2018 CDB Part IB Plant Development Lecture 3 Regulation of gene expression by auxin Jim Haseloff Department of Plant Sciences (www.haseloff-lab.org/education)
OVERVIEW: Regulation of gene expression by auxin 1. Intracellular binding of auxin 2. Targeted degradation of Aux/IAA repressors 3. Selective activation of genes by ARF binding to auxin responsive promoter elements 4. Recruitment of protein co-factors for maintenance of gene expression and chromatin remodelling
1. Intracellular binding of auxin
�������������������������������������������������������� � TIR1-mediated mediated binding of auxin a Auxin Ub AUX/ Domain II IAA Ub Ub Ub AUX/ IAA ARF Ub TIR1 Auxin E2 RBX1 A S response K 1 CUL1 c d
Auxin receptors in Arabidopsis (6) Genetic evidence for role in auxin-mediated Gene Product Function development References TIR1 Transport inhibitor Interacts with ASK1; interacts Loss-of-function mutations N. Dharmasiri et al. 2003, response 1, TIR1 with Aux/IAAs; auxin increases reduce multiple auxin Dharmasiri et al. 2005b, F-box protein Aux/IAA affinity; crystal responses Gray et al. 1999, Kepinski structure shows TIR1-auxin- & Leyser 2005, Ruegger Aux/IAA complex et al. 1998, T an et al. 2007 Auxin F-box protein Member of TIR1/AFB family; Loss of function with tir1 , Dharmasiri et al. 2005b AFB1 1 (AFB1) auxin increases Aux/IAA afb2 , afb3 dramatically affinity impairs development AFB2 Auxin F-box protein Member of TIR1/AFB family; Loss of function with tir1 Dharmasiri et al. 2005b 2 (AFB2) auxin increases Aux/IAA reduces multiple auxin affinity responses Auxin F-box protein Member of TIR1/AFB; auxin Loss of function with tir1 and Dharmasiri et al. 2005b AFB3 3 (AFB3) increases Aux/IAA affinity afb2 dramatically impairs development AFB4 Auxin F-box protein Member of TIR1/AFB family Dharmasiri et al. 2005b 4 (AFB4) AFB5 Auxin F-box protein Member of TIR1/AFB family Loss-of-function mutation Dharmasiri et al. 2005b, 5 (AFB5) confers resistance to auxin Walsh et al. 2006 analogs
�������������������������������������������������������� � TIR1-mediated ubiquitination of AUX/IAA proteins a b Auxin Auxin IAA7 Ub peptide AUX/ Domain II IAA TIR1 Ub Ub C C Ub AUX/ IAA LRR ARF F-box Ub N TIR1 Auxin E2 1 ASK1 InsP 6 X B response R ASK1 CUL1 N GA c d
2. Targeted degradation of AUX/IAA repressors
in Arabidopsis thaliana . �������������������������������������������������������� r a (64) Ub Ub (S DUBs Ub Ub Ub da Ub Ub Ub s Ub Ub dy 26S Ub Ub SH A E2 proteasome Ub Ub SH E3 (>60) ( Lys Lys Lys Amino su Target Target acids T ATP DUBs R es Ub Ub S E3 Ub PH Ub Ub Ub + E3 c Ub (15) o SH E2 SH E1 ATP AMP Pr Ub SH E3 E2 S Ub SH E1 q S E1 (>1,400) Ub (2) Ly AMP SH E2 fo (37) p The ubiquitin–26S proteasome system for protein degradation in Arabidopsis
24 Aux/IAA proteins & diverse functions in Arabidopsis Table 1 Aux/IAA proteins in Arabidopsis thaliana and evidence for their roles in auxin-mediated development Table 1 ( Continued ) Genetic evidence for Genetic evidence for role in auxin-mediated role in auxin-mediated Gene Product Function development References Gene Product Function development References IAA1 IAA1 Auxin decreases protein half-life; axr5-1 degron mutation Abel et al. 1995; Park et al. IAA17 AUXIN RESISTANT 3 Auxin decreases protein half-life; axr3-1 and - 3 degron N. Dharmasiri et al. 2003, axr5-1 gain-of-function reduces multiple auxin 2002; Yang et al. 2004; (AXR3/IAA17) protein can interact with TIR1; mutations reduce Gray et al. 2001, Leyser mutation is in degron responses Zenser et al. 2001, 2003 axr3 mutations are in degron and multiple auxin responses et al. 1996, Ouellet et al. increase protein half-life 2001, Overvoorde et al. IAA2 Contains domain II degron Phylogenetic relationship Abel et al. 1995, Liscum & IAA2 2005, Rouse et al. 1998 Reed 2002 IAA18 IAA18 iaa18-1 mutation is in degron iaa18-1 degron mutation Reed 2001 SUPPRESSOR OF shy2-1 , -2 , -3 , -6 mutations are shy2-1 , -2 , -3 , -6 degron Abel et al. 1995, Kim et al. IAA3 reduces multiple auxin HY2 or SHORT in degron mutations reduce multiple 1996, Reed 2001, Reed responses HYPOCOTYL 2 auxin responses et al. 1998, Soh et al. 1999, (SHY2/IAA3) Tian & Reed 1999, 2003 IAA19 MASSUGU 2 msg2-1 to -4 mutations are in msg2-1 to -4 degron Liscum & Reed 2002, (MSG2/IAA19) degron mutations reduce T atematsu