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Buggiani J, Meinnel T, Giglione C, Frottin F. Advances in nuclear proteostasis of metazoans. Biochimie 2024:S0300-9084(24)00081-6. [PMID: 38642824 DOI: 10.1016/j.biochi.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
The proteostasis network and associated protein quality control (PQC) mechanisms ensure proteome functionality and are essential for cell survival. A distinctive feature of eukaryotic cells is their high degree of compartmentalization, requiring specific and adapted proteostasis networks for each compartment. The nucleus, essential for maintaining the integrity of genetic information and gene transcription, is one such compartment. While PQC mechanisms have been investigated for decades in the cytoplasm and the endoplasmic reticulum, our knowledge of nuclear PQC pathways is only emerging. Recent developments in the field have underscored the importance of spatially managing aberrant proteins within the nucleus. Upon proteotoxic stress, misfolded proteins and PQC effectors accumulate in various nuclear membrane-less organelles. Beyond bringing together effectors and substrates, the biophysical properties of these organelles allow novel PQC functions. In this review, we explore the specificity of the nuclear compartment, the effectors of the nuclear proteostasis network, and the PQC roles of nuclear membrane-less organelles in metazoans.
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Affiliation(s)
- Julia Buggiani
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Frédéric Frottin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
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2
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Wu X, Segall AM, Giglione C, Meinnel T. The complete genome of Vibrio sp. 16 unveils two circular chromosomes and a distinctive 46-kb plasmid. Microbiol Resour Announc 2024; 13:e0122223. [PMID: 38415641 PMCID: PMC11008167 DOI: 10.1128/mra.01222-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
The entire 4.6-Mb genome of Vibrio sp. 16, encoding 4,270 genes, best matches with Vibrio rotiferianus. A 46-kb plasmid (pVDT1), alongside two circular chromosomes, showcases parAB/repB partition genes and three toxin/antitoxin systems potentially linked to phage infection.
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Affiliation(s)
- Xiaofen Wu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Anca M. Segall
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
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3
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Gong X, Boyer JB, Gierlich S, Pożoga M, Weidenhausen J, Sinning I, Meinnel T, Giglione C, Wang Y, Hell R, Wirtz M. HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana. Cell Rep 2024; 43:113768. [PMID: 38363676 DOI: 10.1016/j.celrep.2024.113768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
The ribosome-tethered N-terminal acetyltransferase A (NatA) acetylates 52% of soluble proteins in Arabidopsis thaliana. This co-translational modification of the N terminus stabilizes diverse cytosolic plant proteins. The evolutionary conserved Huntingtin yeast partner K (HYPK) facilitates NatA activity in planta, but in vitro, its N-terminal helix α1 inhibits human NatA activity. To dissect the regulatory function of HYPK protein domains in vivo, we genetically engineer CRISPR-Cas9 mutants expressing a HYPK fragment lacking all functional domains (hypk-cr1) or an internally deleted HYPK variant truncating helix α1 but retaining the C-terminal ubiquitin-associated (UBA) domain (hypk-cr2). We find that the UBA domain of HYPK is vital for stabilizing the NatA complex in an organ-specific manner. The N terminus of HYPK, including helix α1, is critical for promoting NatA activity on substrates starting with various amino acids. Consequently, deleting only 42 amino acids inside the HYPK N terminus causes substantial destabilization of the plant proteome and higher tolerance toward drought stress.
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Affiliation(s)
- Xiaodi Gong
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Simone Gierlich
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 271018 Tai'an, China
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany.
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4
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Etherington RD, Bailey M, Boyer JB, Armbruster L, Cao X, Coates JC, Meinnel T, Wirtz M, Giglione C, Gibbs DJ. Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases. Plant Physiol 2023; 193:2086-2104. [PMID: 37427787 PMCID: PMC10602611 DOI: 10.1093/plphys/kiad406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
The acetylation-dependent (Ac/)N-degron pathway degrades proteins through recognition of their acetylated N-termini (Nt) by E3 ligases called Ac/N-recognins. To date, specific Ac/N-recognins have not been defined in plants. Here we used molecular, genetic, and multiomics approaches to characterize potential roles for Arabidopsis (Arabidopsis thaliana) DEGRADATION OF ALPHA2 10 (DOA10)-like E3 ligases in the Nt-acetylation-(NTA)-dependent turnover of proteins at global- and protein-specific scales. Arabidopsis has two endoplasmic reticulum (ER)-localized DOA10-like proteins. AtDOA10A, but not the Brassicaceae-specific AtDOA10B, can compensate for loss of yeast (Saccharomyces cerevisiae) ScDOA10 function. Transcriptome and Nt-acetylome profiling of an Atdoa10a/b RNAi mutant revealed no obvious differences in the global NTA profile compared to wild type, suggesting that AtDOA10s do not regulate the bulk turnover of NTA substrates. Using protein steady-state and cycloheximide-chase degradation assays in yeast and Arabidopsis, we showed that turnover of ER-localized SQUALENE EPOXIDASE 1 (AtSQE1), a critical sterol biosynthesis enzyme, is mediated by AtDOA10s. Degradation of AtSQE1 in planta did not depend on NTA, but Nt-acetyltransferases indirectly impacted its turnover in yeast, indicating kingdom-specific differences in NTA and cellular proteostasis. Our work suggests that, in contrast to yeast and mammals, targeting of Nt-acetylated proteins is not a major function of DOA10-like E3 ligases in Arabidopsis and provides further insight into plant ERAD and the conservation of regulatory mechanisms controlling sterol biosynthesis in eukaryotes.
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Affiliation(s)
- Ross D Etherington
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Mark Bailey
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Jean-Baptiste Boyer
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Laura Armbruster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Xulyu Cao
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Thierry Meinnel
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Carmela Giglione
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
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Arnesen T, Aksnes H, Giglione C. Protein Termini 2022: central roles of protein ends. Trends Biochem Sci 2023; 48:495-499. [PMID: 36997368 DOI: 10.1016/j.tibs.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023]
Abstract
Although locating at the protein ends, N- and C-termini are at the center of numerous cellular functions. This topic engages an increasing number of scientists, recently forming the International Society of Protein Termini (ISPT). Protein Termini 2022 gathered this interdisciplinary community to discuss how protein ends may steer protein functionality.
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Rivière F, Monassa P, Giglione C, Meinnel T. Kinetic and catalytic features of N-myristoyltransferases. Methods Enzymol 2023; 684:167-190. [DOI: 10.1016/bs.mie.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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7
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Meinnel T, Boyer JB, Giglione C. The Global Acetylation Profiling Pipeline for Quick Assessment of Protein N-Acetyltransferase Specificity In Cellulo. Methods Mol Biol 2023; 2718:137-150. [PMID: 37665458 DOI: 10.1007/978-1-0716-3457-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Global acetylation profiling (GAP) consists of heterologous expression of a given N-acetyltransferase (NAT) in Escherichia coli to assess its specificity. The remarkable sensitivity and robustness of the GAP pipeline relies on the very low frequency of known N-terminal acetylated proteins in E. coli, including their degree of N-terminal acetylation. Using the SILProNAQ mass spectrometry strategy on bacterial protein extracts, GAP permits easy acquisition of both qualitative and quantitative data to decipher the impact of any putative NAT of interest on the N-termini of newly acetylated proteins. This strategy allows rapid determination of the substrate specificity of any NAT.
