1
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Valbuena FM, Fitzgerald I, Strack RL, Andruska N, Smith L, Glick BS. A photostable monomeric superfolder green fluorescent protein. Traffic 2020; 21:534-544. [PMID: 32415747 DOI: 10.1111/tra.12737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 11/30/2022]
Abstract
The green fluorescent protein (GFP) from Aequorea victoria has been engineered extensively in the past to generate variants suitable for protein tagging. Early efforts produced the enhanced variant EGFP and its monomeric derivative mEGFP, which have useful photophysical properties, as well as superfolder GFP, which folds efficiently under adverse conditions. We previously generated msGFP, a monomeric superfolder derivative of EGFP. Unfortunately, compared to EGFP, msGFP and other superfolder GFP variants show faster photobleaching. We now describe msGFP2, which retains monomeric superfolder properties while being as photostable as EGFP. msGFP2 contains modified N- and C-terminal peptides that are expected to reduce nonspecific interactions. Compared to EGFP and mEGFP, msGFP2 is less prone to disturbing the functions of certain partner proteins. For general-purpose protein tagging, msGFP2 may be the best available derivative of A. victoria GFP.
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Affiliation(s)
- Fernando M Valbuena
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Ivy Fitzgerald
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois, USA
| | - Rita L Strack
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Neal Andruska
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Luke Smith
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
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2
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Yang WY, He F, Strack RL, Oh SY, Frazer M, Jaffrey SR, Todd PK, Disney MD. Small Molecule Recognition and Tools to Study Modulation of r(CGG)(exp) in Fragile X-Associated Tremor Ataxia Syndrome. ACS Chem Biol 2016; 11:2456-65. [PMID: 27276216 DOI: 10.1021/acschembio.6b00147] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA transcripts containing expanded nucleotide repeats cause many incurable diseases via various mechanisms. One such disorder, fragile X-associated tremor ataxia syndrome (FXTAS), is caused by a noncoding r(CGG) repeat expansion (r(CGG)(exp)) that (i) sequesters proteins involved in RNA metabolism in nuclear foci, causing dysregulation of alternative pre-mRNA splicing, and (ii) undergoes repeat associated non-ATG translation (RANT), which produces toxic homopolymeric proteins without using a start codon. Here, we describe the design of two small molecules that inhibit both modes of toxicity and the implementation of various tools to study perturbation of these cellular events. Competitive Chemical Cross Linking and Isolation by Pull Down (C-Chem-CLIP) established that compounds bind r(CGG)(exp) and defined small molecule occupancy of r(CGG)(exp) in cells, the first approach to do so. Using an RNA GFP mimic, r(CGG)(exp)-Spinach2, we observe that our optimal designed compound binds r(CGG)(exp) and affects RNA localization by disrupting preformed RNA foci. These events correlate with an improvement of pre-mRNA splicing defects caused by RNA gain of function. In addition, the compounds reduced levels of toxic homopolymeric proteins formed via RANT. Polysome profiling studies showed that small molecules decreased loading of polysomes onto r(CGG)(exp), explaining decreased translation.
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Affiliation(s)
- Wang-Yong Yang
- Departments
of Chemistry and Neuroscience, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Fang He
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Rita L. Strack
- Department
of Pharmacology, Weill Medical College of Cornell University, 1300
York Avenue, Box 70, New York, New York 10065, United States
| | - Seok Yoon Oh
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Michelle Frazer
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Samie R. Jaffrey
- Department
of Pharmacology, Weill Medical College of Cornell University, 1300
York Avenue, Box 70, New York, New York 10065, United States
| | - Peter K. Todd
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Matthew D. Disney
- Departments
of Chemistry and Neuroscience, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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3
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Abstract
The ability to monitor RNAs of interest in living cells is crucial to understanding the function, dynamics, and regulation of this important class of molecules. In recent years, numerous strategies have been developed with the goal of imaging individual RNAs of interest in living cells, each with their own advantages and limitations. This chapter provides an overview of current methods of live-cell RNA imaging, including a detailed discussion of genetically encoded strategies for labeling RNAs in mammalian cells. This chapter then focuses on the development and use of "RNA mimics of GFP" or Spinach technology for tagging mammalian RNAs and includes a detailed protocol for imaging 5S and CGG60 RNA with the recently described Spinach2 tag.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA.
