Scheer Hélène, Almeida Caroline, Ferrier Emilie, Simonnot Quentin, Poirier Laure, Pflieger David, Sement François M., Koechler Sandrine, Piermaria Christina, Krawczyk Paweł, Mroczek Seweryn, Chicher Johana, Kuhn Lauriane, Dziembowski Andrzej, Hammann Philippe, Zuber Hélène, Gagliardi Dominique
The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis Article de journal
Dans: Nature Communications, vol. 12, no. 1, p. 1298, 2021, ISSN: 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: Arabidopsis, Arabidopsis Proteins, Co-Repressor Proteins, DEAD-box RNA Helicases, Gene Expression Regulation, Humans, messenger, Plant, PPSE, Proto-Oncogene Proteins, Ribonucleoproteins, RNA, RNA Nucleotidyltransferases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Small Interfering, Tobacco, transcriptome, Uridine
@article{scheer_tutase_2021,
title = {The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis},
author = {Hélène Scheer and Caroline Almeida and Emilie Ferrier and Quentin Simonnot and Laure Poirier and David Pflieger and François M. Sement and Sandrine Koechler and Christina Piermaria and Paweł Krawczyk and Seweryn Mroczek and Johana Chicher and Lauriane Kuhn and Andrzej Dziembowski and Philippe Hammann and Hélène Zuber and Dominique Gagliardi},
doi = {10.1038/s41467-021-21382-2},
issn = {2041-1723},
year = {2021},
date = {2021-02-01},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {1298},
abstract = {Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.},
keywords = {Arabidopsis, Arabidopsis Proteins, Co-Repressor Proteins, DEAD-box RNA Helicases, Gene Expression Regulation, Humans, messenger, Plant, PPSE, Proto-Oncogene Proteins, Ribonucleoproteins, RNA, RNA Nucleotidyltransferases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Small Interfering, Tobacco, transcriptome, Uridine},
pubstate = {published},
tppubtype = {article}
}
Méteignier Louis-Valentin, Ghandour Rabea, Zimmerman Aude, Kuhn Lauriane, Meurer Jörg, Zoschke Reimo, Hammani Kamel
Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo Article de journal
Dans: Nucleic Acids Research, vol. 49, no. 2, p. 1114–1132, 2021, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: 16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity
@article{meteignier_arabidopsis_2021,
title = {Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo},
author = {Louis-Valentin Méteignier and Rabea Ghandour and Aude Zimmerman and Lauriane Kuhn and Jörg Meurer and Reimo Zoschke and Kamel Hammani},
doi = {10.1093/nar/gkaa1244},
issn = {1362-4962},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Research},
volume = {49},
number = {2},
pages = {1114--1132},
abstract = {The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.},
keywords = {16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity},
pubstate = {published},
tppubtype = {article}
}
Weber-Lotfi Frédérique, Koulintchenko Milana V, Ibrahim Noha, Hammann Philippe, Mileshina Daria V, Konstantinov Yuri M, Dietrich André
Nucleic acid import into mitochondria: New insights into the translocation pathways. Article de journal
Dans: Biochimica et biophysica acta, vol. 1853, no. 12, p. 3165–3181, 2015, ISSN: 0006-3002 0006-3002, (Place: Netherlands).
