Computational Systems Biology Flower development Teemu Teeri 23.2. 2006 23.2. 2006 Flower development

Flower development in four parts ABC and beyond Induction of flowering Meristems and prepatterns Regulatory networks 23.2. 2006 Flower development

Part 1 ABC and beyond Homeotic genes that determine organ identity in flowers 23.2. 2006 Flower development

Arabidopsis Stamen Petal Sepal Carpel 23.2. 2006 Flower development

Homeotic mutants Homeosis: ‘Something has been changed into the likeness of something else’ Bateson 1894 Johannsen: terms ’gene’, ’genotype’, ’phenotype’,... Bateson: terms ’homeosis’, ’genetics’,... Wilhelm Johannsen William Bateson 23.2. 2006 Flower development

Homeotic mutants 23.2. 2006 Flower development

Homeotic mutants grow correct organs in wrong places Normal flower A mutant B mutant C mutant 23.2. 2006 Flower development

ABC model for organ identity determination in flowers sepal petal stamen carpel 23.2. 2006 Flower development

ABC model for organ identity determination in flowers 23.2. 2006 Flower development

The ABC model explains homeotic mutants in flowers sepal petal stamen carpel B C carpel stamen B A sepal petal A C sepal carpel 23.2. 2006 Flower development

Mutant phenotypes in Arabidopsis C sepal petal stamen carpel B C carpel stamen B A sepal petal A C sepal carpel 23.2. 2006 Flower development

Double mutants in Arabidopsis C carpel B- C- A sepal 23.2. 2006 Flower development

Double mutants in Arabidopsis A- B- C- leaf B A C C carpel B- C- A sepal 23.2. 2006 Flower development

ABC genes in Arabidopsis and snapdragon 23.2. 2006 Flower development

MADS domain family of transcription factors K MADS I K C N 56 aa, highly conserved, DNA-binding, dimerisation 27-42 aa, considerable sequence variability 70 aa, moderately conserved, keratin related, protein-protein interactions Poor or no sequence conservation A region present in AG and related MADS proteins 23.2. 2006 Flower development

Expression domains of ABC MADS-box genes correlate with their function AGAMOUS APETALA3 23.2. 2006 Flower development

MADS domain proteins bind DNA as dimers transcription g e n e 23.2. 2006 Flower development

The two B-function genes form an autoregulatory loop globosa DEF GLO deficiens DEF GLO GLO DEF DEF GLO 23.2. 2006 Flower development

ABC MADS-box genes are necessary for development of flower organs leaf B A C Are they sufficient? No, expression of ABC genes in leaves does not convert leaves into flower organs. 23.2. 2006 Flower development

Phylogeny Among the ABC MADS-box genes, phylogenetic position and genetic function correlate. sepal petal anther carpel B A C 23.2. 2006 Flower development

When mutated, there is no change in flower phenotype. Arabidopsis MADS-box genes AGL2, AGL4 and AGL9 group outside of the ABC genes in fylogeny. When mutated, there is no change in flower phenotype. 23.2. 2006 Flower development

In a triple mutant for AGL2, AGL4 and AGL9, all organs in the Arabidopsis flower develop into sepals Wild type Triple mutant Organs W1-W4 23.2. 2006 Flower development

AGL2, AGL4 and AGL9 were renamed to SEPALLATA1, SEPALLATA2 and SEPALLATA3 Wild type Triple mutant Organs W1-W4 23.2. 2006 Flower development

The triple mutant resembles the double mutant where B and C function genes are inactive The SEPALLATA function (SEP1, SEP2 or SEP3) is needed to fulfill both the B function and the C function in Arabidospis. A sepal B- C- 23.2. 2006 Flower development

Quaternary complexes of MADS domain proteins 23.2. 2006 Flower development

The Quartet Model of flower development 23.2. 2006 Flower development

ABC and SEP MADS-box genes are necessary for development of flower organs leaf B A C Are they sufficient? 23.2. 2006 Flower development

Conversion of Arabidopsis leaves into petals Rosette leaves Cotyledons 23.2. 2006 Flower development

Scanning electron microscopy is used to define organ identity 23.2. 2006 Flower development

Unifying principles of flower development ABC model Striking in its simplicity Applicable to a wide range of flowering plants Central role of LEAFY Necessary and sufficient to specify a meristem as floral Integrator of floral induction pathways Key activator of the ABC genes B A C sepal petal stamen carpel 23.2. 2006 Flower development

Part 2 How do we get there? Induction of flowering 23.2. 2006 Flower development

Meristems and phase transitions CO FLC AGL20 AGL24 LFY/FLO Vegetative meristem Inflorescence meristem Flower meristem wt 23.2. 2006 Flower development

Multiple inductive pathways control the timing of flowering Long-day photoperiod Gibberellins (GA) Vernalization Autonomous pathway 23.2. 2006 Flower development

Induction of flowering Multiple cues Figure 1 Plants integrate multiple cues during the switch to flowering. In Arabidopsis input signals influencing the transition are light (photoperiod and quality), ambient temperature, phytohormones and long periods of cold temperature (vernalization). Additionally, floral repressors antagonize the activity of promotive cues. 23.2. 2006 Flower development

