Expanded palette of Nano-lanterns for real-timemulticolor luminescence imagingAkira Takaia,1, Masahiro Nakanob,1, Kenta Saitob, Remi Harunob, Tomonobu M. Watanabec,d, Tatsuya Ohyanagie,Takashi Jine, Yasushi Okadaa,2, and Takeharu Nagaib,d,f,2

Laboratories for aCell Polarity Regulation, cComprehensive Bioimaging, eNano-Bio Probes, and fCell Dynamics Observation, Quantitative Biology Center,RIKEN, Osaka 565-0874, Japan; bThe Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan; and dPRESTO, Japan Scienceand Technology Agency, Tokyo 102-0075, Japan

Edited by Jennifer Lippincott-Schwartz, National Institutes of Health, Bethesda, MD, and approved February 18, 2015 (received for review September25, 2014)

Fluorescence live imaging has become an essential methodology inmodern cell biology. However, fluorescence requires excitationlight, which can sometimes cause potential problems, such asautofluorescence, phototoxicity, and photobleaching. Further-more, combined with recent optogenetic tools, the light illumina-tion can trigger their unintended activation. Because luminescenceimaging does not require excitation light, it is a good candidate asan alternative imaging modality to circumvent these problems.The application of luminescence imaging, however, has been limitedby the two drawbacks of existing luminescent protein probes, suchas luciferases: namely, low brightness and poor color variants. Here,we report the development of bright cyan and orange luminescentproteins by extending our previous development of the brightyellowish-green luminescent protein Nano-lantern. The color changeand the enhancement of brightness were both achieved by bio-luminescence resonance energy transfer (BRET) from enhancedRenilla luciferase to a fluorescent protein. The brightness of thesecyan and orange Nano-lanterns was ∼20 times brighter than wild-type Renilla luciferase, which allowed us to perform multicolor liveimaging of intracellular submicron structures. The rapid dynamics ofendosomes and peroxisomes were visualized at around 1-s temporalresolution, and the slow dynamics of focal adhesions were continu-ously imaged for longer than a few hours without photobleachingor photodamage. In addition, we extended the application of thesemulticolor Nano-lanterns to simultaneous monitoring of multiplegene expression or Ca2+ dynamics in different cellular compartmentsin a single cell.

luciferase | luminescence imaging | luminescent indicator | live imaging |bioluminescence resonance energy transfer

Live imaging with fluorescent proteins (FPs) has revolution-ized modern biology. Applications of FPs have been greatly

expanded by improvements in brightness and development ofcolor variants; however, a fundamental limitation is that fluo-rescence requires excitation light, the power density of which isusually above 0.1 W/cm2 for live-cell imaging. This power iscomparable with direct sunshine (0.13 W/cm2) and can some-times cause problems, such as autofluorescence, phototoxicity,or photobleaching (1). Furthermore, to use FPs with recentlydeveloped optogenetic tools while avoiding unintended opto-genetic stimulation, careful tuning of the spectrum for thestimulation and imaging has been necessary (2).Because luminescence imaging does not depend on excitation

illumination at all, it is a good candidate as an alternative imagingmodality to circumvent these potential problems caused by the ex-citation light. However, most existing luminescent proteins (LPs)are dim because of the low enzymatic activity and the low quantumyield (QY). For example, the QY of WT Renilla luciferase (RLuc)is so small (3) (QY = 0.02 in this report) (Fig. S1 A and B and TableS1) that 2% of the energy derived from the oxidation of the sub-strate, coelenterazine, is converted into photon emission, yieldingonly ∼0.2 photon s−1 molecule−1 photon emission. Long exposure

