Bright and fast multicoloured voltage reporters via electrochromic FRET

Abstract

Genetically encoded fluorescent reporters of membrane potential promise to reveal aspects of neural function not detectable by other means. We present a palette of multicoloured brightly fluorescent genetically encoded voltage indicators with sensitivities from 8-13% ΔF/F per 100 mV, and half-maximal response times from 4-7 ms. A fluorescent protein is fused to an archaerhodopsin-derived voltage sensor. Voltage-induced shifts in the absorption spectrum of the rhodopsin lead to voltage-dependent nonradiative quenching of the appended fluorescent protein. Through a library screen, we identify linkers and fluorescent protein combinations that report neuronal action potentials in cultured rat hippocampal neurons with a single-trial signal-to-noise ratio from 7 to 9 in a 1 kHz imaging bandwidth at modest illumination intensity. The freedom to choose a voltage indicator from an array of colours facilitates multicolour voltage imaging, as well as combination with other optical reporters and optogenetic actuators.

ARTICLE

Received 18 Mar 2014 | Accepted 8 Jul 2014 | Published 13 Aug 2014

Peng Zou1,*, Yongxin Zhao2,*, Adam D. Douglass3, Daniel R. Hochbaum1, Daan Brinks1, Christopher A. Werley1,D. Jed Harrison2, Robert E. Campbell2 & Adam E. Cohen1,4

Genetically encoded uorescent reporters of membrane potential promise to reveal aspects of neural function not detectable by other means. We present a palette of multicoloured brightly uorescent genetically encoded voltage indicators with sensitivities from 813% DF/F per 100 mV, and half-maximal response times from 47 ms. A uorescent protein is fused to an archaerhodopsin-derived voltage sensor. Voltage-induced shifts in the absorption spectrum of the rhodopsin lead to voltage-dependent nonradiative quenching of the appended uorescent protein. Through a library screen, we identify linkers and uorescent protein combinations that report neuronal action potentials in cultured rat hippocampal neurons with a single-trial signal-to-noise ratio from 7 to 9 in a 1 kHz imaging bandwidth at modest illumination intensity. The freedom to choose a voltage indicator from an array of colours facilitates multicolour voltage imaging, as well as combination with other optical reporters and optogenetic actuators.

DOI: 10.1038/ncomms5625

Bright and fast multicoloured voltage reporters via electrochromic FRET

1 Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA.

2 Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2. 3 Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah 84132, USA. 4 Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to R.E.C. (email: mailto:[email protected]

Web End [email protected] ) or to A.E.C. (email: mailto:[email protected]

Web End [email protected] ).

NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications 1

& 2014 Macmillan Publishers Limited. All rights reserved.

ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625

Membrane voltage acts on all transmembrane proteins: the membrane electric eld pulls on charged residues, shifting the free energy landscape for charge-displacing

conformational transitions1. This bioelectric modulation is most famously observed in voltage-gated ion channels in neurons and cardiomyocytes, but voltage also affects the activity of G protein-coupled receptors and some transmembrane enzymes2. Membrane voltage is dynamically regulated in bacteria3, fungi4, plants5 and many cell types and subcellular organelles in the human body, and is dysregulated in states of neuronal, cardiac and metabolic diseases. Thus, there is a need for fast, sensitive, bright and spectrally tunable reporters of membrane voltage.

Recent progress in genetically encoded voltage indicators (GEVIs) has led to several classes of proteins, which robustly report action potentials (APs) in cultured neurons. The rst GEVIs were based on fusion of uorescent proteins to transmembrane voltage-sensing domains6. In some of these, voltage modulates the brightness of a single uorescent moiety710, while in others, voltage modulates the efciency of Frster resonance energy transfer (FRET) between a pair of uorescent moieties11,12. In our measurements of green uorescent protein (GFP)-based GEVIs, described below, the most sensitive was ArcLight8 (DF/F 32% per 100 mV), but this

reporter had half-maximal response times at room temperature of 90 ms (depolarizing step) and 104 ms (hyperpolarizing step). We measured the recently introduced ASAP1 (ref. 9) reporter to have a sensitivity of DF/F 29% per 100 mV, and a half-maximal

response of 2 ms at room temperature. These numbers differ modestly from the original reports, likely due to differences in gene expression protocols and choices of optical lters.

A second class of GEVIs is based on microbial rhodopsin proton pumps3,13,14. In these, the transmembrane voltage modulates the endogenous near infrared uorescence of the retinal chromophore. The most recently developed non-pumping mutants of Archaerhodopsin 3 (Arch), termed QuasArs, have voltage sensitivities between 30 and 90% per 100 mV (depending on the mutant), and half-maximal response times between 50 ms and 1.1 ms at room temperature13.

GFP-based and rhodopsin-based GEVIs have very different spectral properties. GFP-based GEVIs are excited by blue light (470490 nm) and emit green (500530 nm). QuasArs are excited by red light (594640 nm) and emit in the near infrared (peak at 715 nm). GFP-based GEVIs are 3080-fold brighter, and thus are typically imaged with excitation at B10 W cm 2, while QuasArs are typically imaged at 300800 W cm 2 (ref. 13). In a comparison between ArcLight and QuasAr2 in cultured rat hippocampal neurons under their respective standard imaging conditions, QuasAr2 reported single APs with 4.7-fold higher signal-to-noise ratio (SNR) and was 15-fold more photostable13. In organotypic mouse hippocampal slice culture, QuasAr2 reported single APs with 4.5-fold higher SNR than ArcLight13. Nonetheless, the low brightness of Arch-based GEVIs present a challenge for widespread use.

The availability of GEVIs spanning the visible spectrum is important when combining GEVIs with other optical reporters or optogenetic actuators. Having GEVIs of colours between GFP and Arch would facilitate multiplex voltage imaging, for example, to distinguish activity of excitatory and inhibitory neurons in intact tissue. Furthermore, GEVIs spectrally distinct from GFP could be paired with other GFP-based reporters such as GCaMP (Ca2 )

(ref. 15), iGluSnFR (glutamate)16, Perceval (ATP)17, Clomeleon (Cl ) (ref. 18) or Pyronic (pyruvate)19, or with other blue-excited optogenetic actuators. Thus, there is strong motivation to develop a broad palette of GEVI colours.

We sought to combine the speed and sensitivity of Arch-based GEVIs with the brightness and spectral range of conventional

uorescent proteins. Traditionally, FRET is used to measure the physical distance between a donor and acceptor. However, we and others have also used FRET to measure changes in the absorption spectrum of a protein via its inuence on nonradiative quenching of an attached uorescent moiety2022.

Here we use voltage-induced changes in the absorption spectrum of an Arch mutant to alter the degree of nonradiative quenching of a closely fused uorescent protein. We call this mechanism electrochromic FRET (eFRET). We demonstrate fast and sensitive voltage sensing in fusions between QuasAr2 and a broad palette of uorescent proteins: enhanced GFP (EGFP), yellow FP (Citrine), mOrange2, mRuby2. These probes have sensitivities from 813% DF/F per 100 mV, and half-maximal response times from 47 ms, which allows detection of APs in cultured rat hippocampal neurons with a single-trial SNR from 7 to 9 in a 1 kHz imaging bandwidth at modest illumination intensity. A recent paper applied a similar strategy to make voltage sensors based on fusion of uorescent proteins to a mutant of the Leptosphaeria maculans rhodopsin (Mac)23. While other GEVIs offer superior SNR on the blue and far red ends of the spectrum, the present GEVIs ll in the visible spectrum with emission wavelengths between 530640 nm. This spectral range facilitates multicolour voltage imaging with GEVIs, as well as combination with other optical reporters and optogenetic actuators1.

ResultsEngineering eFRET GEVIs. Our electrochromic quencher is a mutant of Arch, termed QuasAr2 (Fig. 1). The direct retinal uorescence of QuasAr2 showed voltage sensitivity of 90% DF/F per 100 mV and a bi-exponential step response with time constants of 1.2 ms (68%) and 11.8 ms (32%) (Table 1) at room temperature13. It has not been feasible to measure directly the voltage-dependent absorption spectra of Arch or its mutants on account of the small quantity of protein found in the plasma membrane of a single cell. However, a mechanistic study of Arch showed that membrane voltage modulated uorescence via a voltage-dependent shift in the acid-base equilibrium of the retinal Schiff base24. Positive membrane voltage favoured the protonated (and uorescent) state. One can thus mimic the voltage-induced absorption changes by changing the pH in a solution of

H+

Retinal

Abs.

+100 mV

100 mV

V

V

FP Em.

FP

Wavelength

H FP

+

Retinal

Abs.

FP Em.

Wavelength

Figure 1 | Proposed mechanism of voltage-dependent uorescence in eFRET GEVIs. Voltage controls the protonation, and thereby the absorption spectrum, of the Schiff base joining the retinal to the protein scaffold. (a) At a depolarizing (positive) voltage, the microbial rhodopsin has a protonated retinal Schiff base, which absorbs strongly with a peak near 600 nm. The retinal absorption quenches the uorescence of the appended uorescent protein (FP). (b) At hyperpolarizing (negative) voltages, the uorescence is not quenched. Spectra shown are cartoons to illustrate mechanism.

2 NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications

& 2014 Macmillan Publishers Limited. All rights reserved.

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625 ARTICLE

Table 1 | Voltage-sensing properties of GEVIs.

Fluorophore HEK Cells Neurons

DF/F per 100 mV (%)

Response to hyperpolarizing step Response to depolarizing step DF/F for single AP (%)

SNR for single AP

sfast(ms) sslow(ms) % fast s1/2 (ms) sfast(ms) sslow(ms) % fast s1/2 (ms)

ECFP 0.8 ND ND

EGFP 7.7 4.3 27 45 7.6 3.0 26 61 3.9 ND

Citrine 13.1 4.8 21 38 7.5 3.1 21 62 3.8 9.7 8.8

mOrange2 10.0 4.3 26 45 7.5 3.9 27 60 5.1 9.9 9.0

mRuby2 8.7 4.3 27 65 4.7 3.6 20 65 3.8 5.4 7.2

mKate2 4.5 2.8 35 25 9.2 4.0 25 44 6.7 ND

ArcLight Q239 31.6 104 283 61 103 28 271 39 90 8.2 9.2

ASAP1 28.8 3.0 29 67 3.5 2.3 39 88 1.9 17.8 13.1

QuasAr2 90 1.0 16 80 0.9 1.2 12 68 1.4 48 41

AP, action potential; ECFP, enhanced cyan uorescent protein; EGFP, enhanced green uorescent protein; SNR, signal-to-noise ratio.

Sensitivity, DF/F per 100 mV, was measured for a voltage step from 70 mV to 30 mV. Response times were characterized either by fast and slow time constants from a bi-exponential t (t and

t ) or by t , the time to reach 50% of the steady-state response to a step of membrane voltage of duration at least 2 t . Half-response times are shorter for steps that do not reach steady state. Hyperpolarizing step: 30 mV to 70 mV; depolarizing step: 70 mV to 30 mV. All measurements were performed at 23 C and represent the average of 69 cells. Illumination intensities were

3 Wcm 2 for all reporters except for QuasAr2. Illumination intensity was 200 Wcm 2 for QuasAr2. (ref. 23).

solubilized protein. At neutral pH, QuasAr2 had a broad absorption band peaked at 587 nm. At higher pH, this band dropped and a band at 411 nm appeared, corresponding to the deprotonated Schiff base (Supplementary Fig. 1).

Based on these spectra, we reasoned that QuasAr2 might mediate voltage-dependent quenching of an appended uorescent protein. The emission spectrum of mOrange2 (ref. 25) has a high degree of overlap with the absorption spectrum of Arch, so we started with this uorophore. To enable efcient FRET, it is critical to optimize the length of the linker, as rate of FRET is proportional to the reciprocal sixth power of the distance between the donor and acceptor chromophores. We examined the crystal structures of Arch-2 (a QuasAr2 homologue) (PDB ID 2EI4) (ref.26) and mOrange (an mOrange2 homologue) (PDB ID 2H5O)27, and found that the last 15 carboxy-terminal residues of Arch-2 and 15 amino-terminal residues of mOrange are largely unstructured (Fig. 2a). We reasoned that those unstructured residues could be removed without disrupting the function of either protein. We created a series of linker libraries by systematically truncating these resectable regions (Fig. 2b and Methods) and randomizing two residues at the junction.

We then developed a hierarchical screening strategy to identify variants with optimal mOrange2 brightness, membrane trafcking and voltage response (Fig. 2c and Methods). We used a customized vector, termed pcDuEx1.0, for gene expression in both prokaryotic and eukaryotic cells. This vector circumvents the laborious cloning typically required to switch between a primary screen in bacteria and a secondary screen in mammalian cells (Methods). Colonies of Escherichia coli were transformed with linker libraries in pcDuEx1.0. The colonies with the brightest mOrange2 uorescence were picked for secondary screening in mammalian cells.

For the mammalian cell-based screen, a green GEVI, ArcLight Q239 (ref. 7), was used as an internal reference for both membrane trafcking and voltage response (Fig. 2cg and Methods). The sensitivity of eFRET variants generally increased as the linker was shortened. The most truncated variants (D31 and D32 libraries) had excellent voltage sensitivity, but substantially decreased brightness of mOrange2, likely due either to poor folding or to high basal quenching by the rhodopsin. In libraries with more than 20 residues truncated, the screen favoured combinations of Arg, Leu, Ala and Gly for the linker. The variant from the D24 library with linker sequence Leu-Arg gave the best overall performance and was used henceforth. We added a trafcking sequence (TS) and endoplasmic reticulum export

motif (ER2) to improve trafcking to the plasma membrane28, although trafcking remained imperfect.

QuasAr2 absorbs strongly from 500640 nm, so we reasoned that eFRET might work for uorescent proteins with a range of emission wavelengths. We created a palette of eFRET constructs by replacing mOrange2 with: ECFP29, EGFP29, Citrine30, mRuby2 (ref. 12) and mKate2 (ref. 31). The emission spectra of these proteins all overlapped to some degree with the absorption spectrum of QuasAr2 (Fig. 3). Spectral properties of these uorophores are given in Supplementary Table 1.

To test the hypothesized eFRET mechanism, we compared the uorescence quantum yield of Citrine in the eFRET fusion and in a membrane-targeted construct lacking the QuasAr2 quencher, both expressed in HEK cells. We used two-photon uorescence excitation and time-correlated single-photon counting to determine the electronic excited state lifetime (Methods). The native Citrine protein had a lifetime of tbare 3.47 ns, while the eFRET

construct had a lifetime of tFRET 2.83 ns (Supplementary Fig. 2).

This difference in lifetime conrms that an additional nonradiative decay pathway exists in the eFRET construct compared to the bare Citrine protein, which we ascribe to FRET from Citrine to retinal. The FRET efciency is given by EFRET 1 tFRET/tbare, from which EFRET 0.18. Maximum

voltage sensitivity occurs at EFRET 0.5, implying that further

optimization of the position and orientation of the FP may improve quenching efciency and thereby voltage sensitivity.

Voltage responses in HEK cells. We characterized the eFRET GEVIs in HEK cells, imaged at 23 C. All eFRET GEVIs trafcked efciently to the plasma membrane (Fig. 4a) and exhibited bright uorescence when excited at 3 W cm 2 with appropriate excitation and emission wavelengths (Supplementary Table 1).

