steroidogenesis. Liver receptor homologue 1 (LRH-1; NR5A2) and steroidogenic factor 1 (SF-1; NR5A1) have therapeutic potential for the treatment of metabolic and neoplastic disease; however, a poor understanding of their ligand regulation has hampered the pursuit of these proteins as pharmaceutical targets. In this study, we dissect how sequence variation among LRH-1 orthologs affects phospholipid (PL) binding and regulation. Both human LRH-1 (hLRH-1) and mouse LRH-1 (mLRH-1) respond to newly discovered medium chain PL agonists to modulate lipid and glucose homeostasis. These PLs activate hLRH-1 by altering receptor dynamics in a newly identified alternate activation function region. Mouse and Drosophila orthologs contain divergent sequences in this region potentially altering PL-driven activation. Structural evidence suggests that these sequence differences in mLRH-1 and Drosophila FTZ-f1 (dmFTZ-f1) confer at least partial ligand independence, making them poor models for hLRH-1 studies; however, the mechanisms of ligand independence remain untested. We show using structural and biochemical methods that the recent evolutionary divergence of the mLRH-1 stabilizes the active conformation in the absence of ligand, yet does not abrogate PL-dependent activation. We also show by mass spectrometry and biochemical assays that FTZ-f1 is incapable of PL binding. This work provides a structural mechanism for the differential tuning of PL sensitivity in NR5A orthologs and supports the use of mice as viable therapeutic models for LRH-1-dependent diseases.
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Affiliation(s)
- Paul M Musille
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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211
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de Vos MGJ, Poelwijk FJ, Battich N, Ndika JDT, Tans SJ. Environmental dependence of genetic constraint. PLoS Genet 2013; 9:e1003580. [PMID: 23825963 PMCID: PMC3694820 DOI: 10.1371/journal.pgen.1003580] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 05/04/2013] [Indexed: 11/25/2022] Open
Abstract
The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.
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212
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Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2013; 2:e00631. [PMID: 23682315 PMCID: PMC3654441 DOI: 10.7554/elife.00631] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/09/2013] [Indexed: 11/28/2022] Open
Abstract
John Maynard Smith compared protein evolution to the game where one word is converted into another a single letter at a time, with the constraint that all intermediates are words: WORD→WORE→GORE→GONE→GENE. In this analogy, epistasis constrains evolution, with some mutations tolerated only after the occurrence of others. To test whether epistasis similarly constrains actual protein evolution, we created all intermediates along a 39-mutation evolutionary trajectory of influenza nucleoprotein, and also introduced each mutation individually into the parent. Several mutations were deleterious to the parent despite becoming fixed during evolution without negative impact. These mutations were destabilizing, and were preceded or accompanied by stabilizing mutations that alleviated their adverse effects. The constrained mutations occurred at sites enriched in T-cell epitopes, suggesting they promote viral immune escape. Our results paint a coherent portrait of epistasis during nucleoprotein evolution, with stabilizing mutations permitting otherwise inaccessible destabilizing mutations which are sometimes of adaptive value. DOI:http://dx.doi.org/10.7554/eLife.00631.001 During evolution, the effect of one mutation on a protein can depend on whether another mutation is also present. This phenomenon is similar to the game in which one word is converted to another word, one letter at a time, subject to the rule that all the intermediate steps are also valid words: for example, the word WORD can be converted to the word GENE as follows: WORD→WORE→GORE→GONE→GENE. In this example, the D must be changed to an E before the W is changed to a G, because GORD is not a valid word. Similarly, during the evolution of a virus, a mutation that helps the virus evade the human immune system might only be tolerated if the virus has acquired another mutation beforehand. This type of mutational interaction would constrain the evolution of the virus, since its capacity to take advantage of the second mutation depends on the first mutation having already occurred. Gong et al. examined whether such interactions have indeed constrained evolution of the influenza virus. Between 1968 and 2007, the nucleoprotein—which acts as a scaffold for the replication of genetic material—in the human H3N2 influenza virus underwent a series of 39 mutations. To test whether all of these mutations could have been tolerated by the 1968 virus, Gong et al. introduced each one individually into the 1968 nucleoprotein. They found that several mutations greatly reduced the fitness of the 1968 virus when introduced on their own, which strongly suggests that these ‘constrained mutations’ became part of the virus’s genetic makeup as a result of interactions with ‘enabling’ mutations. The constrained mutations decreased the stability of the nucleoprotein at high temperatures, while the enabling mutations counteracted this effect. It may, therefore, be possible to identify enabling mutations based on their effects on thermal stability. Intriguingly, the constrained mutations helped the virus overcome one form of human immunity to influenza, suggesting that interactions between mutations might limit the rate at which viruses evolve to evade the immune system. Overall, these results show that interactions among mutations constrain the evolution of the influenza nucleoprotein in a fashion that can be largely understood in terms of protein stability. If the same is true for other proteins and viruses, this work could lead to a deeper understanding of the constraints that govern evolution at the molecular level. DOI:http://dx.doi.org/10.7554/eLife.00631.002
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Affiliation(s)
- Lizhi Ian Gong
- Division of Basic Sciences , Fred Hutchinson Cancer Research Center , Seattle , United States
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213
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Cotterell J, Sharpe J. Mechanistic explanations for restricted evolutionary paths that emerge from gene regulatory networks. PLoS One 2013; 8:e61178. [PMID: 23613807 PMCID: PMC3629181 DOI: 10.1371/journal.pone.0061178] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
The extent and the nature of the constraints to evolutionary trajectories are central issues in biology. Constraints can be the result of systems dynamics causing a non-linear mapping between genotype and phenotype. How prevalent are these developmental constraints and what is their mechanistic basis? Although this has been extensively explored at the level of epistatic interactions between nucleotides within a gene, or amino acids within a protein, selection acts at the level of the whole organism, and therefore epistasis between disparate genes in the genome is expected due to their functional interactions within gene regulatory networks (GRNs) which are responsible for many aspects of organismal phenotype. Here we explore epistasis within GRNs capable of performing a common developmental function--converting a continuous morphogen input into discrete spatial domains. By exploring the full complement of GRN wiring designs that are able to perform this function, we analyzed all possible mutational routes between functional GRNs. Through this study we demonstrate that mechanistic constraints are common for GRNs that perform even a simple function. We demonstrate a common mechanistic cause for such a constraint involving complementation between counter-balanced gene-gene interactions. Furthermore we show how such constraints can be bypassed by means of "permissive" mutations that buffer changes in a direct route between two GRN topologies that would normally be unviable. We show that such bypasses are common and thus we suggest that unlike what was observed in protein sequence-function relationships, the "tape of life" is less reproducible when one considers higher levels of biological organization.
