1
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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2
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. SUBCELLULAR TRANSCRIPTOMICS & PROTEOMICS: A COMPARATIVE METHODS REVIEW. Mol Cell Proteomics 2021; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics. Subcellular information of protein and RNA give insights into molecular function. This review discusses strategies available to measure subcellular information. Hybridization of methods shows promise for exploring the composition of organelles. Advances are aiding understanding of the organisation and dynamics of cells.
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Affiliation(s)
- Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
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3
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Park SY, Moon HC, Park HY. Live-cell imaging of single mRNA dynamics using split superfolder green fluorescent proteins with minimal background. RNA (NEW YORK, N.Y.) 2020; 26:101-109. [PMID: 31641028 PMCID: PMC6913125 DOI: 10.1261/rna.067835.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
The MS2 system, with an MS2 binding site (MBS) and an MS2 coat protein fused to a fluorescent protein (MCP-FP), has been widely used to fluorescently label mRNA in live cells. However, one of its limitations is the constant background fluorescence signal generated from free MCP-FPs. To overcome this obstacle, we used a superfolder GFP (sfGFP) split into two or three nonfluorescent fragments that reassemble and emit fluorescence only when bound to the target mRNA. Using the high-affinity interactions of bacteriophage coat proteins with their corresponding RNA binding motifs, we showed that the nonfluorescent sfGFP fragments were successfully brought close to each other to reconstitute a complete sfGFP. Furthermore, real-time mRNA dynamics inside the nucleus as well as the cytoplasm were observed by using the split sfGFPs with the MS2-PP7 hybrid system. Our results demonstrate that the split sfGFP systems are useful tools for background-free imaging of mRNA with high spatiotemporal resolution.
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Affiliation(s)
- Sung Young Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
| | - Hyungseok C Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea
- Institute of Applied Physics, Seoul National University, Seoul, 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea
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4
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Kim SH, Vieira M, Shim JY, Choi H, Park HY. Recent progress in single-molecule studies of mRNA localization in vivo. RNA Biol 2019; 16:1108-1118. [PMID: 30336727 PMCID: PMC6693552 DOI: 10.1080/15476286.2018.1536592] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022] Open
Abstract
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization in vivo. Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.
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Affiliation(s)
- Songhee H. Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Melissa Vieira
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
| | - Jae Youn Shim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hongyoung Choi
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
- Institute of Applied Physics, Seoul National University, Seoul, Korea
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5
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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6
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Sachdeva G, Myhrvold C, Yin P, Silver PA. Synthetic RNA Scaffolds for Spatial Engineering in Cells. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Gairik Sachdeva
- Harvard John A. Paulson School of Engineering and Applied Sciences, 29 Oxford Street; Cambridge MA 02138 USA
- Harvard University; Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle; Boston MA 02115 USA
- Harvard Medical School; Department of Systems Biology, 200 Longwood Avenue; Boston MA 02115 USA
| | - Cameron Myhrvold
- Harvard University; Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle; Boston MA 02115 USA
- Harvard Medical School; Department of Systems Biology, 200 Longwood Avenue; Boston MA 02115 USA
| | - Peng Yin
- Harvard University; Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle; Boston MA 02115 USA
| | - Pamela A. Silver
- Harvard University; Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle; Boston MA 02115 USA
- Harvard Medical School; Department of Systems Biology, 200 Longwood Avenue; Boston MA 02115 USA
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7
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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8
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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9
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Kellermann SJ, Rentmeister A. A FACS-based screening strategy to assess sequence-specific RNA-binding of Pumilio protein variants in E. coli. Biol Chem 2017; 398:69-75. [DOI: 10.1515/hsz-2016-0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Sequence-specific and programmable binding of proteins to RNA bears the potential to detect and manipulate target RNAs. Applications include analysis of subcellular RNA localization or post-transcriptional regulation but require sequence-specificity to be readily adjustable to any target RNA. The Pumilio homology domain binds an eight nucleotide target sequence in a predictable manner allowing for rational design of variants with new specificities. We describe a high-throughput system for screening Pumilio variants based on fluorescence-activated cell sorting of E. coli. Our approach should help optimizing variants obtained from rational design regarding folding and stability or identifying new variants with alternative binding modes.
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10
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Shigeto H, Nakatsuka K, Ikeda T, Hirota R, Kuroda A, Funabashi H. Continuous Monitoring of Specific mRNA Expression Responses with a Fluorescence Resonance Energy Transfer-Based DNA Nano-tweezer Technique That Does Not Require Gene Recombination. Anal Chem 2016; 88:7894-8. [DOI: 10.1021/acs.analchem.6b02710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hajime Shigeto
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Keisuke Nakatsuka
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
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11
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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12
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Urbanek MO, Galka-Marciniak P, Olejniczak M, Krzyzosiak WJ. RNA imaging in living cells - methods and applications. RNA Biol 2015; 11:1083-95. [PMID: 25483044 PMCID: PMC4615301 DOI: 10.4161/rna.35506] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Numerous types of transcripts perform multiple functions in cells, and these functions are mainly facilitated by the interactions of the RNA with various proteins and other RNAs. Insight into the dynamics of RNA biosynthesis, processing and cellular activities is highly desirable because this knowledge will deepen our understanding of cell physiology and help explain the mechanisms of RNA-mediated pathologies. In this review, we discuss the live RNA imaging systems that have been developed to date. We highlight information on the design of these systems, briefly discuss their advantages and limitations and provide examples of their numerous applications in various organisms and cell types. We present a detailed examination of one application of RNA imaging systems: this application aims to explain the role of mutant transcripts in human disease pathogenesis caused by triplet repeat expansions. Thus, this review introduces live RNA imaging systems and provides a glimpse into their various applications.
