Après moi le Déluge September 29, 2000

Egotism is an exaggerated sense of self-importance. (I'm sure I don't have to explain that term to scientists). Mankind has always fallen prey to this. Doesn't the sun revolve around us and where we chose to live? Well, the Earth may go around the sun but at least our solar system is unique. Well, at least we have life on our planet and we are its pinnacle. Well, at least we make tools. Well, at least we drive cars. We have the Teletubbies.

Today, we are gathering more surprising data regarding the world we live in than ever before. But, little in Nature is static. Almost everything is either increasing or decreasing. It is easy to believe that we are responsible for all of this. We need to understand Nature better to be sure what is our real impact. Several papers this week examine areas of simple life on Earth that could have significant impacts on our understanding. They disclose gaps in our knowledge, even of areas we thought we understood.

One of the first things I did when I started working in the lab in graduate school was purify some restriction enzymes. This was the era when NEB survived by carrying an ice bucket, containing it's products, around to its customers. It did not need a very large bucket either. But for many research labs the cost of restriction enzymes was too expensive, whereas graduate students were cheap. So, our first task was to make some enzymes. (Actually, our first task was to repurify phenol, a job so horrible that I no longer retain any memory of what it entailed.)

The other new graduate student got to purify some EcoRI (from E. coli) and some BspRI, an isoschizomer of HaeIII, from a Bacillus strain he got from someone in Bulgaria. All pretty easy - 37°C, Luria Broth kind of stuff. Here were my enzymes: MboI and MboII from Moraxella bovis and TacI from Themoplasma acidophilum. Moraxella bovis is a bovine pathogen, causing pinkeye. It requires growth on brain-heart infusion (I never wanted to know how this was made). Texas, obviously, regarded work on this organism as more dangerous than most human pathogens. So I got my first introduction to campus safety commissions.

But it was the purification of the other organism that I remember most. The name says it all. You do not even need to know much Latin. Heat loving, acid loving. This organism would only grow at a temperature of 59 °C and a pH of 2-4!! The protocol I had from some European lab gave a quick clue to help make sure you were growing the right bug, as if anything else would grow in a brew at pH 3 and 65°. "If it smells like vomit, you are growing the right bacteria." Sounds like fun. And, in order to get enough enzyme, I had to grow a large amount of it. Luckily, we had access to a 20 liter fermentor. I guess you can call it luck, getting to work with 20 liters of hot, acidic vomit.

I purified enough enzyme to get my work started. By the time I needed more, you could buy them commercially and we had lots more grant money. But the idea that something could survive quite nicely at such extreme conditions was an eye-opener. Life can live almost anywhere.

The latest Nature now describes the complete sequencing of this extremophile. Interestingly, it was first isolated in self-heating ore piles outside mining operations. Much like compost piles generate their own heat due to microbial action, so do these piles. Although T. acidophilum is a member of the Archaea, early work suggested that it has several aspects of its makeup that make it closer to eukaryotic cells than to prokaryotic.

Well, the complete sequence shoots that idea down. T. acidophilum fits well inside the third phylum, the Archaea. What is shocking is the fact that an awfully large amount of its genome appears to have been picked up from other organisms. Over 17% of the ORFs show similarity to another archaean, Sulfolobus solfataricus. Another large fraction seems to be derived from bacterial sequences. The fact that Thermoplasma has no cell wall and may not have any sort of restriction/modification system suggests that it might be quite capable of picking up any sort of DNA molecule that is floating around...at 60 ° C and pH 2!! The authors do not explain how the DNA is able to survive these conditions.

Perhaps it was packaged. A recent meeting on the Origin and Evolution of viruses was described in Science. One of the interesting theories proposed is called the "moron accretion hypothesis" (MAH). And no, it does not deal with people of limited intellect living along the Aegean Sea. We have a lot of evidence that viruses swap genes. Sequencing of their genomes reveals a high degree of mosiacism between viruses - regions of similarity interspersed with dissimilar sequences. It turns out that there are segments of genes in some viruses that resemble bacterial genes, and these carry many of the hallmarks of independent genes. They do not appear to act in concert with other viral genes. Since they represent more DNA than a virus needs, they were dubbed morons (not politically correct but who says scientists do not have a sense of humor?).

