Structure and semi-sequence-specific RNA binding of Nrd1

J 2014

Structure and semi-sequence-specific RNA binding of Nrd1

BAČÍKOVÁ, Veronika, Josef PASULKA, Karel KUBÍČEK and Richard ŠTEFL

Basic information

Original name

Structure and semi-sequence-specific RNA binding of Nrd1

Authors

BAČÍKOVÁ, Veronika (203 Czech Republic, belonging to the institution), Josef PASULKA (203 Czech Republic, belonging to the institution), Karel KUBÍČEK (203 Czech Republic, belonging to the institution) and Richard ŠTEFL (203 Czech Republic, guarantor, belonging to the institution)

Edition

Nucleic Acids Research, United Kingdom, Oxford University Press, 2014, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.112

RIV identification code

RIV/00216224:14740/14:00073612

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gku446

UT WoS

000339713200044

Keywords in English

protein Nrd1; RNA; untranslated RNA; fluorescence analysis; RNA processing; transcription termination; RNA surveillance; RNA recognition motif

Abstract

V originále

In Saccharomyces cerevisiae, the Nrd1-dependent termination and processing pathways play an important role in surveillance and processing of non-coding ribonucleic acids (RNAs). The termination and subsequent processing is dependent on the Nrd1 complex consisting of two RNA-binding proteins Nrd1 and Nab3 and Sen1 helicase. It is established that Nrd1 and Nab3 cooperatively recognize specific termination elements within nascent RNA, GUA[A/G] and UCUU[G], respectively. Interestingly, some transcripts do not require GUA[A/G] motif for transcription termination in vivo and binding in vitro, suggesting the existence of alternative Nrd1-binding motifs. Here we studied the structure and RNA-binding properties of Nrd1 using nuclear magnetic resonance (NMR), fluorescence anisotropy and phenotypic analyses in vivo. We determined the solution structure of a two-domain RNA-binding fragment of Nrd1, formed by an RNA-recognition motif and helix-loop bundle. NMR and fluorescence data show that not only GUA[A/G] but also several other G-rich and AU-rich motifs are able to bind Nrd1 with affinity in a low micromolar range. The broad substrate specificity is achieved by adaptable interaction surfaces of the RNA-recognition motif and helix-loop bundle domains that sandwich the RNA substrates. Our findings have implication for the role of Nrd1 in termination and processing of many non-coding RNAs arising from bidirectional pervasive transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

EE2.3.20.0042, research and development project

Name: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu

EE2.3.30.0037, research and development project

Name: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

GBP305/12/G034, research and development project

Name: Centrum biologie RNA

Files attached

NAR_2014_42_8024.pdf

Request the author's version of the file

Citovat

BAČÍKOVÁ, Veronika, Josef PASULKA, Karel KUBÍČEK and Richard ŠTEFL. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Research. United Kingdom: Oxford University Press, 2014, vol. 42, No 12, p. 8024-8038. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku446.

@article{1182096,
   author = {Bačíková, Veronika and Pasulka, Josef and Kubíček, Karel and Štefl, Richard},
   article_location = {United Kingdom},
   article_number = {12},
   doi = {http://dx.doi.org/10.1093/nar/gku446},
   keywords = {protein Nrd1; RNA; untranslated RNA; fluorescence analysis; RNA processing; transcription termination; RNA surveillance; RNA recognition motif},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Structure and semi-sequence-specific RNA binding of Nrd1},
   url = {http://nar.oxfordjournals.org/content/early/2014/05/23/nar.gku446.long},
   volume = {42},
   year = {2014}
}

TY  - JOUR
ID  - 1182096
AU  - Bačíková, Veronika - Pasulka, Josef - Kubíček, Karel - Štefl, Richard
PY  - 2014
TI  - Structure and semi-sequence-specific RNA binding of Nrd1
JF  - Nucleic Acids Research
VL  - 42
IS  - 12
SP  - 8024-8038
EP  - 8024-8038
PB  - Oxford University Press
SN  - 03051048
KW  - protein Nrd1
KW  - RNA
KW  - untranslated RNA
KW  - fluorescence analysis
KW  - RNA processing
KW  - transcription termination
KW  - RNA surveillance
KW  - RNA recognition motif
UR  - http://nar.oxfordjournals.org/content/early/2014/05/23/nar.gku446.long
L2  - http://nar.oxfordjournals.org/content/early/2014/05/23/nar.gku446.long
N2  - In Saccharomyces cerevisiae, the Nrd1-dependent termination and processing pathways play an important role in surveillance and processing of non-coding ribonucleic acids (RNAs). The termination and subsequent processing is dependent on the Nrd1 complex consisting of two RNA-binding proteins Nrd1 and Nab3 and Sen1 helicase. It is established that Nrd1 and Nab3 cooperatively recognize specific termination elements within nascent RNA, GUA[A/G] and UCUU[G], respectively. Interestingly, some transcripts do not require GUA[A/G] motif for transcription termination in vivo and binding in vitro, suggesting the existence of alternative Nrd1-binding motifs. Here we studied the structure and RNA-binding properties of Nrd1 using nuclear magnetic resonance (NMR), fluorescence anisotropy and phenotypic analyses in vivo. We determined the solution structure of a two-domain RNA-binding fragment of Nrd1, formed by an RNA-recognition motif and helix-loop bundle. NMR and fluorescence data show that not only GUA[A/G] but also several other G-rich and AU-rich motifs are able to bind Nrd1 with affinity in a low micromolar range. The broad substrate specificity is achieved by adaptable interaction surfaces of the RNA-recognition motif and helix-loop bundle domains that sandwich the RNA substrates. Our findings have implication for the role of Nrd1 in termination and processing of many non-coding RNAs arising from bidirectional pervasive transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research
ER  -

BAČÍKOVÁ, Veronika, Josef PASULKA, Karel KUBÍČEK and Richard ŠTEFL. Structure and semi-sequence-specific RNA binding of Nrd1. \textit{Nucleic Acids Research}. United Kingdom: Oxford University Press, 2014, vol.~42, No~12, p.~8024-8038. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gku446.

Detailed Information on Publication Record