As you can see, the RecA story has turned out to be quite interesting and there is plenty more to talk about. But since this blog is not called “The Land of RecA,” I think I’ll give this subject a rest for now. However, as a parting gift, I offer up this bit of research which highlights just what a sophisticated little device we have here:

Read the rest of this entry »

Previously, we have seen that the eukaryotic versions of RecA (Rad51, Rad51B, Rad51C, Rad51D, DMC1, XRCC2, or XRCC3) were spawned when the domain Eukarya probably existed in a unicellular state. We’ve also seen that removal of Rad51 from the mouse genome was lethal. The same holds true for Rad51B, Rad51C, Rad51D, and XRCC2 (such knock-out experiments with XRCC3 have apparently not been done yet). But removal of DMC1 is not lethal. In fact, the phenotype for such a knock-out mouse is as follows:

Homozygotes for targeted mutations are sterile with failure of homologous pairing in meiotic prophase in males and disrupted oogenesis in embryonic females with absence of germ cells in the adult ovary.

DMC1, which stands for Disruption of Meiotic Control, was originally identified in yeast in the early 1990s. Meiosis is the process by which eukaryotic diploid cells form haploid cells that in turn become gametes. In plants and animals, it is the process that generates ova and sperm/pollen. And in the single-celled yeast, this gene also plays a necessary role in facilitating recombination, guiding homologous chromosomes to cross-over during the very early stages of meiosis. Removal of DMC1 leads to arrests in the early stages of meiosis.

Thus, like Rad51, DMC1 is required for meiosis in plants, animals, and fungi. But unlike Rad51, DMC1 function is restricted to meiosis, as not only indicated by gene disruption experiments, but expression studies that find it to be synthesized only during meiosis. In essence then, DMC1 is a marker for meiosis. It is not necessary for meiosis, as fruit flies and the nematode, C. elegans, have lost their copy. But when it is present, meiosis (or the recent ability to carry out meiosis) is strongly indicated.

So that means we can reasonably estimate when meiosis originated simply by surveying the distribution of DMC1 (as least as a first step in our analysis). Thus, I took DMC1 sequence from fungi and used it to search the data bases, pulling out several examples from distantly related protozoa. For example, here it is from an amoeba. Here it is from Trypanosoma. Here it is from a ciliate (YER179W). And most interestingly, here it is from Giardia, thought to be the most “primitive” eukaryote based on the way its genes so deeply branch in the eukaryotic tree. It seems to be rather ubiquitous among the single-celled eukaryotes.

In other words, DMC1 was spawned very early during the evolution of eukaryotes and its birth may very well have coincided with the birth of Eukarya, thus defining Eukarya. Not only may the unfolding of RecA have facilitated the evolution of the complex genomes seen in metazoans, but it may likewise have spawned meiosis. The echo of the evolution genes repeats itself since it is this evolution gene that gave sex to the biotic world.

The very essence of sex is meiotic recombination - Anne Villeneuve and Ken Hillers

In my previous essay, I offered some support for viewing RecA as an evolution gene: it is ubiquitous, ancient, and plays a key role in the important and evolutionarily significant process of recombination. Also, the endosymbionts suggest that it can act like a switch when it comes to genomic integrity over time.

I’ve raised this all as an alternative perspective, where “RecA’s functions are more fully realized across generations, something we would expect from an evolution gene.” In other words, it’s a question of observational scale. If, for some reason, we were restricted to making observations on the scale of milliseconds, we might be under the impression that RecA’s function is to bind ATP, because the DNA repair functions of RecA are dependent on more time and other machinery. Thus, I’m raising a perspective that expands time even further, noting that DNA repair and recombination (what we measure in the lab) is part of the evolution-function of the gene (how an observer with a larger time frame might see it).

In my last essay, I mentioned that RecA was universal among free-living bacteria and that its amino acid sequence was strongly conserved. It’s now time to consider another aspect.

Read the rest of this entry »

If the recA gene is an evolution gene, we would predict that its removal would somehow negatively impact the ability to evolve. So let’s see what happens when RecA function is removed by mutation.

To start off, it does not appear RecA function is essential to unicellular life or reproduction. For example, a commonly used lab strain of E. coli is known as DH5alpha. This strain has a mutation in its recA gene such that it cannot carry out recombination. Researchers exploit this inability to make their genetic transformations more efficient. Yet these bacteria clearly survive and reproduce. The same theme holds true for yeast, a single-celled eukaryote. While yeast without Rad51 function (the eukaryotic version of recA) are quite sensitive to agents that cause DNA damage, they remain viable.

Yet if we focus on eubacteria as a group, we’d find that the distribution of recA is nearly universal. And when we compare the encoded amino acid sequence of various recA genes from distantly related species, it becomes clear this is a highly conserved gene. For example, RecA sequence from E. coli (a gm negative, enteric bacteria) shows 65% identity and 83% similarity with sequence from B. subtilis (gm positive, soil bacteria). If we couple the way RecA is dispensable for life and reproduction in single-celled organisms to the widespread distribution of the gene and strong conservation of sequence, this suggests RecA’s functions are more fully realized across generations, something we would expect from an evolution gene.

But then something changes in the multi-cellular context. Mice that have both copies of their rad51 gene removed show the embryonic lethal phenotype. In other words, such embryos die and are unable to properly develop. Thus, Rad51 function is essential in the complex process of development, at least in mammals.

Could it be that RecA’s role in evolution is to facilitate the generation of complexity? I just noted the distribution of recA is nearly universal among eubacteria. But nearly universal is not universal. So you might be asking yourself about these bacteria that lack recA. It turns out there is a theme that is shared by these few examples of recA-less bacteria – they are endosymbionts (for example, Buchnera sp.). And what characterizes endosymbiotic bacteria is extreme genome reduction and degeneration. In fact, one comparative study indicates that recA (and other DNA repair genes) are lost early in the symbiotic relationship. In other words, it is the removal of recA that might serve as the trigger for genome reduction and thus the glue that establishes the symbiotic existence.

And it is thus from this angle that the hypothesis of front-loading evolution returns, as our evolution gene could be front-loading the appearance and maintenance of multi-cellular life. But that’s the next part of the story.

If we view evolution as a function, it stands to reason that life would be endowed with a tool kit of evolution genes. Such genes would interface with life’s architecture to facilitate evolution. That is, while evolution is inevitable in a population of imperfectly replicating cells, the evolution genes would function to effectively catalyze evolution.

But what part of life’s architecture might be targeted by these evolution genes? An obvious candidate is the DNA itself, as it is the DNA that codes for the machinery of life. For example, when it comes to the evolution of body plans, evo-devo teaches us that changing the pattern of switches in front of a gene is an integral part of such evolution. The switch sets, in turn, are altered over time through the process of genetic recombination. Recombination can remove switches, add switches, or swap different versions of a switch in or out. Afterwards, natural selection behaves merely as the editor to weigh whether or not such alterations are acceptable.

The process of recombination has long been known to be very important in generating variation for evolution. As one scientist notes, “The general feeling would probably be that in some undefined way recombination allows organisms to more effectively evolve to adapt to changing environmental conditions.”

Read the rest of this entry »