scholarly journals The many nuanced evolutionary consequences of duplicated genes

2018 ◽  
Author(s):  
Ashley I. Teufel ◽  
Mackenzie M. Johnson ◽  
Jon M. Laurent ◽  
Aashiq H. Kachroo ◽  
Edward M. Marcotte ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Protein Structures ◽  
Evolutionary Divergence ◽  
Functional Changes ◽  
Binding Interface ◽  
Evolutionary Trajectories ◽  
Conventional Models ◽  
The Many ◽  
Evolutionary Consequences ◽  
Dosage Imbalance

AbstractGene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub- or neofunctionalizaton, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners. We explore this hypothesis by in-silico evolution of a heterodimer when one member of the interacting pair is duplicated. We examine how a range of selection pressures and protein structures leads to differential patterns of evolutionary divergence. We find that a surprising number of distinct evolutionary trajectories can be observed even in a simple three member system. Further, we observe that selection to correct dosage imbalance can affect the evolution of the initial function in several unexpected ways. For example, if a duplicate is under selective pressure to avoid binding its original binding partner, this can lead to changes in the binding interface of a non-duplicated interacting partner to exclude the duplicate. Hence, independent of the fate of the duplicate, its presence can impact how the original function operates. Additionally, we introduce a conceptual framework to describe how interacting partners cope with dosage imbalance after duplication. Contextualizing our results within this framework reveals that the evolutionary path taken by a duplicate’s interacting partners is highly stochastic in nature. Consequently, the fate of duplicate genes may not only be controlled by their own ability to accumulate mutations but also by how interacting partners cope with them.

scholarly journals The Many Nuanced Evolutionary Consequences of Duplicated Genes

2018 ◽  
Vol 36 (2) ◽  
pp. 304-314 ◽  
Author(s):  
Ashley I Teufel ◽  
Mackenzie M Johnson ◽  
Jon M Laurent ◽  
Aashiq H Kachroo ◽  
Edward M Marcotte ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Protein Structures ◽  
Evolutionary Divergence ◽  
Functional Changes ◽  
Binding Interface ◽  
Evolutionary Trajectories ◽  
Conventional Models ◽  
The Many ◽  
Evolutionary Consequences ◽  
Dosage Imbalance

Abstract Gene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub or neofunctionalization, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners. We explore this hypothesis by in silico evolution of a heterodimer when one member of the interacting pair is duplicated. We examine how a range of selection pressures and protein structures leads to differential patterns of evolutionary divergence. We find that a surprising number of distinct evolutionary trajectories can be observed even in a simple three member system. Further, we observe that selection to correct dosage imbalance can affect the evolution of the initial function in several unexpected ways. For example, if a duplicate is under selective pressure to avoid binding its original binding partner, this can lead to changes in the binding interface of a nonduplicated interacting partner to exclude the duplicate. Hence, independent of the fate of the duplicate, its presence can impact how the original function operates. Additionally, we introduce a conceptual framework to describe how interacting partners cope with dosage imbalance after duplication. Contextualizing our results within this framework reveals that the evolutionary path taken by a duplicate’s interacting partners is highly stochastic in nature. Consequently, the fate of duplicate genes may not only be controlled by their own ability to accumulate mutations but also by how interacting partners cope with them.

scholarly journals Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria

2017 ◽  
Author(s):  
Xiaowei Jiang ◽  
Mario A. Fares
Keyword(s):  
Pathogenic Bacteria ◽  
Atp Hydrolysis ◽  
Functional Divergence ◽  
Evolutionary Divergence ◽  
Ecological Diversity ◽  
Secretion Systems ◽  
Membrane Pore ◽  
Functional Changes ◽  
Ecological Diversification ◽  
Ecological Adaptations

AbstractBacteria interact with their environment through the secretion of a specific set of proteins (known as secretome) through various secretion systems. Molecular modifications of these secretion systems may lead to the emergence of new bacterial-environment interactions, although this remains unexplored. In this study we investigate the possible link between molecular and functional changes in secretion proteins and the ecological diversity of bacteria. We studied functional modifications in secretion proteins by identifying events of functional evolutionary divergence—that is, changes at the molecular level that have driven changes of protein’s function. We present data supporting that these functional diversifications occurred in essential secretion proteins in bacteria. In particular, functional divergence of the two most important secretion proteins SecA and SecY in pathogenic bacteria suggests that molecular changes at these proteins are responsible for their adaptations to the host. Functional divergence has mainly occurred at protein domains involved in ATP hydrolysis in SecA and membrane pore formation in SecY. This divergence is stronger in pathogenic bacteria for protein copies resulting from the duplication of SecA/SecY, known as SecA2/SecY2. In concert with these results, we find that the secretome of bacteria with the strongest functional divergence is enriched for proteins specialized in the interaction with specific environments. We unravel evolutionary signatures that link mutations at secretion proteins to the ecological diversification of bacteria.

