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Petrovskaya LE, Siletsky SA, Mamedov MD, Lukashev EP, Balashov SP, Dolgikh DA, Kirpichnikov MP. Features of the Mechanism of Proton Transport in ESR, Retinal Protein from Exiguobacterium sibiricum. Biochemistry Moscow 2023; 88:1544-1554. [PMID: 38105023 DOI: 10.1134/s0006297923100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 12/19/2023]
Abstract
Retinal-containing light-sensitive proteins - rhodopsins - are found in many microorganisms. Interest in them is largely explained by their role in light energy storage and photoregulation in microorganisms, as well as the prospects for their use in optogenetics to control neuronal activity, including treatment of various diseases. One of the representatives of microbial rhodopsins is ESR, the retinal protein of Exiguobacterium sibiricum. What distinguishes ESR from homologous proteins is the presence of a lysine residue (Lys96) as a proton donor for the Schiff base. This feature, along with the hydrogen bond of the proton acceptor Asp85 with the His57 residue, determines functional characteristics of ESR as a proton pump. This review examines the results of ESR studies conducted using various methods, including direct electrometry. Comparison of the obtained data with the results of structural studies and with other retinal proteins allows us to draw conclusions about the mechanisms of transport of hydrogen ions in ESR and similar retinal proteins.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Sergei A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Eugene P Lukashev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Dmitry A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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2
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Ostrovsky MA, Smitienko OA, Bochenkova AV, Feldman TB. Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins. Biochemistry (Mosc) 2023; 88:1528-1543. [PMID: 38105022 DOI: 10.1134/s0006297923100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/20/2023] [Accepted: 08/12/2023] [Indexed: 12/19/2023]
Abstract
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
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Affiliation(s)
- Mikhail A Ostrovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | - Olga A Smitienko
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | | | - Tatiana B Feldman
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
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3
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Xu J, Yang Q, Ma B, Li L, Kong F, Xiao L, Chen D. K +-Dependent Photocycle and Photocurrent Reveal the Uptake of K + in Light-Driven Sodium Pump. Int J Mol Sci 2023; 24:14414. [PMID: 37833864 PMCID: PMC10572131 DOI: 10.3390/ijms241914414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Engineering light-controlled K+ pumps from Na+-pumping rhodopsins (NaR) greatly expands the scope of optogenetic applications. However, the limited knowledge regarding the kinetic and selective mechanism of K+ uptake has significantly impeded the modification and design of light-controlled K+ pumps, as well as their practical applications in various fields, including neuroscience. In this study, we presented K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called Nonlabens dokdonensis rhodopsin 2 (NdR2). As the concentration of K+ increased, we observed the accelerated decay of M intermediate in the wild type (WT) through flash photolysis. In 100 mM KCl, the lifetime of the M decay was approximately 1.0 s, which shortened to around 0.6 s in 1 M KCl. Additionally, the K+-dependent M decay kinetics were also observed in the G263W/N61P mutant, which transports K+. In 100 mM KCl, the lifetime of the M decay was approximately 2.5 s, which shortened to around 0.2 s in 1 M KCl. According to the competitive model, in high KCl, K+ may be taken up from the cytoplasmic surface, competing with Na+ or H+ during M decay. This was further confirmed by the K+-dependent photocurrent of WT liposome. As the concentration of K+ increased to 500 mM, the amplitude of peak current significantly dropped to approximately ~60%. Titration experiments revealed that the ratio of the rate constant of H+ uptake (kH) to that of K+ uptake (kK) is >108. Compared to the WT, the G263W/N61P mutant exhibited a decrease of approximately 40-fold in kH/kK. Previous studies focused on transforming NaR into K+ pumps have primarily targeted the intracellular ion uptake region of Krokinobacter eikastus rhodopsin 2 (KR2) to enhance K+ uptake. However, our results demonstrate that the naturally occurring WT NdR2 is capable of intracellular K+ uptake without requiring structural modifications on the intracellular region. This discovery provides diverse options for future K+ pump designs. Furthermore, we propose a novel photocurrent-based approach to evaluate K+ uptake, which can serve as a reference for similar studies on other ion pumps. In conclusion, our research not only provides new insights into the mechanism of K+ uptake but also offers a valuable point of reference for the development of optogenetic tools and other applications in this field.