Membrane voltage was controlled via whole-cell voltage clamp. Fluorescence traces were extracted from images of cells either by manually dening a region of interest (ROI) comprising the cell body, or by using an automated pixel-weighting algorithm14. Both approaches gave similar results. Fluorescence responses were normalized to uorescence at a holding potential of

70 mV (after background subtraction) and are quoted as DF/F. Voltage sensitivity was calculated as [F(30 mV)

F( 70 mV)]/F( 70 mV). While rhodopsins require retinal

as a cofactor, we found that the culture medium contained sufcient retinal that voltage sensitivity was not enhanced by addition of exogenous retinal (Supplementary Fig. 3).

NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications 3

& 2014 Macmillan Publishers Limited. All rights reserved.

ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625

QuasAr mOrange2

Resectable region

Linker sequence

0 T E A P E P S AGA DV S A ADRP V V A V SKGE ENNMA I I K E F

7 T E A P E P S AGA D X X MV SKGE ENNMA I I K E F

17 T E X X V SKGE ENNMA I I K E F

21 T E X X E ENNMA I I K E F

22 T E X X ENNMA I I K E F

24 T E X X NMA I I K E F

31 T X X E F

32 T X X F

Resectableregion Unstructured QuasAr residues Unstructured mOrange2 residues

mOrange2 N-term truncation

QuasAr C-term truncation

V

F

t t

V

E

F

t

More ordered Less ordered

4 QuasAr1.2mOrange2

E

ArcLight

10 % F/F

2 s

Ratio of F/F

mOrange2 vs. ArcLight

3

2

1

QuasAr1.2

mOrange2

E

20 % F/F

2 s

0 0 5 16 20 24 28 32

Number of truncated residues

Figure 2 | Directed evolution of an eFRET GEVI. (a) A model of QuasArmOrange2 constructs, represented by the crystal structures of Arch-2 (PDB ID 2EI4)ref. 26 and mOrange (PDB ID 2H5O)27. The color scale represents the degree of order in the crystal structure, as reported by the B-factor. Less-ordered regions are presumed more dispensable. (b) Design of linker truncation libraries. QuasAr1.2, the best available variant at the time of the screen, was used as the electrochromic quencher. (c) Hierarchical screen of truncated linker libraries for eFRET GEVIs. Constructs were rst screened inE. coli for mOrange2 brightness and then screened for membrane trafcking in HEK cells. Voltage sensitivity was then tested via eld stimulation in HeLa cells co-expressing the eFRET GEVI, ArcLight (as an internal control), and Kir2.1 (to lower the resting voltage to 60 mV42). (d) ArcLight

uorescence of three HeLa cells. Yellow arrow indicates direction of the applied electric eld. Scale bar, 25 mm. (e) Fluorescence intensity traces of the three regions shown in d. (f) mOrange2 uorescence from the same cells shown in d. (g) Response of mOrange2 uorescence during stimulation as ine. Fluorescence traces show single-trial measurement of cells imaged at 100 frames per second. (h) Effect of linker length on voltage sensitivity in QuasAr1.2mOrange2. For each linker length the most sensitive eFRET GEVI construct was compared with ArcLight measured in the same cells.

Error bars represent s.d. over n 1520 cells in the ratio DF/F.

Fluorescence of all eFRET GEVIs showed approximately linear dependence on applied voltage (Fig. 4b). The most sensitive construct was the Citrine fusion with DF/F 13.11.8% per

100 mV (n 6 cells, all statistics are means.e.m.). The EGFP,

mOrange2 and mRuby2 constructs showed sensitivities between7.7 and 10.0% per 100 mV (Table 1). The bluest and reddest constructs, containing ECFP and mKate2, exhibited poor voltage sensitivity, which we attribute to poor spectral overlap with QuasAr2 absorption. The negative slope of dF/dV was consistent with greater spectral overlap of mOrange2 emission and QuasAr2 absorption at depolarizing voltages.

Fast uorescence response to a change in voltage is essential for detecting neuronal APs. We applied a square wave of voltage ( 70 mV to 30 mV, 5 Hz) and recorded the uorescence at a

frame rate of 1,000 frames per s (Fig. 4c). Fluorescence responses were approximately t by a sum of two exponentials, with a dominant fast and a smaller slow time constant. The fastest

construct was the mRuby2 GEVI, with tfast 3.60.3 ms (65%)

and tslow 202 ms (35%) for depolarizing membrane potential

step (n 8 cells). The GFP, Citrine and mOrange2 had half-

response times between 3.9 and 7.6 ms (Table 1). Response times were similar on rising and falling edges. Response amplitudes to a 5 ms step from 70 to 30 mV are given in Supplementary

Table 2.

We made side-by-side comparisons of the performance of the eFRET GEVIs with two GFP-based GEVIs, ArcLight Q239 (ref. 7), and ASAP1 (ref. 9), and to direct uorescence of QuasAr2 (Fig. 4df). Cell culture, gene expression, electrophysiology, imaging and analysis protocols were identical across constructs (except for changes in illumination wavelength and intensity as noted). ArcLight showed voltage sensitivity of 31.63.5%

DF/F per 100 mV (n 7 cells, Fig. 4e), consistent with previous

reports. The step response of ArcLight followed a bi-exponential decay with time constants of 288 ms (39%) and 2716 ms

4 NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications

& 2014 Macmillan Publishers Limited. All rights reserved.

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625 ARTICLE

QuasAr2 ER2

FP TS

1.0

400 500 600 700 800 Wavelength (nm)

ECFP EGFP Citrine mOrange2 mRuby2 mKate2

Absorption

QuasAr2

Emission

0.8

0.6

0.4

0.2

0.0

Figure 3 | Spectral overlap of uorescent proteins with QuasAr2 absorption. (a) eFRET GEVI domain structure. (b) Overlay of the emission spectra of the uorescent protein donors with the absorption spectrum of the QuasAr2 electrochromic quencher.

(61%) (for a depolarizing voltage step from 70 mV to 30 mV) and a bi-exponential uorescence rise with time constants of 10421 ms (61%) and 28340 ms (39%) (for voltage step from 30 mV to 70 mV) (n 7 cells,

Supplementary Fig. 4). These numbers are slower than in the original report on ArcLight7, due to the difference in measurement temperature: 23 C in our measurements versus 3335 C in the prior report. ASAP1 showed voltage sensitivity of28.81.7% per 100 mV and depolarizing voltage step response time constants of 2.30.1 ms (88%) and 393 ms (12%) (n 6

cells, Fig. 4ef; Table 1).

The voltage response of direct retinal uorescence of QuasAr2 was measured in the QuasAr2-mOrange eFRET GEVI. To achieve comparable levels of QuasAr2 and mOrange2 uorescence required 70-fold greater illumination intensity for QuasAr2 (640 nm, 200 W cm 2 versus 532 nm, 3 W cm 2). Compared with the mOrange2 uorescence, QuasAr2 uorescence was more sensitive to voltage (DF/F 902% per 100 mV, n 6 cells,

Fig. 4eh) and had a somewhat faster response time (double exponential t yielding: t1 1.2 ms, 68%, t2 12 ms, 32%,

Fig. 4eh). The discrepancy in response time between the QuasAr2 and mOrange2 may arise because, in addition to the fast uorescence-determining transition, QuasAr2 may also undergo slower voltage-dependent transitions that change its absorption spectrum but not its uorescence. Alternatively, subtle voltage-induced conformational shifts could change the relative position and orientation of the mOrange2 and the retinal, and thereby change the efciency of nonradiative quenching.

