Because there was some skepticism in the thread about this theory, I emailed one of the top scholars in this area to get his up to date perspective and he delivered this amazing response:

"I'll be happy to give you a succinct summary of my views on this issue.

Molecular evidence (notably DNA sequence) absolutely confirms that the mitochondrial genome is of bacterial origin. The most compelling evidence in this regard comes from the sequence of the mitochondrial DNA (mtDNA) in a group of protists (eukaryotic, mostly single-celled, microbes) called jakobids. Key publications presenting the evidence and the arguments are:

Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493-497.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&d...

Burger G, Gray MW, Forget L, Lang BF. 2013. Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol. Evol. 5:418-438.
http://gbe.oxfordjournals.org/content/5/2/418.abstract

While sequence data firmly support the endosymbiont hypothesis insofar as the mitochondrial genome is concerned, the data also support the conclusion that the mitochondrion originated only once:

Gray MW, Burger G, Lang BF. 1999. Mitochondrial evolution. Science 283:1476-1481.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&d...

Of course, only a few essential mitochondrial proteins are encoded in mtDNA and synthesized inside mitochondria. The vast majority of the 2000+ proteins that make up a mitochondrion are encoded in the nuclear genome, synthesized in the cytoplasm, and imported into mitochondria. So, when we speak about the origin of the mitochondrion, we have to account not only for the mitochondrial genome (which is unquestionably of bacterial origin) as well as the mitochondrial proteome: the collection of proteins that constitute the complete organelle.

Accepting that the mitochondrion originated as a captive bacterium or bacteria-like entity, massive evolutionary restructuring has evidently occurred in the transition from endosymbiont to integrated organelle, including endosymbiotic gene transfer (movement of genes from the endosymbiont genome to the nuclear genome, with loss of the mtDNA copies), recruitment of host proteins, and acquisition of new proteins from outside the host via lateral gene transfer from other organisms. A very complicated business, made even more complicated by the recognition that subsequent mitochondrial evolution has taken different pathways in certain respects in different eukaryotic lineages.

While the CONCEPT of the endosymbiont hypothesis, as outlined above, is strongly supported and accepted, HOW this might have happened is still unclear, and may never be settled to everyone's satisfaction. Did the mitochondrion emerge early in the evolution of the eukaryotic cell through the union, by an unspecified mechanism, of a primitive archaeon (host) and primitive bacterium (endosymbiont), with this union actually being instrumental in the emergence of the eukaryotic cell? Or, did the mitochondrion emerge late, in an evolving archaeon host that already had some of the hallmarks of a typical eukaryotic cell, notably phagocytosis, the well-known mechanism by which modern eukaryotic cells take up bacteria for food? The pros and cons of these two (and many other) scenarios are still being hotly debated.

Hope this helps.

Cheers,

Michael W. Gray, PhD, LLD (h.c.), FRSC

Professor Emeritus

Department of Biochemistry and Molecular Biology

Dalhousie University

Halifax, Nova Scotia B3H 4R2, Canada."