101
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Sciuto MR, Coppola V, Iannolo G, De Maria R, Haas TL. Two-Step Co-Immunoprecipitation (TIP). ACTA ACUST UNITED AC 2018; 125:e80. [DOI: 10.1002/cpmb.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Maria Rita Sciuto
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità; Rome Italy
| | - Valeria Coppola
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità; Rome Italy
| | - Gioacchin Iannolo
- Regenerative Medicine and Biomedical Technologies Unit, Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT; Palermo Italy
| | - Ruggero De Maria
- Institute of General Pathology, Università Cattolica del Sacro Cuore; Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS; Rome Italy
| | - Tobias L. Haas
- Institute of General Pathology, Università Cattolica del Sacro Cuore; Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS; Rome Italy
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102
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Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J. Accurate classification of BRCA1 variants with saturation genome editing. Nature 2018; 562:217-222. [PMID: 30209399 PMCID: PMC6181777 DOI: 10.1038/s41586-018-0461-z] [Citation(s) in RCA: 492] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/26/2018] [Indexed: 12/14/2022]
Abstract
Variants of uncertain significance fundamentally limit the clinical utility of genetic information. The challenge they pose is epitomized by BRCA1, a tumour suppressor gene in which germline loss-of-function variants predispose women to breast and ovarian cancer. Although BRCA1 has been sequenced in millions of women, the risk associated with most newly observed variants cannot be definitively assigned. Here we use saturation genome editing to assay 96.5% of all possible single-nucleotide variants (SNVs) in 13 exons that encode functionally critical domains of BRCA1. Functional effects for nearly 4,000 SNVs are bimodally distributed and almost perfectly concordant with established assessments of pathogenicity. Over 400 non-functional missense SNVs are identified, as well as around 300 SNVs that disrupt expression. We predict that these results will be immediately useful for the clinical interpretation of BRCA1 variants, and that this approach can be extended to overcome the challenge of variants of uncertain significance in additional clinically actionable genes.
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Affiliation(s)
- Gregory M Findlay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melissa D Zhang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anh P Leith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Joseph D Janizek
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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103
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CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9. Metab Eng 2018; 48:288-296. [PMID: 29981865 DOI: 10.1016/j.ymben.2018.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022]
Abstract
Here we describe a method for robust directed evolution using mutagenesis of large sequence spaces in their genomic contexts. The method employs error-prone PCR and Cas9-mediated genome integration of mutant libraries of large-sized donor variants into single or multiple genomic sites with efficiencies reaching 98-99%. From sequencing of genome integrants, we determined that the mutation frequency along the donor fragments is maintained evenly and successfully integrated into the genomic target loci, indicating that there is no bias of mutational load towards the proximity of the double strand break. To validate the applicability of the method for directed evolution of metabolic gene products we engineered two essential enzymes in the mevalonate pathway of Saccharomyces cerevisiae with selected variants supporting up to 11-fold higher production of isoprenoids. Taken together, our method extends on existing CRISPR technologies by facilitating efficient mutagenesis of hundreds of nucleotides in cognate genomic contexts.
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104
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Banks CAS, Thornton JL, Eubanks CG, Adams MK, Miah S, Boanca G, Liu X, Katt ML, Parmely TJ, Florens L, Washburn MP. A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry. Mol Cell Proteomics 2018; 17:1432-1447. [PMID: 29599190 PMCID: PMC6030732 DOI: 10.1074/mcp.tir118.000661] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 01/03/2023] Open
Abstract
Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts because of substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30, or SAP30L and other cellular proteins. Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath. Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison among different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks.
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Affiliation(s)
- Charles A S Banks
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Janet L Thornton
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Mark K Adams
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Sayem Miah
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Gina Boanca
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Xingyu Liu
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Maria L Katt
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Tari J Parmely
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Laurence Florens
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Michael P Washburn
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110;
- §Departments of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
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105
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Beyer T, Bolz S, Junger K, Horn N, Moniruzzaman M, Wissinger Y, Ueffing M, Boldt K. CRISPR/Cas9-mediated Genomic Editing of Cluap1/IFT38 Reveals a New Role in Actin Arrangement. Mol Cell Proteomics 2018; 17:1285-1294. [PMID: 29615496 PMCID: PMC6030719 DOI: 10.1074/mcp.ra117.000487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/28/2018] [Indexed: 12/24/2022] Open
Abstract
CRISPR/Cas9-mediated gene editing allows manipulation of a gene of interest in its own chromosomal context. When applied to the analysis of protein interactions and in contrast to exogenous expression of a protein, this can be studied maintaining physiological stoichiometry, topology, and context. We have used CRISPR/Cas9-mediated genomic editing to investigate Cluap1/IFT38, a component of the intraflagellar transport complex B (IFT-B). Cluap1 has been implicated in human development as well as in cancer progression. Cluap1 loss of function results in early developmental defects with neural tube closure, sonic hedgehog signaling and left-right defects. Herein, we generated an endogenously tagged Cluap1 for protein complex analysis, which was then correlated to the corresponding interactome determined by ectopic expression. Besides IFT-B complex components, new interacting proteins like Ephrin-B1 and TRIP6, which are known to be involved in cytoskeletal arrangement and protein transport, were identified. With the identification of platelet-derived growth factor A (PDGFA) and coiled-coil domain-containing protein 6 (CCDC6) two new interactions were discovered, which link Cluap1 to ciliogenesis and cancer development. The CRISPR/Cas9-mediated knockout of Cluap1 revealed a new phenotype affecting the actin cytoskeleton. Together, these data provide first evidence for a role of Cluap1 not only for cilia assembly and maintenance but also for cytoskeletal rearrangement and intracellular transport processes.
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Affiliation(s)
- Tina Beyer
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany;
| | - Sylvia Bolz
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Katrin Junger
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Nicola Horn
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Muhammad Moniruzzaman
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Yasmin Wissinger
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
- §Thermo Fisher Scientific, Clinical Diagnostics Systems, Neuendorfstr. 25, 16761 Hennigsdorf, Germany
| | - Marius Ueffing
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Karsten Boldt
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany;
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106
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Bontinck M, Van Leene J, Gadeyne A, De Rybel B, Eeckhout D, Nelissen H, De Jaeger G. Recent Trends in Plant Protein Complex Analysis in a Developmental Context. FRONTIERS IN PLANT SCIENCE 2018; 9:640. [PMID: 29868093 PMCID: PMC5962756 DOI: 10.3389/fpls.2018.00640] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/26/2018] [Indexed: 05/30/2023]
Abstract
Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.