Characterization in neurons. The Citrine, mOrange2 and mRuby2 eFRET GEVIs showed sufcient sensitivity and speed to merit testing in neurons. We expressed these via transient transfection in cultured rat hippocampal neurons. Constructs exhibited good trafcking to the plasma membrane (Fig. 5). Injection of current pulses via a patch pipette (500600 pA, 510 ms, 5 Hz) induced trains of APs, which induced downward uorescence transients of 9.71.7% (Citrine), 9.91.3% (mOrange2) and 5.40.4% (mRuby2) (n 711 cells for each,

Table 1). Our eFRET constructs also reported spontaneous activity in cultured neurons (Fig. 6).

Arclight also reported single-trial APs when used at 23 C, with a downward transient of 8.20.7% (n 7 cells), although this

response appeared to be dominated by the response to the slow

subthreshold depolarization as opposed to the fast spike. Thus, despite the greater steady-state voltage sensitivity of ArcLight than the eFRET GEVIs, the slow response of ArcLight acted as a low-pass lter on millisecond-timescale APs, decreasing the uorescence response7. ASAP1 reported single-trial neuronal APs with downward uorescence transients of 17.83.4% (n 5

cells). On account of its greater sensitivity at negative voltages, ASAP1 magnied the subthreshold signal (55% of uorescence response) relative to the AP spike (45% of uorescence response). In a similar assay, Mac-based eFRET GEVIs were reported to resolve single APs with downward transients of 7.2% for MacQmOrange2 and 4.8% for MacQ-mCitrine23.

The SNR of uorescence detection, dened as the ratio of the peak amplitude to s.d. of uorescence at the baseline, was8.81.0 (Citrine), 9.01.2 (mOrange2) and 7.20.6 (mRuby2) (1 kHz frame rate, illumination at 3 W cm 2, 23 C for all eFRET

GEVIs) (n 711 cells for each, Table 1). Parallel measurements

on ArcLight had a single-trial SNR of 9.21.5 and substantially broadened the AP waveform (1 kHz frame rate, illumination at3 W cm 2, 23 C), while ASAP1 had a single-trial SNR of13.12.9. Previous measurements with QuasAr2 reported a single-trial SNR for AP detection of 41 (300 W cm 2) and 70 (800 W cm 2) (ref. 13).

DiscussionWith the proliferation of GEVI constructs, it can be difcult to identify the best construct for a particular experiment. Speed, sensitivity and SNR for single APs for recently reported GEVIs are summarized in Table 1. SNR depends on both voltage sensitivity (DF/F) and overall uorescence counts (F). In the shot noise-limited regime, SNR for AP detection scales as DF=

F

p ,

where DF is the change in uorescence counts for a single AP. Baseline uorescence counts, F, can vary considerably between experiments, depending upon illumination intensity and wavelength, protein expression level, sources of background auto-uorescence, collection efciency of the objective, choice of emission lter, quantum efciency of the detector and selection of the ROI. The SNR values reported here provide a comparative guide for measurements under matched conditions, but will differ for measurements performed under different conditions.

For multicolour voltage imaging, the choice of emission lter is critical. We used the DF=

F

p noise scaling to estimate the SNR for each eFRET GEVI for 30 nm-wide detection bands between 510690 nm. We then determined which eFRET GEVI gave the maximum SNR in each band (Supplementary Fig. 5). This calculation suggests that the eFRET GEVIs enable detection of APs with SNR45 for any 30 nm emission band between 510660 nm. In the GFP spectral band, ASAP1 outperforms the eFRET GEVIs and ArcLight in terms of sensitivity, speed and SNR. In the yellow and orange emission bands, the MacQ-based eFRET GEVIs23 are somewhat more sensitive, while the QuasAr2-based eFRET GEVIs are somewhat faster. For detection of APs in cultured neurons, both types of constructs yield similar SNR. At the far red end of the spectrum, QuasAr2 outperforms both ASAP1 and the eFRET GEVIs in terms of sensitivity, speed, SNR and photostability; but requires intense laser illumination.

The excitation and emission wavelengths of a GEVI or other optical reporter inuence performance when imaging in intact tissue. The excitation and emission spectra of avins, a major contributor to brain autouorescence, overlap strongly with those of GFP32,33. Consequently, a rule of thumb is that the signal-to-background ratio for GFP-based reporters is 10-fold lower in tissue than in cell culture. Redder reporters have signicantly less background in brain tissue. Light scattering in tissue scales with

NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications 5

& 2014 Macmillan Publishers Limited. All rights reserved.

ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625

a

EGFP

Citrine

mOrange2

mRuby2

mKate2

b

5

F/F(%)

0

10

5

15

100 50 0 50 100 Voltage (mV)

100 50 0 50 100Voltage (mV)

100 50 0 50 100 Voltage (mV)

100 50 0 50 100 Voltage (mV)

100 50 0 50 100Voltage (mV)

c

12

10

8

F/F(%)

6

4

2

0

0 80

80 40 40 Time (ms)

0 80

80 40 40 Time (ms)

0 80

80 40 40 Time (ms)

0 80

80 40 40 Time (ms)

0 80

80 40 40 Time (ms)

d g

ASAP1

ArcLight

QuasAr2

16

0 100 200 300 Response speed (s1)

Citrine

EGFP

mRuby2

14

12 mOrange2

% F/Fper 100 mV

% F/Fper 100 mV

10

8

e

6

mKate2

20

20

4

0

0

120

80

0

F/F(%)

F/F(%)

40

2

20

F/F(%)

20

F/F(%)

40

40

0

h

100 50 0 50 100 Voltage (mV)

100 50 0 50 100 Voltage (mV)

100 50 0 50 100 Voltage (mV)

100

0 10 100 1,000 Response speed (s1)

QuasAr2

ASAP1

80

f

30

30

60

60

F/F(%)

F/F(%)

20

20

40

40 ArcLight

20

10

10

20

eFRET GEVIs

0

0

100 50 0 50 100Time (ms) Time (ms) Time (ms)

100 50 0 50 100 100 50 0 50 100

Figure 4 | Voltage sensing with GEVIs in HEK293 cells. Voltage response of eFRET GEVI reporters are shown in (ac) and voltage responses of comparison GEVIs are shown in (df). (a,d) Fluorescence images of HEK cells expressing GEVI reporters. Scale bars, 10 mm. (b,e) Fluorescence as a function of membrane voltage, normalized to uorescence at V 70 mV. Many eFRET-based GEVIs showed a small amount of hysteresis. Each trace

is a single trial with 100 ms exposures. (c,f) Fluorescence response to a step in membrane voltage from 70 mV to 30 mV. Each trace is averaged over

2030 trials with 1 ms exposures. All data were acquired with laser illumination (3 Wcm 2 for eFRET, ASAP1 and ArcLight GEVIs, 200 Wcm 2 for QuasAr2). No temporal ltering was applied. Fluorescence traces were corrected for photobleaching. (g) Quantication of eFRET GEVI sensitivity and speed. Voltage sensitivity of eFRET GEVIs approximately corresponds to the degree of spectral overlap between the emission of the GEVI and the absorption of QuasAr2. (h) eFRET GEVI sensitivity and speed in the context of other GEVIs. Response speed was dened as the inverse of the time to reach 50% of steady-state response to a voltage step from 70 mV to 30 mV. Data in (g) and (h) represents an average of n 69 cells for each

construct. Error bars represent s.e.m.

6 NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications

& 2014 Macmillan Publishers Limited. All rights reserved.

