Imaging Voltage with Microbial Rhodopsins

Chien, M.-P., Brinks, D., Testa-Silva, G., Tian, H., Phil Brooks, F., Adam, Y., et al.

(2021). Photoactivated Voltage Imaging in Tissue with an ArchaerhodopsinDerived Reporter. Sci. Adv. 7, eabe3216. doi:10.1126/sciadv.abe3216

Chow, B. Y., Han, X., Dobry, A. S., Qian, X., Chuong, A. S., Li, M., et al.

(2010). High-performance Genetically Targetable Optical Neural

Silencing by Light-Driven Proton Pumps. Nature 463, 98–102.

doi:10.1038/nature08652

Dana, H., Sun, Y., Mohar, B., Hulse, B. K., Kerlin, A. M., Hasseman, J. P., et al.

(2019). High-performance Calcium Sensors for Imaging Activity in Neuronal

Populations and Microcompartments. Nat. Methods. 16, 649–657. doi:10.1038/

s41592-019-0435-6

Engqvist, M. K. M., McIsaac, R. S., Dollinger, P., Flytzanis, N. C., Abrams, M.,

Schor, S., et al. (2015). Directed Evolution of Gloeobacter Violaceus

Rhodopsin Spectral Properties. J. Mol. Biol. 427, 205–220. doi:10.1016/

j.jmb.2014.06.015

Fan, L. Z., Kheifets, S., Böhm, U. L., Wu, H., Piatkevich, K. D., Xie, M. E., et al.

(2020). All-Optical Electrophysiology Reveals the Role of Lateral Inhibition in

Sensory Processing in Cortical Layer 1. Cell 180, 521–535. doi:10.1016/

j.cell.2020.01.001

Fan, L. Z., Nehme, R., Adam, Y., Jung, E. S., Wu, H., Eggan, K., et al. (2018).

All-optical Synaptic Electrophysiology Probes Mechanism of KetamineInduced Disinhibition. Nat. Methods 15, 823–831. doi:10.1038/s41592018-0142-8

Flytzanis, N. C., Bedbrook, C. N., Chiu, H., Engqvist, M. K. M., Xiao, C., Chan, K.

Y., et al. (2014). Archaerhodopsin Variants with Enhanced Voltage-Sensitive

Fluorescence in Mammalian and Caenorhabditis elegans Neurons. Nat.

Commun. 5. doi:10.1038/ncomms5894

Gong, Y., Huang, C., Li, J. Z., Grewe, B. F., Zhang, Y., Eismann, S., et al. (2015).

High-speed Recording of Neural Spikes in Awake Mice and Flies with a

Fluorescent Voltage Sensor. Science 350, 1361–1366. doi:10.1126/

science.aab0810

Gong, Y., Li, J. Z., and Schnitzer, M. J. (2013). Enhanced Archaerhodopsin

Fluorescent Protein Voltage Indicators. PLoS One 8, e66959. doi:10.1371/

journal.pone.0066959

Gong, Y., Wagner, M. J., Zhong Li, J., and Schnitzer, M. J. (2014). Imaging Neural

Spiking in Brain Tissue Using FRET-Opsin Protein Voltage Sensors. Nat.

Commun. 5, 3674. doi:10.1038/ncomms4674

Gradinaru, V., Zhang, F., Ramakrishnan, C., Mattis, J., Prakash, R., Diester, I., et al.

(2010). Molecular and Cellular Approaches for Diversifying and Extending

Optogenetics. Cell 141, 154–165. doi:10.1016/j.cell.2010.02.037

Grienberger, C., and Konnerth, A. (2012). Imaging Calcium in Neurons. Neuron

73, 862–885. doi:10.1016/j.neuron.2012.02.011

Han, X., and Boyden, E. S. (2007). Multiple-Color Optical Activation, Silencing,

and Desynchronization of Neural Activity, with Single-Spike Temporal

Resolution. PLoS One 2, e299. doi:10.1371/journal.pone.0000299

Herwig, L., Rice, A. J., Bedbrook, C. N., Zhang, R. K., Lignell, A., Cahn, J. K. B., et al.

(2017). Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin

Using a Synthetic Chromophore. Cel. Chem. Biol. 24 (3), 415–425. doi:10.1016/

j.chembiol.2017.02.008

Abdelfattah, A. S., Kawashima, T., Singh, A., Novak, O., Liu, H., Shuai, Y., et al.

