- Open Access
Suitable transfection methods for single particle tracing in plant suspension cells
© Göhring et al.; licensee BioMed Central Ltd. 2014
- Received: 14 April 2014
- Accepted: 15 May 2014
- Published: 31 May 2014
A multitude of different imaging systems are already available to image genetically altered RNA species; however, only a few of these techniques are actually suitable to visualize endogenous RNA. One possibility is to use fluorescently-labelled and hybridization-sensitive probes. In order to yield more information about the exact localization and movement of a single RNA molecule, it is necessary to image such probes with highly sensitive microscope setups. More challenges arise if such experiments are conducted in plant cells due to their high autofluorescence and demanding transfection procedures.
Here, we report in planta imaging of single RNA molecules using fluorescently labeled molecular beacons. We tested three different transfection protocols in order to identify optimal conditions for transfection of fluorescent DNA probes and their subsequent detection at the single molecule level.
We found that an optimized heat shock protocol provided a vastly improved transfection method for small DNA molecules which were used for subsequent single RNA molecule detection in living plant suspension cells.
- Single Molecule
- Molecular Beacon
- Transfection Method
- Single Molecule Level
- Transfection Protocol
Information about the distribution and spatio-temporal dynamics of distinct RNA molecules helps to gain a deeper understanding of a multitude of complex biological processes (e.g., post-transcriptional regulation of gene expression via splicing [1, 2], effects of RNA interference , or RNA’s complex interaction with chromatin ). In vivo imaging of RNA has traditionally required usage of overexpressed tagged proteins, saturated probes, or other reporter systems [5–9]. Often, it is challenging to show that these artificially introduced reporters do not have a negative effect on cellular functions, or a biasing effect on raw data. Labelling using hybridization-sensitive probes would, therefore, provide a nearly unperturbed examination of single endogenous mRNA molecules. In many standard biochemical experiments, bulk populations are analyzed instead of populations of single cells. Subtle and often very interesting effects will only be observable in small subpopulations . A prerequisite for such population statistics is, of course, to refrain from following the dogma of the ‘representative cell’ as the outcome of analysis.
There are several advantages that come with studying biological processes at a single molecule level. Single molecule tracing experiments give accurate information about forces that determine the characteristic motion of an individual molecule. Single molecule diffusion parameters calculated within the fragmented subcellular space (e.g. organelles/compartments ) can be a powerful tool to decipher cellular processes (e.g. protein interactions in cell signaling [12, 13]) or to characterize cell subpopulations . Typically, determination of a single particle trace of an RNA, i.e. one molecule’s diffusion in real time, provides information about direction of movement, step size, and whether there are confined volumes allowing movement within the observed cell volume [15, 16]. By analyzing enough molecules, it can also lead to insights about the percentage of mobile fractions and which kind of movement pattern they are following.
Recently, we successfully used fluorescent hybridization-sensitive probes (Molecular Beacons, MBs) to monitor the distribution of mRNA molecules in living plant cells . A simple workflow followed by a robust statistical pipeline led to the establishment of a tool which provides quantitative information on in vivo RNA localization and abundance. Due to their special conformation, MBs only fluoresce upon binding to their target sequence. This feature makes MBs the ideal tool for imaging of endogenous RNA in living plant cells as it provides a better signal-to-noise ratio; this is beneficial since autofluorescence in plants is, compared to other organisms, drastically increased . However, a severe disadvantage of MBs is the fact that they need to be delivered into the cell. Hitherto used techniques include microinjection and biolistic bombardment [19, 20] which are both laborious, time consuming, and expensive. Moreover, cells become considerably stressed via these invasive transfections. More advanced transfection protocols for mammalian cells make use of nanopore technologies and microfluidics [21, 22]. But, nonetheless, microinjection remains the only convenient method for transiently transfecting intact plant tissue.
In order to use MBs for RNA imaging in living plant protoplasts, we needed to establish a gentle transfection protocol. We chose to test polyethylenglycole (PEG), electroporation, and heat shock mediated transfection methods to investigate the localization of a specific MB against the transcripts of RS2Z33, a plant-specific SR protein, which has been described elsewhere [23, 24].
