TY - JOUR
T1 - Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF
AU - Gao, Ang
AU - Vasilyev, Nikita
AU - Luciano, Daniel J.
AU - Levenson-Palmer, Rose
AU - Richards, Jamie
AU - Marsiglia, William M.
AU - Traaseth, Nathaniel J.
AU - Belasco, Joel G.
AU - Serganov, Alexander
N1 - Funding Information:
This work used funds from National Institutes of Health (NIH) [R01GM112940 to A.S., R01GM035769 to J.G.B., R01AI108889 to N.J.T., F99CA212474 to W.M.M.]; the Northeastern Collaborative Access Team beamlines are funded by NIH [P41 GM103403, S10 RR029205] and resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory [DE-AC02-06CH11357]; beamline 17-ID-2 is supported in part by the DOE Office of Biological and Environmental Research [KP1605010, KC0401040] and NIH [P41GM111244]; NSLS-II is supported in part by the DOE, the Office of Science, and the Office of Basic Energy Sciences Program [DE-SC0012704]. Funding for open access charge: NIH [R01GM112940]. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2018/7/27
Y1 - 2018/7/27
N2 - Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5 termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5-end-dependent mRNA degradation begins with the generation of monophosphorylated 5 termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes.
AB - Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5 termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5-end-dependent mRNA degradation begins with the generation of monophosphorylated 5 termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes.
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U2 - 10.1093/nar/gky327
DO - 10.1093/nar/gky327
M3 - Article
C2 - 29733359
AN - SCOPUS:85054188647
VL - 46
SP - 6841
EP - 6856
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 13
ER -