Microcosm

by Carl Zimmer

  As soon as the basic outlines of molecular biology became clear in the 1960s, scientists decided that DNA, RNA, and proteins did not emerge from the lifeless Earth all at once. But which came first? DNA may be a marvelous repository of information, but without the care provided by proteins and RNA it is just a peculiar string-shaped molecule. Proteins are awesomely versatile, able to snatch atoms drifting by, forge new molecules, and break old ones apart. But they are not so good at storing information for building proteins or for passing that information on to the next generation.

  Francis Crick spent many hours in the mid-1960s speculating on the origin of life with his colleague at Cambridge, the chemist Leslie Orgel. They came to the same basic conclusion, one that Carl Woese came to on his own. Perhaps DNA and proteins emerged well after life began on Earth. Perhaps before life depended on DNA and protein, it was based on RNA alone.

  At the time the suggestion seemed a little bizarre. RNA’s main role in cells appeared to be as a messenger, delivering information from genes to the ribosomes where proteins were made. But Crick, Orgel, and Woese all pointed out that experiments on E. coli showed that RNA molecules also have other jobs. The ribosome, for example, is itself made up of dozens of proteins and a few molecules of RNA. Another kind of RNA, called transfer RNA, helps weld amino acids onto the end of a growing protein. Perhaps, the scientists suggested, RNA has a hidden capacity for the sort of chemical acrobatics proteins are so good at. Perhaps RNA was the first molecule to emerge from the lifeless Earth, with different versions of the molecule playing the roles of DNA and protein. Perhaps DNA and proteins evolved later, proving superior at storing information and carrying out chemical reactions, respectively.

  Years later Crick and Orgel freely admitted that the idea of primordial RNA went nowhere after they published it in 1968. Fifteen years would pass before people began to take it seriously. A year after Crick proposed an RNA origin for life, a young Canadian biochemist named Sydney Altman arrived at Cambridge to work with him on transfer RNA. Altman discovered that when E. coli makes its transfer RNA molecules, it must snip off an extra bit of RNA before they can work properly. Altman named E. coli’s snipping enzyme ribonuclease P (RNase P for short). At Cambridge and then at Yale, Altman slowly teased apart RNase P and was surprised to find that it is a chimera: part protein, part RNA. Altman and his colleagues found that the blade that snips the transfer RNA is itself RNA, not protein. Altman had discovered an RNA molecule behaving like an enzyme—something that had never been reported before.

  Altman would share a Nobel Prize in 1989 with Thomas Cech, a biochemist now at the University of Colorado. Cech found similarly strange RNA in a single-celled eukaryote known as Tetrahymena thermophila, which lives in ponds. Unlike prokaryotes, eukaryotes must edit out large chunks of RNA interspersed in a gene before they can use it for building proteins. Proteins that build the messenger RNA generally edit out these chunks. But Cech discovered that in Tetrahymena, some RNA molecules can splice themselves without any help from a protein. They simply fold precisely back on themselves and cut out their useless parts.

  Cech’s and Altman’s discoveries showed that RNA is far more versatile than anyone had thought. Many biologists turned back to the visionary ideas of Crick, Orgel, and Woese. Perhaps before DNA or proteins evolved, there had existed what Walter Gilbert of Harvard called “the RNA world.”

  If RNA-based life did once swim the seas, its RNA molecules would have had to be a lot more powerful than the ones discovered by Altman and Cech. Some would have had to serve as genes, able to store information and pass it down to new generations. Others would have had to extract the information in those genes and use it to build other RNA molecules that could act like enzymes. These ribozymes, as they were known, had to capture energy and food and replicate genes.

  The possibility of an RNA world spurred a number of scientists to explore the evolutionary potential of this intriguing molecule. In the 1990s, Ronald Breaker, a biochemist at Yale, set out to make RNA-based sensors. He reasoned they would work like the signal detectors found in E. coli. They would have to be able to grab particular molecules or atoms, change their shape in response, and then react with other molecules in the microbe.

