Abstract
Cysteine-RIch Secretory Proteins (CRISPs) constitute a versatile family, with functions in reptilian venom and mammalian reproduction. Mammals generally express three CRISPs, four in mice, and all are highly expressed in male reproductive tissues, either testis or accessory organs. Because reproductive proteins often evolve adaptively in response to post-copulatory sexual selection, we hypothesized that mammalian CRISPs, with important roles in male reproduction, could have undergone positive selection promoting their divergence. We explored the molecular adaptation of mammalian CRISPs applying phylogenetic methods. Our analyses revealed the evidence of positive selection in all mammalian CRISPs. The intensity of positive selection was heterogeneous among CRISP members, being stronger in CRISP3 than in CRISP1 and CRISP2, and also across functional domains, having stronger impact on Pathogenesis-Related 1 (PR-1) in CRISP2 and on Ion Channel Regulator (ICR) in CRISP1 and CRISP3. In addition, we discovered a new CRISP in some rodent species, suggesting that the acquisition of new CRISP components could contribute to male reproductive success or to acquire new physiological roles. Signatures of positive selection were not focused on any particular mammalian group, suggesting that adaptive evolution is a recurrent pattern in mammalian CRISPs. Our findings support a model of CRISP family diversification driven by episodes of duplication and posterior neofunctionalization, and provide potential adaptive changes responsible for interspecific differences in CRISPs activity.
Similar content being viewed by others
References
Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18:1585–1592
Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201
Birkhead TR, Hosken DJ, Pitnick S (2008) Sperm biology: an evolutionary perspective. Academic Press, Oxford
Busso D, Goldweic NM, Hayashi M et al (2007) Evidence for the involvement of testicular protein CRISP2 in mouse sperm-egg fusion. Biol Reprod 76:701–708. https://doi.org/10.1095/biolreprod.106.056770
Bustamante CD, Fledel-Alon A, Williamson S et al (2005) Natural selection on protein-coding genes in the human genome. Nature 437:1153–1157. https://doi.org/10.1038/nature04240
Clark AG, Glanowski S, Nielsen R et al (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960–1963. https://doi.org/10.1126/science.1088821
Cohen DJ, Ellerman DA, Busso D et al (2001) Evidence that human epididymal protein ARP plays a role in gamete fusion through complementary sites on the surface of the human egg. Biol Reprod 1005:1000–1005
Cohen DJ, Maldera JA, Vasen G et al (2011) Epididymal protein CRISP1 plays different roles during the fertilization process. J Androl 32:672–678. https://doi.org/10.2164/jandrol.110.012922
Crespi BJ, Summers K (2006) Positive selection in the evolution of cancer. Biol Rev Camb Philos Soc 81:407–424. https://doi.org/10.1017/S1464793106007056
Da Ros VG, Muñoz MW, Battistone M et al (2015) From the epididymis to the egg: participation of CRISP proteins in mammalian fertilization. Asian J Androl. https://doi.org/10.4103/1008-682X.155769
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772–772. https://doi.org/10.1038/nmeth.2109
Dean MD, Good JM, Nachman MW (2008) Adaptive evolution of proteins secreted during sperm maturation: an analysis of the mouse epididymal transcriptome. Mol Biol Evol 25:383–392. https://doi.org/10.1093/molbev/msm265
Dean MD, Clark NL, Findlay GD et al (2009) Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Mol Biol Evol 26:1733–1743. https://doi.org/10.1093/molbev/msp094
Dewsbury DA (1985) Interactions between males and their sperm during multi-male copulatory episodes of deer mice (Peromyscus maniculatus). Anim Behav 33:1266–1274. https://doi.org/10.1016/S0003-3472(85)80186-X
Dorus S, Busby SA, Gerike U et al (2006) Genomic and functional evolution of the Drosophila melanogaster sperm proteome. Nat Genet. https://doi.org/10.1038/ng1915
Dorus S, Freeman ZN, Parker ER et al (2008) Recent origins of sperm genes in Drosophila. Mol Biol Evol. https://doi.org/10.1093/molbev/msn162
Dorus S, Wasbrough ER, Busby J et al (2010) Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes. Mol Biol Evol 27:1235–1246. https://doi.org/10.1093/molbev/msq007
Dorus S, Wilkin EC, Karr TL (2011) Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm. BMC Genom 12:177. https://doi.org/10.1186/1471-2164-12-177
Ellerman DA, Cohen DJ, Da Ros VG et al (2006) Sperm protein “DE” mediates gamete fusion through an evolutionarily conserved site of the CRISP family. Dev Biol 297:228–237. https://doi.org/10.1016/j.ydbio.2006.05.013
Ernesto JI, Weigel Munoz M, Battistone M et al (2015) CRISP1 as a novel CatSper regulator that modulates sperm motility and orientation during fertilization. J Cell Biol 210:1213–1224. https://doi.org/10.1083/jcb.201412041
Findlay GD, Swanson WJ (2010) Proteomics enhances evolutionary and functional analysis of reproductive proteins. BioEssays 32:26–36. https://doi.org/10.1002/bies.200900127
Findlay GD, Yi X, Maccoss MJ, Swanson WJ (2008) Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol 6:e178. https://doi.org/10.1371/journal.pbio.0060178
Findlay GD, MacCoss MJ, Swanson WJ (2009) Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Res 19:886–896. https://doi.org/10.1101/gr.089391.108
Foley NM, Springer MS, Teeling EC (2016) Mammal madness: is the mammal tree of life not yet resolved? Philos Trans R Soc Lond B 371:20150140. https://doi.org/10.1098/rstb.2015.0140
Gibbs GM, O’Bryan MK (2007) Cysteine rich secretory proteins in reproduction and venom. Soc Reprod Fertil Suppl 65:261–267
Gibbs GM, Scanlon MJ, Swarbrick J et al (2006) The cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ signaling. J Biol Chem 281:4156–4163. https://doi.org/10.1074/jbc.M506849200
Gibbs GM, Roelants K, O’Bryan MK (2008) The CAP superfamily: cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins—roles in reproduction, cancer, and immune defense. Endocr Rev 29:865–897. https://doi.org/10.1210/er.2008-0032
Gibbs GM, Orta G, Reddy T et al (2011) Cysteine-rich secretory protein 4 is an inhibitor of transient receptor potential M8 with a role in establishing sperm function. Proc Natl Acad Sci USA 108:7034–7039. https://doi.org/10.1073/pnas.1015935108
Grayson P, Civetta A (2013) Positive selection in the adhesion domain of Mus sperm Adam genes through gene duplications and function-driven gene complex formations. BMC Evol Biol 13:217. https://doi.org/10.1186/1471-2148-13-217
Guo M, Teng M, Niu L et al (2005) Crystal structure of the cysteine-rich secretory protein stecrisp reveals that the cysteine-rich domain has a K+ channel inhibitor-like fold. Biochemistry 280:12405–12412. https://doi.org/10.1074/jbc.M413566200
Hayashi M, Fujimoto S, Takano H et al (1996) Characterization of a human glycoprotein with a potential role in sperm–egg fusion: cDNA cloning, immunohistochemical localization, and chromosomal assignment of the gene (AEGL1). Genomics 32:367–374. https://doi.org/10.1006/GENO.1996.0131
Jalkanen J, Huhtaniemi I, Poutanen M (2005) Mouse cysteine-rich secretory protein 4 (CRISP4): a member of the crisp family exclusively expressed in the epididymis in an androgen-dependent manner 1. Biol Reprod 1274:1268–1274. https://doi.org/10.1095/biolreprod.104.035758
Karr TL, Dorus S (2012) Evolutionary genomics of the sperm proteome. In: Singh RS, Xu J, Kulathinal RJ (eds) Evolution in the fast lane: rapidly evolving genes and genetic systems. Oxford University Press, Oxford, pp 153–164
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010
Koppers AJ, Reddy T, O’Bryan MK (2011) The role of cysteine-rich secretory proteins in male fertility. Asian J Androl 13:111–117. https://doi.org/10.1038/aja.2010.77
Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276–3278
Maldera JA, Weigel Munoz M, Chirinos M et al (2014) Human fertilization: epididymal hCRISP1 mediates sperm-zona pellucida binding through its interaction with ZP3. Mol Hum Reprod 20:341–349. https://doi.org/10.1093/molehr/gat092
McDonough CE, Whittington E, Pitnick S, Dorus S (2016) Proteomics of reproductive systems: towards a molecular understanding of postmating, prezygotic reproductive barriers. J Proteom 135:26–37. https://doi.org/10.1016/j.jprot.2015.10.015
Murphy WJ, Eizirik E, Johnson WE (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614–618
Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936
