Open Access Highly Accessed Research article

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

Venkatesh Moktali1, Jongsun Park2, Natalie D Fedorova-Abrams3, Bongsoo Park1, Jaeyoung Choi2, Yong-Hwan Lee24 and Seogchan Kang15*

Author Affiliations

1 Integrative Biosciences program in Bioinformatics & Genomics, The Pennsylvania State University, University Park, PA, USA

2 Fungal Bioinformatics Laboratory, Seoul National University, Seoul, Korea

3 Advanced Biomedical Computing Center, SAIC-Frederick, Frederick National Laboratory for Cancer Research, Frederick, MD, USA

4 Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea

5 Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA

For all author emails, please log on.

BMC Genomics 2012, 13:525  doi:10.1186/1471-2164-13-525

Published: 4 October 2012

Abstract

Background

Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable “CYPomes” ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme.

Results

The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson’s P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database.

Conclusions

FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson’s P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.

Keywords:
Cytochrome P450; Genome annotation; Clustering; Fungi; Evolution; Phylogenetics; Mycotoxin