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625 ARTICLE

a b c

50

50

V(mV)

100

0

V(mV)

100

0

50

50

Citrine mOrange2 mRuby2 ASAP1 ArcLight QuasAr2

10%F/F

10%F/F

20 ms

50

100 ms

50

V(mV)

0

0

50

V(mV)

50

100

100

10% F/F

10% F/F

100 ms

20 ms

50

50

0

0

V(mV)

50

V(mV)

50

100

5% F/F

5% F/F

20 ms

100 ms

50

50

V(mV)

0

0

50

V(mV)

100

50

100

100

5% F/F

5% F/F

20 ms

100 ms

50

50

V(mV)

0

V(mV)

0

50

50

100

100

20% F/F

20% F/F

20% F/F

100 ms 20 ms

100

50

50

V(mV)

0

0

50

V(mV)

50

100

20% F/F

100 ms 20 ms

Figure 5 | Single-trial recording of neuronal APs with GEVIs. Each GEVI construct was expressed in primary rat hippocampal neurons under a CaMKIIa promoter. APs were induced by current injections through a patch pipette. (a) Images of neurons expressing the indicated GEVI. Scale bars, 10 mm.

(b) Simultaneous patch clamp and uorescence recordings of AP waveforms. All recordings were acquired with laser illumination (3 Wcm 2 for eFRET, ASAP1, and ArcLight GEVIs, 200 Wcm 2 for QuasAr2) at an exposure time of 1 ms. Fluorescence traces are presented without temporal ltering nor correction for photobleaching. All but the QuasAr2 recording have been inverted (hence photobleaching appears as an upward trend in the mRuby2 trace).

Recordings are representative traces from 511 cells recorded for each construct. (c) Close-up showing single trial, unltered, electrically and optically recorded AP waveforms.

wavelength l approximately as l 2.33, so redder reporters can be imaged deeper34. Illumination at 640 nm propagates nearly1.9-fold further into tissue than does illumination at 488 nm. While two-photon excitation of GFP-based reporters enables even greater depth penetration, this comes at the cost of requiring serial scanning, and a complex optical setup. Absolute brightness is also important when imaging in tissue, due to the need to overcome background autouorescence and to minimize optical power dissipation in the tissue. However, in a comparison between ArcLight and QuasAr2 in rat brain slice, the far dimmer

but redder QuasAr2 reported APs with 4.5-fold higher SNR than ArcLight, albeit at 24-fold higher illumination intensity13. Due to the complex combination of factors that determine GEVI performance in vivo, an empirical test is far preferable to extrapolations from measurements in vitro.

Trafcking remains a key limitation of all GEVIs, despite adoption of trafcking motifs in most. The efciency of trafcking to the plasma membrane often varies dramatically between preparations, between cells of the same type in vitro versus in vivo, and between different cell types from the same

NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications 7

& 2014 Macmillan Publishers Limited. All rights reserved.

ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625

a

50

V(mV)

500

5% F/F

50

500 ms

b

V(mV)

50

500

5% F/F

500 ms

c

V(mV)

50

0

2% F/F

500 ms

Figure 6 | Optical recording of spontaneous neuronal ring with eFRET GEVIs. In neurons synaptically coupled to a spontaneously active circuit, the (a) Citrine, (b) mOrange and (c) mRuby2 eFRET GEVIs clearly revealed single APs. Patch clamp voltage recordings are shown above optical recording traces. All recordings were acquired with laser illumination(3 Wcm 2) at an exposure time of 2 ms. Fluorescence traces are presented without temporal ltering. The optical recordings have been corrected for photobleaching with a linear t.

species. For now, an empirical approach is warranted to identify

the construct best suited to a particular experiment.

The varied F versus V curves for available GEVIs accentuate different aspects of cellular electrophysiology. The more linear GEVIs (eFRET and QuasArs) preserve the waveform of the underlying voltage dynamics, a useful feature for quantication of action potential waveforms. The more sigmoidal GEVIs (ASAP1 and ArcLight) emphasize voltage changes in the region of maximum slope. For ASAP1 and ArcLight this feature would emphasize subthreshold dynamics over APs in population-level recordings averaged over many cells. Due to their slightly different voltages of maximum slope, ASAP1 would show greatest sensitivity for hyperpolarizing potentials while ArcLight would show greatest sensitivity for depolarizing potentials (Fig. 4e). ArcLight variants have been demonstrated with maximum sensitivity over a range of voltages7.

Several challenges remain in genetically encoded voltage imaging. Owing to uncontrolled variation in expression level, none of the GEVIs discussed here reports absolute membrane voltage. To achieve absolute accuracy requires a more complex imaging scheme, either ratiometric35 or time-resolved36. Two-photon voltage imaging, which would facilitate imaging in tissue, also remains a challenge. This goal has been achieved with voltage-sensitive dyes37, but two-photon GEVI imaging has not yet clearly resolved single APs, although some recent work succeeded in detecting activity-evoked signals38.

Further improvements in the eFRET GEVIs are likely to come from optimization of the rhodopsin-based quencher and from improvements in the attachment of the uorescent protein to the rhodopsin. A rhodopsin need not show endogenous uorescence to serve as an efcient eFRET quencher, and thus many rhodopsins that are not suitable as direct voltage indicators may still be useful for eFRET. Thousands of microbial rhodopsin genes have been identied in the wild39,40, and among these improved quenchers are likely to exist. The estimated FRET efciency of 18% in the Citrine construct implies that increases in voltage sensitivity could be attained by improving energy transfer

from the uorescent protein to the rhodopsin. This increase in efciency could come from greater intimacy of contact between the uorescent protein and the rhodopsin, or from optimizing the relative orientation of the donor and acceptor uorophores. To achieve these goals, one may insert circularly permuted uorescent proteins into intracellular loops on the rhodopsin.

With simultaneous multicolour voltage imaging, one could apply genetic targeting to record voltage simultaneously from distinct structures that might otherwise be difcult to distinguish. For instance, wide-eld images that lack single-cell resolution could still distinguish population-average activity levels in intermingled excitatory and inhibitory neurons. The broad palette of eFRET GEVIs also facilitates combination with other GFP-based uorescent reporters or a wide variety of optogenetic actuators.

Methods

Molecular biology. Synthetic DNA oligonucleotides were purchased from Integrated DNA Technologies. PfuUltraII polymerase (Agilent Technologies) or Phusion Polymerase (New England Biolabs) were used for high delity PCR amplications in the buffer supplied by the respective manufacturer. PCR products and products of restriction digests were puried either with PCR clean up kit (Qiagen) or using preparative agarose gel electrophoresis followed by DNA isolation using the Zymoclean gel DNA recovery kit (Zymo Research). Restriction endonucleases were purchased from New England Biolabs and used according to the manufacturers instructions. Ligations were performed using T4 DNA ligase (Invitrogen) or Gibson Assembly (New England Biolabs). Small-scale isolation of plasmid DNA was performed by plasmid Miniprep kit (Qiagen). The cDNA sequences for all fusion constructs were conrmed by sequencing (Genewiz). Site-directed mutagenesis was performed with QuikChange kit (Agilent Technologies).

Construction of linker libraries. A vector for expression in prokaryotic and eukaryotic systems was constructed based on mammalian expression vector pcDNA3.1 ( ). To facilitate prokaryotic expression, a customized constitutive

promoter was introduced 50-ttgctttgtgagcggataacaattataatagattca-30 based on the phage early T5 promoter for prokaryotic transcription41. An E. coli ribosome binding site 50-aggaggaa-30 for prokaryotic translation was also introduced via

QuikChange reactions. The resultant vector, designated pcDuEx1.0, exhibits moderate expression of Arch-mOrange2 fusions in E. coli cells and very similar expression levels in HeLa cells compared with its predecessor. We used pcDuEx1.0 as the vector for screening of linker libraries.

We focused on mOrange2 fusions for determining optimized linker length for FRET efciency. We chose QuasAr1.2 (Arch D95N/D106H, the best available at the time of the screen) as the Arch body. For construction of QuasAr1.2 mOrange2 D0, we fused QuasAr1.2 to the N terminus of mOrange2 fusion via a 5 residue linker (RPVVA) using overlap PCR. The DNA was PCR amplied with the anking restriction sites BamHI and XbaI, followed by double digestion and ligation into pcDuEx1.0 linearized by digestion with the same two enzymes.