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Affiliation(s)
- Thierry Meinnel
- Université Paris Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Jean-Baptiste Boyer
- Université Paris Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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8
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Monassa P, Rivière F, Dian C, Frottin F, Giglione C, Meinnel T. Biochemical and structural analysis of N-myristoyltransferase mediated protein tagging. Methods Enzymol 2023; 684:135-166. [DOI: 10.1016/bs.mie.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. J Exp Bot 2022; 73:6013-6033. [PMID: 35768189 DOI: 10.1093/jxb/erac290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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10
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Miklánková P, Linster E, Boyer JB, Weidenhausen J, Mueller J, Armbruster L, Lapouge K, De La Torre C, Bienvenut W, Sticht C, Mann M, Meinnel T, Sinning I, Giglione C, Hell R, Wirtz M. HYPK promotes the activity of the Nα-acetyltransferase A complex to determine proteostasis of nonAc-X 2/N-degron-containing proteins. Sci Adv 2022; 8:eabn6153. [PMID: 35704578 PMCID: PMC9200280 DOI: 10.1126/sciadv.abn6153] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In humans, the Huntingtin yeast partner K (HYPK) binds to the ribosome-associated Nα-acetyltransferase A (NatA) complex that acetylates ~40% of the proteome in humans and Arabidopsis thaliana. However, the relevance of HsHYPK for determining the human N-acetylome is unclear. Here, we identify the AtHYPK protein as the first in vivo regulator of NatA activity in plants. AtHYPK physically interacts with the ribosome-anchoring subunit of NatA and promotes Nα-terminal acetylation of diverse NatA substrates. Loss-of-AtHYPK mutants are remarkably resistant to drought stress and strongly resemble the phenotype of NatA-depleted plants. The ectopic expression of HsHYPK rescues this phenotype. Combined transcriptomics, proteomics, and N-terminomics unravel that HYPK impairs plant metabolism and development, predominantly by regulating NatA activity. We demonstrate that HYPK is a critical regulator of global proteostasis by facilitating masking of the recently identified nonAc-X2/N-degron. This N-degron targets many nonacetylated NatA substrates for degradation by the ubiquitin-proteasome system.
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Affiliation(s)
- Pavlína Miklánková
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jonas Weidenhausen
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Johannes Mueller
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Carolina De La Torre
- Center of Medical Research, Heidelberg University, Theodor-Kutzer-Ufer, Mannheim, Germany
| | - Willy Bienvenut
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carsten Sticht
- Center of Medical Research, Heidelberg University, Theodor-Kutzer-Ufer, Mannheim, Germany
| | - Matthias Mann
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
- Corresponding author.
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Nyonda MA, Boyer JB, Belmudes L, Krishnan A, Pino P, Couté Y, Brochet M, Meinnel T, Soldati-Favre D, Giglione C. N-Acetylation of secreted proteins is widespread in Apicomplexa and independent of acetyl-CoA ER-transporter AT1. J Cell Sci 2022; 135:275539. [PMID: 35621049 DOI: 10.1242/jcs.259811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Acetyl-CoA participates in post-translational modification of proteins, central carbon and lipid metabolism in several cell compartments. In mammals, the acetyl-CoA transporter 1 (AT1) facilitates the flux of cytosolic acetyl-CoA into the endoplasmic reticulum (ER), enabling the acetylation of proteins of the secretory pathway, in concert with dedicated acetyltransferases including NAT8. However, the implication of the ER acetyl-CoA pool in acetylation of ER-transiting proteins in Apicomplexa is unknown. We identify homologues of AT1 and NAT8 in Toxoplasma gondii and Plasmodium berghei. Proteome-wide analyses revealed widespread N-terminal acetylation marks of secreted proteins in both parasites. Such acetylation profile of N-terminally processed proteins was never observed so far in any other organisms. AT1 deletion resulted in a considerable reduction of parasite fitness. In P. berghei, AT1 is important for growth of asexual blood stages and production of female gametocytes and male gametocytogenesis impaling its requirement for transmission. In the absence of AT1, the lysine and N-terminal acetylation sites remained globally unaltered, suggesting an uncoupling between the role of AT1 in development and active acetylation occurring along the secretory pathway.
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Affiliation(s)
- Mary Akinyi Nyonda
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Paco Pino
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,ExcellGene SA, CH1870 Monthey, Switzerland
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Mathieu Brochet
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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12
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Asensio T, Dian C, Boyer JB, Rivière F, Meinnel T, Giglione C. A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-repressible 5-Related N-Acetyltransferase2 Activity. Front Plant Sci 2022; 13:832144. [PMID: 35273627 PMCID: PMC8902505 DOI: 10.3389/fpls.2022.832144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 05/19/2023]
Abstract
Protein N-acetyltransferases (NATs) belong to the general control non-repressible 5 (Gcn5)-related N-acetyltransferases (GNATs) superfamily. GNATs catalyze the transfer of acetyl from acetyl-CoA to the reactive amine moiety of a wide range of acceptors. NAT sequences are difficult to distinguish from other members of the GNAT superfamily and there are many uncharacterized GNATs. To facilitate the discovery and characterization of new GNATs, we have developed a new continuous, non-radioactive assay. This assay is virtually independent of the substrate and can be used to get substrate specificity hints. We validated first the assay with the well-characterized Schizosaccharomyces pombe NatA (SpNatA). The SpNatA kinetic parameters were determined with various peptides confirming the robustness of the new assay. We reveal that the longer the peptide substrate the more efficient the enzyme. As a proof of concept of the relevance of the new assay, we characterized a NAA90 member from rice (Oryza sativa), OsGNAT2. We took advantage of an in vivo medium-scale characterization of OsGNAT2 specificity to identify and then validate in vitro several specific peptide substrates. With this assay, we reveal long-range synergic effects of basic residues on OsGNAT2 activity. Overall, this new, high-throughput assay allows better understanding of the substrate specificity and activity of any GNAT.
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Giglione C, Meinnel T. Mapping the myristoylome through a complete understanding of protein myristoylation biochemistry. Prog Lipid Res 2021; 85:101139. [PMID: 34793862 DOI: 10.1016/j.plipres.2021.101139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/22/2022]
Abstract
Protein myristoylation is a C14 fatty acid modification found in all living organisms. Myristoylation tags either the N-terminal alpha groups of cysteine or glycine residues through amide bonds or lysine and cysteine side chains directly or indirectly via glycerol thioester and ester linkages. Before transfer to proteins, myristate must be activated into myristoyl coenzyme A in eukaryotes or, in bacteria, to derivatives like phosphatidylethanolamine. Myristate originates through de novo biosynthesis (e.g., plants), from external uptake (e.g., human tissues), or from mixed origins (e.g., unicellular organisms). Myristate usually serves as a molecular anchor, allowing tagged proteins to be targeted to membranes and travel across endomembrane networks in eukaryotes. In this review, we describe and discuss the metabolic origins of protein-bound myristate. We review strategies for in vivo protein labeling that take advantage of click-chemistry with reactive analogs, and we discuss new approaches to the proteome-wide discovery of myristate-containing proteins. The machineries of myristoylation are described, along with how protein targets can be generated directly from translating precursors or from processed proteins. Few myristoylation catalysts are currently described, with only N-myristoyltransferase described to date in eukaryotes. Finally, we describe how viruses and bacteria hijack and exploit myristoylation for their pathogenicity.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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14
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. Trends Plant Sci 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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15
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Linster E, Layer D, Bienvenut WV, Dinh TV, Weyer FA, Leemhuis W, Brünje A, Hoffrichter M, Miklankova P, Kopp J, Lapouge K, Sindlinger J, Schwarzer D, Meinnel T, Finkemeier I, Giglione C, Hell R, Sinning I, Wirtz M. The Arabidopsis N α -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response. New Phytol 2020; 228:554-569. [PMID: 32548857 DOI: 10.1111/nph.16747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Trinh V Dinh
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Felix A Weyer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Wiebke Leemhuis
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Marion Hoffrichter
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Ruediger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
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16
