A eukaryotic cell synthesizes thousands of proteins simultaneously, requiring a distribution system to ensure they arrive at their correct destinations. The endoplasmic reticulum (ER) is a primary hub for processing proteins destined for secretion, insertion into membranes, or delivery to other organelles. For a newly forming protein to be directed to the ER, it requires a molecular “address label.” This signal is the first step in a regulated pathway that ensures proteins are sorted correctly from the start of their existence.
Defining the ER Signal Sequence
The “address label” that directs a protein to the endoplasmic reticulum is a specific stretch of amino acids known as the ER signal sequence. This sequence is typically found at the N-terminus of the polypeptide chain as it is being synthesized. While the exact amino acid composition can vary, these signal sequences share a defining structural feature: a central core of 7 to 25 hydrophobic, or “water-fearing,” amino acids. It is not a rigid structure but a flexible chain whose physical properties are recognized by the cell’s sorting equipment. Once the protein has successfully reached its destination within the ER, this signal sequence is often cleaved off by an enzyme, as it is no longer needed.
The Co-Translational Targeting Pathway
The journey of a protein destined for the ER begins the moment its signal sequence emerges from the ribosome during translation. This process, known as co-translational targeting, ensures the protein is directed to the ER while it is still being built. The first component to interact with the signal sequence is a complex called the Signal Recognition Particle (SRP). The SRP binds to both the hydrophobic signal sequence and the ribosome, which causes a temporary halt in protein synthesis.
The entire assembly, consisting of the SRP, ribosome, and the nascent polypeptide chain, is then guided to the ER membrane and docks with an SRP receptor. This docking triggers a hand-off, transferring the ribosome to a protein channel called the translocon. Once docked, the SRP is released, and protein synthesis resumes. The growing polypeptide chain is threaded through the translocon channel into the ER lumen. For many soluble proteins, the signal sequence is then removed by signal peptidase, freeing the new protein to fold.
Signal Sequences in Transmembrane Proteins
Not all proteins that enter the ER pathway are destined to be secreted. Many are designed to become permanent residents of the cell’s membranes, such as the ER or the plasma membrane. These transmembrane proteins utilize signal sequences in a more complex manner to ensure they are correctly embedded within the lipid bilayer. The process begins similarly, with an N-terminal signal sequence directing the ribosome to the ER and initiating translocation through the translocon.
A primary difference is the presence of a second hydrophobic sequence within the protein, known as a stop-transfer anchor sequence. As the polypeptide chain is threaded through the translocon, this stop-transfer sequence enters the channel and halts the translocation process. This segment then moves laterally out of the translocon and becomes permanently anchored within the ER membrane. The result is a protein that spans the membrane once, with its N-terminal portion inside the ER lumen and its C-terminal portion in the cytosol.
For proteins that pass through the membrane multiple times, these multi-pass proteins possess a series of alternating start-transfer and stop-transfer sequences. An internal, non-cleavable signal sequence can act as a start-transfer signal, initiating translocation in the middle of a protein chain. Subsequent stop-transfer sequences then anchor different segments, allowing the polypeptide to weave back and forth through the membrane.
Consequences of Signal Sequence Dysfunction
When the protein targeting system fails, the consequences for the cell can be significant. Mutations that alter or delete the ER signal sequence can prevent it from being recognized by the Signal Recognition Particle. If the SRP cannot bind to its target, the co-translational targeting pathway is bypassed. The ribosome will complete the protein’s synthesis in the cytoplasm, releasing it into the wrong cellular compartment.
A protein synthesized in the cytosol when it was meant for the ER is often unable to fold correctly and will be non-functional. The cellular environment of the cytosol is very different from that of the ER, lacking the specific enzymes and chaperone proteins required for proper maturation. These misplaced proteins are identified by the cell’s quality control systems and rapidly degraded.
Defects in this pathway have been linked to several human diseases. For instance, certain genetic disorders are caused by mutations in the signal sequence of a protein. This can lead to a deficiency of a specific secreted protein, such as a hormone or enzyme, because it fails to enter the secretory pathway and reach its site of action.