title: A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana.
abstract: BACKGROUND
  The carotenoids are pure isoprenoids that are essential components of the photosynthetic apparatus and are coordinately synthesized with chlorophylls in chloroplasts. However, little is known about the mechanisms that regulate carotenoid biosynthesis or the mechanisms that coordinate this synthesis with that of chlorophylls and other plastidial synthesized isoprenoid-derived compounds, including quinones, gibberellic acid and abscisic acid. Here, a comprehensive transcriptional analysis of individual carotenoid and isoprenoid-related biosynthesis pathway genes was performed in order to elucidate the role of transcriptional regulation in the coordinated synthesis of these compounds and to identify regulatory components that may mediate this process in Arabidopsis thaliana.
  
  
  RESULTS
  A global microarray expression correlation analysis revealed that the phytoene synthase gene, which encodes the first dedicated and rate-limiting enzyme of carotenogenesis, is highly co-expressed with many photosynthesis-related genes including many isoprenoid-related biosynthesis pathway genes. Chemical and mutant analysis revealed that induction of the co-expressed genes following germination was dependent on gibberellic acid and brassinosteroids (BR) but was inhibited by abscisic acid (ABA). Mutant analyses further revealed that expression of many of the genes is suppressed in dark grown plants by Phytochrome Interacting transcription Factors (PIFs) and activated by photoactivated phytochromes, which in turn degrade PIFs and mediate a coordinated induction of the genes. The promoters of PSY and the co-expressed genes were found to contain an enrichment in putative BR-auxin response elements and G-boxes, which bind PIFs, further supporting a role for BRs and PIFs in regulating expression of the genes. In osmotically stressed root tissue, transcription of Calvin cycle, methylerythritol 4-phosphate pathway and carotenoid biosynthesis genes is induced and uncoupled from that of chlorophyll biosynthesis genes in a manner that is consistent with the increased synthesis of carotenoid precursors for ABA biosynthesis. In all tissues examined, induction of β-carotene hydroxylase transcript levels are linked to an increased demand for ABA.
  
  
  CONCLUSIONS
  This analysis provides compelling evidence to suggest that coordinated transcriptional regulation of isoprenoid-related biosynthesis pathway genes plays a major role in coordinating the synthesis of functionally related chloroplast localized isoprenoid-derived compounds.
authors: Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Blvd, West, Bronx, NY 10468, USA.
authors: Stuart
authors: S
authors: Meier
authors: Oren
authors: O
authors: Tzfadia
authors: Ratnakar
authors: R
authors: Vallabhaneni
authors: Chris
authors: C
authors: Gehring
authors: Eleanore T
authors: ET
authors: Wurtzel
references: PLoS Biol. 2004 Sep;2(9):E258
references: 15328536
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9
references: 16845059
references: Genome Res. 2001 Jul;11(7):1143-4
references: 11435394
references: Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14142-6
references: 10570212
references: Plant J. 2003 Jun;34(5):719-31
references: 12787252
references: Arch Biochem Biophys. 2006 Apr 15;448(1-2):45-59
references: 16460663
references: Plant J. 2006 Mar;45(6):982-93
references: 16507088
references: Plant Cell. 1995 Dec;7(12):2139-49
references: 8718624
references: Plant Physiol. 2003 Apr;131(4):1591-601
references: 12692318
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D575-7
references: 14681484
references: Plant J. 2004 Jun;38(5):725-39
references: 15144375
references: Plant Cell. 2001 Dec;13(12):2589-607
references: 11752374
references: Plant Physiol. 1995 Jul;108(3):919-27
references: 7630972
references: Proc Natl Acad Sci U S A. 1988 Oct;85(19):7054-8
references: 16578835
references: Plant Mol Biol. 2010 Mar;72(4-5):445-57
references: 20012672
references: BMC Bioinformatics. 2004 Feb 25;5:18
references: 15053845
references: Annu Rev Plant Biol. 2007;58:321-46
references: 17227226
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6
references: 17478504
references: Plant J. 2009 Nov;60(3):424-35
references: 19594711
references: Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9433-8
references: 18591656
references: Curr Opin Plant Biol. 2004 Dec;7(6):708-11
references: 15491920
references: Metab Eng. 2006 Jul;8(4):291-302
references: 16621640
references: Science. 2000 May 5;288(5467):859-63
references: 10797009
references: Curr Biol. 2008 Dec 9;18(23):1815-23
references: 19062289
references: Planta. 2000 Nov;211(6):846-54
references: 11144270