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Affiliation(s)
- Jikang Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Fei Kong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Lan Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Hagio H, Koyama W, Hosaka S, Song AD, Narantsatsral J, Matsuda K, Shimizu T, Hososhima S, Tsunoda SP, Kandori H, Hibi M. Optogenetic manipulation of neuronal and cardiomyocyte functions in zebrafish using microbial rhodopsins and adenylyl cyclases. eLife 2023; 12:e83975. [PMID: 37589546 PMCID: PMC10435232 DOI: 10.7554/elife.83975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 07/25/2023] [Indexed: 08/18/2023] Open
Abstract
Even though microbial photosensitive proteins have been used for optogenetics, their use should be optimized to precisely control cell and tissue functions in vivo. We exploited GtCCR4 and KnChR, cation channelrhodopsins from algae, BeGC1, a guanylyl cyclase rhodopsin from a fungus, and photoactivated adenylyl cyclases (PACs) from cyanobacteria (OaPAC) or bacteria (bPAC), to control cell functions in zebrafish. Optical activation of GtCCR4 and KnChR in the hindbrain reticulospinal V2a neurons, which are involved in locomotion, induced swimming behavior at relatively short latencies, whereas activation of BeGC1 or PACs achieved it at long latencies. Activation of GtCCR4 and KnChR in cardiomyocytes induced cardiac arrest, whereas activation of bPAC gradually induced bradycardia. KnChR activation led to an increase in intracellular Ca2+ in the heart, suggesting that depolarization caused cardiac arrest. These data suggest that these optogenetic tools can be used to reveal the function and regulation of zebrafish neurons and cardiomyocytes.
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Affiliation(s)
- Hanako Hagio
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
- Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoyaJapan
- Institute for Advanced Research, Nagoya UniversityNagoyaJapan
| | - Wataru Koyama
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
| | - Shiori Hosaka
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
| | | | | | - Koji Matsuda
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
| | - Takashi Shimizu
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
| | - Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of TechnologyNagoyaJapan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of TechnologyNagoyaJapan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of TechnologyNagoyaJapan
| | - Masahiko Hibi
- Graduate School of Science, Nagoya University, JapanNagoyaJapan
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Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. Sequential absorption of two photons creates a bistable form of RubyACR responsible for its strong desensitization. Proc Natl Acad Sci U S A 2023; 120:e2301521120. [PMID: 37186849 PMCID: PMC10214203 DOI: 10.1073/pnas.2301521120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Channelrhodopsins with red-shifted absorption, rare in nature, are highly desired for optogenetics because light of longer wavelengths more deeply penetrates biological tissue. RubyACRs (Anion ChannelRhodopsins), a group of four closely related anion-conducting channelrhodopsins from thraustochytrid protists, are the most red-shifted channelrhodopsins known with absorption maxima up to 610 nm. Their photocurrents are large, as is typical of blue- and green-absorbing ACRs, but they rapidly decrease during continuous illumination (desensitization) and extremely slowly recover in the dark. Here, we show that long-lasting desensitization of RubyACRs results from photochemistry not observed in any previously studied channelrhodopsins. Absorption of a second photon by a photocycle intermediate with maximal absorption at 640 nm (P640) renders RubyACR bistable (i.e., very slowly interconvertible between two spectrally distinct forms). The photocycle of this bistable form involves long-lived nonconducting states (Llong and Mlong), formation of which is the reason for long-lasting desensitization of RubyACR photocurrents. Both Llong and Mlong are photoactive and convert to the initial unphotolyzed state upon blue or ultraviolet (UV) illumination, respectively. We show that desensitization of RubyACRs can be reduced or even eliminated by using ns laser flashes, trains of short light pulses instead of continuous illumination to avoid formation of Llong and Mlong, or by application of pulses of blue light between pulses of red light to photoconvert Llong to the initial unphotolyzed state.
