Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration

Khandia, Rekha; Pandey, Megha; Rzhepakovsky, Igor Vladimirovich; Khan, Azmat Ali; Αλεξίου, Αθανάσιος

doi:10.1007/s12035-022-03081-1

Cited by 3 publications

(1 citation statement)

References 113 publications

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“…GRAVY showed a significant positive correlation with GC composition at all codon positions, while AROMA had no correlation ( Table 1 ). Overall, the analysis revealed that composition significantly influences the hydropathicity and aromaticity of polyproteins encoded by the HCV genome [ 56 ].…”

Section: Resultsmentioning

confidence: 99%

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

et al. 2023

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Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.

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Section: Resultsmentioning

confidence: 99%

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

et al. 2023

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Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer’s Disease as a Part of Host-Pathogen Interaction

Gurjar,

Khan,

Alanazi

et al. 2024

JAD

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Background: Herpes simplex virus type 1 (HSV-1) is associated with Alzheimer’s disease, which goes into a cycle of latency and reactivation. The present study was envisaged to understand the reasons for latency and specific molecular patterns present in the HSV-1. Objective: The objective is the molecular dissection of Herpes simplex virus type 1 to elucidate molecular mechanisms behind latency and compare its codon usage patterns with genes modulated during Alzheimer’s disease as a part of host-pathogen interaction. Methods: In the present study, we tried to investigate the potential reasons for the latency of HSV-1 virus bioinformatically by determining the CpG patterns. Also, we investigated the codon usage pattern, the presence of rare codons, codon context, and protein properties. Results: The top 222 codon pairs graded based on their frequency in the HSV-1 genome revealed that with only one exception (CUG-UUU), all other codon pairs have codons ending with G/C. Considering it an extension of host-pathogen interaction, we compared HSV-1 codon usage with that of codon usage of genes modulated during Alzheimer’s disease, and we found that CGT and TTT are only two codons that exhibited similar codon usage patterns and other codons showed statistically highly significant different codon preferences. Dinucleotide CpG tends to mutate to TpG, suggesting the presence of mutational forces and the imperative role of CpG methylation in HSV-1 latency. Conclusions: Upon comparison of codon usage between HSV-1 and Alzheimer’s disease genes, no similarities in codon usage were found as a part of host-pathogen interaction. CpG methylation plays an imperative role in latency HSV-1.

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Pharmacokinetics of Amikacin in Eye Media Using Various Drugs

Bersanova,

Batkhieva,

Baramiya

et al. 2023

Pharmacophore

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Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration

Cited by 3 publications

References 113 publications

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer’s Disease as a Part of Host-Pathogen Interaction

Pharmacokinetics of Amikacin in Eye Media Using Various Drugs

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