Cargando…

Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry

RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq’s integrity and RNA binding has been challenging to study...

Descripción completa

Detalles Bibliográficos
Autores principales: Sarni, Samantha H., Roca, Jorjethe, Du, Chen, Jia, Mengxuan, Li, Hantian, Damjanovic, Ana, Małecka, Ewelina M., Wysocki, Vicki H., Woodson, Sarah A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704730/
https://www.ncbi.nlm.nih.gov/pubmed/36375072
http://dx.doi.org/10.1073/pnas.2208780119
_version_ 1784840118557736960
author Sarni, Samantha H.
Roca, Jorjethe
Du, Chen
Jia, Mengxuan
Li, Hantian
Damjanovic, Ana
Małecka, Ewelina M.
Wysocki, Vicki H.
Woodson, Sarah A.
author_facet Sarni, Samantha H.
Roca, Jorjethe
Du, Chen
Jia, Mengxuan
Li, Hantian
Damjanovic, Ana
Małecka, Ewelina M.
Wysocki, Vicki H.
Woodson, Sarah A.
author_sort Sarni, Samantha H.
collection PubMed
description RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq’s integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry coupled with surface-induced dissociation and molecular dynamics simulations to disentangle the arrangement of the CTDs and their impact on the stability of Escherichia coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding.
format Online
Article
Text
id pubmed-9704730
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher National Academy of Sciences
record_format MEDLINE/PubMed
spelling pubmed-97047302022-11-29 Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry Sarni, Samantha H. Roca, Jorjethe Du, Chen Jia, Mengxuan Li, Hantian Damjanovic, Ana Małecka, Ewelina M. Wysocki, Vicki H. Woodson, Sarah A. Proc Natl Acad Sci U S A Biological Sciences RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq’s integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry coupled with surface-induced dissociation and molecular dynamics simulations to disentangle the arrangement of the CTDs and their impact on the stability of Escherichia coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding. National Academy of Sciences 2022-11-14 2022-11-22 /pmc/articles/PMC9704730/ /pubmed/36375072 http://dx.doi.org/10.1073/pnas.2208780119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Sarni, Samantha H.
Roca, Jorjethe
Du, Chen
Jia, Mengxuan
Li, Hantian
Damjanovic, Ana
Małecka, Ewelina M.
Wysocki, Vicki H.
Woodson, Sarah A.
Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title_full Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title_fullStr Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title_full_unstemmed Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title_short Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
title_sort intrinsically disordered interaction network in an rna chaperone revealed by native mass spectrometry
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704730/
https://www.ncbi.nlm.nih.gov/pubmed/36375072
http://dx.doi.org/10.1073/pnas.2208780119
work_keys_str_mv AT sarnisamanthah intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT rocajorjethe intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT duchen intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT jiamengxuan intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT lihantian intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT damjanovicana intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT małeckaewelinam intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT wysockivickih intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry
AT woodsonsaraha intrinsicallydisorderedinteractionnetworkinanrnachaperonerevealedbynativemassspectrometry