title: Meta-analyses of microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and their modifying mutants reveal a critical role for the ETT pathway in stabilization of adaxial-abaxial patterning and cell division during leaf development.
abstract: 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.
authors: Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba, 271-8510 Japan.
authors: Hiro
authors: H
authors: Takahashi
authors: Hidekazu
authors: H
authors: Iwakawa
authors: Nanako
authors: N
authors: Ishibashi
authors: Shoko
authors: S
authors: Kojima
authors: Yoko
authors: Y
authors: Matsumura
authors: Pratiwi
authors: P
authors: Prananingrum
authors: Mayumi
authors: M
authors: Iwasaki
authors: Anna
authors: A
authors: Takahashi
authors: Masaya
authors: M
authors: Ikezaki
authors: Lilan
authors: L
authors: Luo
authors: Takeshi
authors: T
authors: Kobayashi
authors: Yasunori
authors: Y
authors: Machida
authors: Chiyoko
authors: C
authors: Machida
mesh_terms: D000465:Algorithms; D019883:Alkyl and Aryl Transferases / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002455:Cell Division; D016000:Cluster Analysis; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000378:metabolism; D018519:Meristem / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D008958:Models, Molecular; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010937:Plant Growth Regulators / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D018520:Plant Shoots / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: C511457:ARF4 protein, Arabidopsis; C463739:AS2 protein, Arabidopsis; C456239:ASYMMETRIC LEAVES1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; C109765:ETT protein, Arabidopsis; D007210:Indoleacetic Acids; D009687:Nuclear Proteins; D010937:Plant Growth Regulators; D014157:Transcription Factors; D019883:Alkyl and Aryl Transferases; C024274:adenylate isopentenyltransferase
references: PLoS One. 2009 Jun 19;4(6):e5980
references: 19543387
references: Plant Cell Physiol. 2001 Jul;42(7):677-85
references: 11479373
references: Genes Dev. 1999 May 1;13(9):1079-88
references: 10323860
references: Plant Cell Physiol. 2010 Apr;51(4):621-34
references: 20208065
references: Biol Open. 2012 Mar 15;1(3):197-207
references: 23213410
references: Genome Res. 2003 Mar;13(3):524-30
references: 12618384
references: Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9972-7
references: 15998742
references: Curr Biol. 2006 May 9;16(9):939-44
references: 16682356
references: Plant Physiol. 2009 Sep;151(1):241-52
references: 19571304
references: J Plant Res. 2012 Sep;125(5):661-8
references: 22351044
references: Genes Dev. 1995 Mar 15;9(6):639-49
references: 7729683
references: Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16392-7
references: 18849474
references: PLoS Genet. 2009 Aug;5(8):e1000613
references: 19696887
references: Plant Cell. 2007 Feb;19(2):445-57
references: 17293570
references: Plant Cell. 2005 Jun;17(6):1723-36
references: 15863515
references: EMBO J. 2004 Aug 18;23(16):3356-64
references: 15282547
references: Plant J. 2012 Mar;69(5):792-808
references: 22026817
references: Plant Cell. 2005 Nov;17(11):2899-910
references: 16199616
references: Plant J. 2011 Mar;65(5):724-36
references: 21251100
references: Development. 2008 Apr;135(7):1315-24
references: 18305008
references: Plant Cell Physiol. 2010 Oct;51(10):1766-76
references: 20802223
references: Development. 2013 May;140(9):1958-69
references: 23571218
references: Development. 1995 May;121(5):1519-32
references: 7789281
references: Genes Dev. 2007 Apr 1;21(7):750-5
references: 17403777
references: Plant Cell. 2001 Jul;13(7):1653-68
references: 11449057
references: Development. 1999 Sep;126(18):4117-28
references: 10457020
references: Cell. 1994 Jul 15;78(1):67-74
references: 8033213
references: Cell Stem Cell. 2011 Sep 2;9(3):262-71
references: 21885021
references: Cold Spring Harb Symp Quant Biol. 2006;71:157-64
references: 17381292
references: J Biosci Bioeng. 2008 Dec;106(6):587-93
references: 19134556
