NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs

  title={NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs},
  author={Hana Cahov{\'a} and Marie-Luise Winz and Katharina H{\"o}fer and Gabriele N{\"u}bel and Andres J{\"a}schke},
A distinctive feature of prokaryotic gene expression is the absence of 5′-capped RNA. In eukaryotes, 5′,5′-triphosphate-linked 7-methylguanosine protects messenger RNA from degradation and modulates maturation, localization and translation. Recently, the cofactor nicotinamide adenine dinucleotide (NAD) was reported as a covalent modification of bacterial RNA. Given the central role of NAD in redox biochemistry, posttranslational protein modification and signalling, its attachment to RNA… 

Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

This work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

A Novel NAD-RNA Decapping Pathway Discovered by Synthetic Light-Up NAD-RNAs

FurNAD-RNAs are introduced as a new research tool for the identification and characterization of novel NAD-RNA decapping enzymes and it is discovered that the eukaryotic glycohydrolase CD38 processes NAD-capped RNA in vitro into ADP-ribose-modified-RNA and nicotinamide and therefore might act as a decapping enzyme in vivo.

NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in Arabidopsis

The development of the method NAD tagSeq for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs) and for revealing the complete sequences of NAD- RNAs using single-molecule RNA sequencing is reported.

Use of NAD tagSeq II to identify growth phase-dependent alterations in E. coli RNA NAD+ capping

Significance Some RNAs in both prokaryotes and eukaryotes were recently found to contain the NAD+ cap, indicating a novel mechanism in gene regulation through noncanonical RNA capping.

Identification of NAD+ capped mRNAs in Saccharomyces cerevisiae

It is demonstrated that 5′ NAD-RNA is found on subsets of nuclear and mitochondrial encoded mRNAs in Saccharomyces cerevisiae, and the presence of an alternative cap structure on mRNA 5′ ends suggests a possible unanticipated level of regulation due to this modification.

Extensive 5’-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

In budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

Identification of NAD-RNAs and ADPR-RNA decapping in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii

This study reports the first characterization of 5’-terminally modified RNA molecules in Archaea and establishes that NAD-RNA modifications, previously only identified in the other two domains of life, are also prevalent in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii.

NAD+ capping of RNA in Archaea and Mycobacteria

It is demonstrated that NAD+ capping exists in the archaeal domain of life, suggesting that it is universal to all living organisms, and the NAD+-capped RNA landscape in mycobacteria is defined, providing a basis for its future exploration.

Noncanonical RNA‐capping: Discovery, mechanism, and physiological role debate

It was demonstrated to affect RNA stability in vivo in bacteria and eukaryotes and to stimulate RNAP promoter escape in vitro in Escherichia coli, and to connect transcription to cellular redox state.



Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases.

The biogenesis of 6S RNA is characterized, revealing that there are two different precursors, a long and a short molecule, which are transcribed from the distal P2 and proximal P1 promoter, respectively, and indicating that the switching of the utilization of both sigma factors and endoribonucleases in the biogenesis is essential in modulating its levels in E.coli.

Efficient incorporation of CoA, NAD and FAD into RNA by in vitro transcription.

  • F. Huang
  • Biology, Chemistry
    Nucleic acids research
  • 2003
A general in vitro transcription procedure has been developed to efficiently prepare RNA with coenzymes CoA, NAD and Fad covalently attached to the 5' end, which provides easy access to CoA-, NAD- and FAD-RNA, which may find broad applications in generating coenzyme- utilizing ribozymes.

Ribonuclease E is a 5′-end-dependent endonuclease

Results show that RNase E has inherent vectorial properties, with its activity depending on the 5′ end of its substrates; this can account for the direction of mRNA decay in E. coli, the phenomenon of ‘all or none’ mRNA decay, and the stabilization provided by 5′ stem–loop structures.

Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA.

The molecular basis for the regulated turnover of GlmZ is revealed, identifying RapZ (RNase adaptor protein for sRNA Glm Z; formerly YhbJ) as a novel type of RNA-binding protein that recruits the major endoribonuclease RNase E to Glmz.

The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

This work shows that the E. coli protein RppH (formerly NudH/YgdP) is the RNA pyrophosphohydrolase that initiates mRNA decay by this 5′-end-dependent pathway and suggests a possible basis for the effect of RPPH and its orthologues on the invasiveness of bacterial pathogens.

Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

A cloning-based screen focused on RNAs of 30–65 nt detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements, and a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5′ or 3′ ends of the mRNAs with perfect complementarity.

Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation

The study reveals hierarchical action of two well-conserved sRNAs in a complex regulatory cascade that controls the glmS mRNA, the first example, to the authors' knowledge, of mRNA expression being controlled by the poly(A) status of a chromosomally encoded sRNA.

The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli

The results suggest that DsrA RNA may enhance the virulence of pathogenic E. coli by playing a regulatory role in acid resistance.

The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior

ABSTRACT Small noncoding regulatory RNAs (sRNAs) play a key role in regulating the expression of many genes in Escherichia coli and other bacteria. Many of the sRNAs identified in E. coli bind to

A DEAD-box RNA helicase in the Escherichia coli RNA degradosome

It is suggested that RhlB acts by unwinding RNA structures that impede the processive activity of PNPase, and is thus an important enzyme in mRNA turnover.