Résumé | Liens | BibTeX | Étiquettes: Arabidopsis/metabolism, Biological Transport, Import factor, mitochondria, Mitochondria/*metabolism, Nucleic acid transport, Nucleic Acids/*metabolism, Permeability transition pore, Plant, PPSE, Saccharomyces cerevisiae/metabolism, Yeast
@article{weber-lotfi_nucleic_2015,
title = {Nucleic acid import into mitochondria: New insights into the translocation pathways.},
author = {Frédérique Weber-Lotfi and Milana V Koulintchenko and Noha Ibrahim and Philippe Hammann and Daria V Mileshina and Yuri M Konstantinov and André Dietrich},
doi = {10.1016/j.bbamcr.2015.09.011},
issn = {0006-3002 0006-3002},
year = {2015},
date = {2015-01-01},
journal = {Biochimica et biophysica acta},
volume = {1853},
number = {12},
pages = {3165--3181},
abstract = {Mitochondria have retained indispensable but limited genetic information and they import both proteins and nucleic acids from the cytosol. RNA import is essential for gene expression and regulation, whereas competence for DNA uptake is likely to contribute to organellar genome dynamics and evolution. Contrary to protein import mechanisms, the way nucleic acids cross the mitochondrial membranes remains poorly understood. Using proteomic, genetic and biochemical approaches with both plant and yeast organelles, we develop here a model for DNA uptake into mitochondria. The first step includes the voltage-dependent anion channel and an outer membrane-located precursor fraction of a protein normally located in the inner membrane. To proceed, the DNA is then potentially recruited in the intermembrane space by an accessible subunit of one of the respiratory chain complexes. Final translocation through the inner membrane remains the most versatile but points to the components considered to make the mitochondrial permeability transition pore. Depending on the size, DNA and RNA cooperate or compete for mitochondrial uptake, which shows that they share import mechanisms. On the other hand, our results imply the existence of more than one route for nucleic acid translocation into mitochondria.},
note = {Place: Netherlands},
keywords = {Arabidopsis/metabolism, Biological Transport, Import factor, mitochondria, Mitochondria/*metabolism, Nucleic acid transport, Nucleic Acids/*metabolism, Permeability transition pore, Plant, PPSE, Saccharomyces cerevisiae/metabolism, Yeast},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Filipowicz W
From RNAi to epigenomes: how RNA rules the world Article de journal
Dans: Chembiochem, vol. 6, no. 2, p. 441-443, 2005, ISBN: 15651038, (1439-4227 (Print) Journal Article).
Liens | BibTeX | Étiquettes: Animals Epigenesis, Genetic *Genome MicroRNAs/genetics/metabolism *Rna *RNA Interference RNA, Plant, Unité ARN, WESTHOF
@article{,
title = {From RNAi to epigenomes: how RNA rules the world},
author = {E Westhof and W Filipowicz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15651038},
isbn = {15651038},
year = {2005},
date = {2005-01-01},
journal = {Chembiochem},
volume = {6},
number = {2},
pages = {441-443},
note = {1439-4227 (Print)
Journal Article},
keywords = {Animals Epigenesis, Genetic *Genome MicroRNAs/genetics/metabolism *Rna *RNA Interference RNA, Plant, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Raya Jésus, Bianco Alberto, Furrer Julien, Briand Jean-Paul, Piotto Martial, Elbayed Karim
Proton dipolar recoupling in resin-bound peptides under high-resolution magic angle spinning Article de journal
Dans: Journal of Magnetic Resonance (San Diego, Calif.: 1997), vol. 157, no. 1, p. 43–51, 2002, ISSN: 1090-7807.
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence, biomolecular, Foot-and-Mouth Disease Virus, I2CT, Nuclear Magnetic Resonance, Peptides, Plant, Resins, Team-Bianco
@article{raya_proton_2002,
title = {Proton dipolar recoupling in resin-bound peptides under high-resolution magic angle spinning},
author = {Jésus Raya and Alberto Bianco and Julien Furrer and Jean-Paul Briand and Martial Piotto and Karim Elbayed},
doi = {10.1006/jmre.2002.2573},
issn = {1090-7807},
year = {2002},
date = {2002-07-01},
journal = {Journal of Magnetic Resonance (San Diego, Calif.: 1997)},
volume = {157},
number = {1},
pages = {43--51},
abstract = {Rotational resonance and radiofrequency-driven dipolar recoupling (RFDR) experiments have been used to recover the weak proton dipolar interaction present in peptides bound to swollen resins spun at the magic angle. The intensity of the correlation peaks obtained using these sequences is shown to be significantly stronger than the one obtained using the classical NOESY experiment. In addition, it is found that during the relatively long mixing times required to transfer magnetization in such soft materials, the RFDR sequence also achieves magnetization transfer via the scalar J-coupling.},
keywords = {Amino Acid Sequence, biomolecular, Foot-and-Mouth Disease Virus, I2CT, Nuclear Magnetic Resonance, Peptides, Plant, Resins, Team-Bianco},
pubstate = {published},
tppubtype = {article}
}
Furrer J, Piotto M, Bourdonneau M, Limal D, Guichard G, Elbayed K, Raya J, Briand J P, Bianco A
Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports Article de journal
Dans: Journal of the American Chemical Society, vol. 123, no. 18, p. 4130–4138, 2001, ISSN: 0002-7863.