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Affiliation(s)
- Michiel Bontinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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107
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Stortz M, Angiolini J, Mocskos E, Wolosiuk A, Pecci A, Levi V. Mapping the dynamical organization of the cell nucleus through fluorescence correlation spectroscopy. Methods 2018; 140-141:10-22. [DOI: 10.1016/j.ymeth.2017.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/01/2017] [Accepted: 12/13/2017] [Indexed: 11/28/2022] Open
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108
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Bernhem K, Blom H, Brismar H. Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging. PLoS One 2018; 13:e0195825. [PMID: 29694368 PMCID: PMC5918999 DOI: 10.1371/journal.pone.0195825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/30/2018] [Indexed: 01/19/2023] Open
Abstract
Transient transfection of fluorescent fusion proteins is a key enabling technology in fluorescent microscopy to spatio-temporally map cellular protein distributions. Transient transfection of proteins may however bypass normal regulation of expression, leading to overexpression artefacts like misallocations and excess amounts. In this study we investigate the use of STORM and PALM microscopy to quantitatively monitor endogenous and exogenous protein expression. Through incorporation of an N-terminal hemagglutinin epitope to a mMaple3 fused Na,K-ATPase (α1 isoform), we analyze the spatial and quantitative changes of plasma membrane Na,K-ATPase localization during competitive transient expression. Quantification of plasma membrane protein density revealed a time dependent increase of Na,K-ATPase, but no increase in size of protein clusters. Results show that after 41h transfection, the total plasma membrane density of Na,K-ATPase increased by 63% while the endogenous contribution was reduced by 16%.
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Affiliation(s)
- Kristoffer Bernhem
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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109
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Masschaele D, Wauman J, Vandemoortele G, De Sutter D, De Ceuninck L, Eyckerman S, Tavernier J. High-Confidence Interactome for RNF41 Built on Multiple Orthogonal Assays. J Proteome Res 2018; 17:1348-1360. [PMID: 29560723 DOI: 10.1021/acs.jproteome.7b00704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ring finger protein 41 (RNF41) is an E3 ubiquitin ligase involved in the ubiquitination and degradation of many proteins including ErbB3 receptors, BIRC6, and parkin. Next to this, RNF41 regulates the intracellular trafficking of certain JAK2-associated cytokine receptors by ubiquitinating and suppressing USP8, which, in turn, destabilizes the ESCRT-0 complex. To further elucidate the function of RNF41 we used different orthogonal approaches to reveal the RNF41 protein complex: affinity purification-mass spectrometry, BioID, and Virotrap. We combined these results with known data sets for RNF41 obtained with microarray MAPPIT and Y2H screens. This way, we establish a comprehensive high-resolution interactome network comprising 175 candidate protein partners. To remove potential methodological artifacts from this network, we distilled the data into a high-confidence interactome map by retaining a total of 19 protein hits identified in two or more of the orthogonal methods. AP2S1, a novel RNF41 interaction partner, was selected from this high-confidence interactome for further functional validation. We reveal a role for AP2S1 in leptin and LIF receptor signaling and show that RNF41 stabilizes and relocates AP2S1.
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Affiliation(s)
- Delphine Masschaele
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Joris Wauman
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Giel Vandemoortele
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Leentje De Ceuninck
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
| | - Jan Tavernier
- Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium.,Center for Medical Biotechnology, VIB , Albert Baertsoenkaai 3 , B-9000 Ghent , Belgium
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110
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Collet B, Collins C, Lester K. Engineered cell lines for fish health research. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 80:34-40. [PMID: 28108246 DOI: 10.1016/j.dci.2017.01.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
As fish farming continues to increase worldwide, the related research areas of fish disease and immunology are also expanding, aided by the revolution in access to genomic information and molecular technology. The genomes of most fish species of economic importance are now available and annotation based on sequence homology with characterised genomes is underway. However, while useful, functional homology is more difficult to determine, there being a lack of widely distributed and well characterised reagents such as monoclonal antibodies, traditionally used in mammalian studies, to help with confirming functions and cellular interactions of fish molecules. In this context, fish cell lines and the possibility of their genetic engineering offer good prospects for studying functional genomics with respect to fish diseases. In this review, we will give an overview of available permanently genetically engineered fish cell lines, as cell-based reporter systems or platforms for expression of endogenous immune or pathogen genes, to investigate interactions and function. The advantages of such systems and the technical challenge for their development will be discussed.
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111
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Butkevich AN, Ta H, Ratz M, Stoldt S, Jakobs S, Belov VN, Hell SW. Two-Color 810 nm STED Nanoscopy of Living Cells with Endogenous SNAP-Tagged Fusion Proteins. ACS Chem Biol 2018; 13:475-480. [PMID: 28933823 DOI: 10.1021/acschembio.7b00616] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A 810 nm STED nanoscopy setup and an appropriate combination of two fluorescent dyes (Si-rhodamine 680SiR and carbopyronine 610CP) have been developed for near-IR live-cell super-resolution imaging. Vimentin endogenously tagged using the CRISPR/Cas9 approach with the SNAP tag, together with a noncovalent tubulin label, provided reliable and cell-to-cell reproducible dual-color confocal and STED imaging of the cytoskeleton in living cells.
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Affiliation(s)
- Alexey N. Butkevich
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Haisen Ta
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Ratz
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Stoldt
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Jakobs
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Department
of Neurology, University of Göttingen Medical Faculty, Robert-Koch-Str.
40, 37075 Göttingen, Germany
| | - Vladimir N. Belov
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department
of NanoBiophotonics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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112
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Shaw J, Leveridge M, Norling C, Karén J, Molina DM, O'Neill D, Dowling JE, Davey P, Cowan S, Dabrowski M, Main M, Gianni D. Determining direct binders of the Androgen Receptor using a high-throughput Cellular Thermal Shift Assay. Sci Rep 2018; 8:163. [PMID: 29317749 PMCID: PMC5760633 DOI: 10.1038/s41598-017-18650-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
Androgen Receptor (AR) is a key driver in prostate cancer. Direct targeting of AR has valuable therapeutic potential. However, the lack of disease relevant cellular methodologies capable of discriminating between inhibitors that directly bind AR and those that instead act on AR co-regulators has made identification of novel antagonists challenging. The Cellular Thermal Shift Assay (CETSA) is a technology enabling confirmation of direct target engagement with label-free, endogenous protein in living cells. We report the development of the first high-throughput CETSA assay (CETSA HT) to identify direct AR binders in a prostate cancer cell line endogenously expressing AR. Using this approach, we screened a pharmacology library containing both compounds reported to directly engage AR, and compounds expected to target AR co-regulators. Our results show that CETSA HT exclusively identifies direct AR binders, differentiating them from co-regulator inhibitors where other cellular assays measuring functional responses cannot. Using this CETSA HT approach we can derive apparent binding affinities for a range of AR antagonists, which represent an intracellular measure of antagonist-receptor Ki performed for the first time in a label-free, disease-relevant context. These results highlight the potential of CETSA HT to improve the success rates for novel therapeutic interventions directly targeting AR.
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Affiliation(s)
- Joseph Shaw
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK.
| | - Mathew Leveridge
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | | | | | | | - Daniel O'Neill
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - James E Dowling
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 35 Gatehouse Park, Waltham, MA, USA
| | - Paul Davey
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - Suzanna Cowan
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | | | - Martin Main
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK
| | - Davide Gianni
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Cambridge, UK.
