1
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Rizzotto A, Tollis S, Pham NT, Zheng Y, Abad MA, Wildenhain J, Jeyaprakash AA, Auer M, Tyers M, Schirmer EC. Reduction in Nuclear Size by DHRS7 in Prostate Cancer Cells and by Estradiol Propionate in DHRS7-Depleted Cells. Cells 2023; 13:57. [PMID: 38201261 PMCID: PMC10778050 DOI: 10.3390/cells13010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Increased nuclear size correlates with lower survival rates and higher grades for prostate cancer. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a biomarker for use in prostate cancer grading because it is largely lost in higher-grade tumors. Here, we found that reduction in DHRS7 from the LNCaP prostate cancer cell line with normally high levels of DHRS7 increases nuclear size, potentially explaining the nuclear size increase observed in higher-grade prostate tumors where it is lost. An exogenous expression of DHRS7 in the PC3 prostate cancer cell line with normally low DHRS7 levels correspondingly decreases nuclear size. We separately tested 80 compounds from the Microsource Spectrum library for their ability to restore normal smaller nuclear size to PC3 cells, finding that estradiol propionate had the same effect as the re-expression of DHRS7 in PC3 cells. However, the drug had no effect on LNCaP cells or PC3 cells re-expressing DHRS7. We speculate that separately reported beneficial effects of estrogens in androgen-independent prostate cancer may only occur with the loss of DHRS7/ increased nuclear size, and thus propose DHRS7 levels and nuclear size as potential biomarkers for the likely effectiveness of estrogen-based treatments.
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Affiliation(s)
- Andrea Rizzotto
- The Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.R.); (A.A.J.)
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland;
| | - Nhan T. Pham
- The Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, UK; (N.T.P.); (Y.Z.); (J.W.); (M.A.)
| | - Yijing Zheng
- The Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, UK; (N.T.P.); (Y.Z.); (J.W.); (M.A.)
| | - Maria Alba Abad
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Jan Wildenhain
- The Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, UK; (N.T.P.); (Y.Z.); (J.W.); (M.A.)
| | - A. Arockia Jeyaprakash
- The Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.R.); (A.A.J.)
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK;
- Gene Center and Department of Biochemistry, LMU-München, 81377 Munich, Germany
| | - Manfred Auer
- The Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, UK; (N.T.P.); (Y.Z.); (J.W.); (M.A.)
- Xenobe Research Institute, P.O. Box 3052, San Diego, CA 92163-1052, USA
| | - Mike Tyers
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric C. Schirmer
- The Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.R.); (A.A.J.)
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2
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Pham NT, Alves J, Sargison FA, Cullum R, Wildenhain J, Fenical W, Butler MS, Mead DA, Duggan BM, Fitzgerald JR, La Clair JJ, Auer M. Nanoscaled Discovery of a Shunt Rifamycin from Salinispora arenicola Using a Three-Color GFP-Tagged Staphylococcus aureus Macrophage Infection Assay. ACS Infect Dis 2023; 9:1499-1507. [PMID: 37433130 PMCID: PMC10425972 DOI: 10.1021/acsinfecdis.3c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 07/13/2023]
Abstract
Antimicrobial resistance has emerged as a global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent. Staphylococcus aureus is a major human and animal pathogen, responsible for high levels of morbidity and mortality worldwide. The intracellular survival of S. aureus in macrophages contributes to immune evasion, dissemination, and resilience to antibiotic treatment. Here, we present a confocal fluorescence imaging assay for monitoring macrophage infection by green fluorescent protein (GFP)-tagged S. aureus as a front-line tool to identify antibiotic leads. The assay was employed in combination with nanoscaled chemical analyses to facilitate the discovery of a new, active rifamycin analogue. Our findings indicate a promising new approach for the identification of antimicrobial compounds with macrophage intracellular activity. The antibiotic identified here may represent a useful addition to our armory in tackling the silent pandemic of antimicrobial resistance.
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Affiliation(s)
- Nhan T. Pham
- School
of Biological Sciences, The University of
Edinburgh, The King’s Buildings, Edinburgh EH9 3BF, U.K.
| | - Joana Alves
- The
Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, U.K.
| | - Fiona A. Sargison
- The
Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, U.K.
| | - Reiko Cullum
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, United
States
| | - Jan Wildenhain
- Exscientia
Oxford Science Park, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
| | - William Fenical
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, United
States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Mark S. Butler
- Xenobe Research Institute, P. O. Box 3052, San Diego, California 92163, United States
| | - David A. Mead
- Terra
Bioforge
Inc., 3220 Deming Way
Suite 100, Middleton, Wisconsin 53562, United States
| | - Brendan M. Duggan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - J. Ross Fitzgerald
- The
Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, U.K.
| | - James J. La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, California 92163, United States
- Department
of Chemistry and Biochemistry, University
of California at San Diego, La
Jolla, California 92093-0358, United States
| | - Manfred Auer
- School
of Biological Sciences, The University of
Edinburgh, The King’s Buildings, Edinburgh EH9 3BF, U.K.
- Xenobe Research Institute, P. O. Box 3052, San Diego, California 92163, United States
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3
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Shave S, Pham NT, Auer M. CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens. J Chem Inf Model 2022; 62:2264-2268. [PMID: 35442032 PMCID: PMC9131445 DOI: 10.1021/acs.jcim.2c00285] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Indexed: 12/02/2022]
Abstract
A simplistic assumption in setting up a competition assay is that a low affinity labeled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a more sensitive assay. An often-cited paper correctly rallies against this assumption and recommends the use of the highest affinity ligand available for experiments aiming to determine competitive inhibitor affinities. However, we have noted this advice being applied incorrectly to competition-based primary screens where the goal is optimum assay sensitivity, enabling a clear yes/no binding determination for even low affinity interactions. The published advice only applies to secondary, confirmatory assays intended for accurate affinity determination of primary screening hits. We demonstrate that using very high affinity ligands in competition-based primary screening can lead to reduced assay sensitivity and, ultimately, the discarding of potentially valuable active compounds. We build on techniques developed in our PyBindingCurve software for a mechanistic understanding of complex biological interaction systems, developing the "CLAffinity tool" for simulating competition experiments using protein, ligand, and inhibitor concentrations common to drug screening campaigns. CLAffinity reveals optimum labeled ligand affinity ranges based on assay parameters, rather than general rules to optimize assay sensitivity. We provide the open source CLAffinity software toolset to carry out assay simulations and a video summarizing key findings to aid in understanding, along with a simple lookup table allowing identification of optimal dynamic ranges for competition-based primary screens. The application of our freely available software and lookup tables will lead to the consistent creation of more performant competition-based primary screens identifying valuable hit compounds, particularly for difficult targets.
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Affiliation(s)
- Steven Shave
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
| | - Nhan T. Pham
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
| | - Manfred Auer
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
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4
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Tollis S, Rizzotto A, Pham NT, Koivukoski S, Sivakumar A, Shave S, Wildenhain J, Zuleger N, Keys JT, Culley J, Zheng Y, Lammerding J, Carragher NO, Brunton VG, Latonen L, Auer M, Tyers M, Schirmer EC. Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion. ACS Chem Biol 2022; 17:680-700. [PMID: 35199530 PMCID: PMC8938924 DOI: 10.1021/acschembio.2c00004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Background: Lower survival rates for many cancer
types correlate with changes in nuclear size/scaling in a tumor-type/tissue-specific
manner. Hypothesizing that such changes might confer an advantage
to tumor cells, we aimed at the identification of commercially available
compounds to guide further mechanistic studies. We therefore screened
for Food and Drug Administration (FDA)/European Medicines Agency (EMA)-approved
compounds that reverse the direction of characteristic tumor nuclear
size changes in PC3, HCT116, and H1299 cell lines reflecting, respectively,
prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous
lung cancer. Results: We found distinct, largely
nonoverlapping sets of compounds that rectify nuclear size changes
for each tumor cell line. Several classes of compounds including,
e.g., serotonin uptake inhibitors, cyclo-oxygenase inhibitors, β-adrenergic
receptor agonists, and Na+/K+ ATPase inhibitors,
displayed coherent nuclear size phenotypes focused on a particular
cell line or across cell lines and treatment conditions. Several compounds
from classes far afield from current chemotherapy regimens were also
identified. Seven nuclear size-rectifying compounds selected for further
investigation all inhibited cell migration and/or invasion. Conclusions: Our study provides (a) proof of concept that
nuclear size might be a valuable target to reduce cell migration/invasion
in cancer treatment and (b) the most thorough collection of tool compounds
to date reversing nuclear size changes specific to individual cancer-type
cell lines. Although these compounds still need to be tested in primary
cancer cells, the cell line-specific nuclear size and migration/invasion
responses to particular drug classes suggest that cancer type-specific
nuclear size rectifiers may help reduce metastatic spread.
