Cao Hong-Wei, Li De-Shan, Zhang Hua
College of Biological Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319 China ; College of Life Science, Northeast Agricultural University, Harbin, 150030 China.
College of Life Science, Northeast Agricultural University, Harbin, 150030 China.
Virusdisease. 2014 Jan;25(1):132-6. doi: 10.1007/s13337-013-0175-7. Epub 2013 Nov 12.
Newcastle disease virus (NDV) hemagglutinin-neuraminidase (HN) is a multifunctional protein, which possesses both the receptor recognition and neuraminidase activities. The fusion (F) protein is a type I membrane glycoprotein that mediates the merger of the viral envelope to the host cell membrane. Although the functions of the HN and F proteins have been well studied, however, the factors shaping synonymous codon usage bias and nucleotide composition in HN and F genes have been few reported. In our study, we analyzed synonymous codon usage using the 69 NDV HN and F genes, respectively. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in HN and F genes. In addition, other factors, such as the aromaticity and hydrophobicity, also influence the codon usage variation among HN and F genes. This study represents the most comprehensive analysis to date of NDV HN and F genes codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.
新城疫病毒（NDV）血凝素神经氨酸酶（HN）是一种多功能蛋白，兼具受体识别和神经氨酸酶活性。融合（F）蛋白是一种I型膜糖蛋白，介导病毒包膜与宿主细胞膜的融合。尽管对HN和F蛋白的功能已进行了充分研究，然而，关于影响HN和F基因同义密码子使用偏好及核苷酸组成的因素却鲜有报道。在我们的研究中，我们分别使用69个NDV的HN和F基因分析了同义密码子的使用情况。碱基组成与密码子使用偏好之间的总体相关性表明，突变压力而非自然选择是决定HN和F基因密码子使用偏好的主要因素。此外，其他因素，如芳香性和疏水性，也会影响HN和F基因间密码子使用的差异。本研究是迄今为止对NDV的HN和F基因密码子使用模式最全面的分析，并为密码子使用偏好机制提供了基本认识。