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Affiliation(s)
- James Cotterell
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation, CRG, Barcelona, Spain.
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214
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Cutter AD, Jovelin R, Dey A. Molecular hyperdiversity and evolution in very large populations. Mol Ecol 2013; 22:2074-95. [PMID: 23506466 PMCID: PMC4065115 DOI: 10.1111/mec.12281] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 02/06/2023]
Abstract
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
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215
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Abstract
There is a wide gap between the generation of large-scale biological data sets and more-detailed, structural and mechanistic studies. However, recent studies that explicitly combine data from systems and structural biological approaches are having a profound effect on our ability to predict how mutations and small molecules affect atomic-level mechanisms, disrupt systems-level networks, and ultimately lead to changes in organismal fitness. In fact, we argue that a shared framework for analysis of nonadditive genetic and thermodynamic responses to perturbations will accelerate the integration of reductionist and global approaches. A stronger bridge between these two areas will allow for a deeper and more-complete understanding of complex biological phenomenon and ultimately provide needed breakthroughs in biomedical research.
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Affiliation(s)
- James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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216
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Oka K, Kohno S, Urushitani H, Guillette LJ, Ohta Y, Iguchi T, Katsu Y. Molecular cloning and characterization of the corticoid receptors from the American alligator. Mol Cell Endocrinol 2013; 365:153-61. [PMID: 23127802 DOI: 10.1016/j.mce.2012.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 01/04/2023]
Abstract
Steroid hormones are essential for health in vertebrates. Corticosteroids, for example, have a regulatory role in many physiological functions, such as osmoregulation, respiration, immune responses, stress responses, reproduction, growth, and metabolism. Although extensively studied in mammals and some non-mammalian species, the molecular mechanisms of corticosteroid hormone (glucocorticoids and mineralocorticoids) action are poorly understood in reptiles. Here, we have evaluated hormone receptor-ligand interactions in the American alligator (Alligator mississippiensis), following the isolation of cDNAs encoding a glucocorticoid receptor (GR) and a mineralocorticoid receptor (MR). The full-length alligator GR (aGR) and aMR cDNAs were obtained using 5' and 3' rapid amplification cDNA ends (RACE). The deduced amino acid sequences exhibited high identity to the chicken orthologs (aGR: 83%; aMR: 90%). Using transient transfection assays of mammalian cells, both aGR and aMR proteins displayed corticosteroid-dependent activation of transcription from keto-steroid hormone responsive, murine mammary tumor virus promoters. We further compared the ligand-specifity of human, chicken, Xenopus, and zebrafish GR and MR. We found that the alligator and chicken GR/MR have very similar amino acid sequences, and this translates to very similar ligand specificity. This is the first report of the full-coding regions of a reptilian GR and MR, and the examination of their transactivation by steroid hormones.
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Affiliation(s)
- Kaori Oka
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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217
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Tóth-Petróczy Á, Tawfik DS. Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space. Mol Biol Evol 2013; 30:761-71. [DOI: 10.1093/molbev/mst003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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218
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Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem J 2013; 449:581-94. [DOI: 10.1042/bj20121221] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The present review focuses on the evolution of proteins and the impact of amino acid mutations on function from a structural perspective. Proteins evolve under the law of natural selection and undergo alternating periods of conservative evolution and of relatively rapid change. The likelihood of mutations being fixed in the genome depends on various factors, such as the fitness of the phenotype or the position of the residues in the three-dimensional structure. For example, co-evolution of residues located close together in three-dimensional space can occur to preserve global stability. Whereas point mutations can fine-tune the protein function, residue insertions and deletions (‘decorations’ at the structural level) can sometimes modify functional sites and protein interactions more dramatically. We discuss recent developments and tools to identify such episodic mutations, and examine their applications in medical research. Such tools have been tested on simulated data and applied to real data such as viruses or animal sequences. Traditionally, there has been little if any cross-talk between the fields of protein biophysics, protein structure–function and molecular evolution. However, the last several years have seen some exciting developments in combining these approaches to obtain an in-depth understanding of how proteins evolve. For example, a better understanding of how structural constraints affect protein evolution will greatly help us to optimize our models of sequence evolution. The present review explores this new synthesis of perspectives.
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219
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Ashenberg O, Laub MT. Using analyses of amino Acid coevolution to understand protein structure and function. Methods Enzymol 2013; 523:191-212. [PMID: 23422431 DOI: 10.1016/b978-0-12-394292-0.00009-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Determining which residues of a protein contribute to a specific function is a difficult problem. Analyses of amino acid covariation within a protein family can serve as a useful guide by identifying residues that are functionally coupled. Covariation analyses have been successfully used on several different protein families to identify residues that work together to promote folding, enable protein-protein interactions, or contribute to an enzymatic activity. Covariation is a statistical signal that can be measured in a multiple sequence alignment of homologous proteins. As sequence databases have expanded dramatically, covariation analyses have become easier and more powerful. In this chapter, we describe how functional covariation arises during the evolution of proteins and how this signal can be distinguished from various background signals. We discuss the basic methodology for performing amino acid covariation analysis, using bacterial two-component signal transduction proteins as an example. We provide practical suggestions for each step of the process including assembly of protein sequences, construction of a multiple sequence alignment, measurement of covariation, and analysis of results.
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Affiliation(s)
- Orr Ashenberg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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220
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Miller PW, Clarke DN, Weis WI, Lowe CJ, Nelson WJ. The evolutionary origin of epithelial cell-cell adhesion mechanisms. CURRENT TOPICS IN MEMBRANES 2013; 72:267-311. [PMID: 24210433 PMCID: PMC4118598 DOI: 10.1016/b978-0-12-417027-8.00008-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A simple epithelium forms a barrier between the outside and the inside of an organism, and is the first organized multicellular tissue found in evolution. We examine the relationship between the evolution of epithelia and specialized cell-cell adhesion proteins comprising the classical cadherin/β-catenin/α-catenin complex (CCC). A review of the divergent functional properties of the CCC in metazoans and non-metazoans, and an updated phylogenetic coverage of the CCC using recent genomic data reveal: (1) The core CCC likely originated before the last common ancestor of unikonts and their closest bikont sister taxa. (2) Formation of the CCC may have constrained sequence evolution of the classical cadherin cytoplasmic domain and β-catenin in metazoa. (3) The α-catenin-binding domain in β-catenin appears to be the favored mutation site for disrupting β-catenin function in the CCC. (4) The ancestral function of the α/β-catenin heterodimer appears to be an actin-binding module. In some metazoan groups, more complex functions of α-catenin were gained by sequence divergence in the non-actin-binding (N-, M-) domains. (5) Allosteric regulation of α-catenin may have evolved for more complex regulation of the actin cytoskeleton.
