The Wiki article reveals a few flaws with the theory symbiogenesis:
1) Genome size. Cyanobacteria and a-proteobacteria are
the most closely related free-living organisms to plastids and mitochondria
respectively. However, plastid and mitochondria exhibit a dramatic
reduction in genome size when compared to their bacterial relatives.
Chloroplast genomes in photosynthetic organisms are normally
120-200kb encoding 20-200 proteins and mitochondrial genomes in humans are
approximately 16kb and encode 37 genes, 13 of which are proteins.
2) Loss of genetic autonomy: The authors, i.e., Keeling and
Archibald, argue that the host cell has assumed control of the regulation of
the former endosymbiont's division, thereby synchronizing it with the cell's
own division. The mechanisms of gene transfer are not fully known;
however, multiple hypotheses exist to explain this phenomenon.
The cDNA hypothesis is based on studies of the genomes
of flowering plants. Protein coding RNAs in mitochondria are spliced and
edited using organelle-specific splice and editing sites. Nuclear copies of
some mitochondrial genes, however, do not contain organelle-specific splice
sites, suggesting a processed mRNA intermediate. The cDNA hypothesis has since
been revised as edited mitochondrial cDNAs are unlikely to recombine with the
nuclear genome and are more likely to recombine with their native mitochondrial
genome. If the edited mitochondrial sequence recombines with the mitochondrial
genome, mitochondrial splice sites would no longer exist in the mitochondrial
genome. Any subsequent nuclear gene transfer would therefore also lack
mitochondrial splice sites.
Bulk-flow hypothesis views escaped DNA, rather than mRNA, as
the mechanism of gene transfer. According to this hypothesis, disturbances
to organelles, including autophagy (normal cell destruction),
gametogenesis (the formation of gametes), and cell stress, release DNA
which is imported into the nucleus and incorporated into the nuclear DNA using
non-homologous end joining (repair of double stranded breaks). For
example, in the initial stages of endosymbiosis, due to a lack of major gene
transfer, the host cell had little to no control over the endosymbiont. The
endosymbiont underwent cell division independently of the host cell, resulting
in many "copies" of the endosymbiont within the host cell. Some
of the endosymbionts lysed and high levels of DNA were incorporated into the
nucleus. A similar mechanism is thought to occur in tobacco plants, who
show a high rate of gene transfer and whose cells contain multiple
chloroplasts. In addition, the bulk flow hypothesis is also supported by
the presence of non-random clusters of organelle genes, suggesting the
simultaneous movement of multiple genes.
3) The hypotheses are demonstrated by mechanisms found in
“near-living relatives,” e.g., Cyanobacteria and a-proteobacteria, as well as
flowering plants and the tobacco plant. However, these processes never
transcend the species barrier, which the endosymbiotic hypothesis suggests.
