51
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Secker C, Kostova S, Niederlechner H, Beetz S, Wendland I, Liebich MJ, Polzer O, Groh M, Schnoegl S, Trepte P, Wanker EE. CellFIE: CRISPR- and Cell Fusion-based Two-hybrid Interaction Mapping of Endogenous Proteins. J Mol Biol 2021; 433:167305. [PMID: 34655654 DOI: 10.1016/j.jmb.2021.167305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/01/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
Numerous genetic methods facilitate the detection of binary protein-protein interactions (PPIs) by exogenous overexpression, which can lead to false results. Here, we describe CellFIE, a CRISPR- and cell fusion-based PPI detection method, which enables the mapping of interactions between endogenously tagged two-hybrid proteins. We demonstrate the specificity and reproducibility of CellFIE in a matrix mapping approach, validating the interactions of VCP with ASPL and UBXD1, and the self-interaction of TDP-43 under endogenous conditions. Furthermore, we show that CellFIE can be used to quantify changes of endogenous PPIs upon stress induction or drug treatment. For the first time, CellFIE facilitates systematic mapping of interactions between endogenously tagged proteins and represents a novel tool to characterize PPIs in live cells under dynamic conditions.
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Affiliation(s)
- Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany. https://twitter.com/Chris_Secker
| | - Simona Kostova
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Hannah Niederlechner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Stephanie Beetz
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ina Wendland
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Mara J Liebich
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Oliver Polzer
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Mirjam Groh
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Philipp Trepte
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
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52
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Dolgalev G, Poverennaya E. Applications of CRISPR-Cas Technologies to Proteomics. Genes (Basel) 2021; 12:1790. [PMID: 34828396 PMCID: PMC8625504 DOI: 10.3390/genes12111790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics.
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53
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Levic DS, Yamaguchi N, Wang S, Knaut H, Bagnat M. Knock-in tagging in zebrafish facilitated by insertion into non-coding regions. Development 2021; 148:dev199994. [PMID: 34495314 PMCID: PMC8513609 DOI: 10.1242/dev.199994] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022]
Abstract
Zebrafish provide an excellent model for in vivo cell biology studies because of their amenability to live imaging. Protein visualization in zebrafish has traditionally relied on overexpression of fluorescently tagged proteins from heterologous promoters, making it difficult to recapitulate endogenous expression patterns and protein function. One way to circumvent this problem is to tag the proteins by modifying their endogenous genomic loci. Such an approach is not widely available to zebrafish researchers because of inefficient homologous recombination and the error-prone nature of targeted integration in zebrafish. Here, we report a simple approach for tagging proteins in zebrafish on their N or C termini with fluorescent proteins by inserting PCR-generated donor amplicons into non-coding regions of the corresponding genes. Using this approach, we generated endogenously tagged alleles for several genes that are crucial for epithelial biology and organ development, including the tight junction components ZO-1 and Cldn15la, the trafficking effector Rab11a, the apical polarity protein aPKC and the ECM receptor Integrin β1b. Our approach facilitates the generation of knock-in lines in zebrafish, opening the way for accurate quantitative imaging studies.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Siyao Wang
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
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54
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Baas FS, Rishi G, Swinkels DW, Subramaniam VN. Genetic Diagnosis in Hereditary Hemochromatosis: Discovering and Understanding the Biological Relevance of Variants. Clin Chem 2021; 67:1324-1341. [PMID: 34402502 DOI: 10.1093/clinchem/hvab130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Hereditary hemochromatosis (HH) is a genetic disease, leading to iron accumulation and possible organ damage. Patients are usually homozygous for p. Cys282Tyr in the homeostatic iron regulator gene but may have mutations in other genes involved in the regulation of iron. Next-generation sequencing is increasingly being utilized for the diagnosis of patients, leading to the discovery of novel genetic variants. The clinical significance of these variants is often unknown. CONTENT Determining the pathogenicity of such variants of unknown significance is important for diagnostics and genetic counseling. Predictions can be made using in silico computational tools and population data, but additional evidence is required for a conclusive pathogenicity classification. Genetic disease models, such as in vitro models using cellular overexpression, induced pluripotent stem cells or organoids, and in vivo models using mice or zebrafish all have their own challenges and opportunities when used to model HH and other iron disorders. Recent developments in gene-editing technologies are transforming the field of genetic disease modeling. SUMMARY In summary, this review addresses methods and developments regarding the discovery and classification of genetic variants, from in silico tools to in vitro and in vivo models, and presents them in the context of HH. It also explores recent gene-editing developments and how they can be applied to the discussed models of genetic disease.
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Affiliation(s)
- Floor S Baas
- Translational Metabolic Laboratory (TML 831), Radboudumc, Nijmegen, the Netherlands.,Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Gautam Rishi
- Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Dorine W Swinkels
- Translational Metabolic Laboratory (TML 831), Radboudumc, Nijmegen, the Netherlands
| | - V Nathan Subramaniam
- Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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55
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Kotarba G, Taracha-Wisniewska A, Miller M, Dabrowski M, Wilanowski T. Transcription factors Krüppel-like factor 4 and paired box 5 regulate the expression of the Grainyhead-like genes. PLoS One 2021; 16:e0257977. [PMID: 34570823 PMCID: PMC8476022 DOI: 10.1371/journal.pone.0257977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Genes from the Grainyhead-like (GRHL) family code for transcription factors necessary for the development and maintenance of various epithelia. These genes are also very important in the development of many types of cancer. However, little is known about the regulation of expression of GRHL genes. Previously, there were no systematic analyses of the promoters of GRHL genes or transcription factors that bind to these promoters. Here we report that the Krüppel-like factor 4 (KLF4) and the paired box 5 factor (PAX5) bind to the regulatory regions of the GRHL genes and regulate their expression. Ectopic expression of KLF4 or PAX5 alters the expression of GRHL genes. In KLF4-overexpressing HEK293 cells, the expression of GRHL1 and GRHL3 genes was upregulated by 32% and 60%, respectively, whereas the mRNA level of GRHL2 gene was lowered by 28% when compared to the respective controls. The levels of GRHL1 and GRHL3 expression were decreased by 30% or 33% in PAX5-overexpressing HEK293 cells. The presence of minor frequency allele of single nucleotide polymorphism rs115898376 in the promoter of the GRHL1 gene affected the binding of KLF4 to this site. The evidence presented here suggests an important role of KLF4 and PAX5 in the regulation of expression of GRHL1-3 genes.
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Affiliation(s)
- Grzegorz Kotarba
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | | | - Michal Miller
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Wilanowski
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
- * E-mail:
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56
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Galloy M, Lachance C, Cheng X, Distéfano-Gagné F, Côté J, Fradet-Turcotte A. Approaches to Study Native Chromatin-Modifying Complex Activities and Functions. Front Cell Dev Biol 2021; 9:729338. [PMID: 34604228 PMCID: PMC8481805 DOI: 10.3389/fcell.2021.729338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
The modification of histones-the structural components of chromatin-is a central topic in research efforts to understand the mechanisms regulating genome expression and stability. These modifications frequently occur through associations with multisubunit complexes, which contain active enzymes and additional components that orient their specificity and read the histone modifications that comprise epigenetic signatures. To understand the functions of these modifications it is critical to study the enzymes and substrates involved in their native contexts. Here, we describe experimental approaches to purify native chromatin modifiers complexes from mammalian cells and to produce recombinant nucleosomes that are used as substrates to determine the activity of the complex. In addition, we present a novel approach, similar to the yeast anchor-away system, to study the functions of essential chromatin modifiers by quickly inducing their depletion from the nucleus. The step-by-step protocols included will help standardize these approaches in the research community, enabling convincing conclusions about the specificities and functions of these crucial regulators of the eukaryotic genome.
