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Sharma A, Dubey PK, Kumar P, Tiwari KN, Tripathi A. Identification and molecular characterization of genes modulating progression of an oocyte from M-I to M-II in rat ovary. Am J Reprod Immunol 2024; 91:e13825. [PMID: 38389407 DOI: 10.1111/aji.13825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/02/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND To achieve oocyte competence for successful fertilization, bidirectional communication between oocyte and granulosa cells is crucial. The acquisition of meiotic competency in oocyte is facilitated by various regulatory genes however, expression pattern of these genes is not well documented during meiotic transition from Metaphase-I to Metaphase-II stage. Therefore, the present research analyzed the expression pattern of regulatory genes that are involved in the transition from M-I to M-II stages in rat oocyte. METHODS The analysis of the data was conducted by applying an array of bioinformatic tools. The investigation of gene group interactions was carried out by employing the STRING database, which relies on co-expression information. The gene ontology (GO) analysis was performed utilizing the comparative GO database. Functional annotation for GO and pathway enrichment analysis were performed for genes involved in networking. The GO obtained through computational simulations was subsequently validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. RESULTS The findings of our study suggest that there is a distinct gene expression pattern in both the oocyte and granulosa cells. This pattern indicates that oocyte-secreted factors, such as BMP15 and GDF9, play a crucial role in regulating the progression of the meiotic cell cycle from the M-I to M-II stages. We have also examined the level of mRNA expression of genes including CYP11A1, CYP19A1, and STAR, which are crucial for the steroidogenesis. CONCLUSIONS It is fascinating to observe that the oscillatory pattern of specific key genes may hold significance in the process of in vitro oocyte maturation, specifically during the transition from the M-I to M-II stage. It might be useful for determining biomarker genes and potential pathways that play a role in attaining oocyte competency, thereby aiding in the assessment of oocyte quality for the purpose of achieving successful fertilization.
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Affiliation(s)
- Alka Sharma
- Zoology Section, MMV, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Pawan K Dubey
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Pradeep Kumar
- Department of Botany, MMV, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Kavindra Nath Tiwari
- Department of Botany, MMV, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Anima Tripathi
- Zoology Section, MMV, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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2
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Yang X, Yang L. Current understanding of the genomic abnormities in premature ovarian failure: chance for early diagnosis and management. Front Med (Lausanne) 2023; 10:1194865. [PMID: 37332766 PMCID: PMC10274511 DOI: 10.3389/fmed.2023.1194865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Premature ovarian failure (POF) is an insidious cause of female infertility and a devastating condition for women. POF also has a strong familial and heterogeneous genetic background. Management of POF is complicated by the variable etiology and presentation, which are generally characterized by abnormal hormone levels, gene instability and ovarian dysgenesis. To date, abnormal regulation associated with POF has been found in a small number of genes, including autosomal and sex chromosomal genes in folliculogenesis, granulosa cells, and oocytes. Due to the complex genomic contributions, ascertaining the exact causative mechanisms has been challenging in POF, and many pathogenic genomic characteristics have yet to be elucidated. However, emerging research has provided new insights into genomic variation in POF as well as novel etiological factors, pathogenic mechanisms and therapeutic intervention approaches. Meanwhile, scattered studies of transcriptional regulation revealed that ovarian cell function also depends on specific biomarker gene expression, which can influence protein activities, thus causing POF. In this review, we summarized the latest research and issues related to the genomic basis for POF and focused on insights gained from their biological effects and pathogenic mechanisms in POF. The present integrated studies of genomic variants, gene expression and related protein abnormalities were structured to establish the role of etiological genes associated with POF. In addition, we describe the design of some ongoing clinical trials that may suggest safe, feasible and effective approaches to improve the diagnosis and therapy of POF, such as Filgrastim, goserelin, resveratrol, natural plant antitoxin, Kuntai capsule et al. Understanding the candidate genomic characteristics in POF is beneficial for the early diagnosis of POF and provides appropriate methods for prevention and drug treatment. Additional efforts to clarify the POF genetic background are necessary and are beneficial for researchers and clinicians regarding genetic counseling and clinical practice. Taken together, recent genomic explorations have shown great potential to elucidate POF management in women and are stepping from the bench to the bedside.
