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Osgerby A, Overton TW. Approaches for high-throughput quantification of periplasmic recombinant proteins. N Biotechnol 2023; 77:149-160. [PMID: 37708933 DOI: 10.1016/j.nbt.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Gram-negative periplasm is a convenient location for the accumulation of many recombinant proteins including biopharmaceutical products. It is the site of disulphide bond formation, required by some proteins (such as antibody fragments) for correct folding and function. It also permits simpler protein release and downstream processing than cytoplasmic accumulation. As such, targeting of recombinant proteins to the E. coli periplasm is a key strategy in biologic manufacture. However, expression and translocation of each recombinant protein requires optimisation including selection of the best signal peptide and growth and production conditions. Traditional methods require separation and analysis of protein compositions of periplasmic and cytoplasmic fractions, a time- and labour-intensive method that is difficult to parallelise. Therefore, approaches for high throughput quantification of periplasmic protein accumulation offer advantages in rapid process development.
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Affiliation(s)
- Alexander Osgerby
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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2
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Cattoglio C, Darzacq X, Tjian R, Hansen AS. Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry. Bio Protoc 2020; 10:e3527. [PMID: 33654751 DOI: 10.21769/bioprotoc.3527] [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: 11/12/2019] [Revised: 12/24/2019] [Accepted: 01/29/2020] [Indexed: 11/02/2022] Open
Abstract
Accurate abundance measurements of cellular proteins are required to achieve a quantitative and predictive understanding of any biological process inside the cell. Existing methods to determine absolute protein abundances are labor-intensive and/or require sophisticated experimental and computational infrastructure (e.g., fluorescence correlation spectroscopy (FCS)-calibrated imaging and quantitative mass spectrometry). Here we detail a straightforward flow cytometry-based method to measure the absolute abundance of any Halo-tagged protein in live cells that uses a standard mammalian cell line with a known number of Halo-CTCF proteins recently characterized in our lab. The protocol only comprises a few steps. First, a cell line expressing the Halo-tagged protein of interest is grown and labeled side-by-side with our standard line. Then, average fluorescence intensities are measured by conventional flow cytometry analysis and finally a simple calculation is applied to estimate the absolute number of the Halo-tagged protein of interest per cell. Once the protein of interest has been endogenously tagged with HaloTag, which we routinely achieve by Cas9-mediated genome editing, the presented protocol is fast, convenient, reproducible, cost-effective and readily accessible.
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Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
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3
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Abstract
This chapter describes advantages and limitations of imaging flow cytometry (IFC) based on Imagestream instrumentation using a hybrid approach of morphometric measurement and quantitation of multiparametric fluorescent intensities' distribution in cells and particles. Brief comparison is given of IFC with conventional flow cytometry and fluorescent microscopy. Some future directions of the IFC technology are described and discussed.
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Affiliation(s)
- Ivan A Vorobjev
- Department of Cell Biology and Histology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Natasha S Barteneva
- Cellular and Molecular Medicine Program, Boston Childrens Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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Su Z, Denu JM. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications. ACTA ACUST UNITED AC 2015; 111:21.32.1-21.32.21. [PMID: 26131849 DOI: 10.1002/0471142727.mb2132s111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications.
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Affiliation(s)
- Zhangli Su
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin.,Wisconsin Institutes for Discovery, University of Wisconsin, Madison, Wisconsin
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin.,Wisconsin Institutes for Discovery, University of Wisconsin, Madison, Wisconsin
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5
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Abstract
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Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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Jia J, Wang W, Meng W, Ding M, Ma S, Wang X. Development of a multiplex autoantibody test for detection of lung cancer. PLoS One 2014; 9:e95444. [PMID: 24755629 PMCID: PMC3995760 DOI: 10.1371/journal.pone.0095444] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 03/27/2014] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths for both men and women. Early diagnosis of lung cancer has a 5-year survival rate of 48.8%, however, nearly 35% of stage I patients relapses after surgical resection, thus portending a poor prognosis. Therefore, detecting lung cancer in early stage and further identifying the high-risk patients would allow the opportunity to provide adjuvant therapy and possibly increase survival. There is considerable evidence that the immune system produces an autoantibody response to neoplastic cells. The detection of such autoantibodies has been shown to have diagnostic and prognostic value. Here we took advantage of the high-throughput Luminex technique to multiplex a total of 14 tumor-associated autoantigens to detect the autoantibody from the patients sera. The 14 antigens were expressed by in vitro transcription/translation system with HaloTag at N-terminus. The fusion proteins were then covalently immobilized onto the Luminex microspheres conjugated by the halo-link ligand, thus eliminating the protein purification procedure. Sera samples from cancer patients and healthy controls were interacted with the microsphere-antigen complex to measure the autoantibodies. We have developed a quick multiplex detection system for measuring autoantibody signature from patient sera with minimal cross-reaction. A panel of seven autoantibody biomarkers has generated an AUC>80% in distinguishing the lung cancers from healthy controls. This study is the first report by combining Luminex platform and HaloTag technology to detect humoral immune response in cancer patients. Due to the flexibility of the Luminex technology, this approach can be applied to others conditions such as infectious, neurological, and metabolic diseases. One can envision that this multiplex Luminex system as well as the panel of seven biomarkers could be used to screen the high-risk population with subsequent CT test based on the blood test result.
