High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example

Souza, Gustavo; Målen, Hiwa; Søfteland, Tina; Sælensminde, Gisle; Prasad, Swati; Jonassen, Inge; Wiker, Harald G.

doi:10.1186/1471-2164-9-316

Cited by 64 publications

(68 citation statements)

References 36 publications

(53 reference statements)

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“…The bioinformatics prediction of the N terminus of HOAS has been revised since the M. tuberculosis enzyme was first studied (14). To ensure that our recombinant protein included the native N terminus, we identified the N-terminal start sequence of endogenous HOAS.…”

Section: Cloning Expression and Purificationmentioning

confidence: 99%

Influence of Allosteric Regulators on Individual Steps in the Reaction Catalyzed by Mycobacterium tuberculosis 2-Hydroxy-3-oxoadipate Synthase

Balakrishnan

Jordan

Nathan

2013

Journal of Biological Chemistry

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Background: 2-Hydroxy-3-oxoadipate synthase is predicted to be essential for growth of Mycobacterium tuberculosis and is subject to allosteric regulation. Results: The role of regulators was characterized by kinetics and detection of thiamin diphosphate-bound covalent intermediate distribution. Conclusion:AcCoA activates steps leading to a predecarboxylation intermediate; GarA chiefly inhibits postdecarboxylation steps. Significance: This novel regulatory regime in thiamin diphosphate enzymes provides new leads to inhibition.

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Section: Cloning Expression and Purificationmentioning

confidence: 99%

Influence of Allosteric Regulators on Individual Steps in the Reaction Catalyzed by Mycobacterium tuberculosis 2-Hydroxy-3-oxoadipate Synthase

Balakrishnan

Jordan

Nathan

2013

Journal of Biological Chemistry

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“…However, there are discrepancies in the annotations for the same genome sequences by different institutions or by using diverse prediction methodologies, which hinders further studies [8]. Recently, mass spectrometry-based approaches have been employed to support the annotations of prokaryotic and eukaryotic genomes, and to more accurately determine the existence and boundaries of genes [15][16][17].…”

Section: Introductionmentioning

confidence: 99%

High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans

Cao

Dai

et al. 2009

Cell Res

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“…MS/MS peak lists from individual RAW files were generated using the DTA SuperCharger package, version 1.29, available in the MSQuant validation tool. We used Mascot Daemon for multiple search submissions on a local Mascot server, version 2.1 (Matrix Science) (4,5). Under our criteria, Mascot indicated a minimal score of 31 for a P value of Յ 0.05.…”

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confidence: 99%

Insulin-Degrading Enzyme Binds to the Nonglycosylated Precursor of Varicella-Zoster Virus gE Protein Found in the Endoplasmic Reticulum

Carpenter

Jackson

Souza

et al. 2010

J Virol

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Insulin degradation enzyme (IDE) is a 110-kDa zinc metalloprotease found in the cytosol of all cells. IDE degrades insulin and a variety of small proteins including amyloid-␤. Recently, IDE has been proposed as the receptor for varicella-zoster virus (VZV) attachment. During our reassessment, some of the original studies were repeated and expanded in scope. We first confirmed that IDE antibody reduced VZV spread. For additional controls, we repeated the same experiments with herpes simplex virus (HSV)-infected cells as well as uninfected cells. There was a visible reduction in HSV spread but less than seen in the VZV system. Of greater importance, IDE antibody also inhibited the growth of uninfected cells. Second, we repeated the coprecipitation assays. We confirmed that antibodies to VZV gE (open reading frame 68) coprecipitated IDE and that anti-IDE antibody coprecipitated gE. However, the detected gE protein was not the mature 98-kDa form; rather, it was a precursor 73-kDa gE form found in the endoplasmic reticulum. Additional control experiments included VZV-infected cell cultures treated with tunicamycin to block gE glycosylation in the endoplasmic reticulum; again, the anti-IDE antibody coprecipitated a 73-kDa gE product. Finally, Orbitrap mass spectrometry analysis of a chromatographically purified gE sample revealed four cellular proteins associated with the unfolded protein response: BiP (HSPA5), HSPA8, HSPD1, and PPIA (peptidyl-propyl cis-trans isomerase). We conclude that IDE protease binds to the 73-kDa gE precursor and that this event occurs in the cytosol but not as a receptor/ligand interaction.Insulin degradation enzyme (IDE) has been proposed as a virus receptor. IDE is a zinc metalloprotease that is known to degrade a number of small proteins (Ͻ6 kDa) including insulin and amyloid-␤ (6, 18). Because of these observations, IDE has been intensively studied as a participant in the pathogenesis of diabetes and Alzheimer's syndrome (9, 30). In 2006, IDE was reported to be a cellular receptor of varicella-zoster virus (VZV), which mediated infection and cell-to-cell spread of the virus (19). This report was based on several experiments. Initially, a truncated VZV gE protein was immobilized onto protein A-Sepharose beads with anti-gE monoclonal antibody (MAb). When the beads were incubated with cell lysates, a protein identified as IDE was attached to the complex. The authors also performed coimmunoprecipitation assays. When gE was precipitated from VZV-infected melanoma cells, the investigators observed that IDE was also detectable in the precipitate. When a rabbit polyclonal anti-IDE antibody was added to a monolayer prior to VZV infection, VZV spread was subsequently inhibited by 30 to 45%. Knockdown of IDE by small interfering RNA (siRNA) inhibited VZV infection and cell-to-cell spread. Similarly, bacitracin, a compound that inhibits IDE, also inhibited VZV infection and cell-to-cell spread. Finally, these deficiencies were corrected by expression of exogenous IDE. In a subsequent publication, the...

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High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example

Cited by 64 publications

References 36 publications

Influence of Allosteric Regulators on Individual Steps in the Reaction Catalyzed by Mycobacterium tuberculosis 2-Hydroxy-3-oxoadipate Synthase

Influence of Allosteric Regulators on Individual Steps in the Reaction Catalyzed by Mycobacterium tuberculosis 2-Hydroxy-3-oxoadipate Synthase

High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans

Insulin-Degrading Enzyme Binds to the Nonglycosylated Precursor of Varicella-Zoster Virus gE Protein Found in the Endoplasmic Reticulum

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