scholarly journals Global proteomic profiling of primary macrophages during M. tuberculosis infection identifies TAX1BP1 as a mediator of autophagy targeting

2019 ◽  
Author(s):  
Jonathan M. Budzik ◽  
Nick E. Garelis ◽  
Teresa Repasy ◽  
Allison W. Roberts ◽  
Lauren M. Popov ◽  
...  
Keyword(s):  
Global Analysis ◽  
Nucleocytoplasmic Transport ◽  
Host Protein ◽  
Protein Abundance ◽  
Proteomic Profiling ◽  
Cell Fates ◽  
Post Translational Modifications ◽  
Functional Capabilities ◽  
Mrna Metabolism ◽  
Adaptor Recruitment

AbstractMacrophages are highly plastic cells that adopt diverse functional capabilities and play critical roles in immunity, cancer, and tissue homeostasis, but how these different cell fates and activities are triggered in response to their environmental cues is not well understood. We used new proteomic tools to identify protein post-translational modifications (PTMs) that control antibacterial responses of macrophages. Here, we report an unbiased and global analysis of the changes in host protein abundance, phosphorylation, and ubiquitylation, during the first 24-hours of Mycobacterium tuberculosis (Mtb) infection of primary macrophages. We discovered 1379 proteins with changes in their phosphorylation state and 591 proteins with changes in their ubiquitylation in response to Mtb infection. We identified pathways regulated by phosphorylation and ubiquitylation that weren’t reflected by changes in protein abundance, indicating that the activity of these pathways was regulated. These include pathways known to be regulated by ubiquitylation and phosphorylation (e.g. autophagy) as well as pathways that were not known to be regulated during Mtb infection (e.g. nucleocytoplasmic transport and mRNA metabolism). We identified an enrichment in phosphorylation of autophagy receptors (TAX1BP1, p62, optineurin, BNIP3L), several of which were not previously implicated in the host response to Mtb infection. We found that p62 deficiency blocks ubiquitylation and TAX1BP1 deficiency enhances ubiquitylation, suggesting p62 ubiquitylation acts as an amplification loop by promoting downstream adaptor recruitment and serves as a platform for recruitment of ubiquitin. Our results show that TAX1BP1 mediates clearance of ubiquitylated Mtb and targets the bacteria to LC3-positive phagophores. Taken together, our proteomic profiling is likely a valuable resource for initiating mechanistic studies of macrophage biology.

Proteomic Profiling and Functional Characterization of Multiple Post-Translational Modifications of Tubulin

2015 ◽  
Vol 14 (8) ◽  
pp. 3292-3304 ◽  
Author(s):  
Ningning Liu ◽  
Yun Xiong ◽  
Yiran Ren ◽  
Linlin Zhang ◽  
Xianfei He ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Proteomic Profiling ◽  
Post Translational Modifications

scholarly journals Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1793
Author(s):  
Aleša Kristan ◽  
Nataša Debeljak ◽  
Tanja Kunej
Keyword(s):  
Target Genes ◽  
Regulatory Elements ◽  
Future Research ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Pas Domain ◽  
Expression Stability ◽  
Post Translational Modifications ◽  
Oxygen Homeostasis ◽  
Cancer Types

Endothelial PAS domain-containing protein 1 (EPAS1), also HIF2α, is an alpha subunit of hypoxia-inducible transcription factor (HIF), which mediates cellular and systemic response to hypoxia. EPAS1 has an important role in the transcription of many hypoxia-responsive genes, however, it has been less researched than HIF1α. The aim of this study was to integrate an increasing number of data on EPAS1 into a map of diverse OMICs elements. Publications, databases, and bioinformatics tools were examined, including Ensembl, MethPrimer, STRING, miRTarBase, COSMIC, and LOVD. The EPAS1 expression, stability, and activity are tightly regulated on several OMICs levels to maintain complex oxygen homeostasis. In the integrative EPAS1 map we included: 31 promoter-binding proteins, 13 interacting miRNAs and one lncRNA, and 16 post-translational modifications regulating EPAS1 protein abundance. EPAS1 has been associated with various cancer types and other diseases. The development of neuroendocrine tumors and erythrocytosis was shown to be associated with 11 somatic and 20 germline variants. The integrative map also includes 12 EPAS1 target genes and 27 interacting proteins. The study introduced the first integrative map of diverse genomics, transcriptomics, proteomics, regulomics, and interactomics data associated with EPAS1, to enable a better understanding of EPAS1 activity and regulation and support future research.

scholarly journals Nucleocytoplasmic Transport of RNA-Binding Proteins Regulates Neural Stem Cell Fates 

2020 ◽  
Author(s):  
Melissa J. MacPherson ◽  
Sarah L Erickson ◽  
Drayden Kopp ◽  
Pengqiang Wen ◽  
Mohammadreza Aghanoori ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Cell Fate ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neurodevelopmental Disorder ◽  
Neural Progenitor ◽  
Nucleocytoplasmic Transport ◽  
Transcriptional Level ◽  
Cell Fates ◽  
Cell Fate Decisions

