Abstract
Background: Ceriporiopsis subvermispora is a white-rot fungus that displays a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. The lignocellulose degrading system from C. subvermispora is formed by genes that encode cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignin in the presence of Mn3+ through the formation of lipoperoxides from unsaturated lipid acids. This highly specific lignin-degrading system is unique among white-rot fungi. Methods: In order to determine if this metabolic specialization has modified codon usage of the ligninolytic system, leading to an increased 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 C. subvermispora, as evaluated by microarray in the presence of two carbon sources, glucose and Aspen wood.Results: General gene expression of C. subvermispora was not correlated with the CAI, tAI, AAtAI, CBP or Nc indexes used to evaluate adaptation to codon bias or the tRNA pool, neither in the presence of glucose or Aspen wood. However, in media containing Aspen wood, the induction of expression of lignin-degrading genes showed a strong correlation with all the former indexes. Lignin-degrading genes, defined as genes whose expression increases at least two-fold in Aspen wood, showed significantly (p<0.001) higher values of CAI, AAtAI, CPB, tAI and lower values of Nc with respect to non-induced genes. Among ligninolytic 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.Conclusions: 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 C. subvermispora. 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 pathway.
Expression of the Laccase Gene from a White Rot Fungus in Pichia pastoris Can Enhance the Resistance of This Yeast to H2O2-Mediated Oxidative Stress by Stimulating the Glutathione-Based Antioxidative System
