The general idea in a eukaryotic origin of mitochondria is that they gradually evolved from the ER , intially without a genome and that mitochondria later acquired DNA. We expect mitochondria with no or only a few genes. We observe several protist species that contain such a minimal mitochondrial genome and that the few genes that are present have a true metabolic/mitochondrial function (instead of a remant housekeeping gene from a putative prokaryote). With Cryptosporidium, the line between intermediate organelles and proto-mitochondria is not clear.
- Oxyrrhis, a dinoflagellate, has only 2 mitochondrial genes of which one fusion protein (here). Assuming the fusion is derived, we have a minimal mitochondrial genome of three proteins: cox1, cob, cox3, all three proteins involved in the fundamental electron transport chain. The presence of only basic metabolic proteins in a minimal genome is in line with continuing specialization of the endomembranbe system for metabolic reactions where genes were added one-by-one.
- Amphidinium, another dinoflagellate, has only three mitochondrial genes (cox1, cob, cox3) but also non-coding DNA that often contain fragments of the same genes (here). This is more in agreement with an acquisition of genes instead of a loss. Its genome can be seen as three genes that have undergone extensive recombination, made possible by inverted repeats and as relics the fragmented genes. In a ‘loss model’ you would expect relics or many more genes.
- The mitochondrion of the apicomplexan Cryptosporidium does not contain any genome and is thus completely dependent on nuclear gene expression for its proteins. It also lacks large parts of the electron transport chain (the oxidative part) and retains the anaerobic pathways. This is in line with the presumed intermediate step towards a true mitochondrion via ER-derived organelles (see here). We see here an organism in an early evolutionary stage of metabolism (no oxidative phosphorylation) and no DNA necessary. The next steps would be the sequential acquisition of DNA coding for proteins involved in oxidative phosphorylation (see here TODO).
- Interestingly, the mitochondrion of Cryptosporidium is enveloped by the ER (here), also in line with being derived from the ER system. One of its proteins show a mitochondrial target sequence in its nuclear DNA (here), showing that it is related to mitochondria and therefore could have been an intermediate where we expect targeting to protomitochondria in a similar fashion as in mitochondria.
- The unicellular green alga Chlamydomonas lacks the genes cox2 and cox3 in their mitochondrial genome. Instead, they are nuclear-encoded and exhibit typical eukaryotic characteristics, including spliceosomal introns and targeting sites (here).
- Also in Chlamydomonas, an important other protein, ATPase subunit 6 is nuclear encoded (here), and this subunit is able to rescue a deficit in this subunit in human cells, since the structure is well conserved. This is in line with the view that older versions of the enzyme would still work (backwards compatibility) since existing functionality is conserved through evolution (cf. design-by-contract).