scholarly journals Correlation between Metabolic Specialization and Codon Preference: Analysis of the Ligninolytic Genes from the White Rot Basidiomycete Ceriporiopsis Subvermispora as A Model System.

2020 ◽  
Author(s):  
Alex R Gonzalez ◽  
Gino R Corsini ◽  
Sergio Lobos ◽  
Daniela Seelenfreund ◽  
Mario Tello
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Hydrolytic Enzymes ◽  
White Rot ◽  
White Rot Fungus ◽  
Lignocellulose Degradation ◽  
Translation Efficiency ◽  
Aspen Wood ◽  
Ceriporiopsis Subvermispora ◽  
Degrading System

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.

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

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1227
Author(s):  
Alex Gonzalez ◽  
Gino Corsini ◽  
Sergio Lobos ◽  
Daniela Seelenfreund ◽  
Mario Tello
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Hydrolytic Enzymes ◽  
High Specificity ◽  
White Rot ◽  
White Rot Fungus ◽  
Lignocellulose Degradation ◽  
Translation Efficiency ◽  
Aspen Wood ◽  
Ceriporiopsis Subvermispora

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.

scholarly journals Massively parallel gene expression variation measurement of a synonymous codon library

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexander Schmitz ◽  
Fuzhong Zhang
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Single Cells ◽  
Massively Parallel ◽  
Protein Abundance ◽  
Translation Efficiency ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Change In Mean ◽  
Adaptation Index

Abstract Background Cell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood. Results Here, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV2), scales with mean protein abundance for low-abundant proteins but does not change at high mean protein abundance. Conclusions Our results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.

scholarly journals 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

2012 ◽  
Vol 78 (16) ◽  
pp. 5845-5854 ◽  
Author(s):  
Yang Yang ◽  
Fangfang Fan ◽  
Rui Zhuo ◽  
Fuying Ma ◽  
Yangmin Gong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Pichia Pastoris ◽  
Oxidative Damage ◽  
White Rot ◽  
Antioxidative System ◽  
White Rot Fungus ◽  
Laccase Gene ◽  
Content Type ◽  
Glutamylcysteine Synthetase

ABSTRACTLaccase is a copper-containing polyphenol oxidase that has great potential in industrial and biotechnological applications. Previous research has suggested that fungal laccase may be involved in the defense against oxidative stress, but there is little direct evidence supporting this hypothesis, and the mechanism by which laccase protects cells from oxidative stress also remains unclear. Here, we report that the expression of the laccase gene from white rot fungus inPichia pastoriscan significantly enhance the resistance of yeast to H2O2-mediated oxidative stress. The expression of laccase in yeast was found to confer a strong ability to scavenge intracellular H2O2and to protect cells from lipid oxidative damage. The mechanism by which laccase gene expression increases resistance to oxidative stress was then investigated further. We found that laccase gene expression inPichia pastoriscould increase the level of glutathione-based antioxidative activity, including the intracellular glutathione levels and the enzymatic activity of glutathione peroxidase, glutathione reductase, and γ-glutamylcysteine synthetase. The transcription of the laccase gene inPichia pastoriswas found to be enhanced by the oxidative stress caused by exogenous H2O2. The stimulation of laccase gene expression in response to exogenous H2O2stress further contributed to the transcriptional induction of the genes involved in the glutathione-dependent antioxidative system, includingPpYAP1,PpGPX1,PpPMP20,PpGLR1, andPpGSH1. Taken together, these results suggest that the expression of the laccase gene inPichia pastoriscan enhance the resistance of yeast to H2O2-mediated oxidative stress by stimulating the glutathione-based antioxidative system to protect the cell from oxidative damage.

Melanoidin-containing wastewaters induce selective laccase gene expression in the white-rot fungus Trametes sp. I-62

2008 ◽  
Vol 159 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Tania González ◽  
María Carmen Terrón ◽  
Susana Yagüe ◽  
Howard Junca ◽  
José María Carbajo ◽  
...  
Keyword(s):  
Gene Expression ◽  
White Rot ◽  
White Rot Fungus ◽  
Laccase Gene

Methane fermentation of Japanese cedar wood pretreated with a white rot fungus, Ceriporiopsis subvermispora