Nielsen R, Bustamante C, Clark AG et al (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3:e170. https://doi.org/10.1371/journal.pbio.0030170
Nolan MA, Wu L, Bang HJ et al (2006) Identification of rat cysteine-rich secretory protein 4 (Crisp4) as the ortholog to human CRISP1 and mouse Crisp4. Biol Reprod 74:984–991. https://doi.org/10.1095/biolreprod.105.048298
Ramm SA, McDonald L, Hurst JL et al (2009) Comparative proteomics reveals evidence for evolutionary diversification of rodent seminal fluid and its functional significance in sperm competition. Mol Biol Evol 26:189–198. https://doi.org/10.1093/molbev/msn237
Reddy T, Gibbs GM, Merriner DJ et al (2008) Cysteine-rich secretory proteins are not exclusively expressed in the male reproductive tract. Dev Dyn 237:3313–3323. https://doi.org/10.1002/dvdy.21738
Roberts KP, Wamstad JA, Ensrud KM, Hamilton DW (2003) Inhibition of capacitation-associated tyrosine phosphorylation signaling in rat sperm by epididymal protein Crisp-1. Biol Reprod 581:572–581. https://doi.org/10.1095/biolreprod.102.013771
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Sunagar K, Johnson WE, O’Brien SJ et al (2012) Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction. Mol Biol Evol 29:1807–1822. https://doi.org/10.1093/molbev/mss058
Suzuki N, Yamazaki Y, Brown RL et al (2008) Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain. Acta Crystallogr D 64:1034–1042. https://doi.org/10.1107/S0907444908023512
Turunen HT, Sipila P, Krutskikh A et al (2012) Loss of cysteine-rich secretory protein 4 (Crisp4) leads to deficiency in sperm-zona pellucida interaction in mice. Biol Reprod 86:1–8. https://doi.org/10.1095/biolreprod.111.092403
Udby L, Calafat J, Sørensen OE et al (2002) Identification of human cysteine-rich secretory protein 3 (CRISP-3) as a matrix protein in a subset of peroxidase-negative granules of neutrophils and in the granules of eosinophils. J Leukoc Biol 72:462–469. https://doi.org/10.1189/JLB.72.3.462
Udby L, Bjartell A, Malm J et al (2005) Characterization and localization of cysteine-rich secretory protein 3 (CRISP-3) in the human male reproductive tract. J Androl. https://doi.org/10.2164/jandrol.04132
Vicens A, Lüke L, Roldan ERS (2014) Proteins involved in motility and sperm-egg interaction evolve more rapidly in mouse spermatozoa. PLoS ONE 9:e91302. https://doi.org/10.1371/journal.pone.0091302
Wagstaff BJ, Begun DJ (2007) Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. Genetics. https://doi.org/10.1534/genetics.107.077503
Weaver S, Shank SD, Spielman SJ et al (2018) Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Mol Biol Evol. https://doi.org/10.1093/molbev/msx335
Wilburn DB, Swanson WJ (2015) From molecules to mating: rapid evolution and biochemical studies of reproductive proteins. J Proteom. https://doi.org/10.1016/j.jprot.2015.06.007
Wolfner MF (2002) The gifts that keep on giving: physiological functions and evolutionary dynamics of male seminal proteins in Drosophila. Heredity 88:85–93. https://doi.org/10.1038/sj/hdy/6800017
Yamazaki Y, Morita T (2004) Structure and function of snake venom cysteine-rich secretory proteins. Toxicon 44:227–231. https://doi.org/10.1016/j.toxicon.2004.05.023
Yamazaki Y, Brown RL, Morita T (2002) Purification and cloning of toxins from elapid venoms that target cyclic nucleotide-gated ion channels. Biochemistry 41:11331–11337
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591. https://doi.org/10.1093/molbev/msm088
Yang Z, Wong WSW, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118. https://doi.org/10.1093/molbev/msi097
Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18:292–298. https://doi.org/10.1016/S0169-5347(03)00033-8
Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479. https://doi.org/10.1093/molbev/msi237
Acknowledgements
The authors would like to thank Jose Luis De la Vega, Paulina Torres, Francisco Herrera, and Shirley Ainsworth for technical assistance; Juan Manuel Hurtado, Roberto Rodríguez, David Santiago Castañeda, Omar Arriaga, and Arturo Ocádiz for computing services; and Miguel Arenas for the critical revision of this manuscript. Computational analyses were supported by the cluster of the Instituto de Biotecnología UNAM (http://teopanzolco.ibt.unam.mx//).
