Mitochondrial transit peptide

BioCodeKb - Bioinformatics Knowledgebase

Mitochondrion is a highly dynamic and complex organelle actively engaged in many important cellular processes. It is important not only for generation of energy but also for thermogenesis, storage of calcium, steroidogenesis and apoptosis. Malfunctioning of mitochondrial processes such as apoptosis is responsible for manifestation of life‐threatening disorders such as cancer and neurodegenerative diseases. Mitochondrial malfunction can occur due to mutations in the mitochondrial DNA or nuclear DNA encoding for mitochondrial proteins or even due to reactive oxygen species‐mediated stress. The treatment of these diseases at the molecular level requires targeting of drugs, genes and functionally active proteins to mitochondria. Therefore, delivery of macromolecules to mitochondria becomes essential for efficient treatment outcomes.


Proteins which have an N-terminal presequence which directs them to an organelle (chloroplast, mitochondria, microbody, cyanelle). The transit peptide is required for their transport across the relevant membranes from their site of synthesis in the cytoplasm. Thus transit peptides are responsible for the transport of a protein encoded by a nuclear gene to a particular organelle.


Transit peptides are for the following organelles:

  • Mitochondrion

  • Apicoplast

  • Chromoplast

  • Chloroplast

  • Cyanelle

  • Thylakoid

  • Amyloplast

  • Peroxisome

  • Glyoxysome

  • Hydrogenosome


Proteins can be targeted to microbodies via an N-terminal transit peptide (which is rare), or via a C-terminal motif (which is more common). Transit peptides are generally cleaved from the mature protein and so will logically be found in proteins tagged with the 'Sequence processing' information.


To carry out protein translocation, unique peptide signals have to be present in the nascent proteins, which function as “zipcodes” that direct the proteins to each of these compartments. Once the proteins are translocated within the organelles, protease cleavage takes place to remove the signal sequences and generate mature proteins.


Peptides targeting mitochondria, for example, are located in the N-terminal region. The sequences are typically twenty to eighty residues long, rich in positively charged residues such as arginines as well as hydroxyl residues such as serines and threonines, but devoid of negatively charged residues and have the tendency to form amphiphilicα-helices. These targeting sequences are cleaved once the precurs or proteins are inside the mitochondria.


Annotation of predicted peptides at UniProt

Transit peptides have been annotated via experimentally proven transit peptides when the cleavage site has been determined by direct protein sequencing.

Large-scale proteomics data are used to annotate transit peptides through the combination of experimental and computational methods, tagged with evidence from 'Combined sources'.


This information can then be propagated 'By similarity' to closely related homologs provided that the transit peptide sequence is conserved.


Transit peptides have been annotated at UniProt, which are predicted by the application of the predictive tools Mitofates, Predotar and TargetP, but only when such predictions are consistent with the known or presumed subcellular location of the protein concerned. The predicted positions of the transit peptide are annotated with evidence 'Sequence analysis'.
When a protein contains a transit peptide (according to experimental data or its similarity with a family of proteins), but the precise cleavage position has not been experimentally determined, we use a question mark instead of a precise position.

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