Journal Article

Meta-Analyses of Microarrays of Arabidopsis <i>asymmetric leaves1</i> (<i>as1</i>), <i>as2</i> and Their Modifying Mutants Reveal a Critical Role for the ETT Pathway in Stabilization of Adaxial–Abaxial Patterning and Cell Division During Leaf Development

Hiro Takahashi, Hidekazu Iwakawa, Nanako Ishibashi, Shoko Kojima, Yoko Matsumura, Pratiwi Prananingrum, Mayumi Iwasaki, Anna Takahashi, Masaya Ikezaki, Lilan Luo, Takeshi Kobayashi, Yasunori Machida and Chiyoko Machida

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 54, issue 3, pages 418-431
Published in print March 2013 | ISSN: 0032-0781
Published online February 2013 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pct027

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial–abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial–abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1–AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1–AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1–AS2–ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana.

Keywords: ASYMMETRIC LEAVES2 (AS2); AUXIN RESPONSE FACTOR3/ETTIN; CDK inhibitors; Cytokinin; Shoot apical meristem

Journal Article.  7792 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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