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Armbruster L, Linster E, Boyer JB, Brünje A, Eirich J, Stephan I, Bienvenut WV, Weidenhausen J, Meinnel T, Hell R, Sinning I, Finkemeier I, Giglione C, Wirtz M. NAA50 Is an Enzymatically Active N α-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses. Plant Physiol 2020; 183:1502-1516. [PMID: 32461302 PMCID: PMC7401105 DOI: 10.1104/pp.20.00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/15/2020] [Indexed: 05/11/2023]
Abstract
Nα-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. In plants, the biological function of NTA remains enigmatic. The dominant N-acetyltransferase (Nat) in Arabidopsis (Arabidopsis thaliana) is NatA, which cotranslationally catalyzes acetylation of ∼40% of the proteome. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-anchoring subunit NAA15. In human (Homo sapiens), fruit fly (Drosophila melanogaster), and yeast (Saccharomyces cerevisiae), this core NatA complex interacts with NAA50 to form the NatE complex. While in metazoa, NAA50 has N-acetyltransferase activity, yeast NAA50 is catalytically inactive and positions NatA at the ribosome tunnel exit. Here, we report the identification and characterization of Arabidopsis NAA50 (AT5G11340). Consistent with its putative function as a cotranslationally acting Nat, AtNAA50-EYFP localized to the cytosol and the endoplasmic reticulum but also to the nuclei. We demonstrate that purified AtNAA50 displays Nα-terminal acetyltransferase and lysine-ε-autoacetyltransferase activity in vitro. Global N-acetylome profiling of Escherichia coli cells expressing AtNAA50 revealed conservation of NatE substrate specificity between plants and humans. Unlike the embryo-lethal phenotype caused by the absence of AtNAA10 and AtNAA15, loss of NAA50 expression resulted in severe growth retardation and infertility in two Arabidopsis transfer DNA insertion lines (naa50-1 and naa50-2). The phenotype of naa50-2 was rescued by the expression of HsNAA50 or AtNAA50. In contrast, the inactive ScNAA50 failed to complement naa50-2 Remarkably, loss of NAA50 expression did not affect NTA of known NatA substrates and caused the accumulation of proteins involved in stress responses. Overall, our results emphasize a relevant role of AtNAA50 in plant defense and development, which is independent of the essential NatA activity.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Annika Brünje
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | | | - Thierry Meinnel
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Carmela Giglione
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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17
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Bienvenut WV, Brünje A, Boyer J, Mühlenbeck JS, Bernal G, Lassowskat I, Dian C, Linster E, Dinh TV, Koskela MM, Jung V, Seidel J, Schyrba LK, Ivanauskaite A, Eirich J, Hell R, Schwarzer D, Mulo P, Wirtz M, Meinnel T, Giglione C, Finkemeier I. Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. Mol Syst Biol 2020; 16:e9464. [PMID: 32633465 PMCID: PMC7339202 DOI: 10.15252/msb.20209464] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
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Affiliation(s)
- Willy V Bienvenut
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Génétique Quantitative et ÉvolutionGif‐sur‐YvetteFrance
| | - Annika Brünje
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Jean‐Baptiste Boyer
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jens S Mühlenbeck
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Gautier Bernal
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute of Plant Sciences Paris‐SaclayGif‐sur‐YvetteFrance
| | - Ines Lassowskat
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Cyril Dian
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Eric Linster
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Trinh V Dinh
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Minna M Koskela
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
- Present address:
Institute of MicrobiologyTřeboňCzech Republic
| | - Vincent Jung
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute IMAGINEParisFrance
| | - Julian Seidel
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Laura K Schyrba
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Aiste Ivanauskaite
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Jürgen Eirich
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Rüdiger Hell
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Paula Mulo
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Markus Wirtz
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Thierry Meinnel
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Carmela Giglione
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Iris Finkemeier
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
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18
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Meinnel T, Dian C, Giglione C. Myristoylation, an Ancient Protein Modification Mirroring Eukaryogenesis and Evolution. Trends Biochem Sci 2020; 45:619-632. [PMID: 32305250 DOI: 10.1016/j.tibs.2020.03.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022]
Abstract
N-myristoylation (MYR) is a crucial fatty acylation catalyzed by N-myristoyltransferases (NMTs) that is likely to have appeared over 2 billion years ago. Proteome-wide approaches have now delivered an exhaustive list of substrates undergoing MYR across approximately 2% of any proteome, with constituents, several unexpected, associated with different membrane compartments. A set of <10 proteins conserved in eukaryotes probably represents the original set of N-myristoylated targets, marking major changes occurring throughout eukaryogenesis. Recent findings have revealed unexpected mechanisms and reactivity, suggesting competition with other acylations that are likely to influence cellular homeostasis and the steady state of the modification landscape. Here, we review recent advances in NMT catalysis, substrate specificity, and MYR proteomics, and discuss concepts regarding MYR during evolution.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Cyril Dian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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19
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Dian C, Pérez-Dorado I, Rivière F, Asensio T, Legrand P, Ritzefeld M, Shen M, Cota E, Meinnel T, Tate EW, Giglione C. High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat Commun 2020; 11:1132. [PMID: 32111831 PMCID: PMC7048800 DOI: 10.1038/s41467-020-14847-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 01/09/2023] Open
Abstract
The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states. Structural comparisons, together with biochemical analysis, provide unforeseen details about how NMT1 reaches a catalytically competent conformation in which the reactive groups are brought into close proximity to enable catalysis. We demonstrate that this mechanism further supports efficient and unprecedented myristoylation of an N-terminal lysine side chain, providing evidence that NMT acts both as N-terminal-lysine and glycine myristoyltransferase.
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Affiliation(s)
- Cyril Dian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
- Evotec Ltd, 114 Innovation Dr, Milton Park, Milton, Abingdon, OX14 4RZ, UK
| | - Frédéric Rivière
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Thomas Asensio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Pierre Legrand
- Synchrotron SOLEIL, Gif-sur-Yvette, Cedex, 91192, France
| | - Markus Ritzefeld
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Evotec SE, Essener Bogen 7, Hamburg, 22419, Germany
| | - Mengjie Shen
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Oakland Innovation, Mill Rd, Harston, Cambridge, CB22 7GG, UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
| | - Edward W Tate
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Rd, London, NW 1AT, UK.
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
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20
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Huber M, Bienvenut WV, Linster E, Stephan I, Armbruster L, Sticht C, Layer D, Lapouge K, Meinnel T, Sinning I, Giglione C, Hell R, Wirtz M. NatB-Mediated N-Terminal Acetylation Affects Growth and Biotic Stress Responses. Plant Physiol 2020; 182:792-806. [PMID: 31744933 PMCID: PMC6997699 DOI: 10.1104/pp.19.00792] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/07/2019] [Indexed: 05/22/2023]
Abstract
N∝-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes. In humans, NTA is catalyzed by seven Nα-acetyltransferases (NatA-F and NatH). Remarkably, the plant Nat machinery and its biological relevance remain poorly understood, although NTA has gained recognition as a key regulator of crucial processes such as protein turnover, protein-protein interaction, and protein targeting. In this study, we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics, and physiological assays to characterize the Arabidopsis (Arabidopsis thaliana) NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of the wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, and naa25-1) caused a 50% decrease in plant growth. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, whereas yeast NAA20 failed to complement naa20-1 Quantitative N-terminomics of approximately 1000 peptides identified 32 bona fide substrates of the plant NatB complex. In vivo, NatB was seen to preferentially acetylate N termini starting with the initiator Met followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. Global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. Indeed, loss of NatB function, but not NatA, increased plant sensitivity toward osmotic and high-salt stress, indicating that NatB is required for tolerance of these abiotic stressors.
