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Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA.

ABSTRACT: Strong positive Darwinian selection acts on two sperm fertilization proteins, lysin and 18-kDa protein, from abalone (Haliotis). To understand the phylogenetic context for this dramatic molecular evolution, we obtained sequences of mitochondrial cytochrome c oxidase subunit I (mtCOI), and genomic sequences of lysin, 18-kDa, and a G protein subunit. Based on mtDNA differentiation, four north Pacific abalone species diverged within the past 2 million years (Myr), and remaining north Pacific species diverged over a period of 4-20 Myr. Between-species nonsynonymous differences in lysin and 18-kDa exons exceed nucleotide differences in introns by 3.5- to 24-fold. Remarkably, in some comparisons nonsynonymous substitutions in lysin and 18-kDa genes exceed synonymous substitutions in mtCOI. Lysin and 18-kDa intron/exon segments were sequenced from multiple red abalone individuals collected over a 1,200-km range. Only two nucleotide changes and two sites of slippage variation were detected in a total of >29,000 nucleotides surveyed. However, polymorphism in mtCOI and a G protein intron was found in this species. This finding suggests that positive selection swept one lysin allele and one 18-kDa allele to fixation. Similarities between mtCOI and lysin gene trees indicate that rapid adaptive evolution of lysin has occurred consistently through the history of the group. Comparisons with mtCOI molecular clock calibrations suggest that nonsynonymous substitutions accumulate 2-50 times faster in lysin and 18-kDa genes than in rapidly evolving mammalian genes.

SUBMITTER: Metz EC

PROVIDER: S-EPMC27954 | biostudies-literature | 1998 Sep

REPOSITORIES: biostudies-literature

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Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA.

Metz E C EC Robles-Sikisaka R R Vacquier V D VD

Proceedings of the National Academy of Sciences of the United States of America 19980901 18

Strong positive Darwinian selection acts on two sperm fertilization proteins, lysin and 18-kDa protein, from abalone (Haliotis). To understand the phylogenetic context for this dramatic molecular evolution, we obtained sequences of mitochondrial cytochrome c oxidase subunit I (mtCOI), and genomic sequences of lysin, 18-kDa, and a G protein subunit. Based on mtDNA differentiation, four north Pacific abalone species diverged within the past 2 million years (Myr), and remaining north Pacific specie ...[more]

PMID: 9724763

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Project description:Pacific abalone, Haliotis discus hannai, is a highly commercial seafood in Southeast Asia. The present study aimed to determine the influence of saccharides and vitamins on post-thaw sperm quality, ATP content, fertilization capacity, hatching capacity, and mRNA content of motility and fertilization-associated genes of Pacific abalone. Sperm cryopreserved using saccharides improved the post-thaw sperm quality including motility, acrosome integrity (AI), plasma membrane integrity (PMI), and mitochondrial membrane potential (MMP). However, vitamins (l-ascorbic acid) did not result in any significant improvement in sperm quality. Sperm cryopreserved using saccharides also improved ATP content, DNA integrity, and mRNA content of motility and fertilization-associated genes of post-thaw sperm than sperm cryopreserved without saccharides. Among sperm cryopreserved using different saccharides, post-thaw sperm quality indicators (except PMI) and mRNA content of motility and fertilization-associated genes did not show significant differences between sperm cryopreserved using 3% sucrose (S) combined with 8% dimethyl sulfoxide (DMSO) and sperm cryopreserved using 1% glucose (G) combined with 8% ethylene glycol (EG). However, sperm cryopreserved using 3% S + 8% DMSO showed higher post-thaw sperm quality (motility: 58.4 ± 2.9%, AI: 57.1 ± 3.2%, PMI: 65.3 ± 3.3%, and MMP: 59.1 ± 3.2%), ATP content (48.4 ± 1.8 nmol/ml), and % DNA in tail (2.09 ± 0.20%) than sperm cryopreserved using other saccharides. When sperms were cryopreserved using 3% S + 8% DMSO, the mRNA content of motility (heat shock protein 70, HSP70; heat shock protein 90, HSP90; protein kinase A, PKA-C; axonemal protein 66.0, Axpp66.0; and tektin-4) and fertilization-associated (sperm protein 18 kDa, SP18 kDa) genes were higher than in sperm cryopreserved using other saccharides. However, changes in the mRNA contents of these genes were insignificant between sperm cryopreserved using 3% S + 8% DMSO and 1% G + 8% EG. Taken together, these results indicate that cryopreservation using 3% S + 8% DMSO can improve post-thaw sperm quality and mRNA contents better than other examined cryoprotectants. The present study suggests that 3% S + 8% DMSO is a suitable cryoprotectant for sperm cryopreservation and molecular conservation of this valuable species.

