SCIENCE
Research Builds Case for Late Evolution of DNA Selective affinities may exist between amino acids, anticodons; microspheres catalyze reactions to make peptides, polynucleotides James H. Krieger, C&EN Washington
"Instead of DNA being the secret of life, life is the secret of DNA." That reversal by Barry Commoner of the more-or-less conventional view of molecular evolution capsules the thrust of work by a number of researchers probing the origin of biological information. Commoner, director of the Center for the Biology of Natural Systems at City University of New York's Queens College, was among a group of those researchers who presented an overview of their
Lacey: underlying molecular logic
work at the annual meeting of the American Association for the Advancement of Science, held in Detroit late last month. The thrust of their work is that the genetic code is a late development in molecular evolution, but that it had to develop because of the intrinsic properties of the molecules involved. First, however, came cellular replication, emerging from the self-ordered, nonrandom organization of amino acids into peptides. In other words, proteins came first, and DNA arose as a convenient way of moderating metabolism and recording the information that already existed at that time. One of the researchers is biochemist James C. Lacey Jr. of the University of Alabama, Birmingham. He has been focusing on the genetic code—the series of nucleotide triplets in nucleic acid that specify the assembly of amino acids into proteins. The four DNA nucleotides— adenine, guanine, cytosine, and thymine (uracil in RNA), abbreviated by their initials—provide 64 possible triplets. Since there are 20 amino acids used, there are several trinucleotide sequences specifying most amino acids, as well as signals for "start" and for "stop" of protein synthesis. In simplest terms, Lacey and his coworker Dail W. Mullins Jr., in work supported by the National Aeronautics & Space Administration, are seeking an answer to the question of why AAA means lysine. The genetic code is an essentially universal system, Lacey argues, which suggests an underlying molecular logic. An answer, Lacey feels, lies in affinities between amino acids and their anticodonic nucleotides. During protein synthesis, messenger RNA in a ribosome carries, for example, an AAA codon specifying that
lysine is to be incorporated. Lysine, however, is brought to the ribosome by a transfer RNA, which carries the base pair complement of AAA, or UUU. Thus, AAA is a codon for lysine, and UUU its nominal anticodon. An examination of the genetic code, Lacey says, shows that those amino acids having U as the middle and most important letter of their codons are all hydrophobic amino acids. Similarly, those amino acids having A as their middle letter are, except for tyrosine, all very hydrophilic amino acids. Lacey was led on a search for evidence that there exists some relationship—possibly "selective affinities"—between amino acids and their anticodonic nucleotides. Taking data from the literature on the relative hydrophobicities of amino acids and mononucleotides, Lacey plotted the hydrophobicities of the homocodonic amino acids versus the hydrophobicities of their anticodonic nucleotides. He found a direct correlation, the hydrophobic amino acids having more hydrophobic anticodons, and vice versa. Similarly, he determined the opposite property, relative hydrophilicity, and found that it also correlates anticodonically for these amino acids. The correlations were later extended to all 20 amino acids and the correlation was found to be generally true using individual sets of data. Recently, Lacey says, he and Mullins worked out a new set of correlation data based upon the collected hydrophobicity estimates from several laboratories that, he says, suggests even more strongly that the fundamental relationships are between amino acids and their anticodons. Plotting the average hydrophobicity ranking of each of the amino acids as a function of the avJune20, 1983 C&EN
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Science erage hydrophobicity ranking of its principal anticodonic dinucleoside monophosphate, gives a "remarkable" correlation coefficient of 0.97 for those points lying within a particular band. Four amino acid-anticodon pairings lie outside this band and correlate only poorly. But two of these noncorrelating anticodon assignments represent the anticodonic equivalents of the common termination codons, and two are those contemporary assignments that are seen to be currently most subject to genetic drift in mitochondria. Beyond such correlations, Lacey says, binding constants are now becoming available that support the idea that weak but selective affinities must have been responsible for the code origin. For example, in one study by others, he says, NMR was used to determine the binding constants of most amino acids for the most hydrophobic nucleotide, adenosine monophosphate, and the results showed that the binding constants for the hydrophobic nucleotide declined as the measure of the hydrophilicity of the amino acid increased. Lacey and Mullins carried out the reverse experiment, taking a hydrophobic amino acid, phenylalanine, and determined its binding constant for the four mononucleotides. The results, Lacey says, show without question that phenylalanine has the highest binding constant for
