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Molecular & Cellular Proteomics

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Microbiology

  • Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System
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    Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System
    Jason Ziveri, Cerina Chhuon, Anne Jamet, Héloïse Rytter, Guénolé Prigent, Fabiola Tros, Monique Barel, Mathieu Coureuil, Claire Lays, Thomas Henry, Nicholas H. Keep, Ida Chiara Guerrera and Alain Charbit
    Molecular & Cellular Proteomics December 1, 2019, First published on October 2, 2019, 18 (12) 2418-2432; https://doi.org/10.1074/mcp.RA119.001532

    KCl stimulation triggers assembly of the Francisella T6SS in culture. Differential whole cell proteomics reveals that the amounts of the T6SS proteins remain unchanged upon KCl stimulation. A phosphoproteomic analysis identifies a phosphorylation on the T6SS sheath, at site Y139 of IglB. Our data demonstrate that site Y139 of IglB plays a critical role in T6SS biogenesis, providing novel mechanistic insight into the role of sheath phosphorylation in T6SS biogenesis.

  • Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning
    Open Access
    Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning
    Florence Roux-Dalvai, Clarisse Gotti, Mickaël Leclercq, Marie-Claude Hélie, Maurice Boissinot, Tabiwang N. Arrey, Claire Dauly, Frédéric Fournier, Isabelle Kelly, Judith Marcoux, Julie Bestman-Smith, Michel G. Bergeron and Arnaud Droit
    Molecular & Cellular Proteomics December 1, 2019, First published on October 4, 2019, 18 (12) 2492-2505; https://doi.org/10.1074/mcp.TIR119.001559

    We have developed a new method for the identification of bacterial species causing Urinary Tract Infections. The first training step used DIA analysis on multiple replicates of bacterial inoculates to define a peptide signature by machine learning classifiers. In a second identification step, the signature is monitored by targeted proteomics on unknown samples. This fast, culture-free and accurate method paves the way of the development of new diagnostic approaches limiting the emergence of antimicrobial resistances.

  • <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
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    ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
    Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
    Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

    Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

  • metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes
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    metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes
    Caleb W. Easterly, Ray Sajulga, Subina Mehta, James Johnson, Praveen Kumar, Shane Hubler, Bart Mesuere, Joel Rudney, Timothy J. Griffin and Pratik D. Jagtap
    Molecular & Cellular Proteomics August 9, 2019, First published on June 24, 2019, 18 (8 suppl 1) S82-S91; https://doi.org/10.1074/mcp.RA118.001240

    metaQuantome enables quantitative analysis of the taxonomic and functional state of a microbiome. Leveraging quantitative mass spectrometry data generated from metaproteomic samples along with taxonomic and functional annotations, metaQuantome unravels the complex and hierarchical data structure of taxonomic and functional ontologies. As a result, metaQuantome enables data exploration, tests hypotheses, and generates high-quality visualizations. metaQuantome deciphers the contribution of taxa to a functional process and vice versa. Its accessibility will pave the way for advanced multi-omic analysis of diverse microbiomes.

  • Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon <em>Sulfolobus islandicus</em>
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    Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus
    Jingjing Cao, Tongkun Wang, Qian Wang, Xiaowei Zheng and Li Huang
    Molecular & Cellular Proteomics August 1, 2019, First published on June 9, 2019, 18 (8) 1572-1587; https://doi.org/10.1074/mcp.RA119.001312

    About 26% of the total proteins and 44% of the identified proteins were acetylated at lysine residues and the N terminus, respectively, in the hyperthermophilic archaeon Sulfolobus islandicus. A Pat homolog preferentially acetylated a group of acyl-CoA synthetases among the acetylated proteins, whereas an Ard1 homolog exhibited broad substrate specificity. A S. islandicus mutant strain lacking the Pat homolog showed no significant growth defects and that lacking the Ard1 homolog grew more slowly than the parent strain.

  • The mRNA-bound Proteome of <em>Leishmania mexicana</em>: Novel Genetic Insight into an Ancient Parasite
    Open Access
    The mRNA-bound Proteome of Leishmania mexicana: Novel Genetic Insight into an Ancient Parasite
    Luis M. de Pablos, Tiago R. Ferreira, Adam A. Dowle, Sarah Forrester, Ewan Parry, Katherine Newling and Pegine B. Walrad
    Molecular & Cellular Proteomics July 1, 2019, First published on April 4, 2019, 18 (7) 1271-1284; https://doi.org/10.1074/mcp.RA118.001307

    A comprehensive, quantified identification of the mRNA-binding and whole cell proteomes in the three main Leishmania lifecycle stages, the first such comparison in kinetoplastid parasites, demonstrates trans-regulator RBPs select distinct, specific mRNA target pools in a stage-regulated manner despite equivalent, constitutive transcript levels available. Results further indicate that in L. mexicana parasites, mRNA levels are not a strong predictor of whole cell expression or RNA binding potential of encoded proteins. Included are the first proteomes from the human-infective metacyclic promastigote stage.

