No description available.

Les plantes induisent des réponses de défense après la perception de pathogènes. Des protéines appelées mitogen-activated protein kinases (MAPKS) sont impliquées dans le réseau complexe de signalisation établi pendant cette défense. Cependant, la connaissance actuelle de leur fonction est encore limitée. L'objectif de ma thèse était de contribuer à une meilleure compréhension de leur rôle et régulation pendant la défense. Premièrement, j'ai participé au décryptage des contributions spécifiques et coopératives de trois MAPKS impliquées dans l'immunité, à savoir MPK3, MPK4 et MPK6. Nous avons montré que ces MAPKS sont d'importants régulateurs de la reprogrammation transcriptionnelle induite pendant la défense. Deuxièmement, nous avons réalisé des approches de phosphoprotéomique et nous avons développé un protocole permettant d'enrichir des protéines associés à la chromatine, ce qui a permis d'identifier de nouveaux phosphosites ainsi que des protéines différemment phosphorylées pendant la défense, notamment de probables substrats des MAPKS. Troisièmement, nous avons identifiés plusieurs dizaines de protéines interagissant potentiellement avec le module MEKKI-MKK2-MPK4. Globalement, ce travail a révélé de nouvelles fonctions des MAPKS dans l'immunité des plantes. Ce travail a aussi permis d'identifier de nouveaux substrats potentiels des MAPKS et suggère que le module MEKK1-MKK2-MPK4 est soumis à une régulation hautement complexe via de multiples interacteurs proétiques et PTMS. / Plants induce defense responses after perception of invading pathogens. Proteins called mitogen-activated protein kinases (MAPKS) are implicated in the complex signaling network occuring in plant immunity. However, the current knowledge of their function is still limited. The objective of my PHD was to contribute to a better understanding of their role and regulation in plant defense. First, i was involved in the deciphering of the specific and cooperative contributions of three MAPKS involved in plant immunity, namely MPK3, MPK4 and MPK6. We charcacterized several hallmarks of defense in WT and MAPK mutant plants. We showed notably that immune MAPKS are important regulators of the transcriptional reprogramming occuring during defense. Second, we applied phosphoproteomic approaches and we developed a protocol to enrich for chromatin-associated proteins which allowed identifying new phosphosites as well as proteins differentially phosphorylated during defense, notably some probable MAPKS substrates. Third, we identified several tens proteins potentially interacting with the immune MEKK1-MKK2-MPK4 module via the purification of protein complexes in vivo. Fourth, we identified diverse post-translational modification (PTMS) on each component of the MEKK1-MKK2-MPK4 module. Overall, this work revealed new functions for MAPKS in plant immunity. This work also provided new candidate MAPK substrates and suggests that the MEKK1-MKK2-MPK4 module is subjected to a highly complex regulation via multiple interacting proteins and PTMS.

Protein phosphorylation governs many regulatory pathways and an increasing number of kinases, proteins that transfer phosphate groups, are in turn activated by cyclic nucleotides. One of the cyclic nucleotides, cyclic adenosine monophosphate (cAMP), has been shown to be a second messenger in abiotic and biotic stress responses. However, little is known about the precise role of cAMP in plants and in the down-stream activation of kinases, and hence cAMP-dependent phosphorylation. To increase our understanding of the role of cAMP, proteomic and phosphoproteomic profiles of Arabidopsis thaliana suspension culture cells were analyzed before and after treatment of cells with two different concentrations of 8-Bromo-cAMP (1 µM and 100 nM) and over a time-course of one hour. A comparative quantitative analysis was undertaken using two- dimensional gel electrophoresis and the Delta 2D software (DECODON) followed by protein spot identification by tandem mass spectrometry combined with Mascot and Scaffold. Differentially expressed proteins and regulated phosphoproteins were categorized according to their biological function using bioinformatics tools. The results revealed that the treatment with 1 µM and 100 nM 8-Bromo-cAMP was sufficient to induce specific concentration- and time-dependent changes at the proteome and phosphoproteome levels. In particular, different phosphorylation patterns were observed overtime preferentially affecting proteins in a number of functional categories, notably phosphatases, proteins that remove phosphate groups. This suggests that cAMP both transiently activates and deactivates proteins through specific phosphorylation events and provides new insight into biological mechanisms and functions at the systems level.