et al. 2004 IAA4 Pea ortholog shows rapid Phylogenetic relationship Abel et al. 1994, 1995; IAA4 multiple auxin responses turnover in vivo Liscum & Reed 2002 IAA26 Phytochrome Contains domain II degron Phylogenetic relationship Liscum & Reed 2002 IAA5 IAA5 Contains domain II degron Phylogenetic relationship Abel et al. 1995, Liscum & interacting protein 1 Reed 2002 (PAP1/IAA26) IAA6 SUPPRESSOR OF Pea ortholog shows rapid shy1-1 -stabilizing mutation Abel et al. 1994, 1995; Kim IAA27 Phytochrome Contains domain II degron Phylogenetic relationship Liscum & Reed 2002 HY1 (SHY1/IAA6) turnover in vivo ; shy1-1 reduces multiple auxin et al. 1996; Ramos et al. interacting protein 2 mutation is in degron responses 2001; Reed 2001 (PAP2/IAA27) IAA7 AUXIN Auxin decreases protein half-life; axr2-1 -stabilizing mutations Abel et al. 1995, IAA28 IAA28 Auxin decreases protein half-life; iaa28-1 degron mutations Dreher et al. 2006, RESISTANT 2 protein can interact with TIR1; reduce multiple auxin N. Dharmasiri et al. 2003, iaa28-1 mutation is in degron reduce multiple auxin Rogg et al. 2001 (AXR2/IAA7) axr2-1 mutation is in degron; responses Gray et al. 2001, Nagpal responses axr2-1 mutation abolishes et al. 2000, Timpte et al. protein interaction with TIR1 1994 IAA29 IAA29 Contains domain II degron Phylogenetic relationship Liscum & Reed 2002 and increases protein half-life IAA31 Auxin decreases protein half-life; Phylogenetic relationship Dreher et al. 2006, IAA31 IAA8 IAA8 Protein shows rapid turnover in Phylogenetic relationship Abel et al. 1995, Dreher et al. imperfect conservation of domain Liscum & Reed 2002 II correlates with a half-life longer vivo; contains domain II degron 2006, Liscum & Reed 2002 than that of other Aux/IAAs in vivo IAA9 IAA9 Protein shows rapid turnover in RNAi-reduced levels in Abel et al. 1995, Dreher vivo; contains domain II degron tomato increase sensitivity et al. 2006, Liscum & Reed to auxin in multiple 2002, Wang et al. 2005 developmental processes IAA10 IAA10 Contains domain II degron Phylogenetic relationship Abel et al. 1995 IAA11 IAA11 Contains domain II degron Phylogenetic relationship Abel et al. 1995, Liscum & Reed 2002 IAA12 BODENLOS bdl mutation is in degron bdl degron mutation reduces Abel et al. 1995; Hamann (BDL/IAA12) multiple auxin responses et al. 1999, 2002; Liscum & Reed 2002 IAA13 Contains domain II degron Degron mutant transgene Abel et al. 1995, Weijers IAA13 impairs auxin-related et al. 2005 development IAA14 SOLITARY ROOT slr-1 mutation is in degron slr-1 degron mutation Abel et al. 1995; Fukaki et al. (SLR/IAA14) reduces multiple auxin 2002, 2005; Vanneste et al. responses 2005 IAA15 IAA15 Contains domain II degron Phylogenetic relationship Liscum & Reed 2002 IAA16 IAA16 Contains domain II degron Phylogenetic relationship Liscum & Reed 2002 ( Continued )
TIR1/AFB Aux/IAA ARF Arabidopsis Rice Physcomitrella Marchantia ? ? ? Green algae (e.g., Spirogyra ) Figure 7 The evolution of the auxin response pathway, showing the distribution of genes encoding TIR1/AFB, Aux/IAA, and ARF proteins in published plant genomes for several plant species. These species represent eudicots ( Arabidopsis ), monocots (rice), mosses ( Physcomitrella ), liverworts ( Marchantia ), and green algae ( Spirogyra , as an example of charophytes). The tree on the left-hand side indicates the divergence order but is not drawn to scale. Protein abbreviations: ARF, AUXIN RESPONSE FACTOR; Aux/IAA, AUXIN/INDOLE-3-ACETIC ACID; TIR1/AFB, TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX.
3. Selective activation of genes by ARF binding to auxin responsive promoters
PLOS Genetics | DOI:10.1371/journal.pgen.1005084 May 28, 2015
Composite and simple auxin responsive elements (AREs)
The protein structure of ARFs. DBD, DNA-binding domain; CTD, C-terminal dimerization domain; MR, middle region; RD, repression domain; AD, activation domain;
4. Recruitment of protein co-factors for maintenance of gene expression
topless ( tpl ) mutant
AuxRE 2x ARF 2x ARF AUX/IAAs AuxRE 4x TPL/TPR corepressors Recognition of composite AuxREs and recruitment of tetrameric TPL/TPR corepressors
Recruitment of Switch/Sucrose Non-Fermenting (SWI/SNF) and Histone Acetyl Transferase (HAT) complexes for remodelling chromatin
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