Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

High-performance genetically targetable optical neural silencing by light-driven proton pumps


The ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 (Arch)1 from Halorubrum sodomense enables near-100% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light. Arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 pA at light powers easily achievable in vivo. Furthermore, Arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. These properties of Arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally relevant timescales. Arch function in neurons is well tolerated because pH excursions created by Arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins2,3 or natural spike firing. To highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue–green light-drivable proton pump from the fungus Leptosphaeria maculans4 (Mac) can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue versus red light. Light-driven proton pumps thus represent a high-performance and extremely versatile class of ‘optogenetic’ voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Optical neural silencing by light-driven proton pumping, revealed by a cross-kingdom functional molecular screen.
Figure 2: Functional properties of the light-driven proton pump Arch in neurons.
Figure 3: High-performance Arch-mediated optical neural silencing of neocortical regions in awake mice.
Figure 4: Multicolour silencing of two neural populations, enabled by blue- and red-light drivable ion pumps of different classes.

Accession codes

Data deposits

Sequences are available to download from GenBank ( under accession numbers: GU045593 (mammalian codon-optimized Arch), GU045594 (mammalian codon-optimized Arch fused to GFP), GU045595 (mammalian codon-optimized Mac), GU045596 (mammalian codon-optimized Mac fused to GFP), GU045597 (ss-Prl-Arch), GU045598 (ss-Arch-GFP-ER2) and GU045599 (ss-Prl-Arch-GFP).


  1. Ihara, K. et al. Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J. Mol. Biol. 285, 163–174 (1999)

    Article  CAS  Google Scholar 

  2. Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neurosci. 8, 1263–1268 (2005)

    Article  CAS  Google Scholar 

  3. Nagel, G. et al. Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc. Natl Acad. Sci. USA 100, 13940–13945 (2003)

    Article  ADS  CAS  Google Scholar 

  4. Waschuk, S. A., Bezerra, A. G., Shi, L. & Brown, L. S. Leptosphaeria rhodopsin: Bacteriorhodopsin-like proton pump from a eukaryote. Proc. Natl Acad. Sci. USA 102, 6879–6883 (2005)

    Article  ADS  CAS  Google Scholar 

  5. Klare, J. P., Chizhov, I. & Engelhard, M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl. Cell Differ. 45, 73–122 (2008)

    Article  CAS  Google Scholar 

  6. Han, X. & Boyden, E. S. Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PLoS One 2, e299 (2007)

    Article  ADS  Google Scholar 

  7. Zhang, F. et al. Multimodal fast optical interrogation of neural circuitry. Nature 446, 633–639 (2007)

    Article  ADS  CAS  Google Scholar 

  8. Zhao, S. et al. Improved expression of halorhodopsin for light-induced silencing of neuronal activity. Brain Cell Biol. 36, 141–154 (2008)

    Article  CAS  Google Scholar 

  9. Gradinaru, V., Thompson, K. R. & Deisseroth, K. eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications. Brain Cell Biol. 36, 129–139 (2008)

    Article  Google Scholar 

  10. Tateno, M., Ihara, K. & Mukohata, Y. The novel ion pump rhodopsins from Haloarcula form a family independent from both the bacteriorhodopsin and archaerhodopsin families/tribes. Arch. Biochem. Biophys. 315, 127–132 (1994)

    Article  CAS  Google Scholar 

  11. Bamberg, E., Tittor, J. & Oesterhelt, D. Light-driven proton or chloride pumping by halorhodopsin. Proc. Natl Acad. Sci. USA 90, 639–643 (1993)

    Article  ADS  CAS  Google Scholar 

  12. Aravanis, A. M. et al. An optical neural interface: in vivo control of rodent motor cortex with integrated fiberoptic and optogenetic technology. J. Neural Eng. 4, S143–S156 (2007)

    Article  Google Scholar 

  13. Bernstein, J. G. et al. Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons. Proc. Soc. Photo Opt. Instrum. Eng. 6854, 68540H (2008)

    Google Scholar 

  14. Lin, J. Y., Lin, M. Z., Steinbach, P. & Tsien, R. Y. Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys. J. 96, 1803–1814 (2009)

    Article  ADS  CAS  Google Scholar 

  15. Berthold, P. et al. Channelrhodopsin-1 initiates phototaxis and photophobic responses in Chlamydomonas by immediate light-induced depolarization. Plant Cell 20, 1665–1677 (2008)

    Article  CAS  Google Scholar 

  16. Bevensee, M. O., Cummins, T. R., Haddad, G. G., Boron, W. F. & Boyarsky, G. pH regulation in single CA1 neurons acutely isolated from the hippocampi of immature and mature rats. J. Physiol. (Lond.) 494, 315–328 (1996)

