Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

Abstract

The hydrolytic deamination of cytosine and 5-methylcytosine residues in DNA appears to contribute significantly to the appearance of spontaneous mutations in microorganisms and in human disease. In the present work, we examined the mechanism of cytosine deamination and the response of the uncatalyzed reaction to changing temperature. The positively charged 1,3-dimethylcytosinium ion was hydrolyzed at a rate similar to the rate of acid-catalyzed hydrolysis of 1-methylcytosine, for which it furnishes a satisfactory kinetic model and a probable mechanism. In agreement with earlier reports, uncatalyzed deamination was found to proceed at very similar rates for cytosine, 1-methylcytosine, cytidine, and cytidine 5′-phosphate, and also for cytosine residues in single-stranded DNA generated from a phagemid, in which we sequenced an insert representing the gene of the HIV-1 protease. Arrhenius plots for the uncatalyzed deamination of cytosine were linear over the temperature range from 90°C to 200°C and indicated a heat of activation (ΔH ‡ ) of 23.4 ± 0.5 kcal/mol at pH 7. Recent evidence indicates that the surface of the earth has been cool enough to support life for more than 4 billion years and that life has been present for almost as long. If the temperature at Earth's surface is assumed to have followed Newton's law of cooling, declining exponentially from 100°C to 25°C during that period, then half of the cytosine-deaminating events per unit biomass would have taken place during the first 0.2 billion years, and <99.4% would have occurred during the first 2 billion years. spontaneous mutation | heat mutagenesis | cytosine deamination | HIV-1 protease I n the absence of enzymes, most biological reactions take place so slowly that they can be followed conveniently only at elevated temperatures (1). Among those reactions are several that may result in spontaneous mutation, notably the hydrolytic deamination of cytosine and 5-methylcytosine, which generate uracil and thymine, respectively. These deamination reactions have been shown to account for many of the single-site mutations that lead to inherited diseases in humans (2) and for the marked bias of spontaneous mutation toward increased AT content in microorganisms (3, 4). Rates of mutation have long been known to increase with increasing temperature, a phenomenon that Drake has termed "heat mutagenesis" (5).There is widespread (6-8), if not universal (9), agreement that life originated when the earth was warmer-perhaps much warmer-than it is today. A recent isotopic analysis of carbon inclusions in zircons from the Jack Hills in Western Australia indicates that life may have emerged as early as 4.1 billion years ago (10), shortly after water first appeared at the surface in liquid form (11). Several present-day organisms thrive at temperatures near the boiling point of water. Thus, Ignisphera aggregans (12) and Pyrococcus horikoshii (13) exhibit optimal growth temperature of 92°and 98°C, respectively, whereas another organism isolated from a hydrothermal vent has be...

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

“…The formation of uracil and thymine from the spontaneous hydrolytic deamination of cytosine and 5-methylcytosine, respectively 1,2 occurs an estimated 100–500 times per cell per day in humans 1 and can result in C•G to T•A mutations, accounting for approximately half of all known pathogenic SNPs (Fig. 1a).…”

Evolutionary dynamics and significance of multiple subclonal mutations in cancer

“…The 50,000 lesions produced per cell per day as a result of spontaneous and/or endogenous chemical reactions [1] are not localized to specific genes but instead are distributed stochastically. Important sources of DNA damage include the chemical instability of the DNA helix by depurination [1, 26–27], deamination of cytidine to thymidine [28], and by cellular reactive molecules (eg, oxygen and nitrogen reactive species) [29]. Damage by environmental agents frequently involves similar chemical alterations, and in order to be a significant cause of human cancer must contribute a comparable number of lesions.…”

Effects of Pressure and pH on the Hydrolysis of Cytosine: Implications for Nucleotide Stability around Deep‐Sea Black Smokers

“…At both ambient and high pressures, the half-life of cytosine decreases significantly as the pH decreases from 7.0 to 6.0. These studies have been augmented very recently by Lewis et al, [12] who reported rate constantsa nd an enthalpy of activation of about 23 kcal mol À1 for the deamination of cytosine andv arious derivatives at pH 2.4 and 7.0 over the temperature range from about 90 to 200 8C.Assuming that earliest life-forms werer ather inefficient and not adapteda nd stripped down for speedy turnover,i nc ontrast to many extant Prokarya and Archaea, these results on the diminished chemical stabilityo fc ytosine at elevated temperatures and the physicali nstability of folded RNA structures have rendered unlikely ah ot-starts cenario for RNA-basedl ifeforms. Many scenarios have RNA-based lifeforms preceding the extant protein-based life-forms, [1] or coevolution of RNA alongside DNA.…”

“…As ingle point of agreement in current( i.e.,s ince % 2012) origin-of-life scenarios invokesar ole for FeS species in redox reactions. These studies have been augmented very recently by Lewis et al, [12] who reported rate constantsa nd an enthalpy of activation of about 23 kcal mol À1 for the deamination of cytosine andv arious derivatives at pH 2.4 and 7.0 over the temperature range from about 90 to 200 8C. [8] With respectt oc hemi-cal stability,s tudies under mesophilic conditions have revealed the susceptibility of cytosine and cytidine to hydrolytic deamination, [9] both as individual molecules and upon incorporation into about 5000 base-pair bacteriophage DNA.…”

“…Separately,i th as long been known that, at least at ambient pressure of 1atm (0.1 MPa), folded RNA structures denature at temperatures less than 70 8Ci nv itro. These studies have been augmented very recently by Lewis et al, [12] who reported rate constantsa nd an enthalpy of activation of about 23 kcal mol À1 for the deamination of cytosine andv arious derivatives at pH 2.4 and 7.0 over the temperature range from about 90 to 200 8C. [10] Subsequently, Levy and Miller found that, at 100 8Ca nd ambient pressure, the nucleobase cytosine hydrolysed to uracil (Scheme 1) with a half-life of just 19 days, compared with 340 years at 25 8C.…”