Protein targeting

From Wikipedia the free encyclopedia

This article deals with protein targeting in eukaryotes except where noted.

Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the cell.[1] Proteins can be targeted to the inner space of an organelle, different intracellular membranes, the plasma membrane, or to the exterior of the cell via secretion.[1] Information contained in the protein itself directs this delivery process.[2] Correct sorting is crucial for the cell; errors have been linked to multiple disease-states.[3][4]


Günter Blobel, awarded the 1999 Nobel Prize in Physiology for his discovery that proteins contain intrinsic signal sequences.

In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. Blobel, then an assistant professor at Rockefeller University, built upon the work of his colleague George Palade.[5] Palade had previously demonstrated that non-secreted proteins were translated by free ribosomes in the cytosol, while secreted proteins (and target proteins, in general) were translated by ribosomes bound to the endoplasmic reticulum.[5] Candidate explanations at the time postulated a processing difference between free and ER-bound ribosomes, but Blobel hypothesized that protein targeting relied on characteristics inherent to the proteins, rather than a difference in ribosomes. Supporting his hypothesis, Blobel discovered that many proteins have a short amino acid sequence at one end that functions like a postal code specifying an intracellular or extracellular destination.[2] He described these short sequences (generally 13 to 36 amino acids residues)[1] as signal peptides or signal sequences and was awarded the 1999 Nobel prize in Physiology for his findings.[6]

Signal peptides[edit]

Signal peptides serve as targeting signals, enabling cellular transport machinery to direct proteins to specific intracellular or extracellular locations. While no consensus sequence has been identified for signal peptides, many nonetheless possess a characteristic tripartite structure:[1]

  1. A positively charged, hydrophilic region near the N-terminal.
  2. A span of 10 to 15 hydrophobic amino acids near the middle of the signal peptide.
  3. A slightly polar region near the C-terminal, typically favoring amino acids with smaller side chains at positions approaching the cleavage site.

After a protein has reached its destination, the signal peptide is generally cleaved by a signal peptidase.[1] Consequently, most mature proteins do not contain signal peptides. While most signal peptides are found at the N-terminal, in peroxisomes the targeting sequence is located on the C-terminal extension.[7] Unlike signal peptides, signal patches are composed by amino acid residues that are discontinuous in the primary sequence but become functional when folding brings them together on the protein surface.[8] Unlike most signal sequences, signal patches are not cleaved after sorting is complete.[9] In addition to intrinsic signaling sequences, protein modifications like glycosylations can also induce targeting to specific intracellular or extra cellular regions.

Protein translocation[edit]

Since the translation of mRNA into protein by a ribosome takes place within the cytosol, proteins destined for secretion or a specific organelle must be translocated.[10] This process can occur during translation, known as co-translational translocation, or after translation is complete, known as post-translational translocation.[11]

Co-translational translocation[edit]

Most secretory and membrane-bound proteins are co-translationally translocated. Proteins that reside in the endoplasmic reticulum (ER), golgi or endosomes also use the co-translational translocation pathway. This process begins while the protein is being synthesized on the ribosome, when a signal recognition particle (SRP) recognizes an N-terminal signal peptide of the nascent protein.[12] Binding of the SRP temporarily pauses synthesis while the ribosome-protein complex is transferred to an SRP receptor on the ER in eukaryotes, and the plasma membrane in prokaryotes.[13] There, the nascent protein is inserted into the translocon, a membrane-bound protein conducting channel composed of the Sec61 translocation complex in eukaryotes, and the homologous SecYEG complex in prokaryotes.[14] In secretory proteins and type I transmembrane proteins, the signal sequence is immediately cleaved from the nascent polypeptide once it has been translocated into the membrane of the ER (eukaryotes) or plasma membrane (prokaryotes) by signal peptidase. The signal sequence of type II membrane proteins and some polytopic membrane proteins are not cleaved off and therefore are referred to as signal anchor sequences. Within the ER, the protein is first covered by a chaperone protein to protect it from the high concentration of other proteins in the ER, giving it time to fold correctly. Once folded, the protein is modified as needed (for example, by glycosylation), then transported to the Golgi for further processing and goes to its target organelles or is retained in the ER by various ER retention mechanisms.

The amino acid chain of transmembrane proteins, which often are transmembrane receptors, passes through a membrane one or several times. These proteins are inserted into the membrane by translocation, until the process is interrupted by a stop-transfer sequence, also called a membrane anchor or signal-anchor sequence.[15] These complex membrane proteins are currently characterized using the same model of targeting that has been developed for secretory proteins. However, many complex multi-transmembrane proteins contain structural aspects that do not fit this model. Seven transmembrane G-protein coupled receptors (which represent about 5% of the genes in humans) mostly do not have an amino-terminal signal sequence. In contrast to secretory proteins, the first transmembrane domain acts as the first signal sequence, which targets them to the ER membrane. This also results in the translocation of the amino terminus of the protein into the ER membrane lumen. This translocation, which has been demonstrated with opsin with in vitro experiments,[16][17] breaks the usual pattern of "co-translational" translocation which has always held for mammalian proteins targeted to the ER. A great deal of the mechanics of transmembrane topology and folding remains to be elucidated.

