Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA

Kudrin, Pavel ; Dzhygyr, Ievgen ; Ishiguro, Kensuke ; Beljantseva, Jelena ; Maksimova, Elena ; Oliveira, Sofia Raquel Alves ; Varik, Vallo ; Payoe, Roshani ; Konevega, Andrey L. and Tenson, Tanel , et al. (2018) In Nucleic Acids Research 46(4). p.1973-1983
Abstract

During amino acid starvation the Escherichia coli stringent response factor RelA recognizes deacylated tRNA in the ribosomal A-site. This interaction activates RelA-mediated synthesis of alarmone nucleotides pppGpp and ppGpp, collectively referred to as (p)ppGpp. These two alarmones are synthesized by addition of a pyrophosphate moiety to the 3 position of the abundant cellular nucleotide GTP and less abundant nucleotide GDP, respectively. Using untagged native RelA we show that allosteric activation of RelA by pppGpp increases the efficiency of GDP conversion to achieve the maximum rate of (p)ppGpp production. Using a panel of ribosomal RNA mutants, we show that the A-site finger structural element of 23S rRNA helix 38 is crucial for... (More)

During amino acid starvation the Escherichia coli stringent response factor RelA recognizes deacylated tRNA in the ribosomal A-site. This interaction activates RelA-mediated synthesis of alarmone nucleotides pppGpp and ppGpp, collectively referred to as (p)ppGpp. These two alarmones are synthesized by addition of a pyrophosphate moiety to the 3 position of the abundant cellular nucleotide GTP and less abundant nucleotide GDP, respectively. Using untagged native RelA we show that allosteric activation of RelA by pppGpp increases the efficiency of GDP conversion to achieve the maximum rate of (p)ppGpp production. Using a panel of ribosomal RNA mutants, we show that the A-site finger structural element of 23S rRNA helix 38 is crucial for RelA binding to the ribosome and consequent activation, and deletion of the element severely compromises (p)ppGpp accumulation in E. coli upon amino acid starvation. Through binding assays and enzymology, we show that E. coli RelA does not form a stable complex with, and is not activated by, deacylated tRNA off the ribosome. This indicates that in the cell, RelA first binds the empty A-site and then recruits tRNA rather than first binding tRNA and then binding the ribosome.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; and (Less)
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
46
issue
4
pages
1973 - 1983
publisher
Oxford University Press
external identifiers
  • pmid:29390134
  • scopus:85043232434
ISSN
0305-1048
DOI
10.1093/nar/gky023
language
English
LU publication?
no
additional info
Funding Information: Estonian Research Council [IUT2-22 to T.T.]; European Regional Development Fund through the Centre of Excellence in Molecular Cell Engineering (to V.H. and T.T.); Swedish Research council (Vetenskapsrådet) [2013-4680 to V.H.]; Ragnar Söderberg foundation (Ragnar Söderberg Fellow in Medicine 2014 to V.H.); Russian Science Foundation Grant [17-14-01416 to A.L.K.]. Funding for open access charge: Ragnar Söderbergs stiftelse grant (to V.H.). Conflict of interest statement. None declared. Publisher Copyright: © 2017 The Author(s). Copyright: Copyright 2018 Elsevier B.V., All rights reserved.
id
317a8e03-6bf3-420d-bbd3-ad90ff780c3a
date added to LUP
2021-09-24 20:37:17
date last changed
2024-06-15 17:17:45
@article{317a8e03-6bf3-420d-bbd3-ad90ff780c3a,
  abstract     = {{<p>During amino acid starvation the Escherichia coli stringent response factor RelA recognizes deacylated tRNA in the ribosomal A-site. This interaction activates RelA-mediated synthesis of alarmone nucleotides pppGpp and ppGpp, collectively referred to as (p)ppGpp. These two alarmones are synthesized by addition of a pyrophosphate moiety to the 3 position of the abundant cellular nucleotide GTP and less abundant nucleotide GDP, respectively. Using untagged native RelA we show that allosteric activation of RelA by pppGpp increases the efficiency of GDP conversion to achieve the maximum rate of (p)ppGpp production. Using a panel of ribosomal RNA mutants, we show that the A-site finger structural element of 23S rRNA helix 38 is crucial for RelA binding to the ribosome and consequent activation, and deletion of the element severely compromises (p)ppGpp accumulation in E. coli upon amino acid starvation. Through binding assays and enzymology, we show that E. coli RelA does not form a stable complex with, and is not activated by, deacylated tRNA off the ribosome. This indicates that in the cell, RelA first binds the empty A-site and then recruits tRNA rather than first binding tRNA and then binding the ribosome.</p>}},
  author       = {{Kudrin, Pavel and Dzhygyr, Ievgen and Ishiguro, Kensuke and Beljantseva, Jelena and Maksimova, Elena and Oliveira, Sofia Raquel Alves and Varik, Vallo and Payoe, Roshani and Konevega, Andrey L. and Tenson, Tanel and Suzuki, Tsutomu and Hauryliuk, Vasili}},
  issn         = {{0305-1048}},
  language     = {{eng}},
  month        = {{02}},
  number       = {{4}},
  pages        = {{1973--1983}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA}},
  url          = {{http://dx.doi.org/10.1093/nar/gky023}},
  doi          = {{10.1093/nar/gky023}},
  volume       = {{46}},
  year         = {{2018}},
}