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4
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Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferré-D'Amaré AR. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 2014; 21:658-63. [PMID: 25026079 DOI: 10.1038/nsmb.2865] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/07/2014] [Indexed: 12/22/2022]
Abstract
GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.
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Affiliation(s)
- Katherine Deigan Warner
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Michael C Chen
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, New York, USA
| | - Rita L Strack
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, New York, USA
| | - Andrea Thorn
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, New York, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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5
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Abstract
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Spinach
and Spinach2 are RNA aptamers that can be used for the
genetic encoding of fluorescent RNA. Spinach2 binds and activates
the fluorescence of (Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (DFHBI), allowing
the dynamic localizations of Spinach2-tagged RNAs to be imaged in
live cells. The spectral properties of Spinach2 are limited by DFHBI,
which produces fluorescence that is bluish-green and is not optimized
for filters commonly used in fluorescence microscopes. Here we characterize
the structural features that are required for fluorophore binding
to Spinach2 and describe novel fluorophores that bind and are switched
to a fluorescent state by Spinach2. These diverse Spinach2–fluorophore
complexes exhibit fluorescence that is more compatible with existing
microscopy filter sets and allows Spinach2-tagged constructs to be
imaged with either GFP or YFP filter cubes. Thus, these “plug-and-play”
fluorophores allow the spectral properties of Spinach2 to be altered
on the basis of the specific spectral needs of the experiment.
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Affiliation(s)
- Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University , New York, New York 10065, United States
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6
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Strack RL, Song W, Jaffrey SR. Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat Protoc 2013; 9:146-55. [PMID: 24356773 DOI: 10.1038/nprot.2014.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically encoded fluorescent sensors can be valuable tools for studying the abundance and flux of molecules in living cells. We recently developed a novel class of sensors composed of RNAs that can be used to detect diverse small molecules and untagged proteins. These sensors are based on Spinach, an RNA mimic of GFP, and they have successfully been used to image several metabolites and proteins in living bacteria. Here we discuss the generation and optimization of these Spinach-based sensors, which, unlike most currently available genetically encoded reporters, can be readily generated to any target of interest. We also provide a detailed protocol for imaging ADP dynamics in living Escherichia coli after a change from glucose-containing medium to other carbon sources. The entire procedure typically takes ∼4 d including bacteria transformation and image analysis. The majority of this protocol is applicable to sensing other metabolites and proteins in living bacteria.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
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7
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Song W, Strack RL, Jaffrey SR. Imaging bacterial protein expression using genetically encoded RNA sensors. Nat Methods 2013; 10:873-5. [PMID: 23872791 PMCID: PMC3758421 DOI: 10.1038/nmeth.2568] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/14/2013] [Indexed: 11/30/2022]
Abstract
We show that the difficulties in imaging the dynamics of protein expression in live bacterial cells can be overcome using fluorescent sensors based on Spinach, an RNA that activates the fluorescence of a small-molecule fluorophore. These RNAs selectively bind target proteins, and exhibit fluorescence increases that enable protein expression to be imaged in living cells. These sensors provide a general strategy to image protein expression in single bacteria in real-time.