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Affiliation(s)
- Phillip W. Miller
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | | | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | | | - W. James Nelson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
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221
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Olson-Manning CF, Wagner MR, Mitchell-Olds T. Adaptive evolution: evaluating empirical support for theoretical predictions. Nat Rev Genet 2012; 13:867-77. [PMID: 23154809 PMCID: PMC3748133 DOI: 10.1038/nrg3322] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adaptive evolution is shaped by the interaction of population genetics, natural selection and underlying network and biochemical constraints. Variation created by mutation, the raw material for evolutionary change, is translated into phenotypes by flux through metabolic pathways and by the topography and dynamics of molecular networks. Finally, the retention of genetic variation and the efficacy of selection depend on population genetics and demographic history. Emergent high-throughput experimental methods and sequencing technologies allow us to gather more evidence and to move beyond the theory in different systems and populations. Here we review the extent to which recent evidence supports long-established theoretical principles of adaptation.
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Affiliation(s)
- Carrie F. Olson-Manning
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Maggie R. Wagner
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Thomas Mitchell-Olds
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
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222
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Wymore T, Brooks CL. From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation. Comput Struct Biotechnol J 2012; 2:e201209018. [PMID: 24688659 PMCID: PMC3962182 DOI: 10.5936/csbj.201209018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 11/22/2022] Open
Affiliation(s)
- Troy Wymore
- Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213 USA
| | - Charles L. Brooks
- University of Michigan, Department of Chemistry and Biophysics, 930 North University Avenue, Ann Arbor, MI 48109 USA
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223
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Wierer M, Schrey AK, Kühne R, Ulbrich SE, Meyer HHD. A single glycine-alanine exchange directs ligand specificity of the elephant progestin receptor. PLoS One 2012; 7:e50350. [PMID: 23209719 PMCID: PMC3507690 DOI: 10.1371/journal.pone.0050350] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/19/2012] [Indexed: 11/18/2022] Open
Abstract
The primary gestagen of elephants is 5α-dihydroprogesterone (DHP), which is unlike all other mammals studied until now. The level of DHP in elephants equals that of progesterone in other mammals, and elephants are able to bind DHP with similar affinity to progesterone indicating a unique ligand-binding specificity of the elephant progestin receptor (PR). Using site-directed mutagenesis in combination with in vitro binding studies we here report that this change in specificity is due to a single glycine to alanine exchange at position 722 (G722A) of PR, which specifically increases DHP affinity while not affecting binding of progesterone. By conducting molecular dynamics simulations comparing human and elephant PR ligand-binding domains (LBD), we observed that the alanine methyl group at position 722 is able to push the DHP A-ring into a position similar to progesterone. In the human PR, the DHP A-ring position is twisted towards helix 3 of PR thereby disturbing the hydrogen bond pattern around the C3-keto group, resulting in a lower binding affinity. Furthermore, we observed that the elephant PR ligand-binding pocket is more rigid than the human analogue, which probably explains the higher affinity towards both progesterone and DHP. Interestingly, the G722A substitution is not elephant-specific, rather it is also present in five independent lineages of mammalian evolution, suggesting a special role of the substitution for the development of distinct mammalian gestagen systems.
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Affiliation(s)
- Michael Wierer
- Physiology Weihenstephan, Technical University Munich, Freising, Germany.
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224
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Smith SD, Wang S, Rausher MD. Functional evolution of an anthocyanin pathway enzyme during a flower color transition. Mol Biol Evol 2012; 30:602-12. [PMID: 23155005 DOI: 10.1093/molbev/mss255] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Dissecting the genetic basis for the evolution of species differences requires a combination of phylogenetic and molecular genetic perspectives. By mapping the genetic changes and their phenotypic effects onto the phylogeny, it is possible to distinguish changes that may have been directly responsible for a new character state from those that fine tune the transition. Here, we use phylogenetic and functional methods to trace the evolution of substrate specificity in dihydroflavonol-4-reductase (Dfr), an anthocyanin pathway gene known to be involved in the transition from blue to red flowers in Iochroma. Ancestral state reconstruction indicates that three substitutions occurred during the flower color transition, whereas several additional substitutions followed the transition. Comparisons of enzymatic function between ancestral proteins in blue- and red-flowered lineages and proteins from present-day taxa demonstrate that evolution of specificity for red pigment precursors was caused by the first three substitutions, which were fixed by positive selection and which differ from previously documented mutations affecting specificity. Two inferred substitutions subsequent to the initial flower color transition were also adaptive and resulted in an additional increase in specificity for red precursors. Epistatic interactions among both sets of substitutions may have limited the order of substitutions along branches of the phylogeny leading from blue-pigmented ancestors to the present-day red-flowered taxa. These results suggest that the species differences in DFR specificity may arise by a combination of selection on flower color and selection for improved pathway efficiency but that the exact series of genetic changes resulting in the evolution of specificity is likely to be highly contingent on the starting state.
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225
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YOKOYAMA SHOZO. Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision. Bioscience 2012; 62:939-948. [PMID: 23483186 PMCID: PMC3593118 DOI: 10.1525/bio.2012.62.11.3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Natural selection has played an important role in establishing various phenotypes, but the molecular mechanisms of phenotypic adaptation are not well understood. The slow progress is a consequence of mutagenesis experiments in which present-day molecules were used and of the limited scope of statistical methods used to detect adaptive evolution. To fully appreciate phenotypic adaptation, the precise roles of adaptive mutations during phenotypic evolution must be elucidated through the engineering and manipulation of ancestral phenotypes. Experimental and quantum chemical analyses of dim-light vision reveal some surprising results and provide a foundation for a productive study of the adaptive evolution of various phenotypes.
