Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data

Abstract

To understand the common gene expression patterns employed by P. placenta during lignocellulose degradation, we have retrieved genome wide transcriptome datasets from NCBI GEO database and analyzed using customized analysis pipeline. We have retrieved the top differentially expressed genes and compared the common significant genes among two different growth conditions. Genes encoding for cellulolytic (GH1, GH3, GH5, GH12, GH16, GH45) and hemicellulolytic (GH10, GH27, GH31, GH35, GH47, GH51, GH55, GH78, GH95) glycoside hydrolase classes were commonly up regulated among all the datasets. Fenton's reaction enzymes (iron homeostasis, reduction, hydrogen peroxide generation) were significantly expressed among all the datasets under lignocellulolytic conditions. Due to the evolutionary loss of genes coding for various lignocellulolytic enzymes (including several cellulases), P. placenta employs hemicellulolytic glycoside hydrolases and Fenton's reactions for the rapid depolymerization of plant cell wall components. Different classes of enzymes involved in aromatic compound degradation, stress responsive and detoxification mechanisms (cytochrome P450 monoxygenases) were found highly expressed in complex plant biomass substrates. We have reported the genome wide expression patterns of genes coding for information, storage and processing (KOG), tentative and predicted molecular networks involved in cellulose, hemicellulose degradation and list of significant protein-ID's commonly expressed among different lignocellulolytic growth conditions.

Keywords: Brown-rot decay; Fenton's reaction; Gene expression; Lignocellulose; NCBI-Gene Expression Omnibus (GEO); Postia placenta.

Figure 1

Pictorial representation of CAZymes distribution (GH-glycoside hydrolases, GT-glycosyl transferases, AA-auxiliary activity, CBM-carbohydrate binding domains, CE-carbohydrate esterases, EXPN-expansin like protiens, PL-polysaccharide lyases) in P. placenta MAD-698- Rv1.0 (A) and the top number denotes for the number of genes coding for particular class of enzymes and each bar internally shows different sub-classes of enzymes and the number of genes encoding for the corresponding enzymes, (B) Comparison of genome wide CAZymes between P. placenta and P. chrysosporium

Figure 2

Customized step by step workflow used for the metadata analysis of Postia placenta gene expression datasets.

Figure 3

Profile plot (GSE12540, GSE69004 and GSE84529) and volcano plots (GSE29656) of the significant and differentially expressed genes among the conditions.

Figure 4

Four-way and three-way Venn diagrams showing the commonly expressed statistically significant CAZymes among the gene expression datasets A) glucose-cellulose, glucose-BMA, BMA-cellulose and GSE29656 B) high lignin and low glucose (A) high glucose and low lignin (B) average lignin and average glucose at incubation periods of 10-days, 20-days and 30-days, C) 15mm-20mm vs 0mm-5mm, 30mm-35mm vs 0mm-5mm and 30mm-35mm vs 15mm-20mm D) GSE29656, GSE69004, GSE12540 and GSE84529 datasets.

Figure 5

Four-way and three-way Venn diagrams showing the commonly expressed statistically significant enzymes among the gene expression datasets A) glucose-cellulose, glucose-BMA, BMA-cellulose and GSE29656 B) high lignin and low glucose (A) high glucose and low lignin (B) average lignin and average glucose at incubation periods of 10-days, 20-days and 30-days, C) 15mm-20mm vs 0mm-5mm, 30mm-35mm vs 0mm-5mm and 30mm-35mm vs 15mm-20mm D) GSE29656, GSE69004, GSE12540 and GSE84529 datasets.

Figure 6

Four-way Venn diagrams showing the commonly expressed statistically significant protein-Ids among the gene expression datasets A) CAZymes among all the datasets B) All InterPro-IDs among all the datasets.

Figure 7

Four-way Venn diagrams showing the commonly expressed statistically significant genes encoding for KOG groups A (RNA Processing and modification), B (Chromatin structure and dynamics), J (Translation, ribosomal structure and biogenesis), K (Transcription) L (Replication, recombination and repair) and heatmap showing total list of significant information storage and processing groups among the datasets.

Figure 8

Tentative representation of Fenton's reaction system observed in P. placenta mainly includes H₂O₂ generating and Iron reduction-homeostasis enzyme systems found to be commonly observed among the gene expression datasets.

Figure 9

Tentative network of genes involved in coding for enzymes involved during cellulose and hemicellulose degradation.