scholarly journals Evolutionary inevitability of sexual antagonism

2014 ◽  
Vol 281 (1776) ◽  
pp. 20132123 ◽  
Author(s):  
Tim Connallon ◽  
Andrew G. Clark
Keyword(s):  
Sex Differences ◽  
Natural Populations ◽  
Evolutionary Divergence ◽  
Sexual Antagonism ◽  
Evolutionary Theories ◽  
Sex Effects ◽  
Evolutionary Trajectories ◽  
Males And Females ◽  
Evolutionary Consequences

Sexual antagonism, whereby mutations are favourable in one sex and disfavourable in the other, is common in natural populations, yet the root causes of sexual antagonism are rarely considered in evolutionary theories of adaptation. Here, we explore the evolutionary consequences of sex-differential selection and genotype-by-sex interactions for adaptation in species with separate sexes. We show that sexual antagonism emerges naturally from sex differences in the direction of selection on phenotypes expressed by both sexes or from sex-by-genotype interactions affecting the expression of such phenotypes. Moreover, modest sex differences in selection or genotype-by-sex effects profoundly influence the long-term evolutionary trajectories of populations with separate sexes, as these conditions trigger the evolution of strong sexual antagonism as a by-product of adaptively driven evolutionary change. The theory demonstrates that sexual antagonism is an inescapable by-product of adaptation in species with separate sexes, whether or not selection favours evolutionary divergence between males and females.

scholarly journals Spanning the gap: unraveling RSC dynamics in vivo

2021 ◽  
Author(s):  
Heinz Neumann ◽  
Bryan J. Wilkins
Keyword(s):  
Cell Cycle ◽  
Posttranslational Modifications ◽  
Transcriptional Activation ◽  
Binding Mode ◽  
Binding Modes ◽  
Binding Domains ◽  
Binding Interface ◽  
The Many ◽  
And Function

AbstractMultiple reports over the past 2 years have provided the first complete structural analyses for the essential yeast chromatin remodeler, RSC, providing elaborate molecular details for its engagement with the nucleosome. However, there still remain gaps in resolution, particularly within the many RSC subunits that harbor histone binding domains.Solving contacts at these interfaces is crucial because they are regulated by posttranslational modifications that control remodeler binding modes and function. Modifications are dynamic in nature often corresponding to transcriptional activation states and cell cycle stage, highlighting not only a need for enriched spatial resolution but also temporal understanding of remodeler engagement with the nucleosome. Our recent work sheds light on some of those gaps by exploring the binding interface between the RSC catalytic motor protein, Sth1, and the nucleosome, in the living nucleus. Using genetically encoded photo-activatable amino acids incorporated into histones of living yeast we are able to monitor the nucleosomal binding of RSC, emphasizing the regulatory roles of histone modifications in a spatiotemporal manner. We observe that RSC prefers to bind H2B SUMOylated nucleosomes in vivo and interacts with neighboring nucleosomes via H3K14ac. Additionally, we establish that RSC is constitutively bound to the nucleosome and is not ejected during mitotic chromatin compaction but alters its binding mode as it progresses through the cell cycle. Our data offer a renewed perspective on RSC mechanics under true physiological conditions.

scholarly journals Functional divergence of bitter taste receptors in a nectar-feeding bird

2019 ◽  
Vol 15 (9) ◽  
pp. 20190461 ◽  
Author(s):  
Yi Wang ◽  
Hengwu Jiao ◽  
Peihua Jiang ◽  
Huabin Zhao
Keyword(s):  
Secondary Metabolites ◽  
Bitter Taste ◽  
Functional Divergence ◽  
Taste Receptor ◽  
Bitter Taste Receptor ◽  
Functional Changes ◽  
Nectar Feeding ◽  
Gene Copies ◽  
Plant Pollinator ◽  
Higher Sensitivity

Nectar may contain many secondary metabolites that are commonly toxic and bitter-tasting. It has been hypothesized that such bitter-tasting secondary metabolites might keep the nectar exclusive to only a few pollinators. To test this hypothesis, we examined functional changes of bitter taste receptor genes ( Tas2r s) in a species of nectar-feeding bird (Anna's hummingbird) by comparing these genes with those from two closely related insect-feeding species (chimney swift and chuck-will's widow). We previously identified a larger number of Tas2r s in the hummingbird than in its close insectivorous relatives. In the present study, we demonstrate higher sensitivity and new functions in the hummingbird Tas2r gene copies generated by a lineage-specific duplication, which has been shaped by positive selection. These results suggest that the bitter taste may lead to increased sensitivities and specialized abilities of the hummingbird to detect bitter-tasting nectar. Moreover, this study potentially supports the hypothesis that bitter-tasting nectar may have been specialized for some pollinators, thus enforcing plant–pollinator mutualism.

scholarly journals ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Rocha ◽  
Jorge Vieira ◽  
Noé Vázquez ◽  
Hugo López-Fernández ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Structures ◽  
Interaction Strength ◽  
Terminal Region ◽  
Spinocerebellar Ataxia Type ◽  
Wild Type ◽  
Binding Interface ◽  
Strength Of Interaction ◽  
The Difference ◽  
Polyq Expansion

