Three Pyrimidine Decarboxylations in the Absence of a Catalyst

Area of Science:

• Biochemistry
• Epigenetics
• Computational Chemistry

Background:

• DNA demethylation involves TET dioxygenases oxidizing 5-methylcytosine to 5-hydroxymethylcytosine and further to 5-formylcytosine and 5-carboxylcytosine (5caC).
• Pyrimidine salvage pathway involves decarboxylation of 5-carboxyuracil (5caU) to uracil.
• The spontaneous decarboxylation rates of 5caC and 5caU are largely unknown, especially compared to the very slow decarboxylation of 6-carboxyuracil (6caU).

Purpose of the Study:

• To determine the spontaneous decarboxylation rates of 5-carboxyuracil (5caU) and 5-carboxycytosine (5caC) in neutral solution.
• To compare these rates with the known slow decarboxylation of 6-carboxyuracil (6caU).
• To elucidate the mechanism of spontaneous decarboxylation using computational simulations.

Main Methods:

• Arrhenius analysis of experimental data at elevated temperatures to determine rate constants and activation enthalpies.
• Kinetic analysis of 5caC decomposition, including intermediate cytosine accumulation and subsequent deamination.
• Ab initio molecular dynamics simulations to model spontaneous decarboxylation mechanisms in water.

Main Results:

• 5caU decomposes with a rate constant of 1.1 × 10^-9 s^-1 at 25 °C.
• 5caC decomposes more slowly (k₂₅ = 5.0 × 10^-11 s^-1), initially forming cytosine, which then deaminates rapidly (k₂₅ = 1.9 × 10^-10 s^-1).
• Both 5caC and 5caU decarboxylate orders of magnitude faster than 6caU (k₂₅ = 1.3 × 10^-17 s^-1).
• Simulations suggest direct CO₂ elimination assisted by a water molecule is the favored spontaneous decarboxylation route for all three compounds.

Conclusions:

• The spontaneous decarboxylation of 5caC and 5caU is significantly faster than previously assumed, impacting understanding of DNA demethylation and pyrimidine metabolism.
• The rapid decarboxylation of 5caC and 5caU suggests these are viable intermediates in biological pathways.
• Spontaneous decarboxylation in water, facilitated by a water molecule, is a key mechanistic pathway.