Molecular Beacons are DNA oligonucleotides with a stem loop structure, whose 5’end is conjugated to a fluorophore (Atto550), and its 3’end to a quencher (BHQ2). The loop sequence targets the RNA of interest (RS2Z33 transcripts), whereas the self-complementary stem keeps the quencher and the fluorophore in close proximity, suppressing any signal. If the MB binds to the target, the stem opens and the fluorophore emits a signal. The MB was designed according to Gohring et al. . 33mRNA_EJ6 (5’-Atto550-GATCGCGCGTGATCGGCTGTAGCTTCGGCCGCGATC-BHQ2-3’).
Cell Culture, Isolation of Protoplasts, and PEG transfection
Arabidopsis cell suspension culture protoplasts (derived from 10d old Col-0 seedlings) were prepared and immediately used for PEG transformation as described in Lorkovic et al. .
Variation of the electroporation buffer in respect to osmolarity, electrical conductivity, and resistance.
Variation of the cell density, washing buffer (PIB or GM buffer, for final buffer composition see below), length of incubation on ice after electroporation
Variation of electrical parameters: voltage, capacity, transferred energy, pulse lengths and intervals.
Further details can be found in the Additional file 1: Data S1. The criteria for the experimental outcome were subjective and included the evaluation of the cellular morphology, presence of cell debris, cell viability, and the state of transfection.
Two hours after protoplast isolation, cells were transfected by electroporation. Approximately 1×105 protoplast cells were washed with 0.275 M Calcium-nitrate and pelleted in a microcentrifuge (150 g for 2 minutes). For electroporation, 0.7 M mannitol (~700 mOsm) was mixed to a final concentration of 500 nM MB. A final volume of 800 μL in a 4 mm cuvette (Biozym Scientific, Oldendorf) was pulsed with following settings of the device Easyject Optima, EquiBio: 240 V, 75 μF, 2 pulses with the length of approximately 7.5 ms and an interval of 20 s. Subsequently, cells were fed with 0.34 M GM-buffer [3163 mg/L Gamborg B5 powder including vitamins (Duchefa), 170 mM D-glucose, 170 mM D-mannitol, 1 mg/L 2.4D, pH 5.5 adjusted with KOH], incubated at room temperature, and kept in the dark for 24 h. Shortly before measurement, cells were washed twice with GM-buffer.
Variation of the osmolarity of the PIB buffer (see below), in order to test the mechanical stress limits of the cellular membrane.
Variation of the cell density, heat shock temperature, length, and subsequent length of incubation on ice.
Variation of the washing buffers (PIB or GM buffer, for final buffer composition see below).
Further details can be found in the Supplementary Data S1. The criteria for experimental outcome were subjective and included the evaluation of the cellular morphology, presence of cell debris, cell viability and the state of transfection.
Two hours after protoplast isolation, cells were transfected by heat shock. The protocol was adjusted from Hicks et al. . Approximately 1×105 protoplast cells were resuspended in 200 μL 2×PIB buffer [2 mM MgAc, 50 mM KAc, 5 mM NaAc, 2 mM PMSF, 20 mM HEPES pH7.2, 1 mM DTT, 225 mM mannitol, 125 mM Spermin, 125 mM Spermidin]. Cells were incubated on ice in the dark for 10 minutes and subsequently pelleted in a microcentrifuge (150 g for 2 minutes). The pellet was resuspended in a solution containing 500 nM MBs in 2xPIB buffer and heat shocked for 30 minutes at 28°C in the dark. Afterwards, cells were immediately put on ice for 4 minutes and 100 μL of 1xPIB were added as fast as possible. Eventually, cells were fed with 0.34 M GM-buffer [3163 mg/L Gamborg B5 powder including vitamins (Duchefa), 170 mM D-glucose, 170 mM D-mannitol, 1 mg/L 2.4D, pH 5.5 adjusted with KOH], incubated at room temperature, and kept in the dark for 24 h. Shortly before measurement, cells were washed twice with GM-buffer.
Imaging of single molecules and analysis
The images were taken on a modified Olympus IX81 inverted microscope. The samples were illuminated through an Olympus UApo N 100×/1.49 NA oil objective with diode laser at 532 nm (Cobolt Calypso 100 TM). The signal acquisition was carried out on an Andor iXonEM + 897 (back illuminated) EMCCD (160 nm pixel size). The experiments were performed using excitation powers of 0.025 kW/cm2 at 532 nm. The samples were illuminated for 5 ms with 35 ms delay time. The illumination protocols were timed with a custom made LabView® based control software. Filter: Overlay (642/532), Dichroic filter: Cy3/Cy5, Emission-filter: Cy3/Cy5 + Bandpass 595/50 (Chroma). The cells were imaged in two illumination configurations, the widefield and highly inclined and laminated optical light sheet (HILO) illumination. The light sheet illumination reduces background fluorescence within the cell, originating from scattered light or other fluorescent molecules .
