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Fungal cytochrome P450 database.

Park J, Lee S, Choi J, Ahn K, Park B, Park J, Kang S, Lee YH - BMC Genomics (2008)

Bottom Line: The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL.The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea. starflr@snu.ac.kr

ABSTRACT

Background: Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.

Results: The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.

Conclusion: The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site http://p450.riceblast.snu.ac.kr/.

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Distribution pattern of 25 major P450 clusters. Cluster names are shown below the X-axis, and the names of fungal phyla are shown at the y-axis. Non-fungi indicate P450s in plants and animals. The Z-axis indicates numbers of P450s in individual groups.
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Figure 4: Distribution pattern of 25 major P450 clusters. Cluster names are shown below the X-axis, and the names of fungal phyla are shown at the y-axis. Non-fungi indicate P450s in plants and animals. The Z-axis indicates numbers of P450s in individual groups.

Mentions: When fungal/oomycetes P450s were combined with 5,447 P450s extracted from 40 other eukaryotic and prokaryotic species and clustered using tribe-MCL (with inflation factor of 5.0; the most strict condition for clustering based on sequence similarity), 141 clusters were identified. Among these, 74 clusters contain only fungal P450s, suggesting that many fungal P450s have a configuration unique to fungi. The taxonomic origins of fungal P450s in the 26 clusters that contain more than 10 fungal P450s were analyzed (Figure 4). P450s in the phylum Ascomycota are dominant because of abundant genome sequences from members of this group. Cluster 19.1 is dominated by P450s encoded members of the subphylum Agricomycotina (phylum Basidiomycota) and Clusters 3.1 and 4.1 are Zygomycota-specific. Cluster 8.1 contains 101 out of 106 oomycetes P450s (95.3%). Nine P450s encoded by Batrachochytrium dendrobatidis, the only sequenced species in the phylum Chitridiomycota, are scattered to 8 clusters, suggesting that they likely have distinct functions and evolutionary origins. Sequences of additional genomes are needed to further investigate the evolution of P450s in this phylum.


Fungal cytochrome P450 database.

Park J, Lee S, Choi J, Ahn K, Park B, Park J, Kang S, Lee YH - BMC Genomics (2008)

Distribution pattern of 25 major P450 clusters. Cluster names are shown below the X-axis, and the names of fungal phyla are shown at the y-axis. Non-fungi indicate P450s in plants and animals. The Z-axis indicates numbers of P450s in individual groups.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2542383&req=5

Figure 4: Distribution pattern of 25 major P450 clusters. Cluster names are shown below the X-axis, and the names of fungal phyla are shown at the y-axis. Non-fungi indicate P450s in plants and animals. The Z-axis indicates numbers of P450s in individual groups.
Mentions: When fungal/oomycetes P450s were combined with 5,447 P450s extracted from 40 other eukaryotic and prokaryotic species and clustered using tribe-MCL (with inflation factor of 5.0; the most strict condition for clustering based on sequence similarity), 141 clusters were identified. Among these, 74 clusters contain only fungal P450s, suggesting that many fungal P450s have a configuration unique to fungi. The taxonomic origins of fungal P450s in the 26 clusters that contain more than 10 fungal P450s were analyzed (Figure 4). P450s in the phylum Ascomycota are dominant because of abundant genome sequences from members of this group. Cluster 19.1 is dominated by P450s encoded members of the subphylum Agricomycotina (phylum Basidiomycota) and Clusters 3.1 and 4.1 are Zygomycota-specific. Cluster 8.1 contains 101 out of 106 oomycetes P450s (95.3%). Nine P450s encoded by Batrachochytrium dendrobatidis, the only sequenced species in the phylum Chitridiomycota, are scattered to 8 clusters, suggesting that they likely have distinct functions and evolutionary origins. Sequences of additional genomes are needed to further investigate the evolution of P450s in this phylum.

Bottom Line: The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL.The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea. starflr@snu.ac.kr

ABSTRACT

Background: Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.

Results: The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.

Conclusion: The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site http://p450.riceblast.snu.ac.kr/.

Show MeSH