  Breaker didn’t design these sensors, though. Instead, he took advantage of the creative powers of evolution. He dumped an assortment of RNA molecules into a flask and then added a particular chemical he wanted his sensor to detect. A few of the RNA molecules bonded clumsily to the chemical while the rest ignored it. Breaker fished out those few good RNA molecules and made new copies of them. He made them sloppily, so that he randomly introduced a few changes to their sequences. In other words, the RNA mutated. When Breaker exposed the mutated RNA molecules to the same chemical again, some of them did an even better job of binding to it. Breaker repeated this cycle of mutation and selection for many rounds, until the RNA molecules could swiftly seize the chemical.

  Eventually Breaker and his colleagues were making RNA molecules that could not only grab the chemical but change their shape. These RNA molecules could act like an enzyme, able to cut other RNA molecules in half. Breaker had created an RNA molecule that could sense something in its environment and use the information to do something to other RNA molecules. He dubbed it a riboswitch.

  In the years that followed, Breaker created a library of riboswitches. Some can respond precisely to cobalt, others to antibiotics, others to ultraviolet light. RNA’s ability to evolve such a range of riboswitches brought more weight to the RNA-world theory. Breaker then had a thought. If the RNA-world theory was right, then RNA-based life had shifted many of the jobs once carried out by RNA to DNA and proteins. But perhaps RNA had not surrendered all those jobs. Perhaps riboswitches still survive in DNA-based organisms. In some cases, an RNA-based sensor might be superior to one made of protein. Riboswitches are easier to make, Breaker noted, since all a cell needs to do is read a gene and make an RNA copy.

  Breaker and his students set out on a search for natural riboswitches. In a few months they had found one in E. coli, which uses this particular riboswitch to sense vitamin B12. E. coli makes its own vitamin B12, which it needs to survive. But above a certain concentration extra B12 is just a waste. E. coli’s riboswitch, Breaker found, binds vitamin B12. The binding causes it to bend into a shape in which it can shut down the protein that makes the vitamin. Breaker couldn’t have fashioned a more elegant riboswitch himself.

  Breaker went on to find more riboswitches in E. coli, and then he found more in other species. Most of them keep levels of chemicals in balance by swiftly shutting down genes. Since Breaker discovered riboswitches, other scientists have found RNA doing many other things in E. coli. Some shut genes off, and others switch them on. Some prevent RNA from being turned into proteins, while others keep its iron in balance. Some RNA molecules allow E. coli to communicate with other microbes, and others help it withstand starvation. These RNA molecules form a hidden control network that’s only now emerging from the shadows. Their discovery has helped make the RNA world even more persuasive.

  Still, the question of exactly how RNA-based life emerged and then gave rise to DNA-based life gives scientists a lot to argue about. Some believe that RNA could have emerged directly from a lifeless Earth. Its ribose backbone, for example, might have been able to form in desert lakes, where borate can keep the fragile sugar stable for decades. Some argue that other replicating molecules came first and that the RNA world was merely one phase of history.

  Like any living thing, RNA life needed some kind of boundary. Some scientists argue that RNA organisms did not make their own membranes but, rather, existed in tiny pores of ocean rocks. As RNA molecules replicated, the new copies spread from chamber to chamber. Other scientists see RNA life packaged in more familiar cells. They are trying to create these organisms from scratch, crafting oily bubbles that can trap RNA molecules. Proof by invention is their strategy.

  There’s probably little to fear from the creation of RNA-based
life. Most experts suspect it would survive only in the confines of the laboratory. DNA-based life is far superior in the evolutionary arena. But that doesn’t mean DNA-based life has abandoned all the ways of its ancestor. RNA may still work best for certain tasks, and that superiority is why it continues to exert control over E. coli and other species. In some ways the RNA world never ended. We still live in it today.

