scholarly journals Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 352 ◽  
Author(s):  
Noel Mesa-Torres ◽  
Isabel Betancor-Fernández ◽  
Elisa Oppici ◽  
Barbara Cellini ◽  
Eduardo Salido ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Protein Quality ◽  
Phenotypic Variability ◽  
Conformational Stability ◽  
Enzyme Inactivation ◽  
Human Populations ◽  
Loss Of Function ◽  
Conformational Diseases ◽  
Adaptive Mutations ◽  
Models Of Disease

Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.

scholarly journals Chemical Chaperone and Inhibitor Discovery: Potential Treatments for Protein Conformational Diseases

2007 ◽  
Vol 1 ◽  
pp. PMC.S212 ◽  
Author(s):  
Jian-Hua Zhao ◽  
Hsuan-Liang Liu ◽  
Hsin-Yi Lin ◽  
Chih-Hung Huang ◽  
Hsu-Wei Fang ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Misfolding ◽  
Protein Quality ◽  
Amyloid Formation ◽  
Loss Of Function ◽  
Chemical Chaperone ◽  
Conformational Diseases ◽  
Chemical Chaperones ◽  
Theoretical Approaches ◽  
Protein Quality Control System

Protein misfolding and aggregation cause a large number of neurodegenerative diseases in humans due to (i) gain of function as observed in Alzheimer's disease, Huntington's disease, Parkinson's disease, and Prion's disease or (ii) loss of function as observed in cystic fibrosis and α1-antitrypsin deficiency. These misfolded proteins could either lead to the formation of harmful amyloids that become toxic for the cells or to be recognized and prematurely degraded by the protein quality control system. An increasing number of studies has indicated that some low-molecular-weight compounds named as chemical chaperones can reverse the mislocalization and/or aggregation of proteins associated with human conformational diseases. These small molecules are thought to non-selectively stabilize proteins and facilitate their folding. In this review, we summarize the probable mechanisms of protein conformational diseases in humans and the use of chemical chaperones and inhibitors as potential therapeutic agents against these diseases. Furthermore, recent advanced experimental and theoretical approaches underlying the detailed mechanisms of protein conformational changes and current structure-based drug designs towards protein conformational diseases are also discussed. It is believed that a better understanding of the mechanisms of conformational changes as well as the biological functions of these proteins will lead to the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.

Abstract 18: Synoviolin, an E3 Ubiquitin Ligase, Modulates Cardiac Myocyte Size and Restores Heart Function in Hypertrophic Cardiomyopathy

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Shirin Doroudgar ◽  
Mirko Völkers ◽  
Donna J Thuerauf ◽  
Ashley Bumbar ◽  
Mohsin Khan ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Protein Misfolding ◽  
Cardiac Myocyte ◽  
Protein Quality ◽  
Heart Function ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
Calcium Handling ◽  
Loss Of Function

The endoplasmic reticulum (ER) is essential for protein homeostasis, or proteostasis, which governs the balance of the proteome. In addition to secreted and membrane proteins, proteins bound for many other cellular locations are also made on ER-bound ribosomes, emphasizing the importance of protein quality and quantity control in the ER. Unlike cytosolic E3 ubiquitin ligases studied in the heart, synoviolin/Hrd1, which has not been studied in the heart, is an ER transmembrane E3 ubiquitin ligase, which we found to be upregulated upon protein misfolding in cardiac myocytes. Given the strategic location of synoviolin in the ER membrane, we addressed the hypothesis that synoviolin is critical for regulating the balance of the proteome, and accordingly, myocyte size. We showed that in vitro, adenovirus-mediated overexpression of synoviolin decreased cardiac myocyte size and protein synthesis, but unlike atrophy-related ubiquitin ligases, synoviolin did not increase global protein degradation. Furthermore, targeted gene therapy using adeno-associated virus 9 (AAV9) showed that overexpression of synoviolin in the left ventricle attenuated maladaptive cardiac hypertrophy and preserved cardiac function in mice subjected to trans-aortic constriction (AAV9-control TAC = 22.5 ± 6.2% decrease in EF vs. AAV9-synoviolin TAC at 6 weeks post TAC; P<0.001), and decreased mTOR activity. Since calcium is a major regulator of cardiac myocyte size, we examined the effects of synoviolin gain- or loss-of-function, using AAV9-synoviolin, or an miRNA designed to knock down synoviolin, respectively. While synoviolin gain-of-function did not affect calcium handling in isolated adult myocytes, synoviolin loss-of-function increased calcium transient amplitude (P<0.01), prolonged spark duration (P<0.001), and increased spark width (P<0.001). Spark frequency and amplitude were unaltered upon synoviolin gain- or loss-of-function. Whereas SR calcium load was unaltered by synoviolin loss-of-function, SERCA-mediated calcium removal was reduced (P<0.05). In conclusion, our studies suggest that in the heart, synoviolin is 1) a critical component of proteostasis, 2) a novel determinant of cardiac myocyte size, and 3) necessary for proper calcium handling.