2006 ◽  
Vol 123 (1) ◽  
pp. 71-77 ◽  
Author(s):  
Rudianto Amirta ◽  
Toshiaki Tanabe ◽  
Takahito Watanabe ◽  
Yoichi Honda ◽  
Masaaki Kuwahara ◽  
...  
Keyword(s):  
Japanese Cedar ◽  
White Rot ◽  
White Rot Fungus ◽  
Methane Fermentation ◽  
Ceriporiopsis Subvermispora

Alkaline-sulfite chemithermomechanical pulping of Eucalyptus grandis biotreated by Ceriporiopsis subvermispora under varied culture conditions

Holzforschung ◽  
2008 ◽  
Vol 62 (4) ◽  
Author(s):  
Marcos Paulo Vicentim ◽  
André Ferraz
Keyword(s):  
Fiber Length ◽  
Corn Steep Liquor ◽  
Eucalyptus Grandis ◽  
Culture Conditions ◽  
Wood Chips ◽  
White Rot ◽  
White Rot Fungus ◽  
Ceriporiopsis Subvermispora ◽  
Fungal Pretreatment ◽  
Chemithermomechanical Pulping

Abstract The effect of different culture conditions have been evaluated concerning the extracellular enzyme activities of the white-rot fungus Ceriporiopsis subvermispora growing on Eucalyptus grandis wood. The consequence of the varied fungal pretreatment on a subsequent chemithermomechanical pulping (CTMP) was addressed. In all cultures, manganese peroxidase (MnP) and xylanase were the predominant extracellular enzymes. The biopulping efficiency was evaluated based on the amount of fiber bundles obtained after the first fiberizing step and the fibrillation levels of refined pulps. It was found that the MnP levels in the cultures correlated positively with the biopulping benefits. On the other hand, xylanase and total oxalate levels did not vary significantly. Accordingly, it was not possible to determine whether MnP accomplishes the effect alone or depends on synergic action of other extracellular agents. Pulp strength and fiber size distribution were also evaluated. The average fiber length of CTMP pulps prepared from untreated wood chips was 623 μm. Analogous values were observed for most of the biopulps; however, significant amounts of shorter fibers were found in the biopulp prepared from wood chips biotreated in cultures supplemented with glucose plus corn-steep liquor. Despite evidence of reduced average fiber length, biopulps prepared from these wood chips presented the highest improvement in tensile indexes (+28% at 23° Schopper-Riegler).

scholarly journals Transcriptomics analysis reveals the high biodegradation efficiency of white-rot fungus Phanerochaete sordida YK-624 on native lignin

2020 ◽  
Author(s):  
Jianqiao Wang ◽  
Tomohiro Suzuki ◽  
Hideo Dohra ◽  
Toshio Mori ◽  
Hirokazu Kawagishi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lignin Degradation ◽  
Ligninolytic Enzymes ◽  
Organic Matrix ◽  
Tca Cycle ◽  
Underlying Mechanism ◽  
White Rot ◽  
White Rot Fungus ◽  
Lignin Biodegradation ◽  
Phanerochaete Sordida

Abstract Background Lignocellulosic biomass is an organic matrix composed of cellulose, hemicellulose, and lignin. In nature, lignin degradation by basidiomycetes is the key step in lignocellulose decay. The white-rot fungus Phanerochaete sordida YK-624 (YK-624) has been extensively studied due to its high lignin degradation ability. In our previous study, it was demonstrated that YK-624 can secrete lignin peroxidase and manganese peroxidase for lignin degradation. However, the underlying mechanism for lignin degradation by YK-624 remains unknown.Results Here, we analyzed YK-624 gene expression following growth under ligninolytic and nonligninolytic conditions and compared the differentially expressed genes in YK-624 to those in the model white-rot fungus P. chrysosporium by next-generation sequencing. More ligninolytic enzymes and lignin-degrading auxiliary enzymes were upregulated in YK-624. This might explain the high degradation efficiency of YK-624. In addition, the genes involved in energy metabolism pathways, such as the TCA cycle, oxidative phosphorylation, lipid metabolism, carbon metabolism and glycolysis, were upregulated under ligninolytic conditions in YK-624.Conclusions In the present study, the first differential gene expression analysis of YK-624 under ligninolytic and nonligninolytic conditions was reported. The results obtained in this study indicated that YK-624 produces more energy- and lignin-degrading enzymes for more efficient lignin biodegradation.

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