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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 tree of angiosperm CYP72A sequences.Shown is the topology from the maximum likelihood analysis of 489 aligned residues using a Jones-Taylor-Thornton substitution model. CYP734A1 from Arabidopsis was used to root the tree. A * indicates nodes with 70% or greater bootstrap support; ** indicates 95% or greater boots strap support (250 maximum likelihood pseudo-replicates). Colored lines indicate sequences from plant orders highlighted on the tree, while colored names indicated the subclades that were used for further analysis. The brown clade represents a “Mixed Clade” with sequences from three plant orders.
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pone.0163024.g002: Phylogenetic tree of angiosperm CYP72A sequences.Shown is the topology from the maximum likelihood analysis of 489 aligned residues using a Jones-Taylor-Thornton substitution model. CYP734A1 from Arabidopsis was used to root the tree. A * indicates nodes with 70% or greater bootstrap support; ** indicates 95% or greater boots strap support (250 maximum likelihood pseudo-replicates). Colored lines indicate sequences from plant orders highlighted on the tree, while colored names indicated the subclades that were used for further analysis. The brown clade represents a “Mixed Clade” with sequences from three plant orders.

Mentions: The CYP72A phylogeny was reconstructed using maximum likelihood, neighbor-joining and maximum parsimony criteria. The neighbor-joining tree and strict consensus tree from the maximum parsimony analysis did not have any supported conflicts when compared to the topology that resulted from the maximum likelihood analysis; here we refer to the maximum likelihood tree (Fig 2). The maximum likelihood tree was chosen because it uses a probabilistic model best fit for protein substitution; assuming different sites evolve independently and that diverged sequences evolve independently after divergence. Maximum likelihood analysis is the best method for our hypothesis that the codons for CYP72A active site amino acids have evolved independent of the codons for other amino acids within each sequence and in other sequences from the same plant. The topology shown supports a common CYP72A ancestor with the deepest nodes having high bootstrap values. The neighbor-joining and maximum parsimony trees are shown in S2 and S3 Figs.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Phylogenetic tree of angiosperm CYP72A sequences.Shown is the topology from the maximum likelihood analysis of 489 aligned residues using a Jones-Taylor-Thornton substitution model. CYP734A1 from Arabidopsis was used to root the tree. A * indicates nodes with 70% or greater bootstrap support; ** indicates 95% or greater boots strap support (250 maximum likelihood pseudo-replicates). Colored lines indicate sequences from plant orders highlighted on the tree, while colored names indicated the subclades that were used for further analysis. The brown clade represents a “Mixed Clade” with sequences from three plant orders.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163024.g002: Phylogenetic tree of angiosperm CYP72A sequences.Shown is the topology from the maximum likelihood analysis of 489 aligned residues using a Jones-Taylor-Thornton substitution model. CYP734A1 from Arabidopsis was used to root the tree. A * indicates nodes with 70% or greater bootstrap support; ** indicates 95% or greater boots strap support (250 maximum likelihood pseudo-replicates). Colored lines indicate sequences from plant orders highlighted on the tree, while colored names indicated the subclades that were used for further analysis. The brown clade represents a “Mixed Clade” with sequences from three plant orders.
Mentions: The CYP72A phylogeny was reconstructed using maximum likelihood, neighbor-joining and maximum parsimony criteria. The neighbor-joining tree and strict consensus tree from the maximum parsimony analysis did not have any supported conflicts when compared to the topology that resulted from the maximum likelihood analysis; here we refer to the maximum likelihood tree (Fig 2). The maximum likelihood tree was chosen because it uses a probabilistic model best fit for protein substitution; assuming different sites evolve independently and that diverged sequences evolve independently after divergence. Maximum likelihood analysis is the best method for our hypothesis that the codons for CYP72A active site amino acids have evolved independent of the codons for other amino acids within each sequence and in other sequences from the same plant. The topology shown supports a common CYP72A ancestor with the deepest nodes having high bootstrap values. The neighbor-joining and maximum parsimony trees are shown in S2 and S3 Figs.

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.