Abstract The formation of the cerebral cortex requires balanced expansion and differentiation of neural progenitor cells, the fate choice of which requires regulation at many steps of gene expression. As progenitor cells often exhibit transcriptomic stochasticity, the ultimate output of cell fate-determining genes must be carefully controlled at the post-transcriptional level, but how this is orchestrated is poorly understood. Here we report that de novo missense variants in an RNA-binding protein CELF2 cause human cortical malformations and perturb neural progenitor cell fate decisions in mice by disrupting the nucleocytoplasmic transport of CELF2. In self-renewing neural progenitors, CELF2 is localized in the cytoplasm where it binds and coordinates mRNAs that encode cell fate regulators and neurodevelopmental disorder-related factors. The translocation of CELF2 into the nucleus releases mRNAs for translation and thereby triggers neural progenitor differentiation. Our results reveal a mechanism by which transport of CELF2 between discrete subcellular compartments orchestrates an RNA regulon to instruct cell fates in cerebral cortical development.

scholarly journals Global Analysis of Myocardial Peptides Containing Cysteines With Irreversible Sulfinic and Sulfonic Acid Post-Translational Modifications

2015 ◽  
Vol 14 (3) ◽  
pp. 609-620 ◽  
Author(s):  
Jana Paulech ◽  
Kiersten A. Liddy ◽  
Kasper Engholm-Keller ◽  
Melanie Y. White ◽  
Stuart J. Cordwell
Keyword(s):  
Sulfonic Acid ◽  
Global Analysis ◽  
Post Translational Modifications

scholarly journals Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5034
Author(s):  
Amol Prakash ◽  
Lorne Taylor ◽  
Manu Varkey ◽  
Nate Hoxie ◽  
Yassene Mohammed ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Human Tumors ◽  
Clinical Proteomics ◽  
Sequence Variants ◽  
Proteomic Profiling ◽  
High Confidence ◽  
Independent Evidence ◽  
Post Translational Modifications ◽  
Web Resource ◽  
Proteomic Data

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

scholarly journals Structural Changes in Proteins With Post-translational Modifications in Female Oncopathologies

2021 ◽  
Author(s):  
Dmitry Tikhonov ◽  
Liudmila Kulikova ◽  
Arthur T. Kopylov ◽  
Vladimir Rudnev ◽  
Alexander Stepanov ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Conformational Changes ◽  
Structural Changes ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Proteomic Profiling ◽  
Dynamics Modeling ◽  
Protein Activity ◽  
Post Translational Modifications ◽  
Elimination Clearance

Abstract Post-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer. Proteomic profiling and analysis of cancer-specific PTM patterns were performed using high-resolution UPLC-MS/MS. Structural analysis, topology, and stability of PTMs associated with sex-specific cancers were analyzed using molecular dynamics modeling. We identified highly specific PTMs, of which 12 modified peptides from eight distinct proteins derived from patients with ovarian cancer and 6 peptides of three proteins favored patients from the group with breast cancer. We found that all defined PTMs were localized in the compact and stable structural motifs exposed outside the solvent environment. PTMs increase the solvent-accessible surface area of the modified moiety and its active environment. The observed conformational changes are still inadequate to activate the structural degradation and enhance protein elimination/clearance; however, it is sufficient for the significant modulation of protein activity.

scholarly journals An infection-activated redox switch promotes tumor growth

2021 ◽  
Author(s):  
Yekaterina Kovalyova ◽  
Daniel W. Bak ◽  
Elizabeth M. Gordon ◽  
Connie Fung ◽  
Jennifer H. B. Shuman ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Xenograft Model ◽  
Tumor Formation ◽  
Host Protein ◽  
Oxygen Species ◽  
Chemical Proteomics ◽  
Post Translational Modifications ◽  
Redox Switch ◽  
Infected Cells ◽  
H Pylori

Oxidative stress is a defining feature of most cancers, including those that stem from carcinogenic infections. Reactive oxygen species (ROS) can drive tumor formation, yet the molecular oxidation events that contribute to tumorigenesis are largely unknown. Here we show that inactivation of a single, redox-sensitive cysteine in the host protease legumain, which is oxidized during infection with the gastric cancer-causing bacterium Helicobacter pylori, accelerates tumor growth. By using chemical proteomics to map cysteine reactivity in human gastric cells, we determined that H. pylori infection induces oxidation of legumain at Cys219. Legumain oxidation, which is enhanced by the ROS-promoting bacterial oncoprotein CagA, dysregulates intracellular legumain processing and localization and decreases legumain activity in H. pylori-infected cells. We further show that the site-specific loss of Cys219 reactivity increases tumor growth and mortality in a xenograft model. Our findings establish a link between the precise oxidation of a host protein and tumorigenic signaling during bacterial infection and demonstrate the importance of oxidative post-translational modifications in tumor growth.

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