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113
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Sciuto MR, Warnken U, Schnölzer M, Valvo C, Brunetto L, Boe A, Biffoni M, Krammer PH, De Maria R, Haas TL. Two-Step Coimmunoprecipitation (TIP) Enables Efficient and Highly Selective Isolation of Native Protein Complexes. Mol Cell Proteomics 2017; 17:993-1009. [PMID: 29217617 DOI: 10.1074/mcp.o116.065920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Coimmunoprecipitation (co-IP) is one of the most frequently used techniques to study protein-protein (PPIs) or protein-nucleic acid interactions (PNIs). However, the presence of coprecipitated contaminants is a well-recognized issue associated with single-step co-IPs. To overcome this limitation, we developed the two-step co-IP (TIP) strategy that enables sequential coimmunoprecipitations of endogenous protein complexes. TIP can be performed with a broad range of mono- and polyclonal antibodies targeting a single protein or different components of a given complex. TIP results in a highly selective enrichment of protein complexes and thus outperforms single-step co-IPs for downstream applications such as mass spectrometry for the identification of PPIs and quantitative PCR for the analysis of PNIs. We benchmarked TIP for the identification of CD95/FAS-interacting proteins in primary human CD4+ T cells, which recapitulated all major known interactors, but also enabled the proteomics discovery of PPM1G and IPO7 as new interaction partners. For its feasibility and high performance, we propose TIP as an advanced tool for the isolation of highly purified protein-protein and protein-nucleic acid complexes under native expression conditions.
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Affiliation(s)
- Maria Rita Sciuto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy;
| | - Uwe Warnken
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Martina Schnölzer
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cecilia Valvo
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Lidia Brunetto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Boe
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mauro Biffoni
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Peter H Krammer
- ‖Department of Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ruggero De Maria
- ¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Tobias L Haas
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; .,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
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114
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Endogenous Gαq-Coupled Neuromodulator Receptors Activate Protein Kinase A. Neuron 2017; 96:1070-1083.e5. [PMID: 29154125 DOI: 10.1016/j.neuron.2017.10.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 09/11/2017] [Accepted: 10/16/2017] [Indexed: 01/09/2023]
Abstract
Protein kinase A (PKA) integrates inputs from G-protein-coupled neuromodulator receptors to modulate synaptic and cellular function. Gαs signaling stimulates PKA activity, whereas Gαi inhibits PKA activity. Gαq, on the other hand, signals through phospholipase C, and it remains unclear whether Gαq-coupled receptors signal to PKA in their native context. Here, using two independent optical reporters of PKA activity in acute mouse hippocampus slices, we show that endogenous Gαq-coupled muscarinic acetylcholine receptors activate PKA. Mechanistically, this effect is mediated by parallel signaling via either calcium or protein kinase C. Furthermore, multiple Gαq-coupled receptors modulate phosphorylation by PKA, a classical Gαs/Gαi effector. Thus, these results highlight PKA as a biochemical integrator of three major types of GPCRs and necessitate reconsideration of classic models used to predict neuronal signaling in response to the large family of Gαq-coupled receptors.
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115
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Drubin DG, Hyman AA. Stem cells: the new "model organism". Mol Biol Cell 2017; 28:1409-1411. [PMID: 28559439 PMCID: PMC5449140 DOI: 10.1091/mbc.e17-03-0183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 01/15/2023] Open
Abstract
Human tissue culture cells have long been a staple of molecular and cell biology research. However, although these cells are derived from humans, they have often lost considerable aspects of natural physiological function. Here we argue that combined advances in genome editing, stem cell production, and organoid derivation from stem cells represent a revolution in cell biology. These advances have important ramifications for the study of basic cell biology mechanisms, as well as for the ways in which discoveries in mechanisms are translated into understanding of disease.
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Affiliation(s)
- David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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116
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Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases. Cell 2017; 171:1326-1339.e14. [PMID: 29103612 DOI: 10.1016/j.cell.2017.10.016] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/17/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022]
Abstract
SCF (Skp1-Cullin-F-box) ubiquitin ligases comprise several dozen modular enzymes that have diverse roles in biological regulation. SCF enzymes share a common catalytic core containing Cul1⋅Rbx1, which is directed toward different substrates by a variable substrate receptor (SR) module comprising 1 of 69 F-box proteins bound to Skp1. Despite the broad cellular impact of SCF enzymes, important questions remain about the architecture and regulation of the SCF repertoire, including whether SRs compete for Cul1 and, if so, how this competition is managed. Here, we devise methods that preserve the in vivo assemblages of SCF complexes and apply quantitative mass spectrometry to perform a census of these complexes (the "SCFome") in various states. We show that Nedd8 conjugation and the SR exchange factor Cand1 have a profound effect on shaping the SCFome. Together, these factors enable rapid remodeling of SCF complexes to promote biased assembly of SR modules bound to substrate.
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117
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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118
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Lolli A, Penolazzi L, Narcisi R, van Osch GJVM, Piva R. Emerging potential of gene silencing approaches targeting anti-chondrogenic factors for cell-based cartilage repair. Cell Mol Life Sci 2017; 74:3451-3465. [PMID: 28434038 PMCID: PMC11107620 DOI: 10.1007/s00018-017-2531-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/18/2022]
Abstract
The field of cartilage repair has exponentially been growing over the past decade. Here, we discuss the possibility to achieve satisfactory regeneration of articular cartilage by means of human mesenchymal stem cells (hMSCs) depleted of anti-chondrogenic factors and implanted in the site of injury. Different types of molecules including transcription factors, transcriptional co-regulators, secreted proteins, and microRNAs have recently been identified as negative modulators of chondroprogenitor differentiation and chondrocyte function. We review the current knowledge about these molecules as potential targets for gene knockdown strategies using RNA interference (RNAi) tools that allow the specific suppression of gene function. The critical issues regarding the optimization of the gene silencing approach as well as the delivery strategies are discussed. We anticipate that further development of these techniques will lead to the generation of implantable hMSCs with enhanced potential to regenerate articular cartilage damaged by injury, disease, or aging.
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Affiliation(s)
- Andrea Lolli
- Department of Orthopaedics, Erasmus MC, University Medical Center, 3015 CN, Rotterdam, The Netherlands.
| | - Letizia Penolazzi
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Roberto Narcisi
- Department of Orthopaedics, Erasmus MC, University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Gerjo J V M van Osch
- Department of Orthopaedics, Erasmus MC, University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Department of Otorhinolaryngology, Erasmus MC, University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Roberta Piva
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy.