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Affiliation(s)
- Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Andrea Rizzotto
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Nhan T. Pham
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Aishwarya Sivakumar
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Jan Wildenhain
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Nikolaj Zuleger
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Jeremy T. Keys
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jayne Culley
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Yijing Zheng
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Jan Lammerding
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Neil O. Carragher
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Valerie G. Brunton
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Eric C. Schirmer
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
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5
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Heckmann M, Klanert G, Sandner G, Lanzerstorfer P, Auer M, Weghuber J. Fluorescence Microscopy-Based Quantitation of GLUT4 Translocation. Methods Appl Fluoresc 2022; 10. [PMID: 35008072 DOI: 10.1088/2050-6120/ac4998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/10/2022] [Indexed: 11/11/2022]
Abstract
Postprandial insulin-stimulated glucose uptake into target tissue is crucial for the maintenance of normal blood glucose homeostasis. This step is rate-limited by the number of facilitative glucose transporters type 4 (GLUT4) present in the plasma membrane. Since insulin resistance and impaired GLUT4 translocation are associated with the development of metabolic disorders such as type 2 diabetes, this transporter has become an important target of antidiabetic drug research. The application of screening approaches that are based on the analysis of GLUT4 translocation to the plasma membrane to identify substances with insulinomimetic properties has gained global research interest in recent years. Here, we review methods that have been implemented to quantitate the translocation of GLUT4 to the plasma membrane. These methods can be broadly divided into two sections: microscopy-based technologies (e.g., immunoelectron, confocal or total internal reflection fluorescence microscopy) and biochemical and spectrometric approaches (e.g., membrane fractionation, photoaffinity labeling or flow cytometry). In this review, we discuss the most relevant approaches applied to GLUT4 thus far, highlighting the advantages and disadvantages of these approaches, and we provide a critical discussion and outlook into new methodological opportunities.
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Affiliation(s)
- Mara Heckmann
- University of Applied Sciences Upper Austria, Stelzhamerstrasse 23, Wels, Oberösterreich, 4600, AUSTRIA
| | - Gerald Klanert
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1C, Tulln, 3430, AUSTRIA
| | - Georg Sandner
- University of Applied Sciences Upper Austria, Stelzhamerstrasse 23, Wels, Oberösterreich, 4600, AUSTRIA
| | - Peter Lanzerstorfer
- University of Applied Sciences Upper Austria, Stelzhamerstrasse 23, Wels, Oberösterreich, 4600, AUSTRIA
| | - Manfred Auer
- Division of Pathway Medicine, University of Edinburgh, University of Edinburgh Medical School, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, Edinburgh, EH8 9AB, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, Stelzhamerstrasse 23, Wels, Oberösterreich, 4600, AUSTRIA
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6
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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7
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Zhu S, Choudhury NR, Rooney S, Pham NT, Koszela J, Kelly D, Spanos C, Rappsilber J, Auer M, Michlewski G. RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels. Nucleic Acids Res 2021; 49:6456-6473. [PMID: 34107032 PMCID: PMC8216281 DOI: 10.1093/nar/gkab484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/01/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
RNA-protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as 'incurable'. Here, we developed a fluorescent on-bead screening platform, RNA Pull-Down COnfocal NAnoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7's primary target is an mRNA of α-synuclein, which contributes to the aetiology of Parkinson's disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-synuclein. This opens up new therapeutic avenues towards treatment of Parkinson's disease as well as provides a novel methodology to search for modulators of RNA-protein interaction.
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Affiliation(s)
- Siran Zhu
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Nila Roy Choudhury
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Saul Rooney
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Nhan T Pham
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Joanna Koszela
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - David Kelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Manfred Auer
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Gracjan Michlewski
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, P.R. China
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8
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Abstract
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Understanding multicomponent
binding interactions in protein–ligand,
protein–protein, and competition systems is essential for fundamental
biology and drug discovery. Hand-deriving equations quickly become
unfeasible when the number of components is increased, and direct
analytical solutions only exist to a certain complexity. To address
this problem and allow easy access to simulation, plotting, and parameter
fitting to complex systems at equilibrium, we present the Python package
PyBindingCurve. We apply this software to explore homodimer and heterodimer
formations culminating in the discovery that under certain conditions,
homodimers are easier to break with an inhibitor than heterodimers
and may also be more readily depleted. This is a potentially valuable
and overlooked phenomenon of great importance to drug discovery. PyBindingCurve
may be expanded to operate on any equilibrium binding system and allows
definition of custom systems using a simple syntax. PyBindingCurve
is available under the MIT license at https://github.com/stevenshave/pybindingcurve as the Python source code accompanied by examples and as an easily
installable package within the Python Package Index.
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Affiliation(s)
- Steven Shave
- University of Edinburgh, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Yan-Kai Chen
- University of Edinburgh, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Nhan T Pham
- University of Edinburgh, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Manfred Auer
- University of Edinburgh, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, United Kingdom
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9
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Zhang J, Hou Z, Wang X, Jiang H, Neng L, Zhang Y, Yu Q, Burwood G, Song J, Auer M, Fridberger A, Hoa M, Shi X. VEGFA165 gene therapy ameliorates blood-labyrinth barrier breakdown and hearing loss. JCI Insight 2021; 6:143285. [PMID: 33690221 PMCID: PMC8119217 DOI: 10.1172/jci.insight.143285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/05/2021] [Indexed: 12/20/2022] Open
Abstract
Millions of people are affected by hearing loss. Hearing loss is frequently caused by noise or aging and often associated with loss of pericytes. Pericytes populate the small vessels in the adult cochlea. However, their role in different types of hearing loss is largely unknown. Using an inducible and conditional pericyte depletion mouse model and noise-exposed mouse model, we show that loss of pericytes leads to marked changes in vascular structure, in turn leading to vascular degeneration and hearing loss. In vitro, using advanced tissue explants from pericyte fluorescence reporter models combined with exogenous donor pericytes, we show that pericytes, signaled by VEGF isoform A165 (VEGFA165), vigorously drive new vessel growth in both adult and neonatal mouse inner ear tissue. In vivo, the delivery of an adeno-associated virus serotype 1-mediated (AAV1-mediated) VEGFA165 viral vector to pericyte-depleted or noise-exposed animals prevented and regenerated lost pericytes, improved blood supply, and attenuated hearing loss. These studies provide the first clear-cut evidence that pericytes are critical for vascular regeneration, vascular stability, and hearing in adults. The restoration of vascular function in the damaged cochlea, including in noise-exposed animals, suggests that VEGFA165 gene therapy could be a new strategy for ameliorating vascular associated hearing disorders.
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Affiliation(s)
- Jinhui Zhang
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Zhiqiang Hou
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Xiaohan Wang
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA.,Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Han Jiang
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Lingling Neng
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Yunpei Zhang
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Qing Yu
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - George Burwood
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Junha Song
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anders Fridberger
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Xiaorui Shi
- Oregon Hearing Research Center, Department of Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, Oregon, USA
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10
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Ambrose AJ, Pham NT, Sivinski J, Guimarães L, Mollasalehi N, Jimenez P, Abad MA, Jeyaprakash AA, Shave S, Costa-Lotufo LV, La Clair JJ, Auer M, Chapman E. A two-step resin based approach to reveal survivin-selective fluorescent probes. RSC Chem Biol 2021; 2:181-186. [PMID: 34458780 PMCID: PMC8342005 DOI: 10.1039/d0cb00122h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
The identification of modulators for proteins without assayable biochemical activity remains a challenge in chemical biology. The presented approach adapts a high-throughput fluorescence binding assay and functional chromatography, two protein-resin technologies, enabling the discovery and isolation of fluorescent natural product probes that target proteins independently of biochemical function. The resulting probes also suggest targetable pockets for lead discovery. Using human survivin as a model, we demonstrate this method with the discovery of members of the prodiginine family as fluorescent probes to the cancer target survivin.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Larissa Guimarães
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
- Departamento de Farmacologia, Universidade de São Paulo São Paulo SP 05508-900 Brazil
| | - Niloufar Mollasalehi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Paula Jimenez
- Instituto do Mar, Universidade Federal de São Paulo Santos SP 11.070-100 Brazil
| | - Maria A Abad
- Wellcome Centre for Cell Biology, University of Edinburgh Edinburgh EH9 3BF UK
| | | | - Steven Shave
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | | | - James J La Clair
- Xenobe Research Institute P. O. Box 3052 San Diego CA 92163-1052 USA
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
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11
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Weis SN, Souza JMF, Hoppe JB, Firmino M, Auer M, Ataii NN, da Silva LA, Gaelzer MM, Klein CP, Mól AR, de Lima CMR, Souza DO, Salbego CG, Ricart CAO, Fontes W, de Sousa MV. In-depth quantitative proteomic characterization of organotypic hippocampal slice culture reveals sex-specific differences in biochemical pathways. Sci Rep 2021; 11:2560. [PMID: 33510253 PMCID: PMC7844295 DOI: 10.1038/s41598-021-82016-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Sex differences in the brain of mammals range from neuroarchitecture through cognition to cellular metabolism. The hippocampus, a structure mostly associated with learning and memory, presents high vulnerability to neurodegeneration and aging. Therefore, we explored basal sex-related differences in the proteome of organotypic hippocampal slice culture, a major in vitro model for studying the cellular and molecular mechanisms related to neurodegenerative disorders. Results suggest a greater prevalence of astrocytic metabolism in females and significant neuronal metabolism in males. The preference for glucose use in glycolysis, pentose phosphate pathway and glycogen metabolism in females and high abundance of mitochondrial respiration subunits in males support this idea. An overall upregulation of lipid metabolism was observed in females. Upregulation of proteins responsible for neuronal glutamate and GABA synthesis, along with synaptic associated proteins, were observed in males. In general, the significant spectrum of pathways known to predominate in neurons or astrocytes, together with the well-known neuronal and glial markers observed, revealed sex-specific metabolic differences in the hippocampus. TEM qualitative analysis might indicate a greater presence of mitochondria at CA1 synapses in females. These findings are crucial to a better understanding of how sex chromosomes can influence the physiology of cultured hippocampal slices and allow us to gain insights into distinct responses of males and females on neurological diseases that present a sex-biased incidence.
