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In Silico Genomics of Fungal Oxidoreductase Genes

Oxidoreductases are found in all living organisms and play essential roles in housekeeping, perception of environmental stress, plant-pathogen interactions, defense reactions, and pathogenicity. In particular, laccase, peroxidases and NADPH oxidase, have been implicated in virulence of phytopathogenic fungi in pathogenicity. Despite its relevance towards plant microbe interaction, the identification and comparative analysis of fungal peroxidase-encoding genes at the genomic level have been limited by the lack of a bioinformatics platform as well as paucity of information on transcript profiling of potential candidate oxidoreductase genes.

The first project of my thesis covered the construction and development of a new bioinformatic platform dedicated to fungal peroxidases database (fPoxDB). fPoxDB facilitated comparative and evolutionary studies on fungal peroxidases at the genomic level. The database includes several bioinformatic tools, such as Blast, BlastMatrix, SignalP 3.0, predictNLS, InterPro Scan and more. Additionally, the database contains 6,113 peroxidases from 25 gene families, covering 331 genomes, which are already pre-computational analyzed with eight different bioinformatic tools.

The second project was focused on in silico comparative analysis of fungal NADPH oxidase (Nox) genes sequences. Nox proteins are transmembrane enzymes found in most eukaryotic organisms and influence many biological processes by generating reactive oxygen species (ROS). In fungi, Nox enzymes play roles in pathogenicity, such as the weakening of plant cell walls by ROS. The enzymes exhibit high sequence similarities to the ferric-reductases (Fre) and ferric-chelate reductases (FRO) proteins, which are involved in reduction of Fe3+ to Fe2+ for iron uptake. A total of 34 eukaryotic genomes, covering 28 fungal, one Oomycota, three animal and two plant species, were subjected to bioinformatic analysis. The results indicate that the properties of fungal Nox genes differ from those of the human and plants, providing novel insights that will enable more accurate identification and characterization of the fungal genes.

In the third project, we explored expression profiling of a typical oxidoreductase gene, laccase, in Heterobasidion – conifer pathosystem. Laccases are multi-copper oxidoreductases catalyzing the oxidation of phenolic substrates, and they play diverse roles in plants and fungi. In fungi, laccase have been shown to be involved in pathogenicity, as well as in lignin degradation. A total of 18 laccases genes were identified in this fungus and the genes were subject to a phylogenetically analysis. Furthermore, the expression levels of the genes, and laccase activities, during growth of H. annosum on its host in the presence or absence of additional carbon source, such as glucose and sucrose, were investigated. Based on increased transcript expression levels eight laccases were considered to be potentially involved in H. annosum virulence.

Taken together, we provide the research community with a database dedicated to fungal peroxidases, and our in silico analysis affords new insights in the structure of fungal NADPH oxidases. Lastly, we present experimental evidence that some H. annosum laccases might be involved in virulence during infection of non-suberized Scots pine seedlings.


Nicolas Détry, Diploma-Biologist will defend the doctoral dissertation entitled "In Silico Genomics of Fungal Oxidoreductase Genes" in the Faculty of Agriculture and Forestry, University of Helsinki, on 7 October 2015 at 12:00. The public examination will take place in lecture room 2, B-building, Latokartanonkaari 9.
Associate Professor Christopher B. Lawrence, Virginia Bioinformatics Institute, USA, will serve as the opponent, and Professor Fred O. Asiegbu as the custos.
The dissertation is also available in electronic form through the E-thesis service.