Fluorescence Activated Cell Sorting of Plant Protoplasts


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A method for isolating specific cell types from plant material is demonstrated. This technique employs transgenic marker lines expressing fluorescent proteins in particular cell types, cellular dissociation and Fluorescence Activated Cell Sorting. Additionally, a growth setup is established here that facilitates treatment of Arabidopsis thaliana seedlings prior to cell sorting.

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Bargmann, B. O., Birnbaum, K. D. Fluorescence Activated Cell Sorting of Plant Protoplasts. J. Vis. Exp. (36), e1673, doi:10.3791/1673 (2010).


High-resolution, cell type-specific analysis of gene expression greatly enhances understanding of developmental regulation and responses to environmental stimuli in any multicellular organism. In situ hybridization and reporter gene visualization can to a limited extent be used to this end but for high resolution quantitative RT-PCR or high-throughput transcriptome-wide analysis the isolation of RNA from particular cell types is requisite. Cellular dissociation of tissue expressing a fluorescent protein marker in a specific cell type and subsequent Fluorescence Activated Cell Sorting (FACS) makes it possible to collect sufficient amounts of material for RNA extraction, cDNA synthesis/amplification and microarray analysis.

An extensive set of cell type-specific fluorescent reporter lines is available to the plant research community. In this case, two marker lines of the Arabidopsis thaliana root are used: PSCR::GFP (endodermis and quiescent center) and PWOX5::GFP (quiescent center). Large numbers (thousands) of seedlings are grown hydroponically or on agar plates and harvested to obtain enough root material for further analysis. Cellular dissociation of plant material is achieved by enzymatic digestion of the cell wall. This procedure makes use of high osmolarity-induced plasmolysis and commercially available cellulases, pectinases and hemicellulases to release protoplasts into solution.

FACS of GFP-positive cells makes use of the visualization of the green versus the red emission spectra of protoplasts excited by a 488 nm laser. GFP-positive protoplasts can be distinguished by their increased ratio of green to red emission. Protoplasts are typically sorted directly into RNA extraction buffer and stored for further processing at a later time.

This technique is revealed to be straightforward and practicable. Furthermore, it is shown that it can be used without difficulty to isolate sufficient numbers of cells for transcriptome analysis, even for very scarce cell types (e.g. quiescent center cells). Lastly, a growth setup for Arabidopsis seedlings is demonstrated that enables uncomplicated treatment of the plants prior to cell sorting (e.g. for the cell type-specific analysis of biotic or abiotic stress responses). Potential supplementary uses for FACS of plant protoplasts are discussed.


1) Preparation of the plant material

  1. Protoplasts can be derived from many different plant species and tissues provided that the right mix of cell wall digesting enzymes is used1. Before a full-scale experiment is undertaken, a small-scale digestion of the material is advisable in order to evaluate the protoplasting efficiency of the tissue, enzymes, etc. and to estimate the percent positive cells for cell sorting. Here, protoplasts derived from the roots of Arabidopsis thaliana seedlings that cell type-specifically express green fluorescent protein (GFP) are used. The endodermis and quiescent center are marked by PSCR::GFP and the quiescent center by PWOX5::GFP2,3 (Figure 1).
  2. Seedlings are grown hydroponically in phytatrays (Sigma; Figure 2a) on a nylon filter (250 μm mesh; NITEX) which lets the roots grow through into the growth medium (0.22% w/v Murashige and Skoog Basal Medium [Sigma], 1% w/v sucrose, 0.05% w/v MES [2-(N-morpholino)ethanesulfonic acid], pH 5.7 with KOH). Alternatively, plants can be grown on top of a nylon filter (100 μm mesh) in vertically positioned 1% agar plates (Figure 2b).
  3. The use of the abovementioned filters not only aids in the harvest of the roots, it also facilitates easy additional treatment of the seedlings, if desired. The filters allow the seedlings to be transferred en masse to new phytatrays or agar plates supplemented with a catalyst of interest. For example, the phytatray set up has been used for cell type-specific analysis of the transcriptional response to nitrogen treatment in Arabidopsis seedlings4.
  4. Ensure microscopically that your fluorescent marker is correctly expressed (especially when using the treatment option, as the cell type-specific markers themselves might be influenced by the treatment). In this case, seedlings are inspected under a fluorescence microscope (Nikon; Figure 1). Note that cell type-specific fluorescent marker lines should be characterized initially under a confocal microscope to determine exactly which cell types are marked and determine variability in expression.