Post-translational translocation[edit]

Even though most secretory proteins are co-translationally translocated, some are translated in the cytosol and later transported to the ER/plasma membrane by a post-translational system. In prokaryotes this process requires certain cofactors such as SecA and SecB and is facilitated by Sec62 and Sec63, two membrane-bound proteins.[18] The Sec63 complex, which is embedded in the ER membrane, causes hydrolysis of ATP, allowing chaperone proteins to bind to an exposed peptide chain and slide the polypeptide into the ER lumen. Once in the lumen the polypeptide chain can be folded properly. This process only occurs in unfolded proteins located in the cytosol.[19]

In addition, proteins targeted to other cellular destinations, such as mitochondria, chloroplasts, or peroxisomes, use specialized post-translational pathways. Proteins targeted for the nucleus are also translocated post-translationally through the addition of a nuclear localization signal (NLS) that promotes passage through the nuclear envelope via nuclear pores.[20]

Sorting of proteins[edit]


Most mitochondrial proteins are synthesized as cytosolic precursors containing uptake peptide signals. Cytosolic chaperones deliver preproteins to channel-linked receptors in the mitochondrial membrane. The preprotein with presequence targeted for the mitochondria is bound by receptors and the general import pore (GIP), collectively known as translocase of the outer membrane (TOM), at the outer membrane. It is then translocated through TOM as hairpin loops. The preprotein is transported through the intermembrane space by small TIMs (which also acts as molecular chaperones) to the TIM23 or TIM22 (translocase of the inner membrane) at the inner membrane. Within the matrix the targeting sequence is cleaved off by mtHsp70.

Three mitochondrial outer membrane receptors are known:

  1. TOM70: Binds to internal targeting peptides and acts as docking point for cytosolic chaperones.
  2. TOM20: Binds presequences.
  3. TOM22: Binds both presequences and internal targeting peptides.

The TOM channel (TOM40) is a cation specific high conductance channel with a molecular weight of 410 kDa and a pore diameter of 21Å.

The presequence translocase23 (TIM23) is localized to the mitochondrial inner membrane and acts as a pore-forming protein which binds precursor proteins with its N-terminus. TIM23 acts as a translocator for preproteins for the mitochondrial matrix, the inner mitochondrial membrane as well as for the intermembrane space. TIM50 is bound to TIM23 at the inner mitochondrial side and found to bind presequences. TIM44 is bound on the matrix side and found binding to mtHsp70.
The presequence translocase22 (TIM22) binds preproteins exclusively bound for the inner mitochondrial membrane.

Mitochondrial matrix targeting sequences are rich in positively charged amino acids and hydroxylated ones.

Proteins are targeted to submitochondrial compartments by multiple signals and several pathways.

Targeting to the outer membrane, intermembrane space, and inner membrane often requires another signal sequence in addition to the matrix targeting sequence.


The preprotein for chloroplasts may contain a stromal import sequence or a stromal and thylakoid targeting sequence. The majority of preproteins are translocated through the Toc and Tic complexes located within the chloroplast envelope. In the stroma the stromal import sequence is cleaved off and folded as well as intra-chloroplast sorting to thylakoids continues. Proteins targeted to the envelope of chloroplasts usually lack cleavable sorting sequence.

Both chloroplasts and mitochondria[edit]

Many proteins are needed in both mitochondria and chloroplasts.[21] In general the dual-targeting peptide is of intermediate character to the two specific ones. The targeting peptides of these proteins have a high content of basic and hydrophobic amino acids, a low content of negatively charged amino acids. They have a lower content of alanine and a higher content of leucine and phenylalanine. The dual targeted proteins have a more hydrophobic targeting peptide than both mitochondrial and chloroplastic ones. However, it is tedious to predict if a peptide is dual-targeted or not based on its physico-chemical characteristics.


All peroxisomal proteins are encoded by nuclear genes.[22] To date there are two types of known Peroxisome Targeting Signals (PTS):[23]

  1. Peroxisome targeting signal 1 (PTS1): a C-terminal tripeptide with a consensus sequence (S/A/C)-(K/R/H)-(L/A). The most common PTS1 is serine-lysine-leucine (SKL). Most peroxisomal matrix proteins possess a PTS1 type signal.
  2. Peroxisome targeting signal 2 (PTS2): a nonapeptide located near the N-terminus with a consensus sequence (R/K)-(L/V/I)-XXXXX-(H/Q)-(L/A/F) (where X can be any amino acid).

