Temporal Quantitative Phosphoproteomics Profiling of Interleukin-33 Signaling Network Reveals Unique Modulators of Monocyte Activation

Interleukin-33 (IL-33), a member of the IL-1 superfamily cytokines, is an endogenous danger signal and a nuclear-associated cytokine. It is one of the essential mediators of both innate and adaptive immune responses. Aberrant IL-33 signaling has been demonstrated to play a defensive role against various infectious and inflammatory diseases. Although the signaling responses mediated by IL-33 have been previously reported, the temporal signaling dynamics are yet to be explored. To this end, we applied quantitative temporal phosphoproteomics analysis to elucidate pathways and proteins induced by IL-33 in THP-1 monocytes. Employing a TMT labeling-based quantitation and titanium dioxide (TiO2)-based phosphopeptide enrichment strategy followed by mass spectrometry analysis, we identified and quantified 9448 unique phosphopeptides corresponding to 3392 proteins that showed differential regulation. Of these, 171 protein kinases, 60 phosphatases and 178 transcription factors were regulated at different phases of IL-33 signaling. In addition to the confirmed activation of canonical signaling modules including MAPK, NFκB, PI3K/AKT modules, pathway analysis of the time-dependent phosphorylation dynamics revealed enrichment of several cellular processes, including leukocyte adhesion, response to reactive oxygen species, cell cycle checkpoints, DNA damage and repair pathways. The detailed quantitative phosphoproteomic map of IL-33 signaling will serve as a potentially useful resource to study its function in the context of inflammatory and pathological conditions.

Download Full-text

Thiol Peroxidase Is an Important Component of Streptococcus pneumoniae in Oxygenated Environments

Infection and Immunity ◽

10.1128/iai.00126-12 ◽

2012 ◽

Vol 80 (12) ◽

pp. 4333-4343 ◽

Cited By ~ 32

Author(s):

Barak Hajaj ◽

Hasan Yesilkaya ◽

Rachel Benisty ◽

Maayan David ◽

Peter W. Andrew ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Mass Spectrometry Analysis ◽

Activity Levels ◽

Content Type ◽

Spectrometry Analysis ◽

Cellular Processes ◽

Thiol Peroxidase ◽

Fine Tune

ABSTRACTStreptococcus pneumoniaeis an aerotolerant Gram-positive bacterium that causes an array of diseases, including pneumonia, otitis media, and meningitis. During aerobic growth,S. pneumoniaeproduces high levels of H2O2. SinceS. pneumoniaelacks catalase, the question of how it controls H2O2levels is of critical importance. Thepsalocus encodes an ABC Mn2+-permease complex (psaBCA) and a putative thiol peroxidase,tpxD. This study shows thattpxDencodes a functional thiol peroxidase involved in the adjustment of H2O2homeostasis in the cell. Kinetic experiments showed that recombinant TpxD removed H2O2efficiently. However,in vivoexperiments revealed that TpxD detoxifies only a fraction of the H2O2generated by the pneumococcus. Mass spectrometry analysis demonstrated that TpxD Cys58undergoes selective oxidationin vivo, under conditions where H2O2is formed, confirming the thiol peroxidase activity. Levels of TpxD expression and synthesisin vitrowere significantly increased in cells grown under aerobic versus anaerobic conditions. The challenge with D39 and TIGR4 with H2O2resulted intpxDupregulation, whilepsaBCAexpression was oppositely affected. However, the challenge of ΔtpxDmutants with H2O2did not affectpsaBCA, implying that TpxD is involved in the regulation of thepsaoperon, in addition to its scavenging activity. Virulence studies demonstrated a notable difference in the survival time of mice infected intranasally with D39 compared to that of mice infected intranasally with D39ΔtpxD. However, when bacteria were administered directly into the blood, this difference disappeared. The findings of this study suggest that TpxD constitutes a component of the organism's fundamental strategy to fine-tune cellular processes in response to H2O2.