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Affiliation(s)
- Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Félix Distéfano-Gagné
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Amelie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
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57
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Manoilov KY, Verkhusha VV, Shcherbakova DM. A guide to the optogenetic regulation of endogenous molecules. Nat Methods 2021; 18:1027-1037. [PMID: 34446923 DOI: 10.1038/s41592-021-01240-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/09/2021] [Indexed: 12/26/2022]
Abstract
Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs.
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Affiliation(s)
- Kyrylo Yu Manoilov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Science Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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58
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de Man SMA, Zwanenburg G, van der Wal T, Hink MA, van Amerongen R. Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics. eLife 2021; 10:e66440. [PMID: 34190040 PMCID: PMC8341982 DOI: 10.7554/elife.66440] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
WNT/CTNNB1 signaling regulates tissue development and homeostasis in all multicellular animals, but the underlying molecular mechanism remains incompletely understood. Specifically, quantitative insight into endogenous protein behavior is missing. Here, we combine CRISPR/Cas9-mediated genome editing and quantitative live-cell microscopy to measure the dynamics, diffusion characteristics and absolute concentrations of fluorescently tagged, endogenous CTNNB1 in human cells under both physiological and oncogenic conditions. State-of-the-art imaging reveals that a substantial fraction of CTNNB1 resides in slow-diffusing cytoplasmic complexes, irrespective of the activation status of the pathway. This cytoplasmic CTNNB1 complex undergoes a major reduction in size when WNT/CTNNB1 is (hyper)activated. Based on our biophysical measurements, we build a computational model of WNT/CTNNB1 signaling. Our integrated experimental and computational approach reveals that WNT pathway activation regulates the dynamic distribution of free and complexed CTNNB1 across different subcellular compartments through three regulatory nodes: the destruction complex, nucleocytoplasmic shuttling, and nuclear retention.
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Affiliation(s)
- Saskia MA de Man
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Gooitzen Zwanenburg
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Tanne van der Wal
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Mark A Hink
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
- van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
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59
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Rodrigues EC, Grawenhoff J, Baumann SJ, Lorenzon N, Maurer SP. Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns. Front Integr Neurosci 2021; 15:692948. [PMID: 34211375 PMCID: PMC8239176 DOI: 10.3389/fnint.2021.692948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized functions. According to current evidence, mRNAs are mostly transported in rather small packages of one to three copies, rarely containing different transcripts. This opens up fascinating logistic problems: how are hundreds of different mRNA cargoes sorted into distinct packages and how are they coupled to and released from motor proteins to produce the observed mRNA distributions? Are all mRNAs transported by the same transport machinery, or are there different adaptors or motors for different transcripts or classes of mRNAs? A variety of often indirect evidence exists for the involvement of proteins in mRNA localization, but relatively little is known about the essential activities required for the actual transport process. Here, we summarize the different types of available evidence for interactions that connect mammalian mRNAs to motor proteins to highlight at which point further research is needed to uncover critical missing links. We further argue that a combination of discovery approaches reporting direct interactions, in vitro reconstitution, and fast perturbations in cells is an ideal future strategy to unravel essential interactions and specific functions of proteins in mRNA transport processes.
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Affiliation(s)
- Elsa C. Rodrigues
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Julia Grawenhoff
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian J. Baumann
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Nicola Lorenzon
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian P. Maurer
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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60
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Cell-type-specific, multicolor labeling of endogenous proteins with split fluorescent protein tags in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2024690118. [PMID: 34074768 DOI: 10.1073/pnas.2024690118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The impact of the Drosophila experimental system on studies of modern biology cannot be understated. The ability to tag endogenously expressed proteins is essential to maximize the use of this model organism. Here, we describe a method for labeling endogenous proteins with self-complementing split fluorescent proteins (split FPs) in a cell-type-specific manner in Drosophila A short fragment of an FP coding sequence is inserted into a specific genomic locus while the remainder of the FP is expressed using an available GAL4 driver line. In consequence, complementation fluorescence allows examination of protein localization in particular cells. Besides, when inserting tandem repeats of the short FP fragment at the same genomic locus, we can substantially enhance the fluorescence signal. The enhanced signal is of great value in live-cell imaging at the subcellular level. We can also accomplish a multicolor labeling system with orthogonal split FPs. However, other orthogonal split FPs do not function for in vivo imaging besides split GFP. Through protein engineering and in vivo functional studies, we report a red split FP that we can use for duplexed visualization of endogenous proteins in intricate Drosophila tissues. Using the two orthogonal split FP systems, we have simultaneously imaged proteins that reside in distinct subsynaptic compartments. Our approach allows us to study the proximity between and localization of multiple proteins endogenously expressed in essentially any cell type in Drosophila.
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61
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Mogensen DJ, Westberg M, Breitenbach T, Etzerodt M, Ogilby PR. Stable Transfection of the Singlet Oxygen Photosensitizing Protein SOPP3: Examining Aspects of Intracellular Behavior †. Photochem Photobiol 2021; 97:1417-1430. [PMID: 33934354 DOI: 10.1111/php.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 01/28/2023]
Abstract
Protein-encased chromophores that photosensitize the production of reactive oxygen species, ROS, have been the center of recent activity in studies of oxidative stress. One potential attribute of such systems is that the local environment surrounding the chromophore, and that determines the chromophore's photophysics, ideally remains constant and independent of the global environment into which the system is placed. Therefore, a protein-encased sensitizer localized in the mitochondria would arguably have the same photophysics as that protein-encased sensitizer at the plasma membrane, for example. One thus obtains a useful tool to study processes modulated by spatially localized ROS. One ROS of interest is singlet oxygen, O2 (a1 Δg ). We recently developed a singlet oxygen photosensitizing protein, SOPP, in which flavin mononucleotide, FMN, is encased in a re-engineered light-oxygen-voltage protein. One goal was to ascertain how a version of this system, SOPP3, which selectively makes O2 (a1 Δg ), in vitro, behaves in a cell. We now demonstrate that SOPP3 undergoes exacerbated irradiation-mediated bleaching when expressed at either the plasma membrane or mitochondria in stable cell lines. We find that the environment around the SOPP3 system affects the bleaching rate, which argues against one of the key suppositions in support of a protein-encased chromophore.
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Affiliation(s)
| | | | | | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University, Aarhus, Denmark
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62
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Khayat MM, Li H, Chander V, Hu J, Hansen AW, Li S, Traynelis J, Shen H, Weissenberger G, Stossi F, Johnson HL, Lupski JR, Posey JE, Sabo A, Meng Q, Murdock DR, Wangler M, Gibbs RA. Phenotypic and protein localization heterogeneity associated with AHDC1 pathogenic protein-truncating alleles in Xia-Gibbs syndrome. Hum Mutat 2021; 42:577-591. [PMID: 33644933 PMCID: PMC8115934 DOI: 10.1002/humu.24190] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/01/2021] [Accepted: 02/14/2021] [Indexed: 12/12/2022]
Abstract
Xia-Gibbs syndrome (XGS) is a rare Mendelian disease typically caused by de novo stop-gain or frameshift mutations in the AT-hook DNA binding motif containing 1 (AHDC1) gene. Patients usually present in early infancy with hypotonia and developmental delay and later exhibit intellectual disability (ID). The overall presentation is variable, however, and the emerging clinical picture is still evolving. A detailed phenotypic analysis of 34 XGS individuals revealed five core phenotypes (delayed motor milestones, speech delay, low muscle tone, ID, and hypotonia) in more than 80% of individuals and an additional 12 features that occurred more variably. Seizures and scoliosis were more frequently associated with truncations that arise before the midpoint of the protein although the occurrence of most features could not be predicted by the mutation position. Transient expression of wild type and different patient truncated AHDC1 protein forms in human cell lines revealed abnormal patterns of nuclear localization including a diffuse distribution of a short truncated form and nucleolar aggregation in mid-protein truncated forms. Overall, both the occurrence of variable phenotypes and the different distribution of the expressed protein reflect the heterogeneity of this syndrome.