2) Preparation of the protoplasting solution

  1. Dissolve 1.25% w/v Cellulase (Yakult), 0.3% w/v Macerozyme (Yakult), 0.4 M D-mannitol, 20 mM MES and 20 mM KCl (from a 1 M stock) in demineralized water and adjust the pH to 5.7 with 1 M Tris/HCl pH 7.5. This solution will be slightly turbid.
  2. Heat the solution to 55° C for 10 minutes (the solution will turn clear) and let it cool down to room temperature before adding 0.1% w/v BSA (bovine serum albumin), 10 mM CaCl2, and 5 mM β-mercaptoethanol.

3) Harvesting and protoplasting of the plant material

  1. The roots are harvested by scraping them off the nylon mesh with a scalpel and deposited into a flask containing the protoplasting solution. Generally, 10 ml of protoplasting solution is used per 1,500 seedling roots.
  2. Shake the flasks gently (75 rpm) at room temperature for one hour. A longer incubation time may increase the protoplast yield but will also add to the effect of protoplasting itself on gene expression.
  3. Filter the protoplast solution with a 40 μm cell strainer (BD Falcon) and divide the solution over conical 15 ml tubes (BD Falcon).
  4. Spin the tubes in a swing-bucket centrifuge for 10 minutes at 500 G. Note that this centrifugation speed will depend on the type of protoplasts used, their fragility and the amount of cell debris produced during enzymatic treatment.
  5. Remove most of the supernatant, resuspend the protoplasts in the remaining solution and inspect them microscopically (Figure 3).
  6. Make use of a hemacytometer to estimate the number and density of protoplasts. The cell density will determine sample injection speed, the events per second rate and therefore the total time needed to sort the cells at the FACS (see also section 4.3).
  7. 3.7) Either proceed directly to FACS or wash and resuspend the protoplasts in an incubation solution, such as W5 (154 mM NaCl, 125 mM CaCl2, 5 mM KCl, 5 mM MES, adjust pH to 5.7 with KOH) or protoplasting solution without the added enzymes. Especially when looking at transcriptional changes, it is of importance to minimize the exposure of the samples to conditions that might influence gene expression, such as changing the buffer the protoplasts are kept in. It is therefore recommended to keep the protoplasts in protoplasting solution and proceed to FACS as soon as possible.

4) Fluorescence Activated Cell Sorting of protoplasts

  1. Turn on and prepare the cell sorter. Here, a FACSAria (BD) is used.
  2. Set up a flow stream with a 100 μm nozzle and a 20 psi sheath pressure.
  3. The cell density and sample injection speed can be adjusted to the particular experiment based on whether a best possible yield or fastest achievable speed is desired. We have sorted successfully with densities up to 10,000,000 cells/ml.
  4. Use the sample agitation option on the FACS to prevent sedimentation of the protoplasts. If clogging of the FACS is an issue, there are three possible troubleshooting steps: 1. Perform a sample-line backflush. 2. Dilute your protoplast suspension to reduce the density. 3. Clean up the protoplast solution by repeating the filtration step (3.3) after centrifugation and resuspension.
  5. Prepare the apparatus to measure forward scatter (FSC), side scatter (SSC) and emission at 530/30 nm for GFP and 610/20 nm for red spectrum autofluorescence (RSA) after excitation by a 488 nm laser. These are in essence the only parameters used to isolate GFP-positive protoplasts. Here, the voltage settings were as follows: FSC - 60V, SSC 250V, GFP 350V and RSA 335V. Note that the optimal voltage settings will be different for every FACS and will even need to be adjusted throughout the lifetime of the cell sorter.
  6. Start by setting up a dotplot for forward scatter versus side scatter. Apply the voltage settings so that the measured events are centered in the plot.
  7. Next, create a dot plot of green versus red fluorescence signals. Apply the voltage settings so that the measured events yield a centered diagonal population in the plot when looking at a wild-type (non-GFP) protoplast suspension. A protoplast suspension derived from a GFP marker line will produce a clear population of green fluorescent events never seen in wild-type samples.
  8. Set compensation constraints to adjust for spectral overlap between GFP and RSA. Proper compensation constraint settings will allow for better separation of the GFP-positive protoplasts from the non-GFP protoplasts and debris. The constraints used here are as follows: RSA, minus 17.91% GFP.
  9. Set up a gate to identify GFP-positive events, a negative control of non-GFP protoplasts should be used to aid in defining the gate boundaries (Figure 4).
  10. Implement a forward scatter cutoff in order to leave small debris out of the analysis. Visualize the GFP-positive events in the FSC vs. SSC plot to help determine the placement of the cutoff. Here, the cutoff was set at 5,000. Note that the FACS will count debris as sort events and a sample with high levels of debris may have a different percent GFP positive events than expected. This is not necessarily a problem. However, the more debris in the sample, the longer the sort will take.
  11. Depending on the experiment and the abundance of the cell type to be analyzed, set the FACS precision mode either for optimal yield or optimal purity of the sorted cells.
  12. For RNA extraction, prepare collection tubes (1.5 ml microfuge tubes) with the appropriate amount of RNA extraction buffer. With this setup, 20,000 sorting events will yield a total volume of approximately 100 μl which were sorted in to 350 μl of extraction buffer (RNeasy micro kit, QIAGEN). Mix samples after completion of the sort as cell suspension can pool at the top.
  13. Store samples or proceed directly to RNA extraction. Successful microarray analyses have been preformed with the RNA extracted from as little as 500 sorted events. Here, we used an RNeasy micro extraction kit (QIAGEN), the WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2 (NuGEN).