Given the heterogeneous background, we have chosen a detection method based on the isotropic undecimated wavelet transform (IUWT) [28, 29]. Wavelet thresholding offers a robust solution for the detection of small bright features, e.g. detection of sub-cellular structures labeled by fluorescent dyes. Since a fluorescent dye can be considered a point light source, its image is the point spread function (PSF) of the optical system that can be approximated by a two-dimensional Gaussian shape.
With n the number of detected photo-electrons and N the number of emitted photons.
Where F represents the excess noise and G the average multiplier gain.
In order to deal with the heterogeneity of the noise, a variance stabilizing transform is applied prior to the IUWT . This step significantly reduces the background and improves the quality of single molecule localization. The method relies on a successive fitting of the noise with a constant kernel wavelet matrix . Subsequently, the fitted background image is subtracted from the original image. After several iterative repeats position of candidates for Gaussian fitting are chosen [28, 33, 34]. Subsequently, the detected molecule’s position was determined with subpixel accuracy by least square fitting of a 2D Gaussian function in the neighborhood of the detected significant pixels [33–36].
The transfection of MBs via heat shock turned out to be a compromise. We optimized the heat shock protocol (oriented along the permeability protocol from Hicks et al. ) in respect of used buffers, heat shock, and recovery time, as well as amount of DNA initially used per cell (see Methods for more details). The investigated cells exhibited good viability with relatively low transfection efficiency (with clearly separated single molecule signals). The detected fluorescent signals were at or below the detection limit of a standard laser scanning microscopy setup. We observed relatively high transfection homogeneity within the cell population, good viability, and a low fluorescent background (comparable to non-transfected cells) (Figure 3B). The average SNR of detected MB single molecule signals in cells was 9.7 ± 2.4 (SNR averaged over all signals), which is sufficient for any single molecule fluorescence experiment e.g. single molecule tracking (Figure 3 and Additional file 3: Figure S2). The transfection efficiency shows a clear dependence on concentration and incubation time, which can be used for a relatively precise adjustment of MB concentration. Consequently, this method seems to be a good approach for transfection of cells with MBs permitting single molecule analysis.
Herein, we report the establishment of two transfection methods for A. thaliana suspension protoplasts optimized for measuring Molecular Beacons with single molecule sensitivity. The standard PEG-based transfection method is not applicable for fluorescent microscopy since PEG-bound MBs remain in an open state and lead to a considerable increase in background fluorescence. Electroporated cells also tend to exhibit high background due to the increased amount of extracellular debris. However, transfection via heat shock turned out to be the optimal transfection method for MBs. The transfection has low material requirements and a smaller work load compared to other described methods e.g., microinjection or bombardment. Heat shocked cells are vital and not influenced in their morphology. The extracellular background is reduced and cells exhibit low transfection efficiencies which are best suited for single molecule measurement. Moreover, we report for the first time the successful measurement of single molecules within living plant suspension cells.
This work was supported by grants to AB of the Austrian Science Fund (FWF) [DK W1207; I-254; SFB RNA-REG F43-P10].