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Affiliation(s)
- Xu Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Yang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
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3
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Ahmad HI, Khan FA, Khan MA, Imran S, Akhtar RW, Pandupuspitasari NS, Negara W, Chen J. Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals. Genes (Basel) 2022; 14:genes14010015. [PMID: 36672756 PMCID: PMC9858190 DOI: 10.3390/genes14010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bactericidal/permeability-increasing protein, a primary factor of the innate immune system of mammals, participates in natural immune protection against invading bacteria. BPIFA1 actively contributes to host defense via multiple mechanisms, such as antibacterial, surfactant, airway surface liquid control, and immunomodulatory activities. However, the evolutionary history and selection forces on the BPIFA1 gene in mammals during adaptive evolution are poorly understood. This study examined the BPIFA1 gene of humans compared with that of other mammalian species to estimate the selective pressure derived by adaptive evolution. To assess whether or not positive selection occurred, we employed several different possibility tests (M1 vs. M2 and M7 vs. M8). The proportions of positively selected sites were significant, with a likelihood log value of 93.63 for the BPIFA1 protein. The Selecton server was used on the same dataset to reconfirm positive selection for specific sites by employing the Mechanistic-Empirical Combination model, thus providing additional evidence supporting the findings of positive selection. There was convincing evidence for positive selection signals in the BPIFA1 genes of mammalian species, which was more significant for selection signs and creating signals. We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. BPIFA1 activates the upper airway's innate immune system in response to numerous genetic signals in the mammalian genome. These findings highlight evolutionary advancements in immunoregulatory effects that play a significant role in the antibacterial and antiviral defenses of mammalian species.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Correspondence: (H.I.A.); (J.C.)
| | - Faheem Ahmed Khan
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore 54000, Pakistan
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Safdar Imran
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Rana Waseem Akhtar
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang 50275, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Correspondence: (H.I.A.); (J.C.)
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Ahmad HI, Iqbal A, Ijaz N, Ullah MI, Asif AR, Rahman A, Mehmood T, Haider G, Ahmed S, Mahmoud SF, Alghamdi FO, Al Amari HA, Simirgiotis MJ, Chen J. Molecular Evolution of the Activating Transcription Factors Shapes the Adaptive Cellular Responses to Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2153996. [PMID: 35873797 PMCID: PMC9300285 DOI: 10.1155/2022/2153996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
Reactive oxygen species (ROS) play an essential part in physiology of individual cell. ROS can cause damage to various biomolecules, including DNA. The systems that have developed to harness the impacts of ROS are antique evolutionary adaptations that are intricately linked to almost every aspect of cellular function. This research reveals the idea that during evolution, rather than being largely conserved, the molecular pathways reacting to oxidative stress have intrinsic flexibility. The coding sequences of the ATF2, ATF3, ATF4, and ATF6 genes were aligned to examine selection pressure on the genes, which were shown to be very highly conserved among vertebrate species. A total of 33 branches were explicitly evaluated for their capacity to diversify selection. After accounting for multiple testing, significance was determined using the likelihood ratio test with a threshold of p ≤ 0.05. Positive selection signs in these genes were detected across vertebrate lineages. In the selected test branches of our phylogeny, the synonymous rate variation revealed evidence (LRT, p value = 0.011 ≤ 0.05) of gene-wide episodic diversifying selection. As a result, there is evidence that diversifying selection occurred at least once on at least one test branch. These findings indicate that the activities of ROS-responsive systems are also theoretically flexible and may be altered by environmental selection pressure. By determining where the genes encoding these processes are "targeted" during evolution, we may better understand the mechanism of adaptation to oxidative stress during evolution.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asia Iqbal
- Department of Wild Life and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nabeel Ijaz
- Department of Clinical Science, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Irfan Ullah
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Akhtar Rasool Asif
- Department of Animal Sciences, University of Veterinary and Animal Sciences, Jhang, Pakistan
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
| | - Abdur Rahman
- Department of Animal Sciences, University of Veterinary and Animal Sciences, Jhang, Pakistan
- Department of Animal Nutrition, Afyon Kocatepe University, Turkey
| | - Tahir Mehmood
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore 53700, Punjab, Pakistan
| | - Ghulam Haider
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shakeel Ahmed
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000 Valdivia, Chile
| | - Samy F. Mahmoud
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fatimah Othman Alghamdi
- National Center for Biotechnology King Abdulaziz City for Science and Technology Riyadh, Saudi Arabia
| | - Hala Abdulrahman Al Amari
- National Center for Biotechnology King Abdulaziz City for Science and Technology Riyadh, Saudi Arabia
| | - Mario Juan Simirgiotis
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000 Valdivia, Chile
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong, Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
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5
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Hosseinzadeh S, Masoudi AA, Torshizi RV, Ehsani A. Identification of differentially expressed long noncoding RNAs in the ovarian tissue of ewes Shal and Sangsari using RNA-seq. Vet Med Sci 2022; 8:2138-2146. [PMID: 35667079 PMCID: PMC9514483 DOI: 10.1002/vms3.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility. Methods Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real‐time PCR to confirm the RNA‐seq. Results Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF‐1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary. Conclusion These results could pave the way for future efforts to address sheep prolificacy barriers.