Download Full-text

Kalirin Interacts with TRAPP and Regulates Rab11 and Endosomal Recycling

Cells ◽

10.3390/cells9051132 ◽

2020 ◽

Vol 9 (5) ◽

pp. 1132

Author(s):

Xiaolong Wang ◽

Meiqian Weng ◽

Yuting Ke ◽

Ellen Sapp ◽

Marian DiFiglia ◽

...

Keyword(s):

Low Frequency ◽

Cell Movement ◽

Mass Spectrometry Analysis ◽

Nucleotide Exchange ◽

Vesicle Budding ◽

Recycling Endosomes ◽

Spectrometry Analysis ◽

Cellular Processes ◽

Nucleotide Exchange Factor ◽

Elevated Expression

Coordinated actions of Rab and Rho are necessary for numerous essential cellular processes ranging from vesicle budding to whole cell movement. How Rab and Rho are choreographed is poorly understood. Here, we report a protein complex comprised of kalirin, a Rho guanine nucleotide exchange factor (GEF) activating Rac1, and RabGEF transport protein particle (TRAPP). Kalirin was identified in a mass spectrometry analysis of proteins precipitated by trappc4 and detected on membranous organelles containing trappc4. Acute knockdown of kalirin did not affect trappc4, but significantly reduced overall and membrane-bound levels of trappc9, which specifies TRAPP toward activating Rab11. Trappc9 deficiency led to elevated expression of kalirin in neurons. Co-localization of kalirin and Rab11 occurred at a low frequency in NRK cells under steady state and was enhanced upon expressing an inactive Rab11 mutant to prohibit the dissociation of Rab11 from the kalirin-TRAPP complex. The small RNA-mediated depletion of kalirin diminished activities in cellular membranes for activating Rab11 and resulted in a shift in size of Rab11 positive structures from small to larger ones and tubulation of recycling endosomes. Our study suggests that kalirin and TRAPP form a dual GEF complex to choreograph actions of Rab11 and Rac1 at recycling endosomes.

Download Full-text

Multiple sclerosis has a distinct lipid signature in plasma and cerebrospinal fluid

Arquivos de Neuro-Psiquiatria ◽

10.1590/0004-282x20190122 ◽

2019 ◽

Vol 77 (10) ◽

pp. 696-704 ◽

Cited By ~ 2

Author(s):

Enedina Maria Lobato de OLIVEIRA ◽

Daniela Antunes MONTANI ◽

Diogo OLIVEIRA-SILVA ◽

André Filipe RODRIGUES-OLIVEIRA ◽

Sandro Luiz de Andrade MATAS ◽

...

Keyword(s):

Multiple Sclerosis ◽

Fatty Acids ◽

Cerebrospinal Fluid ◽

Permutation Test ◽

Inflammatory Diseases ◽

Neurological Diseases ◽

Area Under The Curve ◽

Mass Spectrometry Analysis ◽

Detection Methods ◽

Spectrometry Analysis

ABSTRACT The diagnosis of multiple sclerosis (MS) has changed over the last decade, but remains a composite of clinical assessment and magnetic resonance imaging to prove dissemination of lesions in time and space. The intrathecal synthesis of immunoglobulin may be a nonspecific marker and there are no plasma biomarkers that are useful in the diagnosis of MS, presenting additional challenges to their early detection. Methods We performed a preliminary untargeted qualitative lipidomics mass spectrometry analysis, comparing cerebrospinal fluid (CSF) and plasma samples from patients with MS, other inflammatory neurological diseases and idiopathic intracranial hypertension. Results Lipid identification revealed that fatty acids and sphingolipids were the most abundant classes of lipids in the CSF and that glycerolipids and fatty acids were the main class of lipids in the plasma of patients with MS. The area under the curve was 0.995 (0.912–1) and 0.78 (0.583–0.917), respectively. The permutation test indicated that this ion combination was useful for distinguishing MS from other inflammatory diseases (p < 0.001 and 0.055, respectively). Conclusion This study concluded that the CSF and plasma from patients with MS bear a unique lipid signature that can be useful as a diagnostic biomarker.

