A Detailed Analysis of Codon Usages Bias and Affecting Factors in the Topoisomerase II Gene of Invertebrate iridescent virus 6

Yıl 2024, Cilt: 24 Sayı: 3, 492 - 503, 27.06.2024

Yeşim Aktürk Dizman

https://doi.org/10.35414/akufemubid.1388197

Öz

The topoisomerase II protein (ORF 045L) of invertebrate iridescent virus 6 (IIV6) plays essential roles in managing DNA topology during viral replication and transcription. Considering the importance of the topoisomerase II gene, a comprehensive analysis was conducted to explore the codon usage bias (CUB) of topoisomerase II genes of IIV6 and 9 reference invertebrate iridescent viruses (IIVs). In this research, the findings from the base composition analysis revealed that the IIV6 topoisomerase gene had a high A/T content, with nucleotide A being the most prevalent. The relative synonymous codon usage values for each codon demonstrated the presence of CUB. The effective number of codons (ENC) value for the IIV6 topoisomerase II gene is 34.80, signifying a significant CUB. The ENC plot indicates that all the diverse sequences lie beneath the standard curve, signifying that CUB is influenced not only by mutational pressure but also by other factors, including natural selection. The findings from the neutrality analysis indicate that the codon usage pattern (CUP) is more significantly shaped by natural selection, as evidenced by a regression line slope of 0.1602, compared to the influence of mutation pressure. Furthermore, it has been established that the nucleotide composition and dinucleotide content influence the CUB of the topoisomerase II gene in IIV6. The initial comprehensive analysis of CUB in the IIV6 topoisomerase II gene offers valuable insights into the gene's evolutionary processes.

Anahtar Kelimeler

Invertebrate iridescent virus 6, Topoisomerase II gene, 045L, Codon usage bias

Invertebrate iridescent virüs 6’nın Topoizomeraz II Genindeki Kodon Kullanım Eğiliminin ve Etkileyen Faktörlerin Ayrıntılı Analizi

Öz

Invertebrate iridescent virüs 6 (IIV6)’nın topoizomeraz II proteini (ORF 045L), viral replikasyon ve transkripsiyon sırasında DNA topolojisinin belirlenmesinde önemli roller oynar. Topoizomeraz II geninin önemi göz önünde bulundurularak, IIV6 ve 9 referans invertebrate iridescent virüs (IIVs)’ün topoizomeraz II genlerinin kodon kullanım eğilimini (CUB) araştırmak için kapsamlı bir analiz yapılmıştır. Bu araştırmada, baz bileşimi analizinden elde edilen bulgular, IIV6 topoizomeraz geninin yüksek bir A/T içeriğine sahip olduğunu ve A nükleotidinin en yaygın olduğunu göstermiştir. Her bir kodon için göreli sinonim kodon kullanım değerleri, kodon kullanım eğiliminin varlığını göstermiştir. IIV6 topoizomeraz II geni için etkin kodon sayısı (ENC) değeri 34,80'dir ve bu da önemli bir CUB’ye işaret etmektedir. ENC grafiği, tüm farklı dizilerin standart eğrinin altında yer aldığını ve kodon kullanım eğiliminin sadece mutasyon baskısından değil, doğal seçilim de dahil olmak üzere diğer faktörlerden de etkilendiğini göstermektedir. Nötraliti analizinden elde edilen bulgular, mutasyon baskısının etkisine kıyasla, 0,1602'lik regresyon çizgisi eğiminin de gösterdiği gibi, kodon kullanım modelinin doğal seçilim tarafından daha belirgin bir şekilde şekillendirildiğini göstermektedir. Ayrıca, nükleotid bileşiminin ve dinükleotid içeriğinin IIV6 topoizomeraz II geninin kodon kullanım eğilimini etkilediği tespit edilmiştir. IIV6 topoizomeraz II genindeki kodon kullanım eğiliminin ilk kapsamlı analizi, genin evrimsel süreçleri hakkında değerli bilgiler sunmaktadır.

Anahtar Kelimeler

Invertebrate iridescent virus 6;, Topoisomerase II gene;, 045L;, Codon usage bias

Kaynakça

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