Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa.
World J Microbiol Biotechnol. 2019 Jul 22;35(8):118. doi: 10.1007/s11274-019-2693-y.
The fungal genus Ustilago consists of intimidating pathogens associated with disease manifestations in plants of agricultural importance and gravity. Rapid progress of genome sequencing has opened the floodgates for biological research. Availability of Ustilago genomes provides a scope to explore complex codon and amino acid usage patterns in the genus. An extensive scrutiny of the factors underlying the complex modalities of codon and amino acid usage in Ustilago has been executed in the present analysis. Multivariate statistical analysis revealed a dominant effect of natural selection pressure, aimed at translational accuracy, to be operative on the codon usage behavior. Subtle impact of GC compositional constraint was also evident on the codon usage patterns. Gene expressivity was inferred to be the most crucial determinant governing observed codon usage variations. Amino acid usage patterns were found to be significantly governed by aromatic and hydrophobic characters of the encoded proteins. GC content and length of protein coding sequences also had considerable influence on the amino acid usage signatures. Extensive analysis of codon context variations revealed that UpA dinucleotides were strictly avoided at the codon-codon junctions (cP3-cA1) which might be attributed to reduce the risk of nonsense mutations and subsequently, improve translational finesse. Identification of the optimal codons, employed preferentially among the genes with high expressivity, and estimation of preferred and avoided codon pairs in Ustilago promises to be useful pertaining to mutational experiments at the codonic level, targeted to thwart the growth of Ustilago and combat associated pathogenesis.
黑粉菌属（Ustilago）包含一些令人畏惧的病原体，这些病原体与具有重要农业意义和严重程度的植物疾病表现有关。基因组测序的快速进展为生物研究开辟了大门。黑粉菌基因组的可用性为探索该属中复杂的密码子和氨基酸使用模式提供了机会。本分析对导致黑粉菌复杂密码子和氨基酸使用模式的因素进行了广泛的研究。多变量统计分析表明，自然选择压力的主导作用（旨在提高翻译准确性）对密码子使用行为起作用。GC 组成约束的微妙影响也明显影响了密码子使用模式。基因表达能力被推断为控制观察到的密码子使用变化的最关键决定因素。氨基酸使用模式被发现主要受编码蛋白的芳香族和疏水性特征控制。GC 含量和蛋白质编码序列的长度也对氨基酸使用特征有相当大的影响。对密码子上下文变化的广泛分析表明，在密码子-密码子连接处（cP3-cA1）严格避免了 UpA 二核苷酸，这可能是为了降低无意义突变的风险，从而提高翻译的精细度。鉴定在高表达性基因中优先使用的最优密码子，并估计黑粉菌中偏好和避免的密码子对，有望在针对密码子水平的突变实验中派上用场，旨在阻止黑粉菌的生长并对抗相关的发病机制。