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Affiliation(s)
- Simone Nardin Weis
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil.
| | - Jaques Miranda F Souza
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Juliana Bender Hoppe
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, Brazil
| | - Marina Firmino
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA, 94720, USA
| | - Nassim N Ataii
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA, 94720, USA
| | - Leonardo Assis da Silva
- Laboratory of Electron Microscopy, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | | | - Caroline Peres Klein
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, Brazil
| | - Alan R Mól
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Consuelo M R de Lima
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Diogo Onofre Souza
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, Brazil
| | - Christianne G Salbego
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, Brazil
| | - Carlos André O Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, DF, 70910-900, Brazil
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12
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Song J, Patterson R, Metlagel Z, Krey JF, Hao S, Wang L, Ng B, Sazzed S, Kovacs J, Wriggers W, He J, Barr-Gillespie PG, Auer M. A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1. J Struct Biol 2020; 210:107461. [PMID: 31962158 DOI: 10.1016/j.jsb.2020.107461] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link is expected to anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm, and the apparent filament diameter decreased from 6.4 to 4.8 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.
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Affiliation(s)
- Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roma Patterson
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Metlagel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jocelyn F Krey
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Samantha Hao
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Linshanshan Wang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Ng
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Julio Kovacs
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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13
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Kovacs J, Song J, Auer M, He J, Hunter W, Wriggers W. Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution. J Chem Inf Model 2020; 60:2626-2633. [PMID: 32045242 DOI: 10.1021/acs.jcim.9b01111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cryo-electron tomography maps often exhibit considerable noise and anisotropic resolution, due to the low-dose requirements and the missing wedge in Fourier space. These spurious features are visually unappealing and, more importantly, prevent an automated segmentation of geometric shapes, requiring a subjective and labor-intensive manual tracing. We developed a novel computational strategy for objectively denoising and correcting missing-wedge artifacts in homogeneous specimen areas of tomograms, where it is assumed that a template repeats itself across the volume under consideration, as happens in the case of filaments. In our deconvolution approach, we use a template and a map of corresponding template locations, allowing us to compensate for the information lost in the missing wedge. We applied the method to tomograms of actin-filament bundles of inner-ear stereocilia, which are critical for the senses of hearing and balance. In addition, we demonstrate that our method can be used for cell membrane detection.
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Affiliation(s)
- Julio Kovacs
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Junha Song
- Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Manfred Auer
- Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Wade Hunter
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
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14
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Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS G13D. Nat Commun 2020; 11:499. [PMID: 31980649 PMCID: PMC6981206 DOI: 10.1038/s41467-019-14224-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
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Affiliation(s)
- Susan A Kennedy
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Mohamed-Ali Jarboui
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Werner Siemens Imaging Center, University of Tübingen, Tübingen, Germany
| | - Sriganesh Srihari
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- QIMR-Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Layal Dernayka
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Theodosia Charitou
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Manuel Bernal-Llinares
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | | | | | - David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jasna Curak
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Thierry LeBihan
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Lisa Imrie
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Priyanka Pillai
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Miriam A Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Erik Fasterius
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristina Al-Khalili Szigyarto
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James Breen
- School of Biological Sciences, University of Adelaide Bioinformatics Hub, Adelaide, SA, Australia
- Computational & Systems Biology Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Christina Kiel
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Owen Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Studies, Glasgow University, Glasgow, UK
| | - Steven Shave
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | - David J Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland.
- Conway Institute, University College Dublin, Dublin, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
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15
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Triffo WJ, Palsdottir H, Song J, Morgan DG, McDonald KL, Auer M, Raphael RM. 3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography. Front Cell Neurosci 2019; 13:560. [PMID: 31920560 PMCID: PMC6933316 DOI: 10.3389/fncel.2019.00560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/04/2019] [Indexed: 11/17/2022] Open
Abstract
Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane (PM) and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features.
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Affiliation(s)
- William Jeffrey Triffo
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, George R. Brown School of Engineering, Rice University, Houston, TX, United States.,Department of Radiology, Geisinger, Danville, PA, United States
| | - Hildur Palsdottir
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David Gene Morgan
- Interdisciplinary Center for Electron Microscopy, University of California, Davis, Davis, CA, United States
| | - Kent L McDonald
- Electron Microscope Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert M Raphael
- Department of Bioengineering, George R. Brown School of Engineering, Rice University, Houston, TX, United States
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16
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Lee CH, Griffiths S, Digard P, Pham N, Auer M, Haas J, Grey F. Asparagine Deprivation Causes a Reversible Inhibition of Human Cytomegalovirus Acute Virus Replication. mBio 2019; 10:e01651-19. [PMID: 31594813 PMCID: PMC6786868 DOI: 10.1128/mbio.01651-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/12/2019] [Indexed: 01/03/2023] Open
Abstract
As obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High-throughput small interfering RNA (siRNA) screens provide a systematic approach for the identification of novel host-virus interactions. Here, we report a large-scale screen for host factors important for human cytomegalovirus (HCMV), consisting of 6,881 siRNAs. We identified 47 proviral factors and 68 antiviral factors involved in a wide range of cellular processes, including the mediator complex, proteasome function, and mRNA splicing. Focused characterization of one of the hits, asparagine synthetase (ASNS), demonstrated a strict requirement for asparagine for HCMV replication which leads to an early block in virus replication before the onset of DNA amplification. This effect is specific to HCMV, as knockdown of ASNS had little effect on herpes simplex virus 1 or influenza A virus replication, suggesting that the restriction is not simply due to a failure in protein production. Remarkably, virus replication could be completely rescued 7 days postinfection with the addition of exogenous asparagine, indicating that while virus replication is restricted at an early stage, it maintains the capacity for full replication days after initial infection. This study represents the most comprehensive siRNA screen for the identification of host factors involved in HCMV replication and identifies the nonessential amino acid asparagine as a critical factor in regulating HCMV virus replication. These results have implications for control of viral latency and the clinical treatment of HCMV in patients.IMPORTANCE HCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem, and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals have been developed for use against HCMV since the licensing of ganciclovir, and of these, the same viral genes are often targeted, reducing the usefulness of these drugs against resistant strains. An alternative approach is to target host genes essential for virus replication. Here we demonstrate that HCMV replication is highly dependent on levels of the amino acid asparagine and that knockdown of a critical enzyme involved in asparagine synthesis results in severe attenuation of virus replication. These results suggest that reducing asparagine levels through dietary restriction or chemotherapeutic treatment could limit HCMV replication in patients.
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Affiliation(s)
- Chen-Hsuin Lee
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Samantha Griffiths
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Digard
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nhan Pham
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Juergen Haas
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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17
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Auer M. Ultrastructural cellular signatures: does cellular form follow function? Natl Sci Rev 2019; 6:861-863. [PMID: 31867129 PMCID: PMC6919641 DOI: 10.1093/nsr/nwz057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, USAE-mail:
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18
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Auer M, Edlinger G, Petry T, Pfliegensdörfer J. The role of affective states in potential applicants’ evaluations of employer attractiveness. German Journal of Human Resource Management 2019. [DOI: 10.1177/2397002219854959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
What role do emotions play as a job seeker eyes up a potential employer? Our contribution to research into employer attractiveness explores the role that affective states play in potential applicants’ subjective perceptions of companies’ employer attractiveness in the early phase of job seeking. We adopt a concurrent verbalization approach to inquire into qualified potential applicants’ processes of interpreting employer branding material. Based on these data, we provide insights into the neglected role of emotions in research on potential applicants’ assessments of the appeal of an organization. The findings from a multistep qualitative data analysis produce the following four propositions: (1) strong emotions influence the outcome of the opinion-making process; (2) negative emotions play a crucial role in potential applicants’ evaluations of employer attractiveness; (3) some contents of employer information elicit negative emotions, whereas their complementary counterparts do not elicit positive affective reactions; and (4) expectations towards an employer and comparisons among employers influence potential applicants’ sentiments about individual employers.
