Chapter 10: Plant Hormones & Signaling

Part IV — Hormones & Signaling

10.1 Auxin (IAA): Polar Transport & Signaling

Indole-3-acetic acid (IAA) is the principal auxin. Its polar transportfrom shoot apex to root tip (basipetal) is mediated by PIN efflux carriers and AUX1/LAX influx carriers, creating concentration gradients that direct organogenesis, tropism, and apical dominance.

IAA Biosynthesis (Trp-dependent):

\[\text{Trp} \xrightarrow{TAA1} \text{IPA} \xrightarrow{YUC\text{ (Fd dep.)}} \text{IAA}\]

TAA1 (Trp aminotransferase): Trp → indole-3-pyruvate (IPA)
YUCCAs (flavin monooxygenases): IPA → IAA (rate-limiting step)
Trp-independent pathway also operates in embryos
Stored as IAA-Asp, IAA-Glc conjugates; released by hydrolases

TIR1 Receptor Mechanism (SCF E3 Ubiquitin Ligase):

TIR1: F-box protein, part of SCF^TIR1 E3 ubiquitin ligase complex
IAA binds in an auxin-binding pocket in TIR1
IAA acts as “molecular glue” between TIR1 and AUX/IAA repressors
AUX/IAA ubiquitination → proteasomal degradation
ARF (auxin response factor) TFs de-repressed → gene expression
Polar transport model: chemiosmotic — AHA H⁺ pump lowers apoplast pH; AUX1 (influx, IAAH); PIN (efflux, IAA⁻)

10.2 Major Plant Hormones: Biochemistry Overview

Hormone	Biosynthesis	Receptor	Key Functions
Cytokinin (isopentenyl-Ade)	IPT enzyme; tRNA-IPT; adenosine-5-P + DMAPP → iPMP	AHK1-3 (histidine kinases) → AHP → ARR-A/B	Cell division, shoot organogenesis, chloroplast differentiation, delay senescence
Gibberellins (GA₃, GA₁)	MVA/MEP → GGPP → ent-kaurene (plastid); GA20ox, GA3ox (cytosol)	GID1 (soluble receptor) + DELLA repressors → SCF-ubiquitin	Stem elongation, seed germination, floral transition, fruit development
ABA (abscisic acid)	Carotenoid cleavage by NCED (9-cis-epoxycarotenoid dioxygenase) in plastids	PYR/PYL/RCAR → inhibits PP2C → SnRK2 kinase activated	Stomatal closure, seed dormancy, stress response, seed maturation
Ethylene (C₂H₄)	SAM → ACC (ACS: rate-limiting) → Ethylene + HCN (ACO: O₂-dep.)	ETR1 (ER membrane histidine kinase-like) → CTR1 → EIN2 → EIN3	Fruit ripening, abscission, senescence, triple response to mechanical stress
Brassinosteroids (BR, BL)	Campesterol → campestanol → castasterone (CYP90A-D, DET2)	BRI1 (LRR-RLK) + BAK1 co-receptor → BSK1 → BSU1 → BES1/BZR1 TFs	Hypocotyl elongation, skotomorphogenesis, anther development, immunity
Jasmonate (JA, JA-Ile)	Linolenic acid → OPDA (plastid) → JA (peroxisome) → JA-Ile (cytosol)	COI1 (F-box) + JAZ repressors → SCF degradation → MYC2 TF	Defense vs insects/pathogens, wound response, pollen development, root growth
Salicylate (SA)	Phe → trans-cinnamate → benzoate → SA (or isochorismate pathway)	NPR1 (nuclear receptor) + TGA TFs → PR gene expression	Systemic acquired resistance (SAR), biotrophic pathogen defense, thermotolerance

10.3 ABA Signaling: SnRK2 Kinase Cascade

ABA perception involves a double-negative regulatory cascade where ABA acts as a cofactor to promote receptor–phosphatase interaction, relieving kinase inhibition:

ABA binding: ABA binds PYR/PYL receptor (a START-domain protein) — cap-and-latch mechanism
PP2C inhibition: ABA-PYR complex binds and inhibits PP2C phosphatases (ABI1, ABI2) — the negative regulators
SnRK2 activation: Released SnRK2 kinases (OST1/SnRK2.6) autophosphorylate and become active
SLAC1 activation: SnRK2 phosphorylates SLAC1 anion channel → Cl⁻/malate efflux → guard cell depolarization → K⁺ efflux via GORK → stomatal closure
Gene expression: SnRK2 also phosphorylates ABF/AREB TFs → ABRE-regulated gene expression (stress genes, LEA proteins)

Plant Hormone Signaling Overview

Simulation: Auxin Polar Transport & ABA Dose Response

Finite difference simulation of auxin polar transport along the root axis, and ABA dose-response model for stomatal conductance using the Hill equation.

