Proteome Wide Profiling of N-ε-Lysine Acetylation Reveals a Novel Mechanism of Regulation of the Chitinase Activity in Francisella novicida.

Abstract:

:Francisella tularensis is a Gram-negative bacterium that causes the zoonotic disease tularemia. The historical development of tularemia as a biological weapon has led to it being characterized by the CDC as a category A biothreat agent. Neither posttranslational modification (PTM) of proteins, in particular lysine acetylation, in Francisella nor its subsequent regulation of the protein activity has been well studied. In this work, we analyze N-ε-lysine acetylation of the F. tularensis ssp. novicida proteome by mass spectrometry for the first time. To create a comprehensive acetylation profile, we enriched protein acetylation using two approaches: (1) the addition of glucose or acetate into the culture medium and (2) direct chemical acetylation of N-ε-lysines with acetyl phosphate. We discovered 280 acetylated proteins with 1178 acetylation sites in the F. tularensis ssp. novicida strain U112. Lysine acetylation is an important PTM that regulates multiple cellular processes in bacteria, including metabolism, transcription, translation, stress response, and protein folding. We discovered that Francisella chitinases A and B are acetylated naturally and when chemically induced by acetyl phosphate. Moreover, chemical overacetylation of chitinases results in silencing of the enzymatic activity. Our findings suggest a novel mechanism of posttranslational regulation of the chitinase activity and that acetylation may play a role in Francisella's regulation of the protein activity.

journal_name

J Proteome Res

authors

Marakasova E,Ii A,Nelson KT,van Hoek ML

doi

10.1021/acs.jproteome.9b00512

subject

Has Abstract

pub_date

2020-04-03 00:00:00

pages

1409-1422

issue

4

eissn

1535-3893

issn

1535-3907

journal_volume

19

pub_type

杂志文章
  • iTRAQ protein profile differential analysis between somatic globular and cotyledonary embryos reveals stress, hormone, and respiration involved in increasing plantlet regeneration of Gossypium hirsutum L.

    abstract::Somatic embryo development (SED) in upland cotton shows low frequencies of embryo maturation and plantlet regeneration. Progress in increasing the regeneration rate has been limited. Here a global analysis of proteome dynamics between globular and cotyledonary embryos was performed using isobaric tags for relative and...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500688g

    authors: Ge X,Zhang C,Wang Q,Yang Z,Wang Y,Zhang X,Wu Z,Hou Y,Wu J,Li F

    更新日期:2015-01-02 00:00:00

  • Secretomic Analysis of Host-Pathogen Interactions Reveals That Elongation Factor-Tu Is a Potential Adherence Factor of Helicobacter pylori during Pathogenesis.

    abstract::The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could therefore increase understanding of the mechanisms during initial pathogenesis. The present study...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00584

    authors: Chiu KH,Wang LH,Tsai TT,Lei HY,Liao PC

    更新日期:2017-01-06 00:00:00

  • Lipid Profiling in Epicardial and Subcutaneous Adipose Tissue of Patients with Coronary Artery Disease.

    abstract::Coronary artery disease is one of the most frequent causes of morbidity and mortality worldwide. It is even more prevalent in patients with type 2 diabetes mellitus who suffer from obesity and increased accumulation of epicardial fat with a possible contributing role in the development of coronary artery disease. We p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00269

    authors: Tomášová P,Čermáková M,Pelantová H,Vecka M,Kratochvílová H,Lipš M,Lindner J,Ivák P,Netuka I,Šedivá B,Haluzík M,Kuzma M

    更新日期:2020-10-02 00:00:00

  • ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion.

    abstract::The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elast...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00328

    authors: Hulstaert N,Shofstahl J,Sachsenberg T,Walzer M,Barsnes H,Martens L,Perez-Riverol Y

    更新日期:2020-01-03 00:00:00

  • Establishing a reliable multiple reaction monitoring-based method for the quantification of obesity-associated comorbidities in serum and adipose tissue requires intensive clinical validation.