  AU REVOIR, MON ÉLÉPHANT

  In many ways, Jacques Monod was far more right than he realized when he uttered his famous words about E. coli and the elephant. We share with E. coli a basic genetic code and many proteins essential for getting energy from food. E. coli and our own cells face many of the same challenges. They both need to keep a boundary with the outside world intact yet not too rigid. E. coli has to keep its DNA neatly folded and yet accessible for speed-reading. It has to keep track of its inner geography. It needs to organize its thousands of genes into a network that can respond in a coordinated way to changes in the outside world. Its network has to remain rugged and robust despite the fact that it is swamped with noise. E. coli communicates with other members of its species, allies with some, fights with others, gives up its life. Like us, it grows old.

  Some of these similarities are the result of a common heritage reaching back to the earliest stages of life on Earth. Others are the result of two evolutionary paths that converged on the same solution. Yet even the cases of convergence strengthen Monod’s insight. They are evidence that despite 4 billion years of separate history, we and E. coli are still deeply sculpted by the same evolutionary forces.

  I have met some scientists, however, who simply hate Monod’s quip. It tramples over some fundamental differences between the elephant and E. coli. Elephants—and humans and lichens and all other eukaryotes—have vastly larger genomes than E. coli. Our own genome, for example, has about five times as many genes. It’s also padded with a lot of DNA that does not encode proteins. Another major difference can be found in the proteins we use to replicate DNA. They do not show any clear relationship to the proteins used by E. coli or other bacteria. Eukaryotes do swap a few genes, but much more rarely than E. coli does. We do not shake hands with friends and take up their genes for blue eyes. As animals, we have a way of reproducing that couldn’t be more different from E. coli’s. Only a tiny fraction of the cells in our bodies have the potential to carry our genes successfully to the next generation, and our genomes carry the information necessary for the stately development of a new trillion-celled body complete with 200 cell types and dozens of organs.

  These differences are indeed great and genuine, and yet scientists have surprisingly little idea of how they came to be. Why we’re not more like E. coli is, in some ways, an open question. The answer must be lurking in the early history of life on Earth. Scientists are agreed that life split into three branches very early on, and the differences among them—particularly those that divide eukaryotes from bacteria and archaea—are profound. Yet at the moment, experts are contemplating some radically different explanations for how those divisions emerged. Some have claimed that eukaryotes originated from archaea that swallowed oxygen-breathing bacteria. Others claim that the split occurred long before that, before life crossed into the DNA world.

  I find one explanation particularly intriguing. It comes from Patrick Forterre, an evolutionary biologist at Monod’s Pasteur Institute. He proposes that the profound split between us and E. coli is the work of viruses.

  Forterre’s scenario begins in the RNA world, before the three great divisions of life had yet emerged. RNA-based organisms were promiscuously swapping genes. Some of these genes began to specialize, becoming parasites. They no longer built their own gene-replicating machinery but invaded other organisms to use theirs. These were the first viruses, and they are still around us today, in the form of RNA viruses, such as influenza, HIV, and the common cold.

  It was these RNA viruses, Forterre argues, that invented DNA. For viruses, DNA might have offered a powerful, immediate benefit. It would have allowed them to ward off attacks by their hosts by combining pairs of single-stranded RNA into double-stranded DNA. The vulnerable bases carrying the virus’s genetic information were now nestled on the inside of the double helix while a strong backbone faced outward.

  Early DNA viruses probably evolved a range of relationships with their hosts. E. coli’s viruses are good to keep in mind here: the lethal ones that make the microbe explode with hundreds of viral offspring, the quiet ones that cause trouble only in times of stress, and the beneficial ones that have become fused seamlessly to their hosts. Forterre argues that on several occasions, DNA viruses became permanently established in their RNA hosts. As they became domesticated, they lost the genes they had used to escape and make protein shells. They became nothing more than naked DNA, encoding genes for their own replication.