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence, biomolecular, Capsid, Capsid Proteins, Epitopes, I2CT, Molecular Sequence Data, Nuclear Magnetic Resonance, Peptide Fragments, Plant, Protein Structure, Resins, Secondary, Solvents, Team-Bianco
@article{furrer_evidence_2001,
title = {Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports},
author = {J Furrer and M Piotto and M Bourdonneau and D Limal and G Guichard and K Elbayed and J Raya and J P Briand and A Bianco},
doi = {10.1021/ja003566w},
issn = {0002-7863},
year = {2001},
date = {2001-01-01},
journal = {Journal of the American Chemical Society},
volume = {123},
number = {18},
pages = {4130--4138},
abstract = {The structure of the 19-amino acid peptide epitope, corresponding to the 141-159 sequence of capsid viral protein VP1 of foot-and-mouth disease virus (FMDV), bound to three different resins, namely, polystyrene-MBHA, PEGA, and POEPOP, has been determined by high-resolution magic angle spinning (HRMAS) NMR spectroscopy. A combination of homonuclear and heteronuclear bidimensional experiments was used for the complete peptide resonance assignment and the qualitative characterization of the peptide folding. The influence of the chemicophysical nature of the different polymers on the secondary structure of the covalently attached FMDV peptide was studied in detail. In the case of polystyrene-MBHA and polyacrylamide-PEGA resins, the analysis of the 2D spectra was hampered by missing signals and extensive overlaps, and only a propensity toward a peptide secondary structure could be derived from the assigned NOE correlations. When the FMDV peptide was linked to the polyoxyethylene-based POEPOP resin, it was found to adopt in dimethylformamide a helical conformation encompassing the C-terminal domain from residues 152 to 159. This conformation is very close to that of the free peptide previously analyzed in 2,2,2-trifluoroethanol. Our study clearly demonstrates that a regular helical structure can be adopted by a resin-bound bioactive peptide. Moreover, a change in the folding was observed when the same peptide-POEPOP conjugate was swollen in aqueous solution, displaying the same conformational features as the free peptide in water. The possibility of studying solid-supported ordered secondary structures by the HRMAS NMR technique in a wide range of solvents can be extended either to other biologically relevant peptides and proteins or to new synthetic oligomers.},
keywords = {Amino Acid Sequence, biomolecular, Capsid, Capsid Proteins, Epitopes, I2CT, Molecular Sequence Data, Nuclear Magnetic Resonance, Peptide Fragments, Plant, Protein Structure, Resins, Secondary, Solvents, Team-Bianco},
pubstate = {published},
tppubtype = {article}
}
Brigotti M., Keith G., Pallanca A., Carnicelli D., Alvergna P., Dirheimer G., Montanaro L., Sperti S.
Identification of the tRNAs which up-regulate agrostin, barley RIP and PAP-S, three ribosome-inactivating proteins of plant origin Article de journal
Dans: FEBS Lett, vol. 431, no. 2, p. 259-62, 1998, (0014-5793 Journal Article).