references: Genes Dev. 1999 Jun 15;13(12):1501-12
references: 10385618
references: Curr Biol. 2001 Aug 21;11(16):1251-60
references: 11525739
references: Curr Biol. 2003 Oct 14;13(20):1768-74
references: 14561401
references: Plant J. 2010 Oct;64(2):331-42
references: 21070412
references: Plant J. 2007 Jul;51(2):173-84
references: 17559509
references: Plant Cell Physiol. 2012 Jul;53(7):1180-94
references: 22619472
references: Genes Dev. 1999 Jan 15;13(2):213-24
references: 9925645
references: Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11786-91
references: 9342315
references: Nature. 2000 Dec 21-28;408(6815):967-71
references: 11140682
references: Plant Cell. 2010 Jul;22(7):2113-30
references: 20628155
references: Development. 2008 Apr;135(7):1325-34
references: 18305007
references: Development. 1997 Nov;124(22):4481-91
references: 9409666
references: Curr Opin Plant Biol. 2011 Feb;14(1):24-30
references: 20870452
references: Plant Cell Physiol. 2011 Aug;52(8):1340-53
references: 21690177
references: J Plant Res. 2010 May;123(3):281-90
references: 20369373
references: Plant Cell Physiol. 2002 May;43(5):467-78
references: 12040093
references: Development. 2012 Mar;139(6):1105-9
references: 22296848
references: Plant Cell. 2008 Jan;20(1):48-58
references: 18203921
references: Annu Rev Genet. 2006;40:77-105
references: 17094738
references: Genes Dev. 2008 Sep 15;22(18):2564-77
references: 18794352
references: Mol Gen Genet. 1997 Oct;256(3):231-8
references: 9393447
references: Dev Cell. 2004 Nov;7(5):653-62
references: 15525527
references: Development. 2003 Sep;130(17):4097-107
references: 12874130
references: Nature. 2001 Jun 7;411(6838):706-9
references: 11395775
references: Plant Cell. 2005 Nov;17(11):2940-53
references: 16227452
references: Annu Rev Plant Biol. 2008;59:67-88
references: 18031217
references: Nature. 2001 Jun 7;411(6838):709-13
references: 11395776
references: Cell. 2005 Apr 22;121(2):207-21
references: 15851028
references: Development. 2000 Dec;127(24):5523-32
references: 11076771
references: Plant J. 2010 Jan;61(1):70-82
references: 19891706
references: Development. 1999 Feb;126(3):469-81
references: 9876176
references: Development. 1999 Jun;126(11):2387-96
references: 10225998
references: Development. 1998 Aug;125(15):2935-42
references: 9655815
references: Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9703-8
references: 15980147
references: Plant Cell. 2008 May;20(5):1217-30
references: 18469164
references: J Biosci Bioeng. 2003;96(2):154-60
references: 16233501
references: PLoS Biol. 2009 Nov;7(11):e1000251
references: 19956801
references: Genes Dev. 2009 Mar 1;23(5):549-54
references: 19270155
references: Plant Cell. 2009 Jul;21(7):1957-71
references: 19648297
references: Development. 2006 Aug;133(15):2973-81
references: 16818444
references: Development. 2001 May;128(10):1771-83
references: 11311158
references: Ann Bot. 2004 May;93(5):575-80
references: 15037450
references: Plant Cell Physiol. 2010 Jan;51(1):164-75
references: 20007966
references: Science. 1997 Jun 20;276(5320):1865-8
references: 9188533
references: Annu Rev Plant Biol. 2006;57:477-96
references: 16669771
references: Plant Cell Physiol. 2010 Oct;51(10):1661-73
references: 20739302
references: EMBO J. 2002 Mar 15;21(6):1360-8
references: 11889041
references: Plant Cell Physiol. 2011 Jan;52(1):112-24
references: 21097896
references: Plant Cell Physiol. 2011 Aug;52(8):1259-73
references: 21700721
references: Plant Cell. 1999 Dec;11(12):2263-70
references: 10590156
references: Cell. 1999 Oct 15;99(2):199-209
references: 10535738
references: Plant Cell Physiol. 2011 Oct;52(10):1786-805
references: 21862516
references: Plant Mol Biol. 2012 Aug;79(6):569-81
references: 22684430
references: Plant Mol Biol. 2000 Aug;43(5-6):735-45
references: 11089873
references: Plant Cell Physiol. 2011 Jan;52(1):14-29
references: 20965998
references: J Biol Chem. 2001 Jul 13;276(28):26405-10
references: 11313355
references: Plant Cell Physiol. 2013 Mar;54(3):343-51
references: 22885615