| |
|
|
| |
|
|
Research  |
|
|
|
| |
| |
Systematic and searchable classification of cytochrome P450 proteins encoded
by fungal and oomycete genomes
|
|
|
|
|
|
| |
|
 Authours
|
Venkatesh Moktali, Jongsun Park, Natalie D Fedorova-Abrams, Bongsoo Park, Yong-Hwan Lee, Jaeyoung Choi and Seogchan Kang |
| Title |
Systematic and searchable classification of cytochrome P450 proteins encoded
by fungal and oomycete genomes |
| Journal |
BMC Genomics, 2012 (13) ~ |
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. |
Link
|
 |
|
|
| |
|
|
|
|
| |
|
|
|
|