(typically 1–10 min with conventional luciferase) has, thus, beenrequired, and subcellular spatial resolution has been difficult toachieve. In addition, the color variants of LPs are limited comparedwith those of FPs. Thus, it has been difficult to apply LP for high-speed and multicolor imaging of living cells (4).Recently, we developed a bright yellowish-green LP called Nano-

lantern (5),which is a chimeraofRLuc8-S257G[anenhancedmutant(5) based on the stabilized variant called RLuc8 (3)], and Venus,a bright yellow FP with fast and efficient maturation properties (6).Three properties combined to make Nano-lantern 10 times brighterthan RLuc (5), including (i) increased enzymatic activity of RLuc8-S257G (1.3 times higher than RLuc8), (ii) an optimized linker thatfacilitates efficient intramolecular bioluminescence resonance energytransfer (BRET) fromRLuc8-S257G toVenus, and (iii) the highQYof Venus (QY= 0.57) (6). This enhanced brightness of Nano-lanternsignificantly improved the spatial and temporal resolution of lumi-nescence imaging compared with that of conventional luciferase.In this paper, we extend this BRET-based approach to the

development of color variants of Nano-lantern by using otherFPs, such as cyan and orange FPs, as the BRET acceptor. Wemake use of this expanded color palette of bright LPs in threeproof-of-principle applications of multicolor luminescence imaging.

Significance

The application of luminescence imaging has been limited mainlyby the two drawbacks of luciferases: low brightness and poorcolor variants. Here, we report the development of cyan and or-ange luminescent proteins approximately 20 times brighter thanthe wild-type Renilla luciferase. The color change and en-hancement of brightness were both achieved by exploringbioluminescence resonance energy transfer (BRET) from en-hanced Renilla luciferase to a fluorescent protein, a technologythat we previously reported for the development of the brightyellowish-green luminescent protein Nano-lantern. These cyanand orange Nano-lanterns along with the original yellow Nano-lantern enable monitoring of multiple cellular events, includingdynamics of subcellular structures, gene expressions, and func-tional status, such as intracellular Ca2+ change.

Author contributions: A.T., M.N., K.S., Y.O., and T.N. designed research; A.T., M.N., K.S.,R.H., T.M.W., Y.O., and T.N. performed research; T.O. and T.J. contributed new reagentsA.T., M.N., K.S., R.H., Y.O., and T.N. analyzed data; and A.T., M.N., Y.O., and T.N. wrotethe paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Freely available online through the PNAS open access option.

Data deposition: The sequences reported in this paper have been deposited in the GenBankdatabase (accession nos. AB982072–AB982104 and AB983214–AB983217).1A.T. and M.N. contributed equally to this work.2To whom correspondence may be addressed. Email: ng1@sanken.osaka-u.ac.jp ory.okada@riken.jp.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1418468112/-/DCSupplemental.

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First, we apply the LPs as fusion tags to visualize the dynamics ofsubcellular microstructures, such as cytoskeletons and vesicularorganelles. These submicron structures were continuously visu-alized at ∼1-s temporal resolution for longer than a few hourswithout photobleaching or photodamage. Second, an applicationas a multiple gene expression reporter is shown with photosen-sitive ES cells. Third, Ca2+ indicators were developed based oncyan Nano-lantern (CNL) and orange Nano-lantern (ONL),showing their usefulness as the basis for the development ofluminescent indicators that are fully compatible with optogenetictools and other optical manipulations.

ResultsDevelopment of CNL.We have first replaced Venus of the originalNano-lantern [hereafter, we call it yellow Nano-lantern (YNL)]with mTurquoise2, a cyan FP with the highest QY (QY = 0.93)among all known FPs (7) (Fig. 1A). The chimera of mTurquoise2-RLuc8-S257G emitted bright cyan light (Fig. 1B), and we named itCNL. CNL was about 20 times brighter than RLuc (Fig. 1C). Themeasured QY of CNL was similar to YNL (Table S1), which meansthat the higher QY of mTurquoise2 compensated for the lowerspectral overlap between RLuc8 and mTurquoise2 than between

RLuc8 and Venus. The nearly two times higher brightness ofCNL over YNL, therefore, might reflect the higher enzymaticactivity of CNL.