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Affiliation(s)
- Oleg A. Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Elena G. Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Hai Li
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Yumei Wang
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - John L. Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
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6
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Petrovskaya LE, Lukashev EP, Mamedov MD, Kryukova EA, Balashov SP, Dolgikh DA, Rubin AB, Kirpichnikov MP, Siletsky SA. Oriented Insertion of ESR-Containing Hybrid Proteins in Proteoliposomes. Int J Mol Sci 2023; 24:ijms24087369. [PMID: 37108532 PMCID: PMC10138546 DOI: 10.3390/ijms24087369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in the artificial membranes is rarely observed. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum, ESR, as a model. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized. The photocycle of the hybrid proteins incorporated in proteoliposomes demonstrated a higher pKa of the M state accumulation compared to that of the wild-type ESR. Large negative electrogenic phases and an increase in the relative amplitude of kinetic components in the microsecond time range in the kinetics of membrane potential generation of ESR-Cherry and ESR-Trx indicate a decrease in the efficiency of transmembrane proton transport. On the contrary, Caf-ESR demonstrates a native-like kinetics of membrane potential generation and the corresponding electrogenic stages. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Evgeniy P Lukashev
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Dmitry A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Andrei B Rubin
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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Huang Q, Zhu W, Gao X, Liu X, Zhang Z, Xing B. Nanoparticles-mediated ion channels manipulation: From their membrane interactions to bioapplications. Adv Drug Deliv Rev 2023; 195:114763. [PMID: 36841331 DOI: 10.1016/j.addr.2023.114763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/26/2023]
Abstract
Ion channels are transmembrane proteins ubiquitously expressed in all cells that control various ions (e.g. Na+, K+, Ca2+ and Cl- etc) crossing cellular plasma membrane, which play critical roles in physiological processes including regulating signal transduction, cell proliferation as well as excitatory cell excitation and conduction. Abnormal ion channel function is usually associated with dysfunctions and many diseases, such as neurodegenerative disorders, ophthalmic diseases, pulmonary diseases and even cancers. The precise regulation of ion channels not only helps to decipher physiological and pathological processes, but also is expected to become cutting-edge means for disease treatment. Recently, nanoparticles-mediated ion channel manipulation emerges as a highly promising way to meet the increasing requirements with respect to their simple, efficient, precise, spatiotemporally controllable and non-invasive regulation in biomedicine and other research frontiers. Thanks the advantages of their unique properties, nanoparticles can not only directly block the pore sites or kinetics of ion channels through their tiny size effect, and perturb active voltage-gated ion channel by their charged surface, but they can also act as antennas to conduct or enhance external physical stimuli to achieve spatiotemporal, precise and efficient regulation of various ion channel activities (e.g. light-, mechanical-, and temperature-gated ion channels etc). So far, nanoparticles-mediated ion channel regulation has shown potential prospects in many biomedical fields at the interfaces of neuro- and cardiovascular modulation, physiological function regeneration and tumor therapy et al. Towards such important fields, in this typical review, we specifically outline the latest studies of different types of ion channels and their activities relevant to the diseases. In addition, the different types of stimulation responsive nanoparticles, their interaction modes and targeting strategies towards the plasma membrane ion channels will be systematically summarized. More importantly, the ion channel regulatory methods mediated by functional nanoparticles and their bioapplications associated with physiological modulation and therapeutic development will be discussed. Last but not least, current challenges and future perspectives in this field will be covered as well.
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Affiliation(s)
- Qiwen Huang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weisheng Zhu
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiaoyin Gao
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xinping Liu
- School of Pharmaceutical Science, University of South China, Hengyang 421001, China
| | - Zhijun Zhang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Bengang Xing
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore, 637371, Singapore.
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Boeije Y, Olivucci M. From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023; 52:2643-2687. [PMID: 36970950 DOI: 10.1039/d2cs00719c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.