(2019). Bright and Photostable Chemigenetic Indicators for Extended In Vivo

Voltage Imaging. Science 365, 699–704. doi:10.1126/science.aav6416

Abdelfattah, A. S., Valenti, R., Zheng, J., Wong, A., Chuong, A. S., Hasseman, J. P.,

et al. (2020). A General Approach to Engineer Positive-Going eFRET Voltage

Indicators. Nat. Commun. 11, 3444. doi:10.1038/s41467-020-17322-1

Adam, Y., Kim, J. J., Lou, S., Zhao, Y., Xie, M. E., Brinks, D., et al. (2019). Voltage

Imaging and Optogenetics Reveal Behaviour-dependent Changes in

Hippocampal Dynamics. Nature 569, 413–417. doi:10.1038/s41586-0191166-7

Akemann, W., Mutoh, H., Perron, A., Rossier, J., and Knöpfel, T. (2010). Imaging

Brain Electric Signals with Genetically Targeted Voltage-Sensitive Fluorescent

Proteins. Nat. Methods. 7, 643–649. doi:10.1038/nmeth.1479

Akerboom, J., Chen, T.-W., Wardill, T. J., Tian, L., Marvin, J. S., Mutlu, S., et al.

(2012). Optimization of a GCaMP Calcium Indicator for Neural Activity

Imaging. J. Neurosci. 32, 13819–13840. doi:10.1523/JNEUROSCI.260112.2012

Baker, C. A., Elyada, Y. M., Parra, A., and Bolton, M. M. (2016). Cellular Resolution

Circuit Mapping with Temporal-Focused Excitation of Soma-Targeted

Channelrhodopsin. Elife 5, 1–15. doi:10.7554/eLife.14193

Bando, Y., Sakamoto, M., Kim, S., Ayzenshtat, I., and Yuste, R. (2019).

Comparative Evaluation of Genetically Encoded Voltage Indicators. Cel.

Rep. 26, 802–813. doi:10.1016/j.celrep.2018.12.088

Bayraktar, H., Fields, A. P., Kralj, J. M., Spudich, J. L., Rothschild, K. J., and Cohen,

A. E. (2012). Ultrasensitive Measurements of Microbial Rhodopsin Photocycles

Using Photochromic FRET. Photochem. Photobiol. 88 (1), 90–97. doi:10.1111/

j.1751-1097.2011.01011.x

Beck, C., and Gong, Y. (2019). A High-Speed, Bright, Red Fluorescent Voltage

Sensor to Detect Neural Activity. Sci. Rep. 9, 15878. doi:10.1038/s41598-01952370-8

Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., and Deisseroth, K. (2005).

Millisecond-timescale, Genetically Targeted Optical Control of Neural Activity.

Nat. Neurosci. 8, 1263–1268. doi:10.1038/nn1525

Broussard, G. J., Liang, Y., Fridman, M., Unger, E. K., Meng, G., Xiao, X., et al.

(2018). In Vivo measurement of Afferent Activity with Axon-specific Calcium

Imaging. Nat. Neurosci. 21, 1272–1280. doi:10.1038/s41593-018-0211-4

Cai, C., Friedrich, J., Singh, A., Eybposh, M. H., Pnevmatikakis, E. A., Podgorski, K., et al.

(2021). VolPy: Automated and Scalable Analysis Pipelines for Voltage Imaging

Datasets. PLOS Comput. Biol. 17, e1008806. doi:10.1371/journal.pcbi.1008806

Chamberland, S., Yang, H. H., Pan, M. M., Evans, S. W., Guan, S., Chavarha, M.,

et al. (2017). Fast Two-Photon Imaging of Subcellular Voltage Dynamics in

Neuronal Tissue with Genetically Encoded Indicators. Elife 6, e25690.

doi:10.7554/eLife.25690

Chen, T.-W., Wardill, T. J., Sun, Y., Pulver, S. R., Renninger, S. L., Baohan, A., et al.

(2013). Ultrasensitive Fluorescent Proteins for Imaging Neuronal Activity.

Nature 499, 295–300. doi:10.1038/nature12354

Frontiers in Molecular Biosciences | www.frontiersin.org

August 2021 | Volume 8 | Article 738829

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

Zhang et al.

Voltage Imaging with Microbial Rhodopsins

Nguyen, C., Upadhyay, H., Murphy, M., Borja, G., Rozsahegyi, E. J., Barnett, A.,

et al. (2019). Simultaneous Voltage and Calcium Imaging and Optogenetic

Stimulation with High Sensitivity and a Wide Field of View. Biomed. Opt.

Express. 10, 789. doi:10.1364/BOE.10.000789

Obien, M. E. J., Deligkaris, K., Bullmann, T., Bakkum, D. J., and Frey, U. (2014).

Revealing Neuronal Function through Microelectrode Array Recordings. Front.

