The expanding field of non-canonical RNA capping: new enzymes and mechanisms

Abstract

Recent years witnessed the discovery of ubiquitous and diverse 5′-end RNA cap-like modifications in prokaryotes as well as in eukaryotes. These non-canonical caps include metabolic cofactors, such as NAD + /NADH, FAD, cell wall precursors UDP-GlcNAc, alarmones, e.g. dinucleotides polyphosphates, ADP-ribose and potentially other nucleoside derivatives. They are installed at the 5′ position of RNA via template-dependent incorporation of nucleotide analogues as an initiation substrate by RNA polymerases. However, the discovery of NAD-capped processed RNAs in human cells suggests the existence of alternative post-transcriptional NC capping pathways. In this review, we compiled growing evidence for a number of these other mechanisms which produce various non-canonically capped RNAs and a growing repertoire of capping small molecules. Enzymes shown to be involved are ADP-ribose polymerases, glycohydrolases and tRNA synthetases, and may potentially include RNA 3′-phosphate cyclases, tRNA guanylyl transferases, RNA ligases and ribozymes. An emerging rich variety of capping molecules and enzymes suggests an unrecognized level of complexity of RNA metabolism.

Preparation of RNAs with non-canonical 5′ ends using novel di- and trinucleotide reagents for co-transcriptional capping

“…The best and longestknown examples are eukaryotic mRNAs and snRNAs carrying 7methylguanosine and 2,2,7-trimethylguanosine caps, respectively (Furuichi et al, 1975;Wei et al, 1975;Furuichi and Shatkin, 2000). However, many unconventionally capped RNAs have been recently discovered in both eukaryotic and prokaryotic cells, including RNA 5′-linked to NAD (NAD-RNA) (Chen et al, 2009;Cahová et al, 2015), FAD (FAD-RNA) (Wang et al, 2019), coenzyme-A (CoA-RNA) (Kowtoniuk et al, 2009), dinucleoside polyphosphates (Np n Ns-RNA) (Luciano et al, 2019;Hudecek et al, 2020), vitamins (thiamine-capped RNAs) (Mohler et al, 2020), or nucleotide sugars (Glc-ppRNA and N-AcGlc-ppRNA) (Julius and Yuzenkova, 2017;Wang et al, 2019;Wiedermannova et al, 2021). Access to these 5′-modified RNAs by IVT is often limited by the specificity and promoter sequences of RNA polymerases (Huang, 2003;Benoni et al, 2020).…”

Identification of NAD-RNAs and ADPR-RNA decapping in the archaeal model organismsSulfolobus acidocaldariusandHaloferax volcanii

“…NAD and related dinucleotide metabolites are essential for many physiological processes, and their detection as 5’ caps for different bacterial and eukaryotic RNAs revealed additional layers of complexity (38). Nevertheless, the specific roles of NAD-caps are still being uncovered.…”

Recent insights into noncanonical 5′ capping and decapping of RNA

“…These RNAs are generated by exonucleolytic processing of intronic sequences, and the presence of snoRNAs with a 5′ NAD cap precludes their production through transcriptional initiation. The mechanism of post-transcriptional addition of an NAD cap is still unknown although several potential pathways were recently reviewed ( 49 ), highlighting potential alternative pathways for noncanonical RNA capping with abundant adenosine analogs.…”