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119
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Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. Am J Hum Genet 2017; 101:315-325. [PMID: 28886340 PMCID: PMC5590843 DOI: 10.1016/j.ajhg.2017.07.014] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic. Experimentally measuring a variant's functional consequences can provide clearer guidance, but individual assays performed only after the discovery of the variant are both time and resource intensive. Here, we discuss how multiplex assays of variant effect (MAVEs) can be used to measure the functional consequences of all possible variants in disease-relevant loci for a variety of molecular and cellular phenotypes. The resulting large-scale functional data can be combined with machine learning and clinical knowledge for the development of "lookup tables" of accurate pathogenicity predictions. A coordinated effort to produce, analyze, and disseminate large-scale functional data generated by multiplex assays could be essential to addressing the variant-interpretation crisis.
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Affiliation(s)
- Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Bioinformatics & Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA; Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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120
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Abstract
Fluorescence nanoscopy uniquely combines minimally invasive optical access to the internal nanoscale structure and dynamics of cells and tissues with molecular detection specificity. While the basic physical principles of 'super-resolution' imaging were discovered in the 1990s, with initial experimental demonstrations following in 2000, the broad application of super-resolution imaging to address cell-biological questions has only more recently emerged. Nanoscopy approaches have begun to facilitate discoveries in cell biology and to add new knowledge. One current direction for method improvement is the ambition to quantitatively account for each molecule under investigation and assess true molecular colocalization patterns via multi-colour analyses. In pursuing this goal, the labelling of individual molecules to enable their visualization has emerged as a central challenge. Extending nanoscale imaging into (sliced) tissue and whole-animal contexts is a further goal. In this Review we describe the successes to date and discuss current obstacles and possibilities for further development.
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121
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Pauwels K, Lebrun P, Tompa P. To be disordered or not to be disordered: is that still a question for proteins in the cell? Cell Mol Life Sci 2017; 74:3185-3204. [PMID: 28612216 PMCID: PMC11107661 DOI: 10.1007/s00018-017-2561-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
Abstract
There is ample evidence that many proteins or regions of proteins lack a well-defined folded structure under native-like conditions. These are called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Whether this intrinsic disorder is also their main structural characteristic in living cells has been a matter of intense debate. The structural analysis of IDPs became an important challenge also because of their involvement in a plethora of human diseases, which made IDPs attractive targets for therapeutic development. Therefore, biophysical approaches are increasingly being employed to probe the structural and dynamical state of proteins, not only in isolation in a test tube, but also in a complex biological environment and even within intact cells. Here, we survey direct and indirect evidence that structural disorder is in fact the physiological state of many proteins in the proteome. The paradigmatic case of α-synuclein is used to illustrate the controversial nature of this topic.
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Affiliation(s)
- Kris Pauwels
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Pierre Lebrun
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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122
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Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K. Protein complex analysis: From raw protein lists to protein interaction networks. MASS SPECTROMETRY REVIEWS 2017; 36:600-614. [PMID: 26709718 DOI: 10.1002/mas.21485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purification-mass spectrometry and other co-complex methods have become widely employed experimental techniques to identify protein complexes. These techniques typically suffer from a high number of false negatives and false positive contaminants due to technical shortcomings and purification biases. To support a diverse range of experimental designs and approaches, a large number of computational methods have been proposed to filter, infer and validate protein interaction networks from experimental pull-down MS data. Nevertheless, this expansion of available methods complicates the selection of the most optimal ones to support systems biology-driven knowledge extraction. In this review, we give an overview of the most commonly used computational methods to process and interpret co-complex results, and we discuss the issues and unsolved problems that still exist within the field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:600-614, 2017.
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Affiliation(s)
- Pieter Meysman
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Kevin Titeca
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Sven Eyckerman
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bart Goethals
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- IBioStat, Hasselt University, Hasselt, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
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123
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Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz R, Rafelski SM, Gunawardane RN. Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Mol Biol Cell 2017; 28:2854-2874. [PMID: 28814507 PMCID: PMC5638588 DOI: 10.1091/mbc.e17-03-0209] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
The generation of a collection of human induced pluripotent stem cell (hiPSC) lines expressing endogenously GFP-tagged proteins using CRISPR/Cas9 methods is described. The methods used and the genomic and cell biological data validating the GFP-tagged hiPSC lines are also presented. We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome-editing methodology using Cas9/crRNA ribonuclear protein and donor plasmid coelectroporation, followed by fluorescence-based enrichment of edited cells, typically resulted in <0.1–4% homology-directed repair (HDR). Twenty-five percent of clones generated from each edited population were precisely edited. Furthermore, 92% (36/39) of expanded clonal lines displayed robust morphology, genomic stability, expression and localization of the tagged protein to the appropriate subcellular structure, pluripotency-marker expression, and multilineage differentiation. It is our conclusion that, if cell lines are confirmed to harbor an appropriate gene edit, pluripotency, differentiation potential, and genomic stability are typically maintained during the clonal line–generation process. The data described here reveal general trends that emerged from this systematic gene-tagging approach. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community.
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Affiliation(s)
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109
| | - Rick Horwitz
- Allen Institute for Cell Science, Seattle, WA 98109
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124
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Stepanenko AA, Heng HH. Transient and stable vector transfection: Pitfalls, off-target effects, artifacts. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:91-103. [DOI: 10.1016/j.mrrev.2017.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/09/2017] [Accepted: 05/13/2017] [Indexed: 12/15/2022]
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125
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Abstract
The induced dimerization of two distinct receptors through a heterobifunctional inducer is prevalent among all levels of cellular signaling processes, yet its complexity poses difficulty for systematic quantitative analysis. This paper first shows how to calculate the amount of any possible complex or monomer of heteroligand and two receptors present at equilibrium. The theory is subsequently applied to the determination of three independent equilibrium parameters involved in the rapamycin induced FKBP and FRB dimerization, in which all parameters were simultaneously estimated using one set of fluorescence resonance energy transfer (FRET) experiments. A MATLAB script is provided for parametric fitting.
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Affiliation(s)
- Chang Lu
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University , Beijing 100084, P.R. China
| | - Zhi-Xin Wang
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University , Beijing 100084, P.R. China
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126
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Using nanoBRET and CRISPR/Cas9 to monitor proximity to a genome-edited protein in real-time. Sci Rep 2017; 7:3187. [PMID: 28600500 PMCID: PMC5466623 DOI: 10.1038/s41598-017-03486-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/28/2017] [Indexed: 12/15/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) has been a vital tool for understanding G protein-coupled receptor (GPCR) function. It has been used to investigate GPCR-protein and/or -ligand interactions as well as GPCR oligomerisation. However the utility of BRET is limited by the requirement that the fusion proteins, and in particular the donor, need to be exogenously expressed. To address this, we have used CRISPR/Cas9-mediated homology-directed repair to generate protein-Nanoluciferase (Nluc) fusions under endogenous promotion, thus allowing investigation of proximity between the genome-edited protein and an exogenously expressed protein by BRET. Here we report BRET monitoring of GPCR-mediated β-arrestin2 recruitment and internalisation where the donor luciferase was under endogenous promotion, in live cells and in real time. We have investigated the utility of CRISPR/Cas9 genome editing to create genome-edited fusion proteins that can be used as BRET donors and propose that this strategy can be used to overcome the need for exogenous donor expression.
