Staufen1 reads out structure and sequence features in ARF1
dsRNA for target recognition

J 2020

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition

YADAV, Deepak Kumar, Dagmar ZIGÁČKOVÁ, Maria ZLOBINA, Tomáš KLUMPLER, Christelle BEAUMONT et. al.

Basic information

Original name

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition

Authors

YADAV, Deepak Kumar (356 India, belonging to the institution), Dagmar ZIGÁČKOVÁ (203 Czech Republic, belonging to the institution), Maria ZLOBINA (643 Russian Federation, belonging to the institution), Tomáš KLUMPLER (203 Czech Republic, belonging to the institution), Christelle BEAUMONT (250 France, belonging to the institution), Monika KUBÍČKOVÁ (203 Czech Republic, belonging to the institution), Štěpánka VAŇÁČOVÁ (203 Czech Republic, guarantor, belonging to the institution) and Peter LUKAVSKY (40 Austria, belonging to the institution)

Edition

Nucleic acids research, Oxford, Oxford University Press, 2020, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

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: 16.971

RIV identification code

RIV/00216224:14740/20:00114622

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkz1163

UT WoS

000525957000038

Keywords in English

DOUBLE-STRANDED-RNA; NMR STRUCTURE DETERMINATION; LARGE-SCALE PREPARATION; BICOID MESSENGER-RNA; SECONDARY STRUCTURES; BINDING PROTEIN; DOMAIN; PURIFICATION; NOESY; LOCALIZATION

Abstract

V originále

Staufen1 (STAU1) is a dsRNA binding protein mediating mRNA transport and localization, translational control and STAU1-mediated mRNA decay (SMD). The STAU1 binding site (SBS) within human ADP-ribosylation factorl (ARF1) 3'UTR binds STAU1 and this downregulates ARF1 cytoplasmic mRNA levels by SMD. However, how STAU1 recognizes specific mRNA targets is still under debate. Our structure of the ARF1 SBS-STAU1 complex uncovers target recognition by STAU1. STAU1 dsRNA binding domain (dsRBD) 4 interacts with two pyrimidines and one purine from the minor groove side via helix alpha 1, the beta 1-beta 2 loop anchors the dsRBD at the end of the dsRNA and lysines in helix alpha 2 bind to the phosphodiester backbone from the major groove side. STAU1 dsRBD3 displays the same binding mode with specific recognition of one guanine base. Mutants disrupting minor groove recognition of ARF1 SBS affect in vitro binding and reduce SMD in vivo. Our data thus reveal how STAU1 recognizes minor groove features in dsRNA relevant for target selection.

Links

EE2.3.20.0042, research and development project

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

GA16-21341S, research and development project

Name: Studium úlohy uridylace RNA v lidských buňkách

Investor: Czech Science Foundation

GA18-08153S, research and development project

Name: Molekulární podstata Staufen zprostředkované funkce 3'UTR

Investor: Czech Science Foundation

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

286154, interní kód MU

Name: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Acronym: SYLICA)

Investor: European Union, Capacities

3014, interní kód MU

Name: Molecular basis of aberrant splicing of CFTR exon 9

Investor: EMBO (European Molecular Biology Organization)

630758, interní kód MU

Name: Aberrant Splicing of CFTR Exon 9 (Acronym: ASCE)

Investor: European Union, People

90043, large research infrastructures

Name: CIISB

Citovat

YADAV, Deepak Kumar, Dagmar ZIGÁČKOVÁ, Maria ZLOBINA, Tomáš KLUMPLER, Christelle BEAUMONT, Monika KUBÍČKOVÁ, Štěpánka VAŇÁČOVÁ and Peter LUKAVSKY. Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic acids research. Oxford: Oxford University Press, 2020, vol. 48, No 4, p. 2091-2106. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz1163.

