Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis

Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense

Jeroen Raes; Antje Rohde; Jørgen Holst Christensen; Yves Van de Peer; Wout Boerjan

2003

Scholarcy highlights

  • Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense
  • Enzymatic assays and transgenic plants have contributed extensively to our understanding of the in vivo role of the enzymes, the role of individual gene family members has been more difficult to tackle, a limitation that can only be overcome in plant species such as Arabidopsis, for which the genome sequence and efficient reverse genetics tools are available
  • To get a first insight into whether all these genes are expressed and, more importantly, whether their expression pattern correlates with developmental lignification, their expression was analyzed in a set of tissues and for six developmental stages of inflorescence stem known to contain a high
  • A strong expression of monolignol biosynthesis genes in stems and roots is documented in numerous publications
  • Lignification cDNAs are relatively highly represented in root libraries because of the absence of other very abundant processes, such as photosynthesis, or, as could be concluded from AtC4H::GUS analysis, the phenylpropanoid pathway in roots is active in more cells than the vascular ones to generate compounds not destined for lignification
  • For each of the 10 enzymes of the monolignol biosynthetic pathway, the corresponding genes were annotated in four steps: experimentally certified family members were collected from a variety of species, and a family-specific profile was created; an Arabidopsis protein database was scanned with this profile; true family members were selected; and prediction on the selected genes was improved with information from different sources, such as cDNA and expressed sequence tag sequences and within-family sequence similarity
  • Primers were designed either with the SPADS program that selects specific primers for a particular gene from the Arabidopsis genome or manually, 4CL2, 4CL3, HCT, CCoAOMT1, Caffeic acid O-methyltransferase

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