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Affiliation(s)
- Shahram Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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6
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Silva RF, Lima LF, Ferreira ACA, Silva AFB, Alves DR, Alves BG, Oliveira AC, Morais SM, Rodrigues APR, Santos RR, Figueiredo JR. Eugenol Improves Follicular Survival and Development During in vitro Culture of Goat Ovarian Tissue. Front Vet Sci 2022; 9:822367. [PMID: 35573397 PMCID: PMC9096615 DOI: 10.3389/fvets.2022.822367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the effects of different concentrations (10, 20, or 40 μM) of eugenol (EUG 10, EUG 20, or EUG 40), ascorbic acid (50 μg/mL; AA) or anethole (300 μg/mL; ANE 300) on the in-vitro survival and development of goat preantral follicles and oxidative stress in the cultured ovarian tissue. Ovarian fragments from five goats were cultured for 1 or 7 days in Alpha Minimum Essential Medium (α-MEM+) supplemented or not with AA, ANE 300, EUG 10, EUG 20 or EUG 40. On day 7 of culture, when compared to MEM, the addition of EUG 40 had increased the rate of follicular development, as observed by a decrease in the proportion of primordial follicles alongside with an increase in the rate of normally developing follicles. Furthermore, EUG 40 significantly increased both follicular and oocyte diameters. Subsequently, ovarian fragments from three goats were cultured for 1 or 7 days in α-MEM+ supplemented or not with AA, ANE 300 or EUG 40. All tested antioxidants, except ANE 300, were able to significantly decrease the levels of reactive oxygen species in the ovarian tissue, but EUG 40 could most efficiently neutralize free radicals. All ovarian tissues cultured in the presence of antioxidants, especially EUG 40, presented a significant decrease in H3K4me3 labeling, indicating a silencing of genes that play a role in the inhibition of follicular activation and apoptosis induction. When compared to cultured control tissues, both EUG 40 and ANE 300 significantly increased the intensity of calreticulin labeling in growing follicles. The mRNA relative expression of ERP29 and KDM3A was significantly increased when the culture medium was supplemented with EUG 40, indicating a response to ER stress experienced during culture. In conclusion, EUG 40 improved in-vitro follicle survival, activation and development and decreased ROS production, ER stress and histone lysine methylation in goat ovarian tissue.
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Affiliation(s)
- R. F. Silva
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
- *Correspondence: R. F. Silva
| | - L. F. Lima
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
| | - Anna C. A. Ferreira
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
| | - A. F. B. Silva
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
| | - D. R. Alves
- Natural Product Chemistry Laboratory, State University of Ceara, Fortaleza, Brazil
| | - B. G. Alves
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
| | - A. C. Oliveira
- Superior Institute of Biomedical Science, State University of Ceará, Fortaleza, Brazil
| | - Selene M. Morais
- Natural Product Chemistry Laboratory, State University of Ceara, Fortaleza, Brazil
| | - Ana Paula R. Rodrigues
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
| | | | - J. R. Figueiredo
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary, State University of Ceara, Fortaleza, Brazil
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7
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Ahmad HI, Afzal G, Sadia S, Haider G, Ahmed S, Saeed S, Chen J. Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1144387. [PMID: 35419164 PMCID: PMC9001079 DOI: 10.1155/2022/1144387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022]
Abstract
Oxidative stress is a type of stress that damages DNA and can occur from both endogenous and exogenous sources. Damage to DNA caused by oxidative stress can result in base modifications that promote replication errors and the formation of sites of base loss, which pose unique challenges to the preservation of genomic integrity. However, the adaptive evolution of the DNA repair mechanism is poorly understood in vertebrates. This research aimed to explore the evolutionary relationships, physicochemical characteristics, and comparative genomic analysis of the Nei-like glycosylase gene family involved in DNA base repair in the vertebrates. The genomic sequences of NEIL1, NEIL2, and NEIL3 genes were aligned to observe selection constraints in the genes, which were relatively low conserved across vertebrate species. The positive selection signals were identified in these genes across the vertebrate lineages. We identified that only about 2.7% of codons in these genes were subjected to positive selection. We also revealed that positive selection pressure was increased in the Fapy-DNA-glyco and H2TH domain, which are involved in the base excision repair of DNA that has been damaged by oxidative stress. Gene structure, motif, and conserved domain analysis indicated that the Nei-like glycosylase genes in mammals and avians are evolutionarily low conserved compared to other glycosylase genes in other "vertebrates" species. This study revealed that adaptive selection played a critical role in the evolution of Nei-like glycosylase in vertebrate species. Systematic comparative genome analyses will give key insights to elucidate the links between DNA repair and the development of lifespan in various organisms as more diverse vertebrate genome sequences become accessible.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sehrish Sadia