Development of ONL. We next attempted to develop a longerwavelength variant of Nano-lantern and tried various combina-tions of donor RLuc mutants, including long-wavelength mutantsof RLuc (8), and acceptor FPs, including bright orange and redFPs (9, 10) or FPs with large Stokes shifts (11) (Figs. S2, S3, andS4). We have also tried deletions of the linker between RLuc andFP (Fig. S3). Among all of the tested constructs, the combinationof RLuc8.6–535 (hereafter, RLuc8.6) and mKusabiraOrange2(Fig. 1A) showed the highest BRET efficiency (Table S2). Thisvariant emitted orange light brighter than YNL and more than15 times brighter than RLuc (Fig. 1 B and C), and we named itONL. For the red color variants, the combination of RLuc8.6–545with mCherry or TurboFP635 showed relatively high BRET effi-ciency (Fig. S4), but additional increase of the BRET efficiency isrequired to use it as a fourth color combined with other Nano-lanterns. Nonetheless, these red variants will have a potential benefitfor deep-tissue imaging, because absorption by tissues, especiallyhemoglobin, is reduced at wavelengths longer than 600 nm (12, 13).

Application as Fusion Tags for Subcellular Structures. Next, weexpressed CNL and ONL as fusion proteins to examine whetherthey work as the luminescent fusion tags for subcellular structures(Fig. 2 and Fig. S5). Fusions with histoneH2B, inositol-trisphosphate3-kinase A (ITPKA; F-tractin) (14), β-tubulin, peroxisome targetingsignal 2, zyxin, fibrillarin (Fig. 2), and all tested other various proteinsor peptides (Fig. S5) showed correct localization by both fluores-cence and luminescence imaging, indicating that both CNL andONL (as well as YNL) can be used as fusion tags. Furthermore,because the emission spectrum of each color variant of Nano-lantern has a distinct peak that is distant enough from the others(Fig. 1B), the luminescence signals from these Nano-lantern colorvariants were easily separated by optical filtering (Fig. 2B). It shouldbe noted that the samples were repeatedly illuminated with blue togreen excitation light for CFP, YFP, or OFP excitation for fluores-cence imaging. The images shown in Fig. 2 and Fig. S5 were firsttaken with excitation illumination (fluorescence) and then, withoutillumination (luminescence). Thus, our Nano-lanterns would be fullycompatible with optogenetic tools.To show live-cell imaging of subcellular structures, we examined

three subcellular structures stained with ONL: lysosomes, perox-isomes, and focal adhesions (Movies S1–S3). The rapid dynamics ofperoxisomes and lysosomes were examined, and their trajectorieswere tracked for several minutes (Fig. S6 and Movies S1 and S2),showing that the rapid dynamics of submicrometer structures can beinvestigated by luminescence imaging with ONL.It should be noted that luminescence imaging is free from

photobleaching and photodamage. Therefore, long-term lumines-cence imaging is only limited by the depletion of the substrate.Adding too much substrate coelenterazine-h, however, can increasethe background luminescence because of autooxidation (15). We,therefore, synthesized diacetyl coelenterazine-h, where autoox-idation is inhibited by protective acetyl groups. This inhibition ofautooxidation allows diacetyl coelenterazine-h to be added athigher concentrations without increasing the background autolu-minescence. Diacetyl coelenterazine-h is reverted to coelenter-azine-h in the cell by esterase, which serves as a constant supplyof the substrate. Thus, we can observe the luminescence signalwithout replenishing the substrate for several hours. With thiscondition, the slow dynamics of focal adhesion were observed forabout 4 h continuously with 1-s exposure imaging, which is difficultwith fluorescence imaging because of photobleaching (Movie S3).

Application as Gene Expression Reporters. LPs, such as firefly lu-ciferase (FLuc), have been widely used as a reporter for gene

A

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Fig. 1. Development of multicolor Nano-lanterns and their characterization.(A) Schematics of multicolor Nano-lanterns. Numbers represent the relativeamino acid position in the original protein. (B) Emission spectra of LPs weremeasured in triplicate, and data are presented as means. (Inset) Luminescenceof recombinant Nano-lantern proteins. (C) Luminescence intensities of equi-molar amounts of LPs. Intensities were measured in triplicate, and data arepresented as means ± SDs. One-way ANOVA followed by posthoc Tukey’shonestly significant difference test compared with RLuc. ****P < 0.0001.

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expression with cell lysate-based assays (16, 17). However, the lu-minescence signal from FLuc is much weaker than that from FPs.Extremely long exposure time (1–10 min) and low spatial resolu-tion (4 × 4 to 8 × 8 binning, resulting 2.5–5 μm/pixel) were requiredto collect enough photons. Thus, monitoring the dynamics of geneexpression at single-cell level using FLuc has been difficult.

We, therefore, examined whether Nano-lanterns could beapplied as gene expression reporters (Fig. 3 and Fig. S7). Re-porter plasmids were constructed by introducing cDNA of Nano-lanterns with a nuclear localization signal (NLS) and destabilizationtag (hCL1-PEST) (18) downstream of Wnt-responsive promoter7xTcf (19). The cell line harboring this plasmid responded toWnt-3a

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Fig. 2. Luminescence imaging of intracellular microstructures. (A) Luminescence and fluorescence images of subcellular structures: nuclei in interphase (CNL-H2Band ONL-H2B), F-actin [inositol trisphosphate 3-kinase A (ITPKA) -ONL], microtubules (β-tubulin-ONL), peroxisomes [peroxisome targeting signal 2 (PTS2) -CNL],and focal adhesions (zyxin-ONL). (B) Subnuclear structures visualized by dual-color luminescence imaging: CNL-fibrillarin (nucleoli) and ONL-H2B. Each lumines-cence signal was separated by linear unmixing. (Scale bars: 10 μm.)

LiClWnt-3a

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Fig. 3. Live single-cell luciferase assay for the expression of Wnt target gene. (A) Schematic of Nano-lantern–based Wnt signal reporter. (B) Luminescence ofNLS-tagged Nano-lantern expressed in HEK293A cells harboring Wnt reporter construct. Images were acquired with a 495- to 540-nm band-pass emissionfilter at 16 h after the addition of 200 ng/mL Wnt-3a protein or 10 mM LiCl. Luminescence signals were overlaid with the bright-field image. (Scale bars:10 μm.) (C) Percentages of the positive cells plotted as a bar graph. Cont, control.

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as well as LiCl (Wnt signaling activator through inhibition ofGSK3β). Response was sensitively detected at the single-celllevel as the luminescence signal in the nucleus, even with 0.5 s ofexposure time.We next tried multiple gene expression monitoring. A stable line

ofmurineEScellswas established,whichhave three geneexpressionreporters: Oct4 by CNL, Nanog by YNL, and Sox2 by ONL. Multi-channel luminescence images of differentiating murine ES cellsshowed the expression level of these three genes in each cell andalso, heterogeneity of the differentiation state, even within a singlecolony (Fig. 4). Here, imaging took only 10 s for each channelwithout binning (0.5μm/pixel).This spatial resolution ishighenoughto distinguish single cells in a dense colony, and the temporal reso-lution is fast enough to monitor the dynamics of gene expression.

Application as Ca2+ Indicators. As another application of multicolorluminescence imaging, we constructed Ca2+ indicators by applyingthe complementation of split luciferase technology as reportedpreviously for YNL (3). CNL- and ONL-based Ca2+ indicatorswere expressed as fusion proteins with a mitochondria localizationtag and histone H2B, respectively. After stimulation with 20 μMhistamine, acute Ca2+ spikes followed by Ca2+ oscillations withsmaller amplitudes were observed in both mitochondria and thenucleus (Fig. 5 and Movie S4), thereby showing the same result aswith FP-based Ca2+ indicators in a previous report (20). Theseresults show that our multicolor Nano-lanterns could also be usedas indicators for functional imaging, especially combined withoptogenetic tools, such as channel rhodopsin or photoactivatableCa2+ releaser (21), both of which are activated by blue light.

DiscussionThrough the optimization of the BRET pairs and the linker inbetween them, we have succeeded in making bright cyan andorange LPs, CNL and ONL, in addition to the original YNL.The chemical energy liberated by the oxidation of the substrate

coelenterazine is transferred to the FP, which emits photons withhigh QY. This mechanism does not only enhance the QY ofluciferase but also, changes the color of the emitted light. Thus,the three color variants of Nano-lantern are about 20 timesbrighter than the wild-type RLuc, and their emission spectraare essentially same as those of the acceptor FPs. The enhancedbrightness has enabled luminescence imaging of subcellularorganelles with submicrometer and subsecond resolution. Forthe gene expression reporters, our proof-of-principle experi-ments showed that Nano-lanterns can monitor the expression ofthree different genes at single-cell resolution with an image ac-quisition time shorter than 1 min in total. Furthermore, Nano-lanterns can be applied as indicators for functional imaging, such asCa2+ imaging.Regardless of these successes, luminescence imaging with Nano-

lanterns still has some drawbacks compared with fluorescence im-aging with FPs. First, the signal intensity of Nano-lanterns is stillmore than 100 times weaker than that of FPs. A single FP moleculeemits more than 1,000 photons per 1 s under conditions for singleFP imaging in living cells, whereas a single Nano-lantern emits lessthan 10 photons per 1 s. Therefore, the application as the fusion tagfor low-abundance proteins or the reporter for rapid dynamics(video rate or faster) is a remaining challenge to be overcome byadditional improvements in brightness.Second, luminescence imaging lacks optical sectioning capa-

bilities. FPs emit signals only when illuminated with the excita-tion light. Thus, the signals are stronger near the focal plane withfluorescence imaging. This optical sectioning effect can be fur-ther enhanced by confocal optics, multiphoton excitation, orlight-sheet illumination. Contrastingly, all of the luciferases inthe sample emit signal. The signals of the thick samples areblurred by the haze from the out-of-focus luciferases.Third, different colors of FPs can easily be separated by the

combination of excitation and the emission filters. For example,a pair of FPs with emission spectrum overlap can often be sep-arated by filtering the excitation wavelength. With luminescenceimaging, the signals from different colors of Nano-lanterns canbe separated only by the emission spectrum, and therefore, wehave used a linear unmixing algorithm to achieve better sepa-ration (Fig. S8). Nonetheless, the unmixing algorithm can bemuch simpler than with fluorescence imaging, because auto-fluorescence signals are negligible.Fourth, luminescence imaging requires substrate instead of

excitation light. The supply and the consumption of the substratelimit the imaging. Unlike FLuc, our Nano-lanterns do not re-quire ATP for its reaction, and therefore, the consumption ofintracellular ATP does not compromise its application. However,a constant supply of the substrate coelenterazine is still necessary

Oct4-CNL

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Fig. 4. Inhomogeneous expression of pluripotency markers in a single col-ony of ES cells. Luminescence signals of reporters for (A) Oct4 (CNL),(B) Nanog (YNL), and (C) Sox2 (ONL) were separated by linear unmixing andoverlaid with the bright-field image. (D) Signals of CNL, YNL, and ONL weremerged and overlaid with the bright-field image. (Scale bars: 100 μm.)

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Fig. 5. Simultaneous analysis of Ca2+ dynamics in mitochondria and thenucleus. (A) Dual-channel live bioluminescence imaging of Mito-CNL(Ca2+)(green) and ONL(Ca2+)-H2B (magenta) in HeLa cells. Dual-color luminescenceimage at 55 s in B is shown. (Scale bar: 10 μm.) (B) Simultaneous analysis ofCa2+ dynamics in the mitochondria (blue circle in A) and the nucleus (redcircle in A). Arrow indicates an addition of 20 μM histamine.

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for stable long-term imaging. We have, therefore, synthesizeddiacetyl coelenterazine in this study; however, long-term imag-ing, especially in vivo, is still compromised by its supply. Re-construction of synthesis or recycling of substrate would help toovercome this difficulty.Thus, for many applications, fluorescence imaging still has

many advantages over luminescence imaging. However, our threecolor variants of Nano-lantern are the first, to our knowledge, toenable multicolor luminescence imaging with significantly higherspatial and temporal resolution compared with conventional luci-ferases. Although the temporal resolution of luminescence imaging(0.1–10 s in this paper) is currently one to three orders of magni-tude lower than that of fluorescence imaging (typically, 10–100 ms),the spatial resolution achieved here is comparable with culturedcells (Fig. 2 and Fig. S5). Our proof-of-principle experimentsreported in this paper clearly show that luminescence imaging hasbecome a practical alternative when the side effects by the exci-tation light are not negligible, such as when the samples are verysensitive to photodamage. The combination with optogenetic toolswould be the most effective future application of luminescenceimaging, because the external light illumination can be reserved foroptical stimulation.

Materials and MethodsGeneral. DNA oligonucleotides used for gene cloning and construction werepurchased from Invitrogen or Greiner. KOD-plus-Neo (TOYOBO) was used forPCR. Products of PCR and restriction enzyme digestion were purified byagarose gel electrophoresis followed by the FastGene Gel/PCR Extraction Kit(Nippon Genetics). Restriction enzymes were purchased from New EnglandBiolabs, and the ligase was purchased from TOYOBO (Ligation high version 2)and used as recommended by the manufacturer. Plasmids were preparedfrom the bacterial liquid culture by using either the Fast-n-Easy Plasmid Mini-Prep Kit (Jena Bioscience) or NucleoBond XtraMidi Plus (Machery-Nagel). TheDNA sequences were read by dye terminator cycle sequencing using theBigDye Terminator v3.1 Cycle Sequencing Kit (Life Technologies). Otherreagents, such as buffer salts, were purchased from Wako.

Construction of Color Variants of Nano-Lantern. Unless stated otherwise, weused the term RLuc8.6 as RLuc8.6–535. Based on the design of the originalYNL, cDNA of FPs with or without C-terminal extra amino acids for β-barrelof FPs was PCR-amplified, and cDNA of Venus in pcDNA3-YNL was replacedby the PCR products. Actual amino acid sequences used in this study weremTurquoise2 (1–229 aa), mKusabiraOrange2 (1–218 aa), LSS-mOrange(1–236 aa for FL and 1–226 aa for ΔC10), mKeima-Red (1–218 aa), tdTomato(1–464 aa), mCherry (1–226 aa), TurboFP635 (1–225 aa), mKate2 (1–222 aa),mOrange2 (1–226 aa), TagRFP (1–225 aa), mRuby2 (1–225 aa), and TurboFP650(1–224 aa). The cDNA of TurboFP650 was generated by PCR-based mutagenesis

using cDNA of TurboFP635 as a PCR template. For RLuc8.6- and RLuc8.6–545-based BRET constructs, cDNA of RLuc8.6 and RLuc8.6–545 without N-terminal3 aa (RLuc8.6ΔN3 and RLuc545ΔN3, respectively) was generated by PCR-basedmutagenesis using cDNA of RLuc8 as a PCR template, and cDNA of RLuc8-S257GΔN3 in pcDNA3-YNL was replaced by these PCR products.

Construction of Gene Expression Reporter Genes and Ca2+ Indicators. Wnt-responsive enhancer 7xTcf and CMV minimal promoter were PCR-amplifiedand subcloned into modified pT2-UAS-MCS vector (22) after the removal ofUAS to obtain pT2-7xTcf-MCS. In addition, PGK promoter and puromycinresistance gene were PCR-amplified and subcloned into the vector to obtainpT2-7xTcf-MCS-PGK-Puro. For the construction of pT2-7xTcf-NLS-Nano-lanterns,cDNA of NLS-Nano-lanterns was subcloned into pT2-7xTcf-MCS-PGK-Purovector. For the construction of pT2-7xTcf-NLS-YNL-CP, cDNA of the hCL1-PESTsequence was generated by the synthesized DNA oligonucleotides and PCRamplification and ligated to the C terminus of NLS-YNL of pT2-7xTcf-NLS-YNL.

Transcriptional promoter reporters to mouse Nanog,Oct4, or Sox2 activitywere built based on lentivirus vector to mouse Nanog, Oct4, or Sox2 activity(23). We purchased the plasmid of Mouse Nanog Differentiation Reporter(System Biosciences), which is a commercialized lentivector-based reporterwith Nanog promoter, and replaced the cDNA of RFP in the plasmid with thatof YNL. The Oct4-CNL reporter plasmid was constructed from this Nanog-YNLplasmid by replacing the promoter with Oct4 and the reporter with CNL. TheSox2-ONL reporter plasmid was similarly constructed from pGreenFire1-mCMV(System Biosciences) by replacing minimal CMV promoter and copGFP cDNAwith the Sox2 promoter and ONL cDNA, respectively.

Based on the design of Nano-lantern (Ca2+), we constructed Ca2+ indicators ofCNL and ONL [CNL(Ca2+) and ONL(Ca2+), respectively] by inserting a cDNAfragment encoding the CaM-M13 peptide derived from the Nano-lantern (Ca2+)at the site between 228 and 229 aa of the RLuc variants in CNL and ONL.

ACKNOWLEDGMENTS. We thank the following people for the plasmids:J. Goedhart and T. W. J. Gadella (University of Amsterdam) for mTurquoise2;A. Miyawaki (RIKEN) for mKusabiraOrange2; D. M. Scherbakova andV. Verkhusha (Albert Einstein College of Medicine) for LSSmOrange;M. Z. Lin (Stanford University) formRuby2 (Addgene Plasmid 40260); K. Kawakamifor Tol2; and S. Niwa and N. Hirokawa (University of Tokyo) for β-tubulin andRab11a. We also thank the laboratory members, especially S. Xu, J. Asada,M. Komeno and M. Kakiuchi (Quantitative Biology Center) and K. Sakai(Osaka University) for their technical and secretarial assistance and D. Priest(Quantitative Biology Center) for editing the manuscript. Part of this workwas supported by KAKENHI Grants-in-Aid for Scientific Research 25871128(to A.T.), 24659092 (to Y.O.), 25113723 (to Y.O.), and 25293046 (to Y.O.);RIKEN Incentive Research Grant (to A.T.); Ministry of Education, Science,Sports and Culture Grants-in-Aid for Scientific Research on InnovativeAreas “Spying minority in biological phenomena (no. 3306)” 26115721(to Y.O.) and 23115003 (to T.N.); and the Strategic Programs for R&D (Pres-ident’s Discretionary Fund) of RIKEN (Y.O.), Precursory Research forEmbryonic Science and Technology (T.N.), and Development of Systemsand Technology for Advanced Measurement and Analysis (T.N.) fromJapan Science and Technology Agency.

1. Magidson V, Khodjakov A (2013) Circumventing photodamage in live-cell microscopy.Methods Cell Biol 114:545–560.

2. Akerboom J, et al. (2013) Genetically encoded calcium indicators for multi-colorneural activity imaging and combination with optogenetics. Front Mol Neurosci 6:2.