There are also proteins that possess neither of these signals. Their transport may be based on a so-called "piggy-back" mechanism: such proteins associate with PTS1-possessing matrix proteins and are translocated into the peroxisomal matrix together with them.[24]


Protein transport is defective in the following genetic diseases:

In bacteria and archaea[edit]

As discussed above (see protein translocation), most prokaryotic membrane-bound and secretory proteins are targeted to the plasma membrane by either a co-translation pathway that uses bacterial SRP or a post-translation pathway that requires SecA and SecB. At the plasma membrane, these two pathways deliver proteins to the SecYEG translocon for translocation. Bacteria may have a single plasma membrane (Gram-positive bacteria), or an inner membrane plus an outer membrane separated by the periplasm (Gram-negative bacteria). Besides the plasma membrane the majority of prokaryotes lack membrane-bound organelles as found in eukaryotes, but they may assemble proteins onto various types of inclusions such as gas vesicles and storage granules.

Gram-negative bacteria[edit]

In gram-negative bacteria proteins may be incorporated into the plasma membrane, the outer membrane, the periplasm or secreted into the environment. Systems for secreting proteins across the bacterial outer membrane may be quite complex and play key roles in pathogenesis. These systems may be described as type I secretion, type II secretion, etc.

Gram-positive bacteria[edit]

In most gram-positive bacteria, certain proteins are targeted for export across the plasma membrane and subsequent covalent attachment to the bacterial cell wall. A specialized enzyme, sortase, cleaves the target protein at a characteristic recognition site near the protein C-terminus, such as an LPXTG motif (where X can be any amino acid), then transfers the protein onto the cell wall. Several analogous systems are found that likewise feature a signature motif on the extracytoplasmic face, a C-terminal transmembrane domain, and cluster of basic residues on the cytosolic face at the protein's extreme C-terminus. The PEP-CTERM/exosortase system, found in many Gram-negative bacteria, seems to be related to extracellular polymeric substance production. The PGF-CTERM/archaeosortase A system in archaea is related to S-layer production. The GlyGly-CTERM/rhombosortase system, found in the Shewanella, Vibrio, and a few other genera, seems involved in the release of proteases, nucleases, and other enzymes.

Bioinformatic tools[edit]

  • Minimotif Miner is a bioinformatics tool that searches protein sequence queries for a known protein targeting sequence motifs.
  • Phobius predicts signal peptides based on a supplied primary sequence.
  • SignalP predicts signal peptide cleavage sites.
  • LOCtree predicts the subcellular localization of proteins.

See also[edit]


