Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases

Abstract

RNA, the earliest genetic and catalytic molecule, has a relatively delicate and labile chemical structure, when compared to DNA. It is prone to be damaged by alkali, heat, nucleases, or stress conditions. One mechanism to protect RNA or DNA from damage is through site-specific methylation. Here, we propose that RNA methylation began prior to DNA methylation in the early forms of life evolving on Earth. In this article, the biochemical properties of some RNA methyltransferases (MTases), such as 2'-O-MTases (Rlml/RlmN), spOUT MTases and the NSun2 MTases are dissected for the insight they provide on the transition from an RNA world to our present RNA/DNA/protein world.

Keywords: DNA methylation; RNA methylation; RNA world; RNA-DNA transition; evolution.

FIGURE 1

Prebiotic synthesis of ribose, purines, pyrimidines, and RNA. Simple inorganic molecules such as CO₂, H₂O, HCHO, NH₃, and HCN, can be combined to form organic ribose sugar as well as nitrogenous bases (purines and pyrimidines) by selectively subjecting them to electrical discharges representing the proposed extreme weather conditions in the prebiotic world. The highly reactive molecule formaldehyde (1) can be generated by reacting abundant CO₂ that was present in the reducing world with water molecules. Subsequent reaction of HCHO with itself can give rise to ribose sugar via intermediates such as glycoaldehyde (2) and glyceraldehydes (3) or another reactive molecule HCN by reacting with N₂ under high atmospheric pressure. HCN reacts with itself to produce the purine base adenine and, with HCHO, it produces cyanoacetaldehyde, which can react with urea (H₂NCONH₂) to give rise to two pyrimidine bases, namely cytosine and uracil. Ribose sugar bonds with nitrogenous bases to produce ribonucleosides which might have been phosphorylated by inorganic phosphate (iPO₄) from dissolved minerals to produce ribonucleotides (Costanzo et al., 2007). These ribonucleotides are activated by imidazole (Im) and then polymerize into a long chain without any template on a clay catalyst such as montmorillonite, which was abundantly present in the prebiotic Earth. All these steps vest on the probability of occurrence of all these ingredients and favorable conditions at least in a close proximity to the Earth surface and its proximal atmosphere. Thymine, found only in DNA, is speculated to have been synthesized with more complex reactions at a later evolutionary stage, possibly through methylation of uracil using hydrazine (H₂NNH₂) and HCHO.

FIGURE 2

Possible route of S-adenosyl-L-methionine (SAM) appearance and its metabolic significance. The nitrogenous nucleobase ‘adenine,’ present in the universal methyl donor cofactor SAM, could have been generated by an electric spark reaction in an aqueous solution of NH₃ and HCN (in fact, adenine is merely a pentamer of HCN). The base is highly conspicuous in all life forms in the form of the high energy molecule, Adenosine Triphosphate (ATP), which is the universal energy currency of cells. Likewise, methionine has been reported to be synthesized from a mixture of CH₄, H₂S, NH₃, and CO₂ by providing a similar electric discharge (Van Trump and Miller, 1972; Parker et al., 2011). Methionine is the first amino acid decoded by the genetic code into the biotic proteins. Finally, the ribose sugar present in SAM can be synthesized from formaldehyde by formose reaction using basic substances, neutral clays, heat and various types of radiation. Ribose is the first sugar formed in the anabolic reactions while deoxyribose is synthesized later. Nucleophilic addition reaction of methionine with ATP produces the SAM cofactor, which represents the second most abundant molecule (after ATP) inside all cells and participates in all methylation reactions.

FIGURE 3

Putative chronological appearance of RNA, DNA, MTases, prokaryotes, and eukaryotes. RNA, which functions as a genetic material, as a chaperone, and as a peptide synthesizer, is a likely candidate as the sole common precursor of other biomolecules de novo in the prebiotic world. RNA modification through snoRNA (RNA acting as a ribozyme) would have been the initial step to stabilize and protect RNA from the extreme environmental conditions of the prebiotic soup on Earth. An initial DNA-like molecule would have arisen from the non-enzymatic reduction of 2′-OH of ribose sugar rather than with ribonucleotide reductase which might have manifested after the appearance of the genetic code. The kingdom of prokaryotes and Archaea that arose on early Earth already possessed RNA, DNA, and their modifying enzymes in the course of evolution. There were many RNA MTases that were initially multi-specific, i.e., acting on many RNA species and some of them, later on, may have evolved to act on DNA. With the appearance of cyanobacteria (blue–green algae), the atmospheric CO₂ of the reducing Earth started to be consumed and its concentration gradually decreased while the concentration of O₂ started to build up (leading to the oxidizing atmosphere of the present-day Earth). Many enzymes shifted their mechanism of methylation away from depending on radical SAM (an anaerobic type of methylation; Zhang et al., 2011) to nucleophilic attack (S_N2 type) and evolved to become oxygen tolerant. The presence of oxygen may have triggered the reversibility of methylation reaction since demethylases (TET1-3) are often dioxygenases (Tsukada, 2012).