Delphine Pflieger

Delphine Pflieger
French National Centre for Scientific Research | CNRS · Section de Chimie du vivant et pour le vivant

PhD in analytical chemistry

About

63
Publications
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2,318
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Publications

Publications (63)
Article
Biogenesis of ribonucleoproteins occurs in dynamic subnuclear compartments called Cajal bodies (CBs). COILIN is a critical scaffolding component essential for CB formation, composition and activity. We recently showed that Arabidopsis (Arabidopsis thaliana) AtCOILIN is phosphorylated in response to bacterial elicitor treatment. Here, we further inv...
Article
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(1) Background: The proteomic analysis of histones constitutes a delicate task due to the combination of two factors: slight variations in the amino acid sequences of variants and the multiplicity of post-translational modifications (PTMs), particularly those occurring on lysine residues. (2) Methods: To dissect the relationship between both aspect...
Article
Full-text available
In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphoryl...
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Background: Gametes are highly differentiated cells specialized to carry and protect the parental genetic information. During male germ cell maturation, histone proteins undergo distinct changes that result in a highly compacted chromatin organization. Technical difficulties exclude comprehensive analysis of precise histone mutations during mammal...
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Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and...
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Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approac...
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Mammalian Ras-GTPase–activating protein SH3-domain–binding proteins (G3BPs) are a highly conserved family of RNA-binding proteins that link kinase receptor-mediated signaling to RNA metabolism. Mammalian G3BP1 is a multifunctional protein that functions in viral immunity. Here, we show that the Arabidopsis thaliana homolog of human G3BP1 negatively...
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Background: Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited effi-...
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Abstract Background Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limit...
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In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4 and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. While some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cel...
Poster
Proteomics data is obtained using a combination of liquid chromatography and tandem mass spectrometry (MS/MS) where peptides are most commonly identified by matching MS/MS spectra against theoretical spectra of all candidate peptides represented in a generalist protein sequence reference database. The limitation of this approach is that variant pep...
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Hepatitis C virus (HCV) is a leading cause of liver diseases including the development of hepatocellular carcinoma (HCC). Particularly, core protein has been involved in HCV-related liver pathologies. However, the impact of HCV core on signaling pathways supporting the genesis of HCC remains largely elusive. To decipher the host cell signaling path...
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Background Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which ar...
Article
The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes such as replication, transcription and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites towards a comprehensive understanding of the biological functions accomplished in the nu...
Article
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher-order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by post-translati...
Article
Proteins are major elements participating in all the key functions of the cells. They rarely fulfill their physiological roles in an autonomous way but rather act as part of more complex cellular machines. Indeed they can bind different types of molecules (proteins, nucleic acids, metabolites, etc.), via stable or transient interactions, depending...
Article
Signaling cascades strongly rely on protein kinase-mediated substrate phosphorylation. Currently a major challenge in signal transduction research is to obtain high confidence substrate phosphorylation sites and assign them to specific kinases. In response to bacterial flagellin, a pathogen-associated molecular pattern (PAMP), we searched for rapid...
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Brassinosteroids (BRs) are steroid hormones that coordinate fundamental developmental programs in plants. In this study we show that in addition to the well established roles of BRs in regulating cell elongation and cell division events, BRs also govern cell fate decisions during stomata development in Arabidopsis thaliana. In wild-type A. thaliana...
Article
Phosphopeptide identification is still a challenging task because fragmentation spectra obtained by mass spectrometry do not necessarily contain sufficient fragment ions to establish with certainty the underlying amino acid sequence and the precise phosphosite. To improve upon this, it has been suggested to acquire pairs of spectra from every phosp...
Article
Knowledge of the protein networks interacting with the amyloid precursor protein (APP) in vivo can shed light on the physiological function of APP. To date, most proteins interacting with the APP intracellular domain (AICD) have been identified by Yeast Two Hybrid screens which only detect direct interaction partners. We used a proteomics-based app...
Article
The components that enable cells and organisms to fulfill a plethora of chemical and physical reactions, including their ability to metabolize, replicate, repair and communicate with their environment are mostly based on the functioning of highly complex cellular machines which are to a large extent composed of proteins. With the development of MS...
Article
Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as "systems" rather than collections of individual protein molecules. The abstraction of the intera...
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Full-text available
C1, the complex that triggers the classic pathway of complement, is a 790-kDa assembly resulting from association of a recognition protein C1q with a Ca2+-dependent tetramer comprising two copies of the proteases C1r and C1s. Early structural investigations have shown that the extended C1s-C1r-C1r-C1s tetramer folds into a compact conformation in C...
Article
