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Riaz Z, Hussain M, Parveen S, Sultana M, Saeed S, Ishaque U, Faiz Z, Tayyab M. In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens. Mol Biotechnol 2023:10.1007/s12033-023-00944-3. [PMID: 37914865 DOI: 10.1007/s12033-023-00944-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-β propeptide and TGF-β super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.
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Affiliation(s)
- Zainab Riaz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Punjab, Pakistan.
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
- Institue of Zoology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Urwah Ishaque
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
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Duarte MA, Fernandes CR, Heckel G, da Luz Mathias M, Bastos-Silveira C. Variation and Selection in the Putative Sperm-Binding Region of ZP3 in Muroid Rodents: A Comparison between Cricetids and Murines. Genes (Basel) 2021; 12:genes12091450. [PMID: 34573431 PMCID: PMC8469249 DOI: 10.3390/genes12091450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
In mammals, the zona pellucida glycoprotein 3 (ZP3) is considered a primary sperm receptor of the oocyte and is hypothesized to be involved in reproductive isolation. We investigated patterns of diversity and selection in the putative sperm-binding region (pSBR) of mouse ZP3 across Cricetidae and Murinae, two hyperdiverse taxonomic groups within muroid rodents. In murines, the pSBR is fairly conserved, in particular the serine-rich stretch containing the glycosylation sites proposed as essential for sperm binding. In contrast, cricetid amino acid sequences of the pSBR were much more variable and the serine-rich motif, typical of murines, was generally substantially modified. Overall, our results suggest a general lack of species specificity of the pSBR across the two muroid families. We document statistical evidence of positive selection acting on exons 6 and 7 of ZP3 and identified several amino acid sites that are likely targets of selection, with most positively selected sites falling within or adjacent to the pSBR.
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Affiliation(s)
- Margarida Alexandra Duarte
- Champalimaud Centre for the Uknown, Champalimaud Research, Champalimaud Foundation, Avenida Brasília, 1400-038 Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência, Departamento de Zoologia e Antropologia, Universidade de Lisboa, Rua da Escola Politécnica, 58, Lisboa, 1250-102 Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
- Centro de Estudos de Ambiente e Mar, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Correspondence:
| | - Carlos Rodríguez Fernandes
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (C.R.F.); (C.B.-S.)
- Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland;
- SIB Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Amphipole, CH-1015 Lausanne, Switzerland
| | - Maria da Luz Mathias
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
- Centro de Estudos de Ambiente e Mar, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cristiane Bastos-Silveira
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (C.R.F.); (C.B.-S.)
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Carlisle JA, Swanson WJ. Molecular mechanisms and evolution of fertilization proteins. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:652-665. [PMID: 33015976 DOI: 10.1002/jez.b.23004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022]
Abstract
Sexual reproduction involves a cascade of molecular interactions between the sperm and the egg culminating in cell-cell fusion. Vital steps mediating fertilization include chemoattraction of the sperm to the egg, induction of the sperm acrosome reaction, dissolution of the egg coat, and sperm-egg plasma membrane binding and fusion. Despite decades of research, only a handful of interacting gamete recognition proteins (GRPs) have been identified across taxa mediating each of these steps, most notably in abalone, sea urchins, and mammals. This review outlines and compares notable GRP pairs mediating sperm-egg recognition in these three significant model systems and discusses the molecular basis of species-specific fertilization driven by GRP function. In addition, we explore the evolutionary theory behind the rapid diversification of GRPs between species. In particular, we focus on how the coevolution between interacting sperm and egg proteins may contribute to the formation of boundaries to hybridization. Finally, we discuss how pairing structural information with evolutionary insights can improve our understanding of mechanisms of fertilization and their origins.
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Affiliation(s)
- Jolie A Carlisle
- Department of Genome Sciences, University of Washington Medical School, Seattle, Washington, USA
| | - Willie J Swanson
- Department of Genome Sciences, University of Washington Medical School, Seattle, Washington, USA
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