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Affiliation(s)
- Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
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8
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Strack RL, Jaffrey SR. New approaches for sensing metabolites and proteins in live cells using RNA. Curr Opin Chem Biol 2013; 17:651-5. [PMID: 23746618 DOI: 10.1016/j.cbpa.2013.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
Abstract
Tools to study the abundance, distribution, and flux of intracellular molecules are crucial for understanding cellular signaling and physiology. Although powerful, the current FRET-based technology for imaging cellular metabolites is not easily generalizable. Thus, new platforms for generating genetically encoded sensors are needed. We recently developed a new class of biosensors on the basis of Spinach, an RNA mimic of GFP. In this case, RNA aptamers against a target ligand are modularly fused to Spinach that substantially induce Spinach fluorescence in the presence of ligand. We have used this approach to detect metabolites and proteins both in vitro and in living bacteria, thus providing an alternative to FRET-based sensors and a generalizable approach for generating fluorescent sensors to any ligand of interest.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, 1300 York Avenue, LC 523, New York, NY 10065, USA
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9
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Abstract
Fluorescent proteins (FPs) are invaluable tools for biomedical research. Useful FPs have desirable fluorescence properties such as brightness and photostability, but a limitation is that many orange, red, and far-red FPs are cytotoxic when expressed in the cytosol. This cytotoxicity stems from aggregation. To reduce aggregation, we engineered the surface of DsRed-Express to generate DsRed-Express2, a highly soluble tetrameric FP that is noncytotoxic in bacterial and mammalian cells. Directed evolution of DsRed-Express2 yielded the color variants E2-Orange, E2-Red/Green, and E2-Crimson. These variants can be used to label whole cells for single- and multi-color experiments employing microscopy or flow cytometry. Methods are described for reducing the higher-order aggregation of oligomeric FPs and for analyzing FP cytotoxicity in Escherichia coli and HeLa cells.
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Affiliation(s)
- Rita L. Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E. 58th St., Chicago, IL 60637
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10
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Abstract
Like GFP, the fluorescent protein DsRed has a chromophore that forms autocatalytically within the folded protein, but the mechanism of DsRed chromophore formation has been unclear. It was proposed that an initial oxidation generates a green chromophore, and that a final oxidation yields the red chromophore. However, this model does not adequately explain why a mature DsRed sample contains a mixture of green and red chromophores. We present evidence that the maturation pathway for DsRed branches upstream of chromophore formation. After an initial oxidation step, a final oxidation to form the acylimine of the red chromophore is in kinetic competition with a dehydration to form the green chromophore. This scheme explains why green and red chromophores are alternative end points of the maturation pathway.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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11
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Levi SK, Bhattacharyya D, Strack RL, Austin JR, Glick BS. The yeast GRASP Grh1 colocalizes with COPII and is dispensable for organizing the secretory pathway. Traffic 2010; 11:1168-79. [PMID: 20573068 DOI: 10.1111/j.1600-0854.2010.01089.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In mammalian cells, the 'Golgi reassembly and stacking protein' (GRASP) family has been implicated in Golgi stacking, but the broader functions of GRASP proteins are still unclear. The yeast Saccharomyces cerevisiae contains a single non-essential GRASP homolog called Grh1. However, Golgi cisternae in S. cerevisiae are not organized into stacks, so a possible structural role for Grh1 has been difficult to test. Here, we examined the localization and function of Grh1 in S. cerevisiae and in the related yeast Pichia pastoris, which has stacked Golgi cisternae. In agreement with earlier studies indicating that Grh1 interacts with coat protein II (COPII) vesicle coat proteins, we find that Grh1 colocalizes with COPII at transitional endoplasmic reticulum (tER) sites in both yeasts. Deletion of P. pastoris Grh1 had no obvious effect on the structure of tER-Golgi units. To test the role of S. cerevisiae Grh1, we exploited the observation that inhibiting ER export in S. cerevisiae generates enlarged tER sites that are often associated with the cis Golgi. This tER-Golgi association was preserved in the absence of Grh1. The combined data suggest that Grh1 acts early in the secretory pathway, but is dispensable for the organization of secretory compartments.
