scholarly journals Positive Selection and the Evolution of izumo Genes in Mammals

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Phil Grayson ◽  
Alberto Civetta
Keyword(s):  
Positive Selection ◽  
Protein Function ◽  
Gene Evolution ◽  
Rapid Evolution ◽  
Reproductive Function ◽  
Gene Duplications ◽  
Male Reproductive Function ◽  
Selection For ◽  
Species Specific ◽  
And Control

Most genes linked to male reproductive function have been known to evolve rapidly among species and to show signatures of positive selection. Different male species-specific reproductive strategies have been proposed to underlie positive selection, such as sperm competitive advantage and control over females postmating physiology. However, an underexplored aspect potentially affecting male reproductive gene evolution in mammals is the effect of gene duplications. Here we analyze the molecular evolution of members of the izumo gene family in mammals, a family of four genes mostly expressed in the sperm with known and potential roles in sperm-egg fusion. We confirm a previously reported bout of selection for izumo1 and establish that the bout of selection is restricted to the diversification of species of the superorder Laurasiatheria. None of the izumo genes showed evidence of positive selection in Glires (Rodentia and Lagomorpha), and in the case of the non-testes-specific izumo4, rapid evolution was driven by relaxed selection. We detected evidence of positive selection for izumo3 among Primates. Interestingly, positively selected sites include several serine residues suggesting modifications in protein function and/or localization among Primates. Our results suggest that positive selection is driven by aspects related to species-specific adaptations to fertilization rather than sexual selection.

scholarly journals Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

2020 ◽  
Author(s):  
Asma Awadi ◽  
Hichem Ben Slimen ◽  
Helmut Schaschl ◽  
Felix Knauer ◽  
Franz Suchentrunk
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Protein Function ◽  
Transmembrane Domain ◽  
Proton Translocation ◽  
Introgressive Hybridization ◽  
Vibrational Entropy ◽  
Mutant Type ◽  
Selection For ◽  
Protein Variants

Abstract Background: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. Results: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, the PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. The statistical model runs indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgresson.Conclusions: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.

scholarly journals Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
William C. Beckerson ◽  
Ricardo C. Rodríguez de la Vega ◽  
Fanny E. Hartmann ◽  
Marine Duhamel ◽  
Tatiana Giraud ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Pfam Domain ◽  
Rapid Evolution ◽  
Host Specialization ◽  
Secreted Proteins ◽  
Smut Fungi ◽  
Core Proteins ◽  
Genes Encoding ◽  
Species Specific

ABSTRACT Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses. IMPORTANCE Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

Effects of behaviour selection on litter size, fetal development and plasma progesterone concentrations during pregnancy in silver fox vixens

2002 ◽  
Vol 2002 ◽  
pp. 125-125
Author(s):  
L. V. Osadchuk
Keyword(s):  
Reproductive Function ◽  
Coat Colour ◽  
Performance Potential ◽  
Plasma Progesterone ◽  
Term Selection ◽  
Silver Fox ◽  
In The Wild ◽  
Selection For ◽  
And Control

Animal domestication is a natural selection experiment the important result of which is a great increase in the rate of appearance of new forms and in the wild range of variation of organisms. Analysing different aspects of this problem, D.K. Belyaev has came to a hypothesis that the morphological and physiological reorganisation of domestic animals has been going by the way of unconscious selection of animals on their behaviour, carried out by person at the very first stages of domestication (Belyaev, 1979). To testify this hypothesis, a population of tame silver foxes has been produced in long-term selection for lack of aggression and fear towards humans (domestic behaviour) at the Institute of Cytology and Genetics in Novosibirsk, Russia. In the process of selection the genetic transformation of behaviour and morphology, and physiological functions has been observed (Trut, 1999). In particular, selected animals show no aggressiveness to man, behave amicably towards humans and have some changes in the coat colour and body constitution (Trut, 1999). The important part of Belyaev’s hypothesis was the assumption that selection for domestic behaviour could affect the reproductive function, in particular the pituitary-gonadal axis controlling reproduction and fertility. The aim of this study was to obtain information about possible changes in reproduction between control (C) and domesticated (D) vixens. Reproductive performance, potential fertility, embryonic mortality and fetal viability were analysed for vixens from domesticated and control population. In addition, plasma progesterone concentrations were determined in selected and control females during pregnancy.

Hormonally derived sex pheromones in fish: exogenous cues and signals from gonad to brain

2003 ◽  
Vol 81 (4) ◽  
pp. 329-341 ◽  
Author(s):  
Norm Stacey ◽  
Andrew Chojnacki ◽  
Annapurni Narayanan ◽  
Todd Cole ◽  
Cheryl Murphy
Keyword(s):  
Visual Information ◽  
Reproductive Function ◽  
Great Sensitivity ◽  
Model Systems ◽  
Closely Related Species ◽  
Exogenous Cues ◽  
Selection For ◽  
Olfactory Organs ◽  
The Individual ◽  
Species Specific