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Ghulam Haider
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shakeel Ahmed
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000 Valdivia, Chile
| | - Saba Saeed
- Institute of Physics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
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8
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Ahmad HI, Afzal G, Iqbal MN, Iqbal MA, Shokrollahi B, Mansoor MK, Chen J. Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals. Front Vet Sci 2022; 8:814765. [PMID: 35174241 PMCID: PMC8841730 DOI: 10.3389/fvets.2021.814765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 12/17/2022] Open
Abstract
The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | | | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Muhammad Khalid Mansoor
- Department of Microbiology, Faculty of Veterinary and Animal Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Jinping Chen
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9
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Villegas-Mirón P, Acosta S, Nye J, Bertranpetit J, Laayouni H. Chromosome X-wide Analysis of Positive Selection in Human Populations: Common and Private Signals of Selection and its Impact on Inactivated Genes and Enhancers. Front Genet 2021; 12:714491. [PMID: 34646300 PMCID: PMC8502928 DOI: 10.3389/fgene.2021.714491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic basis of population-specific adaptations genome-wide. Here, we present the analysis of recent selective sweeps, specifically in the X chromosome, in human populations from the third phase of the 1,000 Genomes Project using three different haplotype-based statistics. We describe instances of recent positive selection that fit the criteria of hard or soft sweeps, and detect a higher number of events among sub-Saharan Africans than non-Africans (Europe and East Asia). A global enrichment of neural-related processes is observed and numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection which might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.
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Affiliation(s)
- Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Sandra Acosta
- Department Pathology and Experimental Therapeutics, Medical School, University of Barcelona, Barcelona, Spain
| | - Jessica Nye
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
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10
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Bi Y, Li J, Wang X, He L, Lan K, Qu L, Lan X, Song X, Pan C. Two Novel Rare Strongly Linked Missense SNPs (P27R and A85G) Within the GDF9 Gene Were Significantly Associated With Litter Size in Shaanbei White Cashmere (SBWC) Goats. Front Vet Sci 2020; 7:406. [PMID: 32851004 PMCID: PMC7406713 DOI: 10.3389/fvets.2020.00406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/08/2020] [Indexed: 01/08/2023] Open
Abstract
Growth differentiation factor 9 (GDF9) is a high-fertility candidate gene that plays a crucial role in early folliculogenesis in female mammals. In this study, direct sequencing was used to screen possible SNP loci in the goat GDF9 gene. Three SNP loci, p.proline27alanine (P27R), p.leucine61leucine (L61L), and p.alanine85glycine (A85G), were identified in Shaanbei white cashmere (SBWC) goats. Among the three SNPs, two rare missense SNP loci (P27R and A85G) were discovered to be strongly linked with each other (D′ value = 0.926, r2 value = 0.703). Both P27R and A85G loci had two genotypes: wild type and heterozygous type. A85G exerted a significant effect on litter size (P = 0.029) in SBWC goats, and the heterozygous genotype was superior in comparison with the wild type. The heterozygous genotype was also superior in P27R but no significant association was found. However, the combination genotypes of P27R and A85G were identified to have superior effects on litter size (P = 3.8E−15). This information suggested that these two SNPs influenced litter size in goats synergistically. Combining this information with our previous studies, we propose that the GDF9 gene is the principal high-fertility candidate gene and that the A85G locus is a promising SNP that affects litter size in goats. These results may fill a research gap regarding rare mutations as well as provide crucial molecular markers that could be useful in marker-assisted selection (MAS) goat rearing when selecting superior individuals.