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Affiliation(s)
- Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - Adam W. Hansen
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - Josh Traynelis
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | | | - Fabio Stossi
- Integrated Microscopy Core, Advanced Technology Cores, Dan
L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas,
USA
- Department of Molecular and Cellular Biology, Baylor
College of Medicine, Houston, Texas, USA
| | - Hannah L. Johnson
- Integrated Microscopy Core, Advanced Technology Cores, Dan
L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas,
USA
| | - James R. Lupski
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine,
Houston, Texas, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
| | - David R. Murdock
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, Texas, USA
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63
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Simna SP, Han Z. Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy. Curr Gene Ther 2021; 22:89-103. [PMID: 33874871 DOI: 10.2174/1566523221666210419090357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/22/2022]
Abstract
Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.
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Affiliation(s)
- S P Simna
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
| | - Zongchao Han
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
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64
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Live-cell monitoring of protein localization to membrane rafts using protein-fragment complementation. Biosci Rep 2021; 40:221616. [PMID: 31850494 PMCID: PMC6944658 DOI: 10.1042/bsr20191290] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
The plasma membrane consists of a variety of discrete domains differing from the surrounding membrane in composition and properties. Selective partitioning of protein to these microdomains is essential for membrane functioning and integrity. Studying the nanoscale size and dynamic nature of the membrane microdomains requires advanced imaging approaches with a high spatiotemporal resolution and, consequently, expensive and specialized equipment, unavailable for most researchers and unsuited for large-scale studies. Thus, understanding of protein partitioning to the membrane microdomains in health and disease is still hampered by the lack of inexpensive live-cell approaches with an appropriate spatial resolution. Here, we have developed a novel approach based on Gaussia princeps luciferase protein-fragment complementation assay to quantitively investigate protein partitioning to cholesterol and sphingomyelin-rich domains, sometimes called ‘lipid rafts’, in intact living cells with a high-spatial resolution. In the assay, the reporter construct, carrying one half of the luciferase protein, is targeted to lipid microdomains through the fused acetylation motif from Src-family kinase Fyn. A protein of interest carries the second half of the luciferase protein. Together, this serves as a reversible real-time sensor of raft recruitment for the studied protein. We demonstrated that the assay can efficiently detect the dynamic alterations in raft localization of two disease-associated proteins: Akt and APP. Importantly, this method can be used in high-throughput screenings and other large-scale studies in living cells. This inexpensive, and easy to implement raft localization assay will benefit all researchers interested in protein partitioning in rafts.
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65
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Witting KF, Mulder MP. Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 2021; 11:biom11020255. [PMID: 33578803 PMCID: PMC7916544 DOI: 10.3390/biom11020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.
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66
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Westrich LD, Gotsmann VL, Herkt C, Ries F, Kazek T, Trösch R, Armbruster L, Mühlenbeck JS, Ramundo S, Nickelsen J, Finkemeier I, Wirtz M, Storchová Z, Räschle M, Willmund F. The versatile interactome of chloroplast ribosomes revealed by affinity purification mass spectrometry. Nucleic Acids Res 2021; 49:400-415. [PMID: 33330923 PMCID: PMC7797057 DOI: 10.1093/nar/gkaa1192] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
In plant cells, chloroplast gene expression is predominantly controlled through post-transcriptional regulation. Such fine-tuning is vital for precisely orchestrating protein complex assembly as for the photosynthesis machinery and for quickly responding to environmental changes. While regulation of chloroplast protein synthesis is of central importance, little is known about the degree and nature of the regulatory network, mainly due to challenges associated with the specific isolation of transient ribosome interactors. Here, we established a ribosome affinity purification method, which enabled us to broadly uncover putative ribosome-associated proteins in chloroplasts. Endogenously tagging of a protein of the large or small subunit revealed not only interactors of the holo complex, but also preferential interactors of the two subunits. This includes known canonical regulatory proteins as well as several new proteins belonging to the categories of protein and RNA regulation, photosystem biogenesis, redox control and metabolism. The sensitivity of the here applied screen was validated for various transiently interacting proteins. We further provided evidence for the existence of a ribosome-associated Nα-acetyltransferase in chloroplasts and its ability to acetylate substrate proteins at their N-terminus. The broad set of ribosome interactors underscores the potential to regulate chloroplast gene expression on the level of protein synthesis.
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Affiliation(s)
- Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Tanja Kazek
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Jens Stephan Mühlenbeck
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, 600 16th St, N316, San Francisco, CA 94143, USA
| | - Jörg Nickelsen
- Department of Molecular Plant Science, University of Munich, Grosshaderner-Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
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67
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Castro-Sánchez P, Hernández-Pérez S, Aguilar-Sopeña O, Ramírez-Muñoz R, Rodríguez-Perales S, Torres-Ruiz R, Roda-Navarro P. Fast Diffusion Sustains Plasma Membrane Accumulation of Phosphatase of Regenerating Liver-1. Front Cell Dev Biol 2021; 8:585842. [PMID: 33425892 PMCID: PMC7793866 DOI: 10.3389/fcell.2020.585842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that the accumulation of farnesylated phosphatase of regenerating liver-1 (PRL-1) at the plasma membrane is mediated by static electrostatic interactions of a polybasic region with acidic membrane lipids and assisted by oligomerization. Nonetheless, localization at early and recycling endosomes suggests that the recycling compartment might also contribute to its plasma membrane accumulation. Here, we investigated in live cells the dynamics of PRL-1 fused to the green fluorescent protein (GFP-PRL-1). Blocking the secretory pathway and photobleaching techniques suggested that plasma membrane accumulation of PRL-1 was not sustained by recycling endosomes but by a dynamic exchange of diffusible protein pools. Consistent with this idea, fluorescence correlation spectroscopy in cells overexpressing wild type or monomeric mutants of GFP-PRL-1 measured cytosolic and membrane-diffusing pools of protein that were not dependent on oligomerization. Endogenous expression of GFP-PRL-1 by CRISPR/Cas9 genome edition confirmed the existence of fast diffusing cytosolic and membrane pools of protein. We propose that plasma membrane PRL-1 replenishment is independent of the recycling compartment and the oligomerization state and mainly driven by fast diffusion of the cytosolic pool.
