Publications
2021
Mancera-Martínez Eder, Dong Yihan, Makarian Joelle, Srour Ola, Thiébeauld Odon, Jamsheer Muhammed, Chicher Johana, Hammann Philippe, Schepetilnikov Mikhail, Ryabova Lyubov A.
Phosphorylation of a reinitiation supporting protein, RISP, determines its function in translation reinitiation Journal Article
In: Nucleic Acids Research, vol. 49, no. 12, pp. 6908–6924, 2021, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: Arabidopsis, Arabidopsis Proteins, Caulimovirus, Eukaryotic, Eukaryotic Initiation Factor-2B, Eukaryotic Initiation Factor-3, Large, Peptide Chain Initiation, Phosphorylation, PPSE, Ribosomal Protein S6, Ribosome Subunits, translational
@article{mancera-martinez_phosphorylation_2021,
title = {Phosphorylation of a reinitiation supporting protein, RISP, determines its function in translation reinitiation},
author = {Eder Mancera-Martínez and Yihan Dong and Joelle Makarian and Ola Srour and Odon Thiébeauld and Muhammed Jamsheer and Johana Chicher and Philippe Hammann and Mikhail Schepetilnikov and Lyubov A. Ryabova},
doi = {10.1093/nar/gkab501},
issn = {1362-4962},
year = {2021},
date = {2021-07-01},
journal = {Nucleic Acids Research},
volume = {49},
number = {12},
pages = {6908--6924},
abstract = {Reinitiation supporting protein, RISP, interacts with 60S (60S ribosomal subunit) and eIF3 (eukaryotic initiation factor 3) in plants. TOR (target-of-rapamycin) mediates RISP phosphorylation at residue Ser267, favoring its binding to eL24 (60S ribosomal protein L24). In a viral context, RISP, when phosphorylated, binds the CaMV transactivator/ viroplasmin, TAV, to assist in an exceptional mechanism of reinitiation after long ORF translation. Moreover, we show here that RISP interacts with eIF2 via eIF2β and TOR downstream target 40S ribosomal protein eS6. A RISP phosphorylation knockout, RISP-S267A, binds preferentially eIF2β, and both form a ternary complex with eIF3a in vitro. Accordingly, transient overexpression in plant protoplasts of RISP-S267A, but not a RISP phosphorylation mimic, RISP-S267D, favors translation initiation. In contrast, RISP-S267D preferentially binds eS6, and, when bound to the C-terminus of eS6, can capture 60S in a highly specific manner in vitro, suggesting that it mediates 60S loading during reinitiation. Indeed, eS6-deficient plants are highly resistant to CaMV due to their reduced reinitiation capacity. Strikingly, an eS6 phosphomimic, when stably expressed in eS6-deficient plants, can fully restore the reinitiation deficiency of these plants in cellular and viral contexts. These results suggest that RISP function in translation (re)initiation is regulated by phosphorylation at Ser267.},
keywords = {Arabidopsis, Arabidopsis Proteins, Caulimovirus, Eukaryotic, Eukaryotic Initiation Factor-2B, Eukaryotic Initiation Factor-3, Large, Peptide Chain Initiation, Phosphorylation, PPSE, Ribosomal Protein S6, Ribosome Subunits, translational},
pubstate = {published},
tppubtype = {article}
}
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 Journal Article
In: Nature Communications, vol. 12, no. 1, pp. 1298, 2021, ISSN: 2041-1723.
Abstract | Links | BibTeX | Tags: 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 Journal Article
In: Nucleic Acids Research, vol. 49, no. 2, pp. 1114–1132, 2021, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: 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}
}
2016
Harashima Hirofumi, Dissmeyer Nico, Hammann Philippe, Nomura Yuko, Kramer Katharina, Nakagami Hirofumi, Schnittger Arp
Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1. Journal Article
In: BMC plant biology, vol. 16, no. 1, pp. 209, 2016, ISSN: 1471-2229 1471-2229.
