Results indicate that a high-temperature origin of life may be possible, but …

• Abstract
• Introduction
• Materials and Methods
• Results
• Discussion
• Conclusions
• Acknowledgements
• References
• Figures

Biology Articles » Evolutionary Biology » Origin of Life » The stability of the RNA bases: Implications for the origin of life » Discussion

Discussion

- The stability of the RNA bases: Implications for the origin of life

Calculation of the half-lives for the rates of decomposition of the nucleobases A, U, G, C, and T clearly shows that these compounds are not stable on a geologic time scale at temperatures much above 0°C.

At 350°C, the half-lives for hydrolysis are between 2 and 15 sec, and at 250°C they are between 1 and 35 min. These rates are so fast that it would be impossible for these compounds to accumulate to significant levels, making a heterotrophic origin of life at these temperatures highly unlikely.

At 100°C the half-lives for the decomposition of the nucleobases are still very short. The half-life for A is 1 yr, G is 0.8 yr, U is 12 yr, and T is 56 yr. C is shortest of all with a half-life of only 19 days. Therefore unless these compounds were used immediately after their synthesis, an origin of life at 100°C is also unlikely.

Even at 25°C, the rate of hydrolysis of the compounds are fast on the geologic time scale. The half-lives for A and G are 10,000 yr, whereas that of C is only 340 yr.

At 0°C, the half-life of A is 6 × 10⁵ yr, G is 1.3 × 10⁶ yr, U is 3.8 × 10⁸ yr, and T is 20 × 10⁸ yr. These rates are comparable to the present rate of destruction of organic matter in sea water as it passes through the hydrothermal vents every 10⁷ yr (29). This has been cited as a major limiting factor in the build-up of organic molecules on the early Earth (30, 31), and suggests that at 0°C, A, G, U, and T are sufficiently stable for a low-temperature origin of life. The case for C, however, is different, and is discussed below.

Rates of Synthesis vs. Rates of Decomposition. It is necessary to consider the rates of synthesis as well as the rate of decomposition of the nucleobases to get the steady-state nucleobase concentrations. If the rates of synthesis are temperature dependent and have activation energies similar to those for decomposition, then the steady-state concentrations of the nucleobases would be independent of temperature. For example, the concentration of A is given by:

where A is the concentration of adenine, k_s the rate of synthesis, and k_d the rate of decomposition of the nucleobases. At steady state dA/dt = 0, and where C_s and C_d are the Arrhenius constants. If the H values for k_s and k_d are the same, then k_s/k_d and the steady-state concentration of A are independent of temperature. The value of k_d is strongly dependent on temperature (i.e., H = 28 kcal for A). The rate of synthesis, k_s, consists of two steps, the production of the precursor HCN and its reaction to produce A. The rate of production of A is temperature dependent with  H = 20 kcal (32), but the reaction is very concentration dependent and only proceeds when [HCN] > 0.1 M. (33). At the necessary concentrations, the reaction is fast (hours at 100°C and a few months at 20°C). Therefore the rate-limiting step is the production of HCN by photochemical and electric discharge processes. Because these production rates are independent of temperature, the rate of synthesis of A will be independent as well.

Actually the rate of A synthesis at 100°C is less than that at T  NH₄HCO₂ at higher temperatures, leading to low steady-state HCN concentrations. More importantly, the HCN cannot be concentrated at elevated temperatures (>0°C) as it can at lower temperatures ( restricted to low temperatures. Similar considerations to these would apply to guanine, and to a lesser extent the pyrimidines.

Other Factors Affecting Rates of Decomposition. The rates of decomposition measured here have not been corrected for general acid general base effects of the buffer on the reaction rate. These effects are generally small. For example, at the buffer concentrations used (0.05 M) the rate of decomposition for C is only 1.3 times faster for phosphate, and 1.5 times faster for acetate, than at zero buffer concentration (28, 34). Even relatively large changes in rate (10- to 100-fold), however, would not affect our conclusions on high-temperature theories.

The effects of high pressure on reaction rates are of concern to prebiotic processes in the deep sea and near hydrothermal systems where the pressure may be as high as 300 atm (1 atm = 101.3 kPa). In general, the effects of pressure on reaction rates are small and are given by the equation:

where H is the volume of activation. Typical values for  H are around 20 to 40 cm³/mol (34-36). However, even an extremely large value of 100 cm³/mol only changes the reaction rate by a factor of 2.5 at 300 atm (3,000 m depth) and 100°C. At 1,000 atm and 100°C, the change in rate increases to a factor of only 25. For positive V values the rates decrease by the same factor.

The presence of other compounds in the prebiotic ocean also may have had an affect on reaction rates. The deamination of cytosine to uracil, for example, has been shown to be catalyzed by sulfite (37, 38). Other nucleophiles may act similarly. Nucleophilic addition to the C5-C6 double bond also may increase the rate of hydrolysis of uracil. Therefore the stability of these compounds may be considerably shorter than our values and needs to be corrected for these reactions.

Minerals and mineral surfaces also may affect the rates of decomposition of these compounds. However, it is difficult to predict whether a given mineral or minerals will stabilize on destabilize these compounds. The hydrolysis of adenine to hypoxanthine, for example, has been shown to dramatically increase in the presence of Cu²⁺-montmorillonite (39).

Purines and pyrimidines have been found in sediment cores from both ocean and lake basins (40-42), some dating back as far as 25 × 10⁶ yr (43). However, these measurements are complicated by uncertainties in temperature, microbial activity, and sedimentation rates. The presence of cytosine in 25 × 10⁶-yr-old sediments, however, is surprising and may be the result of contamination or decomposition under anhydrous conditions (43, 44).

The Instability of Cytosine. The instability of C has long been recognized (27, 28, 45-48). For example, it is not found in the Murchison meteorite, whereas A, U, G, xanthine, and hypoxanthine are (49, 50). At 0°C, the half-life for the decomposition of C is 17,000 yr, which is still very short on the geologic time scale.

The instability of cytosine, even at 0°C, raises a serious question of whether it would have been a suitable base for the first genetic material. A steady-state calculation for the relative amounts of C and U in the prebiotic ocean can be done if we assume that all U is produced from the hydrolysis of C (k₁ = 4.1 × 10⁵ yr¹ at 0°C), and that the only other loss channels are the hydrolysis of U (k₂= 1.9 × 10⁹ yr¹ at 0°C) and the destruction of organic compounds by passage through the 350°C hydrothermal vents (k₃ = 6.9 × 10⁸ yr¹ at 0°C). At steady state:

At 0°C, this gives a C/U ratio of 1/600. This ratio is so high that the enolic form of U(0.01% of U), which binds with G (51), would be comparable (1/15) to the concentration of C.

This would require proofreading corrections that would not be likely for the first replicative system. If the rate though the vents was 10 times faster in the past, because of higher heat flow, the ratio would be 1/60, which still would be highly error prone.

One solution to this problem with fidelity may be that the origin of life took place very rapidly after a sterilization event. Such an event would reset the C/U ratio, allowing for a favorable ratio in the first 10⁵ yr, although at the expense of low initial concentrations of C. This suggests that if life arose using C, and its base pair G, it must have done so very quickly ( the previous proposal (31) that life may have evolved in as little as 10⁷ yr.

Another possibility is that some concentration mechanisms were available that raised the concentration of C but not U, or that C may have been stabilized by the incorporation into a hydrogen-bonded polymer structure. This is the case for cytosine in double-stranded DNA, which hydrolyzes to uracil 140 times slower than C in single-stranded DNA (52). It is also possible that the early ocean was largely frozen with the aqueous phase at the NaCl-H₂O eutectic (21°C). This would increase the half-life of C to 8.0 × 10⁵ yr. However, in the absence of any concentration or protective mechanisms, the instability of C suggests that it may not have been used in the first genetic molecule, and this raises questions as to whether G was also absent.

Alternatives To GC. One possibility is that the first genetic material contained a two-letter code consisting of A and U, A and T (53), or A and I (inosine) (54). Although a genetic system based on a two-letter code, in principle, is possible, and attractive in the sense that it is simple, such a system would have more limited coding capabilities than a 2-bp system (53). In addition, a genetic material coded by only two bases would be very sticky, in that it would easily hydrogen-bond to itself. This could lead to problems in early replication.

Do The Purine And Pyrimidine Biosynthetic Pathways Suggest That GC Came After AU? A metabolic argument can be given that guanine and cytosine were incorporated into the genetic material after adenine and uracil (Fig. 4). The biosynthesis of purine nucleoside monophosphates is from aminoimidazole carboxamide riboside monophosphate. The present pathways are indicated in Fig. 4 by solid arrows, and the dotted arrow shows a one-step pathway, instead of the present three-step pathway for the synthesis of GMP. A two-step pathway through XMP is also possible. The shorter route would be expected if GMP, or guanine, were used when the pathways first developed.

Although this type of metabolic argument frequently is used to infer historical biochemical sequences, these arguments are weak in that the origin of the metabolic pathways may have been considerably later than the first use of these bases in the genetic material.

Alternative Bases. If the first genetic material contained a four-base code, then the simplest solution to the instability of C is to use a modified C. 5-Methylcytosine (5-MeC) and 5-hydroxymethylcytosine (5-HMC) were found to be less stable than C at pH 7 and 100°C (t_1/2 5-MeC = 9 days, t_1/2 5-HMC = 13 days). N⁴-methylcytosine is estimated to have t_1/2 = 38 days at 100°C based on the rate of hydrolysis of N⁴-methyldeoxycitidine (55).

Another possibility is that the first genetic material contained a base pair other than GC. A number of alternative base pairs have been proposed. These include isoguanine and isocytosine (53, 56), diaminopurine and U (56), pseudo-diaminopyrimidine (ribose bound to C5 rather than N1) and xanthine (56), A and urazole (1,2,4-triazole-3,5-dione) (57). An even more extreme alternative is suggested by an all-purine helix (54, 58, 59). Eschenmoser and Loewenthal (60) also have shown strong purine-purine binding interactions in their homo-DNA, a DNA analog.

On the basis of stability we can say that xanthine (t_1/2 = 0.4 yr at 100°C, and 0.6 × 10⁶ yr at 0°C), and diaminopurine (t_1/2 = 2 yr at 100°C) are about as stable as A or G. Hypoxanthine (t_1/2 = 12 days at 100°C, and 5,000 yr at 0°C) and isoguanine (t_1/2 = 19 days at 100°C) are about as stable as C. The alternative pyrimidines isocytosine (t_1/2 = 21 days at 100°C; ref. 61) and diaminopyrimidine (t_1/2 = 42 days at 100°C, and 40,000 yr at 0°C) hydrolyze at about the same rate as cytosine. Therefore to get greater stability it may be necessary to use bases other than these pyrimidines (56, 57) or to use an all-purine helix (excluding hypoxanthine and isoguanine). In addition, the instability of all of the alternatives measured (t_1/2  also would be excluded from use in a high-temperature origin of life.

Is There a Role for High Temperatures? We are not suggesting that short-term, high-temperature processes (100°C) such as those that may have occurred in lagoons or on drying beaches did not play a role in the origin of life, but that the temperature of most of the Earth could not have been much above 0°C. However, even small portions of the Earth at high temperatures can lead to the rapid overall decomposition of organic compounds. For example, if 5% of the ocean is at 100°C and the remainder at 0°C, then assuming rapid mixing, the overall half-life for the decomposition of A will be 20 yr instead of the 10⁶ yr at 0°C.

In one scenario, organic compounds would be stored at low temperatures (e.g., 0°C) and may be brought into higher (100°C) temperature regions (i.e., hot rocks, drying lagoons, low-temperature hydrothermal vents) for brief periods of time ( of extreme temperature, such as the hydrothermal vents (350°C), may be excluded from this view because of the very rapid rate of decomposition at these temperatures.