Representative Results

One phytatray of approximately 1,500 one-week-old PSCR::GFP seedlings yielded about 60,000 protoplasts (as measured by hemacytometer). 2.6% of 65,000 FACS-processed events were defined as being GFP-positive and were sorted (Figure 4b).

Eight plates of approximately 1,500 four-day-old PWOX5::GFP seedlings each (12,000 total) yielded about 30,000,000 protoplasts (as measured by hemacytometer). 0.063% of 16,000,000 FACS-processed events were defined as being GFP-positive and were sorted (Figure 4c).

10,000 sorted events are typically used for RNA extraction and can yield from 20 to 140 ng total RNA (Figure 5).

Figure 1
Figure 1. Cell type-specific GFP marker lines in the Arabidopsis root. Fluorescence microscopy images were taken with differential interference contrast (DIC) and a GFP filter on an Eclipse 90i microscope (Nikon) running on Metamorph software (Molecular Devices). The DIC and GFP images were overlaid for visualization purposes. The two marker lines used in this visual experiment are shown; a) PSCR::GFP and b) PWOX5::GFP.

Figure 2
Figure 2. Plant growth conditions. Seedlings were grown in an environmental controller hydroponically in phytatrays (a) or on vertically positioned agar plates (b).

Figure 3
Figure 3. Plant protoplasts expressing GFP. Fluorescence microscopy images were taken with differential interference contrast (DIC) and a GFP filter on an Eclipse 90i microscope (Nikon) running on Metamorph software (Molecular Devices). The DIC and GFP images were overlaid for visualization purposes. Arrows indicate a burst cell, cell debris and a GFP-positive protoplast. The distance between two white lines is 50 μm.

Figure 4
Figure 4. Fluorescence activated cell sorting of GFP-positive protoplasts. Protoplasts derived from wild type (a) PSCR::GFP (b) or PWOX5::GFP (c) marker lines were analyzed and sorted with a FACSAria (BD) using gates defined on a dotplot of green (530/30 nm; x axis) versus red (610/20 nm; y axis) fluorescence. 100,000 events are presented in each plot. The events falling within the GFP sorting gate are highlighted green.

Figure 5
Figure 5. Representative RNA extractions from 10.000 sorted cells. Cells were sorted directly into RNA extraction buffer (QIAGEN), the RNA was purified and checked for concentration, purity and integrity on a 2100 Bioanalyzer (Agilent). Three replicates for both marker lines are shown.

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Protoplasts can, in principle, be derived from a variety of plant tissues, optimizing favorable conditions will greatly enhance RNA quality and quantity. Both the protoplasting solution and the elective incubation buffer used will influence this aspect.

Many different fluorescent proteins can be used, depending on the capabilities of the FACS used, e.g. GFP, RFP, YFP, CFP or their many variants and derivatives. The expression of the markers could be driven not just by cell type-specific promoters or enhancer traps, as shown here, but also by your favorite promoter, e.g. a hormone responsive synthetic reporter gene5. Dual color FACS of plant protoplasts is also feasible. This can, for example, be applied when performing a transient transformation assay using a vector with a fluorescent positive selection marker5.

Protoplasts can also be sorted for the analysis of genomic DNA, proteins or metabolites6. Keeping protoplasts alive after sorting is challenging due to their fragile nature, using a larger (130 μm) nozzle and lower sheath pressure and sorting them into an optimized incubation buffer will enhance post-sort protoplast viability.

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This work was supported by the National Science Foundation (grant no. DBI 0519984) and the National Institutes of Health (grant no. 5R01GM078279)..


Name Company Catalog Number Comments
250 μm nylon mesh Sefar Filtration NITEX 03-250/50
100 μm nylon mesh Sefar Filtration NITEX 03-100/47
Square petri dishes Fisher Scientific 08-757-10k
Phytatrays Sigma-Aldrich P1552
Murashige and Skoog Basal Medium (MS) Sigma-Aldrich M5519
sucrose Fisher Scientific S5-3
MES Sigma-Aldrich M2933
KOH Sigma-Aldrich P1767 10 M stock
Eclipse 90i microscope Nikon Instruments
Cellulase R-10 Yakult Pharmaceutical
Macerozyme R-10 Yakult Pharmaceutical
D-mannitol Sigma-Aldrich M9546
KCl Sigma-Aldrich P8041 1 M stock
BSA Sigma-Aldrich A3912
β-mercapt–thanol Calbiochem 444203
CaCl2 Sigma-Aldrich C2536 1 M stock
orbital shaker Labline Instruments
40 μm cell strainer BD Biosciences 352340
conical 15 ml tubes BD Biosciences 352196
table centrifuge Sorvall, Thermo Scientific Legend RT
NaCl Sigma-Aldrich S3014
FACSAria BD Biosciences
1.5 ml microfuge tubes VWR international 20170-38
RNeasy micro kit Qiagen 74004
WT-Ovation Pico RNA Amplification System NuGEN 3300_12
FL-Ovation cDNA Biotin Module V2 NuGEN 4200_12



  1. Sheen, J. Signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol. 127, 1466-1475 (2001).
  2. Wysocka-Diller, J. W., Helariutta, Y., Fukaki, H., Malamy, J. E., Benfey, P. N. Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development. 127, 595-603 (2000).
  3. Blilou, I., Xu, J., Wildwater, M., Willemsen, V., Paponov, I., Friml, J., Heidstra, R., Aida, M., Palme, K., Scheres, B. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature. 433, 39-44 (2005).
  4. Gifford, M. L., Dean, A., Gutierrez, R. A., Coruzzi, G. M., Birnbaum, K. D. Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A. 105, 803-808 (2008).
  5. Bargmann, B. O. R., Birnbaum, K. D. Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts. Plant Physiol. 149, 1231-1239 (2009).
  6. Petersson, S. V., Johansson, A. I., Kowalczyk, M., Makoveychuk, A., Wang, J. Y., Moritz, T., Grebe, M., Benfey, P. N., Sandberg, G., Ljung, K. An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis. Plant Cell. 21, 1659-1668 (2009).



  1. What is the usual purity of the GFP-positive protoplasts from your sorting experiments? We have sorted protoplasts several times as described here and we cannot get higher than about 50% GFP-positive protoplasts in the sorted material, even when the GFP gate is set very conservatively. We use a promoter that marks about 10% of the cells in the root.

    Posted by: Anonymous
    March 8, 2010 - 12:40 PM
  2. Dear Roger,

    I think the lower than expected purity you are seeing can be explained by the fragile nature of protoplasts. I take it that you are sorting the protoplasts, then rerunning the sorted cells and finding that, in the second run, a lot of the originally sorted events fall outside the gates set in the first run.
    The problem lies in the fact that many protoplasts will burst after (and some also likely during) the sort due to the hypotonicity of the sheath fluid (usually similar to 1xPBS) as compared to the protoplasting solution or protoplasts incubation solution (+/-400 mM Mannitol or a solution of equal osmolarity). In addition, some protoplasts may also perish due to the shearing forces endured while travelling through the apparatus. So, a lot of the GFP-positive protoplasts you sorted in the first run will have lysed and turned into non-GFP cell debris by the time you run them through a second time.
    In the past, we have sorted the protoplasts into a large volume of isotonic (400 mM Mannitol) buffer and then rerun the cells, which gave us a 76% purity readout. Although I believe that the impurities found in that rerun can still be explained by cell lysing during the sort.
    In conclusion, I do not have a precise answer for your question but can pose that the actual purity will be much higher than one would deduce from just looking at a re-sort. Published expression data also support this notion; we can show high levels of enrichment for the expression of certain genes in certain cell types suggesting that the cells must have been isolated to a high degree of purity (Birnbaum K, et al. ²003 A gene expression map of the Arabidopsis root. Science 30²: 1956-60; Brady SM, et al. ²007 A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318: 801-6).
    A way to address this issue experimentally would be to inspect protoplasts visually after the sort and tally the purity of GFP-positive intact cells vs GFP-negative intact cells.
    I hope this resolves the questions you had. Good luck with your experiments!