From the template of QuasAr1.2mOrange2 D0, we constructed linker libraries by systematic truncation of the connecting region between QuasAr1.2 and mOrange2 using Quikchange reactions (Fig. 2). For each library, two randomized amino-acid residues (nucleotide sequence NNKNNK, where N A, G, C, T and

K G, T) were placed between the C terminus of Arch and the N terminus of

mOrange2, to generate 400 amino-acid combinations (1024 nucleotide combinations). The libraries were cloned into pcDuEx1.0 via standard procedure of restriction enzyme digestion and ligation.

Hierarchical screen of linker libraries. E. coli (DH10B, Invitrogen) colonies expressing the linker library exhibited varied intensities of mOrange2 uorescence. For each library, the 24 variants with brightest mOrange2 uorescence were picked and grown in overnight culture at 37 C. The plasmid DNA of each variant was prepared from overnight culture using standard miniprep procedure. For each variant, the plasma membrane trafcking was examined in HEK cells (CRL-1573, ATCC) co-expressing ArcLight, which served as internal reference. The ve variants with the best membrane trafcking were then expressed in HeLa cells for testing of voltage sensitivity.

HeLa cells (CCL2, ATCC) were grown to 4060% conuence on home-made 35 mm glass-bottom dishes or 24-well glass-bottom plates, and transfected with 1 mg of plasmid DNA and 2 ml Turbofect (Thermo Scientic) according to the manufacturers instructions. HeLa cells were transfected with plasmids encoding the QuasAr1.2mOrange2 variant, ArcLight Q239 (Addgene: 36856) and Kir2.1 (Addgene: 32641) in equal weight ratio. Expression of Kir2.1 in HeLa cells maintained the resting potential close to 60 mV, appropriate for a neuronal

voltage indicator42. After 3 h incubation, the media was exchanged to DMEM with 10% fetal bovine serum and the cells were incubated for an additional 24 h at 37 C

8 NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications

& 2014 Macmillan Publishers Limited. All rights reserved.

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625 ARTICLE

in a CO2 incubator. Immediately before imaging, cells were washed twice with Hanks balanced salt solution and then 1 ml of 20 mM HEPES-buffered Hanks balanced salt solution was added. No retinal was added to the bufferloading of retinal into the rhodopsin was presumed to occur from endogenous retinal.

Cell imaging was performed with an inverted Eclipse Ti-E (Nikon) equipped with a Photometrics QuantEM 512SC camera and a 150 W mercury-xenon lamp (Hamamatsu). A home-made parallel platinum electrode pair with a separation distance of 0.5 cm was mounted in a custom plastic support and was placed in the imaging dish or well. The waveforms of voltage pulses were generated by a pulse generator PG 58A (Gould Advance) and amplied by an Agilent 6824A 40V/25A DC Power Supply (Hewlett Packard). The typical waveform had square wave pulses lasting 20 ms with pulse eld strength ranging from 5060 V cm 1. The mOrange2 uorescence was imaged at 100 Hz frame rate in 4 4 binning mode for

10 s using the following lter set: 545/30 nm (excitation), 620/60 nm (emission) and 565 nm (dichroic). For imaging ArcLight, the lter set was: 480/40 nm (excitation), 535/40 nm (emission) and 505 nm (dichroic).

The raw uorescence traces of both mOrange2 and ArcLight were extracted from identical regions of interest in cells expressing both constructs, and exported into a Microsoft Excel spreadsheet using the microscope software NIS-Elements Advanced Research (Nikon). Background subtraction, photobleaching corrections, calculations of average DF/F and calculation of SNR were performed automatically in Excel. The average DF/F and SNR of mOrange2 signals was compared with those of ArcLight signals from the same cells, and the ratios of DF/F of mOrange2 versus ArcLight were reported. At least 20 cells co-expressing mOrange2 fusion and ArcLight were analysed for each variant. The best variant with maximum mean ratio in each library was determined and sequenced.

pH-dependent absorption spectrum of QuasAr2. E. coli cells transformed with a pBAD vector encoding QuasAr2 were grown in 12 ml liquid LB medium with 200 mg ml 1 ampicillin overnight. The next day, 12 ml of liquid LB medium containing 50 mM retinal, 200 mg ml 1 ampicillin and 0.2% L-arabinose was added into the culture to induce expression of QuasAr2, followed by additional incubation at 37 C for 3.5 h. The cell pellets were collected by centrifugation, washed with Tris-buffered saline (30 mM Tris, 150 mM NaCl, pH 7.4), and lysed with a tip sonicator for 10 min. The cytoplasmic fraction was discarded after centrifugation and the coloured insoluble fraction was resuspended in a series of modied Tris-buffered saline buffers (30 mM Tris, 150 mM NaCl, adjusted to the pH value of the spectral measurement) containing 1% N-dodecyl-b-D-maltopyranoside (Affymetrix). The suspension was then centrifuged (17,000 g for 15 min, 4 C). Absorption spectra of QuasAr2 in the supernatant in different pH were recorded on a DU-800 ultraviolet-visible spectrophotometer (Beckman).

Expression vectors for HEK cells and neurons. We chose lentivirus vector FCK-Arch-EGFP (Addgene: 22217) as the backbone for all eFRET constructs. This vector features a CaMKIIa promoter and a Woodchuck hepatitis virus posttranscriptional regulatory element after the 30 end of the open reading frame. To enhance membrane trafcking of fusion proteins, we added a TS and ER export signal peptide sequence (FCYENEV), derived from the inward rectier potassium channel Kir2.1, as previously described28. QuasAr2-FP fusion constructs were made by Gibson Assembly: the vector was linearized by double digestion with BamHI and BsrGI, and QuasAr2 and uorescent protein cDNA segments were generated by PCR amplication.

The linker conguration of all eFRET fusion proteins was constructed based on the optimized linker sequence found by the linker screening. In all eFRET fusion proteins, the N-terminal 2 amino acids of QuasAr2 were changed from DP to VS to facilitate expression, and the C-terminal 14 amino acids of QuasAr2 (APEPSAGADVSAAD) were replaced with a 2-amino-acid linker, Leu-Arg (based on the optimized linker sequence found in linker library D24), to shorten the distance between QuasAr2 and uorescent protein. The N-terminal amino acids in the uorescent proteins were also truncated (Supplementary Table 3). The nucleotide sequences of all constructs are in the Supplementary Note 1.

Two-photon lifetime measurements to determine FRET efciency.

We measured uorescence lifetime on a home-built beam-scanning two-photon microscope with an 80 MHz, 100 fs tunable pulsed laser (SpectraPhysics Insight DeepSee). Pulse compression in the sample plane was performed through maximizing the uorescence intensity of a bead-sample, using the motorized prism compressor built into the laser. The citrine measurements were performed at 1,040 nm excitation wavelength with a time-averaged excitation power of 30 mW, or 0.4 nJ per pulse, focused down to a B500 nm spot with a 1.2 NA water immersion objective (Olympus UplanSapo) for a time-averaged intensity of15 MW cm 2; measurements were performed for linear speeds of the scanned spot varying between 0 and 30 cm s 1 without any measurable effect on uorescence lifetime. Excitation light and uorescence were separated using a FF775-Di01 dichroic mirror and FF01-790/SP-25 Shortpass lter (Both Semrock); uorescence was detected using a Hamamatsu R943-02 photomultiplier tube in photon counting mode, cooled to 20 C. The PMT signal was amplied through an SRS

PR325 amplier and discretized with a Hamamatsu Photon counting unit C9744,

before being fed into a Picoharp 300 TCSPC module (Picoquant). The setup was

controlled by Labview software written in-house.