Fox: thermal protein work 34
June 20, 1983 C&EN
its anticodonic nucleotide, and that the binding constant declines as the hydrophilicity of the nucleotides increases. Assuming, Lacey says, that there is a selective affinity between amino acids and their anticodonic nucleotides, it now seems to be developing that selective affinity can result in selective chemical reactions. Studying the nonenzymic activation of a series of amino acids by adenosine triphosphate (ATP) using M g + + as catalyst, Lacey and Mullins have found that under a wide variety of conditions, phenylalanine, the amino acid of that set having the highest affinity for ATP, is activated most rapidly by it. "We certainly don't have all the answers/' Lacey says. "We don't have all of the binding constants between amino acids and nucleotides we'd like to have. We'd like to build up a catalog of these and see if this model still holds. And we want to study all the reactions . . . and see if we still continue to get selective reaction chemistry." Sidney W. Fox, director of the Institute for Molecular & Cellular Evolution at the University of Miami, Coral Gables, Fla., has been probing the conditions for the emergence of life experimentally for a couple of decades. In his experiments, amino acids—such as can be derived from electrical sparking or ultraviolet irradiation of a simulated primordial gas mixture—are heated together under "geological conditions." The result is what have been termed thermal proteins. These thermal proteins, Fox emphasizes, are specific, nonrandom, and enzymically active, arising from highly precise self-ordering of amino acids. Moreover, when these thermal proteins contact water, they aggregate to form microspheres, units that look like cells. Fox notes that 1 g of the typical thermal protein will give 10 10 of these units. Fox has been studying the properties of the microspheres for some years. "What's astonishing," he says, "is that these have as many properties of modern cells as they do." Recent work, Fox says, has been carried out with microspheres made from the usual thermal protein that was first used, which is an acidic
type, but complexed with a basic type—one that's rich in lysine. The result is a microsphere that has the ability to make offspring peptides and offspring polynucleotides. That is, Fox says, the basic thermal protein, within a cellular type of structure, has the ability to catalyze the reaction of free amino acids in aqueous solution and ATP and to make peptides. It has at the same time the ability to catalyze the reactions of nucleotides to make polynucleotides. "The point is," Fox says, "that here are polynucleotides formed at the same time as peptides, and those are ideal conditions for the beginning of a genetic code." Howard H. Pattee, a systems science professor at State University of New York, Binghamton, works at a higher level of abstraction on the problem of biological information. Pattee explains that he is interested in the theory of self-organization and the theory of information. His approach, he says, is complementary to that of the experimentalists. "All the wet chemistry, so to speak, tells you a lot about what nature does, but it doesn't reveal the essential, theoretical nature of information," Pattee says. What is important, Pattee says, is the idea of where significance, where selective value, comes into the evolutionary picture. It's generally agreed, he says, that it has something to do with the closure of catalytic or other self-sustaining cycles. The problem then is how these self-sustaining cycles evolve to produce the genotype and the phenotype, which are so distinct that they're obvious in highly evolved systems. But at the beginning, he says, it isn't obvious. It isn't that nucleic acids were there and proteins were there and suddenly the nucleic acids became the genotype and the proteins the phenotype. Rather, he says, the two interacted in complicated ways in which it probably isn't clear where the information resided first. "And," Pattee adds, "there's even some argument as to where the information resides now. You can talk about amino acids as informational just as much as you can talk about DNA as informational." D