Cellular functions are largely carried out by noncovalent protein complexes that may exist within the cell as stable modules or as assemblies of dynamically changing composition, whose formation and decomposition are triggered in response to extracellular stimuli. The protein constituents of complexes often exhibit post-translational modifications...
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Full-text available
C1q is a subunit of the C1 complex, a key player in innate immunity that triggers activation of the classical complement pathway. Featuring a unique structural organization and comprising a collagen-like domain with a high level of post-translational modifications, C1q represents a challenging protein assembly for structural biology. We report for...
Article
For twenty years or so now, mass spectrometry has been used to get exact measurements of the mass of biological molecules such as proteins, nucleic acids,oligosaccharides, and so on. Over the past ten years, this technology has followed the trend toward miniaturisation and the samples required can be much smaller. In particular, the nanoelectrospra...
Article
Proteomic analyses have proven to be an invaluable tool in obtaining high-throughput protein identification from low-abundance, complex biological samples. In Organelle Proteomics, detailed protocols provide step-by-step instructions to successfully study organelle proteomes by performing the purification of the various organelles present in eukary...
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Full-text available
Protein complexes have largely been studied by immunoaffinity purification and (mass spectrometric) analysis. Although this approach has been widely and successfully used it is limited because it has difficulties reliably discriminating true from false protein complex components, identifying post-translational modifications, and detecting quantitat...
Article
This chapter describes the purification of ribosomal particles from a mutant strain of Escherichia coli using sucrose gradients and the characterization of their protein composition by a combination of mass spectrometry (MS) techniques. The main objective is to identify the ribosomal proteins that are missing in an aberrant ribosomal particle corre...
Chapter
This chapter describes the purification of ribosomal particles from a mutant strain of Escherichia coli using sucrose gradients and the characterization of their protein composition by a combination of mass spectrometry (MS) techniques. The main objective is to identify the ribosomal proteins that are missing in an aberrant ribosomal particle corre...
Book
Proteomic analyses have proven to be an invaluable tool in obtaining high-throughput protein identification from low-abundance, complex biological samples. In Organelle Proteomics, detailed protocols provide step-by-step instructions to successfully study organelle proteomes by performing the purification of the various organelles present in eukary...
Article
Full-text available
Current methods for phosphoproteome analysis have several limitations. First, most methods for phosphopeptide enrichment lack the specificity to truly purify phosphopeptides. Second, fragmentation spectra of phosphopeptides, in particular those of phosphoserine and phosphothreonine containing peptides, are often dominated by the loss of the phospha...
Article
Full-text available
A thorough analysis, using MS, of aquaporins expressed in plant root PM (plasma membrane) was performed, with the objective of revealing novel post-translational regulations. Here we show that the N-terminal tail of PIP (PM intrinsic protein) aquaporins can exhibit multiple modifications and is differentially processed between members of the PIP1 a...
Article
The hair follicle dermal papilla is composed primarily of extracellular matrix (ECM) proteins secreted by resident fibroblasts. Dermal papilla is endowed with hair morphogenic properties, yet its composition is poorly characterized. In an attempt to understand its specificity better, we compared the protein composition of ECM secreted by cultured d...
Article
Full-text available
Aquaporins are channel proteins that facilitate the diffusion of water across cell membranes. The genome of Arabidopsis thaliana encodes 35 full-length aquaporin homologues. Thirteen of them belong to the plasma membrane intrinsic protein (PIP) subfamily and predominantly sit at the plasma membrane (PM). In the present work we combine separations o...
Article
Ribosome assembly in Escherichia coli involves 54 ribosomal proteins and three RNAs. Whereas functional subunits can be reconstituted in vitro from the isolated components, this process requires long incubation times and high temperatures compared with the in vivo situation, suggesting that non-ribosomal factors facilitate assembly in vivo. Here, w...
Article
The Yap1 transcription factor regulates hydroperoxide homeostasis in S. cerevisiae. Yap1 is activated by oxidation when hydroperoxide levels increase. We show that Yap1 is not directly oxidized by hydroperoxide. We identified the glutathione peroxidase (GPx)-like enzyme Gpx3 as a second component of the pathway, serving the role of sensor and trans...
Article
Proteomics based approaches, which examine the expressed proteins of a tissue or cell type, complement the genome initiatives and are increasingly used to address biomedical questions. Proteins are the main functional output, and post-translational modifications such as phosphorylation are very important in determining protein function. To address...
Article
Proteomics based approaches, which examine the expressed proteins of a tissue or cell type, complement the genome initiatives and are increasingly used to address biomedical questions. Proteins are the main functional output, and post‐translational modifications such as phosphorylation are very important in determining protein function. To address...
Article
In eukaryotic cells, the mitochondrion is the key organelle for cellular respiration. Mitochondrial proteome analysis is difficult to perform by the classical proteomic approach involving two-dimensional gel electrophoresis (2DE), because this organelle contains a large number of membrane-associated and highly alkaline proteins usually requiring sp...

Projects

Projects (4)
Archived project
Extracellular stimuli are perceived by cells and converted into signaling cascades relayed by dynamic phosphorylations of proteins. These cascades finally reach the chromatin, made up of histones and DNA, and impact it, in part by changing the modification pattern of its histone constituents. Ultimately, the gene expression program is revisited, to allow the cells to develop an adequate response to the stimulus. We wish to decipher these iterative steps upon uptake by endothelial cells of extracellular vesicles produced by cancer cells: these vesicles contain microRNAs and proteins, including oncogenes, which can have combined impacts on the recipient cells. The obtained data should allow better understanding how cancer tumors manipulate their environment to ensure their survival, in particular by stimulating angiogenesis.