That is a very interesting question and one which there’s constant research going into.
A few initial points. First, its becoming clearer and clearer that ‘prokaryotes’ is a very poor grouping to use for much of anything. The bacteria most of us think of are the smaller, faster-replicating members of the eubacteria. There’s also the archaebacteria, which are deeply and fundamentally different from the eubacteria in their membrane composition, cell wall structure, DNA organization, and transcription machinery.
Second, it’s becoming more and more clear that the eukaryotes are indeed the result of an early union of eubacteria and archaebacteria. I saw some very cool research at a conference last December bolstering the “eocyte hypothesis”—the idea that the Eukaryotic nuclear genome roots in one particular spot of the archaebacterial tree plus loads of horizontal gene transfer from the eubacteria that became the mitochondria. You can’t root it there just by aligning things, this was long enough ago that base sequence is effectively randomized, you need to look at what sorts of proteins exist, characters that change very rarely as opposed to mere sequence, and its a very hard question that has required a LOT of sequence data from a LOT of organisms. Most of our DNA structure and transcription and some of our protein processing looks like the archaebacteria, but basically all of our metabolism looks like the eubacteria. This is interesting in the light of recent discoveries of symbiotic pairings of archaebacteria and eubacteria in nature in which they exchange metabolic products.
Anyways, the eubacteria and archaebacteria have deeply different transcription machinery and make their membranes in fundamentally different ways. Central carbon metabolism is all but identical though as is a lot of other pathways, and the core biochemistry. I’ve seen work proposing that the eubacteria and archaebacteria may have diverged before living things managed to synthesize their own membrane components rather than scavenging them from the environment. I’ve also seen interesting work to the effect that certain clay minerals can assemble fatty acids and other such membrane-building substances from acetate under the proper energetic conditions.
There’s also a lot of diverstiy in DNA and RNA processing methods that isn’t in any of the cellular life – there are truly bizarre ways of doing this that you only find in viruses. Viruses mutate incredibly rapidly and so you cannot try to root them anywhere, they change too fast. That being said there are proposals that they may be primordial, elements of the very wide range of possible nucleic acid processing mechanisms that existed before the current forms of cellular life really were established and took off. The eubacterial and archaebacterial models may have taken off with remnants of the rest winding up parasitizing them.
Rampant horizontal transfer of genes, especially early when cell identity might not have been so strong, makes all this very complicated.
There’s a school of thought in origin of life research that autocatalytic metabolism was important, and another that replicating polymers were important. The former posits that metal-ion driven cyclical reactions like the citric acid cycle can take off and take over, and wind up producing lots of interesting chemical byproducts that can then capture it and become discrete self-replicating units. The latter points out that elongating polymers in membrane bubbles speed the growth and splitting of these bubbles. They’re both probably important. It should be noted too that these ideas intersect – one of the popular metabolic ideas, polyphosphate, is actually represented in our nucleic acids. Polyphosphate is an interesting substance that can be built up by the right chemial reactions, and can drive other ones when it breaks down. Every ATP, GTP, etc is a nice chemical handle on the end of a chain of three phosphates – a short polyphosphate. By breaking down those polyphosphates you build polymers.
Proteins obviously came very early and gave a huge advantage, and the genetic code is damn near universal with all deviations from the standard one obvioulsy coming in after the fact. Whatever could make proteins probably took over quickly. The initial frenzy, whatever it was, probably eventually lead to a diverse population of compartments processing their nucleic acids in diverse ways and sending pieces of their codes back and forth, which eventually gained advantages by building their own membranes, and eventually cell walls, in different ways. Some of these populations probably took off like mad, making the eubacteria and archaebacteria, and others remained only as horizontally transferred elements like viruses or transposons or the like.
Written in a hurry, may be edited or clarified/extended later.
A clade of archaebacteria found via metagenomics at an undersea vent (uncultured). Contains huge numbers of eukaryotic characteristic genes that are important for formerly eukaryotic specific functions. The eukaryotes cluster within this clade rather than as a sister clade.
Dear CellBioGuy, what is your intuition on what preceded procaryotes?
That is a very interesting question and one which there’s constant research going into.