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Affiliation(s)
- Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jie Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Libang He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kangshu Lan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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11
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Adaptive evolution of peptidoglycan recognition protein family regulates the innate signaling against microbial pathogens in vertebrates. Microb Pathog 2020; 147:104361. [PMID: 32622926 DOI: 10.1016/j.micpath.2020.104361] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/28/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022]
Abstract
The innate immune system is the first line of defense in vertebrates against microbial pathogens. This defense system depends on the peptidoglycan pathogen recognition of receptors (PGRPs) existing in both invertebrates and vertebrates. Although some studies revealed the structural and functional differences between them, however, the evolutionary history and the selection pressures on these genes during adaptive evolution are poorly understood. In this study, we examined four (PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4) genes of 127 vertebrates' species, conserved across vertebrates to evaluate positive selection pressure drives by adaptive evolution. The codons under positive selection were recognized through likelihood tests by comparing different models based on ω ratios in these genes across the vertebrate species. The positive selection test used two sets of models M1a vs. M2a and M7 vs. M8. The results showed that the test of these genes in M1a vs. M2a was not significant with the likelihood value 2ΔlnL = 0, while the likelihood ratios (2ΔlnL) were 2ΔlnL = 12.386, 2ΔlnL = 4.9283, 2ΔlnL = 24.031, and 2ΔlnL = 103.39 for PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4 in M7 vs. M8, respectively. Our study identified the evidence of robust positive selection for these four genes across the vertebrates. These protuberant changes in PGRPs evolution of vertebrates reveal their role in innate immunity. Our study provides an insight based on PGRP genes to understand the evolution of host and pathogens interaction that leads to the progress of the novel conducts for immune diseases that include proteins linked to the recognition of pathogens.
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12
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Adaptive Molecular Evolution of AKT3 Gene for Positive Diversifying Selection in Mammals. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2584627. [PMID: 32550227 PMCID: PMC7256775 DOI: 10.1155/2020/2584627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/12/2020] [Accepted: 02/14/2020] [Indexed: 01/17/2023]
Abstract
The V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) gene is of the serine/threonine-protein kinase family and influences the production of milk fats and cholesterol by acting on the sterol administrative area restricting protein (SREBP). The AKT3 gene is highly preserved in animals, and during lactation in cattle, its expression increases. The AKT3 gene is expressed in the digestive system, mammary gland, and immune cells. A phylogenetic investigation was performed to clarify the evolutionary role of AKT3, by maximum probability. The AKT3 gene sequence data of various mammalian species was evident even with animals undergoing breeding selection. From 39 mammalian species studied, there was a signal of positive diversifying selection with Hominidae at 13Q, 16G, 23R, 24P, 121P, 294K, 327V, 376L, 397K, 445T, and 471F among other codon sites of the AKT3 gene. These sites were codes for amino acids such as arginine, proline, lysine, and leucine indicating major roles for the function of immunological proteins, and in particular, the study highlighted the importance of changes in gene expression of AKT3 on immunity.
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13
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Zhang Z, Tang J, He X, Di R, Chu M. Mutations in NLRP5 and NLRP9 are Associated with Litter Size in Small Tail Han Sheep. Animals (Basel) 2020; 10:ani10040689. [PMID: 32326631 PMCID: PMC7222816 DOI: 10.3390/ani10040689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/02/2020] [Accepted: 04/12/2020] [Indexed: 01/06/2023] Open
Abstract
Previous studies showed that the NLR family pyrin domain-containing 5 (NLRP5) and NLRP9 genes are two important reproductive genes; however, their effects on sheep litter size are unknown. Therefore, in this study, we first genotyped seven sheep breeds via the MassARRAY® SNP system at the loci g.60495375A > G, g.60495363G > A, and g.60499690C > A in NLRP5, and g.59030623T > C and g.59043397A > C in NLRP9. Our results revealed that each locus in most sheep breeds contained three genotypes. Then, we conducted population genetic analysis of single nucleotide polymorphisms in NLRP5 and NLRP9, and we found that the polymorphism information content value in all sheep breeds ranged from 0 to 0.36, and most sheep breeds were under Hardy-Weinberg equilibrium (p > 0.05). Furthermore, association analysis in Small Tail Han sheep indicated that two loci, g.60495363G > A in NLRP5 and g.59030623T > C in NLRP9, were highly associated with litter size. The mutation in g.60495363G > A may decrease interactions of NLRP5 with proteins, such as GDF9, whereas the mutation in g.59030623T > C may enhance the combining capacity of NLRP9 with these proteins; consequently, these mutations may influence the ovulation rate and even litter size. The findings of our study provide valuable genetic markers that can be used to improve the breeding of sheep and even other mammals.
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Affiliation(s)
- Zhuangbiao Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (J.T.); (X.H.); (R.D.)
| | - Jishun Tang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (J.T.); (X.H.); (R.D.)
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (J.T.); (X.H.); (R.D.)
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (J.T.); (X.H.); (R.D.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (J.T.); (X.H.); (R.D.)
