Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton's reaction and wood decay process

Mycology
Ayyappa Kumar Sista Kameshwar, Wensheng Qin

Abstract

Brown-rot fungi are rapid holocellulose degraders and are the most predominant degraders of coniferous wood products in North America. Brown-rot fungi degrades wood by both enzymatic (plant biomass degrading carbohydrate active enzymes-CAZymes) and non-enzymatic systems (Fenton's reaction) mechanisms. Identifying the genes and molecular mechanisms involved in Fenton's reaction would significantly improve our understanding about brown-rot decay. Our present study identifies the common gene expression patterns involved in brown rot decay by performing metadata analysis of fungal transcriptome datasets. We have also analyzed and compared the genome-wide annotations (InterPro and CAZymes) of the selected brown rot fungi. Genes encoding for various oxidoreductases, iron homeostasis, and metabolic enzymes involved in Fenton's mechanism were found to be significantly expressed among all the brown-rot fungal datasets. Interestingly, a higher number of hemicellulases encoding genes were differentially expressed among all the datasets, while a fewer number of cellulases and peroxidases were expressed (especially haem peroxidase and chloroperoxidase). Apart from these lignocellulose degrading enzymes genes encoding for aldo/keto reductase...Continue Reading

References

Nov 1, 1987·Journal of General Microbiology·E LesuisseR R Crichton
Jul 25, 2000·Advances in Microbial Physiology·N G De Luca, P M Wood
Oct 24, 2001·The Journal of Biological Chemistry·O ProtchenkoC C Philpott
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Apr 1, 1965·The Biochemical Journal·G HALLIWELL
Aug 23, 2005·Infection and Immunity·Simon A B KnightAndrew Dancis
Jun 30, 2006·Biochimica Et Biophysica Acta·Caroline C Philpott
Aug 6, 2008·Annual Review of Phytopathology·Hubertus HaasB Gillian Turgeon
Oct 8, 2008·Nucleic Acids Research·Brandi L CantarelBernard Henrissat
Feb 6, 2009·Proceedings of the National Academy of Sciences of the United States of America·Diego MartinezDan Cullen
Apr 20, 2010·Applied and Environmental Microbiology·Amber Vanden WymelenbergDan Cullen
Jun 5, 2010·The Journal of Biological Chemistry·Daniel J Kosman
Oct 15, 2010·Fungal Biology·Ibtissem GrissaPhilippe Silar
Oct 4, 2011·Current Genomics·Ursula Kües, Martin Rühl
Nov 26, 2013·Nucleic Acids Research·Vincent LombardBernard Henrissat
Sep 2, 2014·BMC Bioinformatics·Philippe BardouChristophe Klopp
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Apr 8, 2017·Molecular Biology and Evolution·Sudhir KumarS Blair Hedges

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Citations

Apr 19, 2021·Biotechnology for Biofuels·Fernanda Lopes de FigueiredoAndré Damasio

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Datasets Mentioned

BETA
GSE84529
GSE78007
GSE35333
GSE64897
GSE69012

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Venny
Jvenn
R package edgeR
DESeq
TimeTree
Excel
Linux
DESeq R
GeneSpring®

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