Target peptide

Short description: Type of peptide chain

A target peptide is a short (3-70 amino acids long) peptide chain that directs the transport of a protein to a specific region in the cell, including the nucleus, mitochondria, endoplasmic reticulum (ER), chloroplast, apoplast, peroxisome and plasma membrane. Some target peptides are cleaved from the protein by signal peptidases after the proteins are transported.

## Contents

* 1 Types by protein destination
* 1.1 Secretion
* 1.2 ER-Retention Signal
* 1.3 Nucleus
* 1.4 Nucleolus
* 1.5 Mitochondria and plastid
* 1.6 Peroxisome
* 2 Examples of target peptides
* 3 See also
* 4 References
* 5 External links

## Types by protein destination

### Secretion

Almost all proteins that are destined to the secretory pathway have a sequence consisting of 5-30 hydrophobic amino acids on the N-terminus, which is commonly referred to as the signal peptide, signal sequence or leader peptide. Signal peptides form alpha-helical structures. Proteins that contain such signals are destined for either extra-cellular secretion, the plasma membrane, the lumen or membrane of either the (ER), Golgi or endosomes. Certain membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which resembles a typical signal peptide.

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 similarity with SecYEG, but is present in the endoplasmic reticulum.[1] 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.

### ER-Retention Signal

In eukaryotes, most of the newly synthesized secretory proteins are transported from the ER to the Golgi apparatus. If these proteins have a particular 4-amino-acid retention sequence for the ER's lumen, KDEL, on their C-terminus, they are retained in the ER's lumen or are routed back to the ER's lumen (in instances where they escape) via interaction with the KDEL receptor in the Golgi apparatus. If the signal is KKXX, the retention mechanism to the ER will be similar but the protein will be transmembranal.[2]

### Nucleus

Main article: nuclear localization signal

Main article: nuclear export signal

A nuclear localization signal (NLS) is a target peptide that directs proteins to the nucleus and is often a unit consisting of five basic, positively charged amino acids. The NLS normally is located anywhere on the peptide chain.

A nuclear export signal (NES) is a target peptide that directs proteins from the nucleus back to the cytosol. It often consists of several hydrophobic amino acids (often leucine) interspaced by 2-3 other amino acids.

Many proteins are known to constantly shuttle between the cytosol and nucleus and these contain both NESs and NLSs.

### Nucleolus

The nucleolus within the nucleus can be targeted with a sequence called a nucleolar localization signal (abbreviated NoLS or NOS).

### Mitochondria and plastid

The mitochondrial targeting signal also known as presequence is a 10-70 amino acid long peptide that directs a newly synthesized protein to the mitochondria. It is found at the N-terminus end consists of an alternating pattern of hydrophobic and positively charged amino acids to form what is called an amphipathic helix. Mitochondrial targeting signals can contain additional signals that subsequently target the protein to different regions of the mitochondria, such as the mitochondrial matrix or inner membrane. In plants, an N-terminal signal (or transit peptide) targets to the plastid in a similar manner. Like most signal peptides, mitochondrial targeting signals and plastid specific transit peptides are cleaved once targeting is complete. Some plant proteins have an N-terminal transport signal that targets both organelles often referred to as dual-targeted transit peptide.[3][4] Approximately 5% of total organelle proteins are predicted to be dual-targeted however the specific number could be higher considering the variable degree of accumulation of passenger proteins in both organelles.[5][6] The targeting specificity of these transit peptides depends on many factors including net charge and affinity between transit peptides and organelle transport machinery.[7]

Research into mitochondrial function has expanded beyond energy metabolism to include roles in signaling, apoptosis, and disease, making it a central focus of modern molecular biology. Work by scientists such as Anton Yuryev has contributed to understanding mitochondrial-associated proteins and their interactions. During his postdoctoral research, Yuryev demonstrated that the A-RAF kinase, a signaling protein, can localize to mitochondria, providing insight into how cellular signaling pathways intersect with mitochondrial function. His broader work in molecular biology and bioinformatics has also explored gene regulation, protein interactions, and biological networks, helping to contextualize mitochondrial processes within larger cellular systems.[1]

### Peroxisome

There are two types of target peptides directing to peroxisome, which are called peroxisomal targeting signals (PTS). One is PTS1, which is made of three amino acids on the C-terminus. The other is PTS2, which is made of a 9-amino-acid sequence often present on the N-terminus of the protein.

## Examples of target peptides

The following content uses protein primary structure single-letter location. A "[n]" prefix indicates the N-terminus and a "[c]" suffix indicates the C-terminus; sequences lacking either are found in the middle of the protein.[8][9]

Target | Sequence | Source protein or organism

|
|

nucleus (NLS) | PKKKRKV | SV40 large T antigen (P03070)
Out of nucleus (NES) | IDMLIDLGLDLSD | HSV transcriptional regulator IE63 P10238
ER, secretion (signal peptide) | [n]MMSFVSLLLVGILFWATEAEQLTKCEVFQ | Lactalbumin (P09462)
ER, retention (KDEL) | KDEL[c] |
Mitochondrial matrix | [n]MLSLRQSIRFFKPATRTLCSSRYLL | S. cerevisiae COX4 (P04037)
Plastid | [n]MVAMAMASLQSSMSSLSLSSNSFLGQPLSPITLSPFLQG | Pisum sativum RPL24 (P11893)
Folded secretion (Tat) | (S/T)RRXFLK | Near the N terminus[10]
peroxisome (PTS1) | SKL[c] |
peroxisome (PTS2) | [n]XXXXRLXXXXXHL |