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Affiliation(s)
- Patricia Castro-Sánchez
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Sara Hernández-Pérez
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Oscar Aguilar-Sopeña
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Rocia Ramírez-Muñoz
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Pedro Roda-Navarro
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
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68
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Baldering TN, Karathanasis C, Harwardt MLIE, Freund P, Meurer M, Rahm JV, Knop M, Dietz MS, Heilemann M. CRISPR/Cas12a-mediated labeling of MET receptor enables quantitative single-molecule imaging of endogenous protein organization and dynamics. iScience 2020; 24:101895. [PMID: 33364584 PMCID: PMC7753144 DOI: 10.1016/j.isci.2020.101895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/12/2020] [Accepted: 12/02/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) reports on protein organization in cells with near-molecular resolution and in combination with stoichiometric labeling enables protein counting. Fluorescent proteins allow stoichiometric labeling of cellular proteins; however, most methods either lead to overexpression or are complex and time demanding. We introduce CRISPR/Cas12a for simple and efficient tagging of endogenous proteins with a photoactivatable protein for quantitative SMLM and single-particle tracking. We constructed a HEK293T cell line with the receptor tyrosine kinase MET tagged with mEos4b and demonstrate full functionality. We determine the oligomeric state of MET with quantitative SMLM and find a reorganization from monomeric to dimeric MET upon ligand stimulation. In addition, we measured the mobility of single MET receptors in vivo in resting and ligand-treated cells. The combination of CRISPR/Cas12a-assisted endogenous protein labeling and super-resolution microscopy represents a powerful tool for cell biological research with molecular resolution. CRISPR/Cas12a enables endogenous protein labeling for super-resolution microscopy HEK293T cells were generated with MET endogenously labeled with mEos4b Quantitative PALM microscopy reports efficient dimerization of MET receptor Single-particle tracking shows increased MET immobilization upon ligand treatment
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Affiliation(s)
- Tim N Baldering
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Christos Karathanasis
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Marie-Lena I E Harwardt
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Petra Freund
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Johanna V Rahm
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
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69
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Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies. Proc Natl Acad Sci U S A 2020; 117:30476-30487. [PMID: 33214152 DOI: 10.1073/pnas.2007443117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR (Nb80) is highly immobile and organized in nanoclusters. The Gαs-GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR (Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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70
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Gaertner A, Klauke B, Felski E, Kassner A, Brodehl A, Gerdes D, Stanasiuk C, Ebbinghaus H, Schulz U, Dubowy KO, Tiesmeier J, Laser KT, Bante H, Bergau L, Sommer P, Fox H, Morshuis M, Gummert J, Milting H. Cardiomyopathy-associated mutations in the RS domain affect nuclear localization of RBM20. Hum Mutat 2020; 41:1931-1943. [PMID: 32840935 DOI: 10.1002/humu.24096] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/30/2022]
Abstract
Mutations in RBM20 encoding the RNA-binding motif protein 20 (RBM20) are associated with an early onset and clinically severe forms of cardiomyopathies. Transcriptome analyses revealed RBM20 as an important regulator of cardiac alternative splicing. RBM20 mutations are especially localized in exons 9 and 11 including the highly conserved arginine and serine-rich domain (RS domain). Here, we investigated in several cardiomyopathy patients, the previously described RBM20-mutation p.Pro638Leu localized within the RS domain. In addition, we identified in a patient the novel mutation p.Val914Ala localized in the (glutamate-rich) Glu-rich domain of RBM20 encoded by exon 11. Its impact on the disease was investigated with a novel TTN- and RYR2-splicing assay based on the patients' cardiac messenger RNA. Furthermore, we showed in cell culture and in human cardiac tissue that mutant RBM20-p.Pro638Leu is not localized in the nuclei but causes an abnormal cytoplasmic localization of the protein. In contrast the splicing deficient RBM20-p.Val914Ala has no influence on the intracellular localization. These results indicate that disease-associated variants in RBM20 lead to aberrant splicing through different pathomechanisms dependent on the localization of the mutation. This might have an impact on the future development of therapeutic strategies for the treatment of RBM20-induced cardiomyopathies.
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Affiliation(s)
- Anna Gaertner
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Baerbel Klauke
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Elina Felski
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Astrid Kassner
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Andreas Brodehl
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Désirée Gerdes
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Caroline Stanasiuk
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Hans Ebbinghaus
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Uwe Schulz
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Karl-Otto Dubowy
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Kinderherzzentrum und Zentrum für Angeborene Herzfehler, Bad Oeynhausen, Germany
| | - Jens Tiesmeier
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Kai-Thorsten Laser
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Kinderherzzentrum und Zentrum für Angeborene Herzfehler, Bad Oeynhausen, Germany
| | - Hendrik Bante
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Elektrophysiologie/Rhythmologie, Bad Oeynhausen, Germany
| | - Leonard Bergau
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Elektrophysiologie/Rhythmologie, Bad Oeynhausen, Germany
| | - Philipp Sommer
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Elektrophysiologie/Rhythmologie, Bad Oeynhausen, Germany
| | - Henrik Fox
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Michiel Morshuis
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Jan Gummert
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
| | - Hendrik Milting
- Herz- und Diabeteszentrum NRW, Universitätsklinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
- Klinik für Thorax- und Kardiovaskularchirurgie, Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Bad Oeynhausen, Germany
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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72
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Vece TJ, Wambach JA, Hagood JS. Childhood rare lung disease in the 21st century: "-omics" technology advances accelerating discovery. Pediatr Pulmonol 2020; 55:1828-1837. [PMID: 32533908 PMCID: PMC8711209 DOI: 10.1002/ppul.24809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/28/2020] [Indexed: 01/14/2023]
Abstract
Childhood rare lung diseases comprise a large number of heterogeneous respiratory disorders that are individually rare but are collectively associated with substantial morbidity, mortality, and healthcare resource utilization. Although the genetic mechanisms for several of these disorders have been elucidated, the pathogenesis mechanisms for others remain poorly understood and treatment options remain limited. Childhood rare lung diseases are enriched for genetic etiologies; identification of the disease mechanisms underlying these rare disorders can inform the biology of normal human lung development and has implications for the treatment of more common respiratory diseases in children and adults. Advances in "-omics" technology, such as genomic sequencing, clinical phenotyping, biomarker discovery, genome editing, in vitro and model organism disease modeling, single-cell analyses, cellular imaging, and high-throughput drug screening have enabled significant progress for diagnosis and treatment of rare childhood lung diseases. The most striking example of this progress has been realized for patients with cystic fibrosis for whom effective, personalized therapies based on CFTR genotype are now available. In this chapter, we focus on recent technology advances in childhood rare lung diseases, acknowledge persistent challenges, and identify promising new technologies that will impact not only biological discovery, but also improve diagnosis, therapies, and survival for children with these rare disorders.
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Affiliation(s)
- Timothy J. Vece
- Division of Pediatric Pulmonology, Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer A. Wambach
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - James S. Hagood
- Division of Pediatric Pulmonology, Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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73
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Kim GB, Rincon Fernandez Pacheco D, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Abbasi Akhtar A, Linesch PW, Kobritz N, Chandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Hoang K, Tsyporin J, Gareau DS, Filbin MG, Bannykh S, Santiskulvong C, Wang Y, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements. Cell 2020; 179:251-267.e24. [PMID: 31539496 DOI: 10.1016/j.cell.2019.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
In situ transgenesis methods such as viruses and electroporation can rapidly create somatic transgenic mice but lack control over copy number, zygosity, and locus specificity. Here we establish mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. We provide a toolkit of MADR elements for combination labeling, inducible and reversible transgene manipulation, VCre recombinase expression, and transgenesis of human cells. Further, we demonstrate the versatility of MADR by creating glioma models with mixed reporter-identified zygosity or with "personalized" driver mutations from pediatric glioma. MADR is extensible to thousands of existing mouse lines, providing a flexible platform to democratize the generation of somatic mosaic mice. VIDEO ABSTRACT.