Download Full-text

Rules for PP2A-controlled phosphosignalling and drug responses

10.1101/271841 ◽

2018 ◽

Cited By ~ 5

Author(s):

Otto Kauko ◽

Susumu Y. Imanishi ◽

Evgeny Kulesskiy ◽

Teemu Daniel Laajala ◽

Laxman Yetukuri ◽

...

Keyword(s):

Cancer Cell ◽

Mass Spectrometry Analysis ◽

Drug Responses ◽

Spectrometry Analysis ◽

Cellular Processes ◽

Cell Responses ◽

Systemic Analysis ◽

Phosphatase 2A ◽

Cancer Drivers ◽

Systemic Understanding

AbstractSystemic understanding of protein phosphatase 2A (PP2A)-regulated cellular processes is still at infancy. Here, we present mass-spectrometry analysis of phospho-targets (dephosphorylome) regulated by PP2A modulation. In addition to PP2A-regulated processes and targets, the data reveal important general concepts and rules related to PP2A-mediated phosphoregulation. These include the unidirectionality paradigm of regulation of phosphorylation, and differential spatial distribution of kinase-and phosphatase-dominated phosphotargets. Data also present first systemic analysis of targets of PP2A-modulating oncoproteins, CIP2A, PME-1, and SET; including targets via which PP2A may coordinately regulate activities of cancer drivers and tumor suppressors such as MYC or TP53. To validate functional utility of this dataset, PP2A dephosphorylome activity was correlated with cancer cell responses to over 300 drugs. Notably, we find that cancer therapy responses can be broadly classified based on PP2A dephosphorylome activity, both in quantitative and qualitative manner. In summary, our data characterize rules by which PP2A coordinate cancer cell phosphosignaling and drug responses. The results also may also direct the use of emerging pharmacological approaches for PP2A activity modulation in human diseases.

Download Full-text

The Impact of the ‘Mis-Peptidome’ on HLA Class I-Mediated Diseases: Contribution of ERAP1 and ERAP2 and Effects on the Immune Response

International Journal of Molecular Sciences ◽

10.3390/ijms21249608 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9608

Author(s):

Valentina Tedeschi ◽

Giorgia Paldino ◽

Fabiana Paladini ◽

Benedetta Mattorre ◽

Loretta Tuosto ◽

...

Keyword(s):

Inflammatory Diseases ◽

Association Studies ◽

Strong Association ◽

Hla Class I ◽

Class I ◽

Mass Spectrometry Analysis ◽

Genome Wide Association Studies ◽

Spectrometry Analysis ◽

Hla Class I Molecules ◽

The Impact

The strong association with the Major Histocompatibility Complex (MHC) class I genes represents a shared trait for a group of autoimmune/autoinflammatory disorders having in common immunopathogenetic basis as well as clinical features. Accordingly, the main risk factors for Ankylosing Spondylitis (AS), prototype of the Spondyloarthropathies (SpA), the Behçet’s disease (BD), the Psoriasis (Ps) and the Birdshot Chorioretinopathy (BSCR) are HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02, respectively. Despite the strength of the association, the HLA pathogenetic role in these diseases is far from being thoroughly understood. Furthermore, Genome-Wide Association Studies (GWAS) have highlighted other important susceptibility factors such as Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and, less frequently, ERAP2 that refine the peptidome presented by HLA class I molecules to CD8+ T cells. Mass spectrometry analysis provided considerable knowledge of HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02 immunopeptidome. However, the combined effect of several ERAP1 and ERAP2 allelic variants could generate an altered pool of peptides accounting for the “mis-immunopeptidome” that ranges from suboptimal to pathogenetic/harmful peptides able to induce non-canonical or autoreactive CD8+ T responses, activation of NK cells and/or garbling the classical functions of the HLA class I molecules. This review will focus on this class of epitopes as possible elicitors of atypical/harmful immune responses which can contribute to the pathogenesis of chronic inflammatory diseases.