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Bilbija B, Auer M, Široký P. Long term persistence of introduced Amblyomma geoemydae tick population under indoor conditions in Austria. Med Vet Entomol 2019; 33:317-321. [PMID: 30746727 DOI: 10.1111/mve.12361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
An indoor terrarium population of Amblyomma geoemydae was established subsequent to the import of a single yellow-marginated box turtle Cuora flavomarginata. This indoor tick population revealed an unexpected resistance against de-ticking trials, with persistence between 2010 and 2015, when the ticks were successfully eliminated. Ticks were collected from the bodies and shells of turtles, as well as from terraria soil. Species diagnosis of ticks was carried out according to distinguishable morphological characters and supported by molecular analysis using DNA-barcoding. Introduced exotic ticks are potential vectors of pathogens and can have an impact on wildlife, domestic animals and the human population. This case emphasizes the need for sharp surveillance and control measures on imported reptiles.
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Affiliation(s)
- B Bilbija
- Faculty of Veterinary Hygiene and Ecology, Department of Biology and Wildlife Diseases, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - M Auer
- Senckenberg Natural History Collections Dresden, Museum of Zoology, Dresden, Germany
| | - P Široký
- Faculty of Veterinary Hygiene and Ecology, Department of Biology and Wildlife Diseases, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
- CEITEC-Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
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20
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Pérez-Pi I, Evans DA, Horrocks MH, Pham NT, Dolt KS, Koszela J, Kunath T, Auer M. α-Synuclein-Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation. Anal Chem 2019; 91:5582-5590. [PMID: 30964656 PMCID: PMC6534341 DOI: 10.1021/acs.analchem.8b03842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
α-Synuclein
fibrils are considered a hallmark of Parkinson’s
disease and other synucleinopathies. However, small oligomers that
formed during the early stages of α-synuclein aggregation are
thought to be the main toxic species causing disease. The formation
of α-synuclein oligomers has proven difficult to follow, because
of the heterogeneity and transient nature of the species formed. Here,
a novel bead-based aggregation assay for monitoring the earliest stages
of α-synuclein oligomerization, α-Synuclein–Confocal
Nanoscanning (ASYN-CONA), is presented. The α-synuclein A91C
single cysteine mutant is modified with a trifunctional chemical tag,
which allows simultaneous fluorescent labeling with a green dye (tetramethylrhodamine,
TMR) and attachment to microbeads. Beads with bound TMR-labeled α-synuclein
are then incubated with a red dye (Cy5)-labeled variant of α-synuclein
A91C, and EtOH (20%) to induce aggregation. Aggregation is detected
by confocal scanning imaging, below the equatorial plane of the beads,
which is known as the CONA technique. On-bead TMR-labeled α-synuclein
and aggregated Cy5-labeled α-synuclein from the solution are
quantitatively monitored in parallel by detection of fluorescent halos
or “rings”. α-Synuclein on-bead oligomerization
results in a linear increase of red bead ring fluorescence intensity
over a period of 5 h. Total internal reflection fluorescence microscopy
was performed on oligomers cleaved from the beads, and it revealed
that (i) oligomers are sufficiently stable in solution to investigate
their composition, consisting of 6 ± 1 monomer units, and (ii)
oligomers containing a mean of 15 monomers bind Thioflavin-T. Various
known inhibitors of α-synuclein aggregation were used to validate
the ASYN-CONA assay for drug screening. Baicalein, curcumin, and rifampicin
showed concentration-dependent inhibition of the α-synuclein
aggregation and the IC50 (the concentration of the compound
at which the maxiumum intensity was reduced by one-half) were calculated.
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Affiliation(s)
- Irene Pérez-Pi
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - David A Evans
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom.,UK Dementia Research Institute , University of Edinburgh , Chancellor's Building, Edinburgh Medical School , Edinburgh EH16 4SB , United Kingdom
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Karamjit S Dolt
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Joanna Koszela
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
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21
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Lee CH, Griffiths S, Digard P, Pham N, Auer M, Haas J, Grey F. Identification of novel host factors influencing human cytomegalovirus replication using a two-step siRNA screen. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chen-Hsuin Lee
- 1Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Paul Digard
- 1Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Nhan Pham
- 2University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- 2University of Edinburgh, Edinburgh, United Kingdom
| | - Juergen Haas
- 2University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- 1Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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22
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Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen JH, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SS, Niyogi KK. Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. Plant Cell 2019; 31:579-601. [PMID: 30787178 PMCID: PMC6482638 DOI: 10.1105/tpc.18.00742] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/18/2018] [Accepted: 02/15/2019] [Indexed: 05/04/2023]
Abstract
Light and nutrients are critical regulators of photosynthesis and metabolism in plants and algae. Many algae have the metabolic flexibility to grow photoautotrophically, heterotrophically, or mixotrophically. Here, we describe reversible Glc-dependent repression/activation of oxygenic photosynthesis in the unicellular green alga Chromochloris zofingiensis. We observed rapid and reversible changes in photosynthesis, in the photosynthetic apparatus, in thylakoid ultrastructure, and in energy stores including lipids and starch. Following Glc addition in the light, C. zofingiensis shuts off photosynthesis within days and accumulates large amounts of commercially relevant bioproducts, including triacylglycerols and the high-value nutraceutical ketocarotenoid astaxanthin, while increasing culture biomass. RNA sequencing reveals reversible changes in the transcriptome that form the basis of this metabolic regulation. Functional enrichment analyses show that Glc represses photosynthetic pathways while ketocarotenoid biosynthesis and heterotrophic carbon metabolism are upregulated. Because sugars play fundamental regulatory roles in gene expression, physiology, metabolism, and growth in both plants and animals, we have developed a simple algal model system to investigate conserved eukaryotic sugar responses as well as mechanisms of thylakoid breakdown and biogenesis in chloroplasts. Understanding regulation of photosynthesis and metabolism in algae could enable bioengineering to reroute metabolism toward beneficial bioproducts for energy, food, pharmaceuticals, and human health.
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Affiliation(s)
- Melissa S Roth
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Daniel J Westcott
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Masakazu Iwai
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Maria Mueller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreas Walter
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Fatima Foflonker
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Nassim N Ataii
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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23
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Metlagel Z, Krey JF, Song J, Swift MF, Tivol WJ, Dumont RA, Thai J, Chang A, Seifikar H, Volkmann N, Hanein D, Barr-Gillespie PG, Auer M. Electron cryo-tomography of vestibular hair-cell stereocilia. J Struct Biol 2019; 206:149-155. [PMID: 30822456 DOI: 10.1016/j.jsb.2019.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/13/2019] [Accepted: 02/17/2019] [Indexed: 11/24/2022]
Abstract
High-resolution imaging of hair-cell stereocilia of the inner ear has contributed substantially to our understanding of auditory and vestibular function. To provide three-dimensional views of the structure of stereocilia cytoskeleton and membranes, we developed a method for rapidly freezing unfixed stereocilia on electron microscopy grids, which allowed subsequent 3D imaging by electron cryo-tomography. Structures of stereocilia tips, shafts, and tapers were revealed, demonstrating that the actin paracrystal was not perfectly ordered. This sample-preparation and imaging procedure will allow for examination of structural features of stereocilia in a near-native state.