Simultaneous electrophysiology and uorescence in HEK cells. HEK293t/17 cells (ATCC CRL-11268) were cultured and transfected following standard protocols. Briey, cells were grown at 37 C, 5% CO2, in DMEM supplemented with 10% fetal bovine serum and penicillinstreptomycin. Plasmids were transfected using TransIT-293 reagent (Mirus Bio LLC) following the manufacturers instructions. Twenty-four hours post transfection, cells were re-plated onto glass-bottom dishes (MatTek) at a density of B10,000 cells cm 2. Cells were assayed 4060 h post transfection.

Despite the presence of saturating retinal in the culture medium, cells were supplemented with retinal before measurement to remove a possible source of variability. Cells were supplemented with retinal by preincubating with 5 mM retinal in growth medium (diluted from 40 mM stock solution in dimethyl sulphoxide) in the incubator for 0.51 h immediately before imaging. All imaging and electrophysiology were performed in Tyrodes buffer (containing 125 mM NaCl, 2.5 mM KCl, 3 mM CaCl2, 1 mM MgCl2, 10 mM HEPES, 30 mM glucose, at pH 7.3 and adjusted to 305310 mOsm with sucrose). A gap junction blocker, 2-aminoethoxydiphenyl borate (50 mM, Sigma), was added to eliminate electrical coupling between cells.

Filamented glass micropipettes (WPI) were pulled to a tip resistance of 510 MO, and lled with internal solution containing 125 mM potassium gluconate, 8 mM NaCl, 0.6 mM MgCl2, 0.1 mM CaCl2, 1 mM EGTA, 10 mM

HEPES, 4 mM Mg-ATP, 0.4 mM Na-GTP (pH 7.3); adjusted to 295 mOsm with sucrose. Pipettes were positioned with a Sutter MP285 manipulator. Whole-cell, voltage and current clamp recordings were acquired using a patch clamp amplier (A-M Systems, Model 2400), ltered at 5 kHz with the internal lter and digitized with a National Instruments PCIE-6323 acquisition board at 10 kHz.

Simultaneous whole-cell patch clamp recordings and uorescence recordings were acquired on a home-built, inverted epiuorescence microscope, described below in the section Imaging Apparatus.

Neuronal culture and electrophysiology. All procedures involving animals were in accordance with the National Institutes of Health Guide for the care and use of laboratory animals and were approved by the Institutional Animal Care and Use Committee at the institution at which they were carried out.

Hippocampal neurons from P0 rat pups were dissected and cultured in neurobasal-based medium (NBActiv4, Brainbits) at a density of 40,000 cm 2 on glass-bottom dishes (MatTek) pre-coated with poly-D-lysine (Sigma P7205) and matrigel (BD Biosciences 356234). At 3 days in vitro (DIV), cytarabine was added to the neuronal culture medium at a nal concentration of 2 mM to inhibit glial growth43.

Neurons were transfected on DIV 7 with the eFRET plasmid using Lipofectamine 2000 transfection reagent (Life Technologies). Procedures followed manufacturers instructions but reduced the amount of reagent by 5080% to avoid toxicity.

Measurements were performed on primary cultures at DIV 1020. Experiments were conducted in Tyrodes solution containing 125 mM NaCl, 2.5 mM KCl,3 mM CaCl2, 1 mM MgCl2, 10 mM HEPES, 30 mM glucose (pH 7.3) and adjusted to 305310 mOsm with sucrose. Immediately before imaging, neurons were incubated with 5 mM all-trans retinal in the culture medium for 30 min and then washed with Tyrodes solution. Experiments were performed at 23 C under ambient atmosphere.

Imaging apparatus. Experiments were conducted on a home-built inverted uorescence microscope equipped with 488 nm, 532 nm, 561 nm, 594 nm and 640 nm laser lines and a scientic CMOS camera (Hamamatsu ORCA-Flash 4.0). The power and manufacturer of laser lines are summarized in Supplementary Table 4. Illumination from lasers were combined using dichroic mirrors, sent through an acousto-optic tunable lter (Gooch and Housego 48058-2.5-.55-5W) for intensity modulation, and then expanded and focused onto the back focal plane of a 60 water immersion objective, numerical aperture 1.20 (Olympus UIS2

UPlanSApo 60/1.20 W). Imaging of uorescent proteins was performed at

illumination intensities of 24 W cm 2. Imaging of QuasAr2-direct uorescence was performed at an illumination intensity of 200400 W cm 2. Supplementary

Table 5 summarizes the laser lines, dichroic mirrors and emission lters used for uorescence imaging. For fast data acquisition, a small eld of view around the cell of interest was chosen at the centre of the camera to achieve a frame rate of 1,000 frames per second.

Data analysis. Data was analysed with home-made software written in MATLAB. Fluorescence intensities from raw movies were extracted using a maximum likelihood pixel-weighting algorithm described in ref. 14. Briey, the uorescence at each pixel was correlated with the mean uorescence. Pixels that showed stronger correlation to the mean were preferentially weighted. This algorithm automatically found the pixels carrying the most information, and de-emphasized background pixels. Alternatively, a ROI comprising the cell body was dened by the user, and uorescence intensity was calculated from the unweighted mean of pixel values

NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications 9

& 2014 Macmillan Publishers Limited. All rights reserved.

ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5625

within the ROI. With the improved trafcking of the QuasAr2 mutants resulting from the TS and ER2 motifs, the ROI approach gave similar results as the maximum likelihood pixel-weighting algorithm.

For eFRET speed analysis, the time constants for the step response were calculated by tting a double exponential to the rising and decaying portions of the uorescence traces. All error ranges represent s.e.m.

References

1. Cohen, A. E. & Venkatachalam, V. Bringing bioelectricity to light. Annu. Rev. Biophys. 43, 11.111.22 (2014).

2. Bezanilla, F. How membrane proteins sense voltage. Nat. Rev. Mol. Cell Biol. 9, 323332 (2008).

3. Kralj, J. M., Hochbaum, D. R., Douglass, A. D. & Cohen, A. E. Electrical spiking in Escherichia coli probed with a uorescent voltage indicating protein. Science 333, 345348 (2011).

4. Slayman, C. L. & Slayman, C. W. Depolarization of the plasma membrane of Neurospora during active transport of glucose: evidence for a proton-dependent cotransport system. Proc. Natl Acad. Sci. USA 71, 19351939 (1974).

5. Mousavi, S. A., Chauvin, A., Pascaud, F., Kellenberger, S. & Farmer, E. E. GLUTAMATE RECEPTOR-LIKE genes mediate leaf-to-leaf wound signalling. Nature 500, 422426 (2013).

6. Siegel, M. S. & Isacoff, E. Y. A genetically encoded optical probe of membrane voltage. Neuron 19, 735741 (1997).

7. Jin, L. et al. Single action potentials and subthreshold electrical events imaged in neurons with a uorescent protein voltage probe. Neuron 75, 779785 (2012).

8. Cao, G. et al. Genetically targeted optical electrophysiology in intact neural circuits. Cell 154, 904913 (2013).

9. St-Pierre, F. et al. High-delity optical reporting of neuronal electrical activity with an ultrafast uorescent voltage sensor. Nat. Neurosci. 17, 884889 (2014).

10. Baker, B. J. et al. Genetically encoded uorescent voltage sensors using the voltage-sensing domain of Nematostella and Danio phosphatases exhibit fast kinetics. J. Neurosci. Methods 208, 190196 (2012).

11. Mutoh, H., Akemann, W. & Knpfel, T. Genetically engineered uorescent voltage reporters.. ACS Chem. Neuro. 3, 585592 (2012).

12. Lam, A. J. et al. Improving FRET dynamic range with bright green and red uorescent proteins. Nat. Methods 9, 10051012 (2012).

13. Hochbaum, D. R. et al. All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat. Methods 11, 825833 (2014).14. Kralj, J. M., Douglass, A. D., Hochbaum, D. R., Maclaurin, D. & Cohen, A. E. Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat. Methods 9, 9095 (2012).

15. Chen, T. et al. Ultrasensitive uorescent proteins for imaging neuronal activity. Nature 499, 295300 (2013).

16. Marvin, J. S. et al. An optimized uorescent probe for visualizing glutamate neurotransmission. Nat. Methods 10, 162170 (2013).

17. Tantama, M., Martnez-Franois, J. R., Mongeon, R. & Yellen, G. Imaging energy status in live cells with a uorescent biosensor of the intracellular ATP-to-ADP ratio. Nat. Commun. 4, 2550 (2013).

18. Kuner, T. & Augustine, G. J. A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons. Neuron 27, 447459 (2000).

19. San Martn, A. et al. Imaging mitochondrial ux in single cells with a FRET sensor for pyruvate. PLoS ONE 9, e85780 (2014).

20. Bayraktar, H. et al. Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET. Photochem. Photobiol. 88, 9097 (2011).

21. Barker, S. L., Kopelman, R., Meyer, T. E. & Cusanovich, M. A. Fiber-optic nitric oxide-selective biosensors and nanosensors. Anal. Chem. 70, 971976 (1998).

22. Kuznetsova, S. et al. The enzyme mechanism of nitrite reductase studied at single-molecule level. Proc. Natl Acad. Sci. USA 105, 32503255 (2008).

23. Gong, Y., Wagner, M. J., Li, J. Z. & Schnitzer, M. J. Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors. Nat. Commun. 5, 3674 (2014).

24. Maclaurin, D., Venkatachalam, V., Lee, H. & Cohen, A. E. Mechanism of voltage-sensitive uorescence in a microbial rhodopsin. Proc. Natl Acad. Sci. USA 110, 59395944 (2013).

25. Shaner, N. C. et al. Improving the photostability of bright monomeric orange and red uorescent proteins. Nat. Methods 5, 545551 (2008).

26. Enami, N. et al. Crystal structures of archaerhodopsin-1 and-2: common structural motif in archaeal light-driven proton pumps. J. Mol. Biol. 358, 675685 (2006).

27. Shu, X., Shaner, N. C., Yarbrough, C. A., Tsien, R. Y. & Remington, S. J. Novel chromophores and buried charges control colour in mFruits. Biochemistry 45, 96399647 (2006).

28. Gradinaru, V. et al. Molecular and cellular approaches for diversifying and extending optogenetics. Cell 141, 154165 (2010).

29. Heim, R. & Tsien, R. Y. Engineering green uorescent protein for improved brightness, longer wavelengths and uorescence resonance energy transfer. Curr. Biol. 6, 178182 (1996).

30. Griesbeck, O., Baird, G. S., Campbell, R. E., Zacharias, D. A. & Tsien, R. Y. Reducing the environmental sensitivity of yellow uorescent protein. Mechanism and applications. J. Biol. Chem. 276, 2918829194 (2001).

31. Shcherbo, D. et al. Far-red uorescent tags for protein imaging in living tissues. Biochem. J. 418, 567574 (2009).

32. Chung, Y. G., Schwartz, J. A. & Sawaya, R. E. Diagnostic potential of laser-induced autouorescence emission in brain tissue. J. Korean Med. Sci. 12.2, 135142 (1997).

33. Lin, W., Toms, S. A., Motamedi, M., Jansen, E. D. & Mahadevan-Jansen, A. Brain tumor demarcation using optical spectroscopy; an in vitro study.J. Biomed. Opt. 5, 214220 (2000).34. Flock, S. T., Jacques, S. L., Wilson, B. C., Star, W. M. & van Gemert, M. J. Optical properties of Intralipid: a phantom medium for light propagation studies. Lasers Surg. Med. 12, 510519 (1992).

35. Zhang, J., Davidson, R. M., Wei, M. & Loew, L. M. Membrane electric properties by combined patch clamp and uorescence ratio imaging in single neurons. Biophys. J. 74, 4853 (1998).

36. Hou, J. H., Venkatachalam, V. & Cohen, A. E. Temporal dynamics of microbial rhodopsin uorescence reports absolute membrane voltage. Biophys. J. 106, 639648 (2014).

37. Fisher, J. A. et al. Two-photon excitation of potentiometric probes enables optical recording of action potentials from mammalian nerve terminals in situ.J. Neurophysiol. 99, 15451553 (2008).38. Akemann, W. et al. Two-photon voltage imaging using a genetically encoded voltage indicator. Sci. Rep. 3, 2231 (2013).

39. Beja, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & Delong, E. F. Proteorhodopsin phototrophy in the ocean. Nature 411, 786789 (2001).

40. Spudich, J. L. The multitalented microbial sensory rhodopsins. Trends Microbiol. 14, 480487 (2006).

41. Bujard, H. et al. A T5 promoter-based transcription-translation system for the analysis of proteins in vitro and in vivo. Meth. Enzymol. 155, 416433 (1987).

42. Hille, B. in Ion Channels of Excitable Membranes (Sinauer, 2001).43. Chen, G., Harata, N. C. & Tsien, R. W. Paired-pulse depression of unitary quantal amplitude at single hippocampal synapses. Proc. Natl Acad. Sci. USA 101, 10631068 (2004).

Acknowledgements

We thank V. Nathan and N. Smedemark-Margulies for technical assistance, andV. Venkatachalam, S. Farhi and J. Kralj for helpful discussions. We thank A.Y. Ting,F.St Pierre and M.Z. Lin for plasmids and spectral information. P.Z., A.D.D., D.R.H., D.B., C.A.W. and A.E.C. were supported by the Howard Hughes Medical Institute, the Harvard Center for Brain Science, PECASE award N00014-11-1-0549, US National Institutes of Health grants 1-R01-EB012498-01 and New Innovator grant 1-DP2-OD007428. D.R.H. was supported by an NSF Graduate Fellowship. D.B. was supported by an NWO-Rubicon Fellowship. R.E.C. was supported by the Natural Sciences and Engineering Research Council of Canada (Discovery Grants) and the Canadian Institutes of Health Research. Y.Z. was supported by a graduate scholarship from the University of Alberta and Alberta Innovates. R.E.C. holds a Tier II Canada Research Chair.

Author contributions

P.Z., Y.Z., D.R.H., A.D.D., C.A.W., D.B. conducted experiments and analysed data. R.E.C. supervised the screen for linker length optimization. A.E.C. proposed eFRET for voltage sensing. P.Z., Y.Z., R.E.C. and A.E.C. wrote the paper.

Additional information

Supplementary Information accompanies this paper at http://www.nature.com/naturecommunications

Web End =http://www.nature.com/ http://www.nature.com/naturecommunications

Web End =naturecommunications

Competing nancial interests: AEC is a founder of Q-State Biosciences.

Reprints and permission information is available online at http://npg.nature.com/reprintsandpermissions/

Web End =http://npg.nature.com/ http://npg.nature.com/reprintsandpermissions/

Web End =reprintsandpermissions/

How to cite this article: Zou, P. et al. Bright and fast multicoloured voltage reporters via electrochromic FRET. Nat. Commun. 5:4625 doi: 10.1038/ncomms5625 (2014).

10 NATURE COMMUNICATIONS | 5:4625 | DOI: 10.1038/ncomms5625 | http://www.nature.com/naturecommunications

Web End =www.nature.com/naturecommunications

& 2014 Macmillan Publishers Limited. All rights reserved.