lpetrich
02 Apr 2009, 11:57 AM
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, and those RNA-world features were preserved with it.
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 prokaryotic-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 -- and the chronocyte was a RNA-protein organism.
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" an archaebacterium, which becomes the nucleus
Early eukaryotes eat or otherwise absorb various eubacterial genes
One of them "eats" an alpha-proteobacterium, which becomes the mitochondrion
One of them also "eats" a cyanobacterium, which becomes the chloroplast
Some of them "eat" chloroplast-containing one-celled eukaryotes, sometimes more than once in sequence
References:
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/pubmed/9510246), Martin W, Muller M, 1998
The path from the RNA world (http://www.ncbi.nlm.nih.gov/pubmed/9419221), Poole AM, Jeffares DC, Penny D, 1998
Molecular evolution before the origin of species (http://www.ncbi.nlm.nih.gov:/pubmed/12225777), Brian Davis, 2002
The "hydrogen hypothesis" states that the eukaryotic cell arose from the symbiosis of a eubacterium and an archaebacterium. The eubacterium would produce hydrogen as a result of its metabolism, which the archaebacterium would then consume and combine with oxygen, making methane and water:
4H2 + CO2 -> 2H2O + CH4
The chronocyte hypothesis can easily include the hydrogen hypothesis, it must be said.
The paper "A genomic timescale for the origin of eukaryotes" proposes this scenario:
About 4 billion years ago, the big prokaryote divergence happened, between Eubacteria and Archaea; not long afterward, the ancestor of the eukaryotes diverged from the Archaea.
About 2.7 billion years ago, the first eukaryote endosymbiosis took place, with some early Gram-negative eubacterium; only some genes remain.
About 2.5 billion years ago, O2-releasing cyanobacteria emerged, adding oxygen to the Earth's atmosphere (<1% to >15%), consuming carbon dioxide, and oxidizing methane -- the reduction in the latter two greenhouse gases caused a big ice age at around 2.2-2.4 billion years ago.
Around the time of that ice age, the ancestors of Giardia lamblia diverged. This protist has no mitochondria, but the discovery of mitochondrion-like genes has suggested the possibility of secondary loss -- some of its ancestors had them, then lost them. This paper proposes that these genes were instead from an earlier endosymbiosis, and that Giardia had never had mitochondria. Expect the "never had them" vs. "lost them" controversy to continue.
About 1.8 billion years ago, some protist acquired Rickettsia-like alpha-proteobacteria, with this endosymbiosis producing mitochondria. Rickettsia bacteria like to live inside of cells, suggesting that they are part of the way there. And mitochondrial genes can be distinguished as late arrivals that are close to Rickettsia, rather than early arrivals that branch off lower in the bacterial-relative family tree, as that paper shows.
Some later one acquired cyanobacteria, making chloroplasts and other plastids; this process would sometimes be repeated, with some protist turning a photosynthetic protist into an endosymbiont.
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, and those RNA-world features were preserved with it.
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 prokaryotic-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 -- and the chronocyte was a RNA-protein organism.
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" an archaebacterium, which becomes the nucleus
Early eukaryotes eat or otherwise absorb various eubacterial genes
One of them "eats" an alpha-proteobacterium, which becomes the mitochondrion
One of them also "eats" a cyanobacterium, which becomes the chloroplast
Some of them "eat" chloroplast-containing one-celled eukaryotes, sometimes more than once in sequence
References:
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/pubmed/9510246), Martin W, Muller M, 1998
The path from the RNA world (http://www.ncbi.nlm.nih.gov/pubmed/9419221), Poole AM, Jeffares DC, Penny D, 1998
Molecular evolution before the origin of species (http://www.ncbi.nlm.nih.gov:/pubmed/12225777), Brian Davis, 2002
The "hydrogen hypothesis" states that the eukaryotic cell arose from the symbiosis of a eubacterium and an archaebacterium. The eubacterium would produce hydrogen as a result of its metabolism, which the archaebacterium would then consume and combine with oxygen, making methane and water:
4H2 + CO2 -> 2H2O + CH4
The chronocyte hypothesis can easily include the hydrogen hypothesis, it must be said.
The paper "A genomic timescale for the origin of eukaryotes" proposes this scenario:
About 4 billion years ago, the big prokaryote divergence happened, between Eubacteria and Archaea; not long afterward, the ancestor of the eukaryotes diverged from the Archaea.
About 2.7 billion years ago, the first eukaryote endosymbiosis took place, with some early Gram-negative eubacterium; only some genes remain.
About 2.5 billion years ago, O2-releasing cyanobacteria emerged, adding oxygen to the Earth's atmosphere (<1% to >15%), consuming carbon dioxide, and oxidizing methane -- the reduction in the latter two greenhouse gases caused a big ice age at around 2.2-2.4 billion years ago.
Around the time of that ice age, the ancestors of Giardia lamblia diverged. This protist has no mitochondria, but the discovery of mitochondrion-like genes has suggested the possibility of secondary loss -- some of its ancestors had them, then lost them. This paper proposes that these genes were instead from an earlier endosymbiosis, and that Giardia had never had mitochondria. Expect the "never had them" vs. "lost them" controversy to continue.
About 1.8 billion years ago, some protist acquired Rickettsia-like alpha-proteobacteria, with this endosymbiosis producing mitochondria. Rickettsia bacteria like to live inside of cells, suggesting that they are part of the way there. And mitochondrial genes can be distinguished as late arrivals that are close to Rickettsia, rather than early arrivals that branch off lower in the bacterial-relative family tree, as that paper shows.
Some later one acquired cyanobacteria, making chloroplasts and other plastids; this process would sometimes be repeated, with some protist turning a photosynthetic protist into an endosymbiont.