Identifying the Potential Substrates of the Depalmitoylation Enzyme Acyl-protein Thioesterase 1

2019 ◽  
Vol 19 (5) ◽  
pp. 364-375 ◽  
Author(s):  
Huicong Liu ◽  
Peipei Yan ◽  
Junyan Ren ◽  
Can Wu ◽  
Wei Yuan ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Gene Ontology ◽  
Quantitative Method ◽  
Large Scale ◽  
Biological Pathways ◽  
Protein Enrichment ◽  
Cellular Processes ◽  
Data Independent Acquisition ◽  
Gene Ontology Classification ◽  
Natural Mutation

Background:The homeostasis of palmitoylation and depalmitoylation is involved in various cellular processes, the disruption of which induces severe physiological consequences. Acyl-protein thioesterase (APT) and palmitoyl-protein thioesterases (PPT) catalyze the depalmitoylation process. The natural mutation in human PPT1 caused neurodegenerative disease, yet the understanding of APT1 remains to be elucidated. While the deletion of APT1 in mice turned out to be potentially embryonically lethal, the decoding of its function strictly relied on the identification of its substrates.Objective:To determine the potential substrates of APT1 by using the generated human APT1 knockout cell line.Methods :The combined techniques of palmitoyl-protein enrichment and massspectrometry were used to analyze the different proteins. Palmitoyl-proteins both in HEK293T and APT1-KO cells were extracted by resin-assisted capture (RAC) and data independent acquisition (DIA) quantitative method of proteomics for data collection.Results:In total, 382 proteins were identified. The gene ontology classification segregated these proteins into diverse biological pathways e.g. endoplasmic reticulum process and ubiquitin-mediated proteolysis. A few potential substrates were selected for verification; indeed, major proteins were palmitoylated. Importantly, their levels of palmitoylation were clearly changed in APT1-KO cells. Interestingly, the proliferation of APT1-KO cells escalated dramatically as compared to that of the WT cells, which could be rescued by APT1 overexpression.Conclusion:Our study provides a large scale of potential substrates of APT1, thus facilitating the understanding of its intervened molecular functions.

scholarly journals Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

2020 ◽  
Author(s):  
Fynn M. Hansen ◽  
Maria C. Tanzer ◽  
Franziska Brüning ◽  
Isabell Bludau ◽  
Brenda A. Schulman ◽  
...  
Keyword(s):  
Large Scale ◽  
Tnf Alpha ◽  
Circadian Cycle ◽  
Cellular Processes ◽  
Data Independent Acquisition ◽  
Protein Ubiquitination ◽  
Quantitative Accuracy ◽  
Protein Receptors ◽  
Spectral Libraries ◽  
Acquisition Method

SUMMARYProtein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. We developed a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identified 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF-alpha signaling, the workflow comprehensively captured known sites while adding many novel ones. A first systems-wide investigation of ubiquitination of the circadian cycle uncovered hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting novel connections between metabolism and circadian regulation.

scholarly journals Pregnancy-associated changes in cervical noncoding RNA

Epigenomics ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1013-1025
Author(s):  
Kristin D Gerson ◽  
Miriam J Haviland ◽  
Dayna Neo ◽  
Jonathan L Hecht ◽  
Andrea A Baccarelli ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Cell Adhesion ◽  
Long Noncoding Rna ◽  
Prospective Cohort ◽  
Noncoding Rna ◽  
Normal Pregnancy ◽  
Biological Pathways ◽  
Bonferroni Correction ◽  
Gene Ontology Classification ◽  
Glucocorticoid Signaling

Aim: To identify pregnancy-associated changes in cervical noncoding RNA (ncRNA), including miRNA and long noncoding RNA (lncRNA), and their potential effects on biologic processes. Materials & methods: We enrolled 21 pregnant women with term deliveries (≥37 weeks’ gestation) in a prospective cohort and collected cervical swabs before 28 weeks’ gestation. We enrolled 21 nonpregnant controls. We analyzed miRNA, lncRNA and mRNA expression, applying a Bonferroni correction. Results: Five miRNA and three lncRNA were significantly differentially (>twofold change) expressed. Putative miRNA targets are enriched in genes mediating organogenesis, glucocorticoid signaling, cell adhesion and ncRNA machinery. Conclusion: Differential cervical ncRNA expression occurs in the setting of pregnancy. Gene ontology classification reveals biological pathways through which miRNA may play a biologic role in normal pregnancy physiology.

