"Binary" Enzyme Demonstrates Darwinian Evolution at its Simplest

By Jason Socrates Bardi

Two scientists at The Scripps Research Institute (TSRI), Research Associate John S. Reader and Professor Gerald F. Joyce both of the institute's Department of Molecular Biology, have succeeded in creating an enzyme based on a "binary" genetic code—one containing only two different subunits.

This research, described in the latest issue of the journal Nature, demonstrates that Darwinian evolution can occur in a genetic system with only two bases, and it also supports a theory in the field that an early form of life on earth may have been restricted to two bases.

"Nobody will ever top this because binary systems are the most reduced form of information processing," says Joyce. "Two different subunits are the absolute minimum number you need [for Darwinian evolution]."

Where protein enzymes are polymer strings made up of 20 building blocks (the amino acids), and RNA or DNA enzymes are made up of four different building blocks (the nucleotides), the world's first binary enzyme has but two different building blocks, based on the nucleotides A and U.

This enzyme is functionally equivalent to a "polymerase" molecule. Polymerases are ubiquitous in nature as the enzymes tasked with taking a "template" string of DNA or RNA bits and making copies of it.

Reader and Joyce's binary enzyme is able to join pieces of RNA that are composed of the same two nucleotide symbols. In the test tube, the binary string folds into an active three-dimensional structure and uses a portion of this string as a template. On the template, it "ligates," or joins subunits together, copying the template.

Experimental Approaches to the Origins of Life

If the origins of life are a philosopher's dream, then they are also a historian's nightmare. There are no known "sources," no fossils, that show us what the very earliest life on earth looked like. The earliest fossils we have found are stromatolites—large clumps of single-celled bacteria that grew in abundance in the ancient world three and a half billion years ago in what is now western Australia.

But as simple as the bacteria that formed stromatolites are, they were almost certainly not the very first life forms. Since these bacteria were "evolved" enough to have formed metabolic processes, scientists generally assume that they were preceded by some simpler, precursor life form. But between biological nothingness and bacteria, what was there?

Far from being the subject of armchair philosophy or wild speculation, investigating the origins of life is an active area of research and of interest to many scientists who, like Reader and Joyce, approach the questions experimentally.

Since the fossil record may not show us how life began, what scientists can do is to determine, in a general way, how life-like attributes can emerge within complex chemical systems. The goal is not necessarily to answer how life did emerge in our early, chemical world, but to discover how life does emerge in any chemical world—to ask not just what happens in the past, but what happens in general.

The most important questions are: What is feasible? What chemical systems have the capacity to display signs of life? What is the blueprint for making life in the chemical sense?

One of the great advances in the last few decades has been the notion that at one time life was ruled by RNA-based life—an "RNA world" in which RNA enzymes were the chief catalytic molecules and RNA nucleotides were the building blocks that stored genetic information.

"It's pretty clear that there was a time when life was based on RNA," says Joyce, "not just because it's feasible that RNA can be a gene and an enzyme and can evolve, but because we really think it happened historically."

However, RNA is probably not the initial molecule of life, because one of the four RNA bases—"C"—is chemically unstable. It readily degrades into U, and may not have been abundant enough on early Earth for a four-base genetic system to have been feasible.

Odd Base Out

To address this, Nobel laureate Francis Crick suggested almost 40 years ago that life may have started with two bases instead of four. Now Reader and Joyce have demonstrated that a two-base system is chemically feasible.

Several years ago, Joyce showed that RNA enzymes could be made using only three bases (A, U, and G, but lacking C). The "C minus" enzyme was still able to catalyze reactions, and this work paved the way for creating a two-base enzyme.

In the current study, Reader and Joyce first created a three-base enzyme (A, U, G) and then performed chemical manipulations to convert all the A to D (diaminopurine, a modified form of A) and biochemical manipulations to remove all the G. They were left with an enzyme based on a two-letter code (D and U).

Reader and Joyce insist that their study does not prove life started this way. It does, however, demonstrate that it is possible to have a genetic system of molecules capable of undergoing Darwinian evolution with only two distinct subunits.

The article, "A ribozyme composed of only two different nucleotides," was authored by John S. Reader and Gerald F. Joyce and appears in the December 19, 2002 issue of the journal Nature.

This work was supported by a grant from the National Aeronautics and Space Administration (NASA), the Skaggs Institute for Chemical Biology at The Scripps Research Institute, and through a postdoctoral fellowship from the NASA Specialized Center for Research and Training (NSCORT) in Exobiology.




Sequence and secondary structure of ligase ribozymes containing either three or two different nucleotide subunits. Click to enlarge.