title: Microarray analysis of laser-microdissected tissues indicates the biosynthesis of suberin in the outer part of roots during formation of a barrier to radial oxygen loss in rice (Oryza sativa).
abstract: Internal aeration is crucial for root growth in waterlogged soil. A barrier to radial oxygen loss (ROL) can enhance long-distance oxygen transport via the aerenchyma to the root tip; a higher oxygen concentration at the apex enables root growth into anoxic soil. The ROL barrier is formed within the outer part of roots (OPR). Suberin and/or lignin deposited in cell walls are thought to contribute to the barrier, but it is unclear which compound is the main constituent. This study describes gene expression profiles during ROL barrier formation in rice roots to determine the relative responses of suberin and/or lignin biosyntheses for the barrier. OPR tissues were isolated by laser microdissection and their transcripts were analysed by microarray. A total of 128 genes were significantly up- or downregulated in the OPR during the barrier formation. Genes associated with suberin biosynthesis were strongly upregulated, whereas genes associated with lignin biosynthesis were not. By an ab initio analysis of the promoters of the upregulated genes, the putative cis-elements that could be associated with transcription factors, WRKY, AP2/ERF, NAC, bZIP, MYB, CBT/DREB, and MADS, were elucidated. They were particularly associated with the expression of transcription factor genes containing WRKY, AP2, and MYB domains. A semiquantitative reverse-transcription PCR analysis of genes associated with suberin biosynthesis (WRKY, CYP, and GPAT) confirmed that they were highly expressed during ROL barrier formation. Overall, these results suggest that suberin is a major constituent of the ROL barrier in roots of rice.
authors.affiliation: Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjyojima, Eiheiji, Fukui 910-1195, Japan. shionok@fpu.ac.jp nakazono@agr.nagoya-u.ac.jp.
authors.forename: Katsuhiro
authors.initials: K
authors.lastname: Shiono
authors.affiliation: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
authors.forename: Takaki
authors.initials: T
authors.lastname: Yamauchi
authors.affiliation: Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: So
authors.initials: S
authors.lastname: Yamazaki
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.
authors.forename: Bijayalaxmi
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
authors.forename: Al Imran
authors.initials: AI
authors.lastname: Malik
authors.affiliation: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.affiliation: Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan. Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Nonoichimachi, Ishikawa 921-8836, Japan.
authors.forename: Naoko K
authors.initials: NK
authors.lastname: Nishizawa
authors.affiliation: Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Tsutsumi
authors.affiliation: School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Colmer
authors.affiliation: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan. shionok@fpu.ac.jp nakazono@agr.nagoya-u.ac.jp.
authors.forename: Mikio
authors.initials: M
authors.lastname: Nakazono
mesh_terms: D002473:Cell Wall / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D008055:Lipids / Q000096:biosynthesis*; D042282:Microdissection; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000166:cytology / Q000235:genetics / Q000378:metabolism*; D010100:Oxygen / Q000378:metabolism*; D018517:Plant Roots / Q000166:cytology / Q000378:metabolism
chemical_list: D008055:Lipids; C065875:suberin; D008031:Lignin; D010100:Oxygen
keywords: Exodermis; hypoxia; lignin; plant cell wall; promoter analysis; waterlogging tolerance.