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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 substrate recognition sites.Amino acid residue frequencies from individual clades were illustrated and compared as in Fig 6.
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pone.0163024.g007: Amino acid sequence logo representations of the substrate recognition sites.Amino acid residue frequencies from individual clades were illustrated and compared as in Fig 6.

Mentions: Clade-specific differences are more pronounced in the SRSs (Fig 7). Chemical properties conferred by the SRS amino acids and the shape of the substrate binding pocket determined by the R-groups that line the pocket are critical for substrate selectivity [11]. Distinct differences stand out in the Brassicales SRS regions relative to the other clades. The Brassicales SRS1 lacks a lysine at position 130, and has a more prevalent aspartate at position 141, while SRS3 shows very little conservation with the CYP72A consensus and SRS5 contains a more prevalent glutamine at position 439. The Mixed Clade also stands out for being divergent in SRS3. The Solanales clade is distinguished with a conserved threonine at position 129 in SRS1 and the Vitales clade is defined by a histidine at position 126 and a leucine at position 140 in SRS1. The Vitales leucine at position 140 is smaller than the more typical tyrosine, so it could allow a larger substrate. Similarly, SRS3 and SRS5 are missing several residues in the Gentianales group relative to the consensus, which would constrain the size of the substrate binding pocket in Gentianales CYP72As. These nonsynonymous changes in amino acids within the abovementioned domains reveal potential differences in the binding capabilities and function of the enzymes.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Amino acid sequence logo representations of the substrate recognition sites.Amino acid residue frequencies from individual clades were illustrated and compared as in Fig 6.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163024.g007: Amino acid sequence logo representations of the substrate recognition sites.Amino acid residue frequencies from individual clades were illustrated and compared as in Fig 6.
Mentions: Clade-specific differences are more pronounced in the SRSs (Fig 7). Chemical properties conferred by the SRS amino acids and the shape of the substrate binding pocket determined by the R-groups that line the pocket are critical for substrate selectivity [11]. Distinct differences stand out in the Brassicales SRS regions relative to the other clades. The Brassicales SRS1 lacks a lysine at position 130, and has a more prevalent aspartate at position 141, while SRS3 shows very little conservation with the CYP72A consensus and SRS5 contains a more prevalent glutamine at position 439. The Mixed Clade also stands out for being divergent in SRS3. The Solanales clade is distinguished with a conserved threonine at position 129 in SRS1 and the Vitales clade is defined by a histidine at position 126 and a leucine at position 140 in SRS1. The Vitales leucine at position 140 is smaller than the more typical tyrosine, so it could allow a larger substrate. Similarly, SRS3 and SRS5 are missing several residues in the Gentianales group relative to the consensus, which would constrain the size of the substrate binding pocket in Gentianales CYP72As. These nonsynonymous changes in amino acids within the abovementioned domains reveal potential differences in the binding capabilities and function of the enzymes.

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.