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Accueil > Départements > Biologie des Génomes > Carmela GIGLIONE : Maturation des protéines, destinée cellulaire et thérapeutique

Publications

2017



  • W. V. Bienvenut, J. - P. Scarpelli, J. Dumestier, T. Meinnel, et C. Giglione, « EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples », BMC Bioinformatics, vol. 18, nᵒ 1, 2017.
    Mots-clés : DBG, DIR, PROMTI, SICS.


  • S. Fieulaine, R. Alves de Sousa, L. Maigre, K. Hamiche, M. Alimi, J. - M. Bolla, A. Taleb, A. Denis, J. - M. Pagès, I. Artaud, T. Meinnel, et C. Giglione, « Corrigendum: A unique peptide deformylase platform to rationally design and challenge novel active compounds », Scientific Reports, vol. 7, p. 39365, janv. 2017.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, W. V. Bienvenut, C. Dian, T. Meinnel, et C. Giglione, « The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation », Scientific Reports, vol. 7, nᵒ 1, p. 11041, 2017.
    Résumé : Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.
    Mots-clés : B3S, DBG, IMAPP, PROMTI.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, M. Desmadril, N. Nhiri, A. Van Dorsselaer, S. Cianferani, E. Jacquet, T. Meinnel, et C. Giglione, « Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts », Biochimica Et Biophysica Acta, 2017.
    Résumé : Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 specific activity to values similar to those of bacterial PDFs. We next show that Vp16PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
    Mots-clés : DBG, Enzyme mechanism, N-terminal methionine excision, PDC, Peptide deformylase, PF, PROMTI, structure, Virus.


  • W. V. Bienvenut, C. Giglione, et T. Meinnel, « SILProNAQ: A Convenient Approach for Proteome-Wide Analysis of Protein N-Termini and N-Terminal Acetylation Quantitation », in Protein Terminal Profiling, vol. 1574, O. Schilling, Éd. New York, NY: Springer New York, 2017, p. 17-34.

2016

2015


  • W. V. Bienvenut, C. Giglione, et T. Meinnel, « Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition », Proteomics, vol. 15, nᵒ 14, p. 2503-2518, 2015.
    Résumé : A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions, more than 1000 unique N-termini were identified with 56% showing initiator methionine removal. Additional modifications corresponded to partial or complete Nα-acetylation (10%) and N-formyl retention (5%). Among the proteins undergoing these N-terminal modifications, 140 unique N-termini from translocated membrane proteins were highlighted. The very early time-course impact of actinonin was followed after addition of bacteriostatic concentrations of the drug. Under these conditions, 26% of all proteins did not undergo deformylation any longer after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation ratio measured on individual proteins increased with the same trend. Upon early PDF inhibition, two major categories of proteins retained their N-formyl group: a large number of inner membrane proteins and many proteins involved in protein synthesis including factors assisting the nascent chains in early cotranslational events. All MS data have been deposited in the ProteomeXchange with identifiers PXD001979, PXD002012 and PXD001983 (http://proteomecentral.proteomexchange.org/dataset/PXD001979, http://proteomecentral.proteomexchange.org/dataset/PXD002012 and http://proteomecentral.proteomexchange.org/dataset/PXD001983).
    Mots-clés : Acetylation, Actinonin, Amidohydrolases, Amino Acid Sequence, Anti-Bacterial Agents, Antibiotics, Cotranslational modifications, DBG, Deformylation, Escherichia coli, Escherichia coli Proteins, Hydroxamic Acids, Methionine, Microbiology, Molecular Sequence Data, PROMTI, Proteome.