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Affiliation(s)
- Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Dominik Layer
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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21
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. Annu Rev Plant Biol 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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22
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Apel C, Bignon J, Garcia-Alvarez MC, Ciccone S, Clerc P, Grondin I, Girard-Valenciennes E, Smadja J, Lopes P, Frédérich M, Roussi F, Meinnel T, Giglione C, Litaudon M. N-myristoyltransferases inhibitory activity of ellagitannins from Terminalia bentzoë (L.) L. f. subsp. bentzoë. Fitoterapia 2018; 131:91-95. [PMID: 30342177 DOI: 10.1016/j.fitote.2018.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022]
Abstract
N-myristoylation (Myr) is an eukaryotic N-terminal co- or post-translational protein modification in which the enzyme N-myristoyltransferase (NMT) transfers a fatty acid (C14:0) to the N-terminal glycine residues of several cellular key proteins. Depending on the cellular context, NMT may serve as a molecular target in anticancer or anti-infectious therapy, and drugs that inhibit this enzyme may be useful in the treatment of cancer or infectious diseases. As part of an on-going project to identify natural Homo sapiens N-myristoyltransferase 1 inhibitors (HsNMT1), two ellagitannins, punicalagin (1) and isoterchebulin (2), along with eschweilenol C (3) and ellagic acid (4) were isolated from the bark of Terminalia bentzoë (L.) L. f. subsp. bentzoë. Their structures were determined by means of spectroscopic analyses and comparison with literature data. Punicalagin (1) and isoterchebulin (2) showed significant inhibitory activity towards HsNMT1, and also against Plasmodium falciparum NMT (PfNMT) both in vitro and in cellulo, opening alternative paths for new NMT inhibitors development. This is the first report identifying natural products from a botanical source as inhibitors of HsNMT and PfNMT.
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Affiliation(s)
- Cécile Apel
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France.
| | - Jérôme Bignon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France
| | - María Concepción Garcia-Alvarez
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France
| | - Sarah Ciccone
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Patricia Clerc
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion, 15, Avenue rené Cassin, CS 92003-97744 Saint-Denis cedex 9, France
| | - Isabelle Grondin
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion, 15, Avenue rené Cassin, CS 92003-97744 Saint-Denis cedex 9, France
| | - Emmanuelle Girard-Valenciennes
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion, 15, Avenue rené Cassin, CS 92003-97744 Saint-Denis cedex 9, France
| | - Jacqueline Smadja
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion, 15, Avenue rené Cassin, CS 92003-97744 Saint-Denis cedex 9, France
| | - Philippe Lopes
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France
| | - Michel Frédérich
- Université de Liège, CIRM (Centre Interfacultaire de Recherche sur le Médicament), Laboratoire de Pharmacognosie, Liège, Belgium
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay, 91198 cedex, Gif-sur-Yvette, France.
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Majeran W, Le Caer JP, Ponnala L, Meinnel T, Giglione C. Targeted Profiling of Arabidopsis thaliana Subproteomes Illuminates Co- and Posttranslationally N-Terminal Myristoylated Proteins. Plant Cell 2018; 30:543-562. [PMID: 29453228 PMCID: PMC5894833 DOI: 10.1105/tpc.17.00523] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/02/2018] [Accepted: 02/15/2018] [Indexed: 05/05/2023]
Abstract
N-terminal myristoylation, a major eukaryotic protein lipid modification, is difficult to detect in vivo and challenging to predict in silico. We developed a proteomics strategy involving subfractionation of cellular membranes, combined with separation of hydrophobic peptides by mass spectrometry-coupled liquid chromatography to identify the Arabidopsis thaliana myristoylated proteome. This approach identified a starting pool of 8837 proteins in all analyzed cellular fractions, comprising 32% of the Arabidopsis proteome. Of these, 906 proteins contain an N-terminal Gly at position 2, a prerequisite for myristoylation, and 214 belong to the predicted myristoylome (comprising 51% of the predicted myristoylome of 421 proteins). We further show direct evidence of myristoylation in 72 proteins; 18 of these myristoylated proteins were not previously predicted. We found one myristoylation site downstream of a predicted initiation codon, indicating that posttranslational myristoylation occurs in plants. Over half of the identified proteins could be quantified and assigned to a subcellular compartment. Hierarchical clustering of protein accumulation combined with myristoylation and S-acylation data revealed that N-terminal double acylation influences redirection to the plasma membrane. In a few cases, MYR function extended beyond simple membrane association. This study identified hundreds of N-acylated proteins for which lipid modifications could control protein localization and expand protein function.
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Affiliation(s)
- Wojciech Majeran
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Jean-Pierre Le Caer
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14850
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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Grzela R, Nusbaum J, Fieulaine S, Lavecchia F, Desmadril M, Nhiri N, Van Dorsselaer A, Cianferani S, Jacquet E, Meinnel T, Giglione C. Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts. Biochim Biophys Acta Proteins Proteom 2017; 1866:348-355. [PMID: 29101077 DOI: 10.1016/j.bbapap.2017.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 01/06/2023]
Abstract
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 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF 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.
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Affiliation(s)
- Renata Grzela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Julien Nusbaum
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Francesco Lavecchia
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Michel Desmadril
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, UPR2301, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR2301, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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25
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Grzela R, Nusbaum J, Fieulaine S, Lavecchia F, Bienvenut WV, Dian C, Meinnel T, Giglione C. The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation. Sci Rep 2017; 7:11041. [PMID: 28887476 PMCID: PMC5591237 DOI: 10.1038/s41598-017-11329-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Renata Grzela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Julien Nusbaum
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France
| | - Francesco Lavecchia
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France
| | - Cyril Dian
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, Paris, France.
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26
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Fieulaine S, Alves de Sousa R, Maigre L, Hamiche K, Alimi M, Bolla JM, Taleb A, Denis A, Pagès JM, Artaud I, Meinnel T, Giglione C. Erratum: Corrigendum: A unique peptide deformylase platform to rationally design and challenge novel active compounds. Sci Rep 2017; 7:39365. [PMID: 28074917 PMCID: PMC5225600 DOI: 10.1038/srep39365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Bienvenut WV, Scarpelli JP, Dumestier J, Meinnel T, Giglione C. EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. BMC Bioinformatics 2017; 18:182. [PMID: 28320318 PMCID: PMC5359831 DOI: 10.1186/s12859-017-1595-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 03/10/2017] [Indexed: 01/01/2023] Open
Abstract
Background Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles, such as mitochondria or chloroplast. Protein neo-N-termini can be located up to 100–150 amino acids downstream from the initiator methionine and are not easily predictable. Although some bioinformatics tools are available, they usually require extensive manual validation to identify the exact N-terminal position. The situation becomes even more complex when post-translational modifications take place at the neo-N-terminus. Although N-terminal acetylation occurs mostly in the cytosol, it is also observed in some organelles such as chloroplast. To date, no bioinformatics tool is available to define mature protein starting positions, the associated N-terminus acetylation status and/or yield for each proteoform. In this context, we have developed the EnCOUNTer tool (i) to score all characterized peptides using discriminating parameters to identify bona fide mature protein N-termini and (ii) to determine the N-terminus acetylation yield of the most reliable ones. Results Based on large scale proteomics analyses using the SILProNAQ methodology, tandem mass spectrometry favoured the characterization of thousands of peptides. Data processing using the EnCOUNTer tool provided an efficient and rapid way to extract the most reliable mature protein N-termini. Selected peptides were subjected to N-terminus acetylation yield determination. In an A. thaliana cell lysate, 1232 distinct proteotypic N-termini were characterized of which 648 were located at the predicted protein N-terminus (position 1/2) and 584 were located further downstream (starting at position > 2). A large number of these N-termini were associated with various well-defined maturation processes occurring on organelle-targeted proteins (mitochondria, chloroplast and peroxisome), secreted proteins or membrane-targeted proteins. It was also possible to highlight some protein alternative starts, splicing variants or erroneous protein sequence predictions. Conclusions The EnCOUNTer tool provides a unique way to extract accurately the most relevant mature proteins N-terminal peptides from large scale experimental datasets. Such data processing allows the identification of the exact N-terminus position and the associated acetylation yield. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1595-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Willy Vincent Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Jean-Pierre Scarpelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Johan Dumestier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
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Bienvenut WV, Giglione C, Meinnel T. SILProNAQ: A Convenient Approach for Proteome-Wide Analysis of Protein N-Termini and N-Terminal Acetylation Quantitation. Methods Mol Biol 2017; 1574:17-34. [PMID: 28315241 DOI: 10.1007/978-1-4939-6850-3_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein N-terminal modifications have recently been involved in overall proteostasis through their impact on cell fate and protein life time. This explains the development of new approaches to characterize more precisely the N-terminal end of mature proteins. Although few approaches are available to perform N-terminal enrichment based on positive or negative discriminations, these methods are usually restricted to the enrichment in N-terminal peptides and their characterization by mass spectrometry. Recent investigation highlights both (1) the knowledge of the N-terminal acetylation status of most cytosolic proteins and (2) post-translational addition of this modification on the N-terminus of nuclear coded chloroplast proteins imported in the plastid and after the cleavage of the transit peptide. The workflow involves stable isotope labeling to assess N-acetylation rates followed by Strong Cation eXchange (SCX ) fractionation of the samples to provide protein N-terminal enriched fractions. Combined with mass spectrometry analyses, the technology finally requires extensive data processing. This last step aims first at discriminating the most relevant mature N-termini from the characterized peptides, next at determining its experimental position and then at calculating the N-terminal acetylation yield. Stable-Isotope Protein N-terminal Acetylation Quantification (SILProNAQ) is a complete workflow combining wet-lab techniques together with dry-lab processing to determine the N-terminal acetylation yield of mature proteins for a clearly defined localization.