Download Full-text

Arabidopsis phospholipase Dδ as an initiator of cytoskeleton-mediated signalling to fundamental cellular processes

Functional Plant Biology ◽

10.1071/fp08222 ◽

2009 ◽

Vol 36 (2) ◽

pp. 190 ◽

Cited By ~ 33

Author(s):

Angela Y. Y. Ho ◽

David A. Day ◽

Melissa H. Brown ◽

Jan Marc

Keyword(s):

Potential Interaction ◽

Mass Spectrometry Analysis ◽

Actin Binding ◽

Sequence Alignments ◽

Spectrometry Analysis ◽

Cellular Processes ◽

Plant Signal Transduction ◽

Interaction Partners ◽

Cytoskeletal Rearrangements ◽

Partner Proteins

Phospholipase D (PLD), in combination with the cytoskeleton, plays a key role in plant signal transduction. One isotype of the multigene Arabidopsis PLD family, AtPLDδ, has been implicated in binding microtubules, although the molecular details of the mechanism and identities of potential interaction partners are unclear. We constructed a GFP-AtPLDδ reporter gene, stably transformed it into an Arabidopsis suspension cell line, and used epitope-tagged affinity pull-down assays to isolate a complex of co-purifying proteins. Mass spectrometry analysis of the complex revealed a set of proteins including β-tubulin, actin 7, HSP70, clathrin heavy chain, ATP synthase subunits, and a band 7–4/flotillin homologue. Sequence alignments with defined tubulin- and actin-binding regions from human HsPLD2 revealed highly homologous regions in all 12 AtPLD isotypes, suggesting direct interactions of AtPLDδ with tubulin and actin, while interactions with the remaining partners are likely to be mediated by the cytoskeleton. We propose that AtPLDδ acts through a complex of cytoskeletal and partner proteins to modulate fundamental cellular processes such as cytoskeletal rearrangements, vesicular trafficking, assembly of Golgi apparatus, mitosis and cytokinesis.

Download Full-text

Prediction and collection of protein–metabolite interactions

Briefings in Bioinformatics ◽

10.1093/bib/bbab014 ◽

2021 ◽

Author(s):

Tianyi Zhao ◽

Jinxin Liu ◽

Xi Zeng ◽

Wei Wang ◽

Sheng Li ◽

...

Keyword(s):

Small Molecule ◽

Protein Interactions ◽

Large Scale ◽

Rapid Development ◽

Area Under The Curve ◽

Membrane Receptors ◽

Mass Spectrometry Analysis ◽

Spectrometry Analysis ◽

Cellular Processes ◽

The Rich

Abstract Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors can all be mediated through protein–metabolite interactions (PMIs). Compared with the rich knowledge of protein–protein interactions, little is known about PMIs. To the best of our knowledge, no existing database has been developed for collecting PMIs. The recent rapid development of large-scale mass spectrometry analysis of biomolecules has led to the discovery of large amounts of PMIs. Therefore, we developed the PMI-DB to provide a comprehensive and accurate resource of PMIs. A total of 49 785 entries were manually collected in the PMI-DB, corresponding to 23 small molecule metabolites, 9631 proteins and 4 species. Unlike other databases that only provide positive samples, the PMI-DB provides non-interaction between proteins and metabolites, which not only reduces the experimental cost for biological experimenters but also facilitates the construction of more accurate algorithms for researchers using machine learning. To show the convenience of the PMI-DB, we developed a deep learning-based method to predict PMIs in the PMI-DB and compared it with several methods. The experimental results show that the area under the curve and area under the precision-recall curve of our method are 0.88 and 0.95, respectively. Overall, the PMI-DB provides a user-friendly interface for browsing the biological functions of metabolites/proteins of interest, and experimental techniques for identifying PMIs in different species, which provides important support for furthering the understanding of cellular processes. The PMI-DB is freely accessible at http://easybioai.com/PMIDB.

Download Full-text

New Model for Stacking Monomers in Filamentous Actin from Skeletal Muscles of Oryctolagus cuniculus

International Journal of Molecular Sciences ◽

10.3390/ijms21218319 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8319 ◽

Cited By ~ 1

Author(s):

Anna V. Glyakina ◽

Alexey K. Surin ◽

Sergei Yu. Grishin ◽

Olga M. Selivanova ◽

Mariya Yu. Suvorina ◽

...

