Next Article in Journal
Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq
Next Article in Special Issue
Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny
Previous Article in Journal
Expression Profile of Porcine TRIM26 and Its Inhibitory Effect on Interferon-β Production and Antiviral Response
Previous Article in Special Issue
The New Klebsiella pneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria—Genetic Characteristics by WGS
 
 
Article

Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora

1
Laboratorio de Microbiología Ambiental y Extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5290000, Chile
2
Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile
3
Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile
4
Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170002, Chile
*
Author to whom correspondence should be addressed.
Genes 2020, 11(10), 1227; https://doi.org/10.3390/genes11101227
Received: 11 September 2020 / Revised: 13 October 2020 / Accepted: 14 October 2020 / Published: 20 October 2020
(This article belongs to the Special Issue Microbial Genomics and Evolution)
Ceriporiopsis subvermispora 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 C. subvermispora, 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 (p < 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 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 process. View Full-Text
Keywords: Codon bias; Ceriporiopsis subvermispora; lignocellulose degrading system Codon bias; Ceriporiopsis subvermispora; lignocellulose degrading system
Show Figures

Figure 1

MDPI and ACS Style

Gonzalez, A.; Corsini, G.; Lobos, S.; Seelenfreund, D.; Tello, M. Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora. Genes 2020, 11, 1227. https://doi.org/10.3390/genes11101227

AMA Style

Gonzalez A, Corsini G, Lobos S, Seelenfreund D, Tello M. Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora. Genes. 2020; 11(10):1227. https://doi.org/10.3390/genes11101227

Chicago/Turabian Style

Gonzalez, Alex, Gino Corsini, Sergio Lobos, Daniela Seelenfreund, and Mario Tello. 2020. "Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora" Genes 11, no. 10: 1227. https://doi.org/10.3390/genes11101227

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop