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A 2in1 cloning system enables ratiometric bimolecular fluorescence complementation (rBiFC)
Christopher Grefen and Michael R. Blatt
Laboratory of Plant Physiology and Biophysics, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, UK
BioTechniques, Vol. 53, No. 5, November 2012, pp. 311–314
Full Text (PDF)
Supplementary Material

Gene expression and binary interaction techniques are vital tools that shape our understanding of protein complexes. An inherent flaw, however, with most current protein-protein interaction techniques is the variability in expression levels for fusion proteins when using several individual plasmids. Here, we describe a novel recombination-based cloning strategy called 2in1 that enables co-expression of fusion proteins on a cell-by-cell basis from a single plasmid. We demonstrate the utility of 2in1 through the development of a ratiometric bimolecular fluorescence complementation assay (rBiFC), in which both candidate genes are simultaneously cloned into a single vector backbone containing an internal fluorescent marker for expression control and ratiometric analysis. rBiFC significantly increases the credibility of protein-protein interaction results allowing ratiometric comparison between different protein pairs. In addition to its use in rBiFC, 2in1 can be introduced easily into other vector systems that rely on multiple gene expression and prove feasible in future synthetic biological approaches.

Understanding mechanistic relationships of complex signaling networks requires dissecting protein-protein interactions. Many binary interaction techniques [yeast-2-hybrid (Y2H) (1), split-ubiquitin system (SUS) (2), Förster resonance energy transfer (FRET) (3), and bimolecular fluorescence complementation (BiFC) (4)] rely on expressing two fusion proteins in the same cell at the same time. BiFC is based on splitting a fluorophore [e.g., enhanced yellow fluorescent protein (EYFP) (5)] into two nonfluorescent peptides, fusing these to proteins of interest and their subsequent fluorophor complementation (4, 6). BiFC has become widely used to study protein-protein interactions in many laboratories (7, 8). Advantages compared with other in vivo approaches are that interactions can be monitored in living cells and their subcellular localization determined. However, problems arise where co-transformations lead to different copy numbers, expression level variations, or complete loss of interacting partners. Also, lack of internal controls makes quantitative interpretation of results difficult. These problems become increasingly important when subtle differences among different interaction partners need to be detected (9).

Here, we describe a modification to BiFC vector systems allowing to directly quantify interaction data using a ratiometric approach (rBiFC) through the introduction of multiple expression cassettes within a single vector backbone. To facilitate rBiFC experiments with different combinations of constructs, we elaborated a novel cloning system called 2in1 (Figure 1A) that utilizes recombination technology (10) to allow the simultaneous cloning of two genes into two different independent cloning cassettes on the same vector backbone. To demonstrate the utility of this 2in1 cloning system for establishing rBiFC analysis, we integrated both cloning cassettes within the T-DNA region of a binary expression vector (Supplementary Figure S1A). Cassettes are flanked by N- or C-terminal EYFP halves [nYFP (1–155 amino acids), cYFP (156–239 amino acids)] including myc- or hemagglutinin (HA)-tags to enable biochemical detection and expression is regulated through the viral 35S promoter. To allow ratiometric analysis, the T-DNA also carries a soluble monomeric red fluorescent protein (mRFP1) (11) under control of the same promoter, thereby creating an internal marker for transformation and expression control (see Supplementary materials for details). Introducing enhanced green fluorescent protein (EGFP) and enhanced cyan fluorescent protein (ECFP) (12-15) into both cloning cassettes (Figure 1B), we measured fluorescence intensity using confocal laser scanning microscopy (CLSM) after transient Agrobacterium-mediated transformation in Nicotiana tabacum leaves as described previously (16). GFP and CFP fluorescence were ratioed against RFP to estimate expression differences (Figure 1, C and D) and compared with Western blot analysis of the fusion proteins (Figure 1E), thus verifying equal expression levels within the same T-DNA and on a cell-by-cell basis in this case. However, every gene may behave differently, depending on regulatory sequences, codon-usage, protein turnover, and other factors influencing expression and/or protein stability. Hence, rBiFC experiments, like classical BiFC studies, need always to be accompanied by biochemical analysis verifying protein expression as a basis for ratiometric analysis of interaction.

Method summary

We have devised a novel, Gateway-compatible cloning system named 2in1 that enables single-step transfer of two independent genes into two different expression cassettes on the same vector backbone. Here, we demonstrate how the 2in1 concept ensures the credibility of in vivo protein-protein interaction methods by its application in our ratiometric bimolecular fluorescence complementation (rBiFC) assay. The simultaneous introduction of both fusion proteins on the same plasmid ensures equal gene dosage, and the inclusion of an internal fluorescence marker allows for expression control and ratiometric quantification.

Figure 1.  Ratiometric comparison of three fluorophores expressed from the same T-DNA. (Click to enlarge)

Interactions of the CBL-CIPK network of calcium sensors and protein kinases in Arabidopsis are well documented (17, 18). Calcineurin B-like proteins (CBLs) are membrane-anchored Ca2+ sensors that recruit a specific set of serine-threonine kinases (CIPKs) to their site of action. CBL1 and CBL9, but not CBL6, for example, are known to interact with CIPK23 leading to phosphorylation of the potassium channel AKT1 (17, 18). To analyze the functionality of rBiFC, we cloned CBL1, CBL6, and CBL9 together with CIPK23 in our expression vector pBiFCt-2in1-NC (Figure 2A) and transiently transformed N. tabacum leaves. For each clone, more than 20 image frames were selected at random (Figure 2B). The mean fluorescence of YFP over RFP was plotted and compared (Figure 2C). The positively interacting CBL proteins 1 and 9 were clearly identified through visualizing complemented YFP fluorescence but also through comparing the intensity with constitutively expressed mRFP1. The negative control containing CIPK23-cYFP and untagged nYFP peptide, as well as samples that coexpress CIPK23-cYFP with nYFP-CBL6, showed a weak YFP signal demonstrating the background fluorescencethat is often associated with BiFC. However, when compared with the internal RFP signal, it becomes clear that the ratio is significantly lower than compared with the positive interaction couples and similar to the negative control. This weak YFP signal might otherwise have been recognized as evidence of interaction (Figure 2C), and the results thus emphasize the superiority of the ratiometric approach in detecting true positive interactions. For the sake of comparison, we have included immunoblot analysis confirming equal expression (Figure 2E) of the fusion proteins. To exclude artificial YFP signal detection through RFP activation, a high resolution image of the nucleus of a tobacco cell expressing CBL1-CIPK23 was taken, demonstrating that the interaction takes place outside of the nucleus and that the soluble mRFP1 protein which is abundantly present is not detected in the YFP channel (Figure 2D). It should be noted that for any protein-protein interaction couple, a different orientation of the FP-tags might be necessary as protein stability or interaction might be compromised when termini are masked (19). It is important to be aware of this issue, and when performing protein-protein interaction studies, all possible tag orientations should be tested (20).

Figure 2.  rBiFC proof-of-principle. (Click to enlarge)

rBiFC allows ratiometric analysis of interaction partners and provides an extensive improvement toward the credibility of protein-protein interaction results obtained through fluorescence complementation. The success of rBiFC is based on the 2in1 system, which enables introduction of stoichiometric copy numbers of both interaction partners together with an internal marker. While the proof-of-concept in this manuscript was performed in planta, rBiFC and/or the 2in1 system can be transferred to other cell and expression systems. We have created a set of helper vectors that allows conversion of any expression vector providing high flexibility for the researcher (see Supplementary materials). The use of the 2in1 cloning system is not limited to improving BiFC-based methods; this concept offers advantages for other binary interaction techniques as well, by generally circumventing issues inherent to work with individually cloned interaction partners. It will allow increasing the number of genes to be introduced in a foreign organism as it decreases the number of plasmids, and thereby auxotrophies and other selection markers, necessary for the purpose. Finally, with the 2in1 system, binary interaction assays may be expanded readily to allow screening for ternary interaction partners.


The authors are grateful to Rucha Karnik, Susan Rosser, and Gerhard Thiel for critical comments on the manuscript. M.R.B. is funded through the UK Biotechnology and Biological Sciences Research Council grant BB/HO24867/1.

Competing interests

The authors declare competing financial interests: IP rights of the 2in1 technique are assigned to PBL technology, UK.

Address correspondence to Christopher Grefen, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, UK. Email: [email protected]

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