references: Mol Cell. 2006 Aug 4;23(3):439-46
references: 16885032
references: Plant J. 2003 Jul;35(1):44-56
references: 12834401
references: Plant Physiol. 2009 Oct;151(2):541-58
references: 19675149
references: Plant Physiol. 2008 Jul;147(3):1334-46
references: 18508954
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W534-40
references: 16845065
references: Plant Physiol. 2002 Nov;130(3):1319-34
references: 12427998
references: Plant J. 2010 Apr 1;62(1):39-51
references: 20088898
references: Bioinformatics. 2004 Sep 1;20(13):1993-2003
references: 15044247
references: Plant Mol Biol. 2010 Apr;72(6):659-71
references: 20119844
references: Plant Cell Physiol. 2008 Apr;49(4):604-16
references: 18303110
references: Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):678-83
references: 17202255
references: FEBS Lett. 2006 Oct 2;580(22):5357-62
references: 16989822
references: FASEB J. 1996 Mar;10(4):403-12
references: 8647339
references: Plant Physiol. 2008 May;147(1):367-80
references: 18326788
references: Nature. 2006 Sep 28;443(7110):458-61
references: 17006513
references: Eur J Biochem. 1998 Jan 15;251(1-2):413-7
references: 9492312
references: Plant J. 2006 Nov;48(3):354-66
references: 17010113
references: Bioinformatics. 2004 Mar 1;20(4):578-80
references: 14990455
references: Ann Bot. 2009 Feb;103(4):551-60
references: 18662937
references: Eur J Biochem. 1990 Jul 31;191(2):359-63
references: 2384084
references: EMBO J. 2002 May 15;21(10):2441-50
references: 12006496
references: Plant Cell. 2009 Nov;21(11):3535-53
references: 19920208
references: Biosci Biotechnol Biochem. 2005 Mar;69(3):592-601
references: 15784989
references: Plant Physiol. 2001 Feb;125(2):763-9
references: 11161033
references: J Exp Bot. 2009;60(10):2933-43
references: 19584121
references: Plant J. 2001 Aug;27(4):325-33
references: 11532178
references: Plant J. 1997 Sep;12(3):625-34
references: 9351247
references: Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11626-31
references: 20534526
references: Trends Plant Sci. 2007 Nov;12(11):514-521
references: 17933576
references: Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9437-42
references: 11481498
references: FEBS Lett. 2006 Aug 21;580(19):4718-22
references: 16890225
references: PLoS One. 2010 Jan 26;5(1):e8904
references: 20126659
references: Plant J. 2004 Oct;40(2):188-99
references: 15447646
references: Plant Physiol. 2006 Oct;142(2):762-74
references: 16920875
references: BMC Plant Biol. 2008 Feb 29;8:24
references: 18307823
references: Plant Physiol. 2004 Sep;136(1):2621-32
references: 15375207
references: Plant Physiol. 2000 Apr;122(4):1045-56
references: 10759500
references: Plant Physiol. 2010 May;153(1):66-79
references: 20335404
references: Plant Signal Behav. 2009 Mar;4(3):208-11
references: 19721751
references: Plant Cell. 2005 Dec;17(12):3239-56
references: 16284311
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90
references: 18940857
references: Plant J. 2006 Dec;48(5):728-42
references: 17076805
references: Eur J Biochem. 1985 Dec 2;153(2):341-6
references: 4076182
references: Arch Biochem Biophys. 2010 Dec 1;504(1):118-22
references: 20561506
references: Plant J. 2008 Oct;56(1):86-100
references: 18557838
references: Plant Mol Biol. 2009 Mar;69(4):463-72
references: 19031046
references: J Biol Chem. 2007 Nov 30;282(48):35056-68
references: 17913714
references: Plant Cell. 2006 Aug;18(8):1887-99
references: 16844907
references: Plant Cell. 2002 Feb;14(2):321-32
references: 11884677
references: Planta. 2007 Sep;226(4):1067-73
references: 17569077
references: Mol Plant. 2008 Mar;1(2):198-217
references: 19825533
references: Plant Physiol. 2004 Jul;135(3):1776-83
references: 15247400
references: Plant Physiol. 2003 Dec;133(4):1605-16
references: 14681527
references: Biochem J. 2003 Mar 1;370(Pt 2):679-86
references: 12437513
references: Plant J. 2007 Nov;52(4):752-62
references: 17877699
references: Plant Mol Biol. 2003 Apr;51(6):925-48
references: 12777052
references: Genes Dev. 2004 Mar 15;18(6):700-14
references: 15031265
references: Science. 2003 Oct 10;302(5643):249-55
references: 12934013
references: Plant Cell. 2004 Nov;16(11):3045-58
references: 15486102
references: Science. 1997 Jun 20;276(5320):1865-8
references: 9188533
references: Trends Plant Sci. 2008 Dec;13(12):624-30
references: 19010711
references: Mol Plant. 2009 Jan;2(1):166-82
references: 19529817
references: Annu Rev Plant Biol. 2005;56:165-85
references: 15862093
references: Plant Physiol. 2008 Mar;146(3):1333-45
references: 18162592
references: Mol Ecol. 2006 Oct;15(12):3483-503
references: 17032252
references: Plant Physiol. 2004 Mar;134(3):1050-7
references: 14963246
references: Photochem Photobiol Sci. 2008 Oct;7(10):1131-49
references: 18846277