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Title: The mechanism of RNA 5' capping with NAD +, NADH and desphospho-CoA

Abstract

The chemical nature of the 5' end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. Recently it has been shown that some bacterial RNA species carry a 5'-end structure reminiscent of the 5' 7-methylguanylate ‘cap’ in eukaryotic RNA. In particular, RNA species containing a 5'-end nicotinamide adenine dinucleotide (NAD+) or 3'-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Ourmore » results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1274761
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature (London); Journal Volume: 535; Journal Issue: 7612
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bird, Jeremy G., Zhang, Yu, Tian, Yuan, Panova, Natalya, Barvík, Ivan, Greene, Landon, Liu, Min, Buckley, Brian, Krásný, Libor, Lee, Jeehiun K., Kaplan, Craig D., Ebright, Richard H., and Nickels, Bryce E. The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA. United States: N. p., 2016. Web. doi:10.1038/nature18622.
Bird, Jeremy G., Zhang, Yu, Tian, Yuan, Panova, Natalya, Barvík, Ivan, Greene, Landon, Liu, Min, Buckley, Brian, Krásný, Libor, Lee, Jeehiun K., Kaplan, Craig D., Ebright, Richard H., & Nickels, Bryce E. The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA. United States. doi:10.1038/nature18622.
Bird, Jeremy G., Zhang, Yu, Tian, Yuan, Panova, Natalya, Barvík, Ivan, Greene, Landon, Liu, Min, Buckley, Brian, Krásný, Libor, Lee, Jeehiun K., Kaplan, Craig D., Ebright, Richard H., and Nickels, Bryce E. Wed . "The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA". United States. doi:10.1038/nature18622.
@article{osti_1274761,
title = {The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA},
author = {Bird, Jeremy G. and Zhang, Yu and Tian, Yuan and Panova, Natalya and Barvík, Ivan and Greene, Landon and Liu, Min and Buckley, Brian and Krásný, Libor and Lee, Jeehiun K. and Kaplan, Craig D. and Ebright, Richard H. and Nickels, Bryce E.},
abstractNote = {The chemical nature of the 5' end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. Recently it has been shown that some bacterial RNA species carry a 5'-end structure reminiscent of the 5' 7-methylguanylate ‘cap’ in eukaryotic RNA. In particular, RNA species containing a 5'-end nicotinamide adenine dinucleotide (NAD+) or 3'-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms.},
doi = {10.1038/nature18622},
journal = {Nature (London)},
number = 7612,
volume = 535,
place = {United States},
year = {Wed Jul 06 00:00:00 EDT 2016},
month = {Wed Jul 06 00:00:00 EDT 2016}
}