Neurosci. 8, 423. doi:10.3389/fnins.2014.00423

Ohkura, M., Sasaki, T., Sadakari, J., Gengyo-Ando, K., Kagawa-Nagamura, Y.,

Kobayashi, C., et al. (2012). Genetically Encoded Green Fluorescent Ca2+

Indicators with Improved Detectability for Neuronal Ca2+ Signals. PLoS One. 7,

e51286–10. doi:10.1371/journal.pone.0051286

Ohtani, H., Itoh, H., and Shinmura, T. (1992). Time-resolved Fluorometry of

Purple Membrane of Halobacterium Halobium O640 and an O-like RedShifted Intermediate Q. FEBS Lett. 305, 6–8. doi:10.1016/0014-5793(92)

80643-u

Ota, K., Oisi, Y., Suzuki, T., Ikeda, M., Ito, Y., Ito, T., et al. (2021). Fast, CellResolution, Contiguous-wide Two-Photon Imaging to Reveal Functional

Network Architectures across Multi-Modal Cortical Areas. Neuron 109,

1810–1824. doi:10.1016/j.neuron.2021.03.032

Peterka, D. S., Takahashi, H., and Yuste, R. (2011). Imaging Voltage in Neurons.

Neuron 69, 9–21. doi:10.1016/j.neuron.2010.12.010

Piao, H. H., Rajakumar, D., Kang, B. E., Kim, E. H., and Baker, B. J. (2015).

Combinatorial Mutagenesis of the Voltage-Sensing Domain Enables the

Optical Resolution of Action Potentials Firing at 60 Hz by a Genetically

Encoded Fluorescent Sensor of Membrane Potential. J. Neurosci. 35,

372–385. doi:10.1523/JNEUROSCI.3008-14.2015

Piatkevich, K. D., Bensussen, S., Tseng, H.-A., Shroff, S. N., Lopez-Huerta,

V. G., Park, D., et al. (2019). Population Imaging of Neural Activity in

Awake Behaving Mice. Nature 574, 413–417. doi:10.1038/s41586-0191641-1

Piatkevich, K. D., Jung, E. E., Straub, C., Linghu, C., Park, D., Suk, H.-J., et al.

(2018). A Robotic Multidimensional Directed Evolution Approach Applied to

Fluorescent Voltage Reporters. Nat. Chem. Biol. 14, 352–360. doi:10.1038/

s41589-018-0004-9

Sineshchekov, O. A., Govorunova, E. G., Wang, J., and Spudich, J. L. (2012).

Enhancement of the Long-Wavelength Sensitivity of Optogenetic Microbial

Rhodopsins by 3,4-dehydroretinal. Biochemistry 51, 4499–4506. doi:10.1021/

bi2018859

Smetters, D., Majewska, A., and Yuste, R. (1999). Detecting Action Potentials in

Neuronal Populations with Calcium Imaging. Methods 18, 215–221.

doi:10.1006/meth.1999.0774

Sofroniew, N. J., Flickinger, D., King, J., and Svoboda, K. (2016). A Large Field of

View Two-Photon Mesoscope with Subcellular Resolution for In Vivo Imaging.

Elife 5, 1–20. doi:10.7554/eLife.14472

St-Pierre, F., Marshall, J. D., Yang, Y., Gong, Y., Schnitzer, M. J., and Lin, M. Z.

(2014). High-fidelity Optical Reporting of Neuronal Electrical Activity with an

Ultrafast Fluorescent Voltage Sensor. Nat. Neurosci. 17, 884–889. doi:10.1038/

nn.3709

Stirman, J. N., Smith, I. T., Kudenov, M. W., and Smith, S. L. (2016). Wide

Field-Of-View, Multi-Region, Two-Photon Imaging of Neuronal Activity

in the Mammalian Brain. Nat. Biotechnol. 34, 857–862. doi:10.1038/

nbt.3594

Storace, D., Sepehri Rad, M., Kang, B., Cohen, L. B., Hughes, T., and Baker, B. J.

(2016). Toward Better Genetically Encoded Sensors of Membrane Potential.

Trends Neurosciences 39, 277–289. doi:10.1016/j.tins.2016.02.005

Tian, L., Hires, S. A., Mao, T., Huber, D., Chiappe, M. E., Chalasani, S. H., et al.

(2009). Imaging Neural Activity in Worms, Flies and Mice with Improved

GCaMP Calcium Indicators. Nat. Methods 6, 875–881. doi:10.1038/

nmeth.1398

Tsutsui, H., Jinno, Y., Tomita, A., Niino, Y., Yamada, Y., Mikoshiba, K., et al.

