Lateral Gene Transfer

On the left, in the bacterial sexual reproduction called transformation, DNA is passed from one organism to another. Penicillin-resistant gonorrhea arose from transformation. On the right, small circular pieces of DNA called plasmids move independently and infect cells. They can carry genes that will make bacteria resistant to several drugs. (Courtesy: FDA)

The main feature of a species is that its populations exchange genetic material, and such exchange does not occur outside of the group that defines the species. Now it seems that not only do we consist of modified colonies of ancient types of bacteria, but we also carry at least some genes from certain bacteria, short programs that have inserted themselves into our replication code while we were evolving as species. Apparently, evolution does not strictly proceed within well-defined lineages. Instead "genetic noise" is penetrating the species barrier, introducing an additional component of variability, in addition to internal mutation.

Of course, we are not special in this, it is happening to all the branches in the tree of life. Bacteria routinely exchange portions of their genome; this is their equivalent of sex. In fact, the definition of a species as true and exclusive breeders does not even make sense for bacteria. There are no bacterial species. The same is true for the other prokaryote domain of life, the archaea. It was to be expected that bacteria and archaea also might have exchanged some genes.

As the tools of molecule-by-molecule genetic analysis were applied in the 1990s, it became apparent that many sections of the genomes of eukaryotes (including plants and animals) looked a lot like sections from bacteria and archaea. The similarity is much greater than expected if bacteria, archaea and eukaryotes had diverged by 3.5 Ga, as generally assumed. How could eukaryotes split from the other domains after occurrence of multi-segmented microfossils? Such fossils, found by UCLA paleontologist William Schopf, presumably indicate the presence of metazoans and hence eukaryotes. The discrepancy based on genome comparison is not subtle, but suggests divergence more than a billion years later than indicated by the fossil record. Should we assume that the results of an earlier divergence has fallen victim to catastrophic extinction, so that life history "started over", as it were, 2 Ga ago?

As more full genomes were decoded for organisms from all three domains, including our own, two things became clear. First, we had repeatedly acquired strings of genes by "lateral transfer" from distant taxa; microbes in particular, as evidenced by the different ages measured by small differences in the genetic code sequences. Second, it also became clear that advanced eukaryotes carried excess baggage in their genome, non-working sections called introns.

Bacteria and archaea carry far less of this material; somehow they are able to clean up their genomes. Our DNA seems to be less erasable, but our RNA goes through some transformations in the process of coding proteins that remove the non-coding segments.

Human immunodeficiency virus (HIV) particles on an infected lymphocyte. Note the daughter HIV particles leaving to find a new, uninfected host cell. (Courtesy: CMSP at Custom Medical Stock Photo,Inc. )

Not only do we carry microbes in our bodies, but we depend upon some of them for survival, as with our digestive bacteria. The ones that make us sick we call "germs", a term with also includes viruses. Viruses are non-metabolizing bits of genetic material, and thus, by our previous definition, are not truly "alive". They "hijack" portions of our cellular function by inserting themselves into our DNA ("infection"), and may permanently alter our genetic code.

The fact that genes can cross species barriers, and that some genes insist on duplicating themselves within the genome of a species, supports the suggestion that genes are "selfish", that is, their apparent goal (like that of organisms) is to survive and proliferate into all available space. In this view, the genes are the actors and the organisms provide the background environment.