A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis.

Abstract:

:We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella enterica serovar Typhimurium (Salmonella Typhimurium). This method includes (i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques, (ii) in vivo cross-linking with formaldehyde, (iii) tandem affinity purification of bait proteins under fully denaturing conditions, and (iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions and permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of noncross-linked proteins to bait proteins. Two different negative controls were employed to eliminate the possibility of identifying background and nonspecific proteins as interacting partners, especially those caused by nonspecific binding to the stationary phase used for protein purification. In an initial demonstration of this approach, we tagged three Salmonella proteinsHimD, PduB and PhoPwith known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified for each bait protein, including the known binding partners such as HimA for HimD, as well as unexpected binding partners. Our results suggest that novel protein-protein interactions identified may be critical to pathogenesis by Salmonella.

journal_name

J Proteome Res

authors

Chowdhury SM,Shi L,Yoon H,Ansong C,Rommereim LM,Norbeck AD,Auberry KJ,Moore RJ,Adkins JN,Heffron F,Smith RD

doi

10.1021/pr800865d

subject

Has Abstract

pub_date

2009-03-01 00:00:00

pages

1504-14

issue

3

eissn

1535-3893

issn

1535-3907

pii

10.1021/pr800865d

journal_volume

8

pub_type

杂志文章
  • Interaction network of the 14-3-3 protein in the ancient protozoan parasite Giardia duodenalis.

    abstract::14-3-3s are phosphoserine/phosphotreonine binding proteins that play pivotal roles as regulators of multiple cellular processes in eukaryotes. The flagellated protozoan parasite Giardia duodenalis, the causing agent of giardiasis, is a valuable simplified eukaryotic model. A single 14-3-3 isoform (g14-3-3) is expresse...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr3000199

    authors: Lalle M,Camerini S,Cecchetti S,Sayadi A,Crescenzi M,Pozio E

    更新日期:2012-05-04 00:00:00

  • Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach.

    abstract::Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering o...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00144

    authors: Levitsky LI,Ivanov MV,Lobas AA,Gorshkov MV

    更新日期:2017-02-03 00:00:00

  • 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

  • The Muscle Metabolome Differs between Healthy and Frail Older Adults.

    abstract::Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00840

    authors: Fazelzadeh P,Hangelbroek RW,Tieland M,de Groot LC,Verdijk LB,van Loon LJ,Smilde AK,Alves RD,Vervoort J,Müller M,van Duynhoven JP,Boekschoten MV

    更新日期:2016-02-05 00:00:00

  • Common glycoproteins expressing polylactosamine-type glycans on matched patient primary and metastatic melanoma cells show different glycan profiles.

    abstract::Recently, we reported comparative analysis of glycoproteins which express cancer-specific N-glycans on various cancer cells and identified 24 glycoproteins having polylactosamine (polyLacNAc)-type N-glycans that are abundantly present in malignant cells [ Mitsui et al., J. Pharm. Biomed. Anal. 2012 , 70 , 718 - 726 ]....

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr401015b

    authors: Kinoshita M,Mitsui Y,Kakoi N,Yamada K,Hayakawa T,Kakehi K

    更新日期:2014-02-07 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

  • Beyond linker histones and high mobility group proteins: global profiling of perchloric acid soluble proteins.

    abstract::Extraction with HClO(4) provides an easy method for efficient enrichment of both histone H1 and HMG proteins from a variety of tissues. Usually, the histone and the HMG proteins are the most abundant components of the extracts, however, other proteins have frequently been observed but only seldom studied in more detai...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050415p

    authors: Zougman A,Wiśniewski JR

    更新日期:2006-04-01 00:00:00

  • Serum metabolic signature of minimal hepatic encephalopathy by (1)H-nuclear magnetic resonance.

    abstract::Minimal hepatic encephalopathy (MHE) reduces quality of life of cirrhotic patients, predicts overt hepatic encephalopathy, and is associated with poor prognosis. We hypothesized that MHE arises once metabolic alterations derived from the liver reach a particular threshold. Our aim was to assess whether metabolic profi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100486e

    authors: Jiménez B,Montoliu C,MacIntyre DA,Serra MA,Wassel A,Jover M,Romero-Gomez M,Rodrigo JM,Pineda-Lucena A,Felipo V

    更新日期:2010-10-01 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

  • Online multidimensional separation with biphasic monolithic capillary column for shotgun proteome analysis.