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
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29
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Bienvenut WV, Giglione C, Meinnel T. Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition. Proteomics 2016; 15:2503-18. [PMID: 26017780 DOI: 10.1002/pmic.201500027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022]
Abstract
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).
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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Breiman A, Fieulaine S, Meinnel T, Giglione C. The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks. Biochim Biophys Acta 2015; 1864:531-50. [PMID: 26555180 DOI: 10.1016/j.bbapap.2015.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023]
Abstract
The ribosome is the cell's protein-making factory, a huge protein-RNA complex, that is essential to life. Determining the high-resolution structures of the stable "core" of this factory was among the major breakthroughs of the past decades, and was awarded the Nobel Prize in 2009. Now that the mysteries of the ribosome appear to be more traceable, detailed understanding of the mechanisms that regulate protein synthesis includes not only the well-known steps of initiation, elongation, and termination but also the less comprehended features of the co-translational events associated with the maturation of the nascent chains. The ribosome is a platform for co-translational events affecting the nascent polypeptide, including protein modifications, folding, targeting to various cellular compartments for integration into membrane or translocation, and proteolysis. These events are orchestrated by ribosome-associated protein biogenesis factors (RPBs), a group of a dozen or more factors that act as the "welcoming committee" for the nascent chain as it emerges from the ribosome. In plants these factors have evolved to fit the specificity of different cellular compartments: cytoplasm, mitochondria and chloroplast. This review focuses on the current state of knowledge of these factors and their interaction around the exit tunnel of dedicated ribosomes. Particular attention has been accorded to the plant system, highlighting the similarities and differences with other organisms.
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Affiliation(s)
- Adina Breiman
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sonia Fieulaine
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France.
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Abstract
N-terminal protein modifications correspond to the first modifications which in principle any protein may undergo, before translation is completed by the ribosome. This class of essential modifications can have different nature or function and be catalyzed by a variety of dedicated enzymes. Here, we review the current state of the major N-terminal co-translational modifications, with a particular emphasis to their catalysts, which belong to metalloprotease and acyltransferase clans. The earliest of these modifications corresponds to the N-terminal methionine excision, an ubiquitous and essential process leading to the removal of the first methionine. N-alpha acetylation occurs also in all Kingdoms although its extent appears to be significantly increased in higher eukaryotes. Finally, N-myristoylation is a crucial pathway existing only in eukaryotes. Recent studies dealing on how some of these co-translational modifiers might work in close vicinity of the ribosome is starting to provide new information on when these modifications exactly take place on the elongating nascent chain and the interplay with other ribosome biogenesis factors taking in charge the nascent chains. Here a comprehensive overview of the recent advances in the field of N-terminal protein modifications is given.
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Affiliation(s)
- Carmela Giglione
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
| | - Sonia Fieulaine
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
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Dinh TV, Bienvenut WV, Linster E, Feldman-Salit A, Jung VA, Meinnel T, Hell R, Giglione C, Wirtz M. Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling. Proteomics 2015; 15:2426-35. [PMID: 25951519 PMCID: PMC4692087 DOI: 10.1002/pmic.201500025] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/20/2015] [Accepted: 04/30/2015] [Indexed: 11/07/2022]
Abstract
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).
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Affiliation(s)
- Trinh V Dinh
- Department of Plant Molecular Biology, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Willy V Bienvenut
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-SudGif-sur-Yvette, France
| | - Eric Linster
- Department of Plant Molecular Biology, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School, University of HeidelbergHeidelberg, Germany
| | - Anna Feldman-Salit
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies gGbmHHeidelberg, Germany
| | - Vincent A Jung
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-SudGif-sur-Yvette, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-SudGif-sur-Yvette, France
| | - Rüdiger Hell
- Department of Plant Molecular Biology, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-SudGif-sur-Yvette, France
| | - Markus Wirtz
- Department of Plant Molecular Biology, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
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Xu F, Huang Y, Li L, Gannon P, Linster E, Huber M, Kapos P, Bienvenut W, Polevoda B, Meinnel T, Hell R, Giglione C, Zhang Y, Wirtz M, Chen S, Li X. Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis. Plant Cell 2015; 27:1547-62. [PMID: 25966763 PMCID: PMC4456647 DOI: 10.1105/tpc.15.00173] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/09/2015] [Accepted: 04/16/2015] [Indexed: 05/22/2023]
Abstract
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.
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Affiliation(s)
- Fang Xu
- Michael Smith Laboratories, University of British Columbia, British Columbia V6T 1Z4, Canada Department of Botany, University of British Columbia, British Columbia V6T 1Z4, Canada
| | - Yan Huang
- Michael Smith Laboratories, University of British Columbia, British Columbia V6T 1Z4, Canada Department of Botany, University of British Columbia, British Columbia V6T 1Z4, Canada College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625000, PR China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, PR China
| | - Patrick Gannon
- Michael Smith Laboratories, University of British Columbia, British Columbia V6T 1Z4, Canada Department of Botany, University of British Columbia, British Columbia V6T 1Z4, Canada
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Paul Kapos
- Michael Smith Laboratories, University of British Columbia, British Columbia V6T 1Z4, Canada
| | - Willy Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, 91198 Gif sur Yvette Cedex, France
| | | | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, 91198 Gif sur Yvette Cedex, France
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, 91198 Gif sur Yvette Cedex, France
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, British Columbia V6T 1Z4, Canada
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, PR China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, British Columbia V6T 1Z4, Canada Department of Botany, University of British Columbia, British Columbia V6T 1Z4, Canada
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Kapos P, Xu F, Meinnel T, Giglione C, Li X. N-terminal modifications contribute to flowering time and immune response regulations. Plant Signal Behav 2015; 10:e1073874. [PMID: 26361095 PMCID: PMC4883885 DOI: 10.1080/15592324.2015.1073874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 05/26/2023]
Abstract
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.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
| | - Fang Xu
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS, University Paris-Sud; Gif sur Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS, University Paris-Sud; Gif sur Yvette, France
| | - Xin Li
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
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Stojko J, Fieulaine S, Petiot-Bécard S, Van Dorsselaer A, Meinnel T, Giglione C, Cianférani S. Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes. Analyst 2015; 140:7234-45. [DOI: 10.1039/c5an01311a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Native and ion-mobility mass spectrometry reveal the conformational evolution over time of a peptide deformylase binding different ligands, which is consistent with slow-tight inhibition of the enzyme.
