Massive Thermal Acceleration of the Emergence of Primordial Chemistry, the Incidence of Spontaneous Mutation, and the Evolution of Enzymes

Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution. Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution. Enzymes allow certain reactions to take place take place rapidly as compared with other reactions that confer no selective benefit upon the host organism. Once a substrate is bound, its transformation often transpires in a few milliseconds. In the absence of enzymes, the same reaction takes place relatively slowly, with a half-life that may span many hours, days, or years. Some biological reactions may be slower still in the absence of enzymes. The individual bonds connecting the components of cellulose and other polymers, readily attacked by water in the presence of enzymes, are apparently capable of long term survival in their absence to judge from the survival of submerged Viking ships and paper documents on the S. S. Titanic. If those bonds were not kinetically stable, then proteins, nucleic acids, and polysaccharides would disintegrate too rapidly to be useful for storing energy and maintaining structure and genetic information in the water that surrounds these molecules in living organisms. To appreciate what evolution has accomplished, it would be desirable to know the actual rates at which biological reactions take place in the absence of enzymes. There are more practical reasons for wishing to know the extent to which enzymes enhance reaction rates. The remarkable selectivity of each enzyme for its preferred substrate, as well as its ability to increase the rate of reaction, is believed to depend on a distinguishing property of catalysts that was first recognized by Michael Polanyi in 1921. To enhance the rate of a reaction, the affinity of a catalyst for its substrate must increase, in passing from the ground state to the transition state. The magnitude of that increase matches the factor by which the enzyme enhances the rate of reaction (Fig. 1) (1Wolfenden R. Analog approaches to the transition state in enzyme reactions.Acc. Chem. Res. 1972; 5: 10-18Crossref Scopus (543) Google Scholar). Accordingly, a stable molecule that resembles the altered substrate of an enzyme in the transition state would be expected to be a strong reversible inhibitor, competing with substrates for a place on the enzyme. That principle has provided a useful basis for the design of powerful enzyme inhibitors that include several drugs now used to control hypertension and the spread of HIV, and have been used as haptens to elicit the production of antibodies with catalytic activity. Transition state analogues also furnish a probe that structural biologists can use to unveil the details of the chemical mechanism of action of an enzyme and the changes in enzyme structure that almost invariably accompany catalysis (2Wolfenden R. Thermodynamic and extrathermodynamic requirements of enzyme catalysis.Biophys. Chem. 2003; 105: 559-572Crossref PubMed Scopus (66) Google Scholar). To estimate the minimal binding affinity expected of an ideal transition state analogue inhibitor that perfectly resembles the altered substrate in the transition state, it is necessary to compare the rate of reaction of the enzyme-substrate complex with the rate of the uncatalyzed reaction in water. If one enzyme produces a 100-fold greater rate enhancement than another enzyme, then the first enzyme should show a proportionally higher affinity for a transition state analogue inhibitor. Thus, uncatalyzed reaction rates are expected to be useful in prioritizing enzymes according to their expected sensitivity as targets for drug design. Until fairly recently, the hydrolysis of peptide bonds was the slowest process whose rate had been measured directly in water, with an apparent half-life of 4 years at room temperature (3Kahne D. Still W.C. Hydrolysis of a peptide bond in neutral water.J. Am. Chem. Soc. 1988; 110: 7529-7534Crossref Scopus (178) Google Scholar). That reaction was so slow that its measurement required an extraordinarily sensitive method for detecting extremely early stages in product formation. However, there were reasons to suppose (including, for example, the survival of ancient documents in water) that other biological reactions might be slower still in the absence of a catalyst. An alternative approach to measuring the rates of slow reactions was suggested by a well known rule of thumb, according to which reaction rates tend to double (“Q10 = 2”) when the temperature is raised by 10 °C. In one of the first descriptions of the effect of temperature on the rate of a reaction in water, Harcourt and Esson (4Harcourt A.V. Esson W.T. On the laws of connexion between the conditions of a chemical change and its amount.Phil. Trans. R. Soc. London. 1866; 156: 193-221Crossref Google Scholar) reported a Q10 of 2 for the well known “iodine clock” reaction, in which an abrupt change from colorless to black makes it possible to perform kinetic measurements with the aid of a simple stopwatch. Compounding that increment, one would expect rates of reaction to increase ∼70-fold when the temperature is raised from 25 °C to the boiling point of water. Even at elevated temperatures, however, the prospects for determining the rates of very slow reactions did not seem bright. When that approach was first applied to very slow reactions, the results were a surprise. The rule that Q10 = 2 applies to only a few reactions (e.g. the hydration of CO2) that are rapid and easy to measure at ordinary temperatures. However, slow reactions are vastly more sensitive to temperature. For the decarboxylation of orotidine 5′-phosphate decarboxylase, an intermediate in the biosynthesis of nucleic acids, Q10 is 16. Thus, the rate of this reaction increases not 70-fold as suggested above but 4 million-fold when the temperature is raised from 25° to 100 °C (5Radzicka A. Wolfenden R. A proficient enzyme.Science. 1995; 267: 90-93Crossref PubMed Scopus (733) Google Scholar). Subsequent experiments have shown that Q10 values are 4 for peptide hydrolysis, 6 for the hydrolysis of simple O-glycosides, 13 for the decarboxylation of orotidine 5′-phosphate decarboxylase, and 16 for the P–O cleavage of phosphate monoester dianions: the reaction catalyzed by fructose-1,6-bisphosphatase and inositol phosphatases. The remarkable sensitivity of slow reactions to temperature, together with the linearity of Arrhenius plots in which the logarithm of the rate constant of a reaction is plotted as a function of the reciprocal of absolute temperature (Kelvin), makes it possible to obtain, by extrapolation, the rates of many reactions that are extremely sluggish at ordinary temperatures (supplemental Fig. S1). Representative half-lives at 25 °C are 7 × 105 years for fumarate hydration, 2.3 × 109 years for uroporphyrinogen decarboxylation, and 1.0 × 1012 years for the hydrolysis of the dianions of simple phosphate monoesters (6Wolfenden R. Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes.Annu. Rev. Biochem. 2011; 80: 645-667Crossref PubMed Scopus (108) Google Scholar). The value of t½ for sulfate ester hydrolysis by S–O bond cleavage was recently estimated as 1018 years (7Edwards D.R. Lohman D.C. Wolfenden R. Catalytic proficiency: the extreme case of S–O cleaving sulfatases.J. Am. Chem. Soc. 2012; 134: 525-531Crossref PubMed Scopus (76) Google Scholar). These observations raise two obvious questions. How did such reactions ever get started on the primitive earth? Also, how did enzymes ever evolve to surmount such formidable kinetic obstacles? In a letter to J. D. Hooker, Darwin imagined how life might have originated, perhaps in a “warm little pond” (8Darwin C. Letter to J. D. Hooker. 1871; (February 1, 1871)Google Scholar). Shortly after the publication of The Origin of Species, William Thomson (Lord Kelvin) became interested in the age of the earth and set his students to measuring temperatures at various depths in the soil. He used those results to calculate the rate of heat loss from the earth, assuming that the earth began as a molten mass, and estimated the age of the earth as between 20 and 40 million years. In Kelvin's inaugural address as president of the British Association, he stated his conviction that insufficient time had elapsed on Earth for the chemistry of living systems to have attained its present level of complexity without “intelligent and benevolent design” (9Thomsen W. On the origin of life. Presidential Address to the British Association for the Advancement of Science, Edinburgh, August 1871; reprinted in Kelvin's Popular Lectures and Addresses (2010). Nabu Press, Charleston, SC1871: 132-205Google Scholar). Had he been aware of the generation of heat by the radioactivity of the earth, a phenomenon that would only be discovered much later, Kelvin would not have underestimated the age of the earth (now known to be ∼4.6 billion years) by a factor of ∼100. It should also be added that he was also unaware that life emerged very early during the life of the planet, probably within the first 0.5–1 billion years. Life began, in the words of Philip Ball, “in a blink, almost the instant the oceans were formed. It is as if it was just waiting to happen — as indeed some have suggested. Although Darwinian evolution needed billions of years to find a route from microbe to man, it seems that going from mineral to microbe took barely a moment” (10Ball P. Some like it hot.Nature. 2011; (10.1038/news.2010.590)Google Scholar). If life began so early, then Kelvin's question regains some of its original force. How could biological chemistry have gotten to such a information from Arrhenius (6Wolfenden R. Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes.Annu. Rev. Biochem. 2011; 80: 645-667Crossref PubMed Scopus (108) Google Scholar) that the more sluggish a reaction the more it to The of that if one plots the of of uncatalyzed reactions in water measure of the sensitivity to temperature of a as a function of their of at 25 °C function of the reaction (supplemental Fig. Arrhenius the logarithm of the rate constant of a reaction is plotted as a function of the reciprocal of absolute For most simple reactions, Arrhenius plots are a of temperatures. any temperature, the energy of = = is the rate constant in of is and is The enthalpy of = is the rate is the and is the absolute temperature. The of is from the = the of of these reactions can be plotted their of (Fig. For of the in Fig. 2 show the possible values of and for reactions that at each of several rates at 25 with t½ values of 10 or years. The a reaction with a Q10 of 2 The point in this a value for enzyme reactions, most of which are very as A between that point and any of the other in Fig. 2 the change in the of that the enzyme must be later, enzyme catalysis is by more than by more more point in Fig. 2 a reaction whose of have been and these are to be a of values of but a relatively of values of of a much more in determining the rates of these uncatalyzed reactions than their of Fig. 2 also a of the the = of reaction are to measure if their half-lives between and at ordinary temperatures, their values between 20 and at 25 °C. If between and as is the case for most reactions in water (Fig. then the value of must in the between 10 and to Q10 values between 2 and In of these of it is not that these values in the R. C. The temperature of enzyme rate Am. Chem. Soc. Scopus Google Scholar). It that if chemistry in an environment that was than it is then most chemical would have place much more rapidly than at Also, the rates of the slowest reactions are also the most sensitive to temperature, tend to and at temperatures not from the boiling point of water (supplemental Fig. However, was the earth during the early stages of chemical The early of life on the earth seems with the that life emerged the earth was still Even at temperatures in and and from to his well known C. Rev. PubMed Google Scholar) that the of the of life were by organisms. The of the genetic that the was a The was a or a and 2003; PubMed Scopus (76) Google and the of C. 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