Project description:Our results show that CLK2 undergoes liquid-liquid phase separation (LLPS) in response to heat shock stress. Phosphorylation of CLK2 at T343 prevents the LLPS of CLK2. To identify the proteins that recruited to the CLK2 condensates, we immunoprecipitated CLK2 (WT) or (T343A) proteins with FLAG antibody and performed mass spectrometry to detect the interacting proteins.
Project description:TGFBIp-related corneal dystrophy (CD) is the most common form of stromal corneal dystrophy. Although CD is a group of inheritable and progressive corneal diseases, non-inheritable cases of corneal amyloid deposition are reported. TGFBIp-CD is characterized by the accumulation of insoluble protein deposits consisting smaller proteolytic fragments of TGFBIp in the corneal tissues, eventually leading to progressive corneal opacity. Maximum density of these aggregates is in the corneal center implicating the local absence of amyloid controlling factors. Currently, no other treatment options are available besides the surgical replacement of the affected corneal tissues with a donor’s cornea. Here we show that neuroprotective ATP-independent amyloid β chaperone L-PGDS abundant in cerebrospinal fluid but absent in the corneal tissues can effectively disaggregate amyloids in vitro and in the surgically excised human cornea of patients with TGFBIp-CD.
Project description:We collected samples of Pistil, Plain Valve, Plain lip and Plain calyx from the same period and quenched them in liquid nitrogen. Two biological replications were performed in each sample. TMT labeled quantitative proteomics was used to analyze different proteins in different tissues. GO and KEGG were used to analyze the differentially expressed proteins in different tissues, and the key proteins in the important pathway were found
Project description:Pathogenic microorganisms often secrete proteins or nucleic acids that mimic the structure and/or function of molecules expressed within their host counterparts. This molecular mimicry empowers pathogens to target and subvert critical host processes and helps establish their infectious paradigm. We report here that the intracellular bacterium Legionella pneumophila (L.p.) secretes a toxin named SidI (substrate of icm/dot transporter I) which possesses a transfer RNA (tRNA) like fold and functions as a mannosyl transferase enzyme. The 3.1 Å cryo-EM structure of SidI reveals an N-terminal domain that exhibits a characteristic ‘inverted L-shape’ and charge conservation that is present in two known protein mimics of tRNAs, the bacterial elongation factor EF-G and the mammalian release factor eRF1. In addition, SidI’s C-terminal domain adopts a glycosyl transferase B fold and shares considerable homology to a known mannosyl transferase. This molecular coupling of fold and enzymatic function allows SidI to bind to and enzymatically modify components of the host translational apparatus, including the ribosome, resulting in a robust block of protein synthesis that is comparable to the potency exhibited by the toxin ricin. Additionally, we uncovered that the translational pausing activated by SidI elicits a stress response signature that is highly similar to one activated by elongation inhibitors that target the ribosome and induce ribosome collisions. SidI-mediated perturbations to the ribosome activate the stress kinases ZAKα and p38, that in turn drive the accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus, and subsequently orchestrates the transcription of stress-inducible genes that culminates in the activation of a cell death program. Thus, using Legionella and its effectors as tools, we have unravelled the role of a ribosome to nuclear signaling pathway that regulates cell fate.
Project description:Influenza B virus (IBV) strains are one of the components of seasonal influenza vaccines in both trivalent and quadrivalent formulations. The vast majority of these vaccines are produced in embryonated chickens' eggs. While optimized backbones for vaccine production in eggs exist and are in use for influenza A viruses, no such backbones exist for IBVs, resulting in unpredictable production yields. To generate an optimal vaccine seed virus backbone, we have compiled a panel of 71 IBV strains from 1940 to present day, representing the known temporal and genetic variability of IBV circulating in humans. This panel contains strains from the B/Victoria/2/87-like lineage, B/Yamagata/16/88-like lineage and the ancestral lineage that preceded their split to provide a diverse set that would help to identify a suitable backbone which can be used in combination with hemagglutinin (HA) and neuraminidase (NA) glycoproteins from any IBV strain to be incorporated into the seasonal vaccine. We have characterized and ranked the growth profiles of the 71 IBV strains and the best performing strains were used for co-infection of eggs, followed by serial passaging to select for high-growth reassortant viruses. After serial passaging, we selected 10 clonal isolates based on their growth profiles assessed by hemagglutination and plaque-forming units. We then generated reverse genetics systems for the three clones that performed best in growth curves. The selected backbones were then used to generate different reassortant viruses with HA/NA combinations from high and low titer yielding wild type IBV. When the growth profiles of the recombinant reassortant viruses were tested, the low titer yielding HA/NA viruses with the selected backbones yielded higher titers similar to those from high titer yielding HA/NA combinations. The use of these IBV backbones with improved replication in eggs might increase yields for the influenza B virus components of seasonal influenza virus vaccines.
