What is a plant? (part 2)

Plants are eukaryotes.  'Eu' from the Greek for true and 'karyote' for nut, meaning the nucleus.  Eukaryotes have cells with a nucleus containing their genome in the form of DNA organised in chromosomes.  Eukaryotes, all the plants, animals and other living things, except bacteria and archaea, are thought to have evolved from a single common ancestor, or in other words, eukarya are monophyletic.  Prokaryotes (bacteria and archaea which don't have a nucleus) have their DNA organised differently.  This all sounds very simple and clear, except that things are a bit more complicated (when in life are they not?).  When I said that the eukaryote nucleus contains the genome, this is only partly true.  There are some other organelles (structures within eukaryote cells) that also contain DNA.  The mitochondria, which generate energy for eukaryote cells contain DNA and, in the plants, the chloroplasts, which carry out that most planty of processes, photosynthesis, also contain DNA.

When organisms reproduce sexually, nuclear DNA from two parental cells comes together to make a 'daughter' genome, but the same thing doesn't happen for the organelle DNA - organelle DNA is generally inherited directly from the mother 'egg' cell.  This makes for some very different evolutionary trajectories for the different sets of DNA.  Recombination features strongly as an evolutionary force in nuclear DNA (due to the 'coming together'), but organelle DNA does not recombine in meiosis.  Recombination is still a force in organelle DNA evolution though, but through a different mechanism.  But we need to backtrack a little first, and look at where the organelles came from in the first place.

There's good evidence that the organelles did not start out as part of eukaryote cells.  It seems that they were originally free-living prokaryotes, that either invaded, or were subsumed by an ancient proto-eukaryote.  Somehow, rather than eating, or being eaten by one another, the prokaryote took up residence inside the proto-eukaryote, in either a symbiotic or parasitic arrangement.  We can tell this happened because of the similarities of the DNA in the organelles we find in eukaryotes today, and the DNA in the genomes of some prokaryotes.  The 'host' cell provides some kind of shelter or nutrients and the prokaryote provides energy or photosynthesis.  The question of when this event happened, and whether it happened once for a single cell, from which every eukaryote alive today has evolved, is open to question.

So now we know how the organelles got where they are, living inside the eukaryote cells, back to their DNA, and how recombination acts upon it.  Over the millennia since the endosymbionts took their places, there is very good evidence () that some of the genes from the original nuclear genome have migrated to the organelles, and some of the DNA from the original prokaryote have migrated from the organelle genomes to the nuclear genome of the host cells.    The reason why we can be so sure that this happened is that some of the nuclear genes in some eukaryotes look very much like some prokaryote genes, and some organelle genes look very much like some eukaryote nuclear genes.  There is evidence that this process is still happening in the flowering plants (Adams et al., 2002)

So we have said we know these things about the way genomes are structured, because we have found segments of DNA in different places that are too similar to have arisen by chance, so must have evolved from a common ancestral segment of DNA.  We call this homology - the fact that two biological features share similarity through descent.  But couldn't these things have arisen independently of each other? Isn't it possible that the same DNA evolved twice in separate organisms at random?  Isn't it possible that some gene sequences are so useful that they evolved twice independently by the force of natural selection?  Tricky questions indeed.  There are strong theoretical methods for determining whether we should accept or reject the hypothesis of homology in any given case.  Maybe I'll save the theory for another post on another day.

For now, I'll come back to what a plant is.  There's something about being a eukaryote that seems to help organisms grow bigger and more complex, rather than the apparently simple organisms that are the bacteria and archaea.  Some plants are single cells, but many have adopted multicellularity as a way of getting their heads above the crowd, into the light.

So plants are eukaryotes, with cells having a genome in their nuclei, and having tamed prokaryote chloroplasts harvesting all that lovely sunlight to help them grow and develop. We've also touched on what evolution is here.  I mentioned recombination (where pieces of DNA are exchanged between one DNA segment and another).  Generally DNA is a molecule that can reproduce itself, but if it always reproduced itself identically, there would be no such thing as evolution.  Recombination is one of the forces that act on DNA to cause it to evolve.  The DNA message may be different after the recombination occurs than it was before, and if the DNA is different then the organism might be different.  I'll come back to the other three evolutionary forces another time.

To finish for today, I'd like to share a very interesting paper about recombination that I came across.  I talked about recombination that occurs in meioses, and about recombination between nuclear and organelle DNA, but it does not stop there by any means.  Horizontal gene transfer is one of the other kinds of recombination, that is, the exchange of DNA between non-mating organisms.  Many bacteria regularly swap plastids with each other, and viruses recombine both with each other and with their hosts' DNA.  Single-celled eukaryotes are also known to engage in horizontal gene transfer, but we don't often come across instances of recombination between the genomes of completely unrelated complex eukaryotes.  Richardson and Palmer (2007) review horizontal gene transfer in plants, which has been found in a number of cases between mitochondrial genes in particular.  The extreme example is a very interesting plant, Amborella trichopoda, whose mitochondria may contain more 'foreign', or horizontally transferred genes, apparently 'captured' from a wide range of other mosses and plants, than 'native' genes.  A. trichopoda is endemic to the pacific island of New Caledonia, where it grows as a shrub in the understory of the forest, often covered with mosses, and other epiphytic  plants.  It seems possible that these plants have infiltrated the tissues of our shrub, in the past, and thereby transferred genes, but this isn't really clear, and although some of these 'foreign' genes are expressed in the living shrubs, it also isn't clear whether they are functional  It will be interesting to find out!

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Adams KL, Qui YL, Stoutemyer M, Palmer JD,  2002.  Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.  Proceedings of the National Academy of Sciences, USA 99: 9905-9912.

Richardson AO, Palmer JD.  2007.  Horizontal gene transfer in plants.  Journal of Experimental Botany 58(1): 1-9.