Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering. BMC Genom 6:92-116

University of Cincinnati, Cincinnati, Ohio, United States
BMC Genomics (Impact Factor: 3.99). 02/2005; 6(1):92. DOI: 10.1186/1471-2164-6-92
Source: PubMed


Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning efforts in P. chrysosporium and its subsequent whole genome sequencing have revealed an extraordinary P450 repertoire ("P450ome") containing at least 150 P450 genes with yet unknown function. In order to understand the functional diversity and the evolutionary mechanisms and significance of these hemeproteins, here we report a genome-wide structural and evolutionary analysis of the P450ome of this fungus.
Our analysis showed that P. chrysosporium P450ome could be classified into 12 families and 23 sub-families and is characterized by the presence of multigene families. A genome-level structural analysis revealed 16 organizationally homogeneous and heterogeneous clusters of tandem P450 genes. Analysis of our cloned cDNAs revealed structurally conserved characteristics (intron numbers and locations, and functional domains) among members of the two representative multigene P450 families CYP63 and CYP505 (P450foxy). Considering the unusually complex structural features of the P450 genes in this genome, including microexons (2-10 aa) and frequent small introns (45-55 bp), alternative splicing, as experimentally observed for CYP63, may be a more widespread event in the P450ome of this fungus. Clan-level phylogenetic comparison revealed that P. chrysosporium P450 families fall under 11 fungal clans and the majority of these multigene families appear to have evolved locally in this genome from their respective progenitor genes, as a result of extensive gene duplications and rearrangements.
P. chrysosporium P450ome, the largest known to date among fungi, is characterized by tandem gene clusters and multigene families. This enormous P450 gene diversity has evolved by extensive gene duplications and intragenomic recombinations of the progenitor genes presumably to meet the exceptionally high metabolic demand of this biodegradative group of basidiomycetous fungi in ecological niches. In this context, alternative splicing appears to further contribute to the evolution of functional diversity of the P450ome in this fungus. The evolved P450 diversity is consistent with the known vast biotransformation potential of P. chrysosporium. The presented analysis will help design future P450 functional studies to understand the underlying mechanisms of secondary metabolism and oxidative biotransformation pathways in this model white rot fungus.

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Available from: Jagjit S Yadav
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    • "The availability of whole-genome sequences for a number of fungi opens new research avenues to reach a global understanding of the CYPomes. Currently, a number of studies on fungal CYPomes have extensively performed in model fungi, such as Aspergillus nidulans and Penicillium chrysosporium , and some important fungi such as plant pathogens Fusarium graminearum and Magnaporthe grisea (Doddapaneni et al. 2005; Deng et al. 2007; Kelly et al. 2009). There are two large and systemic public databases for fungal CYPs: CYP Database ( "
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    ABSTRACT: Cytochrome P450 monooxygenase (CYP) superfamily contributes a broad array of biological functions in living organisms. In fungi, CYPs play diverse and pivotal roles in versatile metabolism and fungal adaptation to specific ecological niches. In this report, CYPomes in the 47 genomes of fungi belong to the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota have been studied. The comparison of fungal CYPomes suggests that generally fungi possess abundant CYPs belonging to a variety of families with the two global families CYP51 and CYP61, indicating individuation of CYPomes during the evolution of fungi. Fungal CYPs show highly conserved characteristic motifs, but very low overall sequence similarities. The characteristic motifs of fungal CYPs are distinguishable from those of CYPs in animals, plants, and especially archaea and bacteria. The four representative motifs contribute to the general function of CYPs. Fungal CYP51s and CYP61s can be used as the models for the substrate recognition sites analysis. The CYP proteins are clustered into 15 clades and the phylogenetic analyses suggest that the wide variety of fungal CYPs have mainly arisen from gene duplication. Two large duplication events might have been associated with the booming of Ascomycota and Basidiomycota. In addition, horizontal gene transfer also contributes to the diversification of fungal CYPs. Finally, a possible evolutionary scenario for fungal CYPs along with fungal divergences is proposed. Our results provide the fundamental information for a better understanding of CYP distribution, structure and function, and new insights into the evolutionary events of fungal CYPs along with the evolution of fungi.
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    • "To circumvent this sustainability problem and to achieve higher biodegradation, we employed a different strategy for developing a soil bioremediation process for PAHs, using BaP as the test PAH. Whole genome sequencing of P. chrysosporium has revealed a large repertoire (an estimated 149 P450s) of Cytochrome P450 monooxygenases [9] [16] [17], seven of which have been shown to have the capacity to oxidize a range of PAH compounds including low molecular weight (LMW)-and HMW-PAHs in our recent genome-to-function studies [18] [19] [20]. An upregulated expression of majority of the P450 monooxygenases including these specific PAH-oxidizing P450s under nutrient-sufficient culture conditions [21] [22] [23] and their induction by varying ring size PAHs has been demonstrated in liquid cultures [20]. "
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    ABSTRACT: High molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) such as benzo[a]pyrene (BaP) are resistant to biodegradation in soil. Conventionally, white rot fungus Phanerochaete chrysosporium has been investigated for HMW-PAH degradation in soil primarily using nutrient-deficient (ligninolytic) conditions, albeit with limited and non-sustainable biodegradation outcomes. In this study, we report development of an alternative novel biphasic process initiated under nutrient-sufficient (non-ligninolytic) culture conditions, by employing an advanced experimental design strategy. During the initial nutrient-sufficient non-ligninolytic phase (16 days), the process showed upregulation (3.6- and 22.3-fold, respectively) of two key PAH-oxidizing P450 monooxygenases pc2 (CYP63A2) and pah4 (CYP5136A3) and formation of typical P450-hydroxylated metabolite. This along with abrogation (84.9%) of BaP degradation activity in response to a P450-specific inhibitor implied key role of these monooxygenases. The subsequent phase triggered on continued incubation (to 25 days) switched the process from non-ligninolytic to ligninolytic resulting in a significantly higher net degradation (91.6% as against 67.4% in the control nutrient-limited set) of BaP with concomitant de novo ligninolytic enzyme expression making it a biphasic process yielding improved sustainable bioremediation of PAH-contaminated soil. To our knowledge this is the first report on development of such biphasic process for bioremediation application of a white rot fungus.
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    • "However, not all identified cytochromes may be directly involved in lipid assimilation. For example, B. bassiana CYP655C1 (CYP52 clan) expression was strongly induced by hydrocarbons and insect lipids, but it appears to be involved in tenellin synthesis (with aromatic intermediates) (Doddapaneni et al., 2005), indicating that lipid may act as signals for the biosynthesis of select fungal secondary metabolites. In the basidiomycete , P. chrysosporium, seven members belonging to the CYP63 family have been identified which all can be classified under the CYP52 clan. "
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