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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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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] [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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Ahmad MZ, Ahmad HI, Gul A, Shah Z, Ahmad B, Ahmed S, Al-Ghamdi AA, S. Elshikh M, Jamil A, Nasir JA, Dvořáčková H, Dvořáček J. Genome-wide analysis of sucrose synthase family in soybean and their expression in response to abiotic stress and seed development. PLoS One 2022; 17:e0264269. [PMID: 35213642 PMCID: PMC8880960 DOI: 10.1371/journal.pone.0264269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/07/2022] [Indexed: 01/18/2023] Open
Abstract
The sucrose synthase (SS) is an important enzyme family which play a vital role in sugar metabolism to improve the fruit quality of the plants. In many plant species, the members of SS family have been investigated but the detailed information is not available in legumes particularly and Glycine max specifically. In the present study, we found thirteen SS members (GmSS1-GmSS13) in G. max genome. High conserved regions were present in the GmSS sequences that may due to the selection pressure during evolutionary events. The segmental duplication was the major factor to increase the number of GmSS family members. The identified thirteen GmSS genes were divided into Class I, Class II and Class III with variable numbers of genes in each class. The protein interaction of GmSS gave the co-expression of sucrose synthase with glucose-1-phosphate adenylyltransferase while SLAC and REL test found number of positive sites in the coding sequences of SS family members. All the GmSS family members except GmSS7 and few of class III members, were highly expressed in all the soybean tissues. The expression of the class I members decreased during seed development, whireas, the class II members expression increased during the seed developing, may involve in sugar metabolism during seed development. Solexa sequencing libraries of acidic condition (pH 4.2) stress samples showed that the expression of class I GmSS genes increased 1- to 2-folds in treated samples than control. The differential expression pattern was observed between the members of a paralogous. This study provides detailed genome-wide analysis of GmSS family in soybean that will provide new insights for future evolutionary and soybean breeding to improve the plant growth and development.
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Affiliation(s)
| | - Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asma Gul
- Department of Statistics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Zamarud Shah
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Bushra Ahmad
- Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Shakeel Ahmed
- Institute de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Abdullah Ahmed Al-Ghamdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed S. Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Arshad Jamil
- Department of Plant Breeding and Genetics, University of Agriculture, D.I. Khan, Pakistan
| | - Jamal Abdul Nasir
- Department of Plant Breeding and Genetics, Gomal University, D.I. Khan, Pakistan
| | - Helena Dvořáčková
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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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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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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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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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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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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Tangredi BP, Lawler DF. Osteoarthritis from evolutionary and mechanistic perspectives. Anat Rec (Hoboken) 2019; 303:2967-2976. [PMID: 31854144 DOI: 10.1002/ar.24339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/15/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
Abstract
Developmental osteogenesis and the pathologies associated with tissues that normally are mineralized are active areas of research. All of the basic cell types of skeletal tissue evolved in early aquatic vertebrates. Their characteristics, transcription factors, and signaling pathways have been conserved, even as they adapted to the challenge imposed by gravity in the transition to terrestrial existence. The response to excess mechanical stress (among other factors) can be expressed in the pathologic phenotype described as osteoarthritis (OA). OA is mediated by epigenetic modification of the same conserved developmental gene networks, rather than by gene mutations or new chemical signaling pathways. Thus, these responses have their evolutionary roots in morphogenesis. Epigenetic channeling and heterochrony, orchestrated primarily by microRNAs, maintain the sequence of these responses, while allowing variation in their timing that depends at least partly on the life history of the individual.
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Affiliation(s)
- Basil P Tangredi
- Vermont Institute of Natural Sciences, Quechee, Vermont
- Sustainable Agriculture Program, Green Mountain College, Poultney, Vermont
| | - Dennis F Lawler
- Center for American Archaeology, Kampsville, Illinois
- Illinois State Museum, Springfield, Illinois
- Pacific Marine Mammal Center, Laguna Beach, California
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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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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: 101] [Impact Index Per Article: 16.8] [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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Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, Chen J, Ma Y, Liu X, Du X, Zhao S. Detecting the Population Structure and Scanning for Signatures of Selection in Horses ( Equus caballus) From Whole-Genome Sequencing Data. Evol Bioinform Online 2018; 14:1176934318775106. [PMID: 29899660 PMCID: PMC5990873 DOI: 10.1177/1176934318775106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/14/2018] [Indexed: 12/18/2022] Open
Abstract
Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Pan Ni
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Hafiz Ishfaq Ahmad
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - M Gemingguli
- College of Animal Science, Tarim University, Alar, China
| | | | - D Gulibaheti
- College of Animal Science, Tarim University, Alar, China
| | - Yaping Fang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Haiyang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Akhtar Rasool Asif
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jianhai Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiangdong Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
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