Sunday, February 19, 2012

Biological Revolutions: The Prokaryotes Cometh


(Picture from here.)

Last time we talked about nothing less than the origin of life.

Seems like everything ought to be downhill from that, eh?

"Life" as we defined it consisted of self-replicating metabolizing cellular systems. But what we came up with didn't much resemble life we we know it today. Inheritance was via RNA and not DNA. Catalysis was by RNA enzymes-- ribozymes-- with some proteins. No photosynthesis and nowhere near as complex a system-- or ecology-- as we see today.

So: there are to aspects to the prokaryote revolution: 1) how did it happen? and 2) what did it do to the world? We'll deal with part 2 in another post.

As to how the prokaryotes first came to be we have to think a little about what prokaryotes are.

Currently we define life as being divided into three domains: Bacteria, Archaea and Eucaryotes. Eucaryotes have nuclei containing DNA in the cells. In fact, eucaryotes have lots of little organelles inside them: nuclei, mitochondria, chloroplasts and Golgi apparatus, among others. These are all referred to as membrane bound organelles in that they have their own membrane structures that either are their own or are internal reflections of the cells own membrane. We belong to the Eucaryota and therefore lump all things not us in their own group, the Prokaryotes.

This is analogous to the old way we defined animals as vertebrates (us) and invertebrates (not us.)

However, there is some utility in this discussion in drawing together the Bacteria and Archaea as prokaryotes. The current evidence suggests that something prokaryotic lived 3.8 billion years ago. Eucaryotes are comparative newcomers and appeared only six hundred million years ago. The first life forms appear to be prokaryotes. So the bridge from the RNA world to the Last Universal Common Ancestor (LUCA) and to us appears to have involved the development of the prokaryotes.

Prokaryotes don't carry the baggage of the organelles. Their DNA, ribosomes, enzymes, etc., are more exposed. Prokaryotes have a single loop of stabilized DNA that is stored in something called a nucleoid and is not tightly bound in chromosomes. There may be more than one copy of the DNA existing in the cell at a given time.

Patrick Forterre has delved deep into this area and come up with some very interesting speculations. While I don't think all of his conclusions are supported (viruses being living things is one, for example) he makes some interesting arguments.

Living or not, we know that viral particles are the most abundant biological entities in the current biosphere. They are ten times more abundant than the bacteria in the upper ocean, for example. (See here.) This shouldn't be surprising with a little thought. The ratio of produced virus particles to infected cell is huge. To pick a number of, say, 100k particles/infected cell and an infection rate in a population of, say, 1/10k cells, it would only take 1 cell in 10,000 cells to maintain that ratio. Some viruses replicate and several times that amount and some viruses have a much higher infection rate. Then, there are all those cells dying for lots of reasons. Some of which contain virus particles in their make up.

Forterre suggests this is not a new circumstance. It must also have been true at the time of LUCA. In fact, pretty much as soon as there were cellular organisms with replicating systems were were biological agents (viruses) ready and willing to hijack said systems. So viruses have been with us for a long time.

Viruses also infect all three domains of organisms and with a plethora of different mechanisms. Viruses are also biochemically more related to each other than the cells they infect. Most of their proteins have no specific relationship with their hosts and there are many families of viruses infecting different hosts but produce similar proteins to each other. Viruses, then, show a different biochemical signature from modern organisms.

Viral biochemistry has to come from somewhere. Forterre suggests they came from biochemistry that predates the modern world. Hence, RNA viruses might well be the last relics of the RNA world. DNA viruses might have been instrumental in the creation of the DNA world.

How's that again?

Well, how does a virus work? It has a seed form, a "virion", that attaches to the cell membrane and allows the insertion of a mix of inheritable material (RNA or DNA) and proteins into the cell. That material preps itself-- different viruses do this step different ways-- until it is in a position to make more viruses. Some viruses create actual virus factories that then produce viruses. Others subvert existing machinery to achieve a similar end. At some point the cell extrudes the virus. This can be as simple as the cell exploding ("lysing") or may be a more complex mechanism that leaves the cell membrane intact.

An interruption of any one of these cells can leave the cell in a new state where there is additional protein machinery in place and new heritable material. There's not much intrinsic difference between a DNA strand of a virus and a DNA strand of E. coli. They have genes. They have start and stop codons. Some strands can be recognized as "other" and destroyed and some can't. We've seen-- heck, we've used-- this incorporation of virus DNA into the cell DNA. That's how genetic engineering is often done. What can be done in the lab is often been done before in the field.