Keyword(s):

Electron Microscopy ◽

Mass Spectrometry ◽

Scientific Evidence ◽

Limited Proteolysis ◽

Mass Spectrometry Analysis ◽

Filamentous Actin ◽

X Ray Diffraction ◽

Spectrometry Analysis ◽

Actin Organization ◽

Cellular Processes

To date, some scientific evidence (limited proteolysis, mass spectrometry analysis, electron microscopy (EM)) has accumulated, which indicates that the generally accepted model of double-stranded of filamentous actin (F-actin) organization in eukaryotic cells is not the only one. This entails an ambiguous understanding of many of the key cellular processes in which F-actin is involved. For a detailed understanding of the mechanism of F-actin assembly and actin interaction with its partners, it is necessary to take into account the polymorphism of the structural organization of F-actin at the molecular level. Using electron microscopy, limited proteolysis, mass spectrometry, X-ray diffraction, and structural modeling we demonstrated that F-actin presented in the EM images has no double-stranded organization, the regions of protease resistance are accessible for action of proteases in F-actin models. Based on all data, a new spatial model of filamentous actin is proposed, and the F-actin polymorphism is discussed.

Download Full-text

Ceramide Metabolism and Parkinson’s Disease—Therapeutic Targets

Biomolecules ◽

10.3390/biom11070945 ◽

2021 ◽

Vol 11 (7) ◽

pp. 945

Author(s):

Antía Custodia ◽

Marta Aramburu-Núñez ◽

Clara Correa-Paz ◽

Adrián Posado-Fernández ◽

Ana Gómez-Larrauri ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Second Messengers ◽

Underlying Disease ◽

Mass Spectrometry Analysis ◽

Special Focus ◽

Ionization Mass ◽

Metabolic Dysfunction ◽

Spectrometry Analysis ◽

Cellular Processes

Ceramide is a bioactive sphingolipid involved in numerous cellular processes. In addition to being the precursor of complex sphingolipids, ceramides can act as second messengers, especially when they are generated at the plasma membrane of cells. Its metabolic dysfunction may lead to or be a consequence of an underlying disease. Recent reports on transcriptomics and electrospray ionization mass spectrometry analysis have demonstrated the variation of specific levels of sphingolipids and enzymes involved in their metabolism in different neurodegenerative diseases. In the present review, we highlight the most relevant discoveries related to ceramide and neurodegeneration, with a special focus on Parkinson’s disease.

Download Full-text

PTEN arginine methylation by PRMT6 suppresses PI3K–AKT signaling and modulates pre-mRNA splicing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811028116 ◽

2019 ◽

Vol 116 (14) ◽

pp. 6868-6877 ◽

Cited By ~ 11

Author(s):

Jiawen Feng ◽

Yaping Dang ◽

Weiqi Zhang ◽

Xuyang Zhao ◽

Cong Zhang ◽

...

Keyword(s):

Mass Spectrometry ◽

Alternative Splicing ◽

Posttranslational Modification ◽

Arginine Methylation ◽

Akt Signaling ◽

Mrna Splicing ◽

Mass Spectrometry Analysis ◽

Arginine Methyltransferase ◽

Spectrometry Analysis ◽

Cellular Processes

Arginine methylation is a ubiquitous posttranslational modification that regulates critical cellular processes including signal transduction and pre-mRNA splicing. Here, we report that the tumor-suppressor PTEN is methylated by protein arginine methyltransferase 6 (PRMT6). Mass-spectrometry analysis reveals that PTEN is dimethylated at arginine 159 (R159). We found that PTEN is mutated at R159 in cancers, and the PTEN mutant R159K loses its capability to inhibit the PI3K–AKT cascade. Furthermore, PRMT6 is physically associated with PTEN, promotes asymmetrical dimethylation of PTEN, and regulates the PI3K–AKT cascade through PTEN R159 methylation. In addition, using transcriptome analyses, we found that PTEN R159 methylation is involved in modulation of pre-mRNA alternative splicing. Our results demonstrate that PTEN is functionally regulated by arginine methylation. We propose that PTEN arginine methylation modulates pre-mRNA alternative splicing and influences diverse physiologic processes.

Download Full-text