Résumé | BibTeX | Étiquettes: &, Acid, Adenosine, Base, Conformation, Data, effects/*metabolism, Gov't, Hordeum/metabolism, Hydrolases/*metabolism, Molecular, N-Glycosyl, Non-U.S., Nucleic, Plant, Plant/chemistry/isolation, Proteins/drug, purification/*metabolism, RNA, Sequence, Support, Transfer/chemistry/isolation, Triphosphate/pharmacology, Up-Regulation
@article{,
title = {Identification of the tRNAs which up-regulate agrostin, barley RIP and PAP-S, three ribosome-inactivating proteins of plant origin},
author = { M. Brigotti and G. Keith and A. Pallanca and D. Carnicelli and P. Alvergna and G. Dirheimer and L. Montanaro and S. Sperti},
year = {1998},
date = {1998-01-01},
journal = {FEBS Lett},
volume = {431},
number = {2},
pages = {259-62},
abstract = {Ribosome-inactivating proteins (RIP) are RNA-N-glycosidases widely diffused in plants which depurinate ribosomal RNA at a specific universally conserved position, A4324 in rat ribosomes. A small group of RIPs (cofactor-dependent RIPs) require ATP and tRNA to reach maximal activity on isolated ribosomes. The tRNA which stimulates gelonin was identified as tRNA(Trp). The present paper reports the identification of three other tRNAs which stimulate agrostin (tRNA(Ala)), barley RIP (tRNA(Ala), tRNA(Val)) and PAP-S (tRNA(Gly)), while for tritin-S no particular stimulating tRNA emerged. The sequences of tRNA(Val) and tRNA(Gly) correspond to the already known ones (rabbit and man, respectively). The tRNA(Ala) (anticodon IGC) identifies a new isoacceptor. Only the stimulating activity of the tRNA(Ala) for agrostin approaches the specificity previously observed for the couple gelonin-tRNA(Trp).},
note = {0014-5793
Journal Article},
keywords = {&, Acid, Adenosine, Base, Conformation, Data, effects/*metabolism, Gov't, Hordeum/metabolism, Hydrolases/*metabolism, Molecular, N-Glycosyl, Non-U.S., Nucleic, Plant, Plant/chemistry/isolation, Proteins/drug, purification/*metabolism, RNA, Sequence, Support, Transfer/chemistry/isolation, Triphosphate/pharmacology, Up-Regulation},
pubstate = {published},
tppubtype = {article}
}
Bergdoll M., Remy M. H., Cagnon C., Masson J. M., Dumas P.
Proline-dependent oligomerization with arm exchange Article de journal
Dans: Structure, vol. 5, no. 3, p. 391-401, 1997, (0969-2126 Journal Article).
Résumé | BibTeX | Étiquettes: *Acetyltransferases, *Dimerization, *Protein, Acid, Alignment, Amino, Aminotransferases/chemistry, Animals, Aspartate, ATPase/chemistry, Bacterial, Binding, Cattle, Chickens, Comparative, Conformation, Data, Folding, Heart/enzymology, Human, mitochondria, Models, Molecular, Mutagenesis, Na(+)-K(+)-Exchanging, Pancreatic/chemistry, Plant, Proline/*physiology, Protein, Proteins/chemistry, Pyrophosphatases/chemistry, Ribonuclease, Sequence, Site-Directed, Structural, Study, Viral, Viruses/chemistry
@article{,
title = {Proline-dependent oligomerization with arm exchange},
author = { M. Bergdoll and M. H. Remy and C. Cagnon and J. M. Masson and P. Dumas},
year = {1997},
date = {1997-01-01},
journal = {Structure},
volume = {5},
number = {3},
pages = {391-401},
abstract = {BACKGROUND: Oligomerization is often necessary for protein activity or regulation and its efficiency is fundamental for the cell. The quaternary structure of a large number of oligomers consists of protomers tightly anchored to each other by exchanged arms or swapped domains. However, nothing is known about how the arms can be kept in a favourable conformation before such an oligomerization. RESULTS: Upon examination of such quaternary structures, we observe an extremely frequent occurrence of proline residues at the point where the arm leaves the protomer. Sequence alignment and site-directed mutagenesis confirm the importance of these prolines. The conservation of these residues at the hinge regions can be explained by the constraints that they impose on polypeptide conformation and dynamics: by rigidifying the mainchain, prolines favour extended conformations of arms thus favouring oligomerization, and may prevent interaction of the arms with the core of the protomer. CONCLUSIONS: Hinge prolines can be considered as 'quaternary structure helpers'. The presence of a proline should be considered when searching for a determinant of oligomerization with arm exchange and could be used to engineer synthetic oligomers or to displace a monomers to oligomers equilibrium by mutation of this proline residue.},
note = {0969-2126
Journal Article},
keywords = {*Acetyltransferases, *Dimerization, *Protein, Acid, Alignment, Amino, Aminotransferases/chemistry, Animals, Aspartate, ATPase/chemistry, Bacterial, Binding, Cattle, Chickens, Comparative, Conformation, Data, Folding, Heart/enzymology, Human, mitochondria, Models, Molecular, Mutagenesis, Na(+)-K(+)-Exchanging, Pancreatic/chemistry, Plant, Proline/*physiology, Protein, Proteins/chemistry, Pyrophosphatases/chemistry, Ribonuclease, Sequence, Site-Directed, Structural, Study, Viral, Viruses/chemistry},
pubstate = {published},
tppubtype = {article}
}