title: Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.
abstract: Different stages of vascular and interfascicular fiber differentiation can be identified along the axis of bolting stems in Arabidopsis. To gain insights into the metabolic, developmental, and regulatory events that control this pattern, we applied global transcript profiling employing an Arabidopsis full-genome longmer microarray. More than 5000 genes were differentially expressed, among which more than 3000 changed more than twofold, and were placed into eight expression clusters based on polynomial regression models. Within these, 182 upregulated transcription factors represent candidate regulators of fiber development. A subset of these candidates has been associated with fiber development and/or secondary wall formation and lignification in the literature, making them targets for functional studies and comparative genomic analyses with woody plants. Analysis of differentially expressed phenylpropanoid genes identified a set known to be involved in lignin biosynthesis. These were used to anchor co-expression analyses that allowed us to identify candidate genes encoding proteins involved in monolignol transport and monolignol dehydrogenation and polymerization. Similar analyses revealed candidate genes encoding enzymes that catalyze missing links in the shikimate pathway, namely arogenate dehydrogenase and prephenate aminotransferase.
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Ehlting
authors.forename: Nathalie
authors.initials: N
authors.lastname: Mattheus
authors.forename: Dana S
authors.initials: DS
authors.lastname: Aeschliman
authors.forename: Eryang
authors.initials: E
authors.lastname: Li
authors.forename: Britta
authors.initials: B
authors.lastname: Hamberger
authors.forename: Ian F
authors.initials: IF
authors.lastname: Cullis
authors.forename: Jun
authors.initials: J
authors.lastname: Zhuang
authors.forename: Minako
authors.initials: M
authors.lastname: Kaneda
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
authors.forename: Lacey
authors.initials: L
authors.lastname: Samuels
authors.forename: Kermit
authors.initials: K
authors.lastname: Ritland
authors.forename: Brian E
authors.initials: BE
authors.lastname: Ellis
authors.forename: Jörg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D001692:Biological Transport; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D008031:Lignin / Q000096:biosynthesis*; D010649:Phenylalanine / Q000096:biosynthesis; D018547:Plant Stems / Q000254:growth & development; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors; D010649:Phenylalanine; D008031:Lignin