title: Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis.
abstract: Plants constantly monitor informational light signals using sensory photoreceptors, which include the phytochrome (phy) family (phyA to phyE), and adjust their growth and development accordingly. Following light-induced nuclear translocation, photoactivated phy molecules bind to and induce rapid phosphorylation and degradation of phy-interacting basic Helix Loop Helix (bHLH) transcription factors (PIFs), such as PIF3, thereby regulating the expression of target genes. However, the mechanisms underlying the signal-relay process are still not fully understood. Here, using mass spectrometry, we identify multiple, in vivo, light-induced Ser/Thr phosphorylation sites in PIF3. Using transgenic expression of site-directed mutants of PIF3, we provide evidence that a set of these phosphorylation events acts collectively to trigger rapid degradation of the PIF3 protein in response to initial exposure of dark-grown seedlings to light. In addition, we show that phyB-induced PIF3 phosphorylation is also required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3. This mutually regulatory intermolecular transaction thus provides a mechanism with the dual capacity to promote early, graded, or threshold regulation of the primary, PIF3-controlled transcriptional network in response to initial light exposure, and later, to attenuate global sensitivity to the light signal through reductions in photoreceptor levels upon prolonged exposure.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Weimin
authors.initials: W
authors.lastname: Ni
authors.forename: Shou-Ling
authors.initials: SL
authors.lastname: Xu
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
authors.forename: Thao Nguyen D
authors.initials: TN
authors.lastname: Pham
authors.forename: Shenheng
authors.initials: S
authors.lastname: Guan
authors.forename: Dave A
authors.initials: DA
authors.lastname: Maltby
authors.forename: Alma L
authors.initials: AL
authors.lastname: Burlingame
authors.forename: Zhi-Yong
authors.initials: ZY
authors.lastname: Wang
authors.forename: Peter H
authors.initials: PH
authors.lastname: Quail
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D025461:Feedback, Physiological / Q000528:radiation effects; D015151:Immunoblotting; D008027:Light; D008969:Molecular Sequence Data; D009154:Mutation; D010766:Phosphorylation / Q000528:radiation effects; D051939:Phytochrome B / Q000235:genetics / Q000378:metabolism*; D030821:Plants, Genetically Modified; D059748:Proteolysis / Q000528:radiation effects; D020133:Reverse Transcriptase Polymerase Chain Reaction; D036226:Seedlings / Q000235:genetics / Q000378:metabolism; D012694:Serine / Q000235:genetics / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D013912:Threonine / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D051939:Phytochrome B; D012694:Serine; D013912:Threonine; C497952:PHYB protein, Arabidopsis; C116162:PIF3 protein, Arabidopsis
references.citation: Plant Signal Behav. 2011 Aug;6(8):1119-21
references.pmid: 21758014
references.citation: Plant Cell. 2006 Sep;18(9):2157-71
references.pmid: 16891401
references.citation: J Exp Bot. 2007;58(12):3125-33
references.pmid: 17855731
references.citation: Plant Physiol. 2002 Sep;130(1):442-56
references.pmid: 12226523
references.citation: Nature. 1999 Aug 19;400(6746):781-4
references.pmid: 10466729
references.citation: J Cell Biol. 1999 May 3;145(3):437-45
references.pmid: 10225946
references.citation: Nat Rev Genet. 2007 Mar;8(3):217-30
references.pmid: 17304247
references.citation: Nature. 2011 Oct 12;480(7375):128-31
references.pmid: 21993622
references.citation: Mol Cell Proteomics. 2011 Jan;10(1):M110.004457
references.pmid: 20860994
references.citation: Nat Rev Mol Cell Biol. 2002 Feb;3(2):85-93
references.pmid: 11836510
references.citation: Plant Physiol. 1994 Apr;104(4):1139-1149
references.pmid: 12232154
references.citation: Plant J. 1996 Nov;10(5):859-68
references.pmid: 8953247
references.citation: Nature. 2003 Jul 31;424(6948):571-4
references.pmid: 12891362
references.citation: Nat Methods. 2007 Mar;4(3):207-14
references.pmid: 17327847
references.citation: Plant Cell. 1993 Feb;5(2):147-57
references.pmid: 8453299
references.citation: Plant Cell. 2004 Jun;16(6):1433-45
references.pmid: 15155879
references.citation: Science. 2009 Sep 25;325(5948):1682-6
references.pmid: 19779198
references.citation: Genes Dev. 2012 Aug 15;26(16):1851-63
references.pmid: 22895253
