title: A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis.
abstract: Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point-specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.
authors.affiliation: Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Geng
authors.forename: Rui
authors.initials: R
authors.lastname: Wu
authors.forename: Choon Wei
authors.initials: CW
authors.lastname: Wee
authors.forename: Fei
authors.initials: F
authors.lastname: Xie
authors.forename: Xueliang
authors.initials: X
authors.lastname: Wei
authors.forename: Penny Mei Yeen
authors.initials: PM
authors.lastname: Chan
authors.forename: Cliff
authors.initials: C
authors.lastname: Tham
authors.forename: Lina
authors.initials: L
authors.lastname: Duan
authors.forename: José R
authors.initials: JR
authors.lastname: Dinneny
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism; D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics*; D016000:Cluster Analysis; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D008856:Microscopy, Fluorescence; D020411:Oligonucleotide Array Sequence Analysis; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D030821:Plants, Genetically Modified; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012965:Sodium Chloride / Q000494:pharmacology*; D062211:Spatio-Temporal Analysis; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D013997:Time Factors; D059008:Time-Lapse Imaging; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D029681:Arabidopsis Proteins; D049452:Green Fluorescent Proteins; D012965:Sodium Chloride; D000040:Abscisic Acid
references.citation: Dev Cell. 2010 Jun 15;18(6):1030-40
references.pmid: 20627084
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Nature. 2010 Jul 1;466(7302):128-32
references.pmid: 20596025
references.citation: Annu Rev Plant Biol. 2002;53:247-73
references.pmid: 12221975
references.citation: Plant Cell Environ. 2002 Feb;25(2):239-250
references.pmid: 11841667
references.citation: Plant Physiol. 2004 Apr;134(4):1439-49
references.pmid: 15064374
references.citation: Cell. 1999 Nov 24;99(5):473-83
references.pmid: 10589676
references.citation: Science. 2009 May 22;324(5930):1068-71
references.pmid: 19407142
references.citation: Plant J. 2012 Apr;70(1):5-17
references.pmid: 22449039
references.citation: Plant Cell. 2005 Jul;17(7):1908-25
references.pmid: 15937229
references.citation: Methods Mol Biol. 2009;553:109-26
references.pmid: 19588103
references.citation: Proc Natl Acad Sci U S A. 2012 May 1;109(18):6811-8
references.pmid: 22447775
references.citation: Bioinformatics. 2006 Apr 1;22(7):789-94
references.pmid: 16410320
references.citation: Nat Methods. 2005 Aug;2(8):615-9
references.pmid: 16170893
references.citation: Nature. 2009 Dec 3;462(7273):660-4
references.pmid: 19924127
references.citation: Bioinformatics. 2006 Feb 15;22(4):507-8
references.pmid: 16357033
references.citation: Science. 1998 Jan 30;279(5351):717-20
references.pmid: 9445479
references.citation: J Exp Bot. 2000 Sep;51(350):1575-84
references.pmid: 11006308
references.citation: Science. 2007 Nov 2;318(5851):801-6
references.pmid: 17975066
references.citation: Plant J. 2003 Jul;35(1):44-56
references.pmid: 12834401
references.citation: Plant J. 2007 Oct;52(2):374-81
references.pmid: 17711415
references.citation: Plant Cell. 2010 Jun;22(6):1733-48
references.pmid: 20551347
references.citation: Plant Cell. 2002 Aug;14(8):1833-46
references.pmid: 12172025
references.citation: Arabidopsis Book. 2002;1:e0071
references.pmid: 22303216
references.citation: Bioinformatics. 2004 Feb 12;20(3):307-15
references.pmid: 14960456
references.citation: J Plant Res. 2011 Jul;124(4):509-25
references.pmid: 21416314
references.citation: Plant Physiol. 2004 Jun;135(2):1008-19
references.pmid: 15173565
references.citation: Arabidopsis Book. 2002;1:e0058
references.pmid: 22303212
references.citation: Science. 2003 Dec 12;302(5652):1956-60
references.pmid: 14671301
references.citation: J Exp Bot. 2002 Jan;53(366):33-7
references.pmid: 11741038
references.citation: Science. 2008 May 16;320(5878):942-5
