Protein trafficking and signal sequences

Protein trafficking and signal sequences: Signal sequences are short amino acid sequences that target proteins to specific destinations in the cell. A signal sequence can occur anywhere in a protein, but it’s often found at the N-terminus. Many organelles have membrane pores or translocators that allow proteins with the correct signal sequence to pass through.

Proteins destined for secretion, the plasma membrane, or any organelle in the secretory pathway are first inserted into the endoplasmic reticulum (ER). The signal sequence for ER proteins usually resides at the N-terminus. The signal recognition particle (SRP), a complex of 6 proteins and one RNA, binds the signal sequence as soon as it emerges during translation. Newly synthesized ER proteins are then translocated across the ER membrane through pores (translocators). Once in the ER lumen, proteins fold into their three-dimensional structures.

Protein import into mitochondria requires the translocators TOM and TIM, which mediate passage across the outer and inner mitochondrial membranes, respectively. Proteins that traffic into the nucleus contain a nuclear import signal, and proteins that must also exit the nucleus contain a nuclear export sequence. Proteins targeted to peroxisomes contain a signal sequence recognized by a family of proteins called Pex proteins. Mutations in Pex proteins cause Zellweger syndrome.

Protein trafficking and quality control: Premature stop codons lead to synthesis of a truncated, dysfunctional protein. Cells identify mRNAs with premature stop codons using the exon junction complex in a process called nonsense mediated decay. The exon junction complex is a set of proteins deposited on mRNAs during splicing (when exons are joined and introns are removed). These exon junction complexes are tagged by Upf proteins, which activate factors that remove the 5’ cap and poly A tail from the mRNA, making it susceptible to degradation by exonucleases.

Misfolded and unfolded proteins are toxic to the cell and contribute to diseases such as Alzheimer’s dementia. Unfolded proteins expose hydrophobic domains; chaperones bind these exposed regions to prevent the proteins from aggregating. Misfolded proteins can also be degraded by the proteasome. The proteasome consists of a cylindrical core with proteolytic activity. Caps on either end contain ATPase activity that unfolds proteins before degradation. Proteins targeted to the proteasome are marked by a small peptide called ubiquitin.

In the endoplasmic reticulum, calnexin helps unfolded proteins fold correctly and prevents aggregation. If a protein still has exposed hydrophobic domains, it can’t exit the ER. Instead, it is bound by glucosyl transferase, which adds glucose to the sugar side chain. This allows calnexin to rebind the protein and support another round of folding. If an unfolded protein remains in the ER for a prolonged time, it loses mannose residues, which triggers proteolytic pathways. Mannose-deficient proteins are targeted by EDEM and transferred to a channel called the retro-translocon. After entering the cytosol, the protein is ubiquitinated by enzymes E1, E2, and E3 on the cytoplasmic side of the ER membrane and then degraded by the proteasome.

The ER contains three sensors that detect unfolded proteins: IRE1, PERK, and ATF6. These sensors are activated when levels of the chaperone BiP fall, which happens as rising amounts of unfolded proteins bind and sequester BiP.

Secretory pathways of the cell: Cells use two types of secretion: constitutive and regulated. Constitutive secretion is the default pathway. Regulated secretion involves storing secretory material in vesicles that wait for a signal before releasing their contents. Glycosylation helps ensure proteins are targeted to specific organelles.

N-linked glycosylation: Occurs in the ER, sugar groups like N acetylglucosamine, glucose and mannose are added to asparagine on proteins O-linked glycosylation: Occurs in the Golgi, sugar groups are added to serine or threonine residues of proteins

Vesicles are targeted to the correct compartment by a combination of Rab proteins and SNAREs (which mediate fusion of the vesicular membrane with other membranes). SNARE proteins on vesicles and target membrane compartments interact with specificity. Sec 23-24 proteins in the vesicular membrane are involved with binding to cargo proteins. The coat complex that surrounds vesicles from the ER is called COP II.

The trans-Golgi network targets proteins to their final destination. The default pathway is transport to the plasma membrane. Other proteins are sorted to lysosomes and secretory vesicles. Proteins destined for lysosomes have mannose-6-phosphate (M6P) residues added in the cis-Golgi. These tagged proteins bind M6P receptors in the trans-Golgi. Coat proteins are then added; clathrin forms the coat, lysosomal proteins accumulate, and the vesicles are released from the Golgi by budding. The vesicles fuse with endosomes. The lumen of endosomes has a low pH, which causes the mannose 6-phosphate receptor to dissociate from lysosomal proteins.