Protein trafficking and signal sequences

Protein trafficking and signal sequences: They are short sequences that are used to target specific proteins to their respective destinations. Signal sequences can be localized anywhere in a protein but are often found in the N-terminus. Cytoplasmic organelles contain membrane pores that allow the passage of proteins with the correct signal sequence.

Proteins destined for secretion, the plasma membrane or any organelle of the secretory pathway are first inserted into the 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 immediately after it is translated. Newly synthesized ER proteins will be translocated across the ER membrane via pores or translocators. Once in the ER lumen, proteins will fold into their three dimensional structures.

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

Protein trafficking and quality control: Premature stop codons result in the synthesis of a truncated and dysfunctional protein. Cells identify mRNAs with premature stop codons through the exon junction complex by a process termed nonsense mediated decay. The exon junction complex comprises a set of proteins that is deposited on mRNAs during splicing of exons and removal of introns. Such exon junction complexes are tagged by Upf that activate proteins which remove 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 cause diseases like Alzheimer’s dementia. Unfolded proteins have exposed hydrophobic domains that are bound by chaperones that prevent unfolded proteins from aggregating. They are also degraded by the proteasome. The proteasome consists of a cylindrical core that has proteolytic activity and caps on either end of the core contain an ATPase activity to unfold proteins. Proteins that are to be digested by the proteasome are marked by a small peptide called ubiquitin.

In the endoplasmic reticulum, calnexin facilitates the folding of unfolded proteins and prevents them from aggregating. If the protein contains exposed hydrophobic domains, it cannot exit the ER and is bound by glucosyl transferase that adds glucose to the sugar side chain. Calnexin can rebind the protein and facilitate folding. As an unfolded protein stays longer in the ER, it loses mannose residues which triggers proteolytic enzymes. Mannose deficient proteins are targeted by EDEM and transferred to a channel called the retro-translocon. Upon entering the cytosol, the protein is ubiquitinated by enzymes E1, E2 and E3 present on the cytoplasmic side of the ER membrane and degraded in the proteasome. The ER contains three sensors that detect unfolded proteins - IRE1, PERK and ATF6. The sensors are activated when levels of a chaperone called BiP fall in response to rising amounts of unfolded proteins.

Secretory pathways of the cell: There are two types of secretions - constitutive and regulated. Constitutive secretion is the default pathway while regulated secretion involves the storage of secretory material in vesicles that await a signal to discharge their contents. Glycosylation ensures that 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 (mediate fusion of vesicular membrane with other membranes). SNARE proteins on vesicles and 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 are added mannose-6-phosphate (M6P) residues in the cis-Golgi. Such tagged proteins attach to M6P receptors in the trans-Golgi. Coat proteins are added, clathrin forms the coat, lysosomal proteins accumulate and finally, the vesicles are released from the Golgi by budding. The vesicles fuse with endosomes. The lumen of endosomes has a low pH causing the mannose 6-phosphate receptor to dissociate from lysosomal proteins.