[Retracted] In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

Ahmad, Hafiz Ishfaq; Afzal, Gulnaz; Jamal, Adil; Kiran, Shumaila; Khan, Mueen Alam; Mehmood, Khalid; Kamran, Zahid; Ahmed, Irfan; Ahmad, Shakeel; Ahmad, Asmar; Hussain, Javed; Almas, Sadaf

doi:10.1155/2021/5574789

Cited by 15 publications

(14 citation statements)

References 60 publications

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“…Interestingly, we detected positive selection in most mammalian clades in the data set when looking at the MAVS gene. Given that multi-nucleotide mutations might lead to erroneous positive selection implications in branch-site analysis, we further verified our results using the aBSREL (42). Similar selection patterns were identified between the aBSREL and site-model (Figure 3).…”

Section: Discussionsupporting

confidence: 76%

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Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals

Ahmad

Afzal

Iqbal³

et al. 2022

Front. Vet. Sci.

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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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Section: Discussionsupporting

confidence: 76%

“…MrBayes v3.1.2 (41) was used to summarize the phylogenetic tree, with the top 25% removed. We utilized MEGA6's maximum likelihood (ML) approach to explore the connection between the sampled and related bird species (42). The data were examined using the T92+G model.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals

Ahmad

Afzal

Iqbal³

et al. 2022

Front. Vet. Sci.

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“…The aBS-REL and site models both showed comparable patterns of selection. The findings show that the general selection trends we observed are correct [ 21 , 23 ].…”

Section: Discussionsupporting

confidence: 61%

“…Ensembl and NCBI databases were used to retrieve the genomic sequences of Nei-like DNA glycosylase genes (NEIL1, NEIL2, and NIL3) in the vertebrate species. To extract nonredundant protein sequences, the human Nei-like DNA glycosylase protein sequences (ENSG00000140398, ENSG00000154328, and ENSG00000109674) were utilized in a BLAST search [ 21 ]. The accession numbers of these genes were used to search the NCBI and Ensembl databases for coding sequences (CDS) of vertebrate species (Supplementary Tables S1-S3 ).…”

Section: Methodsmentioning

confidence: 99%

Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates

Ahmad

Afzal

Sadia

et al. 2022

Oxidative Medicine and Cellular Longevity

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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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“…The promoter is the central DNA element separated into distal, proximal, and core regions and is meant to regulate the transcription of genes. To infer the promoter areas of TNP1 , three distinct computational tools were used in this investigation, including Promoter Scan [ 20 ], Promoter 2.0 Prediction Server [ 21 , 22 ], and Neural Network Promoter Prediction [ 23 ]. Promoter Scan is the computer program meant to recognize the high percentage of Pol II promoter sequences while allowing very few false positives.…”

Section: Methodsmentioning

confidence: 99%

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

et al. 2022

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Transition nuclear proteins (TNPs), the principal proteins identified in the condensing spermatids chromatin, have been found to play a key role in histone displacement and chromatin condensation during mammalian spermatogenesis. One such gene belonging to the TNP family called TNP1 gene is abundantly expressed in the regulation of spermatogenesis, and its sequence is remarkably well conserved among mammals. Genomic analysis, by sequencing and computational approach, was used to identify the novel polymorphisms and to evaluate the molecular regulation of TNP1 gene expression in Sahiwal cattle breeding bulls. DNA samples were sequenced to identify novel single nucleotide polymorphisms (SNPs) in the TNP1 gene. Modern computational tools were used to predict putative transcription factor binding in the TNP1 promoter and CpG islands in the TNP1 promoter region. In the TNP1 gene, four SNPs, three TATA boxes, and one CAAT box were identified. One CAAT box was discovered at 89 bp upstream of start site ATG. The computational analyses indicated that the polymorphisms inside the promoter sequence results in an added HNF-1 transcription factor binding site. In contrast, the other variations may remove the naturally occurring SRF transcription factor binding site. The CpG islands in the TNP1 promoter region were predicted to be absent by the MethPrimer program before and after SNP site mutations. These findings pave the way for more research into the TNP1 gene’s promoter activity and the links between these SNPs and reproductive attributes in the Sahiwal breeding bulls.

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[Retracted] In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

Cited by 15 publications

References 60 publications

Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals

Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals

Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

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