Noncanonical features and modifications on the 5′‐end of bacterial sRNAs and mRNAs

Abstract

While many eukaryotic transcripts contain cap structures, it has been long thought that bacterial RNAs do not carry any special modifications on their 5′ ends. In bacteria, primary transcripts are produced by transcription initiated with a nucleoside triphosphate and are therefore triphosphorylated on 5′ ends. Some transcripts are then processed by nucleases that yield monophosphorylated RNAs for specific cellular activities. Many primary transcripts are also converted to monophosphorylated species by removal of the terminal pyrophosphate for 5′-end-dependent degradation. Recent studies surprisingly revealed an expanded repertoire of chemical groups on 5′-ends of bacterial RNAs. In addition to mono- and triphosphorylated moieties, some mRNAs and sRNAs contain cap-like structures and diphosphates on their 5′-ends. Although incorporation and removal of these groups have become better understood in recent years, the physiological significance of these modification remain obscure. This review highlights recent studies aimed at identification and elucidation of novel modifications on the 5′ ends of bacterial RNAs and discusses possible physiological applications of the modified RNAs.

Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

“…In contrast to a m 7 G cap, which is added to nascent RNA by a capping complex that associates with eukaryotic RNA polymerase II (RNAP II) (Ghosh and Lima, 2010; Martinez-Rucobo et al, 2015; Shuman, 1995; Shuman, 2001; Shuman, 2015), an NAD cap is added by RNAP itself during transcription initiation, by serving as a non-canonical initiating nucleotide (NCIN) (Bird et al, 2016) (reviewed in Barvík et al, 2017; Julius et al, 2018; Vasilyev et al, 2018). NCIN-mediated NAD capping has been demonstrated for bacterial RNAP (Bird et al, 2016; Frindert et al, 2018; Julius and Yuzenkova, 2017; Vvedenskaya et al, 2018) and eukaryotic RNAP II (Bird et al, 2016).…”

Recent insights into noncanonical 5′ capping and decapping of RNA

“…The dinucleotide polyphosphate caps were identified in bacteria ( 16 , 17 , 18 , 19 ). Dinucleotide polyphosphates (Np n Ns) were initially discovered as reaction intermediates of aminoacyl-tRNA synthetase–catalyzed reactions in vitro ( 20 ).…”

“…RppH plays a critical role in the 5′-dependent turnover of RNAs in bacteria, where its PPH activity converts 5′-triphosphate RNAs (pppRNAs) to pRNAs for subsequent decay by RNaseE ( 17 , 58 ). E. coli RppH removes a pyrophosphate from pppRNA to produce pRNA ( Fig.…”

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

“…The extent of NC capping and cellular roles of capped RNAs are still unclear A number of potential physiological roles of NC capping are suggested in two recent reviews, including RNA folding and stability, cellular localization, etc. [85,87]. Yet only a few actual examples are published, e.g.…”