Sequence determinants of the folding properties of box C/D kink-turns in RNA

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

Research output: Contribution to journalArticle

3 Citations (Scopus)
92 Downloads (Pure)

Abstract

Folding properties differ markedly between kink-turns (k-turns) that have different biological function. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. By contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.
Original languageEnglish
Pages (from-to)1927-1935
Number of pages9
JournalRNA: a Publication of the RNA Society
Volume23
Issue number12
Early online date27 Sep 2017
DOIs
Publication statusPublished - Dec 2017

Fingerprint

Small Nucleolar Ribonucleoproteins
Riboswitch
Metals
RNA
Ions
Fluorescence Resonance Energy Transfer
Archaea
Computational Biology
Electrophoresis
Carrier Proteins
Gels
Proteins

Keywords

  • RNA structure
  • snoRNP
  • k-turns
  • metal ions
  • L7Ae

Cite this

@article{a67e0286a85a47a7ad1ca2ec3fcae1eb,
title = "Sequence determinants of the folding properties of box C/D kink-turns in RNA",
abstract = "Folding properties differ markedly between kink-turns (k-turns) that have different biological function. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. By contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.",
keywords = "RNA structure, snoRNP, k-turns, metal ions, L7Ae",
author = "Saira Ashraf and Lin Huang and Lilley, {David M. J.}",
note = "Funding: Cancer Research UK for financial support (program grant A18604).",
year = "2017",
month = "12",
doi = "10.1261/rna.063453.117",
language = "English",
volume = "23",
pages = "1927--1935",
journal = "RNA: a Publication of the RNA Society",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "12",

}

TY - JOUR

T1 - Sequence determinants of the folding properties of box C/D kink-turns in RNA

AU - Ashraf, Saira

AU - Huang, Lin

AU - Lilley, David M. J.

N1 - Funding: Cancer Research UK for financial support (program grant A18604).

PY - 2017/12

Y1 - 2017/12

N2 - Folding properties differ markedly between kink-turns (k-turns) that have different biological function. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. By contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.

AB - Folding properties differ markedly between kink-turns (k-turns) that have different biological function. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. By contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.

KW - RNA structure

KW - snoRNP

KW - k-turns

KW - metal ions

KW - L7Ae

U2 - 10.1261/rna.063453.117

DO - 10.1261/rna.063453.117

M3 - Article

C2 - 28956757

VL - 23

SP - 1927

EP - 1935

JO - RNA: a Publication of the RNA Society

JF - RNA: a Publication of the RNA Society

SN - 1355-8382

IS - 12

ER -