The role of RNA structure in translational regulation by L7Ae protein in archaea

Lin Huang, Saira Ashraf, David M. J. Lilley (Lead / Corresponding author)

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Abstract

A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5′′-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem–loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem–loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.

Original languageEnglish
Pages (from-to)60-69
Number of pages10
JournalRNA: a Publication of the RNA Society
Volume25
Issue number1
Early online date16 Oct 2018
DOIs
Publication statusPublished - Jan 2019

Fingerprint

Archaea
Archaeoglobus fulgidus
RNA
Untranslated Regions
Proteins
Nucleic Acid Conformation
Ribosomes
Sequence Analysis
Carrier Proteins
Binding Sites
X-Rays
Messenger RNA
Genes

Keywords

  • Gene regulation
  • Kink-turn
  • RNA structure
  • X-ray crystallography

Cite this

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title = "The role of RNA structure in translational regulation by L7Ae protein in archaea",
abstract = "A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5′′-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem–loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem–loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.",
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author = "Lin Huang and Saira Ashraf and Lilley, {David M. J.}",
note = "We thank Dr Timothy Wilson for discussion, and Cancer Research UK for financial support (program grant A18604).",
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AU - Huang, Lin

AU - Ashraf, Saira

AU - Lilley, David M. J.

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PY - 2019/1

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N2 - A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5′′-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem–loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem–loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.

AB - A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5′′-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem–loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem–loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.

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