scholarly journals Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Bernard Kim ◽  
Kirk E. Lohmueller ◽  
Emilia Huerta-Sánchez
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Genomic Variation ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Modern Humans ◽  
Recombination Rates ◽  
Limited Impact ◽  
Adaptive Mutations ◽  
Adaptive Introgression

AbstractAdmixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.

scholarly journals The evolutionary dynamics of Oropouche Virus (OROV) in South America

2019 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma Wise ◽  
Steven Pullan ◽  
Christopher Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Viral Genome ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Glycosylation Sites ◽  
Variable Evolutionary Rates

AbstractThe Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

scholarly journals Maximum likelihood estimation of fitness components in experimental evolution

2018 ◽  
Author(s):  
Jingxian Liu ◽  
Jackson Champer ◽  
Chen Liu ◽  
Joan Chung ◽  
Riona Reeves ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Likelihood Estimation ◽  
Loss Of Function ◽  
Wild Type ◽  
Fitness Components ◽  
Linked Gene ◽  
Males And Females

AbstractEstimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring selection from allele frequency time series typically assume that evolutionary dynamics at the locus of interest can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability, and distinguishing between these components could be critical in many scenarios. Here we develop a flexible maximum likelihood framework that can disentangle different components of fitness and estimate them individually in males and females from genotype frequency data. As a proof-of-principle, we apply our method to experimentally-evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow. This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

Abstract 88: A Crucial Role of BAG3 in Preventing Dilated Cardiomyopathy

2017 ◽  
Vol 121 (suppl_1) ◽  
Author(s):  
Xi Fang ◽  
Julius Bogomolovas ◽  
Wei Zhang ◽  
Tongbin Wu ◽  
Canzhao Liu ◽  
...  
Keyword(s):  
Heart Failure ◽  
Dilated Cardiomyopathy ◽  
Protein Quality ◽  
Contractile Function ◽  
Metabolic Stress ◽  
Insoluble Fraction ◽  
Therapeutic Benefit ◽  
Loss Of Function ◽  
Specific Subset

Defective protein quality control (PQC) systems are implicated in multiple diseases, with molecular chaperones/co-chaperones being critical to PQC. Cardiomyocytes are constantly challenged by mechanical and metabolic stress, placing great demand on the PQC system. Mutations and downregulation of the co-chaperone protein B cl-2- a ssociated athano g ene 3 (BAG3) are associated with cardiac myopathy and heart failure, and a BAG3 E455K mutation leads to Dilated cardiomyopathy (DCM). However, the role of BAG3 in the heart and mechanisms by which the E455K mutation lead to DCM remained obscure. Here, we found that cardiac-specific BAG3 knockout (CKO) and cardiac-specific E455K BAG3 knockin mice developed DCM. Comparable phenotypes in the two mutants demonstrated that the E455K mutation resulted in loss-of-function, and experiments revealed that the E455K mutation disrupted interaction between BAG3 and HSP70. In both mutants, decreased levels of small heat shock proteins (sHSPs) were observed, and a specific subset of proteins required for metabolic and contractile function of cardiomyocytes was enriched in the insoluble fraction. Together, these observations suggested that interaction between BAG3 and HSP70 was essential for BAG3 to stabilize sHSPs and maintain cardiomyocyte protein homeostasis. Our results provide new insight into the pathogenesis of heart failure caused by defects in BAG3 pathways, suggesting that increasing protein levels of BAG3 may be of therapeutic benefit in heart failure.