- Correspondence: ; Tel.: +86-010-6281-9850
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14
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Ahmad HI, Zhou J, Ahmad MJ, Afzal G, Jiang H, Zhang X, Elokil AA, Khan MA, Li L, Li H, Ping L, Chen J. Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates. Aging (Albany NY) 2020; 12:3516-3557. [PMID: 32045365 PMCID: PMC7066927 DOI: 10.18632/aging.102827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Muhammad Jamil Ahmad
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Abdelmotaleb A. Elokil
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
- Animal Production Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Liu Ping
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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15
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Adaptation to host-specific bacterial pathogens drive rapid evolution of novel PhoP/PhoQ regulation pathway modulating the virulence. Microb Pathog 2020; 141:103997. [PMID: 31982569 DOI: 10.1016/j.micpath.2020.103997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 01/18/2023]
Abstract
The presence of the PhoP-PhoQ system is usually different in various bacterial groups, suggesting that PhoP can control the expression of different genes in species. However, little is known about the evolution of the PhoP-PhoQ system among bacterial pathogens. Here, we study the evolution of PhoP and PhoQ regulation in 15 species of Enterobacteriaceae family. We have determined that the regulatory objectives adopted by PhoP and PhoQ are mainly different, due to the result of horizontal gene transfer events and even the change in the genetic content between closely related species. We have compared many possibilities tests (M1 vs. M2 and M7 with M8) to determine the positive selection. Estimating parameters at M1 and M2, with positive selection in M2 of the two proteins. The proportions of positive selection sites significant with ω = 4.53076 for PhoP and ω = 4.21041 PhQ. M8 was significant for PhoP and PhQ proteins. To further confirm the positive selection results, we used the Selecton server to confer positive selection on individual sites using the Mechanistic-Empirical Combination model, and we noticed that several sites had been identified under selection pressure during the evolution. There was a strong indication for the positive selection in bacterial genes of PhoP and PhoQ showed the results. By the use of REL and IFEL, the positive selection for PhoP was detected 14 and 11 sites respectively at different codon positions. The positively selected sites of amino acids such as Arginine, Alanine, Lysine, and Leucine are more important for the production of signals. Our results suggest that the positive selection of PhoP-PhoQ genes in host adaptation during evolution raises an intriguing possibility causes subtle variations in actions of PhoP-PhoQ and also increases the opportunities that cause modification in protein structure for the evolution of increasing pathogenicity in bacterial pathogens.
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16
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Liu MN, Zhang K, Xu TM. The role of BMP15 and GDF9 in the pathogenesis of primary ovarian insufficiency. HUM FERTIL 2019; 24:325-332. [PMID: 31607184 DOI: 10.1080/14647273.2019.1672107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Endocrine and paracrine signals can be key regulators of ovarian physiology. The oocyte secretes growth factors which directly induce follicular development by a complex paracrine signalling process, and the transforming growth factorβ (TGF-β) superfamily has a pivotal role in this process. The bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) genes are relevant members of the TGF-β superfamily that encode proteins secreted by the oocytes into the ovarian follicles, where they contribute to creating an environment supporting follicle selection and growth. Their main functions include regulating cellular proliferation/differentiation, follicular survival/atresia, and oocyte maturation. Recent functional studies have validated genetic factors (Progesterone receptor membrane component 1 (PGRMC1)), Fragile X mental retardation 1 (FMR1, GDF9 and BMP15) as being causative of primary ovarian insufficiency (POI), BMP15/GDF9 gene variants were found to have a high incidence on the POI phenotype. This review considers the most recent research regarding the role of BMP15 and GDF9 in the genetic control of follicular development, paying special attention to the pathogenesis of POI.