    abstract::Multiple reaction monitoring (MRM)-based mass spectrometric quantification of peptides and their corresponding proteins has been successfully applied for biomarker validation in serum. The option of multiplexing offers the chance to analyze various proteins in parallel, which is especially important in obesity researc...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500722k

    authors: Oberbach A,Schlichting N,Neuhaus J,Kullnick Y,Lehmann S,Heinrich M,Dietrich A,Mohr FW,von Bergen M,Baumann S

    更新日期:2014-12-05 00:00:00

  • Protein expression profiles of necrosis and apoptosis induced by 5-fluoro-2'-deoxyuridine in mouse cancer cells.

    abstract::We have investigated the molecular mechanisms regulating the necrosis and apoptosis that occur on treatment of mouse mammary tumor FM3A cells with 5-fluoro-2'-deoxyuridine (FUdR), a potent anticancer agent, using the original clone F28-7 and its variant F28-7-A cells. Previously, we reported an interesting observation...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr9010537

    authors: Sato A,Satake A,Hiramoto A,Wataya Y,Kim HS

    更新日期:2010-05-07 00:00:00

  • Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus.

    abstract::Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity ha...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr9010684

    authors: Teutschbein J,Albrecht D,Pötsch M,Guthke R,Aimanianda V,Clavaud C,Latgé JP,Brakhage AA,Kniemeyer O

    更新日期:2010-07-02 00:00:00

  • Intrinsic disorder in nuclear hormone receptors.

    abstract::Many proteins possess intrinsic disorder (ID) and lack a rigid three-dimensional structure in at least part of their sequence. ID has been hypothesized to influence protein-protein and protein-ligand interactions. We calculated ID for nearly 400 vertebrate and invertebrate members of the biomedically important nuclear...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8003024

    authors: Krasowski MD,Reschly EJ,Ekins S

    更新日期:2008-10-01 00:00:00

  • Proteomics of nitrogen remobilization in poplar bark.

    abstract::Seasonal nitrogen (N) cycling in temperate deciduous trees involves the accumulation of bark storage proteins (BSPs) in phloem parenchyma and xylem ray cells. BSPs are anabolized using recycled N during autumn leaf senescence and later become a source of N during spring shoot growth as they are catabolized. Little is ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr501090p

    authors: Islam N,Li G,Garrett WM,Lin R,Sriram G,Cooper B,Coleman GD

    更新日期:2015-02-06 00:00:00

  • Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics.

    abstract::Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00165

    authors: Clark DJ,Hu Y,Bocik W,Chen L,Schnaubelt M,Roberts R,Shah P,Whiteley G,Zhang H

    更新日期:2018-06-01 00:00:00

  • Thioridazine Alters the Cell-Envelope Permeability of Mycobacterium tuberculosis.

    abstract::The increasing occurrence of multidrug resistant tuberculosis exerts a major burden on treatment of this infectious disease. Thioridazine, previously used as a neuroleptic, is active against extensively drug resistant tuberculosis when added to other second- and third-line antibiotics. By quantitatively studying the p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b01037

    authors: de Keijzer J,Mulder A,de Haas PE,de Ru AH,Heerkens EM,Amaral L,van Soolingen D,van Veelen PA

    更新日期:2016-06-03 00:00:00

  • Investigating RET RTK signaling pathways using an IAP-based activity-profiling approach.

    abstract::Many neurodegenerative diseases, such as Parkinson's disease, can be directly correlated with the deregulation in neuronal signaling. Hence, it is indispensable for therapy development to understand the participating signaling processes. Because the activity of the involved protein kinases is of major interest for the...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500163r

    authors: Höfener M,Pachl F,Take T,Fischer von Mollard G,Kuster B,Sewald N

    更新日期:2014-08-01 00:00:00

  • Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins.

    abstract::The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00654

    authors: Verkhivker GM

    更新日期:2020-11-06 00:00:00

  • Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.

    abstract::Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues and is shown here to significantly impact the idios...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00468

    authors: Li S,Dabir A,Misal SA,Tang H,Radivojac P,Reilly JP

    更新日期:2016-10-07 00:00:00

  • Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells.