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Affiliation(s)
- Johann Stojko
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Stéphanie Petiot-Bécard
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
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Mardirossian M, Grzela R, Giglione C, Meinnel T, Gennaro R, Mergaert P, Scocchi M. The host antimicrobial peptide Bac71-35 binds to bacterial ribosomal proteins and inhibits protein synthesis. ACTA ACUST UNITED AC 2014; 21:1639-47. [PMID: 25455857 DOI: 10.1016/j.chembiol.2014.10.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/03/2014] [Accepted: 10/06/2014] [Indexed: 11/15/2022]
Abstract
Antimicrobial peptides (AMPs) are molecules from innate immunity with high potential as novel anti-infective agents. Most of them inactivate bacteria through pore formation or membrane barrier disruption, but others cross the membrane without damages and act inside the cells, affecting vital processes. However, little is known about their intracellular bacterial targets. Here we report that Bac71-35, a proline-rich AMP belonging to the cathelicidin family, can reach high concentrations (up to 340 μM) inside the E. coli cytoplasm. The peptide specifically and completely inhibits in vitro translation in the micromolar concentration range. Experiments of incorporation of radioactive precursors in macromolecules with E. coli cells confirmed that Bac71-35 affects specifically protein synthesis. Ribosome coprecipitation and crosslinking assays showed that the peptide interacts with ribosomes, binding to a limited subset of ribosomal proteins. Overall, these results indicate that the killing mechanism of Bac71-35 is based on a specific block of protein synthesis.
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Affiliation(s)
- Mario Mardirossian
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy
| | - Renata Grzela
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy
| | - Peter Mergaert
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy.
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Meinnel T, Castrec B, Traverso J, Majeran W, Giglione C. Protein N‐terminal N‐myristoylation at the proteome scale (587.1). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.587.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Giglione C, Grzela R, Bron P, Lai Kee Him J, Fieulaine S, Nusbaum J, Pozza A, Bienvenut W, Meinnel T. A viral peptide deformylase‐ribosome complex reveals mechanism of host gene expression control (558.2). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.558.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carmela Giglione
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
- Centre DE Biologie Structurale Inserm‐CNRSMontpellierFrance
| | - Renata Grzela
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
| | - Patrick Bron
- Centre DE Biologie Structurale Inserm‐CNRSMontpellierFrance
| | | | - Sonia Fieulaine
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
| | - Julien Nusbaum
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
| | - Alexandre Pozza
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
| | - Willy Bienvenut
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
| | - Thierry Meinnel
- Protein maturation, cell fate and Therapeutics CNRSGif sur YvetteFrance
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Fieulaine S, Desmadril M, Meinnel T, Giglione C. Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart. ACTA ACUST UNITED AC 2014; 70:242-52. [DOI: 10.1107/s1399004713026461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/24/2013] [Indexed: 11/11/2022]
Abstract
Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of theN-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeablein vivoand display similar propertiesin vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.
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Traverso JA, Giglione C, Meinnel T. High-throughput profiling of N-myristoylation substrate specificity across species including pathogens. Proteomics 2013; 13:25-36. [PMID: 23165749 DOI: 10.1002/pmic.201200375] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Abstract
One of the most critical modifications affecting the N-terminus of proteins is N-myristoylation. This irreversible modification affects the membrane-binding properties of crucial proteins involved in signal transduction cascades. This cotranslational modification, catalyzed by N-myristoyl transferase, occurs both in lower and higher eukaryotes and is a validated therapeutic target for several pathologies. However, this lipidation proves very difficult to be evidenced in vivo even with state-of-the-art proteomics approaches or bioinformatics tools. A large part of N-myristoylated proteins remains to be discovered and the rules of substrate specificity need to be established in each organism. Because the peptide substrate recognition occurs around the first eight residues, short peptides are used for modeling the reaction in vitro. Here, we provide a novel approach including a dedicated peptide array for high-throughput profiling protein N-myristoylation specificity. We show that myristoylation predictive tools need to be fine-tuned to organisms and that their poor accuracy should be significantly enhanced. This should lead to strongly improved knowledge of the number and function of myristoylated proteins occurring in any proteome.
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Affiliation(s)
- José A Traverso
- CNRS, Centre de Recherche de Gif, Institut des Sciences du Végétal, Gif-sur-Yvette, France
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Renna L, Stefano G, Majeran W, Micalella C, Meinnel T, Giglione C, Brandizzi F. Golgi traffic and integrity depend on N-myristoyl transferase-1 in Arabidopsis. Plant Cell 2013; 25:1756-73. [PMID: 23673980 PMCID: PMC3694704 DOI: 10.1105/tpc.113.111393] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
N-myristoylation is a crucial irreversible eukaryotic lipid modification allowing a key subset of proteins to be targeted at the periphery of specific membrane compartments. Eukaryotes have conserved N-myristoylation enzymes, involving one or two N-myristoyltransferases (NMT1 and NMT2), among which NMT1 is the major enzyme. In the postembryonic developmental stages, defects in NMT1 lead to aberrant cell polarity, flower differentiation, fruit maturation, and innate immunity; however, no specific NMT1 target responsible for such deficiencies has hitherto been identified. Using a confocal microscopy forward genetics screen for the identification of Arabidopsis thaliana secretory mutants, we isolated STINGY, a recessive mutant with defective Golgi traffic and integrity. We mapped STINGY to a substitution at position 160 of Arabidopsis NMT1 (NMT1A160T). In vitro kinetic studies with purified NMT1A160T enzyme revealed a significant reduction in its activity due to a remarkable decrease in affinity for both myristoyl-CoA and peptide substrates. We show here that this recessive mutation is responsible for the alteration of Golgi traffic and integrity by predominantly affecting the Golgi membrane/cytosol partitioning of ADP-ribosylation factor proteins. Our results provide important functional insight into N-myristoylation in plants by ascribing postembryonic functions of Arabidopsis NMT1 that involve regulation of the functional and morphological integrity of the plant endomembranes.
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Affiliation(s)
- Luciana Renna
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Giovanni Stefano
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Wojciech Majeran
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Chiara Micalella
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Federica Brandizzi
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Address correspondence to
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Traverso JA, Micalella C, Martinez A, Brown SC, Satiat-Jeunemaître B, Meinnel T, Giglione C. Roles of N-terminal fatty acid acylations in membrane compartment partitioning: Arabidopsis h-type thioredoxins as a case study. Plant Cell 2013; 25:1056-77. [PMID: 23543785 PMCID: PMC3634677 DOI: 10.1105/tpc.112.106849] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/22/2013] [Accepted: 03/04/2013] [Indexed: 05/18/2023]
Abstract
N-terminal fatty acylations (N-myristoylation [MYR] and S-palmitoylation [PAL]) are crucial modifications affecting 2 to 4% of eukaryotic proteins. The role of these modifications is to target proteins to membranes. Predictive tools have revealed unexpected targets of these acylations in Arabidopsis thaliana and other plants. However, little is known about how N-terminal lipidation governs membrane compartmentalization of proteins in plants. We show here that h-type thioredoxins (h-TRXs) cluster in four evolutionary subgroups displaying strictly conserved N-terminal modifications. It was predicted that one subgroup undergoes only MYR and another undergoes both MYR and PAL. We used plant TRXs as a model protein family to explore the effect of MYR alone or MYR and PAL in the same family of proteins. We used a high-throughput biochemical strategy to assess MYR of specific TRXs. Moreover, various TRX-green fluorescent protein fusions revealed that MYR localized protein to the endomembrane system and that partitioning between this membrane compartment and the cytosol correlated with the catalytic efficiency of the N-myristoyltransferase acting at the N terminus of the TRXs. Generalization of these results was obtained using several randomly selected Arabidopsis proteins displaying a MYR site only. Finally, we demonstrated that a palmitoylatable Cys residue flanking the MYR site is crucial to localize proteins to micropatching zones of the plasma membrane.