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Affiliation(s)
- Martyna O Urbanek
- a Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Poznan , Poland
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13
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Genetically encoded tools for RNA imaging in living cells. Curr Opin Biotechnol 2015; 31:42-9. [DOI: 10.1016/j.copbio.2014.07.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 07/30/2014] [Indexed: 12/11/2022]
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14
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Abstract
The spectrum of RNA functions in the cell continues to widen and new types of RNA molecules continue to be discovered. However, methods to access and manipulate endogenous RNAs in live cells are limited. Here we describe a universal technique for labeling natural RNAs in live cells with the probes synthesized by the cell. The method is based on fluorescent protein complementation in combination with a split aptamer approach. Two RNA probes containing split aptamer sequences flanked with the antisense RNA target sequences are assembled on the target RNA to form a fluorescent ribonucleoprotein (RNP) complex. The mechanism of complex formation ensures highly sensitive RNA detection allowing visualization of endogenous bacterial mRNAs. We demonstrate the great potential of this method by detecting chromosomally low-level expressed unmodified bacterial mRNA in living bacterial cells. This method holds promise to become a broadly used tool in basic research, and eventually in diagnostics and therapeutics.
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Affiliation(s)
- Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA, 01225, USA,
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15
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Toran P, Smolina I, Driscoll H, Ding F, Sun Y, Cantor CR, Broude NE. Labeling native bacterial RNA in live cells. Cell Res 2014; 24:894-7. [PMID: 24732010 DOI: 10.1038/cr.2014.47] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Paul Toran
- Cell Biology, Molecular Biology and Biochemistry Program, Boston University, Boston, MA 01225, USA
| | - Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA 01225, USA
| | - Harry Driscoll
- Department of Biomedical Engineering, Boston University, Boston, MA 01225, USA
| | - Feng Ding
- Department of Physics and Astronomy, 118 Kinard Lab, Clemson University, Clemson, SC 29634, USA
| | - Yingjie Sun
- Department of Biomedical Engineering, Boston University, Boston, MA 01225, USA
| | - Charles R Cantor
- Sequenom Inc, 3595 John Hopkins Court, San Diego, CA 92121-1331, USA
| | - Natalia E Broude
- 1] Cell Biology, Molecular Biology and Biochemistry Program, Boston University, Boston, MA 01225, USA [2] Department of Biomedical Engineering, Boston University, Boston, MA 01225, USA
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16
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Wu B, Chen J, Singer RH. Background free imaging of single mRNAs in live cells using split fluorescent proteins. Sci Rep 2014; 4:3615. [PMID: 24402470 PMCID: PMC3885884 DOI: 10.1038/srep03615] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/02/2013] [Indexed: 11/13/2022] Open
Abstract
We describe a technique for imaging single mRNAs in living cells based on fluorescent protein (FP) complementation. We employ the high affinity interaction between the bacterial phage MS2/PP7 coat proteins and their respective RNA binding motifs as an RNA scaffold to bring two halves of a split-FP together to image single reporter mRNAs without background fluorescence.
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Affiliation(s)
- Bin Wu
- 1] Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University [2] Gruss Lipper Biophotonic Center, Albert Einstein College of Medicine of Yeshiva University
| | - Jiahao Chen
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University
| | - Robert H Singer
- 1] Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University [2] Gruss Lipper Biophotonic Center, Albert Einstein College of Medicine of Yeshiva University
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17
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Abstract
Molecular imaging has greatly advanced basic biology and translational medicine through visualization and quantification of single/multiple molecular events temporally and spatially in a cellular context and in living organisms. Aptamers, short single-stranded nucleic acids selected in vitro to bind a broad range of target molecules avidly and specifically, are ideal molecular recognition elements for probe development in molecular imaging. This review summarizes the current state of aptamer-based biosensor development (probe design and imaging modalities) and their application in imaging small molecules, nucleic acids and proteins mostly in a cellular context with some animal studies. The article is concluded with a brief discussion on the perspective of aptamer-based molecular imaging.
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Affiliation(s)
- Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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18
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Govindarajan S, Nevo-Dinur K, Amster-Choder O. Compartmentalization and spatiotemporal organization of macromolecules in bacteria. FEMS Microbiol Rev 2012; 36:1005-22. [DOI: 10.1111/j.1574-6976.2012.00348.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022] Open
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19
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Nevo-Dinur K, Govindarajan S, Amster-Choder O. Subcellular localization of RNA and proteins in prokaryotes. Trends Genet 2012; 28:314-22. [DOI: 10.1016/j.tig.2012.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 03/15/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
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20
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Abstract
Visualization of RNA in live cells is a challenging task due to the transient character of most RNA molecules and the lack of adequate methods to label RNA noninvasively. Here, we describe a system for regulated RNA synthesis and visualization of RNA in live Escherichia coli cells based on protein complementation. This method allows for labeling RNA with a relatively small protein complex that becomes fluorescent only when bound to an RNA. This method greatly reduces the high fluorescence background characteristic of methods employing intact fluorescent proteins. A short reporter RNA was shown to localize at the cell periphery in nonrandom patterns.
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21
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Broude NE. Analysis of RNA localization and metabolism in single live bacterial cells: achievements and challenges. Mol Microbiol 2011; 80:1137-47. [DOI: 10.1111/j.1365-2958.2011.07652.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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