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Affiliation(s)
- SHOZO YOKOYAMA
- Department of Biology at Emory University, in Atlanta, Georgia
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226
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Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet 2012; 8:e1002961. [PMID: 23028368 PMCID: PMC3447958 DOI: 10.1371/journal.pgen.1002961] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022] Open
Abstract
Phenotypes that appear to be conserved could be maintained not only by strong purifying selection on the underlying genetic systems, but also by stabilizing selection acting via compensatory mutations with balanced effects. Such coevolution has been invoked to explain experimental results, but has rarely been the focus of study. Conserved expression driven by the unc-47 promoters of Caenorhabditis elegans and C. briggsae persists despite divergence within a cis-regulatory element and between this element and the trans-regulatory environment. Compensatory changes in cis and trans are revealed when these promoters are used to drive expression in the other species. Functional changes in the C. briggsae promoter, which has experienced accelerated sequence evolution, did not lead to alteration of gene expression in its endogenous environment. Coevolution among promoter elements suggests that complex epistatic interactions within cis-regulatory elements may facilitate their divergence. Our results offer a detailed picture of regulatory evolution in which subtle, lineage-specific, and compensatory modifications of interacting cis and trans regulators together maintain conserved gene expression patterns. Some phenotypes, including gene expression patterns, are conserved between distantly related species. However, the molecular bases of those phenotypes are not necessarily conserved. Instead, regulatory DNA sequences and the proteins with which they interact can change over time with balanced effects, preserving expression patterns and concealing regulatory divergence. Coevolution between interacting molecules makes gene regulation highly species-specific, and it can be detected when the cis-regulatory DNA of one species is used to drive expression in another species. In this way, we identified regions of the C. elegans and C. briggsae unc-47 promoters that have coevolved with the lineage-specific trans-regulatory environments of these organisms. The C. briggsae promoter experienced accelerated sequence change relative to related species. All of this evolution occurred without changing the expression pattern driven by the promoter in its endogenous environment.
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227
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Akashi H, Osada N, Ohta T. Weak selection and protein evolution. Genetics 2012; 192:15-31. [PMID: 22964835 PMCID: PMC3430532 DOI: 10.1534/genetics.112.140178] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 06/11/2012] [Indexed: 01/23/2023] Open
Abstract
The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.
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Affiliation(s)
- Hiroshi Akashi
- Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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228
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Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest. G3-GENES GENOMES GENETICS 2012; 2:1085-93. [PMID: 22973546 PMCID: PMC3429923 DOI: 10.1534/g3.112.002733] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 07/03/2012] [Indexed: 11/18/2022]
Abstract
Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm ‘Random Forest’ to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits—autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.
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229
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Andreani J, Faure G, Guerois R. Versatility and invariance in the evolution of homologous heteromeric interfaces. PLoS Comput Biol 2012; 8:e1002677. [PMID: 22952442 PMCID: PMC3431345 DOI: 10.1371/journal.pcbi.1002677] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into protein-protein interaction prediction. Using a database of 1,024 couples of close and remote heteromeric structural interologs, we studied protein-protein interactions from a structural and evolutionary point of view. We systematically and quantitatively analyzed the conservation of different types of interface contacts. Our study highlights astonishing plasticity regarding polar contacts at complex interfaces. It also reveals that up to a quarter of the residues switch out of the interface when comparing two homologous complexes. Despite such versatility, we identify two important interface descriptors which correlate with an increased conservation in the evolution of interfaces: apolar patches and contacts surrounding anchor residues. These observations hold true even when restricting the dataset to transiently formed complexes. We show that a combination of six features related either to sequence or to geometric properties of interfaces can be used to rank positions likely to share similar contacts between two interologs. Altogether, our analysis provides important tracks for extracting meaningful information from multiple sequence alignments of conserved binding partners and for discriminating near-native interfaces using evolutionary information. Unraveling how interfaces of protein complexes coevolved is of major importance to improve our ability to predict their structures and design novel binders. Proteins whose interaction was maintained throughout evolution generally have their homologs binding in a similar manner while their sequences can have significantly diverged. Constraints holding proteins together should be captured from the growing body of available multiple sequence alignments. However, it remains unclear which features of the interfaces provide most tolerance to mutations and it is unknown whether any invariant properties may help to extract meaningful signals from sequence alignments. To solve this issue, we tackled an unprecedented large scale analysis of more than 1000 non-redundant couples of structural interologs. Structural interologs are pairs of complexes of known structure whose chains are homologs. We quantitatively measured how the networks of contacts varied between two interfaces. Although highly versatile, we found that contact networks were more conserved for residues acting as anchors and for apolar contacts when they are clustered into surface patches. Altogether, our results provide major guidelines for exploiting the wealth of evolutionary information contained in the sequences of binding partners. On those bases we developed a method to predict which residues most likely conserve their contacts.
