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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.


Amino acid sequence logo representations of the CYP signature domains.The positions are numbered according to the residue number in the “all CYP72A” alignment used for generating Fig 2. The relative size of the amino acid letters in the logo diagram represents the frequency of that amino acid in the subset of sequences indicated on the left. Amino acid residue frequencies from individual clades (highlighted in Fig 2) were compared to the residue frequencies across the entire set of sequences. The amino acids are colored to indicate functional similarities: (green (polar), purple (neutral), blue (basic), red (acidic), black (hydrophobic). The diagrams were created using WebLogo2 [24].
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pone.0163024.g006: Amino acid sequence logo representations of the CYP signature domains.The positions are numbered according to the residue number in the “all CYP72A” alignment used for generating Fig 2. The relative size of the amino acid letters in the logo diagram represents the frequency of that amino acid in the subset of sequences indicated on the left. Amino acid residue frequencies from individual clades (highlighted in Fig 2) were compared to the residue frequencies across the entire set of sequences. The amino acids are colored to indicate functional similarities: (green (polar), purple (neutral), blue (basic), red (acidic), black (hydrophobic). The diagrams were created using WebLogo2 [24].

Mentions: We used the relationships predicted in the maximum likelihood analysis to focus on subsets of the CYP72As for determining the frequency of particular amino acids within the SRS and structural domains. The sequences whose names are colored in Fig 2 were chosen to represent the plant order from which they came. We show distinct clade-defining differences in amino acid composition within the highly conserved functional domains (Fig 6). For the Poales clade, oxygen binding position 369 shows a clade-defining methionine. The glutamate at position 486 of the PERF domain is less well conserved in Poales than in any of the other clades examined. Most of the Rosales sequences lack a highly conserved tryptophan at position 509 in the heme binding domain.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Amino acid sequence logo representations of the CYP signature domains.The positions are numbered according to the residue number in the “all CYP72A” alignment used for generating Fig 2. The relative size of the amino acid letters in the logo diagram represents the frequency of that amino acid in the subset of sequences indicated on the left. Amino acid residue frequencies from individual clades (highlighted in Fig 2) were compared to the residue frequencies across the entire set of sequences. The amino acids are colored to indicate functional similarities: (green (polar), purple (neutral), blue (basic), red (acidic), black (hydrophobic). The diagrams were created using WebLogo2 [24].
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163024.g006: Amino acid sequence logo representations of the CYP signature domains.The positions are numbered according to the residue number in the “all CYP72A” alignment used for generating Fig 2. The relative size of the amino acid letters in the logo diagram represents the frequency of that amino acid in the subset of sequences indicated on the left. Amino acid residue frequencies from individual clades (highlighted in Fig 2) were compared to the residue frequencies across the entire set of sequences. The amino acids are colored to indicate functional similarities: (green (polar), purple (neutral), blue (basic), red (acidic), black (hydrophobic). The diagrams were created using WebLogo2 [24].
Mentions: We used the relationships predicted in the maximum likelihood analysis to focus on subsets of the CYP72As for determining the frequency of particular amino acids within the SRS and structural domains. The sequences whose names are colored in Fig 2 were chosen to represent the plant order from which they came. We show distinct clade-defining differences in amino acid composition within the highly conserved functional domains (Fig 6). For the Poales clade, oxygen binding position 369 shows a clade-defining methionine. The glutamate at position 486 of the PERF domain is less well conserved in Poales than in any of the other clades examined. Most of the Rosales sequences lack a highly conserved tryptophan at position 509 in the heme binding domain.

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.