@article{1720519,
   author = {Yadav, Deepak Kumar and Zigáčková, Dagmar and Zlobina, Maria and Klumpler, Tomáš and Beaumont, Christelle and Kubíčková, Monika and Vaňáčová, Štěpánka and Lukavsky, Peter},
   article_location = {Oxford},
   article_number = {4},
   doi = {http://dx.doi.org/10.1093/nar/gkz1163},
   keywords = {DOUBLE-STRANDED-RNA; NMR STRUCTURE DETERMINATION; LARGE-SCALE PREPARATION; BICOID MESSENGER-RNA; SECONDARY STRUCTURES; BINDING PROTEIN; DOMAIN; PURIFICATION; NOESY; LOCALIZATION},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition},
   url = {https://watermark.silverchair.com/gkz1163.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArMwggKvBgkqhkiG9w0BBwagggKgMIICnAIBADCCApUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM93m65EaHAul9lvZ3AgEQgIICZgl4kN1MOxCY84aEvwwQEi6vjxrtsNYzBuhYRTUjwbqxdd},
   volume = {48},
   year = {2020}
}

TY  - JOUR
ID  - 1720519
AU  - Yadav, Deepak Kumar - Zigáčková, Dagmar - Zlobina, Maria - Klumpler, Tomáš - Beaumont, Christelle - Kubíčková, Monika - Vaňáčová, Štěpánka - Lukavsky, Peter
PY  - 2020
TI  - Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition
JF  - Nucleic acids research
VL  - 48
IS  - 4
SP  - 2091-2106
EP  - 2091-2106
PB  - Oxford University Press
SN  - 03051048
KW  - DOUBLE-STRANDED-RNA
KW  - NMR STRUCTURE DETERMINATION
KW  - LARGE-SCALE PREPARATION
KW  - BICOID MESSENGER-RNA
KW  - SECONDARY STRUCTURES
KW  - BINDING PROTEIN
KW  - DOMAIN
KW  - PURIFICATION
KW  - NOESY
KW  - LOCALIZATION
UR  - https://watermark.silverchair.com/gkz1163.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArMwggKvBgkqhkiG9w0BBwagggKgMIICnAIBADCCApUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM93m65EaHAul9lvZ3AgEQgIICZgl4kN1MOxCY84aEvwwQEi6vjxrtsNYzBuhYRTUjwbqxdd
L2  - https://watermark.silverchair.com/gkz1163.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArMwggKvBgkqhkiG9w0BBwagggKgMIICnAIBADCCApUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM93m65EaHAul9lvZ3AgEQgIICZgl4kN1MOxCY84aEvwwQEi6vjxrtsNYzBuhYRTUjwbqxdd
N2  - Staufen1 (STAU1) is a dsRNA binding protein mediating mRNA transport and localization, translational control and STAU1-mediated mRNA decay (SMD). The STAU1 binding site (SBS) within human ADP-ribosylation factorl (ARF1) 3'UTR binds STAU1 and this downregulates ARF1 cytoplasmic mRNA levels by SMD. However, how STAU1 recognizes specific mRNA targets is still under debate. Our structure of the ARF1 SBS-STAU1 complex uncovers target recognition by STAU1. STAU1 dsRNA binding domain (dsRBD) 4 interacts with two pyrimidines and one purine from the minor groove side via helix alpha 1, the beta 1-beta 2 loop anchors the dsRBD at the end of the dsRNA and lysines in helix alpha 2 bind to the phosphodiester backbone from the major groove side. STAU1 dsRBD3 displays the same binding mode with specific recognition of one guanine base. Mutants disrupting minor groove recognition of ARF1 SBS affect in vitro binding and reduce SMD in vivo. Our data thus reveal how STAU1 recognizes minor groove features in dsRNA relevant for target selection.
ER  -

YADAV, Deepak Kumar, Dagmar ZIGÁČKOVÁ, Maria ZLOBINA, Tomáš KLUMPLER, Christelle BEAUMONT, Monika KUBÍČKOVÁ, Štěpánka VAŇÁČOVÁ and Peter LUKAVSKY. Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2020, vol.~48, No~4, p.~2091-2106. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz1163.

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