- So MK, Gowrishankar G, Hasegawa S, Chung JK, Rao J: Imaging target mRNA and siRNA-mediated gene silencing in vivo with ribozyme-based reporters. Chembiochem. 2008, 9: 2682-2691. 10.1002/cbic.200800370.View ArticlePubMedGoogle Scholar
- Bhaumik S, Walls Z, Puttaraju M, Mitchell LG, Gambhir SS: Molecular imaging of gene expression in living subjects by spliceosome-mediated RNA trans-splicing. Proc Natl Acad Sci U S A. 2004, 101: 8693-8698. 10.1073/pnas.0402772101.PubMed CentralView ArticlePubMedGoogle Scholar
- Chang E, Zhu MQ, Drezek R: Novel siRNA-based molecular beacons for dual imaging and therapy. Biotechnol J. 2007, 2: 422-425. 10.1002/biot.200600257.View ArticlePubMedGoogle Scholar
- van den Bogaard PT, Tyagi S: Using molecular beacons to study dispersal of mRNPs from the gene locus. Methods Mol Biol. 2009, 464: 91-103.View ArticlePubMedGoogle Scholar
- Stockley PG, Stonehouse NJ, Murray JB, Goodman ST, Talbot SJ, Adams CJ, Liljas L, Valegard K: Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protein. Nucleic Acids Res. 1995, 23: 2512-2518. 10.1093/nar/23.13.2512.PubMed CentralView ArticlePubMedGoogle Scholar
- Daigle N, Ellenberg J: LambdaN-GFP: an RNA reporter system for live-cell imaging. Nat Methods. 2007, 4: 633-636. 10.1038/nmeth1065.View ArticlePubMedGoogle Scholar
- Ozawa T, Natori Y, Sato M, Umezawa Y: Imaging dynamics of endogenous mitochondrial RNA in single living cells. Nat Methods. 2007, 4: 413-419.PubMedGoogle Scholar
- Tyagi S, Kramer FR: Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996, 14: 303-308. 10.1038/nbt0396-303.View ArticlePubMedGoogle Scholar
- Hasegawa S, Gowrishankar G, Rao J: Detection of mRNA in mammalian cells with a split ribozyme reporter. Chembiochem. 2006, 7: 925-928. 10.1002/cbic.200600061.View ArticlePubMedGoogle Scholar
- Muramoto T, Cannon D, Gierlinski M, Corrigan A, Barton GJ, Chubb JR: Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A. 2012, 109: 7350-7355. 10.1073/pnas.1117603109.PubMed CentralView ArticlePubMedGoogle Scholar
- Gombos I, Crul T, Piotto S, Gungor B, Torok Z, Balogh G, Peter M, Slotte JP, Campana F, Pilbat AM, Hunya A, Toth N, Literati-Nagy Z, Vigh L, Glatz A, Brameshuber M, Schütz GJ, Hevener A, Febbraio MA, Horvath I, Vigh L: Membrane-lipid therapy in operation: the HSP co-inducer BGP-15 activates stress signal transduction pathways by remodeling plasma membrane rafts. Plos One. 2011, 6: e28818. 10.1371/journal.pone.0028818.PubMed CentralView ArticlePubMedGoogle Scholar
- Axmann M, Huppa JB, Davis MM, Schutz GJ: Determination of interaction kinetics between the T cell receptor and peptide-loaded MHC class II via single-molecule diffusion measurements. Biophys J. 2012, 103: L17-L19. 10.1016/j.bpj.2012.06.019.PubMed CentralView ArticlePubMedGoogle Scholar
- Serge A, de Keijzer S, Van Hemert F, Hickman MR, Hereld D, Spaink HP, Schmidt T, Snaar-Jagalska BE: Quantification of GPCR internalization by single-molecule microscopy in living cells. Integr Biol Quant Biosci nano macro. 2011, 3: 675-683.Google Scholar
- Brameshuber M, Schutz GJ: Detection and quantification of biomolecular association in living cells using single-molecule microscopy. Methods Enzymol. 2012, 505: 159-186.View ArticlePubMedGoogle Scholar
- Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH: Dynamics of single mRNPs in nuclei of living cells. Science. 2004, 304: 1797-1800. 10.1126/science.1099754.View ArticlePubMedGoogle Scholar
- Vargas DY, Raj A, Marras SA, Kramer FR, Tyagi S: Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci U S A. 2005, 102: 17008-17013. 10.1073/pnas.0505580102.PubMed CentralView ArticlePubMedGoogle Scholar
- Gohring J, Jacak J, Barta A: Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis. The Plant cell. 2014, 26: 754-764. 10.1105/tpc.113.118075.PubMed CentralView ArticlePubMedGoogle Scholar
- Chapman S, Oparka KJ, Roberts AG: New tools for in vivo fluorescence tagging. Curr Opin Plant Biol. 2005, 8: 565-573. 10.1016/j.pbi.2005.09.011.View ArticlePubMedGoogle Scholar