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Affiliation(s)
- Gi Bum Kim
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - David Saxon
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Amy Yang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sara Sabet
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Dutra-Clarke
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rachelle Levy
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ashley Watkins
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hannah Park
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Linesch
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naomi Kobritz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Swasty S Chandra
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Katie Grausam
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alberto Ayala-Sarmiento
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Molina
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kristyna Sedivakova
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kendy Hoang
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Jeremiah Tsyporin
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Daniel S Gareau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY 10065, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serguei Bannykh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chintda Santiskulvong
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yizhou Wang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Moise Danielpour
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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74
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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75
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Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
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Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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76
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Abstract
Mitochondria are essential for eukaryotic life. These double-membrane organelles often form highly dynamic tubular networks interacting with many cellular structures. Their highly convoluted contiguous inner membrane compartmentalizes the organelle, which is crucial for mitochondrial function. Since the diameter of the mitochondrial tubules is generally close to the diffraction limit of light microscopy, it is often challenging, if not impossible, to visualize submitochondrial structures or protein distributions using conventional light microscopy. This renders super-resolution microscopy particularly valuable, and attractive, for studying mitochondria. Super-resolution microscopy encompasses a diverse set of approaches that extend resolution, as well as nanoscopy techniques that can even overcome the diffraction limit. In this review, we provide an overview of recent studies using super-resolution microscopy to investigate mitochondria, discuss the strengths and opportunities of the various methods in addressing specific questions in mitochondrial biology, and highlight potential future developments.
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Affiliation(s)
- Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Peter Ilgen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christian Brüser
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Clinic of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
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77
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Garelja M, Au M, Brimble MA, Gingell JJ, Hendrikse ER, Lovell A, Prodan N, Sexton PM, Siow A, Walker CS, Watkins HA, Williams GM, Wootten D, Yang SH, Harris PWR, Hay DL. Molecular Mechanisms of Class B GPCR Activation: Insights from Adrenomedullin Receptors. ACS Pharmacol Transl Sci 2020; 3:246-262. [PMID: 32296766 PMCID: PMC7155197 DOI: 10.1021/acsptsci.9b00083] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Indexed: 02/07/2023]
Abstract
Adrenomedullin (AM) is a 52 amino acid peptide that plays a regulatory role in the vasculature. Receptors for AM comprise the class B G protein-coupled receptor, the calcitonin-like receptor (CLR), in complex with one of three receptor activity-modifying proteins (RAMPs). The C-terminus of AM is involved in binding to the extracellular domain of the receptor, while the N-terminus is proposed to interact with the juxtamembranous portion of the receptor to activate signaling. There is currently limited information on the molecular determinants involved in AM signaling, thus we set out to define the importance of the AM N-terminus through five signaling pathways (cAMP production, ERK phosphorylation, CREB phosphorylation, Akt phosphorylation, and IP1 production). We characterized the three CLR:RAMP complexes through the five pathways, finding that each had a distinct repertoire of intracellular signaling pathways that it is able to regulate. We then performed an alanine scan of AM from residues 15-31 and found that most residues could be substituted with only small effects on signaling, and that most substitutions affected signaling through all receptors and pathways in a similar manner. We identify F18, T20, L26, and I30 as being critical for AM function, while also identifying an analogue (AM15-52 G19A) which has unique signaling properties relative to the unmodified AM. We interpret our findings in the context of new structural information, highlighting the complementary nature of structural biology and functional assays.
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Affiliation(s)
- Michael
L. Garelja
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Maggie Au
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
| | - Margaret A. Brimble
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
- School
of Chemical Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Joseph J. Gingell
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
| | - Erica R. Hendrikse
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Annie Lovell
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Nicole Prodan
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Patrick M. Sexton
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew Siow
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- School
of Chemical Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Christopher S. Walker
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
| | - Harriet A. Watkins
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
| | - Geoffrey M. Williams
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
- School
of Chemical Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Denise Wootten
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Sung H. Yang
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
| | - Paul W. R. Harris
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
- School
of Chemical Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Debbie L. Hay
- School
of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, 1010, New Zealand
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78
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Kriel NL, Heunis T, Sampson SL, Gey van Pittius NC, Williams MJ, Warren RM. Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. BMC Mol Cell Biol 2020; 21:19. [PMID: 32293251 PMCID: PMC7092591 DOI: 10.1186/s12860-020-00261-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptional responses required to maintain cellular homeostasis or to adapt to environmental stress, is in part mediated by several nucleic-acid associated proteins. In this study, we sought to establish an affinity purification-mass spectrometry (AP-MS) approach that would enable the collective identification of nucleic acid-associated proteins in mycobacteria. We hypothesized that targeting the RNA polymerase complex through affinity purification would allow for the identification of RNA- and DNA-associated proteins that not only maintain the bacterial chromosome but also enable transcription and translation. RESULTS AP-MS analysis of the RNA polymerase β-subunit cross-linked to nucleic acids identified 275 putative nucleic acid-associated proteins in the model organism Mycobacterium smegmatis under standard culturing conditions. The AP-MS approach successfully identified proteins that are known to make up the RNA polymerase complex, as well as several other known RNA polymerase complex-associated proteins such as a DNA polymerase, sigma factors, transcriptional regulators, and helicases. Gene ontology enrichment analysis of the identified proteins revealed that this approach selected for proteins with GO terms associated with nucleic acids and cellular metabolism. Importantly, we identified several proteins of unknown function not previously known to be associated with nucleic acids. Validation of several candidate nucleic acid-associated proteins demonstrated for the first time DNA association of ectopically expressed MSMEG_1060, MSMEG_2695 and MSMEG_4306 through affinity purification. CONCLUSIONS Effective identification of nucleic acid-associated proteins, which make up the RNA polymerase complex as well as other DNA- and RNA-associated proteins, was facilitated by affinity purification of the RNA polymerase β-subunit in M. smegmatis. The successful identification of several transcriptional regulators suggest that our approach could be sensitive enough to investigate the nucleic acid-associated proteins that maintain cellular functions and mediate transcriptional and translational change in response to environmental stress.
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Affiliation(s)
- Nastassja L Kriel
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa.
| | - Tiaan Heunis
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Samantha L Sampson
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Nico C Gey van Pittius
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Monique J Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
- Present address: Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
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79
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Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
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80
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Gouw M, Alvarado-Valverde J, Čalyševa J, Diella F, Kumar M, Michael S, Van Roey K, Dinkel H, Gibson TJ. How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. Methods Mol Biol 2020; 2141:73-102. [PMID: 32696353 DOI: 10.1007/978-1-0716-0524-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few years, it has become apparent that approximately 35% of the human proteome consists of intrinsically disordered regions. Many of these disordered regions are rich in short linear motifs (SLiMs) which mediate protein-protein interactions. Although these motifs are short and often partially conserved, they are involved in many important aspects of protein function, including cleavage, targeting, degradation, docking, phosphorylation, and other posttranslational modifications. The Eukaryotic Linear Motif resource (ELM) was established over 15 years ago as a repository to store and catalogue the scientific discoveries of motifs. Each motif in the database is annotated and curated manually, based on the experimental evidence gathered from publications. The entries themselves are submitted to ELM by filling in two annotation templates designed for motif class and motif instance annotation. In this protocol, we describe the steps involved in annotating new motifs and how to submit them to ELM.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Holger Dinkel
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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81
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Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors. Biophys Rev 2019; 11:745-756. [PMID: 31529362 DOI: 10.1007/s12551-019-00595-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
In the last decades, a promising breakthrough in fluorescence imaging was represented by the advent of super-resolution microscopy (SRM). Super-resolution techniques recently became a popular method to study sub-cellular structures, providing a successful approach to observe cytoskeletal and focal adhesion proteins. Among the SR techniques, single-molecule localization microscopy plays a significant role due to its ability to unveil structures and molecular organizations in biological systems. Furthermore, since they provide information at the molecular level, these techniques are increasingly being used to study the stoichiometry and interaction between several membrane channel proteins and their accessory subunits. The aim of this review is to describe the single-molecule localization-based techniques and their applications relevant to cytoskeletal structures and membrane complexes in order to provide as future prospective an overall picture of their correlation with the mechanosensor channel expression and activity.
