Quality Control of Orphaned Proteins

Abstract

The billions of proteins inside a eukaryotic cell are organized among dozens of sub-cellular compartments, within which they are further organized into protein complexes. The maintenance of both levels of organization is crucial for normal cellular function. Newly made proteins that fail to be segregated to the correct compartment or assembled into the appropriate complex are defined as orphans. In this review, we discuss the challenges faced by a cell of minimizing orphaned proteins, the quality control systems that recognize orphans, and the consequences of excess orphans for protein homeostasis and disease.

Figure 1. Accounting of Protein Localization and Assembly

(A) The approximate percentages of human genes whose proteins are destined for various intracellular compartments are shown. (B) Data from three proteomic studies indicating that roughly half of all proteins in yeast and mammals are in protein complexes.

Figure 2. Recognition Factors for Protein Localization and Mislocalization

Sequence features in a nascent protein can be recognized by various factors that mediate localization to the destinations indicated in parentheses (left side). Not all factors or destinations are shown. Orange indicates hydrophobicity, and blue indicates basic residues. SRP, signal recognition particle; IPO, importin family member; HSP, heat shock protein. The right side shows that the same sequence features used by biosynthesis factors can also be recognized by quality control factors that ultimately lead to degradation at the proteasome.

Figure 3. Recognition of Protein Mislocalization at Organelles

Membrane protein insertion into the wrong organelle can be recognized by its lack of association with an interaction partner. In mitochondria and peroxisomes, the hexameric ATPase Msp1 is involved in extracting such mislocalized proteins to the cytosol for degradation by the proteasome. In the ER, the specific machinery for mislocalized proteins has not been studied, but probably involves known ER-associated degradation (ERAD) pathways. The molecular basis of recognition is not known, but may involve the same features that facilitate assembly into protein complexes, explaining why successful assembly would prevent recognition by quality control factors.

Figure 4. Assembly Interfaces Serve as Degradation Signals

(A) Schematic of hemoglobin assembly in which the α subunit is temporarily shielded by α-hemoglobin-stabilizing protein (AHSP) until it assembles with the β subunit. Free α subunit, generated due to excess or a mutation that prevents assembly, is instead recognized by UBE2O for ubiquitination and targeting to the proteasome for degradation. (B) The assembly interface of α-globin showing hydrophobic (yellow) and basic (blue) surfaces. AHSP is shown in transparent tan to illustrate how this interface is shielded. The positions of two assembly mutants that cause human anemia are indicated. UBE2O is known to bind composite basic/hydrophobic peptides, suggesting that the interface is recognized via these features when assembly fails. (C) An exposed N or C terminus with a destabilizing residue can be shielded in a correctly assembled complex (left) but exposed as an unassembled orphan. N-end and C-end E3 ubiquitin ligases that recognize such residues would then selectively target the orphan for degradation.

Figure 5. Hypothetical Model for Co-translational Monitoring of Protein Assembly

A nascent polypeptide emerging from the ribosome is recognized by an assembly factor, which is recycled when assembly occurs correctly. When assembly fails, the assembly factor is titrated by excess unassembled orphans (right side). The unavailability of this nascent chain binding protein at the ribosome is proposed to trigger ribosome-associated quality control pathway via effects on translation (red arrow), perhaps via factors (not shown) that bind to the sequence motif normally recognized by the assembly factor.