(2013). Improved Detection of Electrical Activity with a Voltage Probe Based on

a Voltage-Sensing Phosphatase. J. Physiol. 591, 4427–4437. doi:10.1113/

jphysiol.2013.257048

Venkatachalam, V., Brinks, D., Maclaurin, D., Hochbaum, D., Kralj, J., and Cohen,

A. E. (2014). Flash Memory: Photochemical Imprinting of Neuronal Action

Potentials onto a Microbial Rhodopsin. J. Am. Chem. Soc. 136, 2529–2537.

doi:10.1021/ja411338t

Hochbaum, D. R., Zhao, Y., Farhi, S. L., Klapoetke, N., Werley, C. A., Kapoor, V.,

et al. (2014). All-optical Electrophysiology in Mammalian Neurons Using

Engineered Microbial Rhodopsins. Nat. Methods. 11, 825–833. doi:10.1038/

nmeth.3000

Hontani, Y., Ganapathy, S., Frehan, S., Kloz, M., de Grip, W. J., and Kennis, J. T. M.

(2018). Strong pH-dependent Near-Infrared Fluorescence in a Microbial

Rhodopsin Reconstituted with a Red-Shifting Retinal Analogue. J. Phys.

Chem. Lett. 9, 6469–6474. doi:10.1021/acs.jpclett.8b02780

Hou, J. H., Venkatachalam, V., and Cohen, A. E. (2014). Temporal Dynamics of

Microbial Rhodopsin Fluorescence Reports Absolute Membrane Voltage.

Biophysical J. 106 (3), 639–648. doi:10.1016/j.bpj.2013.11.4493

Inagaki, S., Tsutsui, H., Suzuki, K., Agetsuma, M., Arai, Y., Jinno, Y., et al. (2017).

Genetically Encoded Bioluminescent Voltage Indicator for Multi-Purpose Use

in Wide Range of Bioimaging. Sci. Rep. 7, 42398. doi:10.1038/srep42398

Inoue, M., Takeuchi, A., Horigane, S.-i., Ohkura, M., Gengyo-Ando, K., Fujii, H.,

et al. (2015). Rational Design of a High-Affinity, Fast, Red Calcium Indicator

R-CaMP2. Nat. Methods. 12, 64–70. doi:10.1038/nmeth.3185

Inoue, M., Takeuchi, A., Manita, S., Horigane, S.-i., Sakamoto, M., Kawakami, R.,

et al. (2019). Rational Engineering of XCaMPs, a Multicolor GECI Suite for In

Vivo Imaging of Complex Brain Circuit Dynamics. Cell 177, 1346–1360.

doi:10.1016/j.cell.2019.04.007

Jin, L., Han, Z., Platisa, J., Wooltorton, J. R. A., Cohen, L. B., and Pieribone, V. A.

(2012). Single Action Potentials and Subthreshold Electrical Events Imaged in

Neurons with a Fluorescent Protein Voltage Probe. Neuron 75, 779–785.

doi:10.1016/j.neuron.2012.06.040

Kannan, M., Vasan, G., Huang, C., Haziza, S., Li, J. Z., Inan, H., et al. (2018). Fast, In

Vivo Voltage Imaging Using a Red Fluorescent Indicator. Nat. Methods. 15,

1108–1116. doi:10.1038/s41592-018-0188-7

Kojima, K., Kurihara, R., Sakamoto, M., Takanashi, T., Kuramochi, H., Zhang, X.

M., et al. (2020). Comparative Studies of the Fluorescence Properties of

Microbial Rhodopsins: Spontaneous Emission versus Photointermediate

Fluorescence. J. Phys. Chem. B. 124, 7361–7367. doi:10.1021/acs.jpcb.0c06560

Kralj, J. M., Douglass, A. D., Hochbaum, D. R., Maclaurin, D., and Cohen, A. E.

(2011a). Optical Recording of Action Potentials in Mammalian Neurons

Using a Microbial Rhodopsin. Nat. Methods. 9, 90–95. doi:10.1038/

nmeth.1782

Kralj, J. M., Hochbaum, D. R., Douglass, A. D., and Cohen, A. E. (2011b). Electrical

Spiking inEscherichia coliProbed with a Fluorescent Voltage-Indicating

Protein. Science 333, 345–348. doi:10.1126/science.1204763

Kwon, T., Sakamoto, M., Peterka, D. S., and Yuste, R. (2017). Attenuation of

Synaptic Potentials in Dendritic Spines. Cel. Rep. 20, 1100–1110. doi:10.1016/

j.celrep.2017.07.012

Liu, S., Lin, C., Xu, Y., Luo, H., Peng, L., Zeng, X., et al. (2021). A Far-Red Hybrid

Voltage Indicator Enabled by Bioorthogonal Engineering of Rhodopsin on Live

Neurons. Nat. Chem. 13, 472–479. doi:10.1038/s41557-021-00641-1

Lou, S., Adam, Y., Weinstein, E. N., Williams, E., Williams, K., Parot, V., et al.