  • T. V. Dinh, W. V. Bienvenut, E. Linster, A. Feldman-Salit, V. A. Jung, T. Meinnel, R. Hell, C. Giglione, et M. Wirtz, « Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling », Proteomics, vol. 15, nᵒ 14, p. 2426-2435, 2015.
    Résumé : Protein N(α) -terminal acetylation represents one of the most abundant protein modifications of higher eukaryotes. In humans, six N(α) -acetyltransferases (Nats) are responsible for the acetylation of approximately 80% of the cytosolic proteins. N-terminal protein acetylation has not been evidenced in organelles of metazoans, but in higher plants is a widespread modification not only in the cytosol but also in the chloroplast. In this study, we identify and characterize the first organellar-localized Nat in eukaryotes. A primary sequence-based search in Arabidopsis thaliana revealed seven putatively plastid-localized Nats of which AT2G39000 (AtNAA70) showed the highest conservation of the acetyl-CoA binding pocket. The chloroplastic localization of AtNAA70 was demonstrated by transient expression of AtNAA70:YFP in Arabidopsis mesophyll protoplasts. Homology modeling uncovered a significant conservation of tertiary structural elements between human HsNAA50 and AtNAA70. The in vivo acetylation activity of AtNAA70 was demonstrated on a number of distinct protein N(α) -termini with a newly established global acetylome profiling test after expression of AtNAA70 in E. coli. AtNAA70 predominately acetylated proteins starting with M, A, S and T, providing an explanation for most protein N-termini acetylation events found in chloroplasts. Like HsNAA50, AtNAA70 displays N(ε) -acetyltransferase activity on three internal lysine residues. All MS data have been deposited in the ProteomeXchange with identifier PXD001947 (http://proteomecentral.proteomexchange.org/dataset/PXD001947).
    Mots-clés : Acetylation, Amino Acid Sequence, Arabidopsis, Arabidopsis thaliana, AtNAA70, Chloroplast, Cloning, Molecular, DBG, Escherichia coli, gene expression, Humans, Models, Molecular, Molecular Sequence Data, N-Terminal Acetyltransferases, Nα-acetyltransferase, Plant proteomics, Plastids, PROMTI, Protein Conformation, proteomics, Tandem Mass Spectrometry.


  • C. Giglione, S. Fieulaine, et T. Meinnel, « N-terminal protein modifications: Bringing back into play the ribosome », Biochimie, vol. 114, p. 134-146, 2015.
    Mots-clés : Amidohydrolases, Amino Acid Sequence, Animals, B3S, Co-translational modifications, DBG, Humans, IMAPP, Methionine aminopeptidase, Methionyl Aminopeptidases, Molecular Sequence Data, N-myristoyltransferase, N-terminal, N-α-acetyltransferase, Peptide deformylase, PROMTI, Protein Biosynthesis, Protein Processing, Post-Translational, Ribosomes.

  • P. Kapos, F. Xu, T. Meinnel, C. Giglione, et X. Li, « N-terminal modifications contribute to flowering time and immune response regulations », Plant Signaling & Behavior, vol. 10, nᵒ 10, p. e1073874, 2015.
    Résumé : A variety of N-terminal co-translational modifications play crucial roles in many cellular processes across eukaryotic organisms. Recently, N-terminal acetylation has been proposed as a regulatory mechanism for the control of plant immunity. Analysis of an N-terminal acetyltransferase complex A (NatA) mutant, naa15-1, revealed that NatA controls the stability of immune receptor Suppressor of NPR1, Constitutive 1 (SNC1) in an antagonistic fashion with NatB. Here, we further report on an antagonistic regulation of flowering time by NatA and NatB, where naa15-1 plants exhibit late flowering, opposite of the early flowering phenotype previously observed in natB mutants. In addition, we provide evidence for the involvement of another N-terminal modification, N-myristoylation, in controlling pathogen-associated molecular pattern (PAMP) triggered immunity (PTI) through the characterization of N-myristoyltransferase 1 (NMT1) defective mutants, which express a low level of NMT1 protein. The mutant line lacks induced production of reactive oxygen species and MAP kinase phosphorylation in response to treatment with the known immune elicitor flg22. NMT1 deficient plants also exhibit increased susceptibility to Pst hrcC, a non-pathogenic Pseudomonas syringae tomato strain lacking a functional type-III secretion system. The potential for the NatA-NatB antagonistic relationship to exist outside of the regulation of SNC1 as well as the disclosing of NMT1s role in PTI further supports the significant contribution of N-terminal co-translational modifications in the regulation of biological processes in plants, and present interesting areas for further exploration.
    Mots-clés : Acetylation, Acyltransferases, Arabidopsis, Arabidopsis Proteins, DBG, Flowers, Gene Expression Regulation, Plant, Methyltransferases, Mutation, N-end Rule, N-terminal acetylation, N-Terminal Acetyltransferase A, N-Terminal Acetyltransferase B, N-terminal myristoylation, Nat, NMT, Pathogen-Associated Molecular Pattern Molecules, Phenotype, Plant Development, Plant Immunity, PROMTI, Protein Modification, Translational, protein regulation, Pseudomonas syringae.

