Was the Eukaryote Cytoplasm Once a Separate Organism?

[lpetrich]

The endosymbiotic origin of mitochondria and chloroplasts ought to need no introduction for many of this forum's readers, but there is some interesting research that suggests further such contributions to early eukaryotic organisms. There is some evidence of additional eubacterial contributions to the eukaryotic genome (Hedges et al 2001), and there is evidence that the eukaryotic informational systems are derived from some archaebacterial ancestor, a circumstance which has provoked the "hydrogen hypothesis" (Martin et al, 1998). In it, some archaebacterium took up residence inside of a eubacterium, and consumed the hydrogen that the eubacterium's metabolism produced. Unlike mitochondria and chloroplasts, it took over the genome.

But an even more dramatic hypothesis has been proposed by Hartman and Fedorov. They have discovered some eukaryotic proteins that have no clear homology with known eubacterial or archaebacterial proteins; they call these proteins "Eukaryotic Signature Proteins". These include proteins like calmodulins associated with such eukaryote-specific mechanisms as a calcium-utilizing internal-signaling system.

They propose that the eukaryotic cytoplasm was once an independent organism, which they have named the "chronocyte", in honor of Kronos, from Greek mythology, who swallowed his children. This organism had had those eukaryote-specific mechanisms, an internal-membrane system, a cytoskeleton, and the ability to practice phagocytosis, which enabled it to acquire endosymbionts.

Hartman and Fedorov go further to propose that the chronocyte had had a RNA genome, and that it had had several RNA-world features like RNA splicing; this RNA-world-preservation hypothesis is also supported in Poole et al. 1998. This genome was partly preserved in the chronocyte's first endosymbiont, an archaebacterium that became the nucleus.

The chronocyte hypothesis requires that proteins came before DNA, a view supported by Davis 2002. That paper examined 10 proteins, and dated their ancestral sequences by the metabolic complexity involved in biosynthesis of their amino acids:

Ferredoxin (Fe-S protein; does redox reactions)
Proteolipid h1 (lives in cell membranes; part of ATPase complex)
FtsZ (involved in cell division)
FEN-1 (flap exonuclease)
RNA polymerase beta'
Reverse transcriptase (RNA -> DNA)
DNA topoisomerase I (alters DNA topology)
Ribonucleotide reductase (Fe) (RNR's make DNA nucleotides from RNA ones)

DNA use was clearly a latecomer, meaning that RNA-protein organisms could have existed.

Here is an approximate chronology:

* RNA world

* RNA-protein organisms. Chronocyte and prokaryote ancestors part ways

* Prokaryote ancestor acquires DNA genome

* Prokaryote ancestor produces eubacterium and archaebacterium ancestors

* Chronocyte develops signaling system, membranes, and phagocytosis

* Chronocyte "eats" archaebacterium, which becomes the nucleus

* Early eukaryotes eat or otherwise absorb various eubacterial genes

* One of them "eats" alpha-proteobacterium, which becomes mitochondron

* One of them also "eats" cyanobacterium, which becomes chloroplast

* Some of them "eat" chloroplast-containing one-celled eukaryotes


Refs:

The origin of the eukaryotic cell: A genomic investigation (http://www.pnas.org/cgi/content/full/032658599v1), Hyman Hartman, and Alexei Fedorov, 2002

A genomic timescale for the origin of eukaryotes (http://www.biomedcentral.com/1471-2148/1/4), S Blair Hedges, Hsiong Chen, Sudhir Kumar, Daniel Y-C Wang, Amanda S Thompson, and Hidemi Watanabe, 2001

The hydrogen hypothesis for the first eukaryote (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9510246&dopt=Abstract), Martin W, Muller M, 1998

The path from the RNA world (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9419221&dopt=Abstract), Poole AM, Jeffares DC, Penny D, 1998

Molecular evolution before the origin of species (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12225777&dopt=Abstract), Brian Davis, 2002

[Nic Tamzek]

Isn't FtsZ a prokaryotic replication protein (the eukaryotic homolog being tubulin)? What then would it have to do with the origin of eukaryotes...or perhaps I'm confused.

[lpetrich]

FtsZ is indeed a cell-division protein, and I mentioned it because it was one of the proteins which Brian Davis had attempted to "date".

The FtsZ-tubulin homology suggests that the prokaryote-eukaryote split happened after that protein got put to work in early cells.

[rlogan]

As always. some very intersting stuff: the duct-tape and bailing wire construction of the early evolutionary junk yard wars.

I didn't realize how "old" this form of cellular constuction hypothesis was, dating back to Mereschowsky's (1910) work.

now tread lightly on me here - I got the abstract on the hydrogen hypothesis, but not the paper.

How was the archaebacterium getting its hydrogen before it met it's friend Mr. eubacterium?

[lpetrich]

Either from other eubacteria in its environment, as present-day methanogens usually do, or from hot springs.

Methanogens extract their energy from this reaction:

CO2 + 4H2 -> CH4 + 2H2O

and sometimes with some other molecules instead of CO2.

So that archaebacterial symbiont could have been a methanogen.