Indiana University-Purdue University Indianapolis (IUPUI) / 2021-11-30

Acute myeloid leukemia (AML) is a clonal malignant disease characterized by a blockage in the differentiation of myeloid cells resulting in the accumulation of highly proliferating immature blast cells. With the success of All Trans Retinoic acid (ATRA) in acute promyelocytic leukemia (AML3), differentiation therapy has become a very attractive treatment option. Ligation of CD44 (a cell surface antigen) with anti-CD44 monoclonal antibodies (mAbs) is reported to reverse the blockage of differentiation and suppress the proliferation of blasts derived from most AML subtypes. However, the molecular mechanisms underlying this apparent ‘normalization’ (reversal) of AML cells induced by CD44 have not been fully elucidated. To expand our understanding of the cellular regulation and circuitry involved, we aimed to apply a quantitative phosphoproteomic approach using Stable Isotope Labeling with Amino acids in Cell culture (SILAC) to monitor dynamic changes of phosphorylation states in HL60 cells following treatment with CD44-mAbs. Phosphoproteomic analysis identified differentially phosphorylated proteins among CD44-mAb treated and control HL60 cells that are involved in a number of major signaling pathways as determined by the Ingenuity Pathway analysis (IPA®) platform. Among others, Rho signaling emerged as a major pathway significantly changed by CD44-mAb treatment. Rho GTPases are well-recognized regulators of the actin cytoskeleton but have also been implicated in diverse cellular events such as cell polarity, microtubule dynamics, membrane trafficking, transcriptional regulation, cell growth control and development. An interesting Rho family member, PAK2 was identified in our search. PAK2 is a ubiquitously expressed serine/threonine protein kinase, which is a direct target for small GTPases and has been identified as a switch between cell survival and cell death signaling depending on its mode of activation. Western-blot analyses of cell lysates of CD44-mAb treated and control HL60 cells confirmed that the phosphorylation of PAK2 ,as well as protein level,were altered as early as 5 minutes following treatment. PAK2 knockdown decreased the effect of CD44-mAb induction of proliferation and inhibition of proliferation proving its importance for mediating it’s signaling transduction. PAK1, a structural homologue of PAK2 had the opposite effect of augmenting CD44-mAb effects suggesting a different mechanism involved. This specificity is attributed to the specific mode of activation that PAK2 exhibits which is not shared with the rest of PAK group I members. Caspase-mediated cleavage of PAK2 producing pro-apoptotic fragments is hypothesized to be the signaling transduction mediated by CD44-mAb. In-Vivo experiments show that PAK2 is essential for leukemic cell migration to the spleen. Additionally, it proved essential for CD44-mAb inhibition of leukemic cells migration to the spleen. Further validation and characterization of PAK2’s activation mode, phosphorylation dynamics, subcellular localization as well as its role in invivo migration are essential in understanding its role in AML.

No description available.

Circadian clocks are endogenous pacemakers found in many organisms including plants, generating approximately 24h rhythms. Knowledge about the plant circadian clock plays a role for crop improvement. The plant circadian clock and its downstream outputs have been studied in detail by transcriptomics, however post-transcriptional and post-translational aspects are still to be researched. In addition, it has recently been shown that a protein modification remains rhythmic when rhythmic transcription is absent. This gives evidence for the existence of two oscillators: a transcription-translation feedback loop and a non-transcriptional oscillator. The aim of this PhD is to gain knowledge about circadian changes in abundance and phosphorylation of proteins as well as protein-protein interaction using the model plant Arabidopsis thaliana. I used high-throughput proteomics and phosphoproteomics methods to identify hundreds of phosposites that change in abundance in WT plants as well as dozens of proteins that exhibit circadian changes in their abundance. I also found significant temporal changes in protein phosphorylation in the transcriptionally arrhythmic mutant CCA1-Ox, albeit with dynamics different from the WT, demonstrating that without transcriptional rhythms, protein modification can still undergo rhythmic changes to some extent. In addition, I found reproducibly that the majority of changing phosphopeptides are most abundant at dawn and this is independent of the presence of a functional transcriptional oscillator. Roles of different kinases and affected phosphoproteins are discussed. I chose one of the rhythmically phosphorylated proteins, the bifunctional enzyme F2KP, for further functional experiments. In vitro experiments demonstrate that the rhythmic phosphosite is important for the activity of the enzyme. This is discussed in the light of circadian regulation of carbon metabolism. In addition to these studies on circadian protein abundance and modification, I investigated time-of-day dependent protein-protein interaction of the clock protein GIGANTEA (GI). Using an interaction proteomics timecourse, I identified about 100 potential new interactors of GI, some of which are candidates for links between diel timing and carbon metabolism. These results will help to generate hypotheses for explaining the surprising pleiotrophy of gi mutants.

