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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 between Poales CYP72A sequences.Species shown include: Zea mays (Zm), Oryza sativa (Os), Sorghum bicolor (Sb), Lolium rigidium (Lr), Brachypodium distachyon (Bd), Triticum aestivum (Ta), Hordeum vulgare (Hv), and Echinochloa phyllopogon (Ep). This clade (extracted from Fig 2) is shown with bootstrap values from 250 pseudoreplicates. Orthologous groups are highlighted to show the potential for functional conservation between species.
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pone.0163024.g003: Phylogenetic relationships between Poales CYP72A sequences.Species shown include: Zea mays (Zm), Oryza sativa (Os), Sorghum bicolor (Sb), Lolium rigidium (Lr), Brachypodium distachyon (Bd), Triticum aestivum (Ta), Hordeum vulgare (Hv), and Echinochloa phyllopogon (Ep). This clade (extracted from Fig 2) is shown with bootstrap values from 250 pseudoreplicates. Orthologous groups are highlighted to show the potential for functional conservation between species.

Mentions: Of the Poales species that we sampled four genomes were not complete; despite that, there is some important diversity in the sequences represented. Closer examination of the structure within clades shows that Poales sequences formed two distinct groups with no specificity to species (Fig 3). All of the Lolium rigidium (rye grass) sequences fell into the well-supported lower portion of the Poales clade that groups separately from the majority of the Poales sequences. Since the L. rigidium genome was not completely sequenced, there could be CYP72As from this species that fall into the upper part of the clade. The topology of the Poales clade reveals well-supported sets of orthologous sequences, suggesting that the CYP72A subfamily expanded prior to speciation within these monocots. Similarly, the Brassicaceae sequences show orthologous pairings in a eudicot clade (Fig 4). Because the tips of a maximum likelihood tree are not necessarily the sequences with the highest percent identity, we verified that sequences labeled as orthologous were indeed more similar to each other than other sequences in our amino acid alignment. Orthologous pairings are also prevalent in Solanales, which is expected from the close sequence similarities between the potato and tomato genomes. Poales, Brassicales, and Solanales patterning suggests functional conservation between species within the same order and functional diversification (i.e. CYP72A expansion) prior to speciation within that order.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Phylogenetic relationships between Poales CYP72A sequences.Species shown include: Zea mays (Zm), Oryza sativa (Os), Sorghum bicolor (Sb), Lolium rigidium (Lr), Brachypodium distachyon (Bd), Triticum aestivum (Ta), Hordeum vulgare (Hv), and Echinochloa phyllopogon (Ep). This clade (extracted from Fig 2) is shown with bootstrap values from 250 pseudoreplicates. Orthologous groups are highlighted to show the potential for functional conservation between species.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163024.g003: Phylogenetic relationships between Poales CYP72A sequences.Species shown include: Zea mays (Zm), Oryza sativa (Os), Sorghum bicolor (Sb), Lolium rigidium (Lr), Brachypodium distachyon (Bd), Triticum aestivum (Ta), Hordeum vulgare (Hv), and Echinochloa phyllopogon (Ep). This clade (extracted from Fig 2) is shown with bootstrap values from 250 pseudoreplicates. Orthologous groups are highlighted to show the potential for functional conservation between species.
Mentions: Of the Poales species that we sampled four genomes were not complete; despite that, there is some important diversity in the sequences represented. Closer examination of the structure within clades shows that Poales sequences formed two distinct groups with no specificity to species (Fig 3). All of the Lolium rigidium (rye grass) sequences fell into the well-supported lower portion of the Poales clade that groups separately from the majority of the Poales sequences. Since the L. rigidium genome was not completely sequenced, there could be CYP72As from this species that fall into the upper part of the clade. The topology of the Poales clade reveals well-supported sets of orthologous sequences, suggesting that the CYP72A subfamily expanded prior to speciation within these monocots. Similarly, the Brassicaceae sequences show orthologous pairings in a eudicot clade (Fig 4). Because the tips of a maximum likelihood tree are not necessarily the sequences with the highest percent identity, we verified that sequences labeled as orthologous were indeed more similar to each other than other sequences in our amino acid alignment. Orthologous pairings are also prevalent in Solanales, which is expected from the close sequence similarities between the potato and tomato genomes. Poales, Brassicales, and Solanales patterning suggests functional conservation between species within the same order and functional diversification (i.e. CYP72A expansion) prior to speciation within that order.

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.