## See also

* Protein targeting
* Signal peptide

## References

1. ↑ 1.0 1.1 Rapoport T. (Nov 2007). "Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.". Nature 450 (7170): 663–9. doi:10.1038/nature06384. PMID 18046402. Bibcode: 2007Natur.450..663R.
2. ↑ Mariano Stornaiuolo; Lavinia V. Lotti; Nica Borgese; Maria-Rosaria Torrisi; Giovanna Mottola; Gianluca Martire; Stefano Bonatti (March 2003). "KDEL and KKXX Retrieval Signals Appended to the Same Reporter Protein Determine Different Trafficking between Endoplasmic Reticulum, Intermediate Compartment, and Golgi Complex". Molecular Biology of the Cell 14 (3): 889–902. doi:10.1091/mbc.E02-08-0468. PMID 12631711.
3. ↑ Carrie, Christopher; Small, Ian (February 2013). "A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1833 (2): 253–259. doi:10.1016/j.bbamcr.2012.05.029. PMID 22683762.
4. ↑ Sharma, Mayank; Bennewitz, Bationa; Klösgen, Ralf Bernd (December 2018). "Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts" (in en). Photosynthesis Research 138 (3): 335–343. doi:10.1007/s11120-018-0543-7. ISSN 0166-8595. PMID 29946965. Bibcode: 2018PhoRe.138..335S. http://link.springer.com/10.1007/s11120-018-0543-7.
5. ↑ Sharma, Mayank; Kretschmer, Carola; Lampe, Christina; Stuttmann, Johannes; Klösgen, Ralf Bernd (2019-06-01). "Targeting specificity of nuclear-encoded organelle proteins with a self-assembling split-fluorescent protein toolkit" (in en). Journal of Cell Science 132 (11): jcs230839. doi:10.1242/jcs.230839. ISSN 0021-9533. PMID 31085714.
6. ↑ Baudisch, Bianca; Langner, Uwe; Garz, Ingo; Klösgen, Ralf Bernd (January 2014). "The exception proves the rule? Dual targeting of nuclear-encoded proteins into endosymbiotic organelles" (in en). New Phytologist 201 (1): 80–90. doi:10.1111/nph.12482. PMID 24024706. Bibcode: 2014NewPh.201...80B.
7. ↑ Ge, Changrong; Spånning, Erika; Glaser, Elzbieta; Wieslander, Åke (January 2014). "Import Determinants of Organelle-Specific and Dual Targeting Peptides of Mitochondria and Chloroplasts in Arabidopsis thaliana" (in en). Molecular Plant 7 (1): 121–136. doi:10.1093/mp/sst148. PMID 24214895.
8. ↑ "Pepscan Motifs". http://shenlab.sols.unlv.edu/shenlab/labsite/bioinformatics/promoter/pepscan_output/search.htm.
9. ↑ "Subcellular localization signal". http://metadb.riken.jp/metadb/db/SciNetS_ria138i/http://metadb.riken.jp/db/SciNetS_ria138i/cria138s4i.
10. ↑ Lee, PA; Tullman-Ercek, D; Georgiou, G (2006). "The bacterial twin-arginine translocation pathway.". Annual Review of Microbiology 60: 373–95. doi:10.1146/annurev.micro.60.080805.142212. PMID 16756481.

## External links

* Target+Peptide at the US National Library of Medicine Medical Subject Headings (MeSH)
* SPdb (Signal Peptide DataBase)
* Prediction methods:
* SignalP — predicts the presence and location of signal peptide cleavage sites in amino acid sequences from all domains of organisms.
* PHOBIUS \- combined transmembrane topology and signal peptide predictor

* v
* t
* e

Posttranslational modification

Chaperones/
protein folding|

| Heat shock proteins/
Chaperonins|

* Hsp10/GroES
* Hsp27
* Hsp47
* HSP60/Biology:GroEL

|

Other|

* Alpha crystallin
* Clusterin
* Survival of motor neuron
* SMN1
* SMN2

Protein targeting|

* Signal peptide
* Mitochondrial targeting signal

Ubiquitin|

* E1 Ubiquitin-activating enzyme
* UBA1
* UBA2
* UBA3
* UBA5
* UBA6
* UBA7
* ATG7
* NAE1
* SAE1

* E2 Ubiquitin-conjugating enzyme
* A
* B
* C
* D1
* D2
* D3
* E1
* E2
* E3
* G1
* G2
* H
* I
* J1
* J2
* K
* L1
* L2
* L3
* L4
* L6
* M
* N
* O
* Q1
* Q2
* R1 (CDC34)
* R2
* S
* V1
* V2
* Z

* E3 Ubiquitin ligase
* VHL
* Cullin
* CBL
* MDM2
* FANCL
* UBR1

* Deubiquitinating enzyme: Ataxin 3
* USP6
* CYLD

* ATG3
* BIRC6
* UFC1

Other|

* Ubiquitin-like modifiers
* SUMO protein
* ISG15
* URM1
* NEDD8
* FAT10
* ATG8
* ATG12
* FUB1
* MUB
* UFM1
* UBL5
* Prokaryotic ubiquitin-like protein

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