Abstract Background Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded (82Q) than the wt (29Q) protein. Methods To understand how the expanded polyQ affects PPI, protein structures were predicted for wt and expanded ATXN1, as well as, for 71 ATXN1 interactors. Then, the binding surfaces of wt and expanded ATXN1 with the reported interactors were inferred. Results Our data supports that the polyQ expansion alters the ATXN1 conformation and that it enhances the strength of interaction with ATXN1 partners. For both ATXN1 variants, the number of residues at the predicted binding interface are greater after the polyQ, mainly due to the AXH domain. Moreover, the difference in the interaction strength of the ATXN1 variants was due to an increase in the number of interactions at the N-terminal region, before the polyQ, for the expanded form. Conclusions There are three regions at the AXH domain that are essential for ATXN1 PPI. The N-terminal region is responsible for the strength of the PPI with the ATXN1 variants. How the predicted motifs in this region affect PPI is discussed, in the context of ATXN1 post-transcriptional modifications.

The Role of MC1R in Speciation & Phylogeny

2013 ◽  
Vol 75 (9) ◽  
pp. 670-676 ◽  
Author(s):  
Susan Offner
Keyword(s):  
G Protein ◽  
Point Mutation ◽  
Solomon Island ◽  
G Protein Coupled Receptors ◽  
Ancestral Population ◽  
Mc1r Gene ◽  
The Many ◽  
Evolutionary Consequences ◽  
G Protein Coupled

A point mutation in the MC1R gene, a G-protein-coupled receptor, has been found that could have led to the formation of two subspecies of Solomon Island flycatcher from a single ancestral population. I discuss the many roles that G-protein-coupled receptors play in vertebrate physiology and how one particular point mutation can have enormous evolutionary consequences.

scholarly journals Evolution of regulatory signatures in primate cortical neurons at cell-type resolution

2020 ◽  
Vol 117 (45) ◽  
pp. 28422-28432
Author(s):  
Alexey Kozlenkov ◽  
Marit W. Vermunt ◽  
Pasha Apontes ◽  
Junhao Li ◽  
Ke Hao ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Brain Evolution ◽  
Cell Types ◽  
Regulatory Elements ◽  
Autism Spectrum ◽  
Projection Neurons ◽  
Evolutionary Divergence ◽  
Cell Type ◽  
Tissue Samples ◽  
Functional Changes

The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype–specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergoes subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type–dependent gene-expression programs, and provides a resource for further exploration of human brain evolution and function.

Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?

1980 ◽  
Vol 13 (3) ◽  
pp. 339-386 ◽  
Author(s):  
O. B. Ptitsyn ◽  
A. V. Finkelstein
Keyword(s):  
Serine Proteases ◽  
Protein Structures ◽  
Three Dimensional ◽  
Sperm Whale ◽  
Globular Protein ◽  
Dimensional Structure ◽  
Evolutionary Divergence ◽  
Functional Convergence ◽  
Primary Structures ◽  
Sperm Whale Myoglobin

(A) Evolutionary similarities of protein structures Two decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrew et al. 1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blake et al. 1965), ribonuclease (Kartha, Bello & Harker, 1967), chymotrypsin (Matthews et al. 1967), carboxypeptidase (Lipscomb et al. 1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew & Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton & Watson, 1970) and trypsin (Stroud, Kay & Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.

scholarly journals The protein structures that shape caspase activity, specificity, activation and inhibition

2004 ◽  
Vol 384 (2) ◽  
pp. 201-232 ◽  
Author(s):  
Pablo FUENTES-PRIOR ◽  
Guy S. SALVESEN
Keyword(s):  
Catalytic Mechanism ◽  
Protein Structures ◽  
Limited Proteolysis ◽  
Point Of View ◽  
Coagulation Cascade ◽  
Structural Basis ◽  
Apoptotic Pathway ◽  
Naturally Occurring ◽  
The Many ◽  
Apoptosis Regulation

The death morphology commonly known as apoptosis results from a post-translational pathway driven largely by specific limited proteolysis. In the last decade the structural basis for apoptosis regulation has moved from nothing to ‘quite good’, and we now know the fundamental structures of examples from the initiator phase, the pre-mitochondrial regulator phase, the executioner phase, inhibitors and their antagonists, and even the structures of some substrates. The field is as well advanced as the best known of proteolytic pathways, the coagulation cascade. Fundamentally new mechanisms in protease regulation have been disclosed. Structural evidence suggests that caspases have an unusual catalytic mechanism, and that they are activated by apparently unrelated events, depending on which position in the apoptotic pathway they occupy. Some naturally occurring caspase inhibitors have adopted classic inhibition strategies, but other have revealed completely novel mechanisms. All of the structural and mechanistic information can, and is, being applied to drive therapeutic strategies to combat overactivation of apoptosis in degenerative disease, and underactivation in neoplasia. We present a comprehensive review of the caspases, their regulators and inhibitors from a structural and mechanistic point of view, and with an aim to consolidate the many threads that define the rapid growth of this field.

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