Omnivore RNA pyrophosphatase: a versatile enzyme that efficiently removes diverse protecting groups from the 5′ end of RNA

The 5' ends of messenger RNAs typically are shielded from ribonuclease attack by protecting groups of various kinds, such as a canonical or noncanonical cap or an oligophosphate, which must often be removed to enable laboratory analysis. However, the deprotecting enzymes that currently are commercially available have limitations with regard to the types of protecting groups that they are able to remove efficiently and their inhibition by 5'-terminal base pairing. Here, we report that a diadenosine oligophosphate hydrolase from Aquifex aeolicus unexpectedly is effective at removing a wide variety of 5' protecting groups from RNA to generate a 5' monophosphate, including triphosphates, diphosphates, canonical N7-methylguanosine triphosphate caps, and noncanonical nicotinamide adenine dinucleotide, flavin adenine dinucleotide, nucleoside tetraphosphate, N-acetylglucosamine, glucose, and galactose caps, and that it is able to do so even when the RNA 5' terminus can be sequestered in a stem-loop. These properties have the potential to make this enzyme a superior alternative for RNA analysis whenever comprehensive deprotection of RNA 5' ends is important.