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Affiliation(s)
- Zoltan Metlagel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jocelyn F Krey
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark F Swift
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, San Diego, USA
| | - William J Tivol
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rachel A Dumont
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jasmine Thai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alex Chang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Helia Seifikar
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Niels Volkmann
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, San Diego, USA
| | - Dorit Hanein
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, San Diego, USA
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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24
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Bsteh G, Hegen H, Teuchner B, Berek K, Wurth S, Auer M, Di Pauli F, Deisenhammer F, Berger T. Peripapillary retinal nerve fibre layer thinning rate as a biomarker discriminating stable and progressing relapsing–remitting multiple sclerosis. Eur J Neurol 2019; 26:865-871. [DOI: 10.1111/ene.13897] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023]
Affiliation(s)
- G. Bsteh
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - H. Hegen
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - B. Teuchner
- Department of Ophthalmology Medical University of Innsbruck Innsbruck Austria
| | - K. Berek
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - S. Wurth
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - M. Auer
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - F. Di Pauli
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - F. Deisenhammer
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
| | - T. Berger
- Department of Neurology Medical University of Innsbruck InnsbruckAustria
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25
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Rojas F, Silvester E, Young J, Milne R, Tettey M, Houston DR, Walkinshaw MD, Pérez-Pi I, Auer M, Denton H, Smith TK, Thompson J, Matthews KR. Oligopeptide Signaling through TbGPR89 Drives Trypanosome Quorum Sensing. Cell 2018; 176:306-317.e16. [PMID: 30503212 PMCID: PMC6333907 DOI: 10.1016/j.cell.2018.10.041] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 02/03/2023]
Abstract
Trypanosome parasites control their virulence and spread by using quorum sensing (QS) to generate transmissible “stumpy forms” in their host bloodstream. However, the QS signal “stumpy induction factor” (SIF) and its reception mechanism are unknown. Although trypanosomes lack G protein-coupled receptor signaling, we have identified a surface GPR89-family protein that regulates stumpy formation. TbGPR89 is expressed on bloodstream “slender form” trypanosomes, which receive the SIF signal, and when ectopically expressed, TbGPR89 drives stumpy formation in a SIF-pathway-dependent process. Structural modeling of TbGPR89 predicts unexpected similarity to oligopeptide transporters (POT), and when expressed in bacteria, TbGPR89 transports oligopeptides. Conversely, expression of an E. coli POT in trypanosomes drives parasite differentiation, and oligopeptides promote stumpy formation in vitro. Furthermore, the expression of secreted trypanosome oligopeptidases generates a paracrine signal that accelerates stumpy formation in vivo. Peptidase-generated oligopeptide QS signals being received through TbGPR89 provides a mechanism for both trypanosome SIF production and reception. Trypanosomes use quorum sensing to differentiate to transmissible stumpy forms A GPR89 protein with oligopeptide transport activity drives parasite differentiation Oligopeptide mixtures and synthetic di- and tripeptides promote stumpy formation Released parasite oligopeptidases generate the paracrine quorum sensing signal in vivo
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Affiliation(s)
- Federico Rojas
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Julie Young
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Rachel Milne
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Mabel Tettey
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Malcolm D Walkinshaw
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Irene Pérez-Pi
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Helen Denton
- School of Biology, BSRC, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Terry K Smith
- School of Biology, BSRC, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Joanne Thompson
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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26
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Koszela J, Pham NT, Evans D, Mann S, Perez-Pi I, Shave S, Ceccarelli DFJ, Sicheri F, Tyers M, Auer M. Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay. BMC Biol 2018; 16:88. [PMID: 30097011 PMCID: PMC6086040 DOI: 10.1186/s12915-018-0554-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/24/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging. RESULTS UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme. CONCLUSIONS As a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.
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Affiliation(s)
- Joanna Koszela
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Nhan T. Pham
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - David Evans
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Stefan Mann
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Irene Perez-Pi
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Derek F. J. Ceccarelli
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7 Canada
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
- Biomedical Sciences, Medical School, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
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27
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Hou Z, Wang X, Cai J, Zhang J, Hassan A, Auer M, Shi X. Platelet-Derived Growth Factor Subunit B Signaling Promotes Pericyte Migration in Response to Loud Sound in the Cochlear Stria Vascularis. J Assoc Res Otolaryngol 2018; 19:363-379. [PMID: 29869048 PMCID: PMC6081892 DOI: 10.1007/s10162-018-0670-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Normal blood supply to the cochlea is critical for hearing. Noise damages auditory sensory cells and has a marked effect on the microvasculature in the cochlear lateral wall. Pericytes in the stria vascularis (strial pericytes) are particularly vulnerable and sensitive to acoustic trauma. Exposure of NG2DsRedBAC transgenic mice (6-8 weeks old) to wide-band noise at a level of 120 dB for 3 h per day for 2 consecutive days produced a significant hearing threshold shift and caused pericytes to protrude and migrate from their normal endothelial attachment sites. The pericyte migration was associated with increased expression of platelet-derived growth factor beta (PDGF-BB). Blockade of PDGF-BB signaling with either imatinib, a potent PDGF-BB receptor (PDGFR) inhibitor, or APB5, a specific PDGFRβ blocker, significantly attenuated the pericyte migration from strial vessel walls. The PDGF-BB-mediated strial pericyte migration was further confirmed in an in vitro cell migration assay, as well as in an in vivo live animal model used in conjunction with confocal fluorescence microscopy. Pericyte migration took one of two different forms, here denoted protrusion and detachment. The protrusion is characterized by pericytes with a prominent triangular shape, or pericytes extending fine strands to neighboring capillaries. The detachment is characterized by pericyte detachment and movement away from vessels. We also found the sites of pericyte migration highly associated with regions of vascular leakage. In particular, under transmission electron microscopy (TEM), multiple vesicles at the sites of endothelial cells with loosely attached pericytes were observed. These data show that cochlear pericytes are markedly affected by acoustic trauma, causing them to display abnormal morphology. The effect of loud sound on pericytes is mediated by upregulation of PDGF-BB. Normal functioning pericytes are required for vascular stability.
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Affiliation(s)
- Zhiqiang Hou
- Oregon Hearing Research Center, Department of Otolaryngology/Head & Neck Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Xiaohan Wang
- Oregon Hearing Research Center, Department of Otolaryngology/Head & Neck Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Jing Cai
- Oregon Hearing Research Center, Department of Otolaryngology/Head & Neck Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Jinhui Zhang
- Oregon Hearing Research Center, Department of Otolaryngology/Head & Neck Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ahmed Hassan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaorui Shi
- Oregon Hearing Research Center, Department of Otolaryngology/Head & Neck Surgery, Oregon Health & Science University, Portland, OR, 97239, USA.
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Haslam D, Sazzed S, Wriggers W, Kovcas J, Song J, Auer M, He J. A Pattern Recognition Tool for Medium-resolution Cryo-EM Density Maps and Low-resolution Cryo-ET Density maps. Bioinform Res Appl (2018) 2018; 10847:233-238. [PMID: 36383494 PMCID: PMC9645795 DOI: 10.1007/978-3-319-94968-0_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cryo-electron microscopy (Cryo-EM) and cryo-electron tomography (cryo-ET) produce 3-D density maps of biological molecules at a range of resolution levels. Pattern recognition tools are important in distinguishing biological components from volumetric maps with the available resolutions. One of the most distinct characters in density maps at medium (5-10 Å) resolution is the visibility of protein secondary structures. Although computational methods have been developed, the accurate detection of helices and β-strands from cryo-EM density maps is still an active research area. We have developed a tool for protein secondary structure detection and evaluation of medium resolution 3-D cryo-EM density maps which combines three computational methods (SSETracer, StrandTwister, and AxisComparison). The program was integrated in UCSF Chimera, a popular visualization software in the cryo-EM community. In related work, we have developed BundleTrac, a computational method to trace filaments in a bundle from lower resolution cryo-ET density maps. It has been applied to actin filament tracing in stereocilia with good accuracy and can be potentially added as a tool in Chimera.
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Affiliation(s)
- Devin Haslam
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
| | - Julio Kovcas
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
| | - Junha Song
- Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Manfred Auer
- Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
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29
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Kamennaya NA, Zemla M, Mahoney L, Chen L, Holman E, Holman HY, Auer M, Ajo-Franklin CM, Jansson C. High pCO 2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial. Nat Commun 2018; 9:2116. [PMID: 29844378 PMCID: PMC5974010 DOI: 10.1038/s41467-018-04588-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 12/05/2014] [Accepted: 04/13/2018] [Indexed: 11/28/2022] Open
Abstract
The contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22-2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO2 pressure (pCO2) representative of the early Paleoproterozoic. We find that high pCO2 boosts generation of acidic extracellular polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.
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Affiliation(s)
- Nina A Kamennaya
- Earth Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, USA.
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Marcin Zemla
- Molecular Biophysics and Integrated Bioimaging Sciences Division, LBNL, Berkeley, CA, 94720, USA
| | - Laura Mahoney
- Earth Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, USA
| | - Liang Chen
- Earth Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, USA
| | - Elizabeth Holman
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Hoi-Ying Holman
- Earth Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Sciences Division, LBNL, Berkeley, CA, 94720, USA
| | | | - Christer Jansson
- Earth Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, USA
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O Box 999, K8-93, Richland, WA, 99352, USA
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30
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Liu W, Luo Z, Wang Y, Pham NT, Tuck L, Pérez-Pi I, Liu L, Shen Y, French C, Auer M, Marles-Wright J, Dai J, Cai Y. Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nat Commun 2018; 9:1936. [PMID: 29789543 PMCID: PMC5964202 DOI: 10.1038/s41467-018-04254-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/11/2018] [Indexed: 12/11/2022] Open
Abstract
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis. A set of loxP mutant pairs was identified to maximize the efficiency of the in vitro diversification. Exemplar pathways of β-carotene and violacein were successfully assembled, diversified, and integrated using this SCRaMbLE-in method. High-throughput sequencing was performed on selected engineered strains to reveal the resulting genotype-to-phenotype relationships. The SCRaMbLE-in method proves to be a rapid, efficient, and universal method to fast track the cycle of engineering biology.
