Molecular Mechanism of Flocculation Self-Recognition in Yeast and Its Role in Mating and Survival

We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca-2(+) takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca-2(+). These results unify the generally accepted lectin hypothesis with the historically first-proposed "Ca-2(+)-bridge" hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. IMPORTANCE Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.

Elucidating the role of post-translational modifications of alpha-synuclein using semisynthesis

Mirva Hejjaoui

Alpha-synuclein (α-syn) is a natively unfolded protein that is closely linked to Parkinson’s disease (PD) by genetic, neuropathologic and biochemical evidence. Aggregated and fibrillar forms of α-syn are the main components of intracellular protein inclusions found in PD patients’ brains, termed Lewy Bodies (LB). Both in animal models and in vitro, α-syn forms fibrillar aggregates that resemble those observed in PD brain tissues. Although disease-associated mutations have been shown to promote the fibrillization of α-syn, the exact mechanisms responsible for triggering α-syn aggregation and toxicity in sporadic PD remain unknown. Addressing this gap of knowledge is crucial for understanding the molecular basis of the disease and developing effective therapies for the treatment of PD and other synucleinopathies. This project was initiated on the basis of the working hypothesis that post-translational modifications (PTM) may play important roles in modulating α-syn function and/or regulating its aggregation and toxicity. More specifically, α-syn is ubiquitously N-terminally acetylated, and phosphorylated (serines 87 and S129), ubiquitinated (lysines 12, 21 and 23) and truncated forms of α-syn have been observed in association with wild-type α-syn in LB and in brain tissues from PD patients and transgenic animals. Other modifications, such as phosphorylation at tyrosine 125 (Y125), were significantly reduced in diseased brains. Despite the discovery of candidate enzymes that mediate α-syn phosphorylation, ubiquitination and truncation, little is known about how each of these modifications alters α-syn structure, function, aggregation and toxicity in vivo. This is primarily due to the lack of tools that allow site-specific introduction of these modifications and the lack of natural mutations that can mimic the effect of these modifications, including phosphorylation. The primary focus of this thesis was to develop strategies to overcome these limitations so as to elucidate the effect of phosphorylation at Y125 and monoubiquitination at lysine 6 (K6) on α-syn structure, fibril formation, membrane binding and subcellular localization. Towards this goal, we developed two semisynthetic strategies that allow site-specific introduction of PTM in α-syn based on the ligation of synthetic peptides containing the desired modified amino acid with recombinantly expressed proteins using Expressed Protein Ligation. This approach enables the introduction of single or multiple PTM in the N- or C-terminal regions of α-syn, and the preparation of modified α-syn in milligram quantities. Using these approaches, we were able to show for the first time that ubiquitination stabilizes the monomeric form of the protein and inhibits, rather than promotes, α-syn aggregation, while phosphorylation at Y125 does not significantly change the structure and aggregation propensity of α-syn. With the semisynthetic pY125 α-syn in our hands, we were also able to investigate for the first time the sub-cellular localization of pY125 α-syn through its microinjection into primary neurons. This was not previously possible due to technical limitations related to the absence of appropriate antibodies against pY125 α-syn for immunocytochemical studies and difficulties in generating sitespecifically modified α-syn. Furthermore, we were able to investigate the effect of α-syn phosphorylation on its interactions with other proteins, by probing the effect of pS129 and pY125 on the binding to a nanobody that was specifically selected by phage-display to tightly bind to the C-terminal domain of α-syn. Accordingly, we demonstrated that phosphorylation at a single residue is capable of disrupting the binding of full-length α-syn to another protein. These results have wide-ranging implications for the potential role of phosphorylation and other PTM in regulating α-syn’s function(s). We also exploited our ability to combine semisynthetic and enzymatic approaches to investigate potential cross-talk between different PTM, namely phosphorylation at Y125 and S129 and monoubiquitination at K6. These advances would eventually allow investigating the effect of cross-talk between other N and C-terminal modifications on α-syn’s properties and to investigate PTM-dependent protein-protein and protein-ligand interactions in vitro and in cellular models of synucleinopathies. Together, our semisynthetic approaches provide novel means for the introduction of site-specific modifications in the N- and C-termini of α-syn. Current efforts in our laboratory are focused on extending these approaches to investigate the dynamics of PTM through the use of photocaged modified amino acids and to prepare novel fluorescently labeled α-syn variants to investigate its folding at the single-molecule level in living cells. The results presented in this thesis and preliminary studies from our group demonstrate that semisynthetic α-syn can provide unique opportunities to investigate structure-function of α-syn and the role of PTM in the biology of α-syn in health and disease.