A few initial points. First, its becoming clearer and clearer that ‘prokaryotes’ is a very poor grouping to use for much of anything. The bacteria most of us think of are the smaller, faster-replicating members of the eubacteria. There’s also the archaebacteria, which are deeply and fundamentally different from the eubacteria in their membrane composition, cell wall structure, DNA organization, and transcription machinery.
Second, it’s becoming more and more clear that the eukaryotes are indeed the result of an early union of eubacteria and archaebacteria. I saw some very cool research at a conference last December bolstering the “eocyte hypothesis”—the idea that the Eukaryotic nuclear genome roots in one particular spot of the archaebacterial tree plus loads of horizontal gene transfer from the eubacteria that became the mitochondria. You can’t root it there just by aligning things, this was long enough ago that base sequence is effectively randomized, you need to look at what sorts of proteins exist, characters that change very rarely as opposed to mere sequence, and its a very hard question that has required a LOT of sequence data from a LOT of organisms. Most of our DNA structure and transcription and some of our protein processing looks like the archaebacteria, but basically all of our metabolism looks like the eubacteria. This is interesting in the light of recent discoveries of symbiotic pairings of archaebacteria and eubacteria in nature in which they exchange metabolic products.
Anyways, the eubacteria and archaebacteria have deeply different transcription machinery and make their membranes in fundamentally different ways. Central carbon metabolism is all but identical though as is a lot of other pathways, and the core biochemistry. I’ve seen work proposing that the eubacteria and archaebacteria may have diverged before living things managed to synthesize their own membrane components rather than scavenging them from the environment. I’ve also seen interesting work to the effect that certain clay minerals can assemble fatty acids and other such membrane-building substances from acetate under the proper energetic conditions.
There’s also a lot of diverstiy in DNA and RNA processing methods that isn’t in any of the cellular life – there are truly bizarre ways of doing this that you only find in viruses. Viruses mutate incredibly rapidly and so you cannot try to root them anywhere, they change too fast. That being said there are proposals that they may be primordial, elements of the very wide range of possible nucleic acid processing mechanisms that existed before the current forms of cellular life really were established and took off. The eubacterial and archaebacterial models may have taken off with remnants of the rest winding up parasitizing them.
Rampant horizontal transfer of genes, especially early when cell identity might not have been so strong, makes all this very complicated.
There’s a school of thought in origin of life research that autocatalytic metabolism was important, and another that replicating polymers were important. The former posits that metal-ion driven cyclical reactions like the citric acid cycle can take off and take over, and wind up producing lots of interesting chemical byproducts that can then capture it and become discrete self-replicating units. The latter points out that elongating polymers in membrane bubbles speed the growth and splitting of these bubbles. They’re both probably important. It should be noted too that these ideas intersect – one of the popular metabolic ideas, polyphosphate, is actually represented in our nucleic acids. Polyphosphate is an interesting substance that can be built up by the right chemial reactions, and can drive other ones when it breaks down. Every ATP, GTP, etc is a nice chemical handle on the end of a chain of three phosphates – a short polyphosphate. By breaking down those polyphosphates you build polymers.
Proteins obviously came very early and gave a huge advantage, and the genetic code is damn near universal with all deviations from the standard one obvioulsy coming in after the fact. Whatever could make proteins probably took over quickly. The initial frenzy, whatever it was, probably eventually lead to a diverse population of compartments processing their nucleic acids in diverse ways and sending pieces of their codes back and forth, which eventually gained advantages by building their own membranes, and eventually cell walls, in different ways. Some of these populations probably took off like mad, making the eubacteria and archaebacteria, and others remained only as horizontally transferred elements like viruses or transposons or the like.
Written in a hurry, may be edited or clarified/extended later.
Of interest!
Even more recent evidence for the eocyte hypothesis!
http://www.the-scientist.com/?articles.view/articleNo/42902/title/Prokaryotic-Microbes-with-Eukaryote-like-Genes-Found/
A clade of archaebacteria found via metagenomics at an undersea vent (uncultured). Contains huge numbers of eukaryotic characteristic genes that are important for formerly eukaryotic specific functions. The eukaryotes cluster within this clade rather than as a sister clade.