references.citation: Mol Cell. 2006 Aug 4;23(3):439-46
references.pmid: 16885032
references.citation: Curr Biol. 2008 Dec 9;18(23):1815-23
references.pmid: 19062289
references.citation: FASEB J. 2003 Mar;17(3):349-68
references.pmid: 12631575
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D1176-84
references.pmid: 23172287
references.citation: Cell. 1998 Nov 25;95(5):657-67
references.pmid: 9845368
references.citation: Nature. 2008 Jan 24;451(7177):475-9
references.pmid: 18216856
references.citation: Plant J. 2003 Sep;35(5):660-4
references.pmid: 12940958
references.citation: Plant Cell. 1991 Dec;3(12):1263-1274
references.pmid: 12324590
references.citation: Plant Cell. 2002 Jul;14(7):1541-55
references.pmid: 12119373
references.citation: EMBO J. 2002 May 15;21(10):2441-50
references.pmid: 12006496
references.citation: Methods Enzymol. 2005;399:287-309
references.pmid: 16338364
references.citation: Plant Cell. 2009 Nov;21(11):3535-53
references.pmid: 19920208
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6069-74
references.pmid: 18420821
references.citation: Nature. 2001 Nov 29;414(6863):514-21
references.pmid: 11734846
references.citation: Plant Cell. 2010 Jul;22(7):2370-83
references.pmid: 20605855
references.citation: Plant Cell. 2008 Feb;20(2):337-52
references.pmid: 18252845
references.citation: Nature. 2007 Jul 19;448(7151):358-61
references.pmid: 17589502
references.citation: Plant J. 2008 Jan;53(2):312-23
references.pmid: 18047474
references.citation: Trends Plant Sci. 2011 Jan;16(1):19-28
references.pmid: 20833098
references.citation: Plant Cell Physiol. 2004 Aug;45(8):1078-86
references.pmid: 15356333
references.citation: Plant Methods. 2010 Nov 25;6:25
references.pmid: 21108821
references.citation: Genes Dev. 2010 Jan 1;24(1):72-85
references.pmid: 20048001
references.citation: Plant Cell. 1999 Aug;11(8):1445-56
references.pmid: 10449579
references.citation: Plant J. 2009 Nov;60(3):449-61
references.pmid: 19619162
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2232-7
references.pmid: 18245378
references.citation: Plant Cell. 2008 Jun;20(6):1586-602
references.pmid: 18539749
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7660-5
references.pmid: 19380720
references.citation: Plant Cell. 2003 Oct;15(10):2399-407
references.pmid: 14508006
references.citation: PLoS One. 2010 Dec 13;5(12):e14029
references.pmid: 21179196
references.citation: Cell. 2003 Jan 24;112(2):243-56
references.pmid: 12553912
references.citation: J Biol Chem. 2011 Apr 8;286(14):12066-74
references.pmid: 21330376
references.citation: Annu Rev Biochem. 2009;78:399-434
references.pmid: 19489725
references.citation: PLoS Genet. 2013;9(1):e1003244
references.pmid: 23382695
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7654-9
references.pmid: 19380736
references.citation: J Proteome Res. 2008 Jun;7(6):2458-70
references.pmid: 18433157
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3287-92
references.pmid: 22328159
references.citation: Plant Physiol. 2007 Nov;145(3):1043-51
references.pmid: 17827270
references.citation: Plant J. 2006 Dec;48(5):728-42
references.pmid: 17076805
references.citation: Science. 2004 Sep 24;305(5692):1937-41
references.pmid: 15448264
references.citation: Eukaryot Cell. 2010 Jan;9(1):31-6
references.pmid: 19897738
references.citation: Mol Plant. 2012 May;5(3):734-49
references.pmid: 22492120
references.citation: Trends Biochem Sci. 2013 Jan;38(1):12-9
references.pmid: 23218751
references.citation: Nat Rev Mol Cell Biol. 2007 Jul;8(7):530-41
references.pmid: 17585314
references.citation: Biochem J. 2012 Sep 1;446(2):271-8
references.pmid: 22631074
references.citation: Plant J. 2012 Jan;69(2):343-54
references.pmid: 21950772
references.citation: Mol Cell. 2007 Dec 14;28(5):730-8
references.pmid: 18082598
references.citation: Plant Cell. 2007 Dec;19(12):3915-29
references.pmid: 18065691
references.citation: Plant Cell. 2004 Nov;16(11):3045-58
references.pmid: 15486102
references.citation: Plant Cell. 2004 Nov;16(11):3033-44
references.pmid: 15486100
references.citation: Mol Cell. 2007 Apr 13;26(1):131-43
references.pmid: 17434132
references.citation: Trends Cell Biol. 2011 Nov;21(11):664-71
references.pmid: 21852137
references.citation: Nature. 2008 Jan 24;451(7177):480-4
references.pmid: 18216857
references.citation: Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16091-8
references.pmid: 15505214
references.citation: Cell. 2001 Dec 28;107(7):819-22
references.pmid: 11779457