Now, the MAH postulates an intriguing origin for viruses. Our story begins - In early cells, there were no chromosomes, the genetic material simply floated free - kind of one gene, one DNA molecule. A mutation in a gene sequence might have resulted in a protein that could self-assemble into a simple 'phage particle'. Picking up the free-floating DNA molecule that coded for it would allow for the connection of phenotype and geneotype in one particle. If this self-assembling protein particle containing the DNA entered another cell, replication and translation of the DNA would create new particles. This theory provides a novel direction of virus genesis. Instead of a virus resulting from the loss of genes in a primitive cell, it comes about through the accretion of many 'moron' sequences. The virus bootstraps itself up from pieces floating around in the medium. Intriguing.

I have always thought that DNA was too unstable to survive for long 'naked', without protein protection. But a recent Science paper belies this point. A group at the Monterey Bay Aquarium Research Institute (what a great place to work) ignored what everyone knew and looked for free-floating DNA in sea water samples. No isolation of an organism first, just clone DNA fragments. Now this is actually a great approach. There are a tremendous number of organisms that can not be grown in the lab. This way, they just fished out the DNA.

They examined a 130 kilobase fragment. It had a rRNA sequence that identified it as coming from a g-Proteobacteria that has never been grown in culture. It was described over 10 years ago but was only known by its rRNA sequence. So, using molecular biology, they have been able to further examine an organism that we have not been able to look at any other way.

And their discoveries went further. For this segment of DNA also contained a gene encoding a bacteriorhodopsin, a membrane-spanning protein often used as a light-driven proton pump. Now, ignore the name, because no bacteriorhodopsin had ever been seen in a bacteria. They have been found in extreme halophile members of the Archaea. But not in bacteria.

The group expressed this bacteriorhodopsin in E. coli, and, sure enough, it transports protons in response to light. And E. coli expressing this protein absorb at the expected wavelength after addition of retinal, a cofactor that known bacteriorhodopsins bind. These bacteria are also a nifty red color. So, they appear to use light to generate ATP. This is a wholly novel environmental niche for marine waters close to the surface. If these organisms can use this energy to fix carbon, as plants do, this will have significant ramifications on our understanding of marine biology.

Aerobic phototrophic bacteria were not expected so close to the surface. Oxygen was believed to be too detrimental to their evolution. In fact, another group went looking to such bacteria near black smokers on the ocean floor. Their technology found nothing there but found a lot of phototrophic bacteria up near the surface. Now recent data indicate that almost 1% of all the surface phytoplankton may be these sorts of bacteria. This is a tremendous amount of organic material, that will lock in CO₂, will provide a food source for other members of the food chain, etc. We are still discovering new data that can have tremendous implications on our view of the world. We still have so much to learn.

In many views only man has tools, language, culture, big brains, upright locomotion, homosexuality, murder. Robert Ardrey popularized the idea that we are unique because we are Killer Apes, and we still retain those murderous instincts. The pivotal scene in 2001 is when the apes learn to use weapons to kill other apes. Most of these ideas have been debunked. In many ways we are just ordinary. But we still need to have something that sets us off completely from other animals.

Perhaps what sets us apart from other animals is the belief that we need to be set apart. As proof, I am going to add my own belief on what sets us apart.

We display an incredible desire to learn about the environment surrounding us. I would venture that mankind's major difference is that we care about what happens next week, next year, next century. No other animal appears to care what happens after it dies. They just work to survive. Anything else is somewhat peripheral. As Mme. Pompadour is supposed to have said, "Après moi le Déluge." (Didn't know how I was going to work the title in, huh?) They can't care about what happens when they are dead. They are spending all their energy living, with some amount dedicated to procreation.

We do care and we have the ability to determine what happens to us. Understanding what is really happening in the world around us increases that ability. But no matter what we do or what happens to us, life on Earth will continue. Life is just too tenacious. So, maybe after us, the deluge may come, but life will still be here and I am sure there will still be bacteria using light to make ATP.