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Affiliation(s)
- Yorrick Boeije
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
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Belikov NE, Petrovskaya LE, Kryukova EA, Dolgikh DA, Lukashev EP, Lukin AY, Demina OV, Varfolomeev SD, Chupin VV, Khodonov AA. Interaction of the Fluorophenyl Analog of Retinal with Proteorhodopsin from Exiguobacterium sibiricum. Russ J Bioorg Chem 2022. [DOI: 10.1134/s1068162022060073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract—
We have developed an alternative method for the synthesis of an analog of natural retinal, which contains the p-fluorophenyl fragment instead of the trimethylcyclohexene ring. The proposed scheme for the synthesis of the target all-E-isomer of the target retinoid consists of using C5-phosphonate that contains the terminal nitrile group under Horner–Emmons reaction conditions. It has been shown that this scheme is more efficient and provides a higher total yield of the target product than the previously described variant. The procedure has been developed for the preparation of an analog of microbial proteorhodopsin ESRh from Exiguobacterium sibiricum, which contains a modified chromophore. It has been found that, as in the case of bacterioopsin from Halobacterium salinarum, the replacement of the trimethylcyclohexene ring in the natural chromophore by the p-fluorophenyl fragment does not prevent the formation of the artificial pigment F-Phe-ESRh from proteorhodopsin ESRh, which preserves the cycle of photochemical reactions. Certain differences have been found between the properties of native recombinant ESRh and its analog F-Phe-ESRh including a shift in the absorption maximum to the short-wavelength region, the formation of M intermediate at lower pH values, the presence of “long-lived M,” and a general slowdown in the photocycle. The reduced stability of the resulting proteorhodopsin analog F-Phe-ESRh to prolonged exposure to visible light has been also demonstrated.
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Muramatsu S, Tokizane T, Inokuchi Y. One-Dimensionally Conjugated Carbocyanine Dyes Isolated under Cold Gas-Phase Conditions: Electronic Spectra and Photochemistry. J Phys Chem A 2022; 126:8127-8135. [DOI: 10.1021/acs.jpca.2c05111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoru Muramatsu
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
| | - Takayuki Tokizane
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
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Walter M, Schubert L, Heberle J, Schlesinger R, Losi A. Time-resolved photoacoustics of channelrhodopsins: early energetics and light-driven volume changes. Photochem Photobiol Sci 2022; 22:477-486. [PMID: 36273368 DOI: 10.1007/s43630-022-00327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022]
Abstract
AbstractIn biological photoreceptors, the energy stored in early transient species is a key feature to drive the photocycle or a chain of reactions. Time-resolved photoacoustics (PA) can explore the energy landscape of transient species formed within few ns after photoexcitation, as well as volumetric changes (ΔV) of these intermediates with respect to the parental state. In this work, PA identified these important parameters for several channelrhodopsins, namely CaChR1 from Chlamydomonas augustae and CrChR2 from Chlamydomonas reinhardtii and various variants. PA has access to the sub-ns formation of the early photoproduct P1 and to its relaxation, provided that this latter process occurs within a few μs. We found that ΔVP1 for CaChR1 is ca. 12 mL/mol, while it is much smaller for CrChR2 (4.7 mL/mol) and for H. salinarum bacteriorhodopsin (HsBR, ΔVK = 2.8 mL/mol). PA experiments on variants strongly indicate that part of this large ΔVP1 value for CaChR1 is caused by the protonation dynamics of the Schiff base counterion complex involving E169 and D299. PA data further show that the energy level of P1 is higher in CrChR2 (ca. 96 kJ/mol) than in CaChr1 (ca. 46 kJ/mol), comparable to the energy level of the K state of HsBR (60 kJ/mol). Instrumental to gain these molecular values from the raw PA data was the estimation of the quantum yield (Φ) for P1 formation via transient spectroscopy; for both channelrhodopsins, ΦP2 was evaluated as ca. 0.4.
Graphical Abstract
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Affiliation(s)
- Maria Walter
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Luiz Schubert
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Ramona Schlesinger
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area Delle Scienze 7/A, 43124, Parma, Italy.
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Doi Y, Watanabe J, Nii R, Tsukamoto T, Demura M, Sudo Y, Kikukawa T. Mutations conferring SO 42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant. Sci Rep 2022; 12:16422. [PMID: 36180556 PMCID: PMC9525653 DOI: 10.1038/s41598-022-20784-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl- and Br-, but SyHR also transports SO42-, despite the close sequence similarity to MrHR. We sought a determinant that could confer SO42- pumping ability on MrHR and found that the removal of a negative charge at the anion entrance is a prerequisite for SO42- transport by MrHR. Consistently, the reverse mutation in SyHR significantly weakened SO42- pump activity. Notably, the MrHR and SyHR mutants did not show SO42- induced absorption spectral shifts or changes in the photoreactions, suggesting no bindings of SO42- in their initial states or the bindings to the sites far from the protein centers. In other words, unlike wild-type SyHR, these mutants take up SO42- into their centers after illumination and release it before the ends of the photoreactions.