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127
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Mining for Micropeptides. Trends Cell Biol 2017; 27:685-696. [PMID: 28528987 DOI: 10.1016/j.tcb.2017.04.006] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 11/23/2022]
Abstract
Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems.
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128
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Jeong DE, Lee D, Hwang SY, Lee Y, Lee JE, Seo M, Hwang W, Seo K, Hwang AB, Artan M, Son HG, Jo JH, Baek H, Oh YM, Ryu Y, Kim HJ, Ha CM, Yoo JY, Lee SJV. Mitochondrial chaperone HSP-60 regulates anti-bacterial immunity via p38 MAP kinase signaling. EMBO J 2017; 36:1046-1065. [PMID: 28283579 DOI: 10.15252/embj.201694781] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondria play key roles in cellular immunity. How mitochondria contribute to organismal immunity remains poorly understood. Here, we show that HSP-60/HSPD1, a major mitochondrial chaperone, boosts anti-bacterial immunity through the up-regulation of p38 MAP kinase signaling. We first identify 16 evolutionarily conserved mitochondrial components that affect the immunity of Caenorhabditis elegans against pathogenic Pseudomonas aeruginosa (PA14). Among them, the mitochondrial chaperone HSP-60 is necessary and sufficient to increase resistance to PA14. We show that HSP-60 in the intestine and neurons is crucial for the resistance to PA14. We then find that p38 MAP kinase signaling, an evolutionarily conserved anti-bacterial immune pathway, is down-regulated by genetic inhibition of hsp-60, and up-regulated by increased expression of hsp-60 Overexpression of HSPD1, the mammalian ortholog of hsp-60, increases p38 MAP kinase activity in human cells, suggesting an evolutionarily conserved mechanism. Further, cytosol-localized HSP-60 physically binds and stabilizes SEK-1/MAP kinase kinase 3, which in turn up-regulates p38 MAP kinase and increases immunity. Our study suggests that mitochondrial chaperones protect host eukaryotes from pathogenic bacteria by up-regulating cytosolic p38 MAPK signaling.
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Affiliation(s)
- Dae-Eun Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Dongyeop Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Sun-Young Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Yujin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Mihwa Seo
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Ara B Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Murat Artan
- Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Heehwa G Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Jay-Hyun Jo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Haeshim Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Young Min Oh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu, Korea
| | - Hyung-Jun Kim
- Research Division, Korea Brain Research Institute, Daegu, Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu, Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Seung-Jae V Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.,Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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129
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Li X, Gao M, Choi JM, Kim BJ, Zhou MT, Chen Z, Jain AN, Jung SY, Yuan J, Wang W, Wang Y, Chen J. Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling. Mol Cell Proteomics 2017; 16:594-607. [PMID: 28174230 DOI: 10.1074/mcp.m116.064543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/25/2017] [Indexed: 12/11/2022] Open
Abstract
Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors.
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Affiliation(s)
- Xu Li
- From the ‡Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Min Gao
- From the ‡Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Jong Min Choi
- ‖Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Beom-Jun Kim
- ‖Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Mao-Tian Zhou
- From the ‡Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Zhen Chen
- From the ‡Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Antrix N Jain
- ‖Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sung Yun Jung
- ‖Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Jingsong Yuan
- **Department of Radiation Oncology, Center for Radiological Research, Columbia University, New York, New York 10032
| | - Wenqi Wang
- ‡‡Department of Developmental and Cell Biology, University of California at Irvine, Irvine, California 92697
| | - Yi Wang
- ‖Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030;
| | - Junjie Chen
- From the ‡Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030;
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130
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Skogs M, Stadler C, Schutten R, Hjelmare M, Gnann C, Björk L, Poser I, Hyman A, Uhlén M, Lundberg E. Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins. J Proteome Res 2016; 16:147-155. [PMID: 27723985 DOI: 10.1021/acs.jproteome.6b00821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins, showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches. In summary, we present a systematic scheme for antibody validation in IF applications using endogenous expression of tagged proteins. This is an important step toward a reproducible approach for context- and application-specific antibody validation and improved reliability of antibody-based experiments and research data.
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Affiliation(s)
- Marie Skogs
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Charlotte Stadler
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Rutger Schutten
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Martin Hjelmare
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Christian Gnann
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Lars Björk
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Ina Poser
- Molecular Cell Biology and Genetics, Max Planck Institute , D- 01307 Dresden, Germany
| | - Anthony Hyman
- Molecular Cell Biology and Genetics, Max Planck Institute , D- 01307 Dresden, Germany
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
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131
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Uemura T, Mori T, Kurihara T, Kawase S, Koike R, Satoga M, Cao X, Li X, Yanagawa T, Sakurai T, Shindo T, Tabuchi K. Fluorescent protein tagging of endogenous protein in brain neurons using CRISPR/Cas9-mediated knock-in and in utero electroporation techniques. Sci Rep 2016; 6:35861. [PMID: 27782168 PMCID: PMC5080626 DOI: 10.1038/srep35861] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/05/2016] [Indexed: 12/23/2022] Open
Abstract
Genome editing is a powerful technique for studying gene functions. CRISPR/Cas9-mediated gene knock-in has recently been applied to various cells and organisms. Here, we successfully knocked in an EGFP coding sequence at the site immediately after the first ATG codon of the β-actin gene in neurons in the brain by the combined use of the CRISPR/Cas9 system and in utero electroporation technique, resulting in the expression of the EGFP-tagged β-actin protein in cortical layer 2/3 pyramidal neurons. We detected EGFP fluorescence signals in the soma and neurites of EGFP knock-in neurons. These signals were particularly abundant in the head of dendritic spines, corresponding to the localization of the endogenous β-actin protein. EGFP knock-in neurons showed no detectable changes in spine density and basic electrophysiological properties. In contrast, exogenously overexpressed EGFP-β-actin showed increased spine density and EPSC frequency, and changed resting membrane potential. Thus, our technique provides a potential tool to elucidate the localization of various endogenous proteins in neurons by epitope tagging without altering neuronal and synaptic functions. This technique can be also useful for introducing a specific mutation into genes to study the function of proteins and genomic elements in brain neurons.
