NudiXes have RNA-decapping activity.

Recent discoveries of various noncanonical RNA caps, such as dinucleoside polyphosphates (Np N), coenzyme A (CoA), and nicotinamide adenine dinucleotide (NAD) in all domains of life have led to a revision of views on RNA cap function and metabolism. Enzymes from the NudiX family capable of hydrolyzing a polyphosphate backbone attached to a nucleoside are the strongest candidates for degradation of noncanonically capped RNA. The model plant organism encodes as many as 28 NudiX enzymes. For most of them, only substrates in the form of small molecules are known. In our study, we focused on four NudiX enzymes (AtNUDT6, AtNUDT7, AtNUDT19 and AtNUDT27), and we studied whether these enzymes can cleave RNA capped with Np Ns (ApA, GpG, ApG, mGpG, mGpA), CoA, ADP-ribose, or NAD(H). While AtNUDT19 preferred NADH-RNA over other types of capped RNA, AtNUDT6 and AtNUDT7 preferentially cleaved ApA-RNA. The most powerful decapping enzyme was AtNUDT27, which cleaved almost all types of capped RNA at a tenfold lower concentration than the other enzymes. We also compared cleavage efficiency of each enzyme on free small molecules with RNA capped with corresponding molecules. We found that AtNUDT6 prefers free ApA, while AtNUDT7 preferentially cleaved ApA-RNA. These findings show that NudiX enzymes may act as RNA-decapping enzymes in and that other noncanonical RNA caps such as ApA and NADH should be searched for in plant RNA.