Python

script.py88 lines

import numpy as np
import matplotlib.pyplot as plt
# output saved as output.png

fig, axes = plt.subplots(1, 2, figsize=(14, 7), facecolor='#0a0f0a')
fig.subplots_adjust(wspace=0.4)

# Panel 1: Auxin polar transport model (finite difference)
ax1 = axes[0]
ax1.set_facecolor('#0d1a0d')
N = 40       # cells along root axis
dx = 1.0     # cell length (arbitrary)
dt = 0.05
T  = 200     # time steps
D  = 0.5     # diffusion coefficient
v  = 1.2     # polar transport velocity (downward)

conc = np.zeros(N)
conc[2:5] = 1.0   # IAA source at shoot-root junction

def apply_boundary(c):
    c[0] = 1.0   # constant source at top
    c[-1] = 0.0  # sink at root tip
    return c

# Snapshots at different times
snapshots = {}
c = conc.copy()
for t in range(T):
    c = apply_boundary(c)
    dc = np.zeros(N)
    # Diffusion: D * d2c/dx2
    dc[1:-1] += D * (c[2:] - 2*c[1:-1] + c[:-2]) / dx**2
    # Polar transport: -v * dc/dx (downward = positive x direction)
    dc[1:-1] -= v * (c[1:-1] - c[:-2]) / dx
    c = c + dt * dc
    c = np.clip(c, 0, None)
    if t in [20, 60, 100, 199]:
        snapshots[t] = c.copy()

positions = np.arange(N)
cols_snap = ['#86efac', '#4ade80', '#a3e635', '#d9f99d']
for (t_val, snap), col in zip(snapshots.items(), cols_snap):
    ax1.plot(positions, snap, color=col, lw=2, label=f't={t_val*0.05:.1f} min')

ax1.set_xlabel('Cell position (root axis)', color='#a3e635', fontsize=9)
ax1.set_ylabel('[IAA] (relative)', color='#a3e635', fontsize=9)
ax1.set_title('Auxin Polar Transport
(Finite Difference Diffusion + Advection)', color='#d9f99d', fontsize=10)
ax1.legend(fontsize=8.5, labelcolor='#d9f99d', facecolor='#0d1a0d', edgecolor='#4ade80')
ax1.tick_params(colors='#a3e635', labelsize=8)
ax1.grid(True, alpha=0.2, color='#4ade80')
ax1.text(0.6, 0.7, 'Source: top
Sink: root tip', transform=ax1.transAxes, color='#d9f99d', fontsize=8.5)
for sp in ax1.spines.values(): sp.set_edgecolor('#4ade80')

# Panel 2: ABA dose-response on stomatal conductance
ax2 = axes[1]
ax2.set_facecolor('#0d1a0d')
aba_conc = np.logspace(-3, 2, 200)  # nM ABA
# Hill equation for stomatal closure
n_hill = 1.8
EC50 = 10.0  # nM ABA for half-maximal closure
gs_max = 0.4  # mol m-2 s-1
gs_min = 0.02

gs = gs_min + (gs_max - gs_min) * (1 - aba_conc**n_hill / (EC50**n_hill + aba_conc**n_hill))
ax2.semilogx(aba_conc, gs, color='#4ade80', lw=2.5)
ax2.fill_between(aba_conc, gs, gs_min, alpha=0.2, color='#4ade80')
ax2.axvline(EC50, color='#fbbf24', lw=1.5, ls='--', label=f'EC50 = {EC50} nM')
ax2.axhline(gs_max/2 + gs_min/2, color='gray', lw=0.8, ls=':', alpha=0.5)
ax2.set_xlabel('[ABA] (nM)', color='#a3e635', fontsize=9)
ax2.set_ylabel('Stomatal Conductance (mol m-2 s-1)', color='#a3e635', fontsize=9)
ax2.set_title('ABA-Induced Stomatal Closure
(Hill Equation Model)', color='#d9f99d', fontsize=10)
ax2.legend(fontsize=9, labelcolor='#d9f99d', facecolor='#0d1a0d', edgecolor='#4ade80')
ax2.tick_params(colors='#a3e635', labelsize=8)
ax2.grid(True, alpha=0.2, color='#4ade80')
ax2.text(0.05, 0.12, f'Hill coeff n = {n_hill}', transform=ax2.transAxes, color='#d9f99d', fontsize=8.5)
for sp in ax2.spines.values(): sp.set_edgecolor('#4ade80')

fig.suptitle('Plant Hormone Modeling: Auxin Transport & ABA Signaling', color='#d9f99d', fontsize=13, fontweight='bold')

plt.savefig('output.png', bbox_inches='tight', facecolor=fig.get_facecolor(), dpi=120)
plt.close()
print('Simulation complete.')

Click Run to execute the Python code

Code will be executed with Python 3 on the server

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