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Affiliation(s)
- Jing Jia
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
| | - Wenzhe Wang
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
| | - Wen Meng
- Hangzhou First People’s Hospital, Hangzhou, Zhejiang, P. R. China
| | - Mingjian Ding
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
| | - Shenglin Ma
- Institute of Lung Cancer, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
- Hangzhou First People’s Hospital, Hangzhou, Zhejiang, P. R. China
- * E-mail: (XW); (SM)
| | - Xiaoju Wang
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
- Institute of Lung Cancer, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, P. R. China
- * E-mail: (XW); (SM)
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 797] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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Fine M, Lu FM, Lin MJ, Moe O, Wang HR, Hilgemann DW. Human-induced pluripotent stem cell-derived cardiomyocytes for studies of cardiac ion transporters. Am J Physiol Cell Physiol 2013; 305:C481-91. [PMID: 23804202 DOI: 10.1152/ajpcell.00143.2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human-induced pluripotent stem cells (hiPSCs) can differentiate into functional cardiomyocytes (iCell Cardiomyocytes) with ion channel activities that are remarkably similar to adult cardiomyocytes. Here, we extend this characterization to cardiac ion transporters. Additionally, we document facile molecular biological manipulation of iCell Cardiomyocytes to overexpress and knockdown transporters and regulatory proteins. Na/Ca exchange (NCX1) and Na/K pump currents were recorded via patch clamp, and Na/H and Cl/OH exchanges were recorded via oscillating proton-selective microelectrodes during patch clamp. Flux densities of all transport systems are similar to those of nonrodent adult cardiomyocytes. NCX1 protein and NCX1 currents decline after NCX1 small interfering (si)RNA transfection with similar time courses (τ ≈ 2 days), and an NCX1-Halo fusion protein is internalized after its extracellular labeling by AlexaFluor488 Ligand with a similar time course. Loss of the cardiac regulatory protein phospholemman (PLM) occurs over a longer time course (τ ≈ 60 h) after PLM small interfering RNA transfection. Similar to multiple previous reports for adult cardiomyocytes, Na/K pump currents in iCell Cardiomyocytes are not enhanced by activating cAMP production with either maximal or submaximal cytoplasmic Na and using either forskolin or isoproterenol to activate adenylate cyclases. Finally, we describe Ca influx-dependent changes of iCell Cardiomyocyte capacitance (Cm). Large increases of Cm occur during Ca influx via NCX1, thereby documenting large internal membrane reserves that can fuse to the sarcolemma, and subsequent declines of Cm document active endocytic processes. Together, these results document a great potential of iCell Cardiomyocytes for both short- and long-term studies of cardiac ion transporters and their regulation.
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Affiliation(s)
- Michael Fine
- Department of Physiology, University of Texas Southwestern Medical School, Dallas, Texas, USA
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Application of HaloTag technology to expression and purification of cannabinoid receptor CB2. Protein Expr Purif 2013; 89:62-72. [PMID: 23470778 DOI: 10.1016/j.pep.2013.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 11/22/2022]
Abstract
Expression of milligram quantities of functional, stable G protein-coupled receptors (GPCR) for high-resolution structural studies remains a challenging task. The goal of this work was to evaluate the usefulness of the HaloTag system (Promega) for expression and purification of the human cannabinoid receptor CB(2), an important target for development of drugs for treatment of immune disorders, inflammation, and pain. Here we investigated expression in Escherichia coli cells of the integral membrane receptor CB(2) as a fusion with the 34 kDa HaloTag at N- or C-terminal location, either in the presence or in the absence of the N-terminal maltose-binding protein (MBP). The CB(2) was flanked at both ends by the tobacco etch virus (TEV) protease cleavage sites to allow for subsequent removal of expression partners. Expression by induction with either IPTG (in E. coli BL21(DE3) cell cultures) or by auto-induction (in E. coli KRX cells) were compared. While the N-terminal location of the HaloTag resulted in high levels of expression of the fusion CB(2), the recombinant receptor was not functional. However, when the HaloTag was placed in the C-terminal location, a fully active receptor was produced irrespective of induction method or bacterial strain used. For purification, the fusion protein was captured onto HaloLink resin in the presence of detergents. Treatment with specific TEV protease released the CB(2) upon washing. To our knowledge, this study represents the first example of expression, surface immobilization and purification of a functional GPCR using HaloTag technology.
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Hoppe S, Bier FF, von Nickisch-Rosenegk M. Microarray-based method for screening of immunogenic proteins from bacteria. J Nanobiotechnology 2012; 10:12. [PMID: 22436172 PMCID: PMC3368735 DOI: 10.1186/1477-3155-10-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 03/21/2012] [Indexed: 12/12/2022] Open
Abstract
Background Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. Results Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168. Conclusions The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria.
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Affiliation(s)
- Sebastian Hoppe
- Fraunhofer Institute for Biomedical Engineering, Branch Potsdam, Am Mühlenberg 13, 14476 Potsdam, Germany.
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