In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins.

5' Untranslated Regions Arabidopsis / genetics Arabidopsis Proteins / genetics Chloroplasts / genetics Gene Expression Plants, Genetically Modified Protein Binding Protein Engineering / methods RNA, Chloroplast / metabolism RNA-Binding Motifs / genetics RNA-Binding Proteins / genetics Recombinant Proteins Ribulose-Bisphosphate Carboxylase / genetics

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
04 06 2021
Historique:
accepted: 28 04 2021
revised: 05 04 2021
received: 09 11 2020
pubmed: 27 5 2021
medline: 29 6 2021
entrez: 26 5 2021
Statut: ppublish

Résumé

Pentatricopeptide repeat (PPR) proteins are helical repeat-proteins that bind RNA in a modular fashion with a sequence-specificity that can be manipulated by the use of an amino acid code. As such, PPR repeats are promising scaffolds for the design of RNA binding proteins for synthetic biology applications. However, the in vivo functional capabilities of artificial PPR proteins built from consensus PPR motifs are just starting to be explored. Here, we report in vivo functions of an artificial PPR protein, dPPRrbcL, made of consensus PPR motifs that were designed to bind a sequence near the 5' end of rbcL transcripts in Arabidopsis chloroplasts. We used a functional complementation assay to demonstrate that this protein bound its intended RNA target with specificity in vivo and that it substituted for a natural PPR protein by stabilizing processed rbcL mRNA. We targeted a second protein of analogous design to the petL 5' UTR, where it substituted for the native stabilizing PPR protein PGR3, albeit inefficiently. These results showed that artificial PPR proteins can be engineered to functionally mimic the class of native PPR proteins that serve as physical barriers against exoribonucleases.

Identifiants

DOI: 10.1093/nar/gkab390 PMID: 34037778 PMC: PMC8191804
pubmed: 34037778
pii: 6284178
doi: 10.1093/nar/gkab390
pmc: PMC8191804
doi:

Substances chimiques

5' Untranslated Regions 0
Arabidopsis Proteins 0
PDM2 protein, Arabidopsis 0
PGR3 protein, Arabidopsis 0
RNA, Chloroplast 0
RNA-Binding Proteins 0
Recombinant Proteins 0
RbcL protein, plastid EC 4.1.1.39
Ribulose-Bisphosphate Carboxylase EC 4.1.1.39

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

5985-5997

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

Nucleic Acids Res. 2013 Oct;41(19):9141-51
pubmed: 23921629
Plant J. 2011 Jul;67(2):318-27
pubmed: 21457370
Nucleic Acids Res. 2019 Apr 23;47(7):3728-3738
pubmed: 30753696
Nucleic Acids Res. 2018 Mar 16;46(5):2613-2623
pubmed: 29294070
Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):415-20
pubmed: 21173259
Nucleic Acids Res. 2012 Apr;40(7):3092-105
pubmed: 22156165
Anal Biochem. 2005 Aug 15;343(2):313-21
pubmed: 15993367
Plant Cell. 2010 Feb;22(2):443-53
pubmed: 20190079
Nat Plants. 2019 May;5(5):505-511
pubmed: 31036912
Nucleic Acids Res. 2016 Sep 6;44(15):7406-17
pubmed: 27235415
Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):196-208
pubmed: 25664731
Mol Plant. 2015 Apr;8(4):667-70
pubmed: 25598142
Plant J. 2017 Nov;92(3):400-413
pubmed: 28805278
Plant Physiol. 2015 Sep;169(1):627-46
pubmed: 26152711
RNA. 2017 Apr;23(4):586-599
pubmed: 28108520
Plant J. 2014 Jun;78(5):772-82
pubmed: 24471963
Plant Cell. 2019 Aug;31(8):1723-1733
pubmed: 31123048
Nucleic Acids Res. 2018 Nov 2;46(19):10448-10459
pubmed: 30125002
Trends Biochem Sci. 2000 Feb;25(2):46-7
pubmed: 10664580
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
Plant Cell. 2013 Aug;25(8):3079-88
pubmed: 23975900
Plant J. 2004 Apr;38(1):152-63
pubmed: 15053768
Plant Cell. 1999 Sep;11(9):1709-16
pubmed: 10488237
Plant J. 2016 Feb;85(4):532-47
pubmed: 26764122
PLoS One. 2013;8(1):e53787
pubmed: 23326506
PLoS Genet. 2012;8(8):e1002910
pubmed: 22916040
EMBO J. 2009 Jul 22;28(14):2042-52
pubmed: 19424177
PLoS One. 2013 Jun 06;8(6):e65343
pubmed: 23762347
PLoS One. 2013;8(3):e57286
pubmed: 23472078
Plant Physiol. 2003 Oct;133(2):462-9
pubmed: 14555774
Nature. 2013 Dec 5;504(7478):168-71
pubmed: 24162847
Annu Rev Plant Biol. 2014;65:415-42
pubmed: 24471833
FEBS Lett. 1998 Jul 10;431(1):39-44
pubmed: 9684861
Mol Biol Evol. 2008 Jun;25(6):1120-8
pubmed: 18343892
Plant Cell. 2010 Jan;22(1):234-48
pubmed: 20097872
Plant Cell. 2014 Feb;26(2):777-87
pubmed: 24585838
Commun Biol. 2018 Oct 11;1:166
pubmed: 30320233
Plant Cell. 2012 Jul;24(7):3087-105
pubmed: 22773745
Nucleic Acids Res. 2019 Dec 16;47(22):11889-11905
pubmed: 31732725
Plant Physiol. 2012 Jan;158(1):156-89
pubmed: 22065420
Nucleic Acids Res. 2012 Apr;40(7):3106-16
pubmed: 22139936
Nat Commun. 2014 Dec 17;5:5729
pubmed: 25517350
Wiley Interdiscip Rev RNA. 2015 Nov-Dec;6(6):597-613
pubmed: 26329122
Plant Cell Physiol. 2021 Jan 13;:
pubmed: 33439244
RNA Biol. 2011 Nov-Dec;8(6):978-83
pubmed: 21941129

Auteurs

Nikolay Manavski (N)

Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.

Sébastien Mathieu (S)

Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.

Margarita Rojas (M)

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA.

Louis-Valentin Méteignier (LV)

Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.

Andreas Brachmann (A)

Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried Germany.

Alice Barkan (A)

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA.

Kamel Hammani (K)

Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
ORCID: 0000-0001-5759-5955

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Régions non traduites › Régions 5' non traduites › In vivo stabilization of endogenous...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Brassicaceae › Arabidopsis › In vivo stabilization of endogenous...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines végétales › Protéines d'Arabidopsis › In vivo stabilization of endogenous...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Plastes › Chloroplastes › In vivo stabilization of endogenous...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › In vivo stabilization of endogenous...
questionsmedicales.fr › Stades d'organismes › Organismes génétiquement modifiés › Végétaux génétiquement modifiés › In vivo stabilization of endogenous...
questionsmedicales.fr › Métabolisme › Liaison aux protéines › In vivo stabilization of endogenous...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Génie génétique › Ingénierie des protéines › In vivo stabilization of endogenous...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN des plantes › ARN des chloroplastes › In vivo stabilization of endogenous...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Éléments structuraux des protéines › Motifs de liaison à l'ARN › In vivo stabilization of endogenous...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines de liaison à l'ARN › In vivo stabilization of endogenous...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines recombinantes › In vivo stabilization of endogenous...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines végétales › Protéines chloroplastiques › Ribulose bisphosphate carboxylase › In vivo stabilization of endogenous...