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Affiliation(s)
- José A. Traverso
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, C/ Profesor Albareda 1, Granada, Spain
| | - Chiara Micalella
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Aude Martinez
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Spencer C. Brown
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Béatrice Satiat-Jeunemaître
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Centre National de la Recherche Scientifique, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
- Address correspondence to
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Bienvenut WV, Sumpton D, Lilla S, Martinez A, Meinnel T, Giglione C. Influence of various endogenous and artefact modifications on large-scale proteomics analysis. Rapid Commun Mass Spectrom 2013; 27:443-450. [PMID: 23280976 DOI: 10.1002/rcm.6474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/16/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Some large-scale proteomics studies in which strong cation exchange chromatography has been applied are used to determine proteomes and post-translational modification dynamics. Although such datasets favour the characterisation of thousands of modified peptides, e.g., phosphorylated and N-α-acetylated, a large fraction of the acquired spectra remain unexplained by standard proteomics approaches. Thus, advanced data processing allows characterisation of a significant part of these unassigned spectra. METHODS Our recent investigation of the N-α-acetylation status of plant proteins gave a dataset of choice to investigate further the in-depth characterisation of peptide modifications using Mascot tools associated with relevant validation processes. Such an approach allows to target frequently occurring modifications such as methionine oxidation, phosphorylation or N-α-acetylation, but also the less usual peptide cationisation. Finally, this dataset offers the unique opportunity to determine the overall influence of some of these modifications on the identification score. RESULTS Although methionine oxidation has no influence and tends to favour the characterisation of protein N-terminal peptides, peptide alkalinisation shows an adverse effect on peptide average score. Nevertheless, peptide cationisation appears to favour the characterisation of protein C-terminal peptides with a limited to no direct influence on the identification score. Unexpectedly, our investigation reveals the unfortunate combination of the molecular weight of N-α-acetylation and potassium cation that mimics the mass increment of a phosphorylation group. CONCLUSIONS Since these characterisations rely upon computational treatment associated with statistical validation approaches such as 'False discovery rates' calculation or post-translational modification position validation, our investigation highlights the limitation of such treatment which is biased by the initial searched hypotheses.
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Affiliation(s)
- Willy V Bienvenut
- CNRS, ISV, UPR2355, Bâtiment 23A, 1 avenue de la Terrasse, F-91198, Gif-sur-Yvette Cedex, France.
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Padovani D, Zeghouf M, Traverso JA, Giglione C, Cherfils J. High yield production of myristoylated Arf6 small GTPase by recombinant N-myristoyl transferase. Small GTPases 2013; 4:3-8. [PMID: 23319116 DOI: 10.4161/sgtp.22895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Small GTP-binding proteins of the Arf family (Arf GTPases) interact with multiple cellular partners and with membranes to regulate intracellular traffic and organelle structure. Understanding the underlying molecular mechanisms requires in vitro biochemical assays to test for regulations and functions. Such assays should use proteins in their cellular form, which carry a myristoyl lipid attached in N-terminus. N-myristoylation of recombinant Arf GTPases can be achieved by co-expression in E. coli with a eukaryotic N-myristoyl transferase. However, purifying myristoylated Arf GTPases is difficult and has a poor overall yield. Here we show that human Arf6 can be N-myristoylated in vitro by recombinant N-myristoyl transferases from different eukaryotic species. The catalytic efficiency depended strongly on the guanine nucleotide state and was highest for Arf6-GTP. Large-scale production of highly pure N-myristoylated Arf6 could be achieved, which was fully functional for liposome-binding and EFA6-stimulated nucleotide exchange assays. This establishes in vitro myristoylation as a novel and simple method that could be used to produce other myristoylated Arf and Arf-like GTPases for biochemical assays.
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Affiliation(s)
- Dominique Padovani
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif (CNRS), Gif-sur-Yvette, France
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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, Pagès JM. New peptide deformylase inhibitors and cooperative interaction: a combination to improve antibacterial activity. J Antimicrob Chemother 2012; 67:1392-400. [PMID: 22378679 DOI: 10.1093/jac/dks058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES Bacterial drug resistance is a worrying public health problem and there is an urgent need for research and development to provide new antibacterial molecules. Peptide deformylase (PDF) is now a well-described intracellular target selected for the design of a new antibiotic group, PDF inhibitors (PDFIs). The initial bacterial susceptibility to an inhibitor of a cytoplasmic target is directly associated with the diffusion of the compound through the membrane barrier of Gram-negative bacteria and with its cytosolic accumulation at the required concentration. METHODS We have recently demonstrated that the activity of different PDFIs is strongly dependent on the accumulation of the active molecules by using permeabilizing agents, efflux inhibitors or efflux-mutated strains. In this work we assessed various combination protocols using different putative inhibitors (PDFIs, methionine aminopeptidase inhibitors etc.) to improve antibacterial activity against various resistant Gram-negative bacteria. RESULTS The maximum effect was observed when combining actinonin with a dual inhibitor of methionine aminopeptidase and PDF, this molecule being also able to interact with the target while actinonin is bound to the PDF active site. CONCLUSIONS Such a combination of inhibitors acting on two tightly associated metabolic steps results in a cooperative effect on bacterial cells and opens an original way to combat multidrug-resistant bacteria.
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Affiliation(s)
- Emilie Goemaere
- UMR-MD1, Transporteurs Membranaires, Chimiorésistance et Drug-Design, Aix-Marseille Université, IRBA, Marseille, France
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Bienvenut WV, Sumpton D, Martinez A, Lilla S, Espagne C, Meinnel T, Giglione C. Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Mol Cell Proteomics 2012; 11:M111.015131. [PMID: 22223895 DOI: 10.1074/mcp.m111.015131] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
N-terminal modifications play a major role in the fate of proteins in terms of activity, stability, or subcellular compartmentalization. Such modifications remain poorly described and badly characterized in proteomic studies, and only a few comparison studies among organisms have been made available so far. Recent advances in the field now allow the enrichment and selection of N-terminal peptides in the course of proteome-wide mass spectrometry analyses. These targeted approaches unravel as a result the extent and nature of the protein N-terminal modifications. Here, we aimed at studying such modifications in the model plant Arabidopsis thaliana to compare these results with those obtained from a human sample analyzed in parallel. We applied large scale analysis to compile robust conclusions on both data sets. Our data show strong convergence of the characterized modifications especially for protein N-terminal methionine excision, co-translational N-α-acetylation, or N-myristoylation between animal and plant kingdoms. Because of the convergence of both the substrates and the N-α-acetylation machinery, it was possible to identify the N-acetyltransferases involved in such modifications for a small number of model plants. Finally, a high proportion of nuclear-encoded chloroplast proteins feature post-translational N-α-acetylation of the mature protein after removal of the transit peptide. Unlike animals, plants feature in a dedicated pathway for post-translational acetylation of organelle-targeted proteins. The corresponding machinery is yet to be discovered.
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Affiliation(s)
- Willy V Bienvenut
- CNRS, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
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Adam Z, Frottin F, Espagne C, Meinnel T, Giglione C. Interplay between N-terminal methionine excision and FtsH protease is essential for normal chloroplast development and function in Arabidopsis. Plant Cell 2011; 23:3745-60. [PMID: 22010036 PMCID: PMC3229147 DOI: 10.1105/tpc.111.087239] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
N-terminal methionine excision (NME) is the earliest modification affecting most proteins. All compartments in which protein synthesis occurs contain dedicated NME machinery. Developmental defects induced in Arabidopsis thaliana by NME inhibition are accompanied by increased proteolysis. Although increasing evidence supports a connection between NME and protein degradation, the identity of the proteases involved remains unknown. Here we report that chloroplastic NME (cNME) acts upstream of the FtsH protease complex. Developmental defects and higher sensitivity to photoinhibition associated with the ftsh2 mutation were abolished when cNME was inhibited. Moreover, the accumulation of D1 and D2 proteins of the photosystem II reaction center was always dependent on the prior action of cNME. Under standard light conditions, inhibition of chloroplast translation induced accumulation of correctly NME-processed D1 and D2 in a ftsh2 background, implying that the latter is involved in protein quality control, and that correctly NME-processed D1 and D2 are turned over primarily by the thylakoid FtsH protease complex. By contrast, inhibition of cNME compromises the specific N-terminal recognition of D1 and D2 by the FtsH complex, whereas the unprocessed forms are recognized by other proteases. Our results highlight the tight functional interplay between NME and the FtsH protease complex in the chloroplast.