Living in a medium that can limit visual information but readily exposes the olfactory organ to hormonal compounds released by conspecifics, fish throughout their long evolutionary history have had both clear cause and ample opportunity to evolve olfactory responsiveness to these potentially important chemical cues (hormonal pheromones). Indeed, water-borne steroids, prostaglandins, and their metabolites are detected with great sensitivity and specificity by the olfactory organs of diverse fishes, and exert important effects on reproductive behavior and physiology in major taxa including carps (goldfish), catfishes, salmon, and gobies. Best understood are goldfish, where periovulatory females sequentially release a preovulatory steroid pheromone and a postovulatory prostaglandin pheromone that dramatically affect male behavior, physiology, and reproductive fitness. Although the diverse array of hormonal products released and detected by fish indicates clear potential for species-specific hormonal pheromones, olfactory recordings showing similar patterns of hormone detection among closely related species provide little evidence of selection for specificity. By demonstrating that the actions of sex hormones and related products are not limited to reproductive synchrony within the individual, the relatively recent discovery of hormonal pheromones has considerably expanded our understanding of fish reproductive function, while providing valuable model systems for future study of olfactory function and pheromone evolution.Key words: pheromone, olfaction, 17α,20β-dihydroxy-4-pregnen-3-one, prostaglandin, sperm competition.

scholarly journals The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies

2020 ◽  
Vol 37 (5) ◽  
pp. 1376-1386
Author(s):  
Henri van Kruistum ◽  
Michael W Guernsey ◽  
Julie C Baker ◽  
Susan L Kloet ◽  
Martien A M Groenen ◽  
...  
Keyword(s):  
Positive Selection ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Gene Duplications ◽  
Genome Wide ◽  
Single Instance ◽  
A Genome ◽  
Livebearing Fish ◽  
Genome Assemblies ◽  
Genome Wide Scan

Abstract The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother–offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10× Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent–offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.

scholarly journals Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations

2015 ◽  
Vol 112 (8) ◽  
pp. 2491-2496 ◽  
Author(s):  
Mingkun Li ◽  
Roland Schröder ◽  
Shengyu Ni ◽  
Burkhard Madea ◽  
Mark Stoneking
Keyword(s):  
Positive Selection ◽  
Protein Function ◽  
Somatic Mutations ◽  
Significant Excess ◽  
High Frequencies ◽  
Mtdna Mutations ◽  
Age Related ◽  
Selection For ◽  
Different Tissues ◽  
Complete Mtdna

Heteroplasmy in human mtDNA may play a role in cancer, other diseases, and aging, but patterns of heteroplasmy variation across different tissues have not been thoroughly investigated. Here, we analyzed complete mtDNA genome sequences at ∼3,500× average coverage from each of 12 tissues obtained at autopsy from each of 152 individuals. We identified 4,577 heteroplasmies (with an alternative allele frequency of at least 0.5%) at 393 positions across the mtDNA genome. Surprisingly, different nucleotide positions (nps) exhibit high frequencies of heteroplasmy in different tissues, and, moreover, heteroplasmy is strongly dependent on the specific consensus allele at an np. All of these tissue-related and allele-related heteroplasmies show a significant age-related accumulation, suggesting positive selection for specific alleles at specific positions in specific tissues. We also find a highly significant excess of liver-specific heteroplasmies involving nonsynonymous changes, most of which are predicted to have an impact on protein function. This apparent positive selection for reduced mitochondrial function in the liver may reflect selection to decrease damaging byproducts of liver mitochondrial metabolism (i.e., “survival of the slowest”). Overall, our results provide compelling evidence for positive selection acting on some somatic mtDNA mutations.

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko
Keyword(s):  
Protein Function ◽  
Intrinsically Disordered Protein ◽  
Structural Basis ◽  
Major Protein ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
Biochemical Journal ◽  
Multiple Binding ◽  
And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

The mechanisms involved in obesity-induced male infertility

2020 ◽  
Vol 16 ◽  
Author(s):  
Hamed Heydari ◽  
Rafighe Ghiasi ◽  
Saber Ghaderpour ◽  
Rana Keyhanmanesh
Keyword(s):  
Oxidative Stress ◽  
Metabolic Disease ◽  
Male Infertility ◽  
Male Fertility ◽  
Reproductive Function ◽  
Disease Development ◽  
Significant Evidence ◽  
Male Reproductive Function ◽  
Negative Effect ◽  
And Oxidative Stress

Introduction: Obesity resulted by imbalance between the intake of energy and energy consumption can lead to growth and metabolic disease development in people. Both in obese men and animal models, several studies indicate that obesity leads to male infertility. Objective: This review has discussed some mechanisms involved in obesity-induced male infertility. Method: Online documents were searched through Science Direct, Pubmed, Scopus, and Google Scholar websites dating from 1959 to recognize studies on obesity, kisspeptin, leptin, and infertility. Results: Obesity induced elevated inflammatory cytokines and oxidative stress can affect male reproductive functions including spermatogenesis disorders, reduced male fertility power and hormones involved in hypothalamus-pituitarygonadal axis. Conclusion: There is significant evidence that obesity resulted in male infertility. obesity has negative effect on male reproductive function via several mechanisms such as inflammation and oxidative stress.

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