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82
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Bukhari H, Müller T. Endogenous Fluorescence Tagging by CRISPR. Trends Cell Biol 2019; 29:912-928. [PMID: 31522960 DOI: 10.1016/j.tcb.2019.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 01/01/2023]
Abstract
Fluorescent proteins have revolutionized biomedical research as they are easy to use for protein tagging, cope without fixation or permeabilization, and thus, enable live cell imaging in various models. Current methods allow easy and quick integration of fluorescent markers to endogenous genes of interest. In this review, we introduce the three central methods, zinc finger nucleases (ZFNs), transcription activator-like effectors (TALENs), and CRISPR, that have been widely used to manipulate cells or organisms. Focusing on CRISPR technology, we give an overview on homology-directed repair (HDR)-, microhomology-mediated end joining (MMEJ)-, and nonhomologous end joining (NHEJ)-based strategies for the knock-in of markers, figure out recent developments of the technique for highly efficient knock-in, and demonstrate pros and cons. We highlight the unique aspects of fluorescent protein knock-ins and pinpoint specific improvements and perspectives, like the combination of editing with stem cell derived organoid development.
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Affiliation(s)
- Hassan Bukhari
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Molecular Biochemistry, Cell Signalling, Ruhr-University Bochum, Bochum, Germany
| | - Thorsten Müller
- Department of Molecular Biochemistry, Cell Signalling, Ruhr-University Bochum, Bochum, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich 80336, Germany.
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83
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Miller M, Wang Y, Bromberg Y. What went wrong with variant effect predictor performance for the PCM1 challenge. Hum Mutat 2019; 40:1486-1494. [PMID: 31268618 PMCID: PMC6744297 DOI: 10.1002/humu.23832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/03/2019] [Accepted: 05/31/2019] [Indexed: 12/31/2022]
Abstract
The recent years have seen a drastic increase in the amount of available genomic sequences. Alongside this explosion, hundreds of computational tools were developed to assess the impact of observed genetic variation. Critical Assessment of Genome Interpretation (CAGI) provides a platform to evaluate the performance of these tools in experimentally relevant contexts. In the CAGI-5 challenge assessing the 38 missense variants affecting the human Pericentriolar material 1 protein (PCM1), our SNAP-based submission was the top performer, although it did worse than expected from other evaluations. Here, we compare the CAGI-5 submissions, and 24 additional commonly used variant effect predictors, to analyze the reasons for this observation. We identified per residue conservation, structural, and functional PCM1 characteristics, which may be responsible. As expected, predictors had a hard time distinguishing effect variants in nonconserved positions. They were also better able to call effect variants in a structurally rich region than in a less-structured one; in the latter, they more often correctly identified benign than effect variants. Curiously, most of the protein was predicted to be functionally robust to mutation-a feature that likely makes it a harder problem for generalized variant effect predictors.
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Affiliation(s)
- Maximilian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
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84
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A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants. Oncogene 2019; 39:30-35. [PMID: 31467430 PMCID: PMC6937211 DOI: 10.1038/s41388-019-0968-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/31/2019] [Accepted: 06/15/2019] [Indexed: 11/26/2022]
Abstract
Genetic mutations in BRCA1, which is crucial for the process of DNA repair and maintenance of genomic integrity, are known to increase markedly the risk of breast and ovarian cancers. Clinical genetic testing has been used to identify new BRCA1 variants; however, functional assessment and determination of their pathogenicity still poses challenges for clinical management. Here, we describe that CRISPR-mediated cytosine base editor, known as BE3, can be used for the functional analysis of BRCA1 variants. We performed CRISPR-mediated base-editing screening using 745 gRNAs targeting all exons in BRCA1 to identify loss-of-function variants and identified variants whose function has heretofore remained unknown, such as c.-97C>T, c.154C>T, c.3847C>T, c.5056C>T, and c.4986+5G>A. Our results show that CRISPR-mediated base editor is a powerful tool for the reclassification of variants of uncertain significance (VUSs) in BRCA1.
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85
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Kruse K, Klomp J, Sun M, Chen Z, Santana D, Huang F, Kanabar P, Maienschein-Cline M, Komarova YA. Analysis of biological networks in the endothelium with biomimetic microsystem platform. Am J Physiol Lung Cell Mol Physiol 2019; 317:L392-L401. [PMID: 31313617 DOI: 10.1152/ajplung.00392.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Here we describe a novel method for studying the protein "interactome" in primary human cells and apply this method to investigate the effect of posttranslational protein modifications (PTMs) on the protein's functions. We created a novel "biomimetic microsystem platform" (Bio-MSP) to isolate the protein complexes in primary cells by covalently attaching purified His-tagged proteins to a solid microscale support. Using this Bio-MSP, we have analyzed the interactomes of unphosphorylated and phosphomimetic end-binding protein-3 (EB3) in endothelial cells. Pathway analysis of these interactomes demonstrated the novel role of EB3 phosphorylation at serine 162 in regulating the protein's function. We showed that phosphorylation "switches" the EB3 biological network to modulate cellular processes such as cell-to-cell adhesion whereas dephosphorylation of this site promotes cell proliferation. This novel technique provides a useful tool to study the role of PTMs or single point mutations in activating distinct signal transduction networks and thereby the biological function of the protein in health and disease.
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Affiliation(s)
- Kevin Kruse
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Jeff Klomp
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Mitchell Sun
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Zhang Chen
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Dianicha Santana
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Fei Huang
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Pinal Kanabar
- Research Informatics Core of the Research Resources Center, University of Illinois at Chicago, Chicago, Illinois.,College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Mark Maienschein-Cline
- Research Informatics Core of the Research Resources Center, University of Illinois at Chicago, Chicago, Illinois.,College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Yulia A Komarova
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
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86
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Abstract
Sensitization of the transient receptor potential ion channel vanilloid 1 (TRPV1) is critically involved in inflammatory pain. To date, manifold signaling cascades have been shown to converge onto TRPV1 and enhance its sensitization. However, many of them also play a role for nociceptive pain, which limits their utility as targets for therapeutic intervention. Here, we show that the vesicle transport through interaction with t-SNAREs homolog 1B (Vti1b) protein promotes TRPV1 sensitization upon inflammation in cell culture but leaves normal functioning of TRPV1 intact. Importantly, the effect of Vti1b can be recapitulated in vivo: Virus-mediated knockdown of Vti1b in sensory neurons attenuated thermal hypersensitivity during inflammatory pain without affecting mechanical hypersensitivity or capsaicin-induced nociceptive pain. Interestingly, TRPV1 and Vti1b are localized in close vicinity as indicated by proximity ligation assays and are likely to bind to each other, either directly or indirectly, as suggested by coimmunoprecipitations. Moreover, using a mass spectrometry-based quantitative interactomics approach, we show that Vti1b is less abundant in TRPV1 protein complexes during inflammatory conditions compared with controls. Alongside, we identify numerous novel and pain state-dependent binding partners of native TRPV1 in dorsal root ganglia. These data represent a unique resource on the dynamics of the TRPV1 interactome and facilitate mechanistic insights into TRPV1 regulation. We propose that inflammation-related differences in the TRPV1 interactome identified here could be exploited to specifically target inflammatory pain in the future.
