Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [85]
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