    Bastiaan Bargmann

    Posted by: Anonymous
    March 8, 2010 - 6:12 PM
  3. Where can i buy a cell sorter for plant protoplasts. Im initiating a project on protoplast fusion in sunflower. What are the price ranges and the best suppliers? Rudo masvodza University of Zimbabwe

    Posted by: Doreen Rudo M.
    August 10, 2010 - 4:37 AM
  4. Dear Rudo,

    In principle, any cell sorter that can be fitted with a 100 micron nozzle can be used. Personally, we only have experience with the FACSAria, mentioned here, and the MoFlo cytometers. Prices may vary widely and will depend on your dealings with the manufacturer.


    -Bastiaan Bargmann

    Posted by: Anonymous
    August 13, 2010 - 1:21 PM
  5. Dear Bastiaan,

    what do you use as mesh support to grow the seedlings hydroponically?

    Thanks in advance.

    Best regards,

    Joana Sequeira Mendes

    Posted by: Anonymous
    May 6, 2011 - 6:59 AM
  6. Dear Joana,

    We use a 100 μm nylon mesh (Sefar Filtration, NITEX 03-100/47). You will have to check with your local supplier. The point is to have an inert, 'sterilizable' screen with holes (+/- 100 μm) that will support the seeds yet let the roots grow through. We built custom supports from pipette-tips and racks (p1000) that can be autoclave-sterilized (see figure ²a and film).

    Good luck with your experiments!

    -Bastiaan Bargmann

    Posted by: Anonymous
    May 10, 2011 - 11:18 AM
  7. Thanks for your quick reply! I'll try to make the home-made supports.

    All the best,


    Posted by: Anonymous
    May 10, 2011 - 11:41 AM
  8. Sorry, correction: we use ²50 μm nylon mesh (Sefar Infiltration, NITEX 03-²50/50) for hydroponic growth.

    The 100 μm mesh dŒs not let the roots through and is used for growing seedlings on agar plates.

    -Bastiaan Bargmann

    Posted by: Anonymous
    May 13, 2011 - 4:31 PM
  9. Dear Bastiaan,

    I assumed it was a mistake as you mention the ²50 μm in the text.

    Thanks again,


    Posted by: Anonymous
    May 17, 2011 - 6:15 AM
  10. Hello Dear authors,
    I have two questions:
    1) what is the minimum concentration of protoplast solution you use for FACS procedure? what is the limitations of volume to be sorted?
    2) after the sorting, what minimum volume and concentration you use for RNA extraction? in case one fraction (for instance, GFP-positive) has a different total amount of RNA compared to the other fraction do you try and bring it to the same concentration?

    thank you very much

    Posted by: alon c.
    December 17, 2013 - 7:32 AM
  11. just to clarify- in question 1 i mean the concentration of protoplasts, not the reagents in the TEX solution...

    Posted by: alon c.
    December 17, 2013 - 7:33 AM
  12. Dear Authors,

    We used MoFlo to isolate GFP cells from Arabidopsis root tips. We could successfully get high quality total RNA from the other cells lines labeled for stele and endodermis (the SCR), however, we failed to get the GFP positive cells from the quiescent center line (we use pAGL42::GFP) after the complementation adjustment on FACS software. From your results, you can get .063% from the WOX5 line. Do you have any suggestion tips for us to isolate the QC cells? Is that because the QC cells are very few and they just sit at the middle at the root tips? I can observe the QC cells marked with GFP under fluorescent microscope and I saw very few of them after protoplasting, but it seems like they are not enough for the FACS sorting. Do you have any advice to improve? Or just to grow more of them?
    Thanks a lot!

    Posted by: Jingyi C.
    March 18, 2014 - 11:44 AM

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