Abstract
Cytochrome P450 93 family (CYP93) belonging to the cytochrome P450 superfamily plays important roles in diverse plant processes. However, no previous studies have investigated the evolution and expression of the members of this family. In this study, we performed comprehensive genome-wide analysis to identify CYP93 genes in 60 green plants. In all, 214 CYP93 proteins were identified; they were specifically found in flowering plants and could be classified into ten subfamilies—CYP93A–K, with the last two being identified first. CYP93A is the ancestor that was derived in flowering plants, and the remaining showed lineage-specific distribution—CYP93B and CYP93C are present in dicots; CYP93F is distributed only in Poaceae; CYP93G and CYP93J are monocot-specific; CYP93E is unique to legumes; CYP93H and CYP93K are only found in Aquilegia coerulea, and CYP93D is Brassicaceae-specific. Each subfamily generally has conserved gene numbers, structures, and characteristics, indicating functional conservation during evolution. Synonymous nucleotide substitution (dN/dS) analysis showed that CYP93 genes are under strong negative selection. Comparative expression analyses of CYP93 genes in dicots and monocots revealed that they are preferentially expressed in the roots and tend to be induced by biotic and/or abiotic stresses, in accordance with their well-known functions in plant secondary biosynthesis.
Highlights
Cytochrome P450 monooxygenases (P450s) are widely distributed in eukaryotes; they form a large and diverse class of enzymes, with more than 35,000 members [1,2]
We searched the NCBI database, including expressed sequence tags (ESTs), and did not find any Cytochrome P450 93 family (CYP93) in the non-flowering species included in this database as well
Our findings suggest that the exon/intron structure of the CYP93 gene family was highly conserved during evolution (Fig 3); the SRSs generally show subfamily-specific amino acid substitutions at some sites (Fig 5), highlighting the nature of their functional diversification in different subfamilies
Summary
Cytochrome P450 monooxygenases (P450s) are widely distributed in eukaryotes; they form a large and diverse class of enzymes, with more than 35,000 members [1,2] (http://drnelson. uthsc.edu/P450.count.April.6.2016.PPTX). Cytochrome P450 monooxygenases (P450s) are widely distributed in eukaryotes; they form a large and diverse class of enzymes, with more than 35,000 members [1,2] P450s are involved in numerous biosynthetic and xenobiotic pathways such as the assimilation of carbon sources, detoxification of xenobiotics, and synthesis of secondary metabolites [2,3]. They have relatively low sequence identity among different organisms (such as plants and animals); they show a common overall topology and tridimensional fold. PLOS ONE | DOI:10.1371/journal.pone.0165020 October 19, 2016
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