  1. ^ a b c d e Nelson DL (January 2017). Lehninger principles of biochemistry. Cox, Michael M.,, Lehninger, Albert L. (Seventh ed.). New York, NY. ISBN 978-1-4641-2611-6. OCLC 986827885.
  2. ^ a b Blobel G, Dobberstein B (December 1975). "Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma". The Journal of Cell Biology. 67 (3): 835–51. doi:10.1083/jcb.67.3.835. PMC 2111658. PMID 811671.
  3. ^ Schmidt V, Willnow TE (February 2016). "Protein sorting gone wrong--VPS10P domain receptors in cardiovascular and metabolic diseases". Atherosclerosis. 245: 194–9. doi:10.1016/j.atherosclerosis.2015.11.027. PMID 26724530.
  4. ^ Guo Y, Sirkis DW, Schekman R (2014-10-11). "Protein sorting at the trans-Golgi network". Annual Review of Cell and Developmental Biology. 30 (1): 169–206. doi:10.1146/annurev-cellbio-100913-013012. PMID 25150009.
  5. ^ a b Leslie M (August 2005). "Lost in translation: the signal hypothesis". The Journal of Cell Biology. 170 (3): 338. doi:10.1083/jcb1703fta1. PMC 2254867. PMID 16167405.
  6. ^ "The Nobel Prize in Physiology or Medicine 1999". Retrieved 2020-09-19.
  7. ^ Wanders RJ (May 2004). "Metabolic and molecular basis of peroxisomal disorders: a review". American Journal of Medical Genetics. Part A. 126A (4): 355–75. doi:10.1002/ajmg.a.20661. PMID 15098234. S2CID 24025032.
  8. ^ Moreira IS, Fernandes PA, Ramos MJ (September 2007). "Hot spots--a review of the protein-protein interface determinant amino-acid residues". Proteins. 68 (4): 803–12. doi:10.1002/prot.21396. PMID 17546660. S2CID 18578313.
  9. ^ Pfeffer SR, Rothman JE (1987-06-01). "Biosynthetic protein transport and sorting by the endoplasmic reticulum and Golgi". Annual Review of Biochemistry. 56 (1): 829–52. doi:10.1146/ PMID 3304148.
  10. ^ Sommer MS, Schleiff E (August 2014). "Protein targeting and transport as a necessary consequence of increased cellular complexity". Cold Spring Harbor Perspectives in Biology. 6 (8): a016055. doi:10.1101/cshperspect.a016055. PMC 4107987. PMID 25085907.
  11. ^ Walter P, Ibrahimi I, Blobel G (November 1981). "Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein". The Journal of Cell Biology. 91 (2 Pt 1): 545–50. doi:10.1083/jcb.91.2.545. PMC 2111968. PMID 7309795.
  12. ^ Voorhees RM, Hegde RS (August 2016). "Toward a structural understanding of co-translational protein translocation". Current Opinion in Cell Biology. 41: 91–9. doi:10.1016/ PMID 27155805.
  13. ^ Nyathi Y, Wilkinson BM, Pool MR (November 2013). "Co-translational targeting and translocation of proteins to the endoplasmic reticulum". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1833 (11): 2392–402. doi:10.1016/j.bbamcr.2013.02.021. PMID 23481039.
  14. ^ Mandon EC, Trueman SF, Gilmore R (August 2009). "Translocation of proteins through the Sec61 and SecYEG channels". Current Opinion in Cell Biology. 21 (4): 501–7. doi:10.1016/ PMC 2916700. PMID 19450960.
  15. ^ Alberts (November 2018). Essential cell biology (Fifth ed.). New York. ISBN 978-0-393-67953-3. OCLC 1048014962.
  16. ^ Kanner EM, Friedlander M, Simon SM. (2003). "Co-translational targeting and translocation of the amino terminus of opsin across the endoplasmic membrane requires GTP but not ATP". J. Biol. Chem. 278 (10): 7920–7926. doi:10.1074/jbc.M207462200. PMID 12486130.
  17. ^ Kanner EM, Klein IK. et al. (2002). "The amino terminus of opsin translocates "posttranslationally" as efficiently as cotranslationally". Biochemistry 41 (24): 7707–7715. doi:10.1021/bi0256882. PMID 12056902.
  18. ^ Rapoport TA (November 2007). "Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes". Nature. 450 (7170): 663–9. Bibcode:2007Natur.450..663R. doi:10.1038/nature06384. PMID 18046402. S2CID 2497138.
  19. ^ Lodish H, Berk A, Kaiser C, Krieger M, Bretscher A, Ploegh H, Amon A, Martin K (2008). Molecular Cell Biology (8th ed.). New York: W.H. Freeman and Company. pp. 591–592. ISBN 978-1-4641-8339-3.
  20. ^ Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH (February 2007). "Classical nuclear localization signals: definition, function, and interaction with importin alpha". The Journal of Biological Chemistry. 282 (8): 5101–5. doi:10.1074/jbc.R600026200. PMC 4502416. PMID 17170104.
  21. ^ Sharma M, Bennewitz B, Klösgen RB (December 2018). "Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts". Photosynthesis Research. 138 (3): 335–343. doi:10.1007/s11120-018-0543-7. PMID 29946965. S2CID 49427254.
  22. ^ Encyclopedia of biological chemistry. Lennarz, William J.,, Lane, M. Daniel (Second ed.). London. 8 January 2013. ISBN 978-0-12-378631-9. OCLC 828743403.CS1 maint: others (link)
  23. ^ Baerends RJ, Faber KN, Kiel JA, van der Klei IJ, Harder W, Veenhuis M (July 2000). "Sorting and function of peroxisomal membrane proteins" (PDF). FEMS Microbiology Reviews. 24 (3): 291–301. doi:10.1111/j.1574-6976.2000.tb00543.x. PMID 10841974.
  24. ^ Saryi NA, Hutchinson JD, Al-Hejjaj MY, Sedelnikova S, Baker P, Hettema EH (February 2017). "Pnc1 piggy-back import into peroxisomes relies on Gpd1 homodimerisation". Scientific Reports. 7 (1): 42579. Bibcode:2017NatSR...742579S. doi:10.1038/srep42579. PMC 5314374. PMID 28209961.
  25. ^ MacLeod DA, Rhinn H, Kuwahara T, Zolin A, Di Paolo G, McCabe BD, et al. (February 2013). "RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson's disease risk". Neuron. 77 (3): 425–39. doi:10.1016/j.neuron.2012.11.033. PMC 3646583. PMID 23395371.
  26. ^ Schmidt V, Willnow TE (February 2016). "Protein sorting gone wrong--VPS10P domain receptors in cardiovascular and metabolic diseases". Atherosclerosis. 245: 194–9. doi:10.1016/j.atherosclerosis.2015.11.027. PMID 26724530.

External links[edit]