  • S. Kraberger, S. G. Kumari, A. A. Hamed, B. Gronenborn, J. E. Thomas, M. Sharman, G. W. Harkins, B. M. Muhire, D. P. Martin, et A. Varsani, « Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains », Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 29, p. 203-215, 2015.
    Résumé : In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
    Mots-clés : Chickpea, Chickpea chlorotic dwarf virus, Cicer, DBG, DNA, Viral, Geminiviridae, Geminivirus, Genetic Variation, Mastrevirus, Molecular Sequence Data, Phylogeny, Plant Diseases, PROMTI, Recombination, Recombination, Genetic, Selection, Genetic, Sequence Analysis, DNA, Sudan.

  • E. Linster, I. Stephan, W. V. Bienvenut, J. Maple-Grødem, L. M. Myklebust, M. Huber, M. Reichelt, C. Sticht, S. G. Møller, T. Meinnel, T. Arnesen, C. Giglione, R. Hell, et M. Wirtz, « Downregulation of N-terminal acetylation triggers ABA-mediated drought responses in Arabidopsis », Nature Communications, vol. 6, p. 7640, 2015.
    Résumé : N-terminal acetylation (NTA) catalysed by N-terminal acetyltransferases (Nats) is among the most common protein modifications in eukaryotes, but its significance is still enigmatic. Here we characterize the plant NatA complex and reveal evolutionary conservation of NatA biochemical properties in higher eukaryotes and uncover specific and essential functions of NatA for development, biosynthetic pathways and stress responses in plants. We show that NTA decreases significantly after drought stress, and NatA abundance is rapidly downregulated by the phytohormone abscisic acid. Accordingly, transgenic downregulation of NatA induces the drought stress response and results in strikingly drought resistant plants. Thus, we propose that NTA by the NatA complex acts as a cellular surveillance mechanism during stress and that imprinting of the proteome by NatA is an important switch for the control of metabolism, development and cellular stress responses downstream of abscisic acid.
    Mots-clés : Abscisic Acid, Acetylation, Arabidopsis, Arabidopsis Proteins, DBG, Down-Regulation, Droughts, Escherichia coli, Gene Expression Regulation, Plant, HEK293 Cells, Humans, N-Terminal Acetyltransferase A, Organisms, Genetically Modified, PROMTI, Real-Time Polymerase Chain Reaction, Stress, Physiological.


  • J. Stojko, S. Fieulaine, S. Petiot-Bécard, A. Van Dorsselaer, T. Meinnel, C. Giglione, et S. Cianférani, « Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes », Analyst, vol. 140, nᵒ 21, p. 7234-7245, 2015.
    Mots-clés : Amidohydrolases, Anti-Bacterial Agents, Arabidopsis, B3S, Binding, Competitive, Buffers, Crystallography, X-Ray, DBG, IMAPP, Ions, Kinetics, Ligands, Mass Spectrometry, PROMTI, Protein Binding, Protein Conformation, Proteins.