- Seki M, Iida A, Morikawa H: Transient expression of the beta-glucuronidase gene in tissues of Arabidopsis thaliana by bombardment-mediated transformation. Mol Biotechnol. 1999, 11: 251-255. 10.1007/BF02788683.View ArticlePubMedGoogle Scholar
- Ueki S, Lacroix B, Krichevsky A, Lazarowitz SG, Citovsky V: Functional transient genetic transformation of Arabidopsis leaves by biolistic bombardment. Nat Protoc. 2009, 4: 71-77.View ArticlePubMedGoogle Scholar
- Li N, Wong PK: Transfection of molecular beacons in microchannels for single-cell gene-expression analysis. Bioanalysis. 2010, 2: 1689-1699. 10.4155/bio.10.116.View ArticlePubMedGoogle Scholar
- Nelson EM, Kurz V, Shim J, Timp W, Timp G: Using a nanopore for single molecule detection and single cell transfection. Analyst. 2012, 137: 3020-3027. 10.1039/c2an35571j.PubMed CentralView ArticlePubMedGoogle Scholar
- Lopato S, Forstner C, Kalyna M, Hilscher J, Langhammer U, Indrapichate K, Lorkovic ZJ, Barta A: Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors. J Biol Chem. 2002, 277: 39989-39998. 10.1074/jbc.M206455200.View ArticlePubMedGoogle Scholar
- Kalyna M, Lopato S, Barta A: Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol Biol Cell. 2003, 14: 3565-3577. 10.1091/mbc.E03-02-0109.PubMed CentralView ArticlePubMedGoogle Scholar
- Lorkovic ZJ, Hilscher J, Barta A: Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells. Mol Biol Cell. 2004, 15: 3233-3243. 10.1091/mbc.E04-01-0055.PubMed CentralView ArticlePubMedGoogle Scholar
- Hicks GR, Smith HM, Lobreaux S, Raikhel NV: Nuclear import in permeabilized protoplasts from higher plants has unique features. Plant cell. 1996, 8: 1337-1352. 10.1105/tpc.8.8.1337.PubMed CentralView ArticlePubMedGoogle Scholar
- Tokunaga M, Imamoto N, Sakata-Sogawa K: Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods. 2008, 5: 159-161. 10.1038/nmeth1171.View ArticlePubMedGoogle Scholar
- Olivo-Marin JC: Extraction of spots in biological images using multiscale products. Pattern Recogn. 2002, 35: 1989-1996. 10.1016/S0031-3203(01)00127-3.View ArticleGoogle Scholar
- Starck JL, Fadili J, Murtagh F: The undecimated wavelet decomposition and its reconstruction. Ieee T Image Process. 2007, 16: 297-309.View ArticleGoogle Scholar
- Hynecek J, Nishiwaki T: Excess noise and other important characteristics of low light level imaging using charge multiplying CCDs. IEEE Trans On Electron Devices. 2003, 50: 239-245. 10.1109/TED.2002.806962.View ArticleGoogle Scholar
- Muresan L, Jacak J, Klement EP, Hesse J, Schutz GJ: Microarray analysis at single-molecule resolution. IEEE Trans Nanobioscience. 9: 51-58.Google Scholar
- Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc. 1995, 57: 289-300.Google Scholar
- Muresan L, Jacak J, Klement EP, Hesse J, Schutz GJ: Microarray Analysis at Single-Molecule Resolution. Ieee T Nanobiosci. 2010, 9: 51-58.View ArticleGoogle Scholar
- Sams M, Silye R, Gohring J, Muresan L, Schilcher K, Jacak J: Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue. J Biomed Opt. 2014, 19: 011021.View ArticlePubMedGoogle Scholar
- Jacak J, Schnidar H, Muresan L, Regl G, Frischauf A, Aberger F, Schutz GJ, Hesse J: Expression analysis of multiple myeloma CD138 negative progenitor cells using single molecule microarray readout. J Biotechnol. 2013, 164: 525-530. 10.1016/j.jbiotec.2013.01.027.PubMed CentralView ArticlePubMedGoogle Scholar
- Hesse J, Jacak J, Kasper M, Regl G, Eichberger T, Winklmayr M, Aberger F, Sonnleitner M, Schlapak R, Howorka S, Muresan L, Frischauf AM, Schütz GJ: RNA expression profiling at the single molecule level. Genome Res. 2006, 16: 1041-1045. 10.1101/gr.4999906.PubMed CentralView ArticlePubMedGoogle Scholar
- Mathur J, Koncz C: PEG-mediated protoplast transformation with naked DNA. Methods Mol Biol. 1998, 82: 267-276.PubMedGoogle Scholar
- Miao Y, Jiang L: Transient expression of fluorescent fusion proteins in protoplasts of suspension cultured cells. Nat Protoc. 2007, 2: 2348-2353. 10.1038/nprot.2007.360.View ArticlePubMedGoogle Scholar
- Bates GW: Genetic transformation of plants by protoplast electroporation. Mol Biotechnol. 1994, 2: 135-145. 10.1007/BF02824806.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.