Abstract | Links | BibTeX | Tags: Arabidopsis, Cell cycle, Kinase, Mitosis, Phosphorylation, PPSE, Substrate
@article{harashima_modulation_2016,
title = {Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1.},
author = {Hirofumi Harashima and Nico Dissmeyer and Philippe Hammann and Yuko Nomura and Katharina Kramer and Hirofumi Nakagami and Arp Schnittger},
doi = {10.1186/s12870-016-0900-7},
issn = {1471-2229 1471-2229},
year = {2016},
date = {2016-01-01},
journal = {BMC plant biology},
volume = {16},
number = {1},
pages = {209},
abstract = {BACKGROUND: Modulation of protein activity by phosphorylation through kinases and subsequent de-phosphorylation by phosphatases is one of the most prominent cellular control mechanisms. Thus, identification of kinase substrates is pivotal for the understanding of many - if not all - molecular biological processes. Equally, the possibility to deliberately tune kinase activity is of great value to analyze the biological process controlled by a particular kinase. RESULTS: Here we have applied a chemical genetic approach and generated an analog-sensitive version of CDKA;1, the central cell-cycle regulator in Arabidopsis and homolog of the yeast Cdc2/CDC28 kinases. This variant could largely rescue a cdka;1 mutant and is biochemically active, albeit less than the wild type. Applying bulky kinase inhibitors allowed the reduction of kinase activity in an organismic context in vivo and the modulation of plant growth. To isolate CDK substrates, we have adopted a two-dimensional differential gel electrophoresis strategy, and searched for proteins that showed mobility changes in fluorescently labeled extracts from plants expressing the analog-sensitive version of CDKA;1 with and without adding a bulky ATP variant. A pilot set of five proteins involved in a range of different processes could be confirmed in independent kinase assays to be phosphorylated by CDKA;1 approving the applicability of the here-developed method to identify substrates. CONCLUSION: The here presented generation of an analog-sensitive CDKA;1 version is functional and represent a novel tool to modulate kinase activity in vivo and identify kinase substrates. Our here performed pilot screen led to the identification of CDK targets that link cell proliferation control to sugar metabolism, proline proteolysis, and glucosinolate production providing a hint how cell proliferation and growth are integrated with plant development and physiology.},
keywords = {Arabidopsis, Cell cycle, Kinase, Mitosis, Phosphorylation, PPSE, Substrate},
pubstate = {published},
tppubtype = {article}
}
2012
Serag Maged F, Kaji Noritada, Tokeshi Manabu, Bianco Alberto, Baba Yoshinobu
The plant cell uses carbon nanotubes to build tracheary elements Journal Article
In: Integrative Biology: Quantitative Biosciences from Nano to Macro, vol. 4, no. 2, pp. 127–131, 2012, ISSN: 1757-9708.
Abstract | Links | BibTeX | Tags: Arabidopsis, Atomic Force, carbon, Cell Differentiation, Confocal, Endocytosis, I2CT, Lignin, Microscopy, Nanotubes, Plant Cells, Team-Bianco
@article{serag_plant_2012,
title = {The plant cell uses carbon nanotubes to build tracheary elements},
author = {Maged F Serag and Noritada Kaji and Manabu Tokeshi and Alberto Bianco and Yoshinobu Baba},
doi = {10.1039/c2ib00135g},
issn = {1757-9708},
year = {2012},
date = {2012-02-01},
journal = {Integrative Biology: Quantitative Biosciences from Nano to Macro},
volume = {4},
number = {2},
pages = {127--131},
abstract = {Since their discovery, carbon nanotubes (CNTs) have been eminent members of the nanomaterial family. Because of their unique physical, chemical and mechanical properties, they are regarded as new potential materials to bring enormous benefits in cell biology studies. Undoubtedly, the first step to prove the advantages of CNTs is to understand the basic behavior of CNTs inside the cells. In a number of studies, CNTs have been demonstrated as new carrier systems for the delivery of DNA, proteins and therapeutic molecules into living cells. However, post-uptake behavior of CNTs inside the cells has not received much consideration. Utilizing the plant cell model, we have shown in this study that the plant cells, differentiating into tracheary elements, incorporate cup-stacked carbon nanotubes (CSCNTs) into cell structure via oxidative cross-linking of monolignols to the nanotubes surface during lignin biosynthesis. This finding highlights the fate of CNTs inside plant cells and provides an example on how the plant cell can handle internalized carbon nanomaterials.},
keywords = {Arabidopsis, Atomic Force, carbon, Cell Differentiation, Confocal, Endocytosis, I2CT, Lignin, Microscopy, Nanotubes, Plant Cells, Team-Bianco},
pubstate = {published},
tppubtype = {article}
}