(2016). Genetically Targeted All-Optical Electrophysiology with a Transgenic

Cre-dependent Optopatch Mouse. J. Neurosci. 36, 11059–11073. doi:10.1523/

JNEUROSCI.1582-16.2016

Maclaurin, D., Venkatachalam, V., Lee, H., and Cohen, A. E. (2013). Mechanism of

Voltage-Sensitive Fluorescence in a Microbial Rhodopsin. Proc. Natl. Acad. Sci.

110, 5939–5944. doi:10.1073/pnas.1215595110

Marshall, J. D., Li, J. Z., Zhang, Y., Gong, Y., St-Pierre, F., Lin, M. Z., et al.

(2016). Cell-Type-Specific Optical Recording of Membrane Voltage

Dynamics in Freely Moving Mice. Cell 167, 1650–1662. doi:10.1016/

j.cell.2016.11.021

Nakai, J., Ohkura, M., and Imoto, K. (2001). A High Signal-To-Noise Ca2+ Probe

Composed of a Single green Fluorescent Protein. Nat. Biotechnol. 19, 137–141.

doi:10.1038/84397

Nakamura, T., Takeuchi, S., Shibata, M., Demura, M., Kandori, H., and

Tahara, T. (2008). Ultrafast Pump−Probe Study of the Primary

Photoreaction Process in Pharaonis Halorhodopsin: Halide Ion

Dependence and Isomerization Dynamics. J. Phys. Chem. B. 112,

12795–12800. doi:10.1021/jp803282s

Neher, E. (1998). Usefulness and Limitations of Linear Approximations to the

Understanding of Ca++ Signals. Cell Calcium. 24, 345–357. doi:10.1016/S01434160(98)90058-6

Frontiers in Molecular Biosciences | www.frontiersin.org

August 2021 | Volume 8 | Article 738829

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

Zhang et al.

Voltage Imaging with Microbial Rhodopsins

Zou, P., Zhao, Y., Douglass, A. D., Hochbaum, D. R., Brinks, D., Werley, C. A., et al.

(2014). Bright and Fast Multicoloured Voltage Reporters via Electrochromic

FRET. Nat. Commun. 5. doi:10.1038/ncomms5625

Villette, V., Chavarha, M., Dimov, I. K., Bradley, J., Pradhan, L., Mathieu, B., et al.

(2019). Ultrafast Two-Photon Imaging of a High-Gain Voltage Indicator in

Awake Behaving Mice. Cell 179, 1590–1608. doi:10.1016/j.cell.2019.11.004

Werley, C. A., Boccardo, S., Rigamonti, A., Hansson, E. M., and Cohen, A. E. (2020).

Multiplexed Optical Sensors in Arrayed Islands of Cells for Multimodal Recordings

of Cellular Physiology. Nat. Commun. 11, 3881. doi:10.1038/s41467-020-17607-5

Xie, M. E., Adam, Y., Fan, L. Z., Böhm, U. L., Kinsella, I., Zhou, D., et al. (2021). Highfidelity Estimates of Spikes and Subthreshold Waveforms from 1-photon Voltage

Imaging In Vivo. Cel Rep. 35, 108954. doi:10.1016/j.celrep.2021.108954

Yuste, R., and Katz, L. C. (1991). Control of Postsynaptic Ca2+ Influx in

Developing Neocortex by Excitatory and Inhibitory Neurotransmitters.

Neuron 6, 333–344. doi:10.1016/0896-6273(91)90243-S

Zhang, H., Reichert, E., and Cohen, A. E. (2016). Optical Electrophysiology for

Probing Function and Pharmacology of Voltage-Gated Ion Channels. Elife 5,

1–20. doi:10.7554/eLife.15202

Zhao, Y., Araki, S., Wu, J., Teramoto, T., Chang, Y.-F., Nakano, M., et al. (2011). An

Expanded Palette of Genetically Encoded Ca2+ Indicators. Science 333,

1888–1891. doi:10.1126/science.1208592

Ziv, Y., Burns, L. D., Cocker, E. D., Hamel, E. O., Ghosh, K. K., Kitch, L. J., et al.

(2013). Long-term Dynamics of CA1 Hippocampal Place Codes. Nat. Neurosci.

16, 264–266. doi:10.1038/nn.3329

Frontiers in Molecular Biosciences | www.frontiersin.org

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