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Affiliation(s)
- Meng-Na Liu
- Department of Clinical Laboratory, Jilin University Second Hospital , Changchun , China
| | - Kun Zhang
- Department of Research Center, Jilin University Second Hospital , Changchun , China
| | - Tian-Min Xu
- Department of Gynecology and Obstetrics, Jilin University Second Hospital , Changchun , China
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17
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Ahmad MJ, Ahmad HI, Adeel MM, Liang A, Hua G, Murtaza S, Mirza RH, Elokil A, Ullah F, Yang L. Evolutionary Analysis of Makorin Ring Finger Protein 3 Reveals Positive Selection in Mammals. Evol Bioinform Online 2019; 15:1176934319834612. [PMID: 31024214 PMCID: PMC6472170 DOI: 10.1177/1176934319834612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 01/12/2023] Open
Abstract
Makorin ring finger proteins (MKRNs) are part the of ubiquitin-proteasome system;
a complex system important for cell functions. Ubiquitin fate through
proteolytic, non-proteolytic pathways varies, depending on covalent linkage
between ubiquitin and protein substrates. Makorin ring finger protein 3 is an
integral part of covalent linkage of ubiquitin to protein substrates. Similar to
others imprinted genes, MKRN3 also evolve under positive selection; however,
which codons are specifically selected in MKRN3 during evolution are needed to
be explored. Different maximum-likelihood (ML) codon-based methodologies were
used to ascertain positive selection signatures in 22 mammalian sequences of
MKRN3 to probe an individual codon for positive selection signatures. By
applying the HyPhy software package implemented in the Data Monkey Web Server
and CODEML implemented in PAML, evolutionary analysis based on two Ml frameworks
were conducted. The analysis was executed by comparing M1a against M2a, M7
against M8, and PAML models and 2∆Lnl (LRT)
was resulted by likelihood logs. M1a contributed ω1 (dN/dS)
with LRT value (∆Lnl) 12.01, and positive
selection was found in M2a with ω3 = 2.23603. To further improve selection test,
M8 was compared to M7 with 2∆Lnl (LRT) 30.17,
and M8 showed positive selection with ω = 1.55759. The data were fit to M8 than
M7, which suggests that M8 was the most significant model of selection. M8 was
judged encouraging for this analysis and used to establish a positive selection
of MKRN3 proteins. We found Gly312 as a positively selected amino acid in a zinc
finger motif/Really Interesting New Gene (RING) finger motif; the former ones’
region is involved in RNA binding and the later ones in ubiquitin ligase
activity of the protein, vital for protein function. Selection analyses of MKRNs
might advance the developments in unique approaches that could lead to genetic
progress over the selection of superior individuals with the breeding values
higher for certain traits as ancestries to get the next generation.
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Affiliation(s)
- Muhammad Jamil Ahmad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Muhammad Muzammal Adeel
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Aixin Liang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Saeed Murtaza
- Faculty of veterinary sciences, Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Riaz Hussain Mirza
- Faculty of veterinary sciences, Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Abdelmotaleb Elokil
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Animal Production Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
| | - Farman Ullah
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Pakistan
| | - Liguo Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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18
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Wang X, Yang Q, Wang K, Yan H, Pan C, Chen H, Liu J, Zhu H, Qu L, Lan X. Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats. Theriogenology 2018; 125:115-121. [PMID: 30414564 DOI: 10.1016/j.theriogenology.2018.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 10/28/2022]
Abstract
Growth differentiation factor 9 (GDF9) gene is an effective intra-ovarian regulator; it plays a crucial role in early folliculogenesis in female mammals. The non synonymous mutations: g.3905A > C (also known as p.Gln320Pro/Q320P) and g.4135G > A (also know as p.Val397Ile/V397I), are two well-known and controversial single nucleotide polymorphisms (SNPs) within GDF9 gene in goats with different prolificacy, and so far, there were no studies on linkage between Q320P and V397I. Therefore, the aim of this work was to study whether Q320P and V397I mutations have a significant effect on litter size, in Shaanbei white cashmere goats (SBWC, n = 1511), and to explore the specific relationship between these two SNPs. The results showed that both of Q320P and V397I mutations exhibited three genotypes; the minor allele frequencies (MAF) of the SNPs were 0.286 and 0.477, respectively; and these two SNPs were in strong linkage disequilibrium (D' = 0.976, r2 = 0.348) in the studied goats. Moreover, association analyses revealed that Q320P was significantly associated with the first-born litter size in goats irrespective of the sample size (n = 1511; P = 0.008), while V397I significantly affected litter size until the sample size crossed 1300 (P = 0.015). Meanwhile, the diplotypes PP-II and QP-VI were observed to have a superior effect on litter size (P = 3.78 × 10-5) to that of the haplotypes (P = 1.12 × 10-7). Thus, the findings led us to assume that Q320P mutation was the major SNP affecting goat litter size. These findings can provide useful DNA markers for selecting superior individuals in marker-assisted selection (MAS) for breeding in relation to fecundity in goats.
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Affiliation(s)
- Xinyu Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Jinwang Liu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China.
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19
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GDF-9 and BMP-15 direct the follicle symphony. J Assist Reprod Genet 2018; 35:1741-1750. [PMID: 30039232 DOI: 10.1007/s10815-018-1268-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/13/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding the physiology underlying the complex dialog between the oocyte and its surrounding somatic cells within the ovarian follicle has been crucial in defining optimal procedures for the development of clinical approaches in ART for women suffering from infertility and ovarian dysfunction. Recent studies have implicated oocyte-secreted factors like growth differentiation factor 9 (GDF-9) and bone morphogenetic protein 15 (BMP-15), members of the transforming growth factor-beta (TGFβ) superfamily, as potent regulators of folliculogenesis and ovulation. These two factors act as biologically active heterodimers or as homodimers in a synergistic cooperation. Through autocrine and paracrine mechanisms, the GDF-9 and BMP-15 system has been shown to regulate growth, differentiation, and function of granulosa and thecal cells during follicular development playing a vital role in oocyte development, ovulation, fertilization, and embryonic competence. The present mini-review provides an overview of recent findings relating GDF-9 and BMP-15 as fundamental factors implicated in the regulation of ovarian function and discusses their potential role as markers of oocyte quality in women.