    Article  CAS  Google Scholar 

  17. Chesler, M. Regulation and modulation of pH in the brain. Physiol. Rev. 83, 1183–1221 (2003)

    Article  CAS  Google Scholar 

  18. Meyer, T. M., Munsch, T. & Pape, H. C. Activity-related changes in intracellular pH in rat thalamic relay neurons. Neuroreport 11, 33–36 (2000)

    Article  CAS  Google Scholar 

  19. Trapp, S., Luckermann, M., Brooks, P. A. & Ballanyi, K. Acidosis of rat dorsal vagal neurons in situ during spontaneous and evoked activity. J. Physiol. (Lond.) 496, 695–710 (1996)

    Article  CAS  Google Scholar 

  20. Leinekugel, X. et al. Correlated bursts of activity in the neonatal hippocampus in vivo . Science 296, 2049–2052 (2002)

    Article  ADS  CAS  Google Scholar 

  21. Wehr, M. & Zador, A. M. Balanced inhibition underlies tuning and sharpens spike timing in auditory cortex. Nature 426, 442–446 (2003)

    Article  ADS  CAS  Google Scholar 

  22. Richter, D. W., Pierrefiche, O., Lalley, P. M. & Polder, H. R. Voltage-clamp analysis of neurons within deep layers of the brain. J. Neurosci. Methods 67, 121–131 (1996)

    Article  CAS  Google Scholar 

  23. Narikawa, K., Furue, H., Kumamoto, E. & Yoshimura, M. In vivo patch-clamp analysis of IPSCs evoked in rat substantia gelatinosa neurons by cutaneous mechanical stimulation. J. Neurophysiol. 84, 2171–2174 (2000)

    Article  CAS  Google Scholar 

  24. Han, X. et al. Millisecond-timescale optical control of neural dynamics in the nonhuman primate brain. Neuron 62, 191–198 (2009)

    Article  CAS  Google Scholar 

  25. Ming, M. et al. pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin. Biophys. J. 90, 3322–3332 (2006)

    Article  ADS  CAS  Google Scholar 

  26. Lukashev, E. P. et al. pH dependence of the absorption spectra and photochemical transformations of the archaerhodopsins. Photochem. Photobiol. 60, 69–75 (1994)

    Article  CAS  Google Scholar 

  27. Lanyi, J. K. Proton transfers in the bacteriorhodopsin photocycle. Biochim. Biophys. Acta 1757, 1012–1018 (2006)

    Article  CAS  Google Scholar 

  28. Enami, N. et al. Crystal structures of archaerhodopsin-1 and -2: common structural motif in archaeal light-driven proton pumps. J. Mol. Biol. 358, 675–685 (2006)

    Article  CAS  Google Scholar 

  29. Mogi, T., Marti, T. & Khorana, H. G. Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin. J. Biol. Chem. 264, 14197–14201 (1989)

    CAS  PubMed  Google Scholar 

  30. Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P. & Lanyi, J. K. Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291, 899–911 (1999)

    Article  CAS  Google Scholar 

Download references


E.S.B. acknowledges funding by the NIH Director’s New Innovator Award (DP2 OD002002-01), as well as the NSF (0835878 and 0848804), the McGovern Institute Neurotechnology Award Program, the Department of Defense, NARSAD, the Alfred P. Sloan Foundation, Jerry and Marge Burnett, the SFN Research Award for Innovation in Neuroscience, the MIT Media Lab, the Benesse Foundation, and the Wallace H. Coulter Foundation. X.H. acknowledges the Helen Hay Whitney Foundation and NIH 1K99MH085944. The authors thank E. Klinman for help with transfections, R. Desimone for advice, J. Lin for technical aid on intracellular pH measurements, K. Ihara for discussions about archaerhodopsins, and M. Hemann and N. Gershenfeld and the Center for Bits and Atoms for use of their respective laboratory facilities.

Author Contributions B.Y.C., X.H. and E.S.B. designed experiments, analysed data and wrote the paper. B.Y.C. and X.H. carried out experiments. A.S.D. assisted with electrophysiological recording. X.Q., M.L. and A.S.C. assisted with molecular biology, virus making, and transfections. M.A.H. performed Monte Carlo modelling. P.E.M., G.M.B. and Y.L. created hippocampal and cortical neural cultures.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Edward S. Boyden.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-3 with Legends, Supplementary Notes, Supplementary Tables 1-3, Supplementary Methods and Supplementary References. (PDF 668 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Chow, B., Han, X., Dobry, A. et al. High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463, 98–102 (2010).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing