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Molecular & Cellular Proteomics

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Table of Contents

February 2019; Volume 18,Issue 2

Research

  • Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes
    You have access
    Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes
    Shinya Ohta, Takako Taniguchi, Nobuko Sato, Mayako Hamada, Hisaaki Taniguchi and Juri Rappsilber
    Molecular & Cellular Proteomics February 1, 2019, First published on September 28, 2018, 18 (2) 169-181; https://doi.org/10.1074/mcp.RA118.000923

    Our quantitative proteomics study determined the protein composition of the mitotic chromosome scaffold. MS results revealed a novel component of the chromosome scaffold, BAZ1B, which was localized to the mitotic chromosome axis. Our results using BAZ1A/B double-KO cells suggest that BAZ1 proteins are essential for timely chromosome condensation at mitosis entry.

  • Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria*
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    Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria*
    Rebeca Kawahara, Livia Rosa-Fernandes, Ancély Ferreira dos Santos, Carla Letícia Bandeira, Jamille G. Dombrowski, Rodrigo M. Souza, Micaella Pereira Da Fonseca, William T. Festuccia, Leticia Labriola, Martin R. Larsen, Claudio R. F. Marinho and Giuseppe Palmisano
    Molecular & Cellular Proteomics February 1, 2019, First published on September 21, 2018, 18 (2) 182-199; https://doi.org/10.1074/mcp.RA118.000907

    This paper investigated the molecular pathways modulated in past P. falciparum-infected placentas. The proteome, phosphoproteome and glycoproteome analysis of P. falciparum-infected placentas that had developed placental malaria during pregnancy but had the parasites cleared by pharmacological treatment, revealed the activation of AKT and ERK signaling pathways and apoptosis. These molecular features open new perspectives towards novel therapeutic solutions.

  • 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.

  • Integrative Proteomic and Phosphoproteomic Profiling of Testis from Wip1 Phosphatase-Knockout Mice: Insights into Mechanisms of Reduced Fertility*
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    Integrative Proteomic and Phosphoproteomic Profiling of Testis from Wip1 Phosphatase-Knockout Mice: Insights into Mechanisms of Reduced Fertility*
    Yinghui Wei, Qian Gao, Pengxia Niu, Kui Xu, Yiqing Qiu, Yanqing Hu, Shasha Liu, Xue Zhang, Miaoying Yu, Zhiguo Liu, Bingyuan Wang, Yulian Mu and Kui Li
    Molecular & Cellular Proteomics February 1, 2019, First published on October 25, 2018, 18 (2) 216-230; https://doi.org/10.1074/mcp.RA117.000479

    Wei et al. apply multi-layer proteomic profiling and systems biology approaches to define Wip1-deficient testis proteome and phosphoproteome landscapes, and they identify cell adhesion/tight junction, sperm motility, and inflammatory response pathways. These data establish the mechanism that proinflammatory cytokines may impair the blood-testis barrier dynamics by decreasing the expression of junction-associated proteins in Wip1 null testes, leading to subfertility and spermatogenesis defects.

  • Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer
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    Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer
    Etna Abad, Yoelsis García-Mayea, Cristina Mir, David Sebastian, Antonio Zorzano, David Potesil, Zbynek Zdrahal, Alex Lyakhovich and Matilde E. Lleonart
    Molecular & Cellular Proteomics February 1, 2019, First published on October 29, 2018, 18 (2) 231-244; https://doi.org/10.1074/mcp.RA118.001102

    Quantitative MS-based proteomics enabled to distinguish metabolic differences of triple negative breast cancer cells and corresponding chemoresistant and cancer stem cells (CSC). This puts mitochondria in a spotlight for cancer therapy and places bactericidal antibiotics; – particularly linezolid- as effective agents for eliminating CSC and resistant cells.

  • Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA)
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    Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA)
    Daiki Kobayashi, Takaho Tokuda, Kyosuke Sato, Hiroki Okanishi, Megumi Nagayama, Mio Hirayama-Kurogi, Sumio Ohtsuki and Norie Araki
    Molecular & Cellular Proteomics February 1, 2019, First published on October 31, 2018, 18 (2) 245-262; https://doi.org/10.1074/mcp.RA118.001014

    Translationally controlled tumor protein (TCTP) is a novel biological target for neurofibromatosis type 1 (NF1)-associated tumors. Here, we identified specific TCTP-interacting proteins by affinity purification and data-independent mass spectrometry acquisition (AP-DIA/SWATH). TCTP mainly interacts with elongation factors in NF1-tumor cells. Interestingly, TCTP directly binds to EF1A2 and activates EF1A2-dependent translation machinery. Inhibiting the TCTP–EF1A2 interaction significantly caused dramatic suppression of growth in NF1-tumor cells. Our findings demonstrate that a translation machinery via TCTP–EF1A2 could represent a therapeutic target of NF1-tumors.

  • Characterization of Proteome Variation During Modern Maize Breeding
    Open Access
    Characterization of Proteome Variation During Modern Maize Breeding
    Lu-Guang Jiang, Bo Li, Sheng-Xue Liu, Hong-Wei Wang, Cui-Ping Li, Shu-Hui Song, Mary Beatty, Gina Zastrow-Hayes, Xiao-Hong Yang, Feng Qin and Yan He
    Molecular & Cellular Proteomics February 1, 2019, First published on November 8, 2018, 18 (2) 263-276; https://doi.org/10.1074/mcp.RA118.001021

    The integrated multi-omics analysis provides insights into variation at different gene expression levels during the adaption of modern maize from tropical to temperate regions. Population-specific proteome variation mirrors genetic variation better than mRNA levels, and a class of cis-QTLs were identified that regulate protein abundance with little or no effect on mRNA levels. Thus, the discordance between protein and mRNA levels indicates far greater evolutionary stability of proteome during modern maize breeding.

  • Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization
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    Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization
    Satu-Marja Myllymäki, Ulla-Reetta Kämäräinen, Xiaonan Liu, Sara Pereira Cruz, Sini Miettinen, Mikko Vuorela, Markku Varjosalo and Aki Manninen
    Molecular & Cellular Proteomics February 1, 2019, First published on November 7, 2018, 18 (2) 277-293; https://doi.org/10.1074/mcp.RA118.001095

    This study characterized the β4-integrin interacting proteome using BioID proximity-dependent biotinylation in epithelial MDCK cells. The analysis identified several novel type II hemidesmosome (HD)-associated proteins and revealed potential connecting protein modules that could orchestrate the observed coordinated coassembly of HDs and focal adhesions (FAs). Curiously, unlike the formation of HDs, the assembly of β4-interactome did not depend on α6β4-heterodimerization.

  • Proteomic Analysis of Baboon Cerebral Artery Reveals Potential Pathways of Damage by Prenatal Alcohol Exposure
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    Proteomic Analysis of Baboon Cerebral Artery Reveals Potential Pathways of Damage by Prenatal Alcohol Exposure
    Shivantika Bisen, David Kakhniashvili, Daniel L. Johnson and Anna N. Bukiya
    Molecular & Cellular Proteomics February 1, 2019, First published on November 9, 2018, 18 (2) 294-307; https://doi.org/10.1074/mcp.RA118.001047

    Proteome analysis was performed to determine whether fetal alcohol exposure during mid-pregnancy would evoke changes in protein profile of fetal cerebral artery in baboons. We detected that levels of 238 proteins differed significantly between control and alcohol-exposed fetuses. Proteins of metabolic pathways represented one of the major targets of alcohol. The differences were detected near term, long after alcohol exposure took place. Our findings point at novel targets of alcohol within developing brain vessels.

  • Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant <em>Arabidopsis thaliana</em>
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    Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana
    Jeremy D. Volkening, Kelly E. Stecker and Michael R. Sussman
    Molecular & Cellular Proteomics February 1, 2019, First published on November 6, 2018, 18 (2) 308-319; https://doi.org/10.1074/mcp.RA118.001124

    Thermal profiles and melting temperatures have been modeled for over 1700 proteins from the model plant Arabidopsis thaliana using six biological replicates, providing a solid groundwork for future thermal shift studies in the species. Highly significant global correlations were found between melting temperature and several protein characteristics, including molecular weight, secondary structure content, and hydrophobic and charged accessible surface areas.

  • Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding
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    Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding
    Filip Trcka, Michal Durech, Pavla Vankova, Josef Chmelik, Veronika Martinkova, Jiri Hausner, Alan Kadek, Julien Marcoux, Tomas Klumpler, Borivoj Vojtesek, Petr Muller and Petr Man
    Molecular & Cellular Proteomics February 1, 2019, First published on November 20, 2018, 18 (2) 320-337; https://doi.org/10.1074/mcp.RA118.001044

    The oligomerization (and particularly dimerization) of Hsp70 proteins plays an important role in their chaperoning activities. Here, we report that human stress-inducible Hsp70 possesses the highest propensity among analyzed Hsp70 homologs to form dimers in the presence of ATP. ATP-bound Hsp70 assembles in solution as an antiparallel dimer closely resembling the dimeric structures captured in DnaK and BiP crystals. ATP-dependent Hsp70 dimerization is necessary for efficient Hsp40 interaction and is differentially affected by TPR cochaperone binding.

  • Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974
    Open Access
    Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974
    Christina Schiza, Dimitrios Korbakis, Keith Jarvi, Eleftherios P. Diamandis and Andrei P. Drabovich
    Molecular & Cellular Proteomics February 1, 2019, First published on November 14, 2018, 18 (2) 338-351; https://doi.org/10.1074/mcp.RA118.001170

    TEX101 protein is a validated biomarker of male infertility and a potential germ cell-surface chaperone. Near-complete degradation of variant G99V TEX101 protein was discovered in men homozygous and heterozygous for the missense variant rs35033974. Differential proteomic profiling revealed TEX101-associated proteins down-regulated in rs35033974hh spermatozoa, including LY6K protein.

  • 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.

  • Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 Family
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    Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 Family
    Huadong Liu, Haiming Huang, Courtney Voss, Tomonori Kaneko, Wen Tao Qin, Sachdev Sidhu and Shawn S.-C. Li
    Molecular & Cellular Proteomics February 1, 2019, First published on November 27, 2018, 18 (2) 372-382; https://doi.org/10.1074/mcp.RA118.001123

    The role of surface loops in encoding SH2 domain specificity has been systematically investigated by characterizing a group of loop variants obtained from screening phage-displayed SH2 domain libraries. The reported results support a general role for the EF loop (which connects the β-strands E and F) and the BG loop (which connects the α-helix B and β-strand G) in encoding SH2 specificity, add to our understanding of the mechanism of target sequence recognition by an SH2 domain in cells, and have general implications for the evolution of binding specificity of protein interaction modules.

Technological Innovation and Resources

  • FlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS*
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    FlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS*
    Sergey I. Kovalchuk, Ole N. Jensen and Adelina Rogowska-Wrzesinska
    Molecular & Cellular Proteomics February 1, 2019, First published on October 29, 2018, 18 (2) 383-390; https://doi.org/10.1074/mcp.TIR118.000953

    FlashPack is a fast and simple protocol for capillary column packing. It is developed for the classical 100 bars pressure bomb setup and ultrahigh sorbent concentrations. It provides a 100-fold increase in packing rate and reduces packing time with sub-2 μm sorbents to a few minutes for HPLC columns and to less than an hour for 50 cm UHPLC columns. Custom-produced columns offer performance on par with commercially available capillary columns.

  • PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome
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    PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome
    Zhiwu An, Linhui Zhai, Wantao Ying, Xiaohong Qian, Fuzhou Gong, Minjia Tan and Yan Fu
    Molecular & Cellular Proteomics February 1, 2019, First published on November 12, 2018, 18 (2) 391-405; https://doi.org/10.1074/mcp.RA118.000812

    PTMiner post-processes the coarse and error-prone results of an open search of MS/MS spectra. It confidently filters and localizes the modifications (mass shifts) using the transfer FDR and an empirical Bayesian method. Evaluated on simulated and synthetic peptide data, PTMiner showed much higher accuracy than two open search engines and the Ascore algorithm. PTMiner was used to comprehensively characterize the PTMs in a draft map of human proteome, resulting in over 1.7 million modifications confidently identified and localized.

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In this issue

Molecular & Cellular Proteomics: 18 (2)
Molecular & Cellular Proteomics
Vol. 18, Issue 2
1 Feb 2019
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Issue highlights

  • Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila
  • Integrative Proteomic and Phosphoproteomic Profiling of Testis from Wip1 Phosphatase-Knockout Mice: Insights into Mechanisms of Reduced Fertility*
  • Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization
  • Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana
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