EPFL2012

Phosphorylation of alpha-Synuclein at Y125 and S129 Alters Its Metal Binding Properties: Implications for Understanding the Role of alpha-Synuclein in the Pathogenesis of Parkinson's Disease and Related Disorders

Bruno Claude Daniel Fauvet, Hubert Girault, Hilal Lashuel, Yu Lu, Michel Prudent

alpha-Synuclein (alpha-syn) is a 140-amino acid protein that plays a central role in the pathogenesis of Parkinson's disease (PD) and other synucleinopathies. However, the molecular determinants that are responsible for triggering and/or propagating alpha-syn aggregation and toxicity remain poorly understood. Several studies have suggested that there are direct interactions between different metals and alpha-syn, but the role of metal ions and alpha-syn in the pathogenesis of PD is not firmly established. Interestingly, the majority of disease-associated post-translational modifications (PTMs) (e.g., truncation, phosphorylation, and nitration) of alpha-syn occur at residues within the C-terminal region (Y125, S129, Y133, and Y136) and in very close proximity to the putative metal binding sites. Therefore, we hypothesized that phosphorylation within this domain could influence the alpha-syn-metal interactions. In this paper, we sought to map the interactions between the di- and trivalent cations, Cu(II), Pb(II), Fe(II), and Fe(III), and the C-terminal region of alpha-syn encompassing residues 107-140 and to determine how phosphorylation at S129 or Y125 alters the specificity and binding affinity of metals using electrospray ionization-mass spectrometry (ESI-MS) and fluorescence spectroscopy. We demonstrate that D115-M116 and P128-S129 act as additional Cu(II) binding sites and show for the first time that the residues P128-S129 and D119 are also involved in Pb(H) and Fe(II) coordination, although D119 is not essential for binding to Fe(II) and Pb(II). Furthermore, we demonstrate that phosphorylation at either Y125 or S129 increases the binding affinity of Cu(II), Pb(II), and Fe(II), but not Fe (III). Additionally, we also show that phosphorylations at these residues lead to a shift in the binding sites of metal ions from the N-terminus to the C-teminus. Together, our findings provide critical insight into and expand our understanding of the molecular and structural bases underlying the interactions between alpha-syn and metal ions, including the identification of novel metal binding sites, and highlight the potential importance of cross-talk between post-translational modifications and metal ion binding in modulating alpha-syn functional and aggregation properties that are regulated by its C-terminal domain.

American Chemical Society2011

Role of Nimrod receptors in the Drosophila melanogaster cellular immune response

Claudia Melcarne

The use of modern molecular biology tools and simple but powerful tractable model organisms such as Drosophila has contributed significantly to our recent advances in the innate immunity field, notably phagocytosis. Since 2001, many phagocytic transmembrane receptors, potential opsonins, and in some cases their ligands, have been discovered. Among them, the Nimrod family, which contains key phagocytic receptors and potential opsonins, deserves special interest as accumulating genetic and biochemical evidence points to their critical role in phagocytosis of both bacteria and apoptotic cells. In this PhD thesis we provided a deeper characterization of two Nimrod transmembrane receptors, Eater and NimC1. In particular, by using single or combined mutations in eater and NimC1, we aimed to further elucidate i) the involvement of each receptor in bacterial phagocytosis and ii) the role of Eater in hemocytes sessility and adhesion. Both receptors have been shown to be specifically expressed in hemocytes, the insect blood cells, and to mediate Gram-positive but not Gram-negative bacteria phagocytosis. In this work we generated a novel NimC1 mutant and demonstrated that the single NimC1 deletion does not affect phagocytosis of bacteria. However, by using the compound NimC1;eater mutant we were able to show that these receptors contribute in a synergistic way to microbes engulfment, but that Eater can bypass the requirement for NimC1. Moreover, we discovered that NimC1, but not Eater, is required for phagocytosis of non-immunogenic particles, namely latex beads and yeast zymosan. Therefore, this work provides evidences of Eater and NimC1 being the main receptors for bacteria phagocytosis, and suggests that those proteins likely play distinct roles in microbial uptake, as tethering and docking receptors. The second part of this thesis re-addresses the role of Eater in hemocyte sessility and adhesion. A previous study showed that this phagocytic receptor is essential to mediate blood cell sessility to the animal integument during larval stages. However, a series of questions about Eater-mediated sessility remains still open. For example, is Eater mediating hemocyte adhesion also in adult flies? And yet, does Eater mediate hemocyte sessility by regulating the expression of cell adhesion genes, therefore functioning as a signalling receptor? By using eater1 mutant adult flies, we showed that, as in larval stages, Eater is required in adult hemocytes to confer adhesion and sessility. Interestingly, we uncovered a potential role of sessility in hemocyte survival during adulthood, since eater1 flies have a decreased number of blood cells. Preliminary transcriptomics analysis led us to hypothesise that this receptor might not work as a signalling molecule, but rather as an adhesion protein providing the initial hemocyte contact to its target surface. In line with Eaterâs role as an adhesion molecule, its over-expression in hemocytes leads to the formation of enlarged cells compared to control. To conclude, this thesis extended our knowledge on the Drosophila cellular immune response, by providing new insights on two Nimrod phagocytic receptors.

EPFL2020