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Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants

View Article: PubMed Central - PubMed

ABSTRACT

Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants.

No MeSH data available.


Phylogenetic relationships within the “Mixed Clade”.The mixed clade from Fig 2 shows the high level of support connecting ten sequences from six different species: Theobroma cacao (Tc), Jatropha curcas (Jc), Ricinus communis (Rc), Solanum lycopersicum (Sl), Solanum tuberosum (St), and Nicotiana plumbaginifolia (Np). This clade was included in further analysis for clade-specific structural features.
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pone.0163024.g005: Phylogenetic relationships within the “Mixed Clade”.The mixed clade from Fig 2 shows the high level of support connecting ten sequences from six different species: Theobroma cacao (Tc), Jatropha curcas (Jc), Ricinus communis (Rc), Solanum lycopersicum (Sl), Solanum tuberosum (St), and Nicotiana plumbaginifolia (Np). This clade was included in further analysis for clade-specific structural features.

Mentions: Probable gene loss is highlighted in a strongly supported eudicot clade comprised of sequences from six unrelated species, the “Mixed Clade” (Fig 5). High bootstrap support suggests a shared common ancestral gene retained in the species represented in the Mixed Clade, while the other plants most likely lost this ancestral gene. For the species J. curcas, N. plumbaginifolia, and T. cacao the only CYP72A sequences we found are grouped in the Mixed Clade. More recent annotations of the T. cacao genome suggest that there could be another CYP72A sequence that is more similar to the P. persica and F. vesca sequences than the Mixed Clade sequences (data not shown). To date, we have not found any additional complete CYP72A sequences in the J. curcas or N. plumbaginifolia genomes even though there is evidence of closely related pseudogenes.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Phylogenetic relationships within the “Mixed Clade”.The mixed clade from Fig 2 shows the high level of support connecting ten sequences from six different species: Theobroma cacao (Tc), Jatropha curcas (Jc), Ricinus communis (Rc), Solanum lycopersicum (Sl), Solanum tuberosum (St), and Nicotiana plumbaginifolia (Np). This clade was included in further analysis for clade-specific structural features.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036807&req=5

pone.0163024.g005: Phylogenetic relationships within the “Mixed Clade”.The mixed clade from Fig 2 shows the high level of support connecting ten sequences from six different species: Theobroma cacao (Tc), Jatropha curcas (Jc), Ricinus communis (Rc), Solanum lycopersicum (Sl), Solanum tuberosum (St), and Nicotiana plumbaginifolia (Np). This clade was included in further analysis for clade-specific structural features.
Mentions: Probable gene loss is highlighted in a strongly supported eudicot clade comprised of sequences from six unrelated species, the “Mixed Clade” (Fig 5). High bootstrap support suggests a shared common ancestral gene retained in the species represented in the Mixed Clade, while the other plants most likely lost this ancestral gene. For the species J. curcas, N. plumbaginifolia, and T. cacao the only CYP72A sequences we found are grouped in the Mixed Clade. More recent annotations of the T. cacao genome suggest that there could be another CYP72A sequence that is more similar to the P. persica and F. vesca sequences than the Mixed Clade sequences (data not shown). To date, we have not found any additional complete CYP72A sequences in the J. curcas or N. plumbaginifolia genomes even though there is evidence of closely related pseudogenes.

View Article: PubMed Central - PubMed

ABSTRACT

Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants.

No MeSH data available.