Module 5 · Lipid and Calcium Biology

Lipids, Ca²⁺ & Contact Sites

Beyond proteostasis, the ER is the cell’s lipid factory and its calcium reservoir. It synthesises the bulk phospholipids, cholesterol, and sphingolipids used throughout the cell; it stores millimolar calcium that is mobilised on second-timescale for signalling; and it physically contacts nearly every other membrane-bound organelle for exchange of lipids and calcium. This module surveys these three interlocking functions.

1. The ER as Lipid Factory

Phospholipids are synthesised on the cytosolic leaflet of the ER via the Kennedy pathway:

Phosphatidic acid (PA) is the universal precursor, generated from glycerol-3-phosphate by GPAT and AGPAT enzymes.
PA → DAG → PC(choline-CDP-DAG pathway), PE(ethanolamine equivalent), PS(via PSS1/PSS2), PI (via PIS).
Sphingolipids are initiated in the ER (SPT, 3-KSR, CerS synthesising ceramide) and elaborated in the Golgi.
Cholesterol synthesis runs entirely in the ER (HMG-CoA reductase is the rate-limiting step and the target of statins; downstream enzymes form the ~30-step mevalonate–lanosterol–cholesterol pathway).

Newly synthesised lipids distribute to other organelles by three mechanisms: vesicular transport (COPII to Golgi and onward), lipid-transfer proteins at contact sites(OSBP, STARD, CERT, VPS13), and lipid scramblases for leaflet redistribution. Flipping between leaflets (within the ER membrane) is catalysed by non-specific scramblases (the TMEM16 and XKR8 families) and ATP-dependent flippases (P4-ATPases).

2. Sterol Homeostasis: SREBP & Insig

Cholesterol sensing is ER-resident. The SREBP (sterol-regulatory element-binding protein) is a membrane-anchored transcription factor, retained in the ER by SCAP–Insig under high sterol. Low sterol releases SCAP from Insig, allowing SREBP/SCAP to traffic to the Golgi, where S1P and S2P cleave it (as with ATF6, Module 4). The released N-terminal domain translocates to the nucleus and activates the cholesterol and fatty-acid synthesis gene programmes. Statin response, LDL receptor biology, and several lipid disorders all trace to this circuit (Brown & Goldstein Nobel 1985).

3. Calcium Storage & Release

ER lumen [Ca²⁺] = 0.5–1 mM; cytosol = 100 nM. The 10⁴-fold gradient is maintained by SERCA(sarco-/endoplasmic reticulum Ca²⁺-ATPase) pumping 2 Ca²⁺ per ATP. Calreticulin and GRP94 buffer luminal Ca²⁺, raising the total storage capacity ~10-fold above free Ca²⁺.

Release proceeds through two channel families:

IP₃ receptors (ITPR1/2/3): activated by inositol-1,4,5-trisphosphate produced at the plasma membrane by PLCβ (GPCR-coupled) or PLCγ (RTK-coupled). Universal second-messenger pathway.
Ryanodine receptors (RYR1/2/3): dominant in skeletal (RYR1) and cardiac (RYR2) muscle; activated by depolarisation via DHPR coupling (skeletal) or Ca²⁺-induced Ca²⁺-release (cardiac).

Calcium release drives countless signalling outputs: muscle contraction, exocytosis, transcription (NFAT via calcineurin), apoptosis (mitochondrial Ca²⁺overload via MAMs, Module 7 of the Organelles course), and synaptic plasticity.

Simulation: ER Ca²⁺ Dynamics

Python

script.py54 lines

import numpy as np, matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

# ER Ca2+ dynamics: store depletion -> STIM1 puncta -> SOCE via Orai1
t = np.linspace(0, 300, 2000)   # seconds

# IP3-triggered release
t_ip3 = 30
release_duration = 20
# Simple model
Ca_ER = np.ones_like(t) * 500   # uM, starting full
Ca_cyto = np.ones_like(t) * 0.1

# IP3R opens at t_ip3
for i, tt in enumerate(t):
    if t_ip3 < tt < t_ip3 + release_duration:
        Ca_ER[i:] -= 5 * np.exp(-(tt - t_ip3)/release_duration)
        Ca_cyto[i] = 0.1 + 1.5 * np.exp(-(tt-t_ip3)/5) * np.heaviside(tt-t_ip3, 1)