3. Loening AM, Fenn TD, Wu AM, Gambhir SS (2006) Consensus guided mutagenesis of Re-nilla luciferase yields enhanced stability and light output. Protein Eng Des Sel 19(9):391–400.

4. Miyawaki A (2007) Bringing bioluminescence into the picture. Nat Methods 4(8):616–617.

5. Saito K, et al. (2012) Luminescent proteins for high-speed single-cell and whole-bodyimaging. Nat Commun 3:1262.

6. Nagai T, et al. (2002) A variant of yellow fluorescent protein with fast and efficientmaturation for cell-biological applications. Nat Biotechnol 20(1):87–90.

7. Goedhart J, et al. (2012) Structure-guided evolution of cyan fluorescent proteins to-wards a quantum yield of 93%. Nat Commun 3:751.

8. Loening AM, Wu AM, Gambhir SS (2007) Red-shifted Renilla reniformis luciferasevariants for imaging in living subjects. Nat Methods 4(8):641–643.

9. Sakaue-Sawano A, et al. (2008) Visualizing spatiotemporal dynamics of multicellularcell-cycle progression. Cell 132(3):487–498.

10. Miranda JG, et al. (2012) New alternately colored FRET sensors for simultaneousmonitoring of Zn²⁺ in multiple cellular locations. PLoS ONE 7(11):e49371.

11. Shcherbakova DM, Hink MA, Joosen L, Gadella TWJ, Verkhusha VV (2012) An orangefluorescent protein with a large Stokes shift for single-excitation multicolor FCCS andFRET imaging. J Am Chem Soc 134(18):7913–7923.

12. Dragulescu-Andrasi A, Chan CT, De A, Massoud TF, Gambhir SS (2011) Bioluminescenceresonance energy transfer (BRET) imaging of protein-protein interactions within deeptissues of living subjects. Proc Natl Acad Sci USA 108(29):12060–12065.

13. Chu J, et al. (2014) Non-invasive intravital imaging of cellular differentiation witha bright red-excitable fluorescent protein. Nat Methods 11(5):572–578.

14. Johnson HW, Schell MJ (2009) Neuronal IP3 3-kinase is an F-actin-bundling protein: Role indendritic targeting and regulation of spine morphology. Mol Biol Cell 20(24):5166–5180.

15. Zhao H, et al. (2004) Characterization of coelenterazine analogs for measurements of

Renilla luciferase activity in live cells and living animals. Mol Imaging 3(1):43–54.16. Takai A, et al. (2010) Anterior neural development requires Del1, a matrix-associated

protein that attenuates canonical Wnt signaling via the Ror2 pathway. Development137(19):3293–3302.

17. Balaskas N, et al. (2012) Gene regulatory logic for reading the Sonic Hedgehog sig-

naling gradient in the vertebrate neural tube. Cell 148(1-2):273–284.18. Metzger MB, Maurer MJ, Dancy BM, Michaelis S (2008) Degradation of a cytosolic

protein requires endoplasmic reticulum-associated degradation machinery. J Biol

Chem 283(47):32302–32316.19. Fuerer C, Nusse R (2010) Lentiviral vectors to probe and manipulate the Wnt signaling

pathway. PLoS ONE 5(2):e9370.20. Nagai T, Sawano A, Park ES, Miyawaki A (2001) Circularly permuted green fluorescent

proteins engineered to sense Ca2+. Proc Natl Acad Sci USA 98(6):3197–3202.21. Fukuda N, Matsuda T, Nagai T (2014) Optical control of the Ca2+ concentration in

a live specimen with a genetically encoded Ca2+-releasing molecular tool. ACS Chem

Biol 9(5):1197–1203.22. Kawakami K, et al. (2004) A transposon-mediated gene trap approach identifies

developmentally regulated genes in zebrafish. Dev Cell 7:133–144.23. Hotta A, et al. (2009) Isolation of human iPS cells using EOS lentiviral vectors to select

for pluripotency. Nat Methods 6(5):370–376.

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