A comparative genomic investigation of niche adaptation in fungi
Open Access
- Author:
- Moktali, Venkatesh Pralhad
- Graduate Program:
- Integrative Biosciences
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- April 23, 2013
- Committee Members:
- Seogchan Kang, Dissertation Advisor/Co-Advisor
Cooduvalli S Shashikant, Committee Member
David Michael Geiser, Committee Member
Anton Nekrutenko, Committee Member
Kateryna Dmytrivna Makova, Committee Member
Dr Yu Zhang, Committee Member - Keywords:
- Cytochrome P450
Fungi
Evolution
Calcium Signaling
Biological Databases
Adaptation
Fungal Niches
Secondary Metabolism - Abstract:
- The Kingdom Fungi has a diverse array of members adapted to very disparate and the most hostile surroundings on earth: such as living plant and/or animal tissues, soil, aquatic environments, other microorganisms, dead animals, and exudates of plants, animals and even nuclear reactors. The ability of fungi to survive in these various niches is supported by the presence of key enzymes/proteins that can metabolize extraneous harmful factors. Characterization of the evolution of these key proteins gives us a glimpse at the molecular mechanisms underpinning adaptations in these organisms. Cytochrome P450 proteins (CYPs) are among the most diversified protein families, they are involved in a number of processed that are critical to fungi. I evaluated the evolution of Cytochrome P450 proteins (CYPs) in order to understand niche adaptation in fungi. Towards this goal, a previously developed database the fungal cytochrome P450 database (FCPD) was improved and several features were added in order to allow for systematic comparative genomic and phylogenomic analysis of CYPs from numerous fungal genomes. Specifically, an in-house platform was developed to standardize and improve the protein sequence clustering procedure, more than 100 fungal and non-fungal genomes were added, putative functional classification of CYPs into three broad categories was added, the CYP clan/family classification was extended to 117 CYP clans and 292 families. With these new features the FCPD 1.2 (http://p450.riceblast.snu.ac.kr/) was published with systematic classification of 22,940 CYPs from 213 species. Using the CYP data from the FCPD 1.2 I carried out detailed phylogenomic analysis of 6108 CYPs belonging to 51 species from the subphylum Pezizomycotina. The analysis revealed CYPomes that were specific to the niches occupied by the different fungi. There was preferential presence of CYP families among pathogenic species. I introduced a putative functional diversification ratio to identify divergence of “CYPomes”, the ratio suggests that the non-pathogenic fungi tended to have comparatively more CYP families/clans compared to the pathogenic fungi. I also identified the CYP clans ancestral to Pezizomycotina fungi, the results confirm previously estimated ancestral CYP clans CYP51, CYP61 and add CYP52 and CYP58 to the set of clans present in the last common ancestor of Pezizomycotina fungi. Putative metabolic classification of CYPs in the group suggests increase in CYPs involved in secondary metabolism among fungal plant pathogens. I also carried out gene family evolution analysis with the CYP data, the analyses suggested high number of gains and losses among serious plant pathogens such as Magnaporthe oryzae and Fusarium spp. Calcium is a ubiquitous ion that plays a major role in myriad processes in the fungal cell. I developed the fungal calcium-signaling database (FCSD: http://fcsd.ifungi.org/) in order to understand the roles of genes interacting directly or indirectly with calcium. The computational pipeline standardized in the FCPD was used to cluster the calcium signaling gene dataset. Comparative genomics analyses of calcium signaling genes indicated varying complexity of the calcium-signaling pathway across fungal phyla. I also carried out detailed gene family analysis of different calcium signaling genes, niche-specific gene gains were observed through this analysis. I believe that the various features built into FCSD encourage community participation and research on understanding calcium signaling in fungi.