Protein phosphorylation is a prevalent reversible post-translational modification that influences protein functions. The advent of phospho-proteomic technologies now enables proteome-wide quantitative detection of residues phosphorylated under different physiological conditions. The functional consequences of the majority of these phosphorylation events are unknown. This calls for endeavors to characterize their molecular functions and cellular effects. This can be facilitated by systematic approaches to categorize phosphorylation events, interpret their importance and infer their functions. I carried out comparative, evolutionary and integrative analyses on in vivo phosphorylation events to address these challenges. First, I performed cross-species comparative phospho-proteomic analysis to identify evolutionarily conserved phosphorylation events in human. A sequence alignment approach was used to identify phosphorylation events conserved at similar sequence positions across orthologous proteins and a network alignment approach was applied to identify potential evolutionarily conserved kinase-substrate interactions. Conserved human phosphoproteins identified are found enriched for proteins encoded by known cancer- and disease-associated genes. Next, I developed a new approach to analyze the sequence conservation of known phosphorylated residues on human, mouse and yeast proteins that factored in the background mutational rates of protein and phosphorylatable residue. Furthermore, sites were analyzed according to (i) characterized functions, (ii) prevalence, (iii) stoichiometry, their occurrence in (iv) structurally disordered/ordered protein regions, in (v) proteins of various abundance and in (vi) proteins with different protein interaction propensity to identify the factors influencing sequence conservation of phosphorylated residues. Importantly, my analysis suggests that false positives and randomly phosphorylated residues are present in existing phosphorylation datasets and they are more common on high abundance proteins. Lastly, I characterized the theoretical maximum phosphorylation capacity in terms of phosphorylatable residues and discovered that genomic tyrosine frequency correlates negatively and significantly with tyrosine kinase frequency and cell type in metazoan. This observation suggests that fidelity of phosphotyrosine signaling occurred partially through global tyrosine depletion.

Protein phosphorylation is a prevalent reversible post-translational modification that influences protein functions. The advent of phospho-proteomic technologies now enables proteome-wide quantitative detection of residues phosphorylated under different physiological conditions. The functional consequences of the majority of these phosphorylation events are unknown. This calls for endeavors to characterize their molecular functions and cellular effects. This can be facilitated by systematic approaches to categorize phosphorylation events, interpret their importance and infer their functions. I carried out comparative, evolutionary and integrative analyses on in vivo phosphorylation events to address these challenges. First, I performed cross-species comparative phospho-proteomic analysis to identify evolutionarily conserved phosphorylation events in human. A sequence alignment approach was used to identify phosphorylation events conserved at similar sequence positions across orthologous proteins and a network alignment approach was applied to identify potential evolutionarily conserved kinase-substrate interactions. Conserved human phosphoproteins identified are found enriched for proteins encoded by known cancer- and disease-associated genes. Next, I developed a new approach to analyze the sequence conservation of known phosphorylated residues on human, mouse and yeast proteins that factored in the background mutational rates of protein and phosphorylatable residue. Furthermore, sites were analyzed according to (i) characterized functions, (ii) prevalence, (iii) stoichiometry, their occurrence in (iv) structurally disordered/ordered protein regions, in (v) proteins of various abundance and in (vi) proteins with different protein interaction propensity to identify the factors influencing sequence conservation of phosphorylated residues. Importantly, my analysis suggests that false positives and randomly phosphorylated residues are present in existing phosphorylation datasets and they are more common on high abundance proteins. Lastly, I characterized the theoretical maximum phosphorylation capacity in terms of phosphorylatable residues and discovered that genomic tyrosine frequency correlates negatively and significantly with tyrosine kinase frequency and cell type in metazoan. This observation suggests that fidelity of phosphotyrosine signaling occurred partially through global tyrosine depletion.

The kinetics of protein phosphorylation and dephosphorylation are tightly controlled by specific kinases and phosphatases; disturbances are often disease-causing. Phosphorylation kinetics are normally monitored using radioactive isotopes of phosphorus, or by using stop-flow techniques. Approaches using mass spectrometry are severely limited by the lack of a stable isotope of phosphorus (other than 31P). The principal aim of this study is to develop a new method to incorporate 18O label into phosphorylation sites of phosphoproteins with a view of applying this method to enhance the detection of phosphorylation by mass spectrometry and to analyze the phosphorylation kinetics of proteins. Aurora-A kinase was selected to explore the possibility of using 18O-labelling to monitor phosphorylation kinetics. The kinase is well characterized, phosphorylated both in human cells and when expressed in recombinant form in E. coli and it contributes to development of some cancers when deregulated. Applying different mass spectrometric approaches resulted in the identification of 19 phosphorylation sites of Aurora-A including five new sites. Using H3P18O4 as a label donor to incorporate 18O into Aurora-A phosphorylation sites showed partial and inconsistent label incorporation. Alternatively, H218O was used to investigate the possibility of label incorporation. Preliminary results, however, showed high complex data which hampered precise identification of phosphopeptides and their labelling state. The labelling experiment was then redesigned in which induction took place in label free medium to allow the light version of the kinase to accumulate, before chasing with 18O label. This design successfully introduced fully labelled P18O3 into Aurora-A phosphorylation sites. LC ESI Q-ToF analysis of 18O labelled Aurora-A sample isolated according to this protocol identified 30 phosphopeptides showing label incorporation, which is double the number of phosphopeptides identified by MASCOT using the same MS analysis. The method was also used to investigate phosphorylation kinetics of Aurora-A. The results suggested differential regulation of phosphorylation sites of Aurora-A as some sites showed early phosphorylation while others were phosphorylated at later stages. Overall, a new approach was developed for enhanced detection of phosphorylation sites and analysis of phosphorylation kinetics.