Project description:Study questionAre sperm mitochondrial DNA copy number (mtDNAcn) and deletion rate (mtDNAdel) associated with odds of fertilization and high embryo quality at Days 3 and 5?Summary answerHigher sperm mtDNAcn and mtDNAdel were associated with lower odds of high quality Day 3 embryos and transfer quality Day 5 embryos, both of which were primarily driven by lowered odds of fertilization.What is known alreadySperm mtDNAcn and mtDNAdel have been previously associated with poor semen parameters and clinical male infertility. One prior study has shown that mtDNAdel is associated with lower fertilization rates. However, it is unknown whether these characteristics are linked with ART outcomes.Study design, size, durationThis prospective observational study included 119 sperm samples collected from men undergoing ART in Western Massachusetts. ART outcomes were observed through to Day 5 post-insemination.Participants/materials, settings, methodsAs part of the Sperm Environmental Epigenetics and Development Study (SEEDS), 119 sperm samples were collected from men undergoing ART in Western Massachusetts. Sperm mtDNAcn and mtDNAdel were measured via triplex probe-based qPCR. Fertilization, Day 3 embryo quality and Day 5 embryo quality measures were fitted with mtDNAcn and mtDNAdel using generalized estimating equations.Main results and the role of chanceAfter adjusting for male age and measurement batches, higher sperm mtDNAcn and mtDNAdel were associated with lower odds of fertilization (P = 0.01 and P < 0.01), high quality Day 3 embryos (P = 0.02 for both) and transfer quality Day 5 embryos (P = 0.01 and P = 0.09). However, the associations of mtDNAcn and mtDNAdel with Day 3 high quality status and Day 5 transfer quality status were attenuated in models restricted to fertilized oocytes. Sperm mtDNAcn and mtDNAdel remained statistically significant in models adjusted for both male age and semen parameters, although models including both mtDNA markers generally favoured mtDNAdel.Limitations, reasons for cautionOur sample only included oocytes and embryos from 119 couples and thus large diverse cohorts are necessary to confirm the association of sperm mtDNA biomarkers with embryo development.Wider implications of the findingsTo our knowledge, our study is the first to assess the associations of sperm mtDNAcn and mtDNAdel with fertilization and embryo quality. The biological mechanism(s) underlying these associations are unknown. Multivariable models suggest that sperm mtDNAcn and mtDNAdel provide discrimination independent of age and semen parameters; therefore, future investigation of the utility of sperm mtDNA as a biomarker for ART outcomes is warranted.Study funding/competing interest(s)This work was supported by Grant (K22-ES023085) from the National Institute of Environmental Health Sciences. The authors declare no competing interests.Trial registration numberN/A.

Project description:Reproductive proteins mediating fertilization commonly exhibit rapid sequence diversification driven by positive selection. This pattern has been observed among nearly all taxonomic groups, including mammals, invertebrates, and plants, and is remarkable given the essential nature of the molecular interactions mediating fertilization. Gene duplication is another important mechanism that facilitates the generation of molecular novelty through functional divergence. Following duplication, paralogs may partition ancestral gene function (subfunctionalization) or acquire new roles (neofunctionalization). However, the contributions of duplication followed by sequence diversification to the molecular diversity of gamete recognition genes has been understudied in many models of fertilization. The marine gastropod mollusk abalone is a classic model for fertilization. Its two acrosomal proteins (lysin and sp18) are ancient gene duplicates with unique gamete recognition functions. Through detailed genomic and bioinformatic analyses we show how duplication events followed by sequence diversification has played an ongoing role in the evolution of abalone acrosomal proteins. The common ancestor of abalone had four members of its acrosomal protein family in a tandem gene array that repeatedly experienced positive selection. We find that both sp18 paralogs contain positively selected sites located in different regions of the paralogs, suggestive of functional divergence where selection acted upon distinct binding interfaces in each paralog. Further, a more recent species-specific duplication of both lysin and sp18 in the European abalone H. tuberculata is described. Despite clade-specific acrosomal protein paralogs, there are no concomitant duplications of egg coat proteins in H. tuberculata, indicating that duplication of egg proteins per se is not responsible for retention of duplicated acrosomal proteins. We hypothesize that, in a manner analogous to host/pathogen evolution, sperm proteins are selected for increased diversity through extensive sequence divergence and recurrent duplication driven by conflict mechanisms.

Project description:BACKGROUND: Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics. RESULTS: We chose human and eleven other high-coverage mammalian genome data-as well as an avian genome as an outgroup-to analyze orthologous protein-coding genes using nonsynonymous (Ka) and synonymous (Ks) substitution rates. After evaluating eight commonly-used methods of Ka and Ks calculation, we observed that these methods yielded a nearly uniform result when estimating Ka, but not Ks (or Ka/Ks). When sorting genes based on Ka, we noticed that fast-evolving and slow-evolving genes often belonged to different functional classes, with respect to species-specificity and lineage-specificity. In particular, we identified two functional classes of genes in the acquired immune system. Fast-evolving genes coded for signal-transducing proteins, such as receptors, ligands, cytokines, and CDs (cluster of differentiation, mostly surface proteins), whereas the slow-evolving genes were for function-modulating proteins, such as kinases and adaptor proteins. In addition, among slow-evolving genes that had functions related to the central nervous system, neurodegenerative disease-related pathways were enriched significantly in most mammalian species. We also confirmed that gene expression was negatively correlated with evolution rate, i.e. slow-evolving genes were expressed at higher levels than fast-evolving genes. Our results indicated that the functional specializations of the three major mammalian clades were: sensory perception and oncogenesis in primates, reproduction and hormone regulation in large mammals, and immunity and angiotensin in rodents. CONCLUSION: Our study suggests that Ka calculation, which is less biased compared to Ks and Ka/Ks, can be used as a parameter to sort genes by evolution rate and can also provide a way to categorize common protein functions and define their interaction networks, either pair-wise or in defined lineages or subgroups. Evaluating gene evolution based on Ka and Ks calculations can be done with large datasets, such as mammalian genomes. REVIEWERS: This article has been reviewed by Drs. Anamaria Necsulea (nominated by Nicolas Galtier), Subhajyoti De (nominated by Sarah Teichmann) and Claus O. Wilke.

Dataset Information

Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA.

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Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA.

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