Induction of flowering Multiple cues Multiple cues are integrated by FLC, SOC1, FT and LFY 23.2. 2006 Flower development

Meristem identity genes Shoot meristem identity genes TERMINAL FLOWER 1 (TFL1) Floral meristem identity genes LEAFY (LFY) APETALA 1 (AP1) 23.2. 2006 Flower development

Snapdragon TFL1 –> CEN, LFY –> FLO Inflorescence meristem Flower meristem CEN FLO cen FLO centroradialis mutant wild type 23.2. 2006 Flower development

Meristem identity genes Vegetative meristem Inflorescence meristem Flower meristem TFL1 LEAFY TFL1 LFY wt 23.2. 2006 Flower development

TFL1 versus LFY and AP1 35S-TFL1 35S-LFY 35S-AP1 LFY ↓ AP1 ↓ TFL1 ↓ 23.2. 2006 Flower development

Part 3 Meristems and prepatterns How ABC is laid down? 23.2. 2006 Flower development

Meristems are stem cells of the plant 23.2. 2006 Flower development

Maintenance of the shoot apical meristem SAM WUS CLA3 CLAVATA3 expression is dependent on WUSCHEL  Stable feedback loop that maintains the size of SAM SAM CLA3 WUS WUS expression gives the meristem a prepattern 23.2. 2006 Flower development

UNUSUAL FLOWER ORGANS (UFO) patterns all meristems Other prepatterns UFO UFO UNUSUAL FLOWER ORGANS (UFO) patterns all meristems 23.2. 2006 Flower development

LEAFY marks the flower meristem Other prepatterns Floral SAM Vegetative SAM LEAFY LEAFY marks the flower meristem 23.2. 2006 Flower development

WUS induces AG AG represses WUS SAM A wus mutant flower: central organs are missing AG WUS 23.2. 2006 Flower development

WUS induces AG AG represses WUS SAM A wus mutant flower: central organs are missing AG WUS + LEAFY Unlike CLAVATA3, AGAMOUS expression is only initially dependent on WUSCHEL 23.2. 2006 Flower development

WUS induces AG AG represses WUS SAM AG LEAFY Repression of the SAM organizer terminates the meristem Unlike CLAVATA3, AGAMOUS expression is only initially dependent on WUSCHEL 23.2. 2006 Flower development

WUS induces AG AG represses WUS SAM ag WUS + LEAFY Failure in repression of the SAM organizer keeps the meristem proliferating 23.2. 2006 Flower development

AP1 is initially expressed throughout the meristem SAM AP1 LEAFY APETALA1 is induced by LEAFY 23.2. 2006 Flower development

AG represses AP1 SAM AG B A C AP1 LEAFY 23.2. 2006 Flower development

B genes use the UFO prepattern AP3 UFO + LEAFY LEAFY and UFO induce AP3 expression in a region where whors 2 and 3 (petals and stamens) will develop 23.2. 2006 Flower development

B genes use the UFO prepattern AP3 PI AP3 PI The B gene autoregulatory loop stabilizes B gene expression PI PI is initially induced also in the center of the flower meristem 23.2. 2006 Flower development

B genes use the UFO prepattern PI AP3+PI PI is initially induced also in the center of the flower meristem The B gene autoregulatory loop stabilizes B gene expression PI AP3 AP3 PI 23.2. 2006 Flower development

Patterning ABC genes SAM sepal petal stamen carpel B A C AG AP3+PI AP1 LEAFY B A C sepal petal stamen carpel 23.2. 2006 Flower development

A complete picture… 23.2. 2006 Flower development

Part 4 Regulatory networks 23.2. 2006 Flower development

Regulatory networks Figure 2. Logical Rules for AP1, AP2, FUL, AP3, and PI. The state of each network node (rightmost column in each table) depends on the combination of activity states of its input nodes (all other columns in each table). X represents any possible value. Comparative symbols (< and >) are used when the relative values are important to determine the state of activity of the target node. AP1 (A), AP2 (B), FUL (C), AP3 (D), and PI (E). 23.2. 2006 Flower development

Regulatory networks Figure 4. Gene Network Architecture for the Arabidopsis Floral Organ Fate Determination. 23.2. 2006 Flower development

Regulatory networks The Steady States of the NetworkModel Coincide with Experimental Gene Expression Profiles The network had 139,968 possible initial conditions, and it attained only 10 fixed-point attractors or steady gene expression states (see supplemental data online for complete basins of attraction). These steady gene states (Table 1) predicted by the model coincide with the gene expression profiles that have been documented experimentally in cells of wild-type Arabidopsis inflorescence meristems and floral organ primordia. For example, in the Infl steady states, floral meristem identity genes (LFY, AP1, and AP2) and floral organ identity genes (AP1, AP2, AP3, PI, SEP, and AG) are off, whereas the inflorescence identity genes (EMF1 and TFL1) are on. 23.2. 2006 Flower development

Reading Jack, T. 2004: Molecular and genetic mechanisms of floral control. Plant Cell 16, S1-S17. Espinosa-Soto et al. 2004: A gene regulatory network model… Plant Cell 16: 2923-2939 23.2. 2006 Flower development