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Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus

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Abstract

The helicase gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is not only involved in viral DNA replication, but also plays a role in viral host range. To identify the codon usage bias of helicase of AcMNPV, the codon usage bias of helicase was especially studies in AcMNPV and 41 reference strains of baculoviruses by calculating the codon adaptation index (CAI), effective number of codon (ENc), relative synonymous codon usage (RSCU), and other indices. The helicase of baculovirus is less biased (mean ENc = 50.539 > 40; mean CAI = 0.246). AcMNPV helicase has a strong bias toward the synonymous codons with G and C at the third codon position (GC3s = 53.6%). The plot of GC3s against ENc values revealed that GC compositional constraints are the main factor that determines the codon usage bias of major of helicase. Several indicators supported that the codon usage pattern of helicase is mainly subject to mutation pressure. Analysis of variation in codon usage and amino acid composition indicated AcMNPV helicase shows the significant preference for one or more postulated codons for each amino acid. A cluster analysis based on RSCU values suggested that AcMNPV is evolutionarily closer to members of group I alphabaculovirus. Comparison of the codon usage pattern among E. coli, yeast, mouse, human and AcMNPV showed that yeast is a suitable expression system for AcMNPV helicase. AcMNPV helicase shows weak codon usage bias. This study may help in elucidating the functional mechanism of AcMNPV helicase and the evolution of baculovirus helicases.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31501701) and the Plant Foundation for Young Scientists of Henan University (CX0000A40557).

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Authors and Affiliations

  1. School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China

    Hongju Wang & Wenqiang Wei

  2. Huaihe Hospital, Henan University, Kaifeng, 475000, Henan, China

    Tao Meng

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  1. Hongju Wang
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  2. Tao Meng
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Correspondence to Wenqiang Wei.

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Author Wenqiang Wei declares that he has no conflict of interest. Author Hongju Wang declares that she has no conflict of interest. Author Tao Meng declares that he has no conflict of interest.

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Wang, H., Meng, T. & Wei, W. Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus. Genes Genom 40, 767–780 (2018). https://doi.org/10.1007/s13258-018-0689-x

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