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 a Richard ŠTEFL

Základní údaje

Originální název

Structure and semi-sequence-specific RNA binding of Nrd1

Autoři

BAČÍKOVÁ, Veronika (203 Česká republika, domácí), Josef PASULKA (203 Česká republika, domácí), Karel KUBÍČEK (203 Česká republika, domácí) a Richard ŠTEFL (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.112

Kód RIV

RIV/00216224:14740/14:00073612

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000339713200044

Klíčová slova anglicky

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

Štítky

kontrola MP, MP, OA, rivok, SCOPUS

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 12. 2014 10:24, Martina Prášilová

Anotace

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

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0042, projekt VaV

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

EE2.3.30.0037, projekt VaV

Název: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

GBP305/12/G034, projekt VaV

Název: Centrum biologie RNA

Přiložené soubory

NAR_2014_42_8024.pdf

Požádat o autorskou verzi souboru

Citovat

BAČÍKOVÁ, Veronika, Josef PASULKA, Karel KUBÍČEK a Richard ŠTEFL. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Research. United Kingdom: Oxford University Press, 2014, roč. 42, č. 12, s. 8024-8038. ISSN 0305-1048. Dostupné z: 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 a Richard ŠTEFL. Structure and semi-sequence-specific RNA binding of Nrd1. \textit{Nucleic Acids Research}. United Kingdom: Oxford University Press, 2014, roč.~42, č.~12, s.~8024-8038. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku446.

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