title: A link among DNA replication, recombination, and gene expression revealed by genetic and genomic analysis of TEBICHI gene of Arabidopsis thaliana.
abstract: Spatio-temporal regulation of gene expression during development depends on many factors. Mutations in Arabidopsis thaliana TEBICHI (TEB) gene encoding putative helicase and DNA polymerase domains-containing protein result in defects in meristem maintenance and correct organ formation, as well as constitutive DNA damage response and a defect in cell cycle progression; but the molecular link between these phenotypes of teb mutants is unknown. Here, we show that mutations in the DNA replication checkpoint pathway gene, ATR, but not in ATM gene, enhance developmental phenotypes of teb mutants, although atr suppresses cell cycle defect of teb mutants. Developmental phenotypes of teb mutants are also enhanced by mutations in RAD51D and XRCC2 gene, which are involved in homologous recombination. teb and teb atr double mutants exhibit defects in adaxial-abaxial polarity of leaves, which is caused in part by the upregulation of ETTIN (ETT)/AUXIN RESPONSIVE FACTOR 3 (ARF3) and ARF4 genes. The Helitron transposon in the upstream of ETT/ARF3 gene is likely to be involved in the upregulation of ETT/ARF3 in teb. Microarray analysis indicated that teb and teb atr causes preferential upregulation of genes nearby the Helitron transposons. Furthermore, interestingly, duplicated genes, especially tandemly arrayed homologous genes, are highly upregulated in teb or teb atr. We conclude that TEB is required for normal progression of DNA replication and for correct expression of genes during development. Interplay between these two functions and possible mechanism leading to altered expression of specific genes will be discussed.
authors.affiliation: Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan. soinagak@lab.nig.ac.jp
authors.forename: Soichi
authors.initials: S
authors.lastname: Inagaki
authors.forename: Kenzo
authors.initials: K
authors.lastname: Nakamura
authors.forename: Atsushi
authors.initials: A
authors.lastname: Morikami
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000235:genetics / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D023281:Genomics; D011995:Recombination, Genetic
chemical_list: D029681:Arabidopsis Proteins; C511743:TEBICHI protein, Arabidopsis; D004259:DNA-Directed DNA Polymerase
references.citation: Plant Cell. 2007 Feb;19(2):445-57
references.pmid: 17293570
references.citation: Plant Cell. 2005 Nov;17(11):2899-910
references.pmid: 16199616
references.citation: Science. 2003 Aug 1;301(5633):653-7
references.pmid: 12893945
references.citation: Plant Cell. 2006 Jan;18(1):85-103
references.pmid: 16326925
references.citation: Cell. 1989 Jul 14;58(1):15-25
references.pmid: 2546672
references.citation: Cell. 2007 Feb 23;128(4):721-33
references.pmid: 17320509
references.citation: Genetics. 1990 Aug;125(4):813-9
references.pmid: 2397884
references.citation: Nature. 2007 May 24;447(7143):407-12
references.pmid: 17522673
references.citation: Cell. 2007 Feb 23;128(4):707-19
references.pmid: 17320508
references.citation: Cell. 2007 Feb 23;128(4):693-705
references.pmid: 17320507
references.citation: Trends Genet. 2004 Mar;20(3):116-22
references.pmid: 15049302
references.citation: Plant J. 2004 Dec;40(6):1007-15
references.pmid: 15584964
references.citation: J Exp Bot. 2004 Mar;55(397):673-84
references.pmid: 14966212
references.citation: PLoS Comput Biol. 2006 Sep 1;2(9):e115
references.pmid: 16948529
references.citation: Plant Cell Physiol. 2005 Sep;46(9):1452-61
references.pmid: 15964904
references.citation: Mol Biol Evol. 2005 Dec;22(12):2444-56
references.pmid: 16120808
references.citation: DNA Repair (Amst). 2007 Jul 1;6(7):953-66
references.pmid: 17531546
references.citation: Plant Cell Physiol. 2005 May;46(5):736-42
references.pmid: 15746155
references.citation: Plant Cell. 2007 Sep;19(9):2929-39
references.pmid: 17890374
references.citation: Curr Opin Struct Biol. 2004 Feb;14(1):36-42
references.pmid: 15102447
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8714-9
references.pmid: 11447285
references.citation: Curr Biol. 2005 Nov 8;15(21):1919-25
