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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.


Conserved CYP domains relevant to functional analysis.Scale diagram of the domains of a CYP class II. The signature domains common in most CYPs are shown in orange. Green boxes indicate the more variable substrate recognition sites. Black and blue indicate the membrane anchor and proline rich hinge domains.
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pone.0163024.g001: Conserved CYP domains relevant to functional analysis.Scale diagram of the domains of a CYP class II. The signature domains common in most CYPs are shown in orange. Green boxes indicate the more variable substrate recognition sites. Black and blue indicate the membrane anchor and proline rich hinge domains.

Mentions: CYPs are defined as heme thiolate monooxygenases and are linked by similarity in the structural fold even though the biochemical reactions they catalyze are quite diverse. The general fold includes domains characteristic of all CYPs and those providing substrate specificity [7]. As diagrammed in Fig 1, most plant CYPs have a membrane anchor tethering them to the endoplasmic reticulum or chloroplast followed by a hinge domain. Each CYP contains domains that facilitate interactions with the heme cofactor and a cytochrome P450 reductase as well as recognition sites that facilitate interactions with various substrates. The heme-binding domain is the most conserved element in the CYP enzyme family, because it provides the cysteine ligand and is rigid enough to hold the heme in place for oxygenation [8]. The glutamate and arginine residues in the ExxR domain and the arginine in the PERF domain are conserved in all plant CYPs and appear to lock the heme pocket into place and stabilize the core structure [9]. The meander region in which the PERF domain lies is also important for protein-protein interactions with the cytochrome P450 reductase [10]. The I-helix contains conserved residues that form a proton groove critical for cleaving the O-O bond to generate the active Fe-O hydroxylating species [8]. The substrate recognition sites (SRSs) are hypervariable regions that have a conserved location in the CYP fold, but vary in amino acid functionality to accommodate diverse substrate sizes and chemistries [11].


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Conserved CYP domains relevant to functional analysis.Scale diagram of the domains of a CYP class II. The signature domains common in most CYPs are shown in orange. Green boxes indicate the more variable substrate recognition sites. Black and blue indicate the membrane anchor and proline rich hinge domains.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163024.g001: Conserved CYP domains relevant to functional analysis.Scale diagram of the domains of a CYP class II. The signature domains common in most CYPs are shown in orange. Green boxes indicate the more variable substrate recognition sites. Black and blue indicate the membrane anchor and proline rich hinge domains.
Mentions: CYPs are defined as heme thiolate monooxygenases and are linked by similarity in the structural fold even though the biochemical reactions they catalyze are quite diverse. The general fold includes domains characteristic of all CYPs and those providing substrate specificity [7]. As diagrammed in Fig 1, most plant CYPs have a membrane anchor tethering them to the endoplasmic reticulum or chloroplast followed by a hinge domain. Each CYP contains domains that facilitate interactions with the heme cofactor and a cytochrome P450 reductase as well as recognition sites that facilitate interactions with various substrates. The heme-binding domain is the most conserved element in the CYP enzyme family, because it provides the cysteine ligand and is rigid enough to hold the heme in place for oxygenation [8]. The glutamate and arginine residues in the ExxR domain and the arginine in the PERF domain are conserved in all plant CYPs and appear to lock the heme pocket into place and stabilize the core structure [9]. The meander region in which the PERF domain lies is also important for protein-protein interactions with the cytochrome P450 reductase [10]. The I-helix contains conserved residues that form a proton groove critical for cleaving the O-O bond to generate the active Fe-O hydroxylating species [8]. The substrate recognition sites (SRSs) are hypervariable regions that have a conserved location in the CYP fold, but vary in amino acid functionality to accommodate diverse substrate sizes and chemistries [11].

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.