references.pmid: 18436742
references.citation: Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8
references.pmid: 18180456
references.citation: Plant Physiol. 2010 Jan;152(1):226-44
references.pmid: 19906889
references.citation: Nat Rev Mol Cell Biol. 2007 Jun;8(6):491-501
references.pmid: 17522592
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13446-51
references.pmid: 22847438
references.citation: Science. 2006 Jan 6;311(5757):91-4
references.pmid: 16400150
references.citation: Ann Bot. 2005 Nov;96(6):989-96
references.pmid: 16192293
references.citation: Curr Biol. 2011 Jun 7;21(11):990-7
references.pmid: 21620700
references.citation: Plant Physiol. 2000 Mar;122(3):967-76
references.pmid: 10712561
references.citation: Plant Cell. 2012 Jun;24(6):2483-96
references.pmid: 22739828
references.citation: Plant J. 2007 Apr;50(2):347-63
references.pmid: 17376166
references.citation: Plant Cell. 2011 Sep;23(9):3335-52
references.pmid: 21954460
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12837-42
references.pmid: 16141318
references.citation: Plant Physiol. 1999 Nov;121(3):743-52
references.pmid: 10557222
references.citation: Dev Cell. 2002 Apr;2(4):505-13
references.pmid: 11970900
references.citation: Plant J. 2001 Aug;27(4):325-33
references.pmid: 11532178
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):6055-60
references.pmid: 16581911
references.citation: Plant Cell. 1992 Oct;4(10):1251-61
references.pmid: 1359917
references.citation: Dev Cell. 2011 Oct 18;21(4):770-82
references.pmid: 22014526
references.citation: Cell. 2006 Aug 11;126(3):467-75
references.pmid: 16901781
references.citation: PLoS One. 2007 Aug 08;2(8):e718
references.pmid: 17684564
references.citation: Plant Cell. 2009 Jun;21(6):1659-68
references.pmid: 19491238
references.citation: Plant Cell Environ. 2010 Apr;33(4):543-51
references.pmid: 19843253
references.citation: Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):10101-6
references.pmid: 22665765
references.citation: Science. 2009 May 22;324(5930):1064-8
references.pmid: 19407143
references.citation: Plant Physiol. 2010 Jan;152(1):206-16
references.pmid: 19923240
references.citation: Biotechnol Lett. 2010 Oct;32(10):1361-71
references.pmid: 20502944
references.citation: Nature. 2007 Aug 9;448(7154):666-71
references.pmid: 17637675
references.citation: Plant J. 2010 Apr;62(2):179-91
references.pmid: 20088903
references.citation: Cell. 2000 May 26;101(5):555-67
references.pmid: 10850497
references.citation: Nat Cell Biol. 2012 Aug;14(8):810-7
references.pmid: 22820377
references.citation: Cell. 2010 Nov 12;143(4):606-16
references.pmid: 21074051
references.citation: Nature. 2011 May 19;473(7347):380-3
references.pmid: 21593871
references.citation: EMBO J. 2004 Apr 7;23(7):1647-56
references.pmid: 15044947
references.citation: Arabidopsis Book. 2002;1:e0048
references.pmid: 22303210
references.citation: Neural Netw. 1996 Jul;9(5):787-796
references.pmid: 12662563
references.citation: Plant Cell. 2013 Jan;25(1):324-41
references.pmid: 23341337
references.citation: Genes Dev. 2003 Feb 1;17(3):354-8
references.pmid: 12569126
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references.pmid: 12883005
references.citation: Plant Physiol. 2013 Feb;161(2):931-41
references.pmid: 23370718
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 2000 Jun;51:501-531
references.pmid: 15012200
references.citation: Arabidopsis Book. 2002;1:e0101
references.pmid: 22303222
references.citation: Science. 2005 Mar 11;307(5715):1634-8
references.pmid: 15681342
references.citation: Plant Physiol. 1997 Mar;113(3):881-893
references.pmid: 12223650
references.citation: Planta. 2004 May;219(1):41-7
references.pmid: 14986139
references.citation: Nat Cell Biol. 2012 Aug;14(8):802-9
references.pmid: 22820378
references.citation: Nat Protoc. 2011 Jan;6(1):56-68
references.pmid: 21212783
references.citation: Genome Res. 2012 Jan;22(1):163-76
references.pmid: 21940835
references.citation: Plant Cell. 2011 May;23(5):1876-88
references.pmid: 21558544