How the initiating ribosome copes with ppGpp to translate mRNAs
Vinogradova, Daria S ; Zegarra, Victor ; Maksimova, Elena ; Nakamoto, Jose Alberto LU
; Kasatsky, Pavel
; Paleskava, Alena
; Konevega, Andrey L
and Milón, Pohl
(2020)
In PLoS Biology
18(1).
p.1-25
- Abstract
During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the initiating ribosome senses the cellular pool of guanosine nucleotides and regulates the progression towards protein synthesis. Our results show that the affinity of guanosine triphosphate (GTP) and the inhibitory concentration of ppGpp for the 30S-bound initiation factor IF2 vary depending on the programmed mRNA. The TufA mRNA enhanced GTP affinity for 30S complexes, resulting in improved ppGpp tolerance and allowing efficient protein synthesis. Conversely, the InfA mRNA allowed ppGpp to compete with GTP for IF2, thus stalling 30S complexes. Structural modeling... (More)
During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the initiating ribosome senses the cellular pool of guanosine nucleotides and regulates the progression towards protein synthesis. Our results show that the affinity of guanosine triphosphate (GTP) and the inhibitory concentration of ppGpp for the 30S-bound initiation factor IF2 vary depending on the programmed mRNA. The TufA mRNA enhanced GTP affinity for 30S complexes, resulting in improved ppGpp tolerance and allowing efficient protein synthesis. Conversely, the InfA mRNA allowed ppGpp to compete with GTP for IF2, thus stalling 30S complexes. Structural modeling and biochemical analysis of the TufA mRNA unveiled a structured enhancer of translation initiation (SETI) composed of two consecutive hairpins proximal to the translation initiation region (TIR) that largely account for ppGpp tolerance under physiological concentrations of guanosine nucleotides. Furthermore, our results show that the mechanism enhancing ppGpp tolerance is not restricted to the TufA mRNA, as similar ppGpp tolerance was found for the SETI-containing Rnr mRNA. Finally, we show that IF2 can use pppGpp to promote the formation of 30S initiation complexes (ICs), albeit requiring higher factor concentration and resulting in slower transitions to translation elongation. Altogether, our data unveil a novel regulatory mechanism at the onset of protein synthesis that tolerates physiological concentrations of ppGpp and that bacteria can exploit to modulate their proteome as a function of the nutritional shift happening during stringent response and infection.
(Less)
- author
- Vinogradova, Daria S
; Zegarra, Victor
; Maksimova, Elena
; Nakamoto, Jose Alberto
LU
; Kasatsky, Pavel
; Paleskava, Alena
; Konevega, Andrey L
and Milón, Pohl
- publishing date
- 2020
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Binding, Competitive, Escherichia coli/genetics, Escherichia coli Proteins/metabolism, Guanosine Tetraphosphate/metabolism, Guanosine Triphosphate/metabolism, Host-Pathogen Interactions/physiology, Kinetics, Nucleic Acid Conformation, Peptide Chain Initiation, Translational/drug effects, Peptide Elongation Factor Tu/metabolism, Protein Biosynthesis/drug effects, RNA, Messenger/chemistry, Ribosomes/drug effects
- in
- PLoS Biology
- volume
- 18
- issue
- 1
- article number
- e3000593
- pages
- 1 - 25
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- scopus:85078947441
- pmid:31995552
- ISSN
- 1545-7885
- DOI
- 10.1371/journal.pbio.3000593
- language
- English
- LU publication?
- no
- id
- 2f88ef9e-ac24-450c-9c1e-0b3c415f3ed9
- date added to LUP
- 2022-10-13 10:35:35
- date last changed
- 2024-04-18 15:43:31
@article{2f88ef9e-ac24-450c-9c1e-0b3c415f3ed9,
abstract = {{<p>During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the initiating ribosome senses the cellular pool of guanosine nucleotides and regulates the progression towards protein synthesis. Our results show that the affinity of guanosine triphosphate (GTP) and the inhibitory concentration of ppGpp for the 30S-bound initiation factor IF2 vary depending on the programmed mRNA. The TufA mRNA enhanced GTP affinity for 30S complexes, resulting in improved ppGpp tolerance and allowing efficient protein synthesis. Conversely, the InfA mRNA allowed ppGpp to compete with GTP for IF2, thus stalling 30S complexes. Structural modeling and biochemical analysis of the TufA mRNA unveiled a structured enhancer of translation initiation (SETI) composed of two consecutive hairpins proximal to the translation initiation region (TIR) that largely account for ppGpp tolerance under physiological concentrations of guanosine nucleotides. Furthermore, our results show that the mechanism enhancing ppGpp tolerance is not restricted to the TufA mRNA, as similar ppGpp tolerance was found for the SETI-containing Rnr mRNA. Finally, we show that IF2 can use pppGpp to promote the formation of 30S initiation complexes (ICs), albeit requiring higher factor concentration and resulting in slower transitions to translation elongation. Altogether, our data unveil a novel regulatory mechanism at the onset of protein synthesis that tolerates physiological concentrations of ppGpp and that bacteria can exploit to modulate their proteome as a function of the nutritional shift happening during stringent response and infection.</p>}},
author = {{Vinogradova, Daria S and Zegarra, Victor and Maksimova, Elena and Nakamoto, Jose Alberto and Kasatsky, Pavel and Paleskava, Alena and Konevega, Andrey L and Milón, Pohl}},
issn = {{1545-7885}},
keywords = {{Binding, Competitive; Escherichia coli/genetics; Escherichia coli Proteins/metabolism; Guanosine Tetraphosphate/metabolism; Guanosine Triphosphate/metabolism; Host-Pathogen Interactions/physiology; Kinetics; Nucleic Acid Conformation; Peptide Chain Initiation, Translational/drug effects; Peptide Elongation Factor Tu/metabolism; Protein Biosynthesis/drug effects; RNA, Messenger/chemistry; Ribosomes/drug effects}},
language = {{eng}},
number = {{1}},
pages = {{1--25}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS Biology}},
title = {{How the initiating ribosome copes with ppGpp to translate mRNAs}},
url = {{http://dx.doi.org/10.1371/journal.pbio.3000593}},
doi = {{10.1371/journal.pbio.3000593}},
volume = {{18}},
year = {{2020}},
}