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20
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Ahmad HI, Ahmad MJ, Adeel MM, Asif AR, Du X. Positive selection drives the evolution of endocrine regulatory bone morphogenetic protein system in mammals. Oncotarget 2018; 9:18435-18445. [PMID: 29719616 PMCID: PMC5915083 DOI: 10.18632/oncotarget.24240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
The rapid evolution of reproductive proteins might be driven by positive Darwinian selection. The bone morphogenetic protein family is the largest within the transforming growth factor (TGF) superfamily. A little have been known about the molecular evolution of bone morphogenetic proteins exhibiting potential role in mammalian reproduction. In this study we investigated mammalian bone morphogenetic proteins using maximum likelihood approaches of codon substitutions to identify positive Darwinian selection in various species. The proportion of positively selected sites was tested by different likelihood models for individual codon, and M8 were found to be the best model. The percentage of positively elected sites under M8 are 2.20% with ω = 1.089 for BMP2, 1.6% with ω = 1.61 for BMP 4 0.53% for BMP15 with ω = 1.56 and 0.78% for GDF9 with ω = 1.93. The percentage of estimated selection sites under M8 is strong statistical confirmation that divergence of bone morphogenetic proteins is driven by Darwinian selection. For the proteins, model M8 was found significant for all proteins with ω > 1. To further test positive selection on particular amino acids, the evolutionary conservation of amino acid were measured based on phylogenetic linkage among sequences. For exploring the impact of these somatic substitution mutations in the selection region on human cancer, we identified one pathogenic mutation in human BMP4 and one in BMP15, possibly causing prostate cancer and six neutral mutations in BMPs. The comprehensive map of selection results allows the researchers to perform systematic approaches to detect the evolutionary footprints of selection on specific gene in specific species.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Muhammad Jamil Ahmad
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Muhammad Muzammal Adeel
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Akhtar Rasool Asif
- University of Veterinary and Animal Sciences, Lahore, Sub Campus Jhang, Pakistan
| | - Xiaoyong Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Ahmad HI, Liu G, Jiang X, Edallew SG, Wassie T, Tesema B, Yun Y, Pan L, Liu C, Chong Y, Yu ZJ, Jilong H. Maximum-likelihood approaches reveal signatures of positive selection in BMP15 and GDF9 genes modulating ovarian function in mammalian female fertility. Ecol Evol 2017; 7:8895-8902. [PMID: 29177034 PMCID: PMC5689494 DOI: 10.1002/ece3.3336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) and the growth factors (GDFs) play an important role in ovarian folliculogenesis and essential regulator of processes of numerous granulosa cells. BMP15 gene variations linked to various ovarian phenotypic consequences subject to the species, from infertility to improved prolificacy in sheep, primary ovarian insufficiency in women or associated with minor subfertility in mouse. To study the evolving role of BMP15 and GDF9, a phylogenetic analysis was performed. To find out the candidate gene associated with prolificacy in mammals, the nucleotide sequence of BMP15 and GDF9 genes was recognized under positive selection in various mammalian species. Maximum‐likelihood approaches used on BMP15 and GDF9 genes exhibited a robust divergence and a prompted evolution as compared to other TGFβ family members. Furthermore, among 32 mammalian species, we identified positive selection signals in the hominidae clade resulting to 132D, 147E, 163Y, 191W, and 236P codon sites of BMP15 and 162F, 188K, 206R, 240A, 244L, 246H, 248S, 251D, 253L, 254F and other codon sites of GDF9. The positively selected amino acid sites such as Alanine, Lucien, Arginine, and lysine are important for signaling. In conclusion, this study evidences that GDF9 and BMP15 genes have rapid evolution than other TGFß family members and was subjected to positive selection in the mammalian clade. Selected sites under the positive selection are of remarkable significance for the particular functioning of the protein and consequently for female fertility.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Guiqiong Liu
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Xunping Jiang
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Shishay Girmay Edallew
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Teketay Wassie
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Birhanu Tesema
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Yu Yun
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Liu Pan
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Chenhui Liu
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Yuqing Chong
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Zhao Jia Yu
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
| | - Han Jilong
- Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of the Ministry of Education College of Animal Science and Technology Huazhong Agricultural University Wuhan China
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