Lesson 6: Life's Origins 6.6 Lateral Gene Transfers - Crossing the Species Border From the foregoing it is already clear that the concept of "species" is of limited use in elucidating the origin of life and its evolution during the early stages of history. The term species refers to interbreeding populations who produce fertile offspring, or to potentially interbreeding populations (if they were at the same place at the same time). It is a concept well suited for the classification of domesticated plants and animals and all the other life forms which have similar life histories. It is good to remember that the species concept originated in the 18th century, when species were still considered immutable and bacteria were unknown. When it became clear that species are not immutable, the concept became fuzzy. Genetic changes accumulate over time. Eventually, once-related populations have evolved into separate and distinct species. But to draw the line where one species ends and another begins in such a series is an arbitrary exercise. Fortunately, evolution proceeds sometimes very slowly and sometimes quite rapidly, based on the changing morphology seen in fossil lineages, which makes it easier to draw a line. (This circumstance has been celebrated by the impressive label "punctuated equilibrium".) 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. Figure 6.6.1 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. As the tools of molecule-by-molecule genetic analysis were applied in the 1990's (see section 5.3), 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. (See http://exobio.ucsd.edu/Space_Sciences/genome.htm 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. 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. Figure 6.6.2 Human immunodeficiency virus (HIV) particles on an infected lymphocyte. Note the daughter HIV particles leaving to find a new, uninfected host cell. 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. The basics of making a eukaryotic cell according to SET are as follows. The first step was the merger of a heat and acid-loving archaeon with a swimming bacterium like a spirochete to form the nucleocytoplasm, found in all fungal, plant and animal cells. The conversion of free-swimming spirochetes to cell-propelling undulipodia, cilia and so on is one of the more controversial aspects of SET. The other steps seem to have been confirmed by study of cell component genomes. The combined cell was the first swimming organism with a nucleus, a protist; neither plant nor animal nor fungus. It lived without oxygen, and was in fact poisoned by it. The nucleus arose not from engulfing another organism, but from the symbiotic merger of the first two organisms. There are no free-living bacteria that look much like bare nuclei. The next step the combined organism had to achieve was the development of mitosis, the division of cell components during replication. The next symbiotic acquisition was the capture of an oxygen-breathing bacterium. Next came the ability to surround food material and create an interior space, a vacuole, where the food might be consumed at leisure. This was obviously a big improvement over the previous technique of nuzzling up to food, secreting digestive fluids and re-absorbing them. The first organism using internal digestion first appeared around 2 Ga, that is, 2,000 million years ago. The final component was incorporated, presumably, when food became a partner. The now three-part cell efficiently engulfed and digested green photosynthetic bacteria. Some green bacteria lingered on and photosynthesized within their host, before being digested. Some hosts learned to hold back the digestive process, to give the bacteria more time to do their thing. A partnership was born, and eventually the green bacteria became chloroplasts. The merged cell now was a green micro-alga. Eventually it became the ancestor to the familiar macro-algae and plants. Several other classes of membrane-bounded organelles occurring in the cytoplasm between the nucleus wall and the outer cell wall resemble bacteria in their behavior and metabolism. Examples are plastids, mitochrondria, and microtubules. Further study will reveal the ancestry of these highly modified colonies of symbionts. We are their descendants.