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Affiliation(s)
- Stephanie K Levi
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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12
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Strack RL, Hein B, Bhattacharyya D, Hell SW, Keenan RJ, Glick BS. Correction to A Rapidly Maturing Far-Red Derivative of DsRed-Express2 for Whole-Cell Labeling. Biochemistry 2009. [DOI: 10.1021/bi901587v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Strack RL, Hein B, Bhattacharyya D, Hell SW, Keenan RJ, Glick BS. A rapidly maturing far-red derivative of DsRed-Express2 for whole-cell labeling. Biochemistry 2009; 48:8279-81. [PMID: 19658435 PMCID: PMC2861903 DOI: 10.1021/bi900870u] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/17/2009] [Indexed: 11/30/2022]
Abstract
Fluorescent proteins (FPs) with far-red excitation and emission are desirable for multicolor labeling and live-animal imaging. We describe E2-Crimson, a far-red derivative of the tetrameric FP DsRed-Express2. Unlike other far-red FPs, E2-Crimson is noncytotoxic in bacterial and mammalian cells. E2-Crimson is brighter than other far-red FPs and matures substantially faster than other red and far-red FPs. Approximately 40% of the E2-Crimson fluorescence signal is remarkably photostable. With an excitation maximum at 611 nm, E2-Crimson is the first FP that is efficiently excited with standard far-red lasers. We show that E2-Crimson has unique applications for flow cytometry and stimulated emission depletion (STED) microscopy.
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Affiliation(s)
- Rita L. Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Birka Hein
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| | - Dibyendu Bhattacharyya
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637
| | - Stefan W. Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637
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14
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Strack RL, Bhattacharyya D, Glick BS, Keenan RJ. Noncytotoxic orange and red/green derivatives of DsRed-Express2 for whole-cell labeling. BMC Biotechnol 2009; 9:32. [PMID: 19344508 PMCID: PMC2678115 DOI: 10.1186/1472-6750-9-32] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 04/03/2009] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Whole-cell labeling is a common application of fluorescent proteins (FPs), but many red and orange FPs exhibit cytotoxicity that limits their use as whole-cell labels. Recently, a tetrameric red FP called DsRed-Express2 was engineered for enhanced solubility and was shown to be noncytotoxic in bacterial and mammalian cells. Our goal was to create derivatives of this protein with different spectral properties. RESULTS Building on previous studies of DsRed mutants, we created two DsRed-Express2 derivatives: E2-Orange, an orange FP, and E2-Red/Green, a dual-color FP with both red and green emission. We show that these new FPs retain the low cytotoxicity of DsRed-Express2. In addition, we show that these new FPs are useful as second or third colors for flow cytometry and fluorescence microscopy. CONCLUSION E2-Orange and E2-Red/Green will facilitate the production of healthy, stably fluorescent cell lines and transgenic organisms for multi-color labeling studies.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
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15
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Strack RL, Strongin DE, Bhattacharyya D, Tao W, Berman A, Broxmeyer HE, Keenan RJ, Glick BS. A noncytotoxic DsRed variant for whole-cell labeling. Nat Methods 2008; 5:955-7. [PMID: 18953349 DOI: 10.1038/nmeth.1264] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/23/2008] [Indexed: 11/09/2022]
Abstract
A common application of fluorescent proteins is to label whole cells, but many RFPs are cytotoxic when used with standard high-level expression systems. We engineered a rapidly maturing tetrameric fluorescent protein called DsRed-Express2 that has minimal cytotoxicity. DsRed-Express2 exhibits strong and stable expression in bacterial and mammalian cells, and it outperforms other available RFPs with regard to photostability and phototoxicity.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center W238, Chicago, Illinois 60637, USA
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16
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Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ. Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants. Protein Eng Des Sel 2007; 20:525-34. [PMID: 17962222 DOI: 10.1093/protein/gzm046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The red fluorescent protein DsRed has been extensively engineered for use as an in vivo research tool. In fast maturing DsRed variants, the chromophore maturation half-time is approximately 40 min, compared to approximately 12 h for wild-type DsRed. Further, DsRed has been converted from a tetramer into a monomer, a task that entailed mutating approximately 20% of the amino acids. These engineered variants of DsRed have proven extremely valuable for biomedical research, but the structural basis for the improved characteristics has not been thoroughly investigated. Here we present a 1.7 A crystal structure of the fast maturing tetrameric variant DsRed.T4. We also present a biochemical characterization and 1.6 A crystal structure of the monomeric variant DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures suggests that rearrangements of Ser69 and Glu215 contribute to fast maturation, and that positioning of the Lys70 side chain modulates fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A between the two structures. We propose that novel intramolecular interactions in DsRed.M1 partially compensate for the loss of intermolecular interactions found in the tetramer.
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Affiliation(s)
- Daniel E Strongin
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA
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