  • F. Xu, Y. Huang, L. Li, P. Gannon, E. Linster, M. Huber, P. Kapos, W. Bienvenut, B. Polevoda, T. Meinnel, R. Hell, C. Giglione, Y. Zhang, M. Wirtz, S. Chen, et X. Li, « Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis », The Plant Cell, vol. 27, nᵒ 5, p. 1547-1562, 2015.
    Résumé : Nod-like receptors (NLRs) serve as immune receptors in plants and animals. The stability of NLRs is tightly regulated, though its mechanism is not well understood. Here, we show the crucial impact of N-terminal acetylation on the turnover of one plant NLR, Suppressor of NPR1, Constitutive 1 (SNC1), in Arabidopsis thaliana. Genetic and biochemical analyses of SNC1 uncovered its multilayered regulation by different N-terminal acetyltransferase (Nat) complexes. SNC1 exhibits a few distinct N-terminal isoforms generated through alternative initiation and N-terminal acetylation. Its first Met is acetylated by N-terminal acetyltransferase complex A (NatA), while the second Met is acetylated by N-terminal acetyltransferase complex B (NatB). Unexpectedly, the NatA-mediated acetylation serves as a degradation signal, while NatB-mediated acetylation stabilizes the NLR protein, thus revealing antagonistic N-terminal acetylation of a single protein substrate. Moreover, NatA also contributes to the turnover of another NLR, RESISTANCE TO P. syringae pv maculicola 1. The intricate regulation of protein stability by Nats is speculated to provide flexibility for the target protein in maintaining its homeostasis.
    Mots-clés : Acetylation, Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Chromosome Mapping, Cloning, Molecular, DBG, Models, Biological, Molecular Sequence Data, Mutation, N-Terminal Acetyltransferases, PROMTI, Protein Stability, Seedlings, Sequence Alignment, Tobacco.
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Publications Principales avant 2015

-  Fieulaine S, Desmadril M, Meinnel T, Giglione C (2014) Understanding the high efficient catalysis of prokaryote peptide defomylases by shedding light on the determinants specifying the low activity of the human counterpart. Acta Crystallographica Section D. 70 : 242-252

-  Renna L., Stefano G, Micalella C., Majeran W, Meinnel T, Giglione C, Brandizzi, F. (2013) Golgi traffic and integrity depend on N-myristoyltransferase-1 in Arabidopsis thaliana. The Plant Cell 25 : 1756-1773

-  Traverso JA, Micalella C, Martinez A, Brown SC, Satiat-Jeunemaitre B, Meinnel T, Giglione C (2013) Roles of N-terminal fatty acid acylations in membrane compartment partitioning : Arabidopsis h-TRXs as a case study. The Plant Cell 25 : 1056-1077

-  Traverso JA, Giglione* C, Meinnel T* (2013) High-throughput profiling of N-myristoylation substrate specificity across species including pathogens. Proteomics 13 : 25-36

-  Goemaere E, Melet A, Larue V, Lieutaud A, Alves de Sousa R, Chevalier J, Yimga-Djapa L, Giglione C, Huguet F, Alimi M, Meinnel T, Dardel F, Artaud I, Pages JM (2012) New peptide deformylase inhibitors and cooperative interaction : a combination to improve antibacterial activity. J Antimicrob Chemother 67 : 1392-1400

-  Bienvenut WV, Sumpton D, Martinez A, Lilla S, Espagne C, Meinnel T, Giglione C (2012) Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-alpha-acetylation features. Mol Cell Proteomics 11 : M111 015131

-  Adam Z, Frottin F, Espagne C, Meinnel T, Giglione C (2011) Interplay between N-terminal methionine excision and FtsH protease is essential for normal chloroplast development and function in Arabidopsis. Plant Cell 23 : 3745-3760

-  Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C (2011) Trapping conformational states along ligand-binding dynamics of peptide deformylase : the impact of induced fit on enzyme catalysis. PLoS Biol 9 : e1001066

-  Sharon I, Battchikova N, Aro EM, Giglione C, Meinnel T, Glaser F, Pinter RY, Breitbart M, Rohwer F, Beja O (2011) Comparative metagenomics of microbial traits within oceanic viral communities. ISME J 5 : 1178-1190

-  Frottin F, Espagne C, Traverso JA, Mauve C, Valot B, Lelarge-Trouverie C, Zivy M, Noctor G, Meinnel T, Giglione C (2009) Cotranslational proteolysis dominates glutathione homeostasis to support proper growth and development. Plant Cell 21 : 3296-3314

-  Giglione C, Fieulaine S, Meinnel T (2009) Cotranslational processing mechanisms : towards a dynamic 3D model. Trends Biochem Sci 34 : 417-426

-  Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, Lukowitz W (2009) Paternal control of embryonic patterning in Arabidopsis thaliana. Science 323 : 1485-1488

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