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  • 1
    Publication Date: 2009-09-26
    Description: The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bridgham, Jamie T -- Ortlund, Eric A -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Sep 24;461(7263):515-9. doi: 10.1038/nature08249.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779450" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CHO Cells ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; Epistasis, Genetic ; *Evolution, Molecular ; Hormones/metabolism ; *Models, Biological ; Models, Molecular ; Mutation/genetics ; Protein Engineering ; Receptors, Glucocorticoid/*chemistry/*genetics/metabolism ; Sequence Alignment ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2006-04-08
    Description: According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system-the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor-evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation-recruitment of an older molecule, previously constrained for a different role, into a new functional complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bridgham, Jamie T -- Carroll, Sean M -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 7;312(5770):97-101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601189" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/chemistry/*metabolism ; Amino Acid Substitution ; Animals ; Bayes Theorem ; Binding Sites ; Desoxycorticosterone/metabolism ; *Evolution, Molecular ; Gene Duplication ; Hagfishes ; Hydrocortisone/metabolism ; Lampreys ; Ligands ; Mutation ; Perciformes ; Phylogeny ; Rats ; Receptors, Glucocorticoid/chemistry/genetics/metabolism ; Receptors, Mineralocorticoid/chemistry/*genetics/*metabolism ; Receptors, Steroid/chemistry/*genetics/*metabolism ; Skates (Fish)
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2003-09-23
    Description: Receptors for sex and adrenal steroid hormones are absent from fully sequenced invertebrate genomes and have not been recovered from other invertebrates. Here we report the isolation of an estrogen receptor ortholog from the mollusk Aplysia californica and the reconstruction, synthesis, and experimental characterization of functional domains of the ancestral protein from which all extant steroid receptors (SRs) evolved. Our findings indicate that SRs are extremely ancient and widespread, having diversified from a primordial gene before the origin of bilaterally symmetric animals, and that this ancient receptor had estrogen receptor-like functionality. This gene was lost in the lineage leading to arthropods and nematodes and became independent of hormone regulation in the Aplysia lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thornton, Joseph W -- Need, Eleanor -- Crews, David -- 41770/PHS HHS/ -- New York, N.Y. -- Science. 2003 Sep 19;301(5640):1714-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA. joet@uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14500980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aplysia/chemistry/genetics/*metabolism ; Biological Evolution ; CHO Cells ; Cloning, Molecular ; Cricetinae ; DNA/metabolism ; Estrogens/*metabolism/pharmacology ; *Evolution, Molecular ; Gene Duplication ; Humans ; Ligands ; Likelihood Functions ; Molecular Sequence Data ; Mutation ; *Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Receptors, Estrogen/chemistry/genetics/isolation & purification/*metabolism ; Receptors, Steroid/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Steroids/metabolism/pharmacology ; Transcription, Genetic ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-01-11
    Description: Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine--the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump--increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979732/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finnigan, Gregory C -- Hanson-Smith, Victor -- Stevens, Tom H -- Thornton, Joseph W -- R01 GM038006/GM/NIGMS NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- R01-GM38006/GM/NIGMS NIH HHS/ -- T32-GM007257/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jan 9;481(7381):360-4. doi: 10.1038/nature10724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22230956" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology ; *Evolution, Molecular ; Extinction, Biological ; Fungi/classification/*enzymology/genetics ; Gene Duplication ; *Models, Biological ; Mutagenesis ; Phylogeny ; Protein Conformation ; Saccharomyces cerevisiae/enzymology ; Vacuolar Proton-Translocating ATPases/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-06-17
    Description: Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447330/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447330/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harms, Michael J -- Thornton, Joseph W -- F32-GM090650/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM104397/GM/NIGMS NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- R01-GM104397/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Aug 14;512(7513):203-7. doi: 10.1038/nature13410. Epub 2014 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute of Molecular Biology and Department of Chemistry &Biochemistry, University of Oregon, Eugene, Oregon 97403, USA [2] Departments of Human Genetics and Ecology &Evolution, University of Chicago, Chicago, Illinois 60637, USA. ; 1] Departments of Human Genetics and Ecology &Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24930765" target="_blank"〉PubMed〈/a〉
    Keywords: Biophysics ; *Evolution, Molecular ; Genotype ; Mutation/genetics ; Protein Conformation ; Protein Stability ; Receptors, Glucocorticoid/*chemistry/*genetics ; Saccharomyces cerevisiae ; Substrate Specificity ; Two-Hybrid System Techniques
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2007-08-19
    Description: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ortlund, Eric A -- Bridgham, Jamie T -- Redinbo, Matthew R -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM081592-01/GM/NIGMS NIH HHS/ -- R01 GM081592-02/GM/NIGMS NIH HHS/ -- R01-DK622229/DK/NIDDK NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702911" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Crystallography, X-Ray ; Epistasis, Genetic ; *Evolution, Molecular ; Humans ; Hydrocortisone/metabolism ; Ligands ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/*chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/*chemistry/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 110 (1963), S. 0 
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 30 (1965), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The influence of breed, sex, and fatness on the quantity and eating quality of loins from 119 Duroc and 111 Yorkshire pigs was studied. Duroc pigs had significantly more intramuscular fat, smaller longissimus dorsi area, more tender, juicier loins, and less separable lean in the ham than Yorkshire pigs. Among Durocs, barrows had more desirable lean flavor than gilts. Among Yorkshires, barrows had more desirable fat flavor than gilts. In both breeds, an increase in backfat thickness was accompanied by a significant linear decrease in separable lean and increase in separable fat of the ham. Correlations among quantity indices and eating quality indicated that indices of quantity were not related to eating quality.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 30 (1965), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Certain cross-sectional variations in tenderness were studied among 97 pork loin roasts by panel, Warner-Bratzler shear, and the slice tenderness evaluator (STE). This instrument, used with a universal testing machine and load cell, first punctures and then shears off circular meat wafers 3/8-inch in diameter. Longissimus dorsi (loin-eye) slices from heated roasts were graphically partitioned into six locations (two each from the dorsal, medial, and lateral areas) and resistances to STE puncture and shear were recorded. The lateral locations were the most tender, and medial locations the least tender. Correlation of panel scores with STE values was greatest for the toughest areas. Simple correlations between STE values and panel score were highly significant, with stronger relationships being noted between panel and STE shear. The noticeable difference in tenderness observed among the six pork loin-eye locations emphasizes the importance of careful and consistent sampling methods.
    Type of Medium: Electronic Resource
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  • 10
    Publication Date: 2013-06-24
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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