Arabidopsis thaliana NudiXes have RNA-decapping activity. Issue 3 (17th January 2023)

• Record Type: Journal Article
• Authors: Mititelu, Maria-Bianca; Hudeček, Oldřich; Gozdek, Agnieszka; Benoni, Roberto; Nešuta, Ondřej; Krasnodębski, Szymon; Kufel, Joanna; Cahová, Hana
• Is Part Of: RSC chemical biology. Volume 4:Issue 3(2023)
• Page Start: 223
• Page End: 228
• Publication Date: 2023-01-17
• Subjects: 572
• DOI: 10.1039/d2cb00213b
• Languages: English
• ISSNs: 2633-0679

Abstract

Abstract : In light of recent discoveries of noncanonical RNA caps, we studied substrate specificity of potential plant RNA decapping enzymes - NudiXes. We have found that some are very selective, while others function as general RNA decapping enzymes. Abstract : Recent discoveries of various noncanonical RNA caps, such as dinucleoside polyphosphates (Np n 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 Arabidopsis thaliana encodes as many as 28 NudiX enzymes. For most of them, only in vitro substrates in the form of small molecules are known. In our study, we focused on four A. thaliana NudiX enzymes (AtNUDT6, AtNUDT7, AtNUDT19 and AtNUDT27), and we studied whether these enzymes can cleave RNA capped with Np n Ns (Ap2–5 A, Gp3–4 G, Ap3–5 G, m 7 Gp3 G, m 7 Gp3 A), CoA, ADP-ribose, or NAD(H). While AtNUDT19 preferred NADH-RNA over other types of capped RNA, AtNUDT6 and AtNUDT7 preferentially cleaved Ap4 A-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 Ap4 A, while AtNUDT7 preferentially cleaved Ap4 A-RNA. These findings show that NudiX enzymes may act as RNA-decapping enzymes in A. thaliana and that other noncanonical RNA caps such as Ap4 A and NADH should be searched for in plant RNA.