references.pmid: 16271868
references.citation: Development. 1995 May;121(5):1519-32
references.pmid: 7789281
references.citation: Nat Rev Mol Cell Biol. 2002 May;3(5):317-27
references.pmid: 11988766
references.citation: Plant Cell. 2004 May;16(5):1091-104
references.pmid: 15075397
references.citation: Plant Cell. 2003 Jan;15(1):119-32
references.pmid: 12509526
references.citation: Plant Cell Physiol. 2006 Jul;47(7):853-63
references.pmid: 16699177
references.citation: Plant Cell. 2006 Apr;18(4):879-92
references.pmid: 16517762
references.citation: Nature. 2007 May 24;447(7143):425-32
references.pmid: 17522676
references.citation: DNA Repair (Amst). 2007 Jul 1;6(7):1042-61
references.pmid: 17412649
references.citation: Plant Cell. 2006 Oct;18(10):2431-42
references.pmid: 16980538
references.citation: J Cell Biol. 2006 Mar 13;172(6):823-34
references.pmid: 16520385
references.citation: PLoS Genet. 2007 Jun;3(6):e86
references.pmid: 17542647
references.citation: Genetics. 2003 Mar;163(3):1031-40
references.pmid: 12663541
references.citation: Plant Physiol. 2007 May;144(1):105-20
references.pmid: 17351056
references.citation: Genes Dev. 2004 Oct 1;18(19):2368-79
references.pmid: 15466488
references.citation: Plant Cell. 2006 Jul;18(7):1750-65
references.pmid: 16766691
references.citation: Genetics. 1989 Oct;123(2):261-8
references.pmid: 2684745
references.citation: Curr Biol. 2006 May 9;16(9):933-8
references.pmid: 16682355
references.citation: Nature. 2005 Nov 17;438(7066):379-83
references.pmid: 16292314
references.citation: Nature. 2007 Jun 21;447(7147):951-8
references.pmid: 17581578
references.citation: Plant J. 2006 Dec;48(6):947-61
references.pmid: 17227549
references.citation: Mol Cell. 2004 Oct 8;16(1):69-79
references.pmid: 15469823
references.citation: Genes Cells. 2006 Feb;11(2):111-21
references.pmid: 16436048
references.citation: Cell. 2005 Apr 22;121(2):207-21
references.pmid: 15851028
references.citation: Plant Cell. 2003 Nov;15(11):2592-602
references.pmid: 14555697
references.citation: Nat Genet. 2005 Sep;37(9):997-1002
references.pmid: 16056225
references.citation: Nat Rev Genet. 2007 Jan;8(1):77-84
references.pmid: 17173059
references.citation: Development. 2007 Mar;134(5):813-23
references.pmid: 17251271
references.citation: Plant Cell. 2006 Feb;18(2):350-65
references.pmid: 16399800
references.citation: Cell. 1996 Sep 20;86(6):887-96
references.pmid: 8808624
references.citation: Plant J. 2004 May;38(4):673-84
references.pmid: 15125773
references.citation: Plant Cell. 2005 Aug;17(8):2157-71
references.pmid: 16006579
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):4223-7
references.pmid: 17360504
references.citation: Cell. 2006 Sep 22;126(6):1189-201
references.pmid: 16949657
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9703-8
references.pmid: 15980147
references.citation: EMBO J. 2006 Nov 29;25(23):5579-90
references.pmid: 17110925
references.citation: Plant J. 1999 Nov;20(4):503-8
references.pmid: 10607302
references.citation: Curr Biol. 2005 Nov 8;15(21):1912-8
references.pmid: 16271867
references.citation: Mol Biol Evol. 2007 Nov;24(11):2515-24
references.pmid: 17890239
references.citation: Genes Dev. 2004 Apr 1;18(7):782-93
references.pmid: 15082530
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):9068-73
references.pmid: 15951422
references.citation: Cell. 2001 Jan 12;104(1):131-42
references.pmid: 11163246
references.citation: Genetics. 2004 Dec;168(4):2207-15
references.pmid: 15611187
references.citation: EMBO J. 2003 Jul 15;22(14):3737-48
references.pmid: 12853488
references.citation: Annu Rev Biochem. 2004;73:39-85
references.pmid: 15189136
references.citation: Plant Cell. 2002 Oct;14(10):2451-62
references.pmid: 12368497
references.citation: Plant J. 2005 Feb;41(4):533-45
references.pmid: 15686518
references.citation: J Biol Chem. 2006 Apr 7;281(14):9560-8
references.pmid: 16452472
references.citation: DNA Repair (Amst). 2006 Sep 8;5(9-10):1010-20
references.pmid: 16798113
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13986-91
references.pmid: 16172387
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8650-5
references.pmid: 15939881