    abstract::Enzyme-mediated 18O/16O differential labeling of proteome samples often suffers from incomplete exchange of the carboxy-terminus oxygen atoms, resulting in ambiguity in the measurable abundance differences. In this study, an 18O/16O labeling strategy was optimized for and applied to the solution-based comparative anal...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049790s

    authors: Blonder J,Hale ML,Chan KC,Yu LR,Lucas DA,Conrads TP,Zhou M,Popoff MR,Issaq HJ,Stiles BG,Veenstra TD

    更新日期:2005-03-01 00:00:00

  • Andromeda: a peptide search engine integrated into the MaxQuant environment.

    abstract::A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial s...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101065j

    authors: Cox J,Neuhauser N,Michalski A,Scheltema RA,Olsen JV,Mann M

    更新日期:2011-04-01 00:00:00

  • EpiC: an open resource for exploring epitopes to aid antibody-based experiments.

    abstract::Antibodies are a primary research tool for a diverse range of experiments in biology, from development to pathology. Their utility is derived from their ability to specifically identify proteins at a high level of sensitivity. This diversity of experimental requirements stretches the capabilities of these key research...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100029f

    authors: Haslam NJ,Gibson TJ

    更新日期:2010-07-02 00:00:00

  • Proteomic analysis of lipid microdomains from lipopolysaccharide-activated human endothelial cells.

    abstract::The endothelium plays a critical role in orchestrating the inflammatory response seen during sepsis. Many of the inflammatory effects of Gram-negative sepsis are elicited by lipopolysaccharide (LPS), a glycolipid component of bacterial cell walls. Lipid-rich microdomains have been shown to concentrate components of th...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049824w

    authors: Karsan A,Blonder J,Law J,Yaquian E,Lucas DA,Conrads TP,Veenstra T

    更新日期:2005-03-01 00:00:00

  • Role of proteomics to differentiate between benign and potentially malignant pancreatic cysts.

    abstract::Pancreatic cystic neoplasms represent 10-15% of primary cystic masses of the pancreas. While pancreatic cysts are detected with an increasing frequency due to the use of advanced imaging modalities in clinical practice, the diagnosis of pancreatic cystic neoplasms remains unsatisfactory because available diagnostic te...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr2000557

    authors: Cuoghi A,Farina A,Z'graggen K,Dumonceau JM,Tomasi A,Hochstrasser DF,Genevay M,Lescuyer P,Frossard JL

    更新日期:2011-05-06 00:00:00

  • High performance liquid chromatography-mass spectrometry for metabonomics: potential biomarkers for acute deterioration of liver function in chronic hepatitis B.

    abstract::Metabonomics methods have been successfully applied to the drug discovery, toxicology, phytochemistry, and clinical fields. Here, we report a self-developed metabonomics platform which is based on high performance liquid chromatography-mass spectrometry (HPLC-MS) technique and applied to the investigation of acute det...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050364w

    authors: Yang J,Zhao X,Liu X,Wang C,Gao P,Wang J,Li L,Gu J,Yang S,Xu G

    更新日期:2006-03-01 00:00:00

  • Identification of chromatophore membrane protein complexes formed under different nitrogen availability conditions in Rhodospirillum rubrum.

    abstract::The chromatophore membrane of the photosynthetic diazotroph Rhodospirillum rubrum is of vital importance for a number of central processes, including nitrogen fixation. Using a novel amphiphile, we have identified protein complexes present under different nitrogen availability conditions by the use of two-dimensional ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100838x

    authors: Selao TT,Branca R,Chae PS,Lehtiö J,Gellman SH,Rasmussen SG,Nordlund S,Norén A

    更新日期:2011-06-03 00:00:00

  • Proteomic Investigation of Ram Spermatozoa and the Proteins Conferred by Seminal Plasma.

    abstract::Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility afte...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00530

    authors: Pini T,Leahy T,Soleilhavoup C,Tsikis G,Labas V,Combes-Soia L,Harichaux G,Rickard JP,Druart X,de Graaf SP

    更新日期:2016-10-07 00:00:00

  • Poly(glycidyl methacrylate/divinylbenzene)-IDA-FeIII in phosphoproteomics.

    abstract::The study of protein phosphorylation has grown exponentially in recent years, as it became evident that important cellular functions are regulated by phosphorylation and dephosphorylation of proteins on serine, threonine and tyrosine residues. The use of immobilized metal affinity chromatography (IMAC) to enrich phosp...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050224m

    authors: Aprilita NH,Huck CW,Bakry R,Feuerstein I,Stecher G,Morandell S,Huang HL,Stasyk T,Huber LA,Bonn GK

    更新日期:2005-11-01 00:00:00

  • A Shotgun Proteomic Approach Reveals That Fe Deficiency Causes Marked Changes in the Protein Profiles of Plasma Membrane and Detergent-Resistant Microdomain Preparations from Beta vulgaris Roots.

    abstract::In the present study we have used label-free shotgun proteomic analysis to examine the effects of Fe deficiency on the protein profiles of highly pure sugar beet root plasma membrane (PM) preparations and detergent-resistant membranes (DRMs), the latter as an approach to study microdomains. Altogether, 545 proteins we...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00026

    authors: Gutierrez-Carbonell E,Takahashi D,Lüthje S,González-Reyes JA,Mongrand S,Contreras-Moreira B,Abadía A,Uemura M,Abadía J,López-Millán AF

    更新日期:2016-08-05 00:00:00

  • Application of a Novel Mass Spectral Data Acquisition Approach to Lipidomic Analysis of Liver Extracts from Sitaxentan-Treated Liver-Humanized PXB Mice.

    abstract::The application of a data-independent acquisition (DIA) method ("SONAR") that employs a rapidly scanning quadrupole is described for the lipidomic analysis of complex biological extracts. Using this approach, the MS acquisition window can be varied between 1 and 25 Da, enabling the isolation of ions prior to their ent...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00334

    authors: King A,Baginski M,Morikawa Y,Rainville PD,Gethings LA,Wilson ID,Plumb RS

    更新日期:2019-11-01 00:00:00

  • Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.

    abstract::Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the a...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100035b

    authors: Iwai LK,Benoist C,Mathis D,White FM

    更新日期:2010-06-04 00:00:00

  • A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis.

    abstract::Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00927

    authors: Rudolph JD,Cox J

    更新日期:2019-05-03 00:00:00

  • Mapping glycans onto specific N-linked glycosylation sites of Pyrus communis PGIP redefines the interface for EPG-PGIP interactions.

    abstract::Polygalacturonase inhibiting proteins (PGIPs) are members of the leucine rich repeat family of proteins, involved in plant defense against fungal pathogens. PGIPs exhibit a remarkable degree of specificity in terms of their ability to bind and inhibit their target molecules, the endopolygalacturonases (EPGs). This spe...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800855f

    authors: Lim JM,Aoki K,Angel P,Garrison D,King D,Tiemeyer M,Bergmann C,Wells L

    更新日期:2009-02-01 00:00:00

  • Liquid chromatography-mass spectrometry based metabolomics study of cloned versus normal pigs fed either restricted or ad libitum high-energy diets.

    abstract::Genetically identical cloned pigs should in principle eliminate biological variation and provide more pronounced effects when subjected to, e.g., dietary interventions, but little is known about how phenotype and phenotypic variation is affected by cloning. Therefore, an investigation of the metabolome of cloned pigs ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201253h

    authors: Christensen KL,Hedemann MS,Jørgensen H,Stagsted J,Knudsen KE

    更新日期:2012-07-06 00:00:00

  • Investigating the dynamic nature of the interactions between nuclear proteins and histones upon DNA damage using an immobilized peptide chemical proteomics approach.

    abstract::As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060278b

    authors: Dirksen EH,Pinkse MW,Rijkers DT,Cloos J,Liskamp RM,Slijper M,Heck AJ

    更新日期:2006-09-01 00:00:00