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Molecular & Cellular Proteomics

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Ribosomes*

  • PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms
    Open Access
    PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms
    Steven Verbruggen, Elvis Ndah, Wim Van Criekinge, Siegfried Gessulat, Bernhard Kuster, Mathias Wilhelm, Petra Van Damme and Gerben Menschaert
    Molecular & Cellular Proteomics August 9, 2019, First published on April 30, 2019, 18 (8 suppl 1) S126-S140; https://doi.org/10.1074/mcp.RA118.001218

    The PROTEOFORMER pipeline feeds ribosome profiling-driven information into an MS/MS search space. The pipeline has been greatly expanded and updated since its first publication. These novelties are presented and validated with matching MS/MS data, leading to the endorsement of a set of new proteoforms on MS/MS level and to a collection of general considerations for the ribosome profiling-based proteogenomics community.

  • Complexome Profiling Reveals Association of PPR Proteins with Ribosomes in the Mitochondria of Plants
    You have access
    Complexome Profiling Reveals Association of PPR Proteins with Ribosomes in the Mitochondria of Plants
    Nils Rugen, Henryk Straube, Linda E. Franken, Hans-Peter Braun and Holger Eubel
    Molecular & Cellular Proteomics July 1, 2019, First published on April 25, 2019, 18 (7) 1345-1362; https://doi.org/10.1074/mcp.RA119.001396

    Plant mitochondrial protein expression is complex and routinely involves pentatricopeptide repeat proteins for processing of transcripts. Although the composition and structure of the mitoribosomes in other eukaryotic kingdoms of life is well established, plant mitochondria have so far eluded a detailed analysis. Using a complexome profiling approach, this study provides an early glimpse on the composition of plant mitochondrial ribosomes and sheds new light on the process of mitochondrial gene expression in plants. Mitochondrial subunits were found to possess several additional proteins carrying pentatricopeptide repeats potentially involved in RNA editing. Other proteins are potentially involved in the processing of nascent proteins.

  • In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly
    Open Access
    In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly
    Han Hu, Gebreamlak Bezabih, Mao Feng, Qiaohong Wei, Xufeng Zhang, Fan Wu, Lifeng Meng, Yu Fang, Bin Han, Chuan Ma and Jianke Li
    Molecular & Cellular Proteomics April 1, 2019, First published on January 7, 2019, 18 (4) 606-621; https://doi.org/10.1074/mcp.RA118.001257

    The hitherto depth proteomes of the hypopharyngeal glands (HGs) across the adult life of two stocks of honeybees with low (ITBs) and high royal jelly production (RJBs) uncover the molecular landscapes of the gland ontogeny and activity to match with gland age-specific tasks. Pathways involved in protein and energy metabolism are induced in HGs of RJB nurse bees to enhance royal jelly (RJ) secretion relative to ITBs. Our finding gains a novel mechanistic insight of the augment RJ-output in RJBs.

  • Open Access
    Doxorubicin-induced DNA Damage Causes Extensive Ubiquitination of Ribosomal Proteins Associated with a Decrease in Protein Translation*
    Vincentius A. Halim, Iraia García-Santisteban, Daniel O. Warmerdam, Bram van den Broek, Albert J. R. Heck, Shabaz Mohammed and René H. Medema
    Molecular & Cellular Proteomics December 1, 2018, First published on February 8, 2018, 17 (12) 2297-2308; https://doi.org/10.1074/mcp.RA118.000652

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