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Affiliation(s)
- Jessica Andreani
- CEA, iBiTecS, Service de Bioenergetique Biologie Structurale et Mecanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
- CNRS, UMR 8221, Gif sur Yvette, France
- Université Paris Sud, UMR 8221, Orsay, France
| | - Guilhem Faure
- CEA, iBiTecS, Service de Bioenergetique Biologie Structurale et Mecanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
- CNRS, UMR 8221, Gif sur Yvette, France
- Université Paris Sud, UMR 8221, Orsay, France
| | - Raphaël Guerois
- CEA, iBiTecS, Service de Bioenergetique Biologie Structurale et Mecanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
- CNRS, UMR 8221, Gif sur Yvette, France
- Université Paris Sud, UMR 8221, Orsay, France
- * E-mail:
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230
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Li Y, Sturm A, Cunningham P, Bury NR. Evidence for a divergence in function between two glucocorticoid receptors from a basal teleost. BMC Evol Biol 2012; 12:137. [PMID: 22862956 PMCID: PMC3457903 DOI: 10.1186/1471-2148-12-137] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 07/26/2012] [Indexed: 01/17/2023] Open
Abstract
Background Duplicated glucocorticoid receptors (GR) are present in most teleost fish. The evolutionary advantage of retaining two GRs is unclear, as no subtype specific functional traits or physiological roles have been defined. To identify factors driving the retention of duplicate GRs in teleosts, the current study examined GRs in representatives of two basal ray-finned fish taxa that emerged either side of the teleost lineage whole genome duplication event (WGD) event, the acipenseriform, Acipenser ruthenus, (pre-WGD) and the osteoglossimorph, Pantodon buchholzi, (post-WGD). Results The study identified a single GR in A. ruthenus (ArGR) and two GRs in P. buchholzi (PbGR1 and PbGR2). Phylogenetic analyses showed that ArGR formed a distinct branch separate from the teleosts GRs. The teleost GR lineage was subdivded into two sublineages, each of which contained one of the two P. buchholzi GRs. ArGR, PbGR1 and PbGR2 all possess the unique 9 amino acid insert between the zinc-fingers of the DNA-binding domain that is present in one of the teleost GR lineages (GR1), but not the other (GR2). A splice variant of PbGR2 produces an isoform that lacked these 9 amino acids (PbGR2b). Cortisol stimulated transactivation activity of ArGR, PbGR2b and PbGR1 in vitro; with PbGR2b and PbGR1, the glucocorticoid 11-deoxycortisol was a more potent agonist than cortisol. The hormone sensitivity of PbGR2b and PbGR1 differed in the transactivation assay, with PbGR2b having lower EC50 values and greater fold induction. Conclusions The difference in transactivation activity sensitivity between duplicated GRs of P. buchholzi suggests potential functional differences between the paralogs emerged early in the teleost lineage. Given the pleiotropic nature of GR function in vertebrates, this finding is in accordance with the hypothesis that duplicated GRs were potentially retained through subfunctionalisation followed by gene sharing. A 9 amino acid insert in the DNA-binding domain emerged in basal ray-finned fish GRs. However, the presence of a PbGR2 splice variant that lacks this insert, as well as the loss of the exon encoding these amino acids in the genes encoding for other teleost GR2 suggests the selection of two receptors with different DNA-binding domain structures in teleosts.
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Affiliation(s)
- Yi Li
- Nutritional Sciences Research Division, King's College London, Franklin Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
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231
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Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. PLoS Comput Biol 2012; 8:e1002629. [PMID: 22876172 PMCID: PMC3410847 DOI: 10.1371/journal.pcbi.1002629] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 06/18/2012] [Indexed: 11/23/2022] Open
Abstract
Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail. An improved ability to predict realistic backbone changes in response to engineered mutations would be of great utility for the blossoming field of rational protein design. One model that has recently grown in acceptance is the backrub motion, a low-energy dipeptide rotation with single-peptide counter-rotations, that is coupled to dynamic two-state sidechain rotamer jumps, as evidenced by alternate conformations in very high-resolution crystal structures. It has been speculated that backrubs may facilitate sequence changes equally well as rotamer changes. However, backrub-induced shifts and experimental uncertainty are of similar magnitude for backbone atoms in even high-resolution structures, so comparison of wildtype-vs.-mutant crystal structure pairs is not sufficient to directly link backrubs to mutations. In this study, we use two alternative approaches that bypass this limitation. First, we use a quality-filtered structure database to aggregate many examples for precisely defined motifs with single amino acid differences, and find that the effectively amplified backbone differences closely resemble backrubs. Second, we directly apply a provably-accurate, backrub-enabled protein design algorithm to idealized versions of these motifs, and discover that the lowest-energy computed models match the average-coordinate experimental structures. These results support the hypothesis that backrubs participate in natural protein evolution and validate their continued use for design of synthetic proteins. Protein design has the potential to generate useful molecules for medicine and chemistry, including sensors, drugs, and catalysts for arbitrary reactions. When protein design is carried out starting from an experimentally determined structure, as is often the case, one important aspect to consider is backbone flexibility, because in response to a mutation the backbone often must shift slightly to reconcile the new sidechain with its environment. In principle, one may model the backbone in many ways, but not all are physically realistic or experimentally validated. Here we study the "backrub" motion, which has been previously documented in atomic detail, but only for sidechain movements within single structures. By a twopronged approach involving both structural bioinformatics and computation with a principled design algorithm, we demonstrate that backrubs are sufficient to explain the backbone differences between mutation-related sets of very precisely defined motifs from the protein structure database. Our findings illustrate that backrubs are useful for describing evolutionary sequence change and, by extension, suggest that they are also appropriate for rational protein design calculations.
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Affiliation(s)
- Daniel A Keedy
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America.
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232
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Abstract
Plants possess multifunctional and rapidly evolving specialized metabolic enzymes. Many metabolites do not appear to be immediately required for survival; nonetheless, many may contribute to maintaining population fitness in fluctuating and geographically dispersed environments. Others may serve no contemporary function but are produced inevitably as minor products by single enzymes with varying levels of catalytic promiscuity. The dominance of the terrestrial realm by plants likely mirrored expansion of specialized metabolism originating from primary metabolic pathways. Compared with their evolutionarily constrained counterparts in primary metabolism, specialized metabolic enzymes may be more tolerant to mutations normally considered destabilizing to protein structure and function. If this is true, permissiveness may partially explain the pronounced chemodiversity of terrestrial plants.
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233
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Transformation of a transposon into a derived prolactin promoter with function during human pregnancy. Proc Natl Acad Sci U S A 2012; 109:11246-51. [PMID: 22733751 DOI: 10.1073/pnas.1118566109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Transposable elements (TEs) are known to provide DNA for host regulatory functions, but the mechanisms underlying the transformation of TEs into cis-regulatory elements are unclear. In humans two TEs--MER20 and MER39--contribute the enhancer/promoter for decidual prolactin (dPRL), which is dramatically induced during pregnancy. We show that evolution of the strong human dPRL promoter was a multistep process that took millions of years. First, MER39 inserted near MER20 in the primate/rodent ancestor, and then there were two phases of activity enhancement in primates. Through the mapping of causal nucleotide substitutions, we demonstrate that strong promoter activity in apes involves epistasis between transcription factor binding sites (TFBSs) ancestral to MER39 and derived sites. We propose a mode of molecular evolution that describes the process by which MER20/MER39 was transformed into a strong promoter, called "epistatic capture." Epistatic capture is the stabilization of a TFBS that is ancestral but variable in outgroup lineages, and is fixed in the ingroup because of epistatic interactions with derived TFBSs. Finally, we note that evolution of human promoter activity coincides with the emergence of a unique reproductive character in apes, highly invasive placentation. Because prolactin communicates with immune cells during pregnancy, which regulate fetal invasion into maternal tissues, we speculate that ape dPRL promoter activity evolved in response to increased invasiveness of ape fetal tissue.
