Phylogenetic Analysis of Putative Genes Involved in the Tryptophan-Dependent Pathway of Auxin Biosynthesis in Rice

• Published in: Applied biochemistry and biotechnology Vol. 172; no. 5; pp. 2480 - 2495
• Main Author: Abu-Zaitoon, Yousef M.
• Format: Journal Article
• Language: English
• Published: Boston Springer US 01.03.2014; Springer; Springer Nature B.V
• Subjects: Aldehyde Oxidase - classification; Aldehyde Oxidase - genetics; Aldehyde Oxidase - metabolism; Amino Acid Sequence; Aminohydrolases - classification; Aminohydrolases - genetics; Aminohydrolases - metabolism; Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Aromatic-L-Amino-Acid Decarboxylases - classification; Aromatic-L-Amino-Acid Decarboxylases - genetics; Aromatic-L-Amino-Acid Decarboxylases - metabolism; Biochemistry; Bioinformatics; Biological and medical sciences; Biosynthesis; Biotechnology; Brassicaceae; Chemistry; Chemistry and Materials Science; Data Mining; Databases, Protein; Detoxification; Embryonic growth stage; Enzymes; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Gene Expression; Genes, Plant; Indoleacetic Acids - metabolism; Molecular Sequence Data; Oryza - genetics; Oryza - metabolism; Oryza sativa; Oxygenases - classification; Oxygenases - genetics; Oxygenases - metabolism; Phylogenetics; Phylogeny; Plant biology; Plant growth; Plant Proteins - classification; Plant Proteins - genetics; Plant Proteins - metabolism; Rice; Sequence Alignment; Tryptophan - metabolism; Yucca; Phylogenetic analysis; Flavin monooxygenase; Tryptophan decarboxylase; Aldehyde oxidase; Indole-3-acetic acid; Nitrilase; Monocotyledones; Auxin; Indole; Lyases; Biosynthesis; Phylogeny; Oryza sativa; Flavin; Gene; Gramineae; Carboxy-lyases; Angiospermae; Rice; Enzyme; Tryptophan; Carbon-carbon lyases; Hydrolases; Aromatic-L-amino-acid decarboxylase; Spermatophyta; Oxidoreductases; Acetic acid
• ISSN: 0273-2289; 1559-0291
• DOI: 10.1007/s12010-013-0710-4

Plant proteome databases were mined for a flavin monooxygenase (YUCCA), tryptophan decarboxylase (TDC), nitrilase (NIT), and aldehyde oxidase (AO) enzymes that could be involved in the tryptophan-dependent pathway of auxin biosynthesis. Phylogenetic trees for enzyme sequences obtained were constructed. The YUCCA and TDC trees showed that these enzymes were conserved across the plant kingdom and therefore could be involved in auxin synthesis. YUCCAs branched into two clades. Most experimentally studied YUCCAs were found in the first clade. The second clade which has representatives from only seed plants contained Arabidopsis sequences linked to embryonic development. Therefore, sequences in this clade were suggested to be evolved with seed development. Examination of TDC activity and expression had previously linked this enzyme to secondary products synthesis. However, the phylogenetic finding of a conserved TDC clade across land plants suggested its essential role in plant growth. Phylogenetic analysis of AOs showed that plants inherited one AO. Recent gene duplication was suggested as AO sequences from each species were similar to each other rather than to AO from other species. Taken together and based on the experimental support of the involvement of AO in abscisic synthesis, AO was excluded as an intermediate in IAA production. Phylogenetic tree for NIT showed that the first clade contained sequences from species across the plant kingdom whereas the second branch contained sequences from only Brassicaceae. Even though NIT4 orthologues were conserved in the second clade, their major role seems to be detoxification of hydrogen cyanide rather than producing IAA.