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Affiliation(s)
- Takeshi Uemura
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano 390-8621, Japan
- CREST, JST, Saitama 332-0012, Japan
| | - Takuma Mori
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
| | - Taiga Kurihara
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
| | - Shiori Kawase
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
- CREST, JST, Saitama 332-0012, Japan
| | - Rie Koike
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
- CREST, JST, Saitama 332-0012, Japan
| | - Michiru Satoga
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
| | - Xueshan Cao
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
| | - Xue Li
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
| | - Toru Yanagawa
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Takayuki Sakurai
- Department of Cardiovascular Research, Shinshu University Graduate School of Medicine, Nagano 390-8621, Japan
| | - Takayuki Shindo
- Department of Cardiovascular Research, Shinshu University Graduate School of Medicine, Nagano 390-8621, Japan
| | - Katsuhiko Tabuchi
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano 390-8621, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano 390-8621, Japan
- PRESTO, JST, Saitama 332-0012, Japan
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132
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Eyckerman S, Impens F, Van Quickelberghe E, Samyn N, Vandemoortele G, De Sutter D, Tavernier J, Gevaert K. Intelligent Mixing of Proteomes for Elimination of False Positives in Affinity Purification-Mass Spectrometry. J Proteome Res 2016; 15:3929-3937. [PMID: 27640904 DOI: 10.1021/acs.jproteome.6b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein complexes are essential in all organizational and functional aspects of the cell. Different strategies currently exist for analyzing such protein complexes by mass spectrometry, including affinity purification (AP-MS) and proximal labeling-based strategies. However, the high sensitivity of current mass spectrometers typically results in extensive protein lists mainly consisting of nonspecifically copurified proteins. Finding the true positive interactors in these lists remains highly challenging. Here, we report a powerful design based on differential labeling with stable isotopes combined with nonequal mixing of control and experimental samples to discover bona fide interaction partners in AP-MS experiments. We apply this intelligent mixing of proteomes (iMixPro) concept to overexpression experiments for RAF1, RNF41, and TANK and also to engineered cell lines expressing epitope-tagged endogenous PTPN14, JIP3, and IQGAP1. For all baits, we confirmed known interactions and found a number of novel interactions. The results for RNF41 and TANK were compared to a classical affinity purification experiment, which demonstrated the efficiency and specificity of the iMixPro approach.
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Affiliation(s)
- Sven Eyckerman
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Francis Impens
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,VIB Proteomics Expertise Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Emmy Van Quickelberghe
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Noortje Samyn
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Giel Vandemoortele
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Delphine De Sutter
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Jan Tavernier
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
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133
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Thomson RB, Thomson CL, Aronson PS. N-glycosylation critically regulates function of oxalate transporter SLC26A6. Am J Physiol Cell Physiol 2016; 311:C866-C873. [PMID: 27681177 DOI: 10.1152/ajpcell.00171.2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/22/2016] [Indexed: 11/22/2022]
Abstract
The brush border Cl--oxalate exchanger SLC26A6 plays an essential role in mediating intestinal secretion of oxalate and is crucial for the maintenance of oxalate homeostasis and the prevention of hyperoxaluria and calcium oxalate nephrolithiasis. Previous in vitro studies have suggested that SLC26A6 is heavily N-glycosylated. N-linked glycosylation is known to critically affect folding, trafficking, and function in a wide variety of integral membrane proteins and could therefore potentially have a critical impact on SLC26A6 function and subsequent oxalate homeostasis. Through a series of enzymatic deglycosylation studies we confirmed that endogenously expressed mouse and human SLC26A6 are indeed glycosylated, that the oligosaccharides are principally attached via N-glycosidic linkage, and that there are tissue-specific differences in glycosylation. In vitro cell culture experiments were then used to elucidate the functional significance of the addition of the carbohydrate moieties. Biotinylation studies of SLC26A6 glycosylation mutants indicated that glycosylation is not essential for cell surface delivery of SLC26A6 but suggested that it may affect the efficacy with which it is trafficked and maintained in the plasma membrane. Functional studies of transfected SLC26A6 demonstrated that glycosylation at two sites in the putative second extracellular loop of SLC26A6 is critically important for chloride-dependent oxalate transport and that enzymatic deglycosylation of SLC26A6 expressed on the plasma membrane of intact cells strongly reduced oxalate transport activity. Taken together, these studies indicated that oxalate transport function of SLC26A6 is critically dependent on glycosylation and that exoglycosidase-mediated deglycosylation of SLC26A6 has the capacity to profoundly modulate SLC26A6 function.
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Affiliation(s)
- R Brent Thomson
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Claire L Thomson
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Peter S Aronson
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
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134
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Banks CAS, Boanca G, Lee ZT, Eubanks CG, Hattem GL, Peak A, Weems LE, Conkright JJ, Florens L, Washburn MP. TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. Mol Cell Proteomics 2016; 15:3435-3449. [PMID: 27609421 DOI: 10.1074/mcp.m116.060509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/06/2022] Open
Abstract
The NF-κB family of transcription factors is pivotal in controlling cellular responses to environmental stresses; abnormal nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling features in many autoimmune diseases and cancers. Several components of the NF-κB signaling pathway have been reported to interact with the protein TNIP2 (also known as ABIN2), and TNIP2 can both positively and negatively regulate NF-κB- dependent transcription of target genes. However, the function of TNIP2 remains elusive and the cellular machinery associating with TNIP2 has not been systematically defined. Here we first used a broad MudPIT/Halo Affinity Purification Mass Spectrometry (AP-MS) approach to map the network of proteins associated with the NF-κB transcription factors, and establish TNIP2 as an NF-κB network hub protein. We then combined AP-MS with biochemical approaches in a more focused study of truncated and mutated forms of TNIP2 to map protein associations with distinct regions of TNIP2. NF-κB interacted with the N-terminal region of TNIP2. A central region of TNIP2 interacted with the endosomal sorting complex ESCRT-I via its TSG101 subunit, a protein essential for HIV-1 budding, and a single point mutant in TNIP2 disrupted this interaction. The major gene ontology category for TNIP2 associated proteins was mRNA metabolism, and several of these associations, like KHDRBS1, were lost upon depletion of RNA. Given the major association of TNIP2 with mRNA metabolism proteins, we analyzed the RNA content of affinity purified TNIP2 using RNA-Seq. Surprisingly, a specific limited number of mRNAs was associated with TNIP2. These RNAs were enriched for transcription factor binding, transcription factor cofactor activity, and transcription regulator activity. They included mRNAs of genes in the Sin3A complex, the Mediator complex, JUN, HOXC6, and GATA2. Taken together, our findings suggest an expanded role for TNIP2, establishing a link between TNIP2, cellular transport machinery, and RNA transcript processing.
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Affiliation(s)
- Charles A S Banks
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Gina Boanca
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Zachary T Lee
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Cassandra G Eubanks
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Gaye L Hattem
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Allison Peak
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Lauren E Weems
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Juliana J Conkright
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Laurence Florens
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Michael P Washburn
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and .,§Departments of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
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135
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Ali MR, Ali HR, Rankin CR, El-Sayed MA. Targeting heat shock protein 70 using gold nanorods enhances cancer cell apoptosis in low dose plasmonic photothermal therapy. Biomaterials 2016; 102:1-8. [DOI: 10.1016/j.biomaterials.2016.06.017] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 01/12/2023]
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136
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Daetwyler S, Huisken J. Fast Fluorescence Microscopy with Light Sheets. THE BIOLOGICAL BULLETIN 2016; 231:14-25. [PMID: 27638692 DOI: 10.1086/689588] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In light sheet microscopy, optical sectioning by selective fluorescence excitation with a sheet of light is combined with fast full-frame acquisition. This illumination scheme provides minimal photobleaching and phototoxicity. Complemented with remote focusing and multi-view acquisition, light sheet microscopy is the method of choice for acquisition of very fast biological processes, large samples, and high-throughput applications in areas such as neuroscience, plant biology, and developmental biology. This review explains why light sheet microscopes are much faster and gentler than other established fluorescence microscopy techniques. New volumetric imaging schemes and highlights of selected biological applications are also discussed.
