A signal peptide (sometimes referred to as signal sequence, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, the majority of type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved.
In prokaryotes, signal peptides direct the newly synthesized protein to the SecYEG protein-conducting channel, which is present in the plasma membrane. A homologous system exists in eukaryotes, where the signal peptide directs the newly synthesized protein to the Sec61 channel, which shares structural and sequence homology with SecYEG, but is present in the endoplasmic reticulum. Both the SecYEG and Sec61 channels are commonly referred to as the translocon, and transit through this channel is known as translocation. While secreted proteins are threaded through the channel, transmembrane domains may diffuse across a lateral gate in the translocon to partition into the surrounding membrane.
Signal Peptide Structure 
The core of the signal peptide contains a long stretch of hydrophobic amino acids that has a tendency to form a single alpha-helix. In addition, many signal peptides begin with a short positively charged stretch of amino acids, which may help to enforce proper topology of the polypeptide during translocation by what is known as the positive-inside rule. At the end of the signal peptide there is typically a stretch of amino acids that is recognized and cleaved by signal peptidase. However this cleavage site is absent from transmembrane-domains that serve as signal peptides, which are sometimes referred to as signal anchor sequences. Signal peptidase may cleave either during or after completion of translocation to generate a free signal peptide and a mature protein. The free signal peptides are then digested by specific proteases.
Co-translational versus Post-translational Translocation 
In both prokaryotes and eukaryotes signal sequences may act co-translationally or post-translationally.
The co-translational pathway is initiated when the signal peptide emerges from the ribosome and is recognized by the signal-recognition particle (SRP). SRP then halts further translation and directs the signal sequence-ribosome-mRNA complex to the SRP receptor, which is present on the surface of either the plasma membrane (in prokaryotes) or the ER (in eukaryotes). Once membrane-targeting is completed, the signal sequence is inserted into the translocon. Ribosomes are then physically docked onto the cytoplasmic face of the translocon and protein synthesis resumes.
The post-translational pathway is initiated after protein synthesis is completed. In prokaryotes, the signal sequence of post-translational substrates is recognized by the SecB chaperone protein that transfers the protein to the SecA ATPase, which in turns pumps the protein through the translocon. Although post-translational translocation is known to occur in eukaryotes, it is poorly understood. It is however known that in yeast post-translational translocation requires the translocon and two additional membrane-bound proteins, Sec62 and Sec63.
Signal Peptides are determining the Secretion Efficiency 
Signal peptides are extremely heterogeneous and many prokaryotic and eukaryotic signal peptides are functionally interchangeable even between different species however the efficiency of protein secretion is stongly determined by the signal peptide. 
Nucleotide Level Features 
In vertebrates, the region of the mRNA that codes for the signal peptide (i.e. the signal sequence coding region, or SSCR) can function as an RNA element with specific activities. SSCRs promote nuclear mRNA export and the proper localization to the surface of the endoplasmic reticulum. In addition SSCRs have specific sequence features: they have low adenine-content, are enriched in certain motifs, and tend to be present in the first exon at a frequency that is higher than expected.
See also 
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- Gilmore R, Blobel G, Walter P. (Nov. 1982). "Protein translocation across the endoplasmic reticulum. I. Detection in the microsomal membrane of a receptor for the signal recognition particle.". JCB 95 (2 Pt1): 463–9. doi:10.1083/jcb.95.2.463. PMC 2112970. PMID 6292235.
- Görlich D, Prehn S, Hartmann E, Kalies KU, Rapoport TA. (Oct. 1992). "A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation.". Cell 71 (3): 489–503. doi:10.1016/0092-8674(92)90517-G. PMID 1423609.
- Panzner, S (1995). "Posttranslational protein transport in yeast reconstituted with a purified complex of Sec proteins and Kar2p". Cell 81 (4): 561–570. doi:10.1016/0092-8674(95)90077-2. ISSN 00928674.
- Kober L, Zehe C, Bode J (April 2013). "Optimized signal peptides for the development of high expressing CHO cell lines". Biotechnol. Bioeng. 110 (4): 1164–73. doi:10.1002/bit.24776. PMID 23124363.
- von Heijne G (Jul 1985). "Signal sequences: The limits of variation". J Mol Biol 184 (1): 99–105. doi:10.1016/0022-2836(85)90046-4. PMID 4032478.
- Palazzo, Alexander F.; Springer, Michael; Shibata, Yoko; Lee, Chung-Sheng; Dias, Anusha P.; Rapoport, Tom A. (2007). "The Signal Sequence Coding Region Promotes Nuclear Export of mRNA". PLoS Biology 5 (12): e322. doi:10.1371/journal.pbio.0050322. ISSN 1544-9173.
- Cenik, Can; Chua, Hon Nian; Zhang, Hui; Tarnawsky, Stefan P.; Akef, Abdalla; Derti, Adnan; Tasan, Murat; Moore, Melissa J.; Palazzo, Alexander F.; Roth, Frederick P. (2011). "Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes". PLoS Genetics 7 (4): e1001366. doi:10.1371/journal.pgen.1001366. ISSN 1553-7404.
- Signal Peptide at the US National Library of Medicine Medical Subject Headings (MeSH)
- SPdb (Signal Peptide DataBase)
- SignalP — predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.