Thursday, October 4, 2012

Microbiome Part 2: Lateral Gene Transfer (aka Bump and Grind)

Note this program first aired September 15, 2012.

Bacteria are thought to be the original gangsters, the form in which life sprung forth from the primordial soup. And that was nearly 3.5 billion years ago. One line of questioning in the current fervor of microbial research is then “what is the evolutionary history of the prokaryotic clades?”—those groups of microorganisms with no membrane to keep their DNA nice and tidy, who may or may not be closely related to each other. And when we say evolutionary history, we mean how did the prokaryotic diversity we see today arise, who evolved from whom and which groups are more closely related, meaning, which groups evolved from a common ancestor relatively recently.

It turns out, this question is much easier to ask than it is to answer. And the reason for this is that we have to compare the genes of these various organisms in order to determine how related they are. The more genes they share, the more closely related we can assume them to be. It actually is quite complicated trying to decide which genes to compare. Some have said, why not compare them all? Well in some cases that is exactly what is going on. Researchers are comparing entire geneomes  from various prokaryotes. The trick is to get them all lined up correctly, so you are comparing the similar areas of each genome. And this only really works for organisms that have relatively few genes. Even the super computers get overwhelmed relatively quickly with large amounts of genetic data. Other researcher pick out specific types of genes, and compare just those. These minutia lead to terrific and heated debates about the relationships of various groups of organisms we can’t even see!

The real reason though, that reconstructing the evolutionary history of bacteria is so difficult is that they don’t behave the same way we do with respect to our genetic legacy. Pretty much all of us Eukaryotes reproduce sexually. We find a mate, combine our genetic material, and produce offspring that carries a mix of our DNA, some from one parent, and some from the other. That is the only way our genes move from individual to individual, through direct heredity. Tracing and comparing genes gives us a picture of lineage.

The problem is that prokaryotes don’t behave that way, when it comes to their DNA. Instead of finding that special someone to settle down with and start a family, they are all about one night stands. And infact, not only one night stands, but trans specific hook ups. Prokaryotes are willing and able to swap chunks of DNA with any other prokaryotic cell they encounter, regardless of whether or not it is the same species as them. This promiscuity is quite frankly, a little shocking.  This bump and grind life style is known as lateral gene transfer, and is the reason it is so hard to reconstruct the evolution of bacteria and archea. They don’t follow the lineage based model of our own genetic methodology. They swap genes all over the place, all the time, so the presence of a gene in a particular bacteria may not be telling you anything about that cell’s parent, it may just indicate that that cell happened to bump into some other prokaryotic species and they did a quick genetic switcheroo when no one was looking. Theoretically this MO, and not sexual recombination, accounts for diversification in early prokaryote evolution.

So what this means is that our models for piecing together the puzzle of the early evolution of prokaryotes doesn’t work. The chaos that is lateral gene transfer makes this virtually impossible at least for now. It also has some incredibly important implications for human health, all of which we will be talking about on future episodes of the World Around Us.

Timeline of early life on Earth from the New Scientist:

More than you ever wanted to know about comparing bacterial DNA:
“Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution” Se-Ran Juna, Gregory E. Simsa, Guohong A. Wua, and Sung-Hou Kim,

The pros and cons: “The advantages and disadvantages of horizontal gene transfer and the emergence of the first species” Aaron A Vogan and Paul G Higgs*