Funding
This work was supported by Dirección General de Asuntos de Personal Académico/Universidad Nacional Autónoma de México (DGAPA/UNAM) (Contract Grant Number IN203116 to C.T. and postdoctoral fellowship to A.V.), the Alexander von Humboldt Foundation (w/o Grant Number to C.T.), and Juan de la Cierva postdoctoral fellowship (IJCI-2016-29550) from Spanish Government to A.V.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no competing interests.
Electronic supplementary material
Below is the link to the electronic supplementary material.
239_2018_9872_MOESM1_ESM.png
Supplementary Figure S1 Phylogenetic tree of mammalian CRISP1 inferred by ML. Terminal branches are presented with the accession sequence and species name. Taxonomic groups are indicated on right of tree. Node labels indicate the number of replicates of bootstrap support, based on 1000 iterations. The Eulipotyphla Sorex araneus was used to root the tree (PNG 2107 KB)
239_2018_9872_MOESM2_ESM.png
Supplementary Figure S2 Phylogenetic tree of mammalian CRISP2 inferred by ML. Terminal branches are presented with the accession sequence and species name. Taxonomic groups are indicated on right of tree. Node labels indicate the number of replicates of bootstrap support, based on 1000 iterations. The Eulipotyphla Sorex araneus was used to root the tree (PNG 1647 KB)
239_2018_9872_MOESM3_ESM.png
Supplementary Figure S3 Phylogenetic tree of mammalian CRISP3 inferred by ML. Terminal branches are presented with the accession sequence and species name. Taxonomic groups are indicated on right of the tree. Branches corresponding to rodent CRISP 3 duplications are colored in red. The rodent CRISP3 clade, in the box, was analyzed separately for positive selection. Node labels indicate the number of replicates of bootstrap support, based on 1000 iterations. The Afrotheria Echinops telfairi and Chrysochloris asiatica were used to root the tree (PNG 1473 KB)
239_2018_9872_MOESM4_ESM.png
Supplementary Figure S4 Histogram representing the site-specific ω estimates under neutral (below alignment) and selection (above alignment) branch-site models on one CRISP3 paralog of prairie vole (Microtus ochrogaster). The tested branch is indicated with a red box. Rodent CRISP3 phylogeny (on left) was used as background. The species names are indicated on terminal branches in species with a single CRISP3 or on internal branches in species with two CRISP3 paralogs, these indicated with bold labels. Significant PSSs are indicated with colored bars (yellow: BEB probability > 0.95; red: BEB probability > 0.99). Domain scheme of the CRISP3 protein is shown above the histogram (PNG 2079 KB)
239_2018_9872_MOESM11_ESM.pdf
Supplementary Table S1 List of CRISP sequences retrieved for this study. Information about CRISP gene, accession number and organisms is indicated (PDF 57 KB)
239_2018_9872_MOESM13_ESM.pdf
Supplementary Table S3 Positive selection sites identified by the likelihood site models implemented in Datamonkey server (PDF 28 KB)
Rights and permissions
About this article
Cite this article
Vicens, A., Treviño, C.L. Positive Selection in the Evolution of Mammalian CRISPs. J Mol Evol 86, 635–645 (2018). https://doi.org/10.1007/s00239-018-9872-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00239-018-9872-6