Some virus families that parasitize Archaea, Bacteria and Eucaryota have enough common ground between them to suggest they evolved from an ancestor that predated LUCA.

DNA is harder to manipulate than RNA. So there needed to be complex proteins available before it could be used. RNA has no such issue since RNA by itself has enzymatic activity. So the DNA world could not have happened without a prior ancestor that was not DNA dependent. And finally, we need to somehow bring proteins into this process.

If LUCA used DNA for inheritance, used RNA to encode proteins and used RNA and proteins to catalyze processes, that organization had to come from somewhere. And, since heritage is all in biology, something had to have it first and propagate it. Viruses have some neat potential solutions to these problems.

For one thing, viruses drive down enormously the cost of change. Cells must create other cells. They are discrete entities. Loss of that unit organization is synonymous with death. Viruses do not have that limitation. They are concerned with encapsulating an infectious capsid. For the capsid's contents to survive it need only find a compatible cells. Since cells are fighting back, it is in the interest of virus to mix it up as much as possible.

Consequently, viruses inherently evolve more quickly and take more chances in their evolution than cell based system. In addition, replication is a dirty business with lots of leftover bits and mistakes. Cells invest in systems to prevent these. Viruses have no such incentive-- to them the mistakes are opportunities to try something new. Hey, if thirty percent of your capsids aren't infective, who cares? There's seventy thousand that are and a lot of them are different. (See here and here.)

So. Here we have an RNA world with a sea of viruses and cells. Lots of variation in both cells and viruses. Some viruses are capturing RNA from their hosts and propagating it. Some viruses are injecting new RNA into their cells and the cells capture it. Some are doing both. Cells themselves are variable in construction. Some use lipid membranes. Some membranes are inorganic. Some chemical reactions might be taking place outside of cells entirely. Everything is exchanging with everything else-- much more than now. Even then, however, capsid exchange is inherently more rapid than cellular exchange. The whole genome pool is parasitic on itself.

For example, consider a capsid containing protein production machinery (encoded in RNA) injects itself into a cell that uses ribozymes. Let's say it's defective; it can't encode other capsids. But the machinery itself can metabolize. This cell now has a selective advantage of neighboring cells that only use ribozymes. That cell might absorb/digest/exchange the encoding of a membrane. The chemistry doesn't care. It produces membrane.

Large viruses (such as the mimivirus) have biochemical systems that rival the size of biochemical systems of their host. The viral factory of the mimivirus is nearly as large as the nucleus of its amoeba host. (see here.) One wonders if, long ago, a similarly large virus infected a host and stayed there, its biochemical pathways replacing those of its host. Eventually, the cell divides and it's the virus genome, not the original host, that is preserved.

At some point, some members of this ancient pool become organized. Genes that encode replication are linked to genes that encode accessory functions such as metabolism. Expression of that encoding (such as proteins) become more uniform as a result. At this point the cooperative nature of the primordial pool becomes competitive as something resembling cell lines appear. It's to the advantage of a cell line to propagate itself and compete with other systems and cell lines for resources. What had been more of a chemical selection becomes natural selection and both cells and capsids participate.

All of this could have happened without DNA. The RNA world could have become quite complex. Fast cellular evolution. Faster virus evolution. The RNA cellular fights back and the virus has to change in order to remain competitive.

DNA has a greater replication fidelity than RNA-- it's a much less noisy chemical reaction. A virus that changed the transported RNA into DNA as part of the infection process is more assured of retaining identity while under attack by cellular defense mechanisms. When this first happened it would be a powerful tool since the DNA would not necessarily even be recognized as dangerous material by cellular defenses. Like many virally induced changes, this could have been incorporated in the cellular genome. (See here.)

Using DNA instead of RNA slows the pace of evolution while it increases constancy across generations.

These sorts of things happened not once but many times. Eventually, a cell line stayed viable and became honed through natural selection into LUCA. After LUCA, exchange of DNA slowed and out of those cell lines arose something resembling species-- though the concept is blurry and vague at this point.

It doesn't matter. The prokaryotes were born.

They were about to take over the world.

Cited works and additional reading:





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