Laboratorio de Microbiología Ambiental y Extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5290000, Chile.
Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile.
Genes (Basel). 2020 Oct 20;11(10):1227. doi: 10.3390/genes11101227.
is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of , in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly ( < 0.001) higher values of CAI, AAtAI, CPB, tAI, and lower values of Nc than non-induced genes. Cellulose-binding proteins and manganese peroxidases presented the highest adaptation values. We also identified an expansion of genes encoding glycine and glutamic acid tRNAs. Our results suggest that the metabolic specialization to use wood as the sole carbon source has introduced a bias in the codon usage of genes involved in lignocellulose degradation. This bias reduces codon diversity and increases codon usage adaptation to the tRNA pool available in . To our knowledge, this is the first study showing that codon usage is modified to improve the translation efficiency of a group of genes involved in a particular metabolic process.
是一种白腐真菌，在定殖枯木或木质纤维素化合物时对木质素矿化具有高度特异性。其木质纤维素降解系统由纤维素水解酶、锰过氧化物酶和漆酶组成，可催化木质纤维素的有效解聚和矿化。为了确定这种代谢特化是否改变了木质纤维素降解系统的密码子使用，从而提高其对真菌翻译机器的适应性，我们分析了对宿主密码子使用（CAI）、tRNA 池（tAI 和 AAtAI）、密码子对偏好性（CPB）和有效密码子数（Nc）的适应。这些指标与 在存在葡萄糖和山杨木时的基因表达相关。一般基因表达与指数值不相关。然而，在含有山杨木的培养基中，木质纤维素降解基因的表达诱导显示出明显（<0.001）更高的 CAI、AAtAI、CPB、tAI 值和更低的 Nc 值，而非诱导基因。纤维素结合蛋白和锰过氧化物酶表现出最高的适应值。我们还发现编码甘氨酸和谷氨酸 tRNA 的基因扩展。我们的结果表明，将木材作为唯一碳源的代谢特化导致木质纤维素降解基因的密码子使用出现偏差。这种偏差降低了密码子的多样性，增加了密码子使用对 中可用 tRNA 池的适应性。据我们所知，这是第一项表明密码子使用被修改以提高参与特定代谢过程的一组基因的翻译效率的研究。