  • Proteomics Reveals Multiple Phenotypes Associated with <em>N</em>-linked Glycosylation in <em>Campylobacter jejuni</em>
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    Proteomics Reveals Multiple Phenotypes Associated with N-linked Glycosylation in Campylobacter jejuni
    Joel A. Cain, Ashleigh L. Dale, Paula Niewold, William P. Klare, Lok Man, Melanie Y. White, Nichollas E. Scott and Stuart J. Cordwell
    Molecular & Cellular Proteomics April 1, 2019, First published on January 7, 2019, 18 (4) 715-734; https://doi.org/10.1074/mcp.RA118.001199

    N-linked protein glycosylation (Pgl) in Campylobacter jejuni is required for chicken colonization and human virulence, yet its biological role remains unknown. pgl gene deletion resulted in a significant rearrangement of the C. jejuni proteome that leads to alterations in crucial phenotypes including stress response, nutrient uptake, electron transport and chemotaxis, and is essential for full activity of the Nap nitrate reductase. N-glycosylation therefore contributes to multiple “virulence” phenotypes in C. jejuni.

  • You have access
    The Unique Features of Proteins Depicting the Chicken Amniotic Fluid
    Mylène Da Silva, Clara Dombre, Aurélien Brionne, Philippe Monget, Magali Chessé, Marion De Pauw, Maryse Mills, Lucie Combes-Soia, Valérie Labas, Nicolas Guyot, Yves Nys and Sophie Réhault-Godbert
    Molecular & Cellular Proteomics March 15, 2019, First published on February 14, 2018, 18 (Supplement 1) S174-S190; https://doi.org/10.1074/mcp.RA117.000459
  • Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of <em>Aeromonas hydrophila</em>
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    Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila
    Zujie Yao, Zhuang Guo, Yuqian Wang, Wanxin Li, Yuying Fu, Yuexu Lin, Wenxiong Lin and Xiangmin Lin
    Molecular & Cellular Proteomics February 1, 2019, First published on October 23, 2018, 18 (2) 200-215; https://doi.org/10.1074/mcp.RA118.001035

    The affinity antibody purification combined with LC MS/MS was used to investigate the lysine succinylome profile of A. hydrophila ATCC7966. A total of 666 lysine succinylation proteins were identified and analyzed in depth to better understand its regulatory roles. Lysine succinylation modifications on S-ribosylhomocysteine lyase were further studied and shown to regulate its cellular physiology and affect bacterial quorum sensing behavior of A. hydrophila.

  • Carcinogenic <em>Helicobacter pylori</em> Strains Selectively Dysregulate the <em>In Vivo</em> Gastric Proteome, Which May Be Associated with Stomach Cancer Progression
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    Carcinogenic Helicobacter pylori Strains Selectively Dysregulate the In Vivo Gastric Proteome, Which May Be Associated with Stomach Cancer Progression
    Jennifer M. Noto, Kristie L. Rose, Amanda J. Hachey, Alberto G. Delgado, Judith Romero-Gallo, Lydia E. Wroblewski, Barbara G. Schneider, Shailja C. Shah, Timothy L. Cover, Keith T. Wilson, Dawn A. Israel, Juan Carlos Roa, Kevin L. Schey, Yana Zavros, M. Blanca Piazuelo and Richard M. Peek
    Molecular & Cellular Proteomics February 1, 2019, First published on November 19, 2018, 18 (2) 352-371; https://doi.org/10.1074/mcp.RA118.001181

    Helicobacter pylori is the strongest risk factor for gastric cancer. Initial interactions between H. pylori and its host occur at the epithelial cell surface, and this activates signaling pathways that drive oncogenesis. This manuscript defines strain-specific gastric epithelial proteomic changes induced by H. pylori in vivo that are critical for initiation of the gastric carcinogenesis. Protein targets were validated in human gastric epithelial cells in vitro, primary human gastric epithelial monolayers, and H. pylori-infected gerbil and human tissue in vivo.

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