Predicting evolution in diverse communities

2019 ◽  
pp. 167-188
Author(s):  
Timothy G. Barraclough
Keyword(s):  
Microbial Community ◽  
Ecosystem Functioning ◽  
Evolutionary Dynamics ◽  
Control Measures ◽  
Living Systems ◽  
Human Populations ◽  
Focal Species ◽  
Diverse Communities ◽  
Challenges And Opportunities ◽  
Disease Agent

Following the outline of basic theory and evidence in chapters 7 and 8, this chapter sets the challenge of attempting to predict evolutionary dynamics in realistically diverse communities. Many challenges and opportunities facing human populations rely on being able to predict living systems. Even when a single focal species such as a pest or disease agent is of particular concern, its dynamics and responses to control measures always depend on interactions with a diverse set of other species. Even when the focus is on whole-ecosystem functioning, that depends on trait responses of constituent species. The chapter outlines several case studies where a multispecies evolutionary approach is required, including managing marine fisheries, controlling crop pests, and managing human microbiomes for improved health. To illustrate possible ways forwards, a model of evolution in a microbial community is presented, and possible methods for tracking evolution in diverse communities are discussed.

scholarly journals Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Fang Wang ◽  
Shujia Huang ◽  
Rongsui Gao ◽  
Yuwen Zhou ◽  
Changxiang Lai ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Phenotypic Variability ◽  
Missense Variant ◽  
Pedigree Analysis ◽  
Chinese Patients ◽  
Genetic Contribution ◽  
Loss Of Function ◽  
Genomic Study ◽  
Significant Gene ◽  
Host Genetic

Abstract The COVID-19 pandemic has accounted for millions of infections and hundreds of thousand deaths worldwide in a short-time period. The patients demonstrate a great diversity in clinical and laboratory manifestations and disease severity. Nonetheless, little is known about the host genetic contribution to the observed interindividual phenotypic variability. Here, we report the first host genetic study in the Chinese population by deeply sequencing and analyzing 332 COVID-19 patients categorized by varying levels of severity from the Shenzhen Third People’s Hospital. Upon a total of 22.2 million genetic variants, we conducted both single-variant and gene-based association tests among five severity groups including asymptomatic, mild, moderate, severe, and critical ill patients after the correction of potential confounding factors. Pedigree analysis suggested a potential monogenic effect of loss of function variants in GOLGA3 and DPP7 for critically ill and asymptomatic disease demonstration. Genome-wide association study suggests the most significant gene locus associated with severity were located in TMEM189–UBE2V1 that involved in the IL-1 signaling pathway. The p.Val197Met missense variant that affects the stability of the TMPRSS2 protein displays a decreasing allele frequency among the severe patients compared to the mild and the general population. We identified that the HLA-A*11:01, B*51:01, and C*14:02 alleles significantly predispose the worst outcome of the patients. This initial genomic study of Chinese patients provides genetic insights into the phenotypic difference among the COVID-19 patient groups and highlighted genes and variants that may help guide targeted efforts in containing the outbreak. Limitations and advantages of the study were also reviewed to guide future international efforts on elucidating the genetic architecture of host–pathogen interaction for COVID-19 and other infectious and complex diseases.

scholarly journals Myotonia in a patient with a mutation in an S4 arginine residue associated with hypokalaemic periodic paralysis and a concomitant synonymous CLCN1 mutation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Michael G. Thor ◽  
Vinojini Vivekanandam ◽  
Marisol Sampedro-Castañeda ◽  
S. Veronica Tan ◽  
Karen Suetterlin ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Phenotypic Variability ◽  
Transmembrane Helix ◽  
Periodic Paralysis ◽  
Loss Of Function ◽  
Leak Current ◽  
Muscle Action Potential ◽  
Arginine Residues ◽  
Pore Domain ◽  
Clcn1 Mutation

AbstractThe sarcolemmal voltage gated sodium channel NaV1.4 conducts the key depolarizing current that drives the upstroke of the skeletal muscle action potential. It contains four voltage-sensing domains (VSDs) that regulate the opening of the pore domain and ensuing permeation of sodium ions. Mutations that lead to increased NaV1.4 currents are found in patients with myotonia or hyperkalaemic periodic paralysis (HyperPP). Myotonia is also caused by mutations in the CLCN1gene that result in loss-of-function of the skeletal muscle chloride channel ClC-1. Mutations affecting arginine residues in the fourth transmembrane helix (S4) of the NaV1.4 VSDs can result in a leak current through the VSD and hypokalemic periodic paralysis (HypoPP), but these have hitherto not been associated with myotonia. We report a patient with an Nav1.4 S4 arginine mutation, R222Q, presenting with severe myotonia without fulminant paralytic episodes. Other mutations affecting the same residue, R222W and R222G, have been found in patients with HypoPP. We show that R222Q channels have enhanced activation, consistent with myotonia, but also conduct a leak current. The patient carries a concomitant synonymous CLCN1 variant that likely worsens the myotonia and potentially contributes to the amelioration of muscle paralysis. Our data show phenotypic variability for different mutations affecting the same S4 arginine that have implications for clinical therapy.

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