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A eukaryotic origin of mitochondria assumes that they were derived from the endomembrane system in a gradual fashion, and that intermediates have existed. Our general proposed mechanism (working hypothesis) for the evolution of mitochondria is that progressive specializations of the endomembrane system and the incorporation of DNA would lead to more complex organelles eventually leading to our modern mitochondria. All these intermediates had to be fully functional and therefore, it can be assumed that organisms still exist that harbour these intermediate mitochondria, and these intermdiates may be found specifically organisms that are considered to be primitive eukaryotes.

In a gradual evolution of mitochondria, we assume a gradual targeting of metabolic enzymes to specialized endomembrane-derived organelles as well as a gradual increase in the number of genes inside the mitochondrion. Thus, we would expect to find organelles that are derived from the endoplasmic reticulum, contain no DNA and only a few metabolic enzymes, but also organelles with more functionality that contain no or just a few genes. We can find these putative precursor and primitive mitochondria in extant single-cell eukaryotes in the form of mitosomes, hydrogenosomes and other organelles. Amitochondriate organisms and organisms with mitochondria that contain no genome are the obvious representatives of these intermediates. 

  • Type II amitochondriates with hydrogenosomes. Many anaerobic protists exist with organelles that produce molecular hydrogen as well as ATP: hydrogenosomes (here). Although most do not contain DNA, some have a small genome. Both the habitat (anaerobic) as contain no or a small genome (Nyctotherus) is in line with a gradual evolution through the endomembrane system. The hydrogenosome contain not all parts of the mitochondrial respiratory chain and no ubiquinone but another stronger reducing agent rhodoquinone (here). So hydrogenosomes could also be a good intermediate based on metabolic grounds. Hydrogenosomes generate energy for the cell.
  • Type I amitochondriate with mitosomes as found in microsporidia has no genome, has only a function in synthesizing iron-sulfur clusters (ISC) and does not contain the enzymes for oxidative phosphorylation. Also the proteins contain a targeting sequence similar to mitochondrial proteins which can form the basis for evolution to a true mitochondrial import (here). Also, Entamoebe has mitosomes that do not generate energy for the cell, have a role in Fe-S cluster (here). Mitosomes have mitochondria-like chaperonin genes. Contain no DNA. Giardia has also specialized membranes with electron transport functions (mitosomes) and has mitochondrial-like chaperonin genes, a nuclear coded valyl-tRNA synthetase and a fully functional mitochondrial iron–sulphur cluster assembly pathway involving the proteins IscS and IscU which are present in a double membrane-bound organelle (here). Contain no DNA. A mitosome (mitochondria-related organelle) has also been described in Cryptosporidia and Cryptosporidium parvum has genes (IscS and IscU) encoding a mitochondrial-type iron–sulphur cluster biosynthetic pathway and that these proteins target the proposed organelle (here).
  • In Entamoebe, DNA-containing cytoplasmic structures (EhKOs) can be present that emanate from the cell nucleus, to be cell-cycle-regulated and to contain eukaryotic-type rRNA, a pyruvate:ferredoxin oxidoreductase-like protein and a number of eukaryotic-type transcriptional regulators (here). Although the evolutionary relationship with for instance mitosomes is unclear at the moment, these structures show that endomembrane-derived structures with DNA are indeed possible.
  • Functional and phylogenetic analyses show that hydrogenosomes and mitochondria are likely related and share a common ancestor (see here). Based on a Fe-S cluster is was shown that the hydrogenosomal, mitochondrial and mitosomal (?) protein clustered in phylogenetic analyses (here). Also, these three different organelles are mutually exclusive in cells, in line with an evolution towards mitochondria from mitosomes. (The other way around, you would expect organisms woth both a normal mitochondrion and reduced/remnant one.) Similarities in mitochondrial, hydrogenosomal and mitosomal N-terminal targeting peptides also hint at a shared derived import machinery in all three organelle types suggesting a common origin of these organelles (van der Giezen and Tovar 2005).
  • The relation of mitochondria to mitosome is supported by (i) presence of two membranes surrounding these organelles, (ii) localization of proteins of iron sulfur cluster assembly machinery within these organelles (IscU, IscS, ferredoxin), (iii) targeting of proteins into the mitosome by means of N-terminal leader sequences with similar properties of mitochondrial leader sequences, (iv) FeS cluster assembly activity idetified in mitosome-rich cell fraction (see here).