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Affiliation(s)
- Wei Liu
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Zhouqing Luo
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Nhan T Pham
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Laura Tuck
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Irene Pérez-Pi
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Longying Liu
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Yue Shen
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China.,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Chris French
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,Edinburgh Medical School, Biomedical Sciences, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle upon, Tyne, NE1 7RX, UK
| | - Junbiao Dai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
| | - Yizhi Cai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China. .,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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31
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Suppan C, Brcic I, Heitzer E, Tiran V, Mueller H, Auer M, Cote R, Datar R, Dandachi N, Balic M. Prognostic impact of tumor fractions in plasma assessed with mFAST-SeqS on overall survival of metastatic breast cancer undergoing systemic treatment. Eur J Cancer 2018. [DOI: 10.1016/s0959-8049(18)30632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Shave S, McGuire K, Pham NT, Mole DJ, Webster SP, Auer M. Diclofenac Identified as a Kynurenine 3-Monooxygenase Binder and Inhibitor by Molecular Similarity Techniques. ACS Omega 2018; 3:2564-2568. [PMID: 30023839 PMCID: PMC6044753 DOI: 10.1021/acsomega.7b02091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
In this study, we apply a battery of molecular similarity techniques to known inhibitors of kynurenine 3-monooxygenase (KMO), querying each against a repository of approved, experimental, nutraceutical, and illicit drugs. Four compounds are assayed against KMO. Subsequently, diclofenac (also known by the trade names Voltaren, Voltarol, Aclonac, and Cataflam) has been confirmed as a human KMO protein binder and inhibitor in cell lysate with low micromolar KD and IC50, respectively, and low millimolar cellular IC50. Hit to drug hopping, as exemplified here for one of the most successful anti-inflammatory medicines ever invented, holds great promise for expansion into new disease areas and highlights the not-yet-fully-exploited potential of drug repurposing.
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Affiliation(s)
- Steven Shave
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
| | - Kris McGuire
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Nhan T. Pham
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
| | - Damian J. Mole
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Scott P. Webster
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Manfred Auer
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
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33
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Shave S, Mann S, Koszela J, Kerr A, Auer M. PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries. PLoS One 2018; 13:e0193332. [PMID: 29474422 PMCID: PMC5825087 DOI: 10.1371/journal.pone.0193332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 10/18/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022] Open
Abstract
The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.
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Affiliation(s)
- Steven Shave
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland, United Kingdom
| | - Stefan Mann
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland, United Kingdom
| | - Joanna Koszela
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland, United Kingdom
| | - Alastair Kerr
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland, United Kingdom
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland, United Kingdom
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34
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Wilson K, Webster SP, Iredale JP, Zheng X, Homer NZ, Pham NT, Auer M, Mole DJ. Detecting drug-target binding in cells using fluorescence-activated cell sorting coupled with mass spectrometry analysis. Methods Appl Fluoresc 2017; 6:015002. [PMID: 28901950 DOI: 10.1088/2050-6120/aa8c60] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The assessment of drug-target engagement for determining the efficacy of a compound inside cells remains challenging, particularly for difficult target proteins. Existing techniques are more suited to soluble protein targets. Difficult target proteins include those with challenging in vitro solubility, stability or purification properties that preclude target isolation. Here, we report a novel technique that measures intracellular compound-target complex formation, as well as cellular permeability, specificity and cytotoxicity-the toxicity-affinity-permeability-selectivity (TAPS) technique. The TAPS assay is exemplified here using human kynurenine 3-monooxygenase (KMO), a challenging intracellular membrane protein target of significant current interest. TAPS confirmed target binding of known KMO inhibitors inside cells. We conclude that the TAPS assay can be used to facilitate intracellular hit validation on most, if not all intracellular drug targets.
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Affiliation(s)
- Kris Wilson
- Drug Discovery Core, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom
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35
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Hegen H, Walde J, Auer M, Deisenhammer F. Cerebrospinal fluid:serum glucose ratio in the ventricular and lumbar compartments: implications for clinical practice. Eur J Neurol 2017; 25:373-379. [DOI: 10.1111/ene.13513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/02/2017] [Indexed: 11/30/2022]
Affiliation(s)
- H. Hegen
- Department of Neurology Medical University of Innsbruck Innsbruck Austria
| | - J. Walde
- Department of Statistics Faculty of Economics and Statistics University of Innsbruck Innsbruck Austria
| | - M. Auer
- Department of Neurology Medical University of Innsbruck Innsbruck Austria
| | - F. Deisenhammer
- Department of Neurology Medical University of Innsbruck Innsbruck Austria
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36
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Dantoft W, Martínez-Vicente P, Jafali J, Pérez-Martínez L, Martin K, Kotzamanis K, Craigon M, Auer M, Young NT, Walsh P, Marchant A, Angulo A, Forster T, Ghazal P. Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses. Front Immunol 2017; 8:1146. [PMID: 28993767 PMCID: PMC5622154 DOI: 10.3389/fimmu.2017.01146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022] Open
Abstract
Neonates and especially premature infants are highly susceptible to infection but still can have a remarkable resilience that is poorly understood. The view that neonates have an incomplete or deficient immune system is changing. Human neonatal studies are challenging, and elucidating host protective responses and underlying cognate pathway biology, in the context of viral infection in early life, remains to be fully explored. In both resource rich and poor settings, human cytomegalovirus (HCMV) is the most common cause of congenital infection. By using unbiased systems analyses of transcriptomic resources for HCMV neonatal infection, we find the systemic response of a preterm congenital HCMV infection, involves a focused IFN regulatory response associated with dendritic cells. Further analysis of transcriptional-programming of neonatal dendritic cells in response to HCMV infection in culture revealed an early dominant IFN-chemokine regulatory subnetworks, and at later times the plasticity of pathways implicated in cell-cycle control and lipid metabolism. Further, we identify previously unknown suppressed networks associated with infection, including a select group of GPCRs. Functional siRNA viral growth screen targeting 516-GPCRs and subsequent validation identified novel GPCR-dependent antiviral (ADORA1) and proviral (GPR146, RGS16, PTAFR, SCTR, GPR84, GPR85, NMUR2, FZ10, RDS, CCL17, and SORT1) roles. By contrast a gene family cluster of protocadherins is significantly differentially induced in neonatal cells, suggestive of possible immunomodulatory roles. Unexpectedly, programming responses of adult and neonatal dendritic cells, upon HCMV infection, demonstrated comparable quantitative and qualitative responses showing that functionally, neonatal dendritic cell are not overly compromised. However, a delay in responses of neonatal cells for IFN subnetworks in comparison with adult-derived cells are notable, suggestive of subtle plasticity differences. These findings support a set-point control mechanism rather than immaturity for explaining not only neonatal susceptibility but also resilience to infection. In summary, our findings show that neonatal HCMV infection leads to a highly plastic and functional robust programming of dendritic cells in vivo and in vitro. In comparison with adults, a minimal number of subtle quantitative and temporal differences may contribute to variability in host susceptibility and resilience, in a context dependent manner.
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Affiliation(s)
- Widad Dantoft
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Pablo Martínez-Vicente
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - James Jafali
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lara Pérez-Martínez
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Quantitative Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kim Martin
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Synexa Life Sciences, Cape Town, South Africa
| | - Konstantinos Kotzamanis
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Marie Craigon
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,SynthSys-Centre for Synthetic and Systems Biology, School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil T Young
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Paul Walsh
- NSilico Life Science and Department of Computing, Institute of Technology, Cork, Ireland
| | - Arnaud Marchant
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Thorsten Forster
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Ghazal
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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37
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Portal C, Hintersteiner M, Barbeau O, Dodd P, Huggett M, Pérez-Pi I, Evans D, Auer M. Facile Synthesis of a Next Generation Safety-Catch Acid-Labile Linker, SCAL-2, Suitable for Solid-Phase Synthesis, On-Support Display and for Post-Synthesis Tagging. ChemistrySelect 2017; 2:6658-6662. [PMID: 29104911 PMCID: PMC5661701 DOI: 10.1002/slct.201701519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 11/27/2022]
Abstract
The SCAL linker, a safety catch linker, is amongst the most versatile linkers for solid phase synthesis. It was originally described in 1991 by Pátek and Lebl. Yet, its application has been hindered by the low yields of published synthetic routes. Over time, the exceptional versatility of this linker has been demonstrated in several applications of advanced solid phase synthesis of peptides and peptidomimetics. Recently, an updated synthesis of the original linker has also been presented at the 22nd American Peptide Symposium, comprising 10 steps. Herein, the design and synthesis of a next generation SCAL linker, SCAL‐2, is reported. SCAL‐2 features a simplified molecular architecture, which allows for a more efficient synthesis in 8 steps with superior yields. Both linkers, SCAL and SCAL‐2 are compared in terms of their cleavage properties adding valuable information on how to best utilize the versatility of these linkers for solid phase synthesis.