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Affiliation(s)
- Zach Adam
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Frédéric Frottin
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Christelle Espagne
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
- Address correspondence to
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Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biol 2011; 9:e1001066. [PMID: 21629676 PMCID: PMC3101196 DOI: 10.1371/journal.pbio.1001066] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 04/14/2011] [Indexed: 11/18/2022] Open
Abstract
For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally “zipped up” by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A “movie” that reconstructs this entire process can be further extrapolated to catalysis. The notion of induced fit when a protein binds its ligand—like a glove adapting to the shape of a hand—is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the “conformational change.” In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the “slow, tight-binding” of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis.
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Affiliation(s)
| | | | - Isabelle Artaud
- Université Paris Descartes, UMR8601, Paris, France
- CNRS, UMR8601, Paris, France
| | - Michel Desmadril
- Université Paris-Sud, IBBMC, UMR8619, Orsay, France
- CNRS, IBBMC, UMR8619, Orsay, France
| | - Frédéric Dardel
- Université Paris Descartes, UMR8015, Paris, France
- CNRS, UMR8015, Paris, France
| | - Thierry Meinnel
- CNRS, ISV, UPR2355, Gif-sur-Yvette, France
- * E-mail: (TM); (CG)
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Bienvenut WV, Espagne C, Martinez A, Majeran W, Valot B, Zivy M, Vallon O, Adam Z, Meinnel T, Giglione C. Dynamics of post-translational modifications and protein stability in the stroma of Chlamydomonas reinhardtii chloroplasts. Proteomics 2011; 11:1734-50. [PMID: 21462344 DOI: 10.1002/pmic.201000634] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 11/10/2010] [Accepted: 11/29/2010] [Indexed: 01/09/2023]
Abstract
The proteome of any system is a dynamic entity dependent on the intracellular concentration of the entire set of expressed proteins. In turn, this whole protein concentration will be reliant on the stability/turnover of each protein as dictated by their relative rates of synthesis and degradation. In this study, we have investigated the dynamics of the stromal proteome in the model organism Chlamydomonas reinhardtii by characterizing the half-life of the whole set of proteins. 2-DE stromal proteins profiling was set up and coupled with MS analyses. These identifications featuring an average of 26% sequence coverage and eight non-redundant peptides per protein have been obtained for 600 independent samples related to 253 distinct spots. An interactive map of the global stromal proteome, of 274 distinct protein variants is now available on-line at http://www.isv.cnrs-gif.fr/gel2dv2/. N-α-terminal-Acetylation (NTA) was noticed to be the most frequently detectable post-translational modification, and new experimental data related to the chloroplastic transit peptide cleavage site was obtained. Using this data set supplemented with series of pulse-chase experiments, elements directing the relationship between half-life and N-termini were analyzed. Positive correlation between NTA and protein half-life suggests that NTA could contribute to protein stabilization in the stroma.
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Frottin F, Espagne C, Traverso JA, Mauve C, Valot B, Lelarge-Trouverie C, Zivy M, Noctor G, Meinnel T, Giglione C. Cotranslational proteolysis dominates glutathione homeostasis to support proper growth and development. Plant Cell 2009; 21:3296-314. [PMID: 19855051 PMCID: PMC2782297 DOI: 10.1105/tpc.109.069757] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/17/2009] [Accepted: 10/05/2009] [Indexed: 05/18/2023]
Abstract
The earliest proteolytic event affecting most proteins is the excision of the initiating Met (NME). This is an essential and ubiquitous cotranslational process tightly regulated in all eukaryotes. Currently, the effects of NME on unknown complex cellular networks and the ways in which its inhibition leads to developmental defects and cell growth arrest remain poorly understood. Here, we provide insight into the earliest molecular mechanisms associated with the inhibition of the NME process in Arabidopsis thaliana. We demonstrate that the developmental defects induced by NME inhibition are caused by an increase in cellular proteolytic activity, primarily induced by an increase in the number of proteins targeted for rapid degradation. This deregulation drives, through the increase of the free amino acids pool, a perturbation of the glutathione homeostasis, which corresponds to the earliest limiting, reversible step promoting the phenotype. We demonstrate that these effects are universally conserved and that the reestablishment of the appropriate glutathione status restores growth and proper development in various organisms. Finally, we describe a novel integrated model in which NME, protein N-alpha-acylation, proteolysis, and glutathione homeostasis operate in a sequentially regulated mechanism that directs both growth and development.
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Affiliation(s)
- Frédéric Frottin
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Unité Propre de Recherche2355, Protein Maturation, Cell Fate, and Therapeutics, F-91198 Gif-sur-Yvette cedex, France
| | - Christelle Espagne
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Unité Propre de Recherche2355, Protein Maturation, Cell Fate, and Therapeutics, F-91198 Gif-sur-Yvette cedex, France
| | - José A. Traverso
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Unité Propre de Recherche2355, Protein Maturation, Cell Fate, and Therapeutics, F-91198 Gif-sur-Yvette cedex, France
| | - Caroline Mauve
- Université Paris-Sud, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, F-91405 Orsay, France
- Centre National de la Recherche Scientifique, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, Unité Mixte de Recherche 8618, F-91405 Orsay, France
| | - Benoît Valot
- Université Paris-Sud, Plateforme de Protéomique, Institut Fédératif de Recherche87, Centre National de la Recherche Scientifique/Université Paris-Sud/Institut National de la Recherche Agronomique, F-91190 Gif-sur-Yvette, France
- Centre National de la Recherche Scientifique, Plateforme de Protéomique, Institut Fédératif de Recherche87, F-91190 Gif-sur-Yvette, France
- Institut National de la Recherche Agronomique, Plateforme de Protéomique, Institut Fédératif de Recherche87, F-91190 Gif-sur-Yvette, France
| | - Caroline Lelarge-Trouverie
- Université Paris-Sud, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, F-91405 Orsay, France
- Centre National de la Recherche Scientifique, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, Unité Mixte de Recherche 8618, F-91405 Orsay, France
| | - Michel Zivy
- Université Paris-Sud, Plateforme de Protéomique, Institut Fédératif de Recherche87, Centre National de la Recherche Scientifique/Université Paris-Sud/Institut National de la Recherche Agronomique, F-91190 Gif-sur-Yvette, France
- Centre National de la Recherche Scientifique, Plateforme de Protéomique, Institut Fédératif de Recherche87, F-91190 Gif-sur-Yvette, France
- Institut National de la Recherche Agronomique, Plateforme de Protéomique, Institut Fédératif de Recherche87, F-91190 Gif-sur-Yvette, France
| | - Graham Noctor
- Université Paris-Sud, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, F-91405 Orsay, France
- Centre National de la Recherche Scientifique, Institut Fédératif de Recherche87, Institut de Biotechnologie des Plantes, Plateforme Métabolisme-Métabolome, Unité Mixte de Recherche 8618, F-91405 Orsay, France
| | - Thierry Meinnel
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Unité Propre de Recherche2355, Protein Maturation, Cell Fate, and Therapeutics, F-91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Unité Propre de Recherche2355, Protein Maturation, Cell Fate, and Therapeutics, F-91198 Gif-sur-Yvette cedex, France
- Address correspondence to
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