# SOCE refill (slower)
t_soce = 120
for i, tt in enumerate(t):
    if tt > t_soce:
        Ca_ER[i] = max(Ca_ER[i], 500 * (1 - np.exp(-(tt-t_soce)/80)))
        if tt < t_soce + 50:
            Ca_cyto[i] = 0.1 + 0.3 * np.exp(-(tt-t_soce)/30)

Ca_ER = np.maximum(Ca_ER, 50)

fig, ax1 = plt.subplots(figsize=(12, 5), facecolor='#0a0a1a')
ax1.set_facecolor('#111827'); ax1.tick_params(colors='#cbd5e1')
for s in ax1.spines.values(): s.set_color('#334155')
ax1.grid(True, color='#334155', alpha=0.3)

ax1.plot(t, Ca_ER, color='#34d399', lw=2.4, label='[Ca2+] ER (uM)')
ax1.set_xlabel('Time (s)', color='#cbd5e1')
ax1.set_ylabel('ER [Ca2+] (uM)', color='#34d399')
ax1.tick_params(axis='y', labelcolor='#34d399')
ax1.axvspan(30, 50, color='#f87171', alpha=0.15, label='IP3R release')
ax1.axvspan(120, 200, color='#fbbf24', alpha=0.15, label='SOCE refill')

ax2 = ax1.twinx()
ax2.plot(t, Ca_cyto*1000, color='#f87171', lw=2.4, label='[Ca2+] cyto (nM)')
ax2.set_ylabel('Cyto [Ca2+] (nM)', color='#f87171')
ax2.tick_params(axis='y', labelcolor='#f87171')

ax1.set_title('ER Ca2+ dynamics: store depletion and SOCE refill',
              color='#6ee7b7', fontweight='bold')

plt.tight_layout()
plt.savefig('output.png', dpi=120, bbox_inches='tight', facecolor='#0a0a1a')
print('ER stores ~0.5 mM Ca2+ vs 100 nM cytosolic (4-log gradient)')
print('IP3R opens -> rapid release -> STIM1 oligomerises -> SOCE via Orai1 refills')

Click Run to execute the Python code

Code will be executed with Python 3 on the server

4. Store-Operated Ca²⁺ Entry (SOCE) & STIM-Orai

When ER Ca²⁺ stores deplete, the ER-resident luminal Ca²⁺sensor STIM1 oligomerises. STIM1 clusters trafficking to ER–PM junctions physically engage Orai1 (CRAC channel) in the plasma membrane, opening it and allowing Ca²⁺ entry from the extracellular space to refill ER stores.

This pathway was elegantly reconstructed 2005–2010 (Feske, Rao, Lewis, Prakriya). Loss-of-function mutations in Orai1 or STIM1 cause severe combined immunodeficiency (T-cell Ca²⁺-signalling failure) and muscular dystrophy. Gain-of-function mutations cause tubular-aggregate myopathy and Stormorken syndrome. The STIM-Orai CRAC channel is a successful drug target (CM4620 in trials for pancreatitis).

5. Membrane Contact Sites

The ER contacts every other membrane-bound organelle through dedicated contact sites (10–30 nm gaps, tethered by protein bridges but not fused):

ER-Mitochondria (MAMs): Mfn2, VAPB-PTPIP51, IP₃R-GRP75-VDAC. Ca²⁺ transfer, lipid exchange, mitochondrial fission site.
ER-PM: E-Syt1/2/3, STIM-Orai, ORP5/8 (lipid-transfer via PI4P/PS exchange).
ER-endosome/lysosome: STARD3 (cholesterol), VPS13A-D, ORP1L.
ER-Golgi: VAP-OSBP sterol/PI4P exchange.
ER-peroxisome: ACBD5-VAP.

Contact sites are now recognised as the central integrator of interorganellar communication — a full treatment is in Module 7 of theOrganelles course.

6. Non-Vesicular Lipid Transfer

At contact sites, lipid-transfer proteins shuttle specific lipids between closely apposed membranes: CERT (ceramide, ER-Golgi); OSBP (cholesterol in exchange for PI4P, ER-Golgi); VPS13 family (bulk lipid transfer via a hydrophobic groove running along a ~25 nm-long scaffold). VPS13 mutations cause multiple neurodegenerative conditions (chorea acanthocytosis, VPS13A; Cohen syndrome, VPS13B). The scale of non-vesicular lipid traffic is now estimated to rival or exceed vesicular traffic in several cell types (Prinz 2020 review), overturning the classical COPI/COPII-centred picture.

← Module 4 Module 6: ER in Disease →