  Only at that point, Forterre argues, could RNA-based life have made the transition to DNA. From time to time, mutations caused genes from the RNA chromosome to be pasted on the virus’s DNA chromosome. The transferred genes could then enjoy all the benefits of DNA-based replication. They were more stable and less prone to devastating mutations. Natural selection favored organisms that carried more genes in DNA than in RNA. Over time, the RNA chromosome shriveled while the DNA chromosome grew. Eventually the organism became completely DNA based. Even the genes for riboswitches and other relics of the RNA world were converted to DNA. Forterre proposes that this viral takeover occurred three times. Each infection gave rise to one of the three domains of life.

  Forterre argues that his scenario can account for the deep discord between the genes that all three domains share and the ones that are different. Forterre started his scientific career studying the enzymes E. coli uses to build DNA. Related versions of those enzymes exist in other species of bacteria, but they are nowhere to be found in archaea or eukaryotes. The difference, Forterre argues, lies in the fact that the ancestors of E. coli and other bacteria got their DNA-building enzymes from one strain of virus and the eukaryotes and archaea didn’t.

  Once the three domains split, they followed different trajectories. Our own ancestors, the early eukaryotes, may have acquired their nucleus and other traits from other viruses. Eukaryotes grew to be larger than bacteria or archaea, and as a result their populations grew smaller. In small populations it’s easier for slightly harmful mutations to spread, thanks merely to chance. It may have been only then that the eukaryote genome began to expand. Interspersing noncoding DNA within genes may have been harmful at first, but over time it may have given eukaryotes the ability to shuffle segments of their genes to encode different proteins. We humans have 18,000 genes, but we can make 100,000 proteins out of them.

  Forterre’s proposal is as radical as the suggestion in 1968 that life was once based on RNA. It will demand just as much research to test. In the meantime, it is intriguing to think about what it would mean if Forterre is right. The differences between the elephant and E. coli would actually be the sign of yet another fundamental similarity: we—all living things—are different only because we got sick from different viruses.

  Ten

  PLAYING NATURE

  PORTRAIT IN PROTOPLASM

  IN CHRISTOPHER VOIGT’S LABORATORY at the University of California, San Francisco, you can have your picture taken by E. coli. Voigt will place a photograph of you before a hooded contraption. The reflected light from the picture strikes a tray covered with a thin, gummy layer of E. coli. It’s a special strain that Voigt and his colleagues created in 2005. They inserted genes into the bacteria, some of which let the bacteria detect light and some of which cause them to produce a dark pigment. The genes are wired so that if a microbe detects light—such as the light reflected from a photograph—it shuts down the genes for making pigment. The bacteria that catch photons from light parts of the picture remain clear. The ones that don’t churn out pigment and turn sepia. A picture emerges, soft, fuzzy, but recognizably you.

  Voigt is an assistant pr
ofessor with a long list of scientific papers on his résumé. But he is also a child of the biotechnological age. He had not yet been born when scientists first learned how to insert genes in E. coli in the 1970s. That breakthrough was one of the most important in the history of biology. Genetic engineering allowed scientists to decipher some of the genome’s most baffling features. They turned E. coli into an industrial workhorse and created a $75 billion industry. Once scientists had mastered the art of inserting genes into E. coli, they began putting them in other microbes and then in animals and plants. Now goats produce drugs in their milk. Now 250 million acres of farmland are covered in crops carrying genes that make them resistant to pesticides and herbicides.

  But as genetic engineering spreads to other species, E. coli has not faded into the background. It remains the species of choice for scientists who want to develop new tools for manipulating life. Voigt’s work, for example, is part of a new kind of genetic engineering called synthetic biology. Instead of simply moving a single gene from one species to another, synthetic biologists seek to create entire circuits of genes. They wire together genes from various species and fine-tune them to carry out new functions. For now synthetic biologists have learned enough only to create eye-catching proofs of principle, like Voigt’s microbial camera. But these lessons could lead to microbes that act as solar-power generators, or that can produce drugs when the conditions are right—call them thinking drugs. Some synthetic biologists are even trying to dismantle E. coli and use its parts to rebuild life from scratch.