Protein Sorting Map (Nucleus, ER, Mitochondria, Lysosome, Peroxisome)

Core Concept

Eukaryotic proteins are delivered to their correct compartment by sorting signals — short amino-acid sequences (or, for lysosomal enzymes, an added sugar tag) that are read by specific receptors and routed through dedicated translocation machinery. Nuclear proteins carry a nuclear localization signal (NLS) and are imported through nuclear pore complexes; secretory and membrane proteins carry an N-terminal signal sequence and enter the ER co-translationally via SRP; mitochondrial proteins use an amphipathic presequence and TOM/TIM complexes; lysosomal enzymes are tagged with mannose-6-phosphate and sorted at the Golgi; peroxisomal proteins carry PTS1/PTS2 signals recognized by Pex receptors. Each route uses a distinct energy source (GTP, ATP, or membrane potential), and the signal plus its receptor jointly determine the destination.

Key Components

Mechanism

1. Signal recognition. A receptor (importin, SRP, Tom20, M6P receptor, or Pex5) binds the protein's sorting signal, committing it to a route.
2. Targeting. The receptor–cargo complex docks at the destination's machinery (NPC, translocon, TOM, coated vesicle, or PEX translocon).
3. Translocation. The protein is threaded through a channel — through NPC gating, a translocon, TOM/TIM, or the peroxisomal translocon (which can admit folded proteins).
4. Release/reset. A switch (Ran-GTP in the nucleus, signal cleavage in ER/mitochondria, low pH in endosomes, receptor recycling) releases cargo and recycles the receptor for another round.

Energy and Directionality

Each pathway is vectorial — cargo moves one way — and the energy source enforces that direction. Nuclear transport uses the Ran-GTP gradient: Ran-GTP is high in the nucleus, and its binding to importin discharges cargo, while GTP hydrolysis (Ran-GAP) resets the cycle. ER import is driven by GTP (SRP/SRP receptor) plus the translation machinery. Mitochondrial import consumes the inner-membrane electrochemical potential (Δψ) and matrix ATP (Hsp70 pulling). Lysosomal sorting and peroxisomal import consume ATP (coat dynamics and AAA ATPases). In every case, removing the energy source (or the signal) blocks import — a useful experimental test.

Experimental Evidence

• Classical experiments: pulse-chase autoradiography (Palade) showed secreted proteins move ER → Golgi → vesicles → surface; in vitro reconstitution (Blobel) proved signal-sequence-dependent ER targeting and SRP function.
• Cell-free import assays: mitochondrial proteins imported only with a presequence + membrane potential; ionophores that collapse Δψ block import.
• Signal-swap experiments: attaching an ER signal to a cytosolic protein redirects it to the ER; appending an NLS sends a reporter into the nucleus — direct proof that signals are both necessary and sufficient.
• Disease evidence: I-cell disease (mucolipidosis II), caused by defective M6P tagging, misroutes lysosomal enzymes — proving the M6P tag's role; Zellweger syndrome (PEX mutations) shows peroxisomal import failure.
• What this proves vs. not: these experiments establish where a protein goes and what signal directs it, but not the protein's function at the destination.

Common confusions

• "All import needs ATP" — Nuclear import is driven by the Ran-GTP gradient (GTP, not ATP); mitochondrial import needs Δψ plus ATP.
• "ER and mitochondrial import are the same" — ER import is co-translational (during synthesis via SRP); mitochondrial import is post-translational (unfolded protein threads through TOM/TIM).
• "The NLS and ER signal sequence are interchangeable" — They are different sequences read by different receptors; each routes to a different organelle.
• "Lysosomal enzymes are sorted by an amino-acid signal" — They use a sugar tag, mannose-6-phosphate, added in the Golgi.
• "Peroxisomes import only unfolded proteins" — Peroxisomes can import folded and oligomeric proteins, unlike mitochondria/ER.

Quick review

• Each organelle = specific signal + receptor + machinery + energy source.
• Nucleus (NLS/importin/Ran-GTP), ER (signal/SRP/Sec61/GTP), mitochondria (presequence/TOM-TIM/Δψ+ATP), lysosome (M6P/M6P-receptor/clathrin/ATP), peroxisome (PTS1/Pex5/PEX/ATP).
• Signals are necessary and sufficient; mutation → mislocalization → disease.