title: Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives.
abstract: Lignin, most complex and abundant biopolymer on the earth's surface, attains its stability from intricate polyphenolic units and non-phenolic bonds, making it difficult to depolymerize or separate from other units of biomass. Eccentric lignin degrading ability and availability of annotated genome make Phanerochaete chrysosporium ideal for studying lignin degrading mechanisms. Decoding and understanding the molecular mechanisms underlying the process of lignin degradation will significantly aid the progressing biofuel industries and lead to the production of commercially vital platform chemicals. In this study, we have performed a large-scale metadata analysis to understand the common gene expression patterns of P. chrysosporium during lignin degradation. Gene expression datasets were retrieved from NCBI GEO database and analyzed using GEO2R and Bioconductor packages. Commonly expressed statistically significant genes among different datasets were further considered to understand their involvement in lignin degradation and detoxification mechanisms. We have observed three sets of enzymes commonly expressed during ligninolytic conditions which were later classified into primary ligninolytic, aromatic compound-degrading and other necessary enzymes. Similarly, we have observed three sets of genes coding for detoxification and stress-responsive, phase I and phase II metabolic enzymes. Results obtained in this study indicate the coordinated action of enzymes involved in lignin depolymerization and detoxification-stress responses under ligninolytic conditions. We have developed tentative network of genes and enzymes involved in lignin degradation and detoxification mechanisms by P. chrysosporium based on the literature and results obtained in this study. However, ambiguity raised due to higher expression of several uncharacterized proteins necessitates for further proteomic studies in P. chrysosporium.
authors.affiliation: Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada.
authors.forename: Ayyappa Kumar Sista
authors.initials: AKS
authors.lastname: Kameshwar
authors.affiliation: Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada. wqin@lakeheadu.ca.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Qin
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D008658:Inactivation, Metabolic; D008031:Lignin / Q000378:metabolism*; D050216:Metabolic Detoxication, Phase I; D050217:Metabolic Detoxication, Phase II; D010084:Oxidation-Reduction; D020075:Phanerochaete / Q000235:genetics* / Q000378:metabolism*; D064210:Secondary Metabolism; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D008031:Lignin
keywords: Detoxification responses; GEO2R; Gene expression omnibus (GEO); Lignocellulose; Phanerochaete chrysosporium; Phase I and phase II metabolic enzymes; Transcriptome