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Affiliation(s)
- Christophe Portal
- Edinburgh BioQuarter 9 Little France Road, Edinburgh Scotland EH16 4UX U.K
| | - Martin Hintersteiner
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - Olivier Barbeau
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - Peter Dodd
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - Margaret Huggett
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - Irene Pérez-Pi
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - David Evans
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences University of Edinburgh, The King's Buildings, Edinburgh Scotland EH9 3BF U.K
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38
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Rojas F, Koszela J, Búa J, Llorente B, Burchmore R, Auer M, Mottram JC, Téllez-Iñón MT. The ubiquitin-conjugating enzyme CDC34 is essential for cytokinesis in contrast to putative subunits of a SCF complex in Trypanosoma brucei. PLoS Negl Trop Dis 2017; 11:e0005626. [PMID: 28609481 PMCID: PMC5507466 DOI: 10.1371/journal.pntd.0005626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 12/05/2016] [Revised: 07/11/2017] [Accepted: 05/06/2017] [Indexed: 12/31/2022] Open
Abstract
The ubiquitin-proteasome system is a post-translational regulatory pathway for controlling protein stability and activity that underlies many fundamental cellular processes, including cell cycle progression. Target proteins are tagged with ubiquitin molecules through the action of an enzymatic cascade composed of E1 ubiquitin activating enzymes, E2 ubiquitin conjugating enzymes, and E3 ubiquitin ligases. One of the E3 ligases known to be responsible for the ubiquitination of cell cycle regulators in eukaryotes is the SKP1-CUL1-F-box complex (SCFC). In this work, we identified and studied the function of homologue proteins of the SCFC in the life cycle of Trypanosoma brucei, the causal agent of the African sleeping sickness. Depletion of trypanosomal SCFC components TbRBX1, TbSKP1, and TbCDC34 by RNAi resulted in decreased growth rate and contrasting cell cycle abnormalities for both procyclic (PCF) and bloodstream (BSF) forms. Depletion of TbRBX1 in PCF cells interfered with kinetoplast replication, whilst depletion of TbSKP1 arrested PCF and BSF cells in the G1/S transition. Silencing of TbCDC34 in BSF cells resulted in a block in cytokinesis and caused rapid clearance of parasites from infected mice. We also show that TbCDC34 is able to conjugate ubiquitin in vitro and in vivo, and that its activity is necessary for T. brucei infection progression in mice. This study reveals that different components of a putative SCFC have contrasting phenotypes once depleted from the cells, and that TbCDC34 is essential for trypanosome replication, making it a potential target for therapeutic intervention. African sleeping sickness is a neglected tropical disease caused by infection with the protozoan parasite Trypanosoma brucei, which is transmitted to humans by tsetse flies (Glossina genus). Treatment of the disease is complex and relies on limited pharmaceutical options. Understanding how T. brucei regulates cell cycle progression at a molecular level when alternating between the mammalian host and the insect vector could lead to better therapies. In this study, we examined different T. brucei proteins with homology to components of the SKP1-CUL1-F-box ubiquitin ligase complex (SCFC), previously characterized in other eukaryotes as a regulator of cell cycle progression. We found that depletion of the homologues of a putative SCFC cause T. brucei to develop abnormally, generating different phenotypes of the mammalian and insect stages. Interestingly, depletion of the ubiquitin conjugating enzyme TbCDC34 arrest cells in a pre-cytokinesis stage, indicating that this protein is essential for cytokinesis. In addition to improving our fundamental understanding of the molecular regulation underlying the sophisticated life cycle of T. brucei, this work pinpoints a potential target for drug development against trypanosomiasis.
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Affiliation(s)
- Federico Rojas
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
- * E-mail:
| | - Joanna Koszela
- Institute of Quantitative Biology Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Jacqueline Búa
- Instituto Nacional de Parasitología ‘Dr. M. Fatala Chabén’, A.N.L.I.S., ‘Dr. Carlos G. Malbrán’, Buenos Aires, Argentina
| | - Briardo Llorente
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Manfred Auer
- Institute of Quantitative Biology Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Jeremy C. Mottram
- Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
| | - María Teresa Téllez-Iñón
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
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39
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Abstract
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Use
of a heterobifunctional photoactivatable cross-linker, sulfo-SDA
(diazirine), has yielded high-density data that facilitated structure
modeling of individual proteins. We expand the photoactivatable chemistry
toolbox here with a second reagent, sulfo-SBP (benzophenone). This
further increases the density of photo-cross-linking to a factor of
20× over conventional cross-linking. Importantly, the two different
photoactivatable groups display orthogonal directionality, enabling
access to different protein regions, unreachable with a single cross-linker.
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Affiliation(s)
- Adam Belsom
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Gemma Mudd
- School of Biological Sciences and Medical School, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Sven Giese
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
| | - Manfred Auer
- School of Biological Sciences and Medical School, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
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40
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Kim KH, Brown RC, Daugaard T, Tivol WF, Auer M, Simmons B, Singh S. Strategy for Extending the Stability of Bio-oil-Derived Phenolic Oligomers by Mild Hydrotreatment with Ionic-Liquid-Stabilized Nanoparticles. ChemSusChem 2017; 10:884-893. [PMID: 27992678 DOI: 10.1002/cssc.201601515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 12/17/2016] [Indexed: 06/06/2023]
Abstract
The development of catalytic transformations and processes is essential to utilize bio-oil and lignin derivatives. Metal nanoparticles (M-NPs) stabilized in ionic liquids (ILs) are promising for the catalytic hydrotreatment of bio-oil because the properties of the catalyst system can be customized by combining the appropriate IL and metal nanoparticles. Herein, we demonstrate an experimental approach to stabilize lignin-derived phenolics isolated from bio-oil with ruthenium NPs stabilized by an ionic copolymer in 1-ethyl-3-methylimidazolium acetate ([C2 C1 Im][OAc]). The mild hydrotreatment of phenolic oligomers (POs) was performed with the synthesized M-NP catalyst at 100 °C for 6 h. Hydrotreatment of the POs resulted in enhanced thermal stability of the POs by as much as a factor of three, as determined by the aging index and by reducing reactive functionalities, which was also confirmed by NMR spectroscopy and GC analysis. The results support our hypothesis that M-NPs stabilized in ILs can effectively stabilize POs under mild conditions, which could be applicable to any lignin-derived phenolic.
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Affiliation(s)
- Kwang Ho Kim
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA, USA
| | - Robert C Brown
- Bioeconomy Institute, Iowa State University, Ames, IA, USA
| | | | - William F Tivol
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Manfred Auer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Blake Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA, USA
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41
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Bsteh G, Monz E, Zamarian L, Hagspiel S, Hegen H, Auer M, Wurth S, Di Pauli F, Deisenhammer F, Berger T. Combined evaluation of personality, risk and coping in MS patients: A step towards individualized treatment choice - The PeRiCoMS-Study I. J Neurol Sci 2017; 376:71-75. [PMID: 28431632 DOI: 10.1016/j.jns.2017.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/13/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic inflammatory neurological disease requiring disease-modifying treatment (DMT). To provide patients with the optimal individual therapeutic option, treatment recommendations should be based not only on individual disease course and DMT specific benefit-risk estimates, but also on patient's individual characteristics such as personality, risk attitude and coping strategies. However, these characteristics are difficult to objectify in clinical routine practice without the support of appropriate evaluation instruments. OBJECTIVE To identify and to assemble an objective test battery measuring personality, risk attitude and coping strategies in MS patients. METHODS A comprehensive literature search was performed to obtain all questionnaires assessing personality, risk attitude and coping strategies. Availability in German language, validation in a published normative collective and a reliability of >0.70 were required for our purposes. Based on these criteria, we chose the Big-Five-Personality Test, UPPS Impulsive Behaviour Scale, Domain-Specific Risk-Taking scale (DOSPERT), Brief-COPE and Stress & Coping Inventory (SCI). Results were compared to published normative controls of the respective questionnaires. RESULTS Out of 22 MS patients (7 males, 15 females) participating in this study, 19 (86.4%) completed all questionnaires. The median completion time was 45min (min-max range: 25-60min). The median scores of the MS group were within the average range of published control samples in all questionnaires. CONCLUSIONS We report that traits of personality, risk attitude and coping strategies can be effectively and feasibly tested in MS patients by the instruments used in our exploratory study. There were no differences between MS patients and healthy controls, thus enabling assessment without being influenced by the diagnosis of MS. After validation in a larger cohort the "PeRiCoMS"-battery will be useful as another step towards a more individualized shared-decision-making in every day routine practice.