Project description:The Tau (MAPT) protein drives neuronal dysfunction and toxicity in the brain in Alzheimer’s disease (AD) and other Tauopathies. To dissect the complexity of the Tau interactome that underlies this process we used two proteomic approaches to characterize the dynamic and multifaceted nature of Tau protein-protein interactions in human induced pluripotent stem cell (iPSC)-derived neurons. We used engineered ascorbic acid peroxidase (APEX) for spatiotemporally restricted mapping of Tau interaction proteins in combination with quantitative affinity purification mass spectrometry (AP-MS) to interrogate disease-related changes in the Tau interactome. The APEX method resolved subcellular interactions of wild-type Tau at amino acid level resolution in living neurons as well as novel activity-dependent interactions of Tau with presynaptic vesicle proteins that occurred during Tau secretion from neurons. Among the many Tau interacting proteins revealed by AP-MS, the interaction of mitochondrial proteins with wild-type Tau (TauWT) was more robust than with TauV337M or TauP301L. The mitochondrial proteins that preferentially interacted with TauWT comprised a protein module that is downregulated in multi-omics analyses of human AD brains. Mitochondrial bioenergetics were altered in TauV337M compared to TauWT human iPSC-derived neurons confirming the impact of Tau on mitochondria. These Tau interactome analyses open up novel disease-related processes as potential therapeutic targets to block Tau-mediated pathogenesis.
Project description:Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protein concentrations, a tandem depletion technique consisting of ammonium sulfate precipitation and Protein A affinity chromatography was developed. Using this method, 50 % of albumin, together with other high abundant proteins such as alpha-1-antitrypin, was depleted from the plasma sample at 20 % to 40 % ammonium sulfate saturation levels. In combination with immunoglobulin removal using a Protein A column, this technique delivered up to 40 new low- to medium abundance protein identifications when performing a shotgun mass spectrometry analysis. Compared to non-depleted plasma, 270 additional protein spots were observed during 2D-PAGE analysis. These results illustrate that this tandem depletion method is equivalent to commercial kits which are based on immune-affinity chromatography. Moreover, this method using protein A immunoglobulin depletion was shown to be highly reproducible and a minimal amount of non-target proteins was depleted. The combination of ammonium sulfate precipitation and Protein A affinity chromatography offers a low cost, efficient, straightforward and reproducible alternative to commercial kits, with proteins remaining in native conformation, allowing protein activity and protein interaction studies.
Project description:The presence of large protein inclusions is a hallmark of neurodegeneration, and yet the precise molecular factors that contribute to their formation remain poorly understood. Screens using aggregation-prone proteins have commonly relied on downstream toxicity as a readout rather than the direct formation of aggregates. Here, we combined a genome-wide CRISPR knockout screen with Pulse Shape Analysis, a FACS-based method for inclusion detection, to identify direct modifiers of TDP-43 aggregation in human cells. Our screen revealed both canonical and novel proteostasis genes, and unearthed SRRD,a poorly characterized protein, as a top regulator of protein inclusion formation. APEX biotin labeling reveals that SRRD resides in proximity to proteins that are involved in the formation and breakage of disulfide bonds and to intermediate filaments, suggesting a role in regulation of the spatial dynamics of the intermediate filament network. Indeed, loss of SRRD results in aberrant intermediatefilament fibrils and the impaired formation of aggresomes, including blunted vimentin cage structure, during proteotoxic stress. Interestingly, SRRD also localizes to aggresomes and unfolded proteins, and rescues proteotoxicity in yeast whereby the its N-terminal low complexity domain is sufficient to induce this affect. Altogether this suggests an unanticipated and broad role for SRRD in cytoskeletal organization and cellular proteostasis.
Project description:During infection, virus-specific CD8+ T cells undergo rapid bursts of proliferation and differentiate into effector cells that kill virus infected cells and reduce viral load. This rapid clonal expansion can put T cells at significant risk for replication-induced DNA damage. We found that c-Myc utilizes the E3 ubiquitin ligase, Cul4b, to inextricably link CD8+ T cell expansion to DNA damage response pathways. Following activation, c-Myc increased levels of Cul4b and other members of the CRL4 complex. Despite having abundant c-Myc expression, Cul4b-deficient CD8+ T cells were unable to expand and clear virus. Cul4b-deficient CD8+ T cells accrued DNA damage and succumbed to proliferative catastrophe early after antigen encounter. Mechanistically, Cul4b ablation induced a protracted accumulation of p21 and Cyclin E2 resulting in replication stress. Our data show that, to support cell proliferation, c-Myc must employ Cul4b to maintain genome stability, thereby directly coupling these two interdependent pathways. These data clarify how CD8+ T cells use c-Myc and Cul4b to sustain their potential for extraordinary population expansion, longevity and antiviral responses.
Project description:Here we use unbiased abundance proteomics and phosphoproteomics to assess global changes to host and viral proteins in Calu-3 cells at 10 and 24 hours post infection with either the B.1.1.7 UK variant or early-lineage SARS-CoV-2 viruses VIC and IC19.