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87
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Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Cell Host Microbe 2019; 26:86-99.e7. [PMID: 31253590 DOI: 10.1016/j.chom.2019.05.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 12/24/2018] [Accepted: 04/26/2019] [Indexed: 12/29/2022]
Abstract
The Cullin-RING E3 ligase (CRL) family is commonly hijacked by pathogens to redirect the host ubiquitin proteasome machinery to specific targets. During HIV infection, CRL5 is hijacked by HIV Vif to target viral restriction factors of the APOBEC3 family for ubiquitination and degradation. Here, using a quantitative proteomics approach, we identify the E3 ligase ARIH2 as a regulator of CRL5-mediated APOBEC3 degradation. The CUL5Vif/CBFß complex recruits ARIH2 where it acts to transfer ubiquitin directly to the APOBEC3 targets. ARIH2 is essential for CRL5-dependent HIV infectivity in primary CD4+ T cells. Furthermore, we show that ARIH2 cooperates with CRL5 to prime other cellular substrates for polyubiquitination, suggesting this may represent a general mechanism beyond HIV infection and APOBEC3 degradation. Taken together, these data identify ARIH2 as a co-factor in the Vif-hijacked CRL5 complex that contributes to HIV infectivity and demonstrate the operation of the E1-E2-E3/E3-substrate ubiquitination mechanism in a viral infection context.
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Affiliation(s)
- Ruth Hüttenhain
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA.
| | - Jiewei Xu
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - Lily A Burton
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David E Gordon
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA; Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey R Johnson
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - Laura Satkamp
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kheewoong Baek
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Arno F Alpi
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA.
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88
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Quantitative proteomics of MDCK cells identify unrecognized roles of clathrin adaptor AP-1 in polarized distribution of surface proteins. Proc Natl Acad Sci U S A 2019; 116:11796-11805. [PMID: 31142645 PMCID: PMC6575629 DOI: 10.1073/pnas.1821076116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Epithelial cells perform critical protective, secretory, absorptive, and sensory functions, for which they require plasma membrane polarization into apical and basolateral domains. Impaired polarity causes cancer and developmental and degenerative disorders. Research on fundamental polarity mechanisms has been hindered by the paucity of model proteins and by the use of overexpression systems. Here, we introduce a high-throughput surface proteomics approach based on domain-selective biotinylation and quantitative mass spectrometry that provides candidate proteins to study polarity under normal expression levels. Using this approach, we described that clathrin adaptors mediate apical and basolateral distribution of surface proteins, expanding the traditional notion that clathrin adaptors mediate only basolateral polarity. Our results establish quantitative surface proteomics as a powerful tool to study epithelial polarity. The current model of polarized plasma membrane protein sorting in epithelial cells has been largely generated on the basis of experiments characterizing the polarized distribution of a relatively small number of overexpressed model proteins under various experimental conditions. Thus, the possibility exists that alternative roles of various types of sorting machinery may have been underestimated or missed. Here, we utilize domain-selective surface biotinylation combined with stable isotope labeling with amino acids in cell culture (SILAC) and mass spectrometry to quantitatively define large populations of apical and basolateral surface proteins in Madin-Darby canine kidney (MDCK) cells. We identified 313 plasma membrane proteins, of which 38% were apical, 51% were basolateral, and 11% were nonpolar. Silencing of clathrin adaptor proteins (AP) AP-1A, AP-1B, or both caused redistribution of basolateral proteins as expected but also, of a large population of apical proteins. Consistent with their previously reported ability to compensate for one another, the strongest loss of polarity was observed when we silenced AP-1A and AP-1B simultaneously. We found stronger evidence of compensation in the apical pathway compared with the basolateral pathway. Surprisingly, we also found subgroups of proteins that were affected after silencing just one adaptor, indicating previously unrecognized independent roles for AP-1A and AP-1B. While AP-1B silencing mainly affected basolateral polarity, AP-1A silencing seemed to cause comparable loss of apical and basolateral polarity. Our results uncover previously overlooked roles of AP-1 in polarized distribution of apical and basolateral proteins and introduce surface proteomics as a method to examine mechanisms of polarization with a depth not possible until now.
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89
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Pick a Tag and Explore the Functions of Your Pet Protein. Trends Biotechnol 2019; 37:1078-1090. [PMID: 31036349 DOI: 10.1016/j.tibtech.2019.03.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Protein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.
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90
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Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM. The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair. Sci Rep 2019; 9:6539. [PMID: 31024071 PMCID: PMC6483993 DOI: 10.1038/s41598-019-42990-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
The chromosome 21 encoded protein kinase DYRK1A is essential for normal human development. Mutations in DYRK1A underlie a spectrum of human developmental disorders, and increased dosage in trisomy 21 is implicated in Down syndrome related pathologies. DYRK1A regulates a diverse array of cellular processes through physical interactions with substrates and binding partners in various subcellular compartments. Despite recent large-scale protein-protein interaction profiling efforts, DYRK1A interactions specific to different subcellular compartments remain largely unknown, impeding progress toward understanding emerging roles for this kinase. Here, we used immunoaffinity purification and quantitative mass spectrometry to identify nuclear interaction partners of endogenous DYRK1A. This interactome was enriched in DNA damage repair factors, transcriptional elongation factors and E3 ubiquitin ligases. We validated an interaction with RNF169, a factor that promotes homology directed repair upon DNA damage, and found that DYRK1A expression and kinase activity are required for maintenance of 53BP1 expression and subsequent recruitment to DNA damage loci. Further, DYRK1A knock out conferred resistance to ionizing radiation in colony formation assays, suggesting that DYRK1A expression decreases cell survival efficiency in response to DNA damage and points to a tumor suppressive role for this kinase.
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Affiliation(s)
- Steven E Guard
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Zachary C Poss
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Christopher C Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Maria Pagratis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Helen Simpson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA.
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91
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Roberts B, Hendershott MC, Arakaki J, Gerbin KA, Malik H, Nelson A, Gehring J, Hookway C, Ludmann SA, Yang R, Haupt A, Grancharova T, Valencia V, Fuqua MA, Tucker A, Rafelski SM, Gunawardane RN. Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs. Stem Cell Reports 2019; 12:1145-1158. [PMID: 30956114 PMCID: PMC6522946 DOI: 10.1016/j.stemcr.2019.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
We describe a multistep method for endogenous tagging of transcriptionally silent genes in human induced pluripotent stem cells (hiPSCs). A monomeric EGFP (mEGFP) fusion tag and a constitutively expressed mCherry fluorescence selection cassette were delivered in tandem via homology-directed repair to five genes not expressed in hiPSCs but important for cardiomyocyte sarcomere function: TTN, MYL7, MYL2, TNNI1, and ACTN2. CRISPR/Cas9 was used to deliver the selection cassette and subsequently mediate its excision via microhomology-mediated end-joining and non-homologous end-joining. Most excised clones were effectively tagged, and all properly tagged clones expressed the mEGFP fusion protein upon differentiation into cardiomyocytes, allowing live visualization of these cardiac proteins at the sarcomere. This methodology provides a broadly applicable strategy for endogenously tagging transcriptionally silent genes in hiPSCs, potentially enabling their systematic and dynamic study during differentiation and morphogenesis.
