Comprehensive CYP72A Protein Sequence Analysis

A total of 209 CYP72A protein sequences were acquired via five methods: the cytochrome P450 homepage BLAST server [33 (link)], The Arabidopsis Information Resource page (TAIR; https://www.arabidopsis.org/), MaizeGDB BLAST server (http://www.maizegdb.org/), Dr. David Nelson, and through BLAST searching sequence databases (NCBI Genbank). An incomplete protein complement of CYP72A sequences had been previously identified in sacred lotus and papaya [33 (link),34 ] and rice [13 (link)]. These sequences were obtained from the Cytochrome P450 Homepage. A. thaliana and S. lycopersicum sequences were used in extensive BLAST searches in Genbank to identify additional CYP72A sequences. Z. mays sequences were utilized in BLAST searches in MaizeGDB to identify the full set of CYP72A in the maize B73 genome. The CYP names used in the analysis were assigned by Dr. David Nelson; otherwise, unnamed sequences were assigned sequence tags containing the corresponding species and accession number (e.g. Tc_EOX99507). The following plant species are represented: Zea mays (maize), Oryza sativa (rice), Sorghum bicolor (sorghum), Lolium rigidium (rye grass), Brachypodium distachyon (purple false brome), Triticum aestivum (common wheat), Hordeum vulgare (barley), Echinochloa phyllopogon (late watergrass), Coptis japonica (gold thread), Nelumbo nucifera (sacred lotus), Vitis vinifera (grape), Jatropha curcas (barbados nut), Ricinus communis (castor bean), Populus richocarpa (black cottonwood), Glycyrrhiza uralensis (Chinese licorice), Glycine max (soy bean), Medicago truncatula (barrel clover), Glycyrrhiza echinata (licorice), Cicer arietinum (chick pea), Lotus japonicas (lotus), Fragaria vesca (strawberry), Prunus persica (peach), Theobroma cacao (cocoa tree), Arabidopsis thaliana, Capsella rubella (red shepherd’s purse), Brassica rapa (oil Seed), Carica papaya (papaya), Catharanthus roseus (Madagascar periwinkle), Nicotiana tabacum (tobacco), Nicotiana plumbaginifolia (tex mex tobacco), Solanum lycopersicum (tomato), Solanum tuberosum (potato), and Panax ginseng (ginseng) (Table 1). To be included in the set, sequences had to be >55% identical and appear to be entire. Sequences with large gaps (particularly in important structural motifs) or insertions relative to the entire set were excluded. In order to root the CYP72A phylogenetic tree, A. thaliana sequence CYP734A1 was chosen as an outlier based on previous phylogenies [12 ].

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Prall W., Hendy O, & Thornton L.E. (2016). Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants. PLoS ONE, 11(9), e0163024.

Publication 2016

Arabidopsis Arabidopsis thaliana Barley Brassica rapa Capsella Castor bean Chick pea Chinese licorice Cicer arietinum Clover Cocoa Common wheat Coptis japonica Cottonwood Echinochloa Fragaria vesca Genome Ginseng Glycyrrhiza Gold Grape Hordeum vulgare Insertions Jatropha curcas Licorice Lotus Madagascar periwinkle Maize Medicago truncatula Nicotiana tabacum Oryza sativa Papaya Peach Plant Populus Potato Protein sequences Purple false brome Rice Ricinus communis Root Rubella Rye grass Sacred lotus Shepherd purse Sorghum Sorghum bicolor Soy bean Strawberry Tobacco Tomato Tree Vitis

Corresponding Organization : College of New Jersey

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Variable analysis

independent variables

The five methods used to acquire the 209 CYP72A protein sequences: the cytochrome P450 homepage BLAST server, The Arabidopsis Information Resource page (TAIR), MaizeGDB BLAST server, Dr. David Nelson, and BLAST searching sequence databases (NCBI Genbank)

dependent variables

The 209 CYP72A protein sequences obtained from the various sources

control variables

The criteria used to include sequences in the set: sequences had to be >55% identical and appear to be entire, and sequences with large gaps or insertions relative to the entire set were excluded
The use of the Arabidopsis thaliana sequence CYP734A1 as an outlier to root the CYP72A phylogenetic tree

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