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234
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Sandhya S, Mudgal R, Jayadev C, Abhinandan KR, Sowdhamini R, Srinivasan N. Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. MOLECULAR BIOSYSTEMS 2012; 8:2076-84. [PMID: 22692068 DOI: 10.1039/c2mb25113b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of 'protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a 'roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.
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Affiliation(s)
- S Sandhya
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560065, India
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235
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Park K, Kim D. Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1484-9. [PMID: 22684088 DOI: 10.1016/j.bbapap.2012.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/01/2012] [Accepted: 05/31/2012] [Indexed: 10/28/2022]
Abstract
Correlated mutation analysis (CMA) has been used to investigate protein functional sites. However, CMA has suffered from low signal-to-noise ratio caused by meaningless phylogenetic signals or structural constraints. We present a new method, Structure-based Correlated Mutation Analysis (SCMA), which encodes coevolution scores into a protein structure network. A path-based network model is adapted to describe information transfer between residues, and the statistical significance is estimated by network shuffling. This model intrinsically assumes that residues in physical contact have a more reliable coevolution score than distant residues, and that coevolution in distant residues likely arises from a series of contacting and coevolving residues. In addition, coevolutionary coupling is statistically controlled to remove the structural effects. When applied to the rhodopsin structure, the SCMA method identified a much higher percentage of functional residues than the typical coevolution score (61% vs. 22%). In addition, statistically significant residues are used to construct the coevolved residue-residue subnetwork. The network has one highly connected node (retinal bound Lys296), indicating that Lys296 can induce and regulate most other coevolved residues in a variety of locations. The coevolved network consists of a few modular clusters which have distinct functional roles. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.
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Affiliation(s)
- Keunwan Park
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
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Lai J, Jin J, Kubelka J, Liberles DA. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. J Mol Biol 2012; 422:442-59. [PMID: 22651983 DOI: 10.1016/j.jmb.2012.05.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/26/2012] [Accepted: 05/22/2012] [Indexed: 12/24/2022]
Abstract
Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity.
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Affiliation(s)
- Jason Lai
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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237
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Koren L, Whiteside D, Fahlman S, Ruckstuhl K, Kutz S, Checkley S, Dumond M, Wynne-Edwards K. Cortisol and corticosterone independence in cortisol-dominant wildlife. Gen Comp Endocrinol 2012; 177:113-9. [PMID: 22449618 DOI: 10.1016/j.ygcen.2012.02.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 02/07/2012] [Accepted: 02/28/2012] [Indexed: 12/12/2022]
Abstract
Species have traditionally been defined as cortisol-dominant or corticosterone-dominant, depending on the glucocorticoid that is reported. To assess the degree of covariance versus independence between cortisol and corticosterone, 245 serum samples belonging to 219 individuals from 18 cortisol-dominant, non-domesticated species (6 mammalian orders) were compared by mass spectrometry. In these samples, which were elevated above baseline, concentration ranges were overlapping for cortisol and corticosterone although cortisol was dominant in every sample except one of 17 bighorn sheep with a corticosterone-biased cortisol-to-corticosterone ratio of 0.17. As expected, cortisol and corticosterone were strongly associated among species (r(2)=0.8; species with high absolute cortisol tend to have high absolute corticosterone concentrations), with wide variation in the species-average cortisol-to-corticosterone ratio (range 7.5-49) and an even wider ratio range across individuals (0.2-341). However, only 9 out of 13 species with >7 individuals showed a positive association between cortisol and corticosterone among individuals, and repeated measures of the cortisol-to-corticosterone ratio within individuals were weakly associated (CV range 3-136%). We conclude that corticosterone, although at lower concentrations, has the potential to signal independently of cortisol, and should be included in integrated endocrine models of stress responses.
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Affiliation(s)
- Lee Koren
- Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada.
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238
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Glembo TJ, Farrell DW, Gerek ZN, Thorpe MF, Ozkan SB. Collective dynamics differentiates functional divergence in protein evolution. PLoS Comput Biol 2012; 8:e1002428. [PMID: 22479170 PMCID: PMC3315450 DOI: 10.1371/journal.pcbi.1002428] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 01/30/2012] [Indexed: 12/29/2022] Open
Abstract
Protein evolution is most commonly studied by analyzing related protein sequences and generating ancestral sequences through Bayesian and Maximum Likelihood methods, and/or by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function. Structural and dynamic evolution have largely been left out of molecular evolution studies. Here we incorporate both structure and dynamics to elucidate the molecular principles behind the divergence in the evolutionary path of the steroid receptor proteins. We determine the likely structure of three evolutionarily diverged ancestral steroid receptor proteins using the Zipping and Assembly Method with FRODA (ZAMF). Our predictions are within ∼2.7 Å all-atom RMSD of the respective crystal structures of the ancestral steroid receptors. Beyond static structure prediction, a particular feature of ZAMF is that it generates protein dynamics information. We investigate the differences in conformational dynamics of diverged proteins by obtaining the most collective motion through essential dynamics. Strikingly, our analysis shows that evolutionarily diverged proteins of the same family do not share the same dynamic subspace, while those sharing the same function are simultaneously clustered together and distant from those, that have functionally diverged. Dynamic analysis also enables those mutations that most affect dynamics to be identified. It correctly predicts all mutations (functional and permissive) necessary to evolve new function and ∼60% of permissive mutations necessary to recover ancestral function. Proteins are remarkable machines of the living systems that show diverse biochemical functions. Biochemical diversity has grown over time via molecular evolution. In order to understand how diversity arose, it is fundamental to understand how the earliest proteins evolved and served as templates for the present diverse proteome. The one sequence - one structure - one function paradigm is being extended to a new view: an ensemble of different conformations in equilibrium can evolve new function and the analysis of inherent structural dynamics is crucial to give a more complete understanding of protein evolution. Therefore, we aim to bring structural dynamics into protein evolution through our zipping and assembly method with FRODA. (ZAMF). We apply ZAMF to simultaneously obtain structures and structural dynamics of three ancestral sequences of steroid receptor proteins. By comparative dynamics analysis among the three ancestral steroid hormone receptors: (i) we show that changes in the structural dynamics indicates functional divergence and (ii) we identify all functionally critical and most of the permissive mutations necessary to evolve new function. Overall, all these findings suggest that conformational dynamics may play an important role where new functions evolve through novel molecular interactions.