scholarly journals Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw155 ◽  
Author(s):  
Marc Feuermann ◽  
Pascale Gaudet ◽  
Huaiyu Mi ◽  
Suzanna E. Lewis ◽  
Paul D. Thomas
Keyword(s):  
Gene Ontology ◽  
Gene Function ◽  
Large Scale ◽  
Cellular Processes

The Research of Production Process Statistical Steady-State Based on the Hypothesis Test

2011 ◽  
Vol 314-316 ◽  
pp. 2433-2438
Author(s):  
Wei Zhi Wang
Keyword(s):  
Quality Control ◽  
Steady State ◽  
Production Process ◽  
Quantitative Method ◽  
Large Scale ◽  
Hypothesis Test ◽  
Influence Factors ◽  
Normal Operation ◽  
Scale Production ◽  
Large Scale Production

By only applying a after the event exam in the quality control of the batch production is not enough to meet the needs of modern large-scale production. To a certain extent, modern quality control is a dynamic process of the steady-state judge and adjustment. A simple and reliable steady-state judge rule and method is the premise to guarantee the normal operation. This paper provides a quantitative method to evaluate production process steady-state by analyzing influence factors based on mathematical statistics. The method is both suitable for simple production process and complex production process with sub-processes.

scholarly journals A Potential of microRNAs for High-Content Screening

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Andrius Serva ◽  
Christoph Claas ◽  
Vytaute Starkuviene
Keyword(s):  
Large Scale ◽  
Cellular Processes ◽  
Comprehensive Knowledge ◽  
Functional Models ◽  
Rapid Accumulation ◽  
Health And Disease ◽  
Temporal And Spatial ◽  
And Function ◽  
Functional Analyses ◽  
Immense Potential

In the last years miRNAs have increasingly been recognised as potent posttranscriptional regulators of gene expression. Possibly, miRNAs exert their action on virtually any biological process by simultaneous regulation of numerous genes. The importance of miRNA-based regulation in health and disease has inspired research to investigate diverse aspects of miRNA origin, biogenesis, and function. Despite the recent rapid accumulation of experimental data, and the emergence of functional models, the complexity of miRNA-based regulation is still far from being well understood. In particular, we lack comprehensive knowledge as to which cellular processes are regulated by which miRNAs, and, furthermore, how temporal and spatial interactions of miRNAs to their targets occur. Results from large-scale functional analyses have immense potential to address these questions. In this review, we discuss the latest progress in application of high-content and high-throughput functional analysis for the systematic elucidation of the biological roles of miRNAs.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals Nothing Regular about the Regulins: Distinct Functional Properties of SERCA Transmembrane Peptide Regulatory Subunits

2021 ◽  
Vol 22 (16) ◽  
pp. 8891
Author(s):  
Nishadh Rathod ◽  
Jessi J. Bak ◽  
Joseph O. Primeau ◽  
M’Lynn E. Fisher ◽  
Lennane Michel Espinoza-Fonseca ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Functional Properties ◽  
Transmembrane Helices ◽  
Regulatory Subunits ◽  
Reading Frame ◽  
Endoplasmic Reticulum Calcium ◽  
Cellular Processes ◽  
Functional Consequences ◽  
Differential Binding ◽  
Dynamics Simulations

The sarco-endoplasmic reticulum calcium ATPase (SERCA) is responsible for maintaining calcium homeostasis in all eukaryotic cells by actively transporting calcium from the cytosol into the sarco-endoplasmic reticulum (SR/ER) lumen. Calcium is an important signaling ion, and the activity of SERCA is critical for a variety of cellular processes such as muscle contraction, neuronal activity, and energy metabolism. SERCA is regulated by several small transmembrane peptide subunits that are collectively known as the “regulins”. Phospholamban (PLN) and sarcolipin (SLN) are the original and most extensively studied members of the regulin family. PLN and SLN inhibit the calcium transport properties of SERCA and they are required for the proper functioning of cardiac and skeletal muscles, respectively. Myoregulin (MLN), dwarf open reading frame (DWORF), endoregulin (ELN), and another-regulin (ALN) are newly discovered tissue-specific regulators of SERCA. Herein, we compare the functional properties of the regulin family of SERCA transmembrane peptide subunits and consider their regulatory mechanisms in the context of the physiological and pathophysiological roles of these peptides. We present new functional data for human MLN, ELN, and ALN, demonstrating that they are inhibitors of SERCA with distinct functional consequences. Molecular modeling and molecular dynamics simulations of SERCA in complex with the transmembrane domains of MLN and ALN provide insights into how differential binding to the so-called inhibitory groove of SERCA—formed by transmembrane helices M2, M6, and M9—can result in distinct functional outcomes.

