Enzymes can catalyze biochemical reactions that cannot occur by themselves. In nature, most proteins can play the role of enzymes. However, other molecules, such as RNA molecules, can also perform enzyme reactions. In the former era of modern life based on DNA and proteins, RNA was considered to have functioned both as primary genetic material and as a catalyst or ribozyme. Ribozymes have been found in nature, where they catalyze RNA cleavage and ligation reactions—mostly in the context of RNA splicing and retrotransposition. In vitro-selected ribozymes have been evolved to act as RNA ligases and replicases that can reproduce themselves or their ancestors, and that are able to produce functional RNAs (including aptamers and ribozymes).
Recently, in a research report published in the international journal Nature, scientists from Julius-Maximilians-Universität Würzburg identified a new ribozyme that catalyzes the site-specific installation of 1-methyladenosine in a substrate RNA, using O6-methylguanine as a small-molecule cofactor. The ribozyme displays a wide range of RNA-sequence, such as site-specific adenosine methylation in various RNAs. This new ribozyme may become the first known methyltransferase in the world, and researchers named it MTR1.
Figure 1. In vitro selection of methyltransferase ribozymes. (Scheitl C P M, et al., 2020)
In this study, the researchers described the details of this new ribozyme. In the targeted RNA, it can produce methylated nucleoside-1-methyladenosine (m1A), and the methyl group can be transferred from the free methylguanine nucleic acid base (O6-methylguanine, m6G)) into the ribozyme binding bag. The methyl-group donor of the MTR1 methyltransferase ribozyme is a simple methylated nucleobase. Conceptually, the ribozyme mimics RNA-guided RNA methylation by RNA-protein complexes, such as CD-box RNPs involved in 2'-O-methylation of ribosomal RNA. The ribozyme combines both functions—guide and enzyme—in a single molecule of RNA. The cofactor-binding site in the catalytic core of the in vitro-selected ribozyme may be similar to the binding site of guanine or m6G in purine riboswitches. Therefore, it is conceivable that methyltransferase ribozymes could be evolved from riboswitch RNAs that are known to bind modern methyltransferase cofactors, including S-adenosylmethionine (SAM) and methylene tetrahydrofolate (THF) derivatives. The discovery of this new ribozyme illustrates a very interesting aspect of its evolution. According to the RNA world hypothesis, RNA is one of the earliest molecules to store information and have enzyme activity. The ribozyme developed by the researchers may produce methylated RNAs in the process of evolution, which in turn may lead to the emergence of larger structural and functional diversity of RNA molecules.
RNA methylation is considered to be the on or off switch of the biochemical reaction. And it plays a key role in the function of RNA structure and controls many life processes in cells. The new ribozyme MTR1 could not only attach a single methyl group to synthetic RNA structures, but also to natural RNA strands in cells. Therefore, this result may attract the attention of many cell biologists.
The newly developed ribozyme mtr1 is believed to be a useful tool in many research fields in the future, such as helping to better understand the methylation of RNA, the interaction between structure and function, etc. The reported findings have implications for scrutinizing the evolution of catalytic RNA as well as studying fundamental aspects of RNA methylation in contemporary biology. In view of the activity of MTR1 with m6dG, it seems likely that an analogous ribozyme activity can be developed to catalyze the removal of a methyl group from RNA (or DNA), thus mimicking repair enzymes of alkylation damage-response pathways. Such hypothetical RNA repair ribozymes could have been beneficial catalysts in an RNA world, helping the evolution of RNA replicases by releasing mutagenic methylation blocks derived from environmental damage and interfered with faithful Watson-Crick base-pairing. The next step is to reveal the structure of these new ribozymes and the detailed chemical mechanism of RNA catalyzed methylation. With the development of new methods, researchers will also develop ribozymes with diverse reactions.