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Affiliation(s)
- Tyler J. Glembo
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Daniel W. Farrell
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Z. Nevin Gerek
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona, United States of America
| | - M. F. Thorpe
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona, United States of America
| | - S. Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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239
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Huyet J, Pinon GM, Fay MR, Rafestin-Oblin ME, Fagart J. Structural determinants of ligand binding to the mineralocorticoid receptor. Mol Cell Endocrinol 2012; 350:187-95. [PMID: 21820032 DOI: 10.1016/j.mce.2011.07.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 07/15/2011] [Accepted: 07/17/2011] [Indexed: 11/15/2022]
Abstract
The first and critical step in the mechanism of aldosterone action is its binding to the mineralocorticoid receptor (MR), a member of the nuclear receptor superfamily. Over the last 40 years, numerous studies have attempted to determine the structural determinants of ligand-binding to MR. An initial set of data showed that hsp90 is bound to the receptor via specific regions and maintains it in a ligand-binding competent state. Site-directed mutagenesis and functional studies guided by a 3D model of the MR ligand-binding domain (LBD) made it possible to identify the residues responsible for the high affinity and selectivity for aldosterone, and to characterize the mechanisms of MR activation and inactivation. The recent determination of the X-ray crystal structures of the LBD of the wild-type MR and MR(S810L), which is responsible for a familial form of hypertension, has made it possible to elucidate the peculiar mechanism of activation of MR(S810L) and established a clear structure/activity relationship for steroidal and non-steroidal MR antagonists.
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Affiliation(s)
- Jessica Huyet
- INSERM U773, Centre de Recherche Biomédicale Bichat-Beaujon, CRB3, Paris, France
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240
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Kohn JA, Deshpande K, Ortlund EA. Deciphering modern glucocorticoid cross-pharmacology using ancestral corticosteroid receptors. J Biol Chem 2012; 287:16267-75. [PMID: 22437833 DOI: 10.1074/jbc.m112.346411] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Steroid receptors (SRs) are the largest family of metazoan transcription factors and control genes involved in development, endocrine signaling, reproduction, immunity, and cancer. The entire hormone receptor system is driven by a molecular switch triggered by the binding of small lipophilic ligands. This makes the SRs ideal pharmaceutical targets, yet even the best clinically approved synthetic steroidal agonists are prone to cross-reactivity and off-target pharmacology. The mechanism underlying this promiscuity is derived from the fact that SRs share common structural features derived from their evolutionary relationship. More often than not, rational attempts to probe SR drug selectivity via mutagenesis fail even when high quality structural and functional data are available due to the fact that important mutations often result in nonfunctional receptors. This highlights the fact that SRs suffer from instability, preventing in-depth mutational analysis and hampering crystallization of key receptor-ligand complexes. We have taken a unique approach to address this problem by using a resurrected ancestral protein to determine the structure of a previously intractable complex and identified the structural mechanisms that confer activation and selectivity for a widely used glucocorticoid, mometasone furoate. Moreover, we have identified a single residue located outside of the ligand-binding pocket that controls mometasone furoate antagonism versus agonism in the human mineralocorticoid receptor.
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Affiliation(s)
- Jeffrey A Kohn
- Department of Biochemistry and the Discovery and Developmental Therapeutics Program, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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241
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242
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Huang R, Hippauf F, Rohrbeck D, Haustein M, Wenke K, Feike J, Sorrelle N, Piechulla B, Barkman TJ. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc Natl Acad Sci U S A 2012; 109:2966-71. [PMID: 22315396 PMCID: PMC3286912 DOI: 10.1073/pnas.1019605109] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (k(cat)/K(M)) for competing substrates, even though adaptive substitutions may affect K(M) and k(cat) separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities.
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Affiliation(s)
- Ruiqi Huang
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008; and
| | - Frank Hippauf
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Diana Rohrbeck
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Maria Haustein
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Katrin Wenke
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Janie Feike
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Noah Sorrelle
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008; and
| | - Birgit Piechulla
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Todd J. Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008; and
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243
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Buzón V, Carbó LR, Estruch SB, Fletterick RJ, Estébanez-Perpiñá E. A conserved surface on the ligand binding domain of nuclear receptors for allosteric control. Mol Cell Endocrinol 2012; 348:394-402. [PMID: 21878368 DOI: 10.1016/j.mce.2011.08.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 08/08/2011] [Accepted: 08/12/2011] [Indexed: 12/26/2022]
Abstract
Nuclear receptors (NRs) form a large superfamily of transcription factors that participate in virtually every key biological process. They control development, fertility, gametogenesis and are misregulated in many cancers. Their enormous functional plasticity as transcription factors relates in part to NR-mediated interactions with hundreds of coregulatory proteins upon ligand (e.g., hormone) binding to their ligand binding domains (LBD), or following covalent modification. Some coregulator association relates to the distinct residues that shape a coactivator binding pocket termed AF-2, a surface groove that primarily determines the preference and specificity of protein-protein interactions. However, the highly conserved AF-2 pocket in the NR superfamily appears to be insufficient to account for NR subtype specificity leading to fine transcriptional modulation in certain settings. Additional protein-protein interaction surfaces, most notably on their LBD, may contribute to modulating NR function. NR coregulators and chaperones, normally much larger than the NR itself, may also bind to such interfaces. In the case of the androgen receptor (AR) LBD surface, structural and functional data highlighted the presence of another site named BF-3, which lies at a distinct but topographically adjacent surface to AF-2. AR BF-3 is a hot spot for mutations involved in prostate cancer and androgen insensitivity syndromes, and some FDA-approved drugs bind at this site. Structural studies suggested an allosteric relationship between AF-2 and BF-3, as occupancy of the latter affected coactivator recruitment to AF-2. Physiological relevant partners of AR BF-3 have not been described as yet. The newly discovered site is highly conserved among the steroid receptors subclass, but is also present in other NRs. Several missense mutations in the BF-3 regions of these human NRs are implicated in pathology and affect their function in vitro. The fact that AR BF-3 pocket is a druggable site evidences its pharmacological potential. Compounds that may affect allosterically NR function by binding to BF-3 open promising avenues to develop type-specific NR modulators.