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Affiliation(s)
- Stephan Daetwyler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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137
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Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Dumoulin L, Wojsznis N, Gevaert K, Vandenabeele S, De Jaeger G. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. PLANT MOLECULAR BIOLOGY 2016; 91:341-354. [PMID: 27003905 DOI: 10.1007/s11103-016-0471-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lies Dumoulin
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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138
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Bouhy D, Geuens T, De Winter V, Almeida-Souza L, Katona I, Weis J, Hochepied T, Goossens S, Haigh JJ, Janssens S, Timmerman V. Characterization of New Transgenic Mouse Models for Two Charcot-Marie-Tooth-Causing HspB1 Mutations using the Rosa26 Locus. J Neuromuscul Dis 2016; 3:183-200. [DOI: 10.3233/jnd-150144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Delphine Bouhy
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Thomas Geuens
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Vicky De Winter
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Leonardo Almeida-Souza
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Istvan Katona
- Institute of Neuropathology, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Joachim Weis
- Institute of Neuropathology, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Tino Hochepied
- Transgenic Mouse Core Facility, VIB Inflammation Research Center, Ghent University, Gent, Belgium
- Department for Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Steven Goossens
- Department for Biomedical Molecular Biology, Ghent University, Gent, Belgium
- Unit for Molecular and Cellular Oncology, VIB Inflammation Research Center, Ghent University, Gent, Belgium
| | - Jody J. Haigh
- Department for Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Sophie Janssens
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
- Laboratory for Mucosal Immunology and Immunoregulation, VIB Inflammation Research Centre, Ghent University, Gent, Belgium
- Department of Internal Medicine, Ghent University, Gent, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Group, VIB Department of Molecular Genetics and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
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139
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Cairns TC, Sidhu YS, Chaudhari YK, Talbot NJ, Studholme DJ, Haynes K. Construction and high-throughput phenotypic screening ofZymoseptoria tritici over-expression strains. Fungal Genet Biol 2016; 79:110-7. [PMID: 26092797 PMCID: PMC4502453 DOI: 10.1016/j.fgb.2015.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/20/2015] [Accepted: 04/15/2015] [Indexed: 11/17/2022]
Abstract
Targeted gene deletion has been instrumental in elucidating many aspects of Zymoseptoria tritici pathogenicity. Gene over-expression is a complementary approach that is amenable to rapid strain construction and high-throughput screening, which has not been exploited to analyze Z. tritici, largely due to a lack of available techniques. Here we exploit the Gateway® cloning technology for rapid construction of over-expression vectors and improved homologous integration efficiency of a Z. tritici Δku70 strain to build a pilot over-expression library encompassing 32 genes encoding putative DNA binding proteins, GTPases or kinases. We developed a protocol using a Rotor-HDA robot for rapid and reproducible cell pinning for high-throughput in vitro screening. This screen identified an over-expression strain that demonstrated a marked reduction in hyphal production relative to the isogenic progenitor. This study provides a protocol for rapid generation of Z. tritici over-expression libraries and a technique for functional genomic screening in this important pathogen.
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Affiliation(s)
- T C Cairns
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Y S Sidhu
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Y K Chaudhari
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - N J Talbot
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - D J Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - K Haynes
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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140
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Abstract
Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC)
- Brussels
- Belgium
- Vrije Universiteit Brussel
- Brussels
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141
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Stains JP, Civitelli R. A Functional Assay to Assess Connexin 43-Mediated Cell-to-Cell Communication of Second Messengers in Cultured Bone Cells. Methods Mol Biol 2016; 1437:193-201. [PMID: 27207296 PMCID: PMC4959905 DOI: 10.1007/978-1-4939-3664-9_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cell-to-cell transfer of small molecules is a fundamental way by which multicellular organisms coordinate function. Recent work has highlighted the complexity of biologic responses downstream of gap junctions. As the connexin-regulated effectors are coming into focus, there is a need to develop functional assays that allow specific testing of biologically relevant second messengers. Here, we describe a modification of the classic gap junction parachute assay to assess biologically relevant molecules passed through gap junctions.
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Affiliation(s)
- Joseph P. Stains
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roberto Civitelli
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University, St Louis, MO, USA
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142
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Vandemoortele G, Gevaert K, Eyckerman S. Proteomics in the genome engineering era. Proteomics 2015; 16:177-87. [DOI: 10.1002/pmic.201500262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Giel Vandemoortele
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
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143
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Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal 2015; 13:42. [PMID: 26581338 PMCID: PMC4652402 DOI: 10.1186/s12964-015-0121-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 12/17/2022] Open
Abstract
It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the “tip of the iceberg” has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany. .,Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
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144
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SW480 colorectal cancer cells that naturally express Lgr5 are more sensitive to the most common chemotherapeutic agents than Lgr5-negative SW480 cells. Anticancer Drugs 2015. [PMID: 26196680 DOI: 10.1097/cad.0000000000000270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Leucine-rich repeat containing G protein-coupled receptor 5 (Lgr5) is a colorectal cancer (CRC) stem cell marker. The role of Lgr5-expressing stem cells in resistance to chemotherapy is controversial. The notion that Lgr5-expressing cells are more chemotherapy resistant is supported by some data; other data do not support this notion. We hypothesized that Lgr5-expressing cells would be more chemotherapy sensitive, as Lgr5 is usually a marker of dividing cells. We tested this hypothesis by exploiting two natural variants of SW480 CRC cells: the less-differentiated Lgr5-expressing floating fraction and the more-differentiated Lgr5-depleted attached fraction. We estimated chemotherapy sensitivity using an XTT Cell Proliferation Assay Kit. We confirmed that the detected chemotherapy sensitivity differences were Lgr5-driven by overexpressing Lgr5. SW480 CRC cells that naturally express Lgr5 are those that are floating, and they are more sensitive to the chemotherapeutic compounds irinotecan (maximum difference approximately two times, 0.0001<P<0.0052) and oxaliplatin (maximum difference ∼1.5 times, 0.0001<P<0.0024) than Lgr5-negative (attached) SW480 cells. At IC50, the difference in sensitivity between these two fractions of SW480 cells to the drugs was twice as prominent with irinotecan as with oxaliplatin (P<0.0001). SW480 cells that naturally express Lgr5 were slightly more sensitive to 5-fluorouracil than non-Lgr5-expressing cells (0.0002<P<0.0344). Transfected Lgr5-overexpressing attached cells showed similar results with irinotecan and oxaliplatin, confirming that the detected differences in sensitivity to these drugs were Lgr5 driven. Most likely, Lgr5 makes cells vulnerable to chemotherapy, increasing their propensity to divide through activation of the Wnt/β-catenin pathway. There is one exception, Lgr5-overexpressing cells did not show this increase in sensitivity to 5-fluorouracil. Remarkably, Lgr5 reduced the number of floating cells two-fold (instead of increasing it, as one would expect from a stemness-determining factor) and slightly increased the number of attached differentiated cells at a significantly high transfection efficiency for these SW480 cells (∼30%). These results suggest that Lgr5, although purported to be a cancer stem cell marker, is not sufficient to promote floating in these colon cancer cells. In conclusion, CRC cells that naturally express Lgr5 are more sensitive to the most commonly used CRC chemotherapeutic compounds than those that are naturally Lgr5 negative.
