John Spudich, Ph.D.

Robert A. Welch Distinguished Chair in Chemistry; Director, Center for Membrane Biology; Professor, Biochemistry & Molecular Biology
Fellow, American Academy of Arts & Sciences; President, International Union of Photobiology


Description of Research

STRUCTURE AND FUNCTION OF MICROBIAL AND ANIMAL RHODOPSINS

The primary interests in our laboratory are the mechanisms by which photosensory receptors sense and transmit information concerning the color, intensity, and pattern of light in the environment. We study a widespread class of photoactive receptor proteins (rhodopsins) that consist of seven transmembrane helices connected by interhelical loops. The helices form a pocket for the photosensitive molecule vitamin-A aldehyde (retinal) that attaches in a covalent linkage to a lysine residue in the middle of the 7th helix buried in the core of the protein. These proteins are used for visual processes of various degrees of sophistication, ranging from detection of light-dark boundaries, light gradients, and light direction by single-cell microorganisms to high-resolution color image detection by higher animal eyes.

Photoisomerization of the retinylidene chromophore initiates a variety of types of signaling reactions. Mammalian visual pigments signal by binding and activating heterotrimeric G-proteins. Four distinctly different modes of signaling have been demonstrated for microbial rhodopsins: conformational coupling to bound membrane transducer subunits that relay signals to sensory pathways in the cytoplasm, binding to a cytoplasmic transducer, light-gated ion channel conduction, and light-regulated enzymatic activity encoded by the sensory rhodopsin protein. In addition, homologous microbial rhodopsins pumps drive active ion transport. Our laboratory studies in terms of structure/function how evolution has produced these distinctly different molecular functions from a shared protein scaffold.

Demonstrated Functions of Microbial Rhodopsins in Nature. BR, bacteriorhodopsins; HR, halorhodopsins; NaR, sodium ion pumping rhodopsin; SRI & SRII, sensory rhodopsins I & II; ASR, Anabaena sensory rhodopsin; CCRs, cation-conducting channelrhodopsins; ACRs, anion-conducting channelrhodopsins; SR enzymes, sensory rhodopsin enzymes. Demonstrated functions are illustrated in green. (?) denotes that the indicated functions of ASR and ACRs are suggested but have not been proven. One SR enzyme, a guanylyl cyclase, has been shown to mediate phototaxis in the flagellated swimming zoospores of a fungus; other SR enzymes are of unknown physiological function.

Demonstrated Functions of Microbial Rhodopsins in Nature. BR, bacteriorhodopsins; HR, halorhodopsins; NaR, sodium ion pumping rhodopsin; SRI & SRII, sensory rhodopsins I & II; ASR, Anabaena sensory rhodopsin; CCRs, cation-conducting channelrhodopsins; ACRs, anion-conducting channelrhodopsins; SR enzymes, sensory rhodopsin enzymes. Demonstrated functions are illustrated in green. (?) denotes that the indicated functions of ASR and ACRs are suggested but have not been proven. One SR enzyme, a guanylyl cyclase, has been shown to mediate phototaxis in the flagellated swimming zoospores of a fungus; other SR enzymes are of unknown physiological function.

OPTOGENETICS: Expressing microbial rhodopsins in genetically targeted neurons enables control of the neurons’ membrane potential with the high temporal and spatial precision of light, a technique called optogenetics. Over the past decade, light-gated cation-conducting channelrhodopsins from chlorophyte algae (CCRs) have transformed neuroscience research, especially study of brain circuitry, through their use as membrane-depolarizing tools for targeted photoactivation of neuron firing. Photoinhibition of neuronal action potentials had been limited by the lack of efficient tools for membrane hyperpolarization until the recent discovery of natural anion-conducting channelrhodopsins (ACRs) in cryptophyte alga (Govorunova et al. Science 2015). The CCR structure is from PDB 3ug9, the image of the neuron expressing a GFP-tagged channelrhodopsin from Roger Janz (McGovern Medical School), and the neural activation and inhibition data from the Spudich lab. The image is from the Cover of Photochemistry & Photobiology Mar-Apr 2016 issue.

OPTOGENETICS: Expressing microbial rhodopsins in genetically targeted neurons enables control of the neurons’ membrane potential with the high temporal and spatial precision of light, a technique called optogenetics. Over the past decade, light-gated cation-conducting channelrhodopsins from chlorophyte algae (CCRs) have transformed neuroscience research, especially study of brain circuitry, through their use as membrane-depolarizing tools for targeted photoactivation of neuron firing. Photoinhibition of neuronal action potentials had been limited by the lack of efficient tools for membrane hyperpolarization until the recent discovery of natural anion-conducting channelrhodopsins (ACRs) in cryptophyte alga (Govorunova et al. Science 2015). The CCR structure is from PDB 3ug9, the image of the neuron expressing a GFP-tagged channelrhodopsin from Roger Janz (McGovern Medical School), and the neural activation and inhibition data from the Spudich lab. The image is from the Cover of Photochemistry & Photobiology Mar-Apr 2016 issue.

Contact Information

John.L.Spudich@uth.tmc.edu

UTHealth Medical School
Department of Biochemistry and Molecular Biology
Center for Membrane Biology
6431 Fannin Street, MSB 6.200
Houston, Texas 77030

713-500-5473 Direct  713-500-0652 Fax

Education

Ph.D. - University of California, Berkeley

Jane Coffin Childs Postdoctoral Fellow - Harvard Medical School

Research Interests

Light sensors & photosensory transduction, Microbial rhodopsins, Membrane receptor structure/function, Optogenetics

Publications

In vitro activity of a purified natural anion channelrhodopsin

Li H, Sineshchekov OA, Wu G, Spudich JL.

J Biol Chem. 2016 Dec 2;291(49):25319-25325. doi: 10.1074/jbc.C116.760041. Epub 2016 Oct 27.

PMID: 27789708

 

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Natural light-gated anion channels: A family of microbial rhodopsins for advanced optogenetics

Govorunova EG, Sineshchekov OA, Janz R, Liu X, Spudich JL.

Science. 2015 Aug 7;349(6248):647-50. doi: 10.1126/science.aaa7484. Epub 2015 Jun 25.

PMID: 26113638
Govorunova et al. 2015 Science
Govorunova et al. 2015 Science Supplement

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Gating Mechanisms of a Natural Anion Channelrhodopsin

Sineshchekov OA, Govorunova EG, Li H, Spudich JL.

Proc Natl Acad Sci USA. 2015 Nov 17;112(46):14236-41. doi: 10.1073/pnas.1513602112. Epub 2015 Nov 2.

PMID: 26578767

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Photochemical Reaction Cycle Transitions During Anion Channelrhodopsin Gating

Sineshchekov OA, Li H, Govorunova EG, Spudich JL.

Proc Natl Acad Sci USA. 2016 Mar 21. pii: 201525269. [Epub ahead of print]

PMID: 27001860

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Structurally Distinct Cation Channelrhodopsins from Cryptophyte Algae

Govorunova EG, Sineshchekov OA, Spudich JL.

Biophys J. 2016 Jun 7;110(11):2302-4. doi: 10.1016/j.bpj.2016.05.001. Epub 2016 May 24.

PMID: 27233115

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