title: Genome-wide characterization of the lignification toolbox in Arabidopsis.
abstract: Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants, and functional genomics tools, Arabidopsis constitutes an excellent model system to profoundly unravel the monolignol biosynthetic pathway. In a genome-wide bioinformatics survey of the Arabidopsis genome, 34 candidate genes were annotated that encode genes homologous to the 10 presently known enzymes of the monolignol biosynthesis pathway, nine of which have not been described before. By combining evolutionary analysis of these 10 gene families with in silico promoter analysis and expression data (from a reverse transcription-polymerase chain reaction analysis on an extensive tissue panel, mining of expressed sequence tags from publicly available resources, and assembling expression data from literature), 12 genes could be pinpointed as the most likely candidates for a role in vascular lignification. Furthermore, a possible novel link was detected between the presence of the AC regulatory promoter element and the biosynthesis of G lignin during vascular development. Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies.
authors: Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
authors: Jeroen
authors: J
authors: Raes
authors: Antje
authors: A
authors: Rohde
authors: Jørgen Holst
authors: JH
authors: Christensen
authors: Yves
authors: Y
authors: Van de Peer
authors: Wout
authors: W
authors: Boerjan
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics; D000445:Aldehyde Oxidoreductases / Q000235:genetics; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins; D003066:Coenzyme A Ligases / Q000235:genetics; D019295:Computational Biology; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D020869:Gene Expression Profiling; D018745:Genome, Plant; D008031:Lignin / Q000096:biosynthesis*; D008780:Methyltransferases / Q000235:genetics; D006899:Mixed Function Oxygenases / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics; D010802:Phylogeny; D050564:Trans-Cinnamate 4-Monooxygenase
chemical_list: D029681:Arabidopsis Proteins; C493362:CYP73A5 protein, Arabidopsis; D008031:Lignin; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; D000429:Alcohol Oxidoreductases; C018656:cinnamyl alcohol dehydrogenase; C097486:CYP84A1 protein, Arabidopsis; C438015:CYP98A3 protein, Arabidopsis; D050564:Trans-Cinnamate 4-Monooxygenase; D000445:Aldehyde Oxidoreductases; C019904:cinnamoyl CoA reductase; D008780:Methyltransferases; C059825:caffeoyl-CoA O-methyltransferase; C019608:caffeate O-methyltransferase; D010650:Phenylalanine Ammonia-Lyase; D003066:Coenzyme A Ligases; C019943:4-coumarate-CoA ligase