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Affiliation(s)
- Brock Roberts
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Jamie Gehring
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | | | - Andrew Tucker
- Allen Institute for Cell Science, Seattle, WA 98109, USA
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92
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Logan S, Arzua T, Canfield SG, Seminary ER, Sison SL, Ebert AD, Bai X. Studying Human Neurological Disorders Using Induced Pluripotent Stem Cells: From 2D Monolayer to 3D Organoid and Blood Brain Barrier Models. Compr Physiol 2019; 9:565-611. [PMID: 30873582 PMCID: PMC6705133 DOI: 10.1002/cphy.c180025] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurological disorders have emerged as a predominant healthcare concern in recent years due to their severe consequences on quality of life and prevalence throughout the world. Understanding the underlying mechanisms of these diseases and the interactions between different brain cell types is essential for the development of new therapeutics. Induced pluripotent stem cells (iPSCs) are invaluable tools for neurological disease modeling, as they have unlimited self-renewal and differentiation capacity. Mounting evidence shows: (i) various brain cells can be generated from iPSCs in two-dimensional (2D) monolayer cultures; and (ii) further advances in 3D culture systems have led to the differentiation of iPSCs into organoids with multiple brain cell types and specific brain regions. These 3D organoids have gained widespread attention as in vitro tools to recapitulate complex features of the brain, and (iii) complex interactions between iPSC-derived brain cell types can recapitulate physiological and pathological conditions of blood-brain barrier (BBB). As iPSCs can be generated from diverse patient populations, researchers have effectively applied 2D, 3D, and BBB models to recapitulate genetically complex neurological disorders and reveal novel insights into molecular and genetic mechanisms of neurological disorders. In this review, we describe recent progress in the generation of 2D, 3D, and BBB models from iPSCs and further discuss their limitations, advantages, and future ventures. This review also covers the current status of applications of 2D, 3D, and BBB models in drug screening, precision medicine, and modeling a wide range of neurological diseases (e.g., neurodegenerative diseases, neurodevelopmental disorders, brain injury, and neuropsychiatric disorders). © 2019 American Physiological Society. Compr Physiol 9:565-611, 2019.
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Affiliation(s)
- Sarah Logan
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago Arzua
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Scott G. Canfield
- Department of Cellular & Integrative Physiology, IU School of Medicine-Terre Haute, Terre Haute, IN, USA
| | - Emily R. Seminary
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Samantha L. Sison
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Allison D. Ebert
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Xiaowen Bai
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
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93
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Abstract
It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic datasets from affinity purifications. Data is analyzed in a parallel fashion where a prey protein is scored in an individual affinity purification by aggregating information from the entire dataset. Topological scores span a broad range of values indicating the enrichment of an individual protein in every bait protein purification. TopS is applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS highlights potential direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides important insights into protein interaction networks. Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of each bait relative to the other baits.
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94
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Padmanabhan P, Bademosi AT, Kasula R, Lauwers E, Verstreken P, Meunier FA. Need for speed: Super-resolving the dynamic nanoclustering of syntaxin-1 at exocytic fusion sites. Neuropharmacology 2019; 169:107554. [PMID: 30826343 DOI: 10.1016/j.neuropharm.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Communication between cells relies on regulated exocytosis, a multi-step process that involves the docking, priming and fusion of vesicles with the plasma membrane, culminating in the release of neurotransmitters and hormones. Key proteins and lipids involved in exocytosis are subjected to Brownian movement and constantly switch between distinct motion states which are governed by short-lived molecular interactions. Critical biochemical reactions between exocytic proteins that occur in the confinement of nanodomains underpin the precise sequence of priming steps which leads to the fusion of vesicles. The advent of super-resolution microscopy techniques has provided the means to visualize individual molecules on the plasma membrane with high spatiotemporal resolution in live cells. These techniques are revealing a highly dynamic nature of the nanoscale organization of the exocytic machinery. In this review, we focus on soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) syntaxin-1, which mediates vesicular fusion. Syntaxin-1 is highly mobile at the plasma membrane, and its inherent speed allows fast assembly and disassembly of syntaxin-1 nanoclusters which are associated with exocytosis. We reflect on recent studies which have revealed the mechanisms regulating syntaxin-1 nanoclustering on the plasma membrane and draw inferences on the effect of synaptic activity, phosphoinositides, N-ethylmaleimide-sensitive factor (NSF), α-soluble NSF attachment protein (α-SNAP) and SNARE complex assembly on the dynamic nanoscale organization of syntaxin-1. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Ravikiran Kasula
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia.
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95
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Vandemoortele G, De Sutter D, Moliere A, Pauwels J, Gevaert K, Eyckerman S. A Well-Controlled BioID Design for Endogenous Bait Proteins. J Proteome Res 2018; 18:95-106. [PMID: 30525648 DOI: 10.1021/acs.jproteome.8b00367] [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: 12/27/2022]
Abstract
The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
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Affiliation(s)
- Giel Vandemoortele
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Aline Moliere
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
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96
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White CW, Johnstone EKM, See HB, Pfleger KDG. NanoBRET ligand binding at a GPCR under endogenous promotion facilitated by CRISPR/Cas9 genome editing. Cell Signal 2018; 54:27-34. [PMID: 30471466 DOI: 10.1016/j.cellsig.2018.11.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/10/2018] [Accepted: 11/20/2018] [Indexed: 01/14/2023]
Abstract
Bioluminescence resonance energy transfer (BRET) is a versatile tool used to investigate membrane receptor signalling and function. We have recently developed a homogenous NanoBRET ligand binding assay to monitor interactions between G protein-coupled receptors and fluorescent ligands. However, this assay requires the exogenous expression of a receptor fused to the nanoluciferase (Nluc) and is thus not applicable to natively-expressed receptors. To overcome this limitation in HEK293 cells, we have utilised CRISPR/Cas9 genome engineering to insert Nluc in-frame with the endogenous ADORA2B locus this resulted in HEK293 cells expressing adenosine A2B receptors under endogenous promotion tagged on their N-terminus with Nluc. As expected, we found relatively low levels of endogenous (gene-edited) Nluc/A2B receptor expression compared to cells transiently transfected with expression vectors coding for Nluc/A2B. However, in cells expressing gene-edited Nluc/A2B receptors we observed clear saturable ligand binding of a non-specific fluorescent adenosine receptor antagonist XAC-X-BY630 (Kd = 21.4 nM). Additionally, at gene-edited Nluc/A2B receptors we derived pharmacological parameters of ligand binding; Kd as well as Kon and Koff for binding of XAC-X-BY630 by NanoBRET association kinetic binding assays. Lastly, cells expressing gene-edited Nluc/A2B were used to determine the pKi of unlabelled adenosine receptor ligands in competition ligand binding assays. Utilising CRISPR/Cas9 genome engineering here we show that NanoBRET ligand binding assays can be performed at gene-edited receptors under endogenous promotion in live cells, therefore overcoming a fundamental limitation of NanoBRET ligand assays.
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Affiliation(s)
- Carl W White
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia; Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia; Australian Research Council Centre for Personalised Therapeutics Technologies, Australia.
| | - Elizabeth K M Johnstone
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia; Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia; Australian Research Council Centre for Personalised Therapeutics Technologies, Australia
| | - Heng B See
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia; Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia; Australian Research Council Centre for Personalised Therapeutics Technologies, Australia
| | - Kevin D G Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia; Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia; Australian Research Council Centre for Personalised Therapeutics Technologies, Australia; Dimerix Limited, Nedlands, Western Australia 6009, Australia.
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97
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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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98
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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: 474] [Impact Index Per Article: 79.0] [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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99
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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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100
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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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