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Hua AB, Sweasy JB. Functional roles and cancer variants of the bifunctional glycosylase NEIL2. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:40-56. [PMID: 37310399 DOI: 10.1002/em.22555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Over 70,000 DNA lesions occur in the cell every day, and the inability to properly repair them can lead to mutations and destabilize the genome, resulting in carcinogenesis. The base excision repair (BER) pathway is critical for maintaining genomic integrity by repairing small base lesions, abasic sites and single-stranded breaks. Monofunctional and bifunctional glycosylases initiate the first step of BER by recognizing and excising specific base lesions, followed by DNA end processing, gap filling, and finally nick sealing. The Nei-like 2 (NEIL2) enzyme is a critical bifunctional DNA glycosylase in BER that preferentially excises cytosine oxidation products and abasic sites from single-stranded, double-stranded, and bubble-structured DNA. NEIL2 has been implicated to have important roles in several cellular functions, including genome maintenance, participation in active demethylation, and modulation of the immune response. Several germline and somatic variants of NEIL2 with altered expression and enzymatic activity have been reported in the literature linking them to cancers. In this review, we provide an overview of NEIL2 cellular functions and summarize current findings on NEIL2 variants and their relationship to cancer.
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Affiliation(s)
- Anh B Hua
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
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Ghazi BK, Bangash MH, Razzaq AA, Kiyani M, Girmay S, Chaudhary WR, Zahid U, Hussain U, Mujahid H, Parvaiz U, Buzdar IA, Nawaz S, Elsadek MF. In Silico Structural and Functional Analyses of NLRP3 Inflammasomes to Provide Insights for Treating Neurodegenerative Diseases. BIOMED RESEARCH INTERNATIONAL 2023; 2023:9819005. [PMID: 36726838 PMCID: PMC9886462 DOI: 10.1155/2023/9819005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/08/2022] [Accepted: 11/24/2022] [Indexed: 01/24/2023]
Abstract
Inflammasomes are cytoplasmic intracellular multiprotein complexes that control the innate immune system's activation of inflammation in response to derived chemicals. Recent advancements increased our molecular knowledge of activation of NLRP3 inflammasomes. Although several studies have been done to investigate the role of inflammasomes in innate immunity and other diseases, structural, functional, and evolutionary investigations are needed to further understand the clinical consequences of NLRP3 gene. The purpose of this study is to investigate the structural and functional impact of the NLRP3 protein by using a computational analysis to uncover putative protein sites involved in the stabilization of the protein-ligand complexes with inhibitors. This will allow for a deeper understanding of the molecular mechanism underlying these interactions. It was found that human NLRP3 gene coexpresses with PYCARD, NLRC4, CASP1, MAVS, and CTSB based on observed coexpression of homologs in other species. The NACHT, LRR, and PYD domain-containing protein 3 is a key player in innate immunity and inflammation as the sensor subunit of the NLRP3 inflammasome. The inflammasome polymeric complex, consisting of NLRP3, PYCARD, and CASP1, is formed in response to pathogens and other damage-associated signals (and possibly CASP4 and CASP5). Comprehensive structural and functional analyses of NLRP3 inflammasome components offer a fresh approach to the development of new treatments for a wide variety of human disorders.
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Affiliation(s)
| | | | | | | | - Shishay Girmay
- Department of Animal Science, College of Dryland Agriculture, Samara University, Ethiopia
| | | | - Usman Zahid
- Acute & Specialty Medicine Hospital Epsom & St. Helier University Hospitals NHS Trust Medical College, Faisalabad Medical University, Pakistan
| | | | - Huma Mujahid
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Usama Parvaiz
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Shah Nawaz
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Mohamed Farouk Elsadek
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Saudi Arabia
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Parveen S, Zhu P, Shafique L, Lan H, Xu D, Ashraf S, Ashraf S, Sherazi M, Liu Q. Molecular Characterization and Phylogenetic Analysis of Casein Gene Family in Camelus ferus. Genes (Basel) 2023; 14:genes14020256. [PMID: 36833182 PMCID: PMC9957437 DOI: 10.3390/genes14020256] [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: 10/24/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Camel milk is known for its exceptional medical uses. It has been used since ancient times to treat infant diarrhea, hepatitis, insulin-dependent diabetes (IDDM), lactose intolerance, alcohol-induced liver damage, allergies, and autism. It has the power to treat several diseases, with cancer being the most significant. This study investigated the evolutionary relationship, physiochemical characteristics, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in Camelus ferus. Molecular phylogenetics showing the camelid species clustered casein nucleotide sequences into four groups: CSN1S1, CSN2, CSN1S2, and CSN3. The casein proteins from camels were evaluated and found to be unstable, thermostable, and hydrophilic. CSN1S2, CSN2, and CSN3 were acidic, but CSN1S1 was basic. CSN1S1 showed positive selection for one amino acid (Q), CSN1S2 and CSN2 for three (T, K, Q), and CSN3 showed no positive selection. We also compared high-milk-output species such as cattle (Bos Tarus) and low-milk-yield species such as sheep (Ovies Aries) with camels (Camel ferus) and discovered that YY1 sites are more frequent in sheep than in camels and very low in cattle. We concluded that the ratio of YY1 sites in these species may affect milk production.
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Affiliation(s)
- Shakeela Parveen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
- Correspondence: (L.S.); (Q.L.)
| | - Hong Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Dingyun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Sana Ashraf
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Saba Ashraf
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Maryam Sherazi
- Department of Dairy Technology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Correspondence: (L.S.); (Q.L.)
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A Simulation Analysis and Screening of Deleterious Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) in Sheep LEP Gene. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7736485. [PMID: 35978633 PMCID: PMC9377880 DOI: 10.1155/2022/7736485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Leptin is a polypeptide hormone produced in the adipose tissue and governs many processes in the body. Recently, polymorphisms in the LEP gene revealed a significant change in body weight regulation, energy balance, food intake, and reproductive hormone secretion. This study considers its crucial role in the regulation of the economically important traits of sheep. Several computational tools, including SIFT, Predict SNP2, SNAP2, and PROVEAN, have been used to screen out the deleterious nsSNPs. Following the screening of 11 nsSNPs in the sheep genome, 5 nsSNPs, T86M (C → T), D98N (G → A), N136T (A → C), R142Q (G → A), and P157Q (C → A), were predicted to have a significant deleterious effect on the LEP protein function, leading to phenotypic difference. The analysis of proteins’ stability change due to amino acid substitution using the I-stable, SDM, and DynaMut consistently confirmed that three nsSNPs (T86M (C → T), D98N (G → A), and P157Q (C → A)) increased protein stability. It is suggested that these three nsSNPs may enhance the evolvability of LEP protein, which is vital for the evolutionary adaptation of sheep. Our findings demonstrate that the five nsSNPs reported in this study might be responsible for sheep’s structural and functional modifications of LEP protein. This is the first comprehensive report on the sheep LEP gene. It narrow downs the candidate nsSNPs for in vitro experiments to facilitate the development of reliable molecular markers for associated traits.
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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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