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Affiliation(s)
- Víctor Buzón
- Institut de Biomedicina, Universitat de Barcelona, Baldiri Reixac 15-21, Parc Científic de Barcelona, 08028 Barcelona, Spain
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244
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The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. J Mol Evol 2012; 74:1-34. [PMID: 22210458 DOI: 10.1007/s00239-011-9480-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 12/12/2011] [Indexed: 12/20/2022]
Abstract
The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.
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245
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Faure G, Andreani J, Guerois R. InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res 2012; 40:D847-56. [PMID: 22053089 PMCID: PMC3245184 DOI: 10.1093/nar/gkr845] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/15/2011] [Accepted: 09/21/2011] [Indexed: 11/12/2022] Open
Abstract
Capturing how the structures of interacting partners evolved at their binding interfaces is a fundamental issue for understanding interactomes evolution. In that scope, the InterEvol database was designed for exploring 3D structures of homologous interfaces of protein complexes. For every chain forming a complex in the protein data bank (PDB), close and remote structural interologs were identified providing essential snapshots for studying interfaces evolution. The database provides tools to retrieve and visualize these structures. In addition, pre-computed multiple sequence alignments of most likely interologs retrieved from a wide range of species can be downloaded to enrich the analysis. The database can be queried either directly by pdb code or keyword but also from the sequence of one or two partners. Interologs multiple sequence alignments can also be recomputed online with tailored parameters using the InterEvolAlign facility. Last, an InterEvol PyMol plugin was developed to improve interactive exploration of structures versus sequence alignments at the interfaces of complexes. Based on a series of automatic methods to extract structural and sequence data, the database will be monthly updated. Structures coordinates and sequence alignments can be queried and downloaded from the InterEvol web interface at http://biodev.cea.fr/interevol/.
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Affiliation(s)
- Guilhem Faure
- CEA, iBiTecS, F-91191 Gif sur Yvette and CNRS, F-91191 Gif sur Yvette, France
| | - Jessica Andreani
- CEA, iBiTecS, F-91191 Gif sur Yvette and CNRS, F-91191 Gif sur Yvette, France
| | - Raphaël Guerois
- CEA, iBiTecS, F-91191 Gif sur Yvette and CNRS, F-91191 Gif sur Yvette, France
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246
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Baker ME, Uh KY, Asnaashari P. 3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone. Steroids 2011; 76:1451-7. [PMID: 21840328 DOI: 10.1016/j.steroids.2011.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/17/2022]
Abstract
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone. Only 11-deoxycortisol has high affinity [K(d) ~ 3 nM] for the corticoid receptor [CR] in lamprey gill cytosol. To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone. These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17α-hydroxyl on 11-deoxycortisol. Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR]. Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5. Mutant human MR and GR containing a van der Waals contact between helix 3 and helix 5 display enhanced responses to progesterone and glucocorticoids, respectively. We propose that this interaction was present in the CR and lost during the evolution of the MR and GR, leading to changes in their response to progesterone and corticosteroids, respectively.
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Affiliation(s)
- Michael E Baker
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0693, USA.
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247
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Abstract
Although the mechanisms by which complex cellular features evolve constitute one of the great unsolved problems of evolutionary biology, it is clear that the emergence of new protein-protein interactions, often accompanied by the diversification of duplicate genes, is involved. Using information on the levels of protein multimerization in major phylogenetic groups as a guide to the patterns that must be explained and relying on results from population-genetic theory to define the relative plausibility of alternative evolutionary pathways, a framework for understanding the evolution of dimers is developed. The resultant theory demonstrates that the likelihoods of alternative pathways for the emergence of protein complexes depend strongly on the effective population size. Nonetheless, it is equally clear that further advancements in this area will require comparative studies on the fitness consequences of alternative monomeric and dimeric proteins.
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248
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O'Donnell CW, Waldispühl J, Lis M, Halfmann R, Devadas S, Lindquist S, Berger B. A method for probing the mutational landscape of amyloid structure. ACTA ACUST UNITED AC 2011; 27:i34-42. [PMID: 21685090 PMCID: PMC3117379 DOI: 10.1093/bioinformatics/btr238] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods. Results: We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aβ and its highly-toxic ‘Iowa’ mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments. Availability: Our tool is publically available on the web at http://amyloid.csail.mit.edu/. Contact:lindquist_admin@wi.mit.edu; bab@csail.mit.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Charles W O'Donnell
- Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA
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249
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Peralta H, Guerrero G, Aguilar A, Mora J. Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins. Biol Direct 2011; 6:48. [PMID: 21970442 PMCID: PMC3198989 DOI: 10.1186/1745-6150-6-48] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 10/04/2011] [Indexed: 12/03/2022] Open
Abstract
Background Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements. Results We analyzed 7080 genes (five groups of 1416 orthologs each) from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen). We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS) and nonsynonymous (dN) substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition), we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive values of polarity, volume and electrostatic charge. Conclusions These findings revealed that even when orthologs perform the same function in each genomic background, their sequences reveal important evolutionary tendencies and differences related to adaptation. This article was reviewed by: Dr. Purificación López-García, Prof. Jeffrey Townsend (nominated by Dr. J. Peter Gogarten), and Ms. Olga Kamneva.
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Affiliation(s)
- Humberto Peralta
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo, postal 565-A, Cuernavaca, Morelos, México
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250
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Konno A, Kitagawa A, Watanabe M, Ogawa T, Shirai T. Tracing protein evolution through ancestral structures of fish galectin. Structure 2011; 19:711-21. [PMID: 21565705 DOI: 10.1016/j.str.2011.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 02/08/2011] [Accepted: 02/16/2011] [Indexed: 11/16/2022]
Abstract
Ancestral structures of fish galectins (congerins) were determined. The extant isoforms I and II of congerin are the components of a fish biological defense system and have rapidly differentiated under natural selection pressure, by which congerin I has experienced a protein-fold evolution. The dimer structure of the ancestral congerin demonstrated intermediate features of the extant isoforms. The protein-fold evolution was not observed in the ancestral structure, indicating it specifically occurred in congerin I lineage. Details of hydrogen bonding pattern at the dimer interface and the carbohydrate-binding site of the ancestor were different from the current proteins. The differences implied these proteins were under selection pressure for stabilizing dimer structure and differentiation in carbohydrate specificity. The ancestor had rather low cytotoxic activity than offspring, indicating selection was made to enhance this activity of congerins. Combined with functional analyses, the structure revealed atomic details of the differentiation process of the proteins.
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Affiliation(s)
- Ayumu Konno
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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