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Affiliation(s)
- G Bsteh
- Department of Neurology, Medical University of Innsbruck, Austria.
| | - E Monz
- Department of Neurology, Medical University of Innsbruck, Austria
| | - L Zamarian
- Department of Neurology, Medical University of Innsbruck, Austria
| | - S Hagspiel
- Department of Neurology, Medical University of Innsbruck, Austria
| | - H Hegen
- Department of Neurology, Medical University of Innsbruck, Austria
| | - M Auer
- Department of Neurology, Medical University of Innsbruck, Austria
| | - S Wurth
- Department of Neurology, Medical University of Innsbruck, Austria
| | - F Di Pauli
- Department of Neurology, Medical University of Innsbruck, Austria
| | - F Deisenhammer
- Department of Neurology, Medical University of Innsbruck, Austria
| | - T Berger
- Department of Neurology, Medical University of Innsbruck, Austria
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42
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Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci 2017; 12:23. [PMID: 28194258 PMCID: PMC5299692 DOI: 10.1186/s40793-017-0233-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/08/2017] [Indexed: 01/21/2023] Open
Abstract
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.
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Affiliation(s)
| | - Hannah Woo
- University Of Tennessee, Knoxville, TN USA
| | | | - Robert Walker
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcin Zemla
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Lynne A Goodwin
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Terry C Hazen
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,University Of Tennessee, Knoxville, TN USA
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43
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Graier T, Auer M, Heitzer E, Ulz P, Perakis S, Speicher M, Geigl J. Rapid single-cell copy-number aberration analysis using high-throughput sequencing. Eur J Cancer 2017. [DOI: 10.1016/s0959-8049(17)30159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Suppan C, Tiran V, Heitzer E, Auer M, Cote R, Datar R, Dandachi N, Balic M. Serial blood draws in metastatic breast cancer patients undergoing systemic treatment analysed by size based CTC detection and mFAST Seq cell free DNA analysis. Eur J Cancer 2017. [DOI: 10.1016/s0959-8049(17)30211-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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45
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Jorgens DM, Inman JL, Wojcik M, Robertson C, Palsdottir H, Tsai WT, Huang H, Bruni-Cardoso A, López CS, Bissell MJ, Xu K, Auer M. Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture. J Cell Sci 2017; 130:177-189. [PMID: 27505896 PMCID: PMC5394780 DOI: 10.1242/jcs.190967] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/28/2016] [Indexed: 02/04/2023] Open
Abstract
The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growth-arrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect to the outer nuclear envelope. The cytoskeleton is also connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues.
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Affiliation(s)
- Danielle M Jorgens
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Wojcik
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Claire Robertson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hildur Palsdottir
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Wen-Ting Tsai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Haina Huang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Alexandre Bruni-Cardoso
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Claudia S López
- Department of Biomedical Engineering, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mina J Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ke Xu
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
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46
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Shamir ER, Coutinho K, Georgess D, Auer M, Ewald AJ. Twist1-positive epithelial cells retain adhesive and proliferative capacity throughout dissemination. Biol Open 2016; 5:1216-28. [PMID: 27402962 PMCID: PMC5051642 DOI: 10.1242/bio.019703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Dissemination is the process by which cells detach and migrate away from a multicellular tissue. The epithelial-to-mesenchymal transition (EMT) conceptualizes dissemination in a stepwise fashion, with downregulation of E-cadherin leading to loss of intercellular junctions, induction of motility, and then escape from the epithelium. This gain of migratory activity is proposed to be mutually exclusive with proliferation. We previously developed a dissemination assay based on inducible expression of the transcription factor Twist1 and here utilize it to characterize the timing and dynamics of intercellular adhesion, proliferation and migration during dissemination. Surprisingly, Twist1(+) epithelium displayed extensive intercellular junctions, and Twist1(-) luminal epithelial cells could still adhere to disseminating Twist1(+) cells. Although proteolysis and proliferation were both observed throughout dissemination, neither was absolutely required. Finally, Twist1(+) cells exhibited a hybrid migration mode; their morphology and nuclear deformation were characteristic of amoeboid cells, whereas their dynamic protrusive activity, pericellular proteolysis and migration speeds were more typical of mesenchymal cells. Our data reveal that epithelial cells can disseminate while retaining competence to adhere and proliferate.
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Affiliation(s)
- Eliah R Shamir
- Departments of Cell Biology and Oncology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA
| | - Kester Coutinho
- Departments of Cell Biology and Oncology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Dan Georgess
- Departments of Cell Biology and Oncology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Andrew J Ewald
- Departments of Cell Biology and Oncology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA
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47
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Mori H, Bhat R, Bruni-Cardoso A, Chen EI, Jorgens DM, Coutinho K, Louie K, Bowen BB, Inman JL, Tecca V, Lee SJ, Becker-Weimann S, Northen T, Seiki M, Borowsky AD, Auer M, Bissell MJ. New insight into the role of MMP14 in metabolic balance. PeerJ 2016; 4:e2142. [PMID: 27478693 PMCID: PMC4950575 DOI: 10.7717/peerj.2142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Membrane-anchored matrix metalloproteinase 14 (MMP14) is involved broadly in organ development through both its proteolytic and signal-transducing functions. Knockout of Mmp14 (KO) in mice results in a dramatic reduction of body size and wasting followed by premature death, the mechanism of which is poorly understood. Since the mammary gland develops after birth and is thus dependent for its functional progression on systemic and local cues, we chose it as an organ model for understanding why KO mice fail to thrive. A global analysis of the mammary glands' proteome in the wild type (WT) and KO mice provided insight into an unexpected role of MMP14 in maintaining metabolism and homeostasis. We performed mass spectrometry and quantitative proteomics to determine the protein signatures of mammary glands from 7 to 11 days old WT and KO mice and found that KO rudiments had a significantly higher level of rate-limiting enzymes involved in catabolic pathways. Glycogen and lipid levels in KO rudiments were reduced, and the circulating levels of triglycerides and glucose were lower. Analysis of the ultrastructure of mammary glands imaged by electron microscopy revealed a significant increase in autophagy signatures in KO mice. Finally, Mmp14 silenced mammary epithelial cells displayed enhanced autophagy. Applied to a systemic level, these findings indicate that MMP14 is a crucial regulator of tissue homeostasis. If operative on a systemic level, these findings could explain how Mmp14KO litter fail to thrive due to disorder in metabolism.
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Affiliation(s)
- Hidetoshi Mori
- Department of Pathology, Center for Comparative Medicine, University of California,Davis,CA,USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory,Berkeley,CA,USA
| | - Ramray Bhat
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory,Berkeley,CA,USA; Calcutta Medical College, University of Calcutta, Calcutta, India
| | - Alexandre Bruni-Cardoso
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory,Berkeley,CA,USA; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo,São Paulo,Brazil
| | - Emily I Chen
- Department of Pharmacology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center , New York , NY , USA
| | - Danielle M Jorgens
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kester Coutinho
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin Ben Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Victoria Tecca
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah J Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sabine Becker-Weimann
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Motoharu Seiki
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Alexander D Borowsky
- Department of Pathology, Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mina J Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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48
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Belic J, Ulz P, Graf R, Auer M, Fischereder K, Hoefler G, Bauernhofer T, Geigl J, Heitzer E, Speicher M. Whole-genome sequencing of circulating tumor DNA reveals relevance of focal amplifications for the management of metastatic prostate cancer. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Heitzer E, Auer M, Suppan C, Dandachi N, Balic M. Changes in ctDNA levels established with the untargeted mFAST-SeqS method reflect response to therapy in metastasized breast cancer patients. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61725-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Heusermann W, Ludin B, Pham NT, Auer M, Weidemann T, Hintersteiner M. A Wide-Field Fluorescence Microscope Extension for Ultrafast Screening of One-Bead One-Compound Libraries Using a Spectral Image Subtraction Approach. ACS Comb Sci 2016; 18:209-19. [PMID: 27057765 DOI: 10.1021/acscombsci.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increasing involvement of academic institutions and biotech companies in drug discovery calls for cost-effective methods to identify new bioactive molecules. Affinity-based on-bead screening of combinatorial one-bead one-compound libraries combines a split-mix synthesis design with a simple protein binding assay operating directly at the bead matrix. However, one bottleneck for academic scale on-bead screening is the unavailability of a cheap, automated, and robust screening platform that still provides a quantitative signal related to the amount of target protein binding to individual beads for hit bead ranking. Wide-field fluorescence microscopy has long been considered unsuitable due to significant broad spectrum autofluorescence of the library beads in conjunction with low detection sensitivity. Herein, we demonstrate how such a standard microscope equipped with LED-based excitation and a modern CMOS camera can be successfully used for selecting hit beads. We show that the autofluorescence issue can be overcome by an optical image subtraction approach that yields excellent signal-to-noise ratios for the detection of bead-associated target proteins. A polymer capillary attached to a semiautomated bead-picking device allows the operator to efficiently isolate individual hit beads in less than 20 s. The system can be used for ultrafast screening of >200,000 bead-bound compounds in 1.5 h, thereby making high-throughput screening accessible to a wider group within the scientific community.
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Affiliation(s)
- Wolf Heusermann
- IMCF
Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Beat Ludin
- Life Imaging Services, Efringerstrasse
79, 4057 Basel, Switzerland
| | - Nhan T Pham
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Manfred Auer
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Thomas Weidemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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