    abstract::A biphasic monolithic capillary column with 10 cm segment of strong-cation exchange monolith and 65 cm segment of reversed-phase monolith was prepared within a single 100 microm i.d. capillary. Separation performance of this column was evaluated by a five-cycle online multidimensional separation of 10 microg tryptic d...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr700562b

    authors: Wang F,Dong J,Ye M,Jiang X,Wu R,Zou H

    更新日期:2008-01-01 00:00:00

  • A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12.

    abstract::The bacterial ribosomal protein S12 contains a universally conserved D88 residue on a loop region thought to be critically involved in translation due to its proximal location to the A site of the 30S subunit. While D88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioa...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr3009435

    authors: Strader MB,Hervey WJ 4th,Costantino N,Fujigaki S,Chen CY,Akal-Strader A,Ihunnah CA,Makusky AJ,Court DL,Markey SP,Kowalak JA

    更新日期:2013-03-01 00:00:00

  • Western honeybee drones and workers (Apis mellifera ligustica) have different olfactory mechanisms than eastern honeybees (Apis cerana cerana).

    abstract::The honeybees Apis mellifera ligustica (Aml) and Apis cerana cerana (Acc) are two different western and eastern bee species that evolved in distinct ecologies and developed specific antennal olfactory systems for their survival. Knowledge of how their antennal olfactory systems function in regards to the success of ea...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300298w

    authors: Woltedji D,Song F,Zhang L,Gala A,Han B,Feng M,Fang Y,Li J

    更新日期:2012-09-07 00:00:00

  • Proteomic profiling of plasma in Huntington's disease reveals neuroinflammatory activation and biomarker candidates.

    abstract::Huntington's disease (HD) causes widespread CNS changes and systemic abnormalities including endocrine and immune dysfunction. HD biomarkers are needed to power clinical trials of potential treatments. We used multiplatform proteomic profiling to reveal plasma changes with HD progression. Proteins of interest were eva...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0700753

    authors: Dalrymple A,Wild EJ,Joubert R,Sathasivam K,Björkqvist M,Petersén A,Jackson GS,Isaacs JD,Kristiansen M,Bates GP,Leavitt BR,Keir G,Ward M,Tabrizi SJ

    更新日期:2007-07-01 00:00:00

  • Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics.

    abstract::Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049886m

    authors: Chang J,Van Remmen H,Ward WF,Regnier FE,Richardson A,Cornell J

    更新日期:2004-11-01 00:00:00

  • Altered chaperone and protein turnover regulators expression in cultured skin fibroblasts from type 1 diabetes mellitus with nephropathy.

    abstract::In type-1 diabetes mellitus (T1DM) with diabetic nephropathy (DN), accumulation of abnormal proteins in the kidney and other tissues may derive from constitutive alterations of intracellular protein recognition, assembly, and turnover. We characterized the proteins involved in these functions in cultured skin fibrobla...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060443n

    authors: Tessari P,Puricelli L,Iori E,Arrigoni G,Vedovato M,James P,Coracina A,Millioni R

    更新日期:2007-03-01 00:00:00

  • Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications.

    abstract::Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0602803

    authors: Ndassa YM,Orsi C,Marto JA,Chen S,Ross MM

    更新日期:2006-10-01 00:00:00

  • Single-step procedure for the isolation of proteins at near-native conditions from mammalian tissue for proteomic analysis on antibody microarrays.

    abstract::The process of extracting comprehensive proteome representations is a crucial step for many proteomic studies. While antibody microarrays are an evolving and promising methodology in proteomics, the issue of protein extraction from tissues for this kind of analysis has never been addressed. Here, we describe a single-...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900844q

    authors: Alhamdani MS,Schröder C,Werner J,Giese N,Bauer A,Hoheisel JD

    更新日期:2010-02-05 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

  • Metabolomics approach for enzyme discovery.

    abstract::The search for novel enzymes is an important but difficult task in functional genomics. Here, we present a systematic method based on in vitro assays in combination with metabolite profiling to discover novel enzymatic activities. A complex mixture of metabolites is incubated with purified candidate proteins and the r...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0600576

    authors: Saito N,Robert M,Kitamura S,Baran R,Soga T,Mori H,Nishioka T,Tomita M

    更新日期:2006-08-01 00:00:00

  • Integrative transcriptome and proteome study to identify the signaling network regulated by POPX2 phosphatase.

    abstract::POPX2 is a serine/threonine phosphatase belonging to the protein phosphatase 2C (PP2C) family that has been found to be elevated in invasive breast cancer cells. Silencing of POPX2 results in lower cell motility and invasiveness. The molecular mechanism of POPX2-regulated cell motility is not well understood. To ident...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr301113c

    authors: Zhang S,Guo T,Chan H,Sze SK,Koh CG

    更新日期:2013-06-07 00:00:00

  • Empirical Bayesian random censoring threshold model improves detection of differentially abundant proteins.

    abstract::A challenge in proteomics is that many observations are missing with the probability of missingness increasing as abundance decreases. Adjusting for this informative missingness is required to assess accurately which proteins are differentially abundant. We propose an empirical Bayesian random censoring threshold (EBR...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500171u

    authors: Koopmans F,Cornelisse LN,Heskes T,Dijkstra TM

    更新日期:2014-09-05 00:00:00

  • Comparative proteomic analysis reveals sex and estrogen receptor β effects in the pressure overloaded heart.

    abstract::In pressure overload (PO), sex differences in humans and rodents have been well documented and estrogen receptor (ER) β is considered cardioprotective. However, the underlying mechanisms are poorly understood. Our aim was to investigate sex- and ERβ-specific effects in protein abundance in PO employing a 2-dimensional...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500749j

    authors: Kararigas G,Fliegner D,Forler S,Klein O,Schubert C,Gustafsson JÅ,Klose J,Regitz-Zagrosek V

    更新日期:2014-12-05 00:00:00

  • Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition.

    abstract::To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, incl...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8006478

    authors: Keshamouni VG,Jagtap P,Michailidis G,Strahler JR,Kuick R,Reka AK,Papoulias P,Krishnapuram R,Srirangam A,Standiford TJ,Andrews PC,Omenn GS

    更新日期:2009-01-01 00:00:00

  • Two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling approach revealed first proteome profiles of pulmonary alveolar macrophages infected with porcine reproduct

    abstract::Porcine reproductive and respiratory syndrome (PRRS) has devastated the pig industry worldwide for almost 25 years, and its virus (PRRSV) preferentially infects and replicates in pulmonary alveolar macrophages (PAMs). To discover cellular protein responses in PRRSV-infected PAMs, two-dimensional liquid chromatography-...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201266z

    authors: Lu Q,Bai J,Zhang L,Liu J,Jiang Z,Michal JJ,He Q,Jiang P

    更新日期:2012-05-04 00:00:00

  • Deciphering the Molecular Diversity of an Ant Venom Peptidome through a Venomics Approach.

    abstract::The peptide toxins in the venoms of small invertebrates such as stinging ants have rarely been studied due to the limited amount of venom available per individual. We used a venomics strategy to identify the molecular diversity of the venom peptidome for the myrmicine ant Tetramorium bicarinatum. The methodology inclu...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00452

    authors: Touchard A,Téné N,Song PCT,Lefranc B,Leprince J,Treilhou M,Bonnafé E

    更新日期:2018-10-05 00:00:00

  • Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome.

    abstract::Recent advances in genome editing technologies have enabled the insertion of epitope tags at endogenous loci with relative efficiency. We describe an approach for investigation of protein interaction dynamics of the AMP-activated kinase complex AMPK using a catalytic subunit AMPKα2 (PRKAA2 gene) as the bait, based on ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00378

    authors: Stein BD,Herzig S,Martínez-Bartolomé S,Lavallée-Adam M,Shaw RJ,Yates JR 3rd

    更新日期:2019-10-04 00:00:00

  • Characterization of human tear proteome using multiple proteomic analysis techniques.

    abstract::Tear proteome profiling may generate useful information for the understanding of the interaction between an eye and its contacting objects, such as a contact lens or a lens implant. This is important for designing improved eye-care devices and maintaining the health of an eye. Proteome profiles of tear fluids may also...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0501970

    authors: Li N,Wang N,Zheng J,Liu XM,Lever OW,Erickson PM,Li L

    更新日期:2005-11-01 00:00:00

  • Minimizing Laboratory-Induced Decay in Bone Proteomics.

    abstract::Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00564

    authors: Procopio N,Buckley M

    更新日期:2017-02-03 00:00:00

  • Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry.

    abstract::A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-re...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr025551y

    authors: Mawuenyega KG,Kaji H,Yamuchi Y,Shinkawa T,Saito H,Taoka M,Takahashi N,Isobe T

    更新日期:2003-01-01 00:00:00

  • Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion.

    abstract::Growing appreciation for astrocytes as active participants in nervous system development, neurovascular metabolic coupling, and neurological disease progression has stimulated recent investigation into specific astrocyte-secreted proteins that may mediate these functions. The current work utilized SILAC-generated isot...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100134n

    authors: Greco TM,Seeholzer SH,Mak A,Spruce L,Ischiropoulos H

    更新日期:2010-05-07 00:00:00