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145
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Zheng M, Mitra RN, Filonov NA, Han Z. Nanoparticle-mediated rhodopsin cDNA but not intron-containing DNA delivery causes transgene silencing in a rhodopsin knockout model. FASEB J 2015; 30:1076-86. [PMID: 26564956 DOI: 10.1096/fj.15-280511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022]
Abstract
Previously, we compared the efficacy of nanoparticle (NP)-mediated intron-containing rhodopsin (sgRho) vs. intronless cDNA in ameliorating retinal disease phenotypes in a rhodopsin knockout (RKO) mouse model of retinitis pigmentosa. We showed that NP-mediated sgRho delivery achieved long-term expression and phenotypic improvement in RKO mice, but not NP housing cDNA. However, the protein level of the NP-sgRho construct was only 5-10% of wild-type at 8 mo postinjection. To have a better understanding of the reduced levels of long-term expression of the vectors, in the present study, we evaluated the epigenetic changes of subretinal delivering NP-cDNA vs. NP-sgRho in the RKO mouse eyes. Following the administration, DNA methylation and histone status of specific regions (bacteria plasmid backbone, promoter, rhodopsin gene, and scaffold/matrix attachment region) of the vectors were evaluated at various time points. We documented that epigenetic transgene silencing occurred in vector-mediated gene transfer, which were caused by the plasmid backbone and the cDNA of the transgene, but not the intron-containing transgene. No toxicity or inflammation was found in the treated eyes. Our results suggest that cDNA of the rhodopsin transgene and bacteria backbone interfered with the host defense mechanism of DNA methylation-mediated transgene silencing through heterochromatin-associated modifications.
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Affiliation(s)
- Min Zheng
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Rajendra N Mitra
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Nazar A Filonov
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Zongchao Han
- *Department of Ophthalmology and Carolina Institute for NanoMedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Molecular Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
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146
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Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 2015; 163:712-23. [PMID: 26496610 DOI: 10.1016/j.cell.2015.09.053] [Citation(s) in RCA: 902] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023]
Abstract
The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis.
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Affiliation(s)
- Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nina C Hubner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Ina Weisswange
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Eupheria Biotech GmbH, 01307 Dresden, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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147
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Hasse S, Hyman AA, Sarov M. TransgeneOmics--A transgenic platform for protein localization based function exploration. Methods 2015; 96:69-74. [PMID: 26475212 DOI: 10.1016/j.ymeth.2015.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 12/17/2022] Open
Abstract
The localization of a protein is intrinsically linked to its role in the structural and functional organization of the cell. Advances in transgenic technology have streamlined the use of protein localization as a function discovery tool. Here we review the use of large genomic DNA constructs such as bacterial artificial chromosomes as a transgenic platform for systematic tag-based protein function exploration.
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Affiliation(s)
- Susanne Hasse
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
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148
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Cooper DE, Young PA, Klett EL, Coleman RA. Physiological Consequences of Compartmentalized Acyl-CoA Metabolism. J Biol Chem 2015; 290:20023-31. [PMID: 26124277 DOI: 10.1074/jbc.r115.663260] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Meeting the complex physiological demands of mammalian life requires strict control of the metabolism of long-chain fatty acyl-CoAs because of the multiplicity of their cellular functions. Acyl-CoAs are substrates for energy production; stored within lipid droplets as triacylglycerol, cholesterol esters, and retinol esters; esterified to form membrane phospholipids; or used to activate transcriptional and signaling pathways. Indirect evidence suggests that acyl-CoAs do not wander freely within cells, but instead, are channeled into specific pathways. In this review, we will discuss the evidence for acyl-CoA compartmentalization, highlight the key modes of acyl-CoA regulation, and diagram potential mechanisms for controlling acyl-CoA partitioning.
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Affiliation(s)
| | | | - Eric L Klett
- From the Departments of Nutrition and Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
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149
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Wong A, Gehring C, Irving HR. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites. Front Bioeng Biotechnol 2015; 3:82. [PMID: 26106597 PMCID: PMC4460814 DOI: 10.3389/fbioe.2015.00082] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022] Open
Abstract
Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.
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Affiliation(s)
- Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University , Melbourne, VIC , Australia
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150
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Burkart GM, Baskin TI, Bezanilla M. A family of ROP proteins that suppresses actin dynamics, and is essential for polarized growth and cell adhesion. J Cell Sci 2015; 128:2553-64. [PMID: 26045445 DOI: 10.1242/jcs.172445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 05/31/2015] [Indexed: 01/22/2023] Open
Abstract
In plants, the ROP family of small GTPases has been implicated in the polarized growth of tip-growing cells, such as root hairs and pollen tubes; however, most of the data derive from overexpressing ROP genes or constitutively active and dominant-negative isoforms, whereas confirmation by using loss-of-function studies has generally been lacking. Here, in the model moss Physcomitrella patens, we study ROP signaling during tip growth by using a loss-of-function approach based on RNA interference (RNAi) to silence the entire moss ROP family. We find that plants with reduced expression of ROP genes, in addition to failing to initiate tip growth, have perturbed cell wall staining, reduced cell adhesion and have increased actin-filament dynamics. Although plants subjected to RNAi against the ROP family also have reduced microtubule dynamics, this reduction is not specific to loss of ROP genes, as it occurs when actin function is compromised chemically or genetically. Our data suggest that ROP proteins polarize the actin cytoskeleton by suppressing actin-filament dynamics, leading to an increase in actin filaments at the site of polarized secretion.
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Affiliation(s)
- Graham M Burkart
- Department of Biology, University of Massachusetts-Amherst, 611 N. Pleasant Street, Amherst, MA 01003, USA Plant Biology Graduate Program, University of Massachusetts-Amherst, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Tobias I Baskin
- Department of Biology, University of Massachusetts-Amherst, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Magdalena Bezanilla
- Department of Biology, University of Massachusetts-Amherst, 611 N. Pleasant Street, Amherst, MA 01003, USA
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