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O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM. A proteomic survey of widespread protein aggregation in yeast. Mol Biosyst 2014; 10:851-861. [PMID: 24488121 DOI: 10.1039/c3mb70508k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many normally cytosolic yeast proteins form insoluble intracellular bodies in response to nutrient depletion, suggesting the potential for widespread protein aggregation in stressed cells. Nearly 200 such bodies have been found in yeast by screening libraries of fluorescently tagged proteins. In order to more broadly characterize the formation of these bodies in response to stress, we employed a proteome-wide shotgun mass spectrometry assay in order to measure shifts in the intracellular solubilities of endogenous proteins following heat stress. As quantified by mass spectrometry, heat stress tended to shift the same proteins into insoluble form as did nutrient depletion; many of these proteins were also known to form foci in response to arsenic stress. Affinity purification of several foci-forming proteins showed enrichment for co-purifying chaperones, including Hsp90 chaperones. Tests of induction conditions and co-localization of metabolic enzymes participating in the same metabolic pathways suggested those foci did not correspond to multi-enzyme organizing centers. Thus, in yeast, the formation of stress bodies appears common across diverse, normally diffuse cytoplasmic proteins and is induced by multiple types of cell stress, including thermal, chemical, and nutrient stress.
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Affiliation(s)
- Jeremy D O'Connell
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Mark Tsechansky
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge, UK
| | - Ariel Royal
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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Abstract
Some metabolic pathway enzymes are known to organize into multi-enzyme complexes for reasons of catalytic efficiency, metabolite channeling, and other advantages of compartmentalization. It has long been an appealing prospect that de novo purine biosynthesis enzymes form such a complex, termed the "purinosome." Early work characterizing these enzymes garnered scarce but encouraging evidence for its existence. Recent investigations led to the discovery in human cell lines of purinosome bodies-cytoplasmic puncta containing transfected purine biosynthesis enzymes, which were argued to correspond to purinosomes. New discoveries challenge both the functional and physiological relevance of these bodies in favor of protein aggregation.
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Affiliation(s)
- Alice Zhao
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM. Transiently transfected purine biosynthetic enzymes form stress bodies. PLoS One 2013; 8:e56203. [PMID: 23405267 PMCID: PMC3566086 DOI: 10.1371/journal.pone.0056203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/10/2013] [Indexed: 01/02/2023] Open
Abstract
It has been hypothesized that components of enzymatic pathways might organize into intracellular assemblies to improve their catalytic efficiency or lead to coordinate regulation. Accordingly, de novo purine biosynthesis enzymes may form a purinosome in the absence of purines, and a punctate intracellular body has been identified as the purinosome. We investigated the mechanism by which human de novo purine biosynthetic enzymes might be organized into purinosomes, especially under differing cellular conditions. Irregardless of the activity of bodies formed by endogenous enzymes, we demonstrate that intracellular bodies formed by transiently transfected, fluorescently tagged human purine biosynthesis proteins are best explained as protein aggregation.
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Affiliation(s)
- Alice Zhao
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Mark Tsechansky
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Jagannath Swaminathan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Lindsey Cook
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Abstract
Many genes are toxic when overexpressed, but general mechanisms for this toxicity have proven elusive. Vavouri et al. (2009) find that intrinsic protein disorder and promiscuous molecular interactions are strong determinants of dosage sensitivity, explaining in part the toxicity of dosage-sensitive oncogenes in mice and humans.
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Affiliation(s)
- Edward M Marcotte
- Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1064, USA.
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Saar-Tsechansky M, Pliskin N, Rabinowitz G, Tsechansky M, Porath A. Monitoring quality of health care with relational patterns. Top Health Inf Manage 2001; 22:24-35. [PMID: 11680275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
This paper describes the extraction of relational patterns from hospital discharge data for the purpose of monitoring the quality of health care. We discuss what relational patterns are and how they support the extraction of meaningful patterns from data that are expressive, comprehensive, and easy to interpret. We demonstrate how relational patterns can be applied to identify poor practices embedded in hospitalization processes, for instance, help trigger subsequent inquiries and support decision-making processes.
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Affiliation(s)
- M Saar-Tsechansky
- Department of Information Systems, Leonard N. Stern School of Business, New York University, New York City, New York, USA
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