scholarly journals Miga-mediated endoplasmic reticulum–mitochondria contact sites regulate neuronal homeostasis

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Lingna Xu ◽  
Xi Wang ◽  
Jia Zhou ◽  
Yunyi Qiu ◽  
Weina Shang ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Mammalian Cells ◽  
Mitochondrial Dynamics ◽  
Molecular Organization ◽  
Lipid Transport ◽  
Cellular Processes ◽  
Contact Sites ◽  
Neuronal Homeostasis ◽  
Higher Eukaryotes ◽  
Lateral Sclerosis

Endoplasmic reticulum (ER)–mitochondria contact sites (ERMCSs) are crucial for multiple cellular processes such as calcium signaling, lipid transport, and mitochondrial dynamics. However, the molecular organization, functions, regulation of ERMCS, and the physiological roles of altered ERMCSs are not fully understood in higher eukaryotes. We found that Miga, a mitochondrion located protein, markedly increases ERMCSs and causes severe neurodegeneration upon overexpression in fly eyes. Miga interacts with an ER protein Vap33 through its FFAT-like motif and an amyotrophic lateral sclerosis (ALS) disease related Vap33 mutation considerably reduces its interaction with Miga. Multiple serine residues inside and near the Miga FFAT motif were phosphorylated, which is required for its interaction with Vap33 and Miga-mediated ERMCS formation. The interaction between Vap33 and Miga promoted further phosphorylation of upstream serine/threonine clusters, which fine-tuned Miga activity. Protein kinases CKI and CaMKII contribute to Miga hyperphosphorylation. MIGA2, encoded by the miga mammalian ortholog, has conserved functions in mammalian cells. We propose a model that shows Miga interacts with Vap33 to mediate ERMCSs and excessive ERMCSs lead to neurodegeneration.

A Quantitative Method for Measuring Health of Authoritative Name Servers

2022 ◽  
Vol 16 (1) ◽  
pp. 0-0
Keyword(s):  
Quantitative Method ◽  
Large Scale ◽  
Critical Infrastructure ◽  
Research Work ◽  
Abnormal Behavior ◽  
The Internet ◽  
Large Component ◽  
Internet Community ◽  
Critical Components ◽  
Typical User

The Domain Name System - DNS is regarded as one of the critical infrastructure component of the global Internet because a large-scale DNS outage would effectively take a typical user offline. Therefore, the Internet community should ensure that critical components of the DNS ecosystem - that is, root name servers, top-level domain registrars and registries, authoritative name servers, and recursive resolvers - function smoothly. To this end, the community should monitor them periodically and provide public alerts about abnormal behavior. The authors propose a novel quantitative approach for evaluating the health of authoritative name servers – a critical, core, and a large component of the DNS ecosystem. The performance is typically measured in terms of response time, reliability, and throughput for most of the Internet components. This research work proposes a novel list of parameters specifically for determining the health of authoritative name servers: DNS attack permeability, latency comparison, and DNSSEC validation.

scholarly journals PINK1/Parkin Mediated Mitophagy, Ca2+ Signalling, and ER–Mitochondria Contacts in Parkinson’s Disease

2020 ◽  
Vol 21 (5) ◽  
pp. 1772 ◽  
Author(s):  
Lucia Barazzuol ◽  
Flavia Giamogante ◽  
Marisa Brini ◽  
Tito Calì
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Endoplasmic Reticulum ◽  
Neurodegenerative Diseases ◽  
Current Knowledge ◽  
Phosphatase And Tensin Homolog ◽  
Cellular Processes ◽  
Selective Degradation ◽  
Contact Sites ◽  
Tensin Homolog

Endoplasmic reticulum (ER)–mitochondria contact sites are critical structures for cellular function. They are implicated in a plethora of cellular processes, including Ca2+ signalling and mitophagy, the selective degradation of damaged mitochondria. Phosphatase and tensin homolog (PTEN)-induced kinase (PINK) and Parkin proteins, whose mutations are associated with familial forms of Parkinson’s disease, are two of the best characterized mitophagy players. They accumulate at ER–mitochondria contact sites and modulate organelles crosstalk. Alterations in ER–mitochondria tethering are a common hallmark of many neurodegenerative diseases including Parkinson’s disease. Here, we summarize the current knowledge on the involvement of PINK1 and Parkin at the ER–mitochondria contact sites and their role in the modulation of Ca2+ signalling and mitophagy.

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