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Affiliation(s)
- Yuhei Doi
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jo Watanabe
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Ryota Nii
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Takashi Tsukamoto
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Makoto Demura
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Kikukawa
- School of Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
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13
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Abstract
Microbial channelrhodopsins are light-gated ion channels widely used for optogenetic manipulation of neuronal activity. ChRmine is a bacteriorhodopsin-like cation channelrhodopsin (BCCR) more closely related to ion pump rhodopsins than other channelrhodopsins. ChRmine displays unique properties favorable for optogenetics including high light sensitivity, a broad, red-shifted activation spectrum, cation selectivity, and large photocurrents, while its slow closing kinetics impedes some applications. The structural basis for ChRmine function, or that of any other BCCR, is unknown. Here, we present cryo-EM structures of ChRmine in lipid nanodiscs in apo (opsin) and retinal-bound (rhodopsin) forms. The structures reveal an unprecedented trimeric architecture with a lipid filled central pore. Large electronegative cavities on either side of the membrane facilitate high conductance and selectivity for cations over protons. The retinal binding pocket structure suggests channel properties could be tuned with mutations and we identify ChRmine variants with ten-fold decreased and two-fold increased closing rates. A T119A mutant shows favorable properties relative to wild-type and previously reported ChRmine variants for optogenetics. These results provide insight into structural features that generate an ultra-potent microbial opsin and provide a platform for rational engineering of channelrhodopsins with improved properties that could expand the scale, depth, and precision of optogenetic experiments.
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Affiliation(s)
- Kyle Tucker
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, 94720, USA
| | - Savitha Sridharan
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Hillel Adesnik
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA.
| | - Stephen G Brohawn
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA.
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, 94720, USA.
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14
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Siletsky SA, Mamedov MD, Lukashev EP, Balashov SP, Petrovskaya LE. Application of direct electrometry in studies of microbial rhodopsins reconstituted in proteoliposomes. Biophys Rev. [PMID: 36124261 PMCID: PMC9481854 DOI: 10.1007/s12551-022-00986-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/15/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial rhodopsins are the family of retinal-containing proteins that perform primarily the light-driven transmembrane ion transport and sensory functions. They are widely distributed in nature and can be used for optogenetic control of the cellular activities by light. Functioning of microbial rhodopsins results in generation of the transmembrane electric potential in response to a flash that can be measured by direct time-resolved electrometry. This method was developed by L. Drachev and his colleagues at the Belozersky Institute and successfully applied in the functional studies of microbial rhodopsins. First measurements were performed using bacteriorhodopsin from Halobacterium salinarum-the prototype member of the microbial retinal protein family. Later, direct electrometric studies were conducted with proteorhodopsin from Exiguobacterium sibiricum (ESR), the sodium pump from Dokdonia, and other proteins. They allowed detailed characterization of the charge transfer steps during the photocycle of microbial rhodopsins and provided new insights for profound understanding of their mechanism of action.
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15
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Govorunova EG, Gou Y, Sineshchekov OA, Li H, Lu X, Wang Y, Brown LS, St-Pierre F, Xue M, Spudich JL. Kalium channelrhodopsins are natural light-gated potassium channels that mediate optogenetic inhibition. Nat Neurosci 2022; 25:967-974. [PMID: 35726059 PMCID: PMC9854242 DOI: 10.1038/s41593-022-01094-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 05/12/2022] [Indexed: 02/02/2023]
Abstract
Channelrhodopsins are used widely for optical control of neurons, in which they generate photoinduced proton, sodium or chloride influx. Potassium (K+) is central to neuron electrophysiology, yet no natural K+-selective light-gated channel has been identified. Here, we report kalium channelrhodopsins (KCRs) from Hyphochytrium catenoides. Previously known gated potassium channels are mainly ligand- or voltage-gated and share a conserved K+-selectivity filter. KCRs differ in that they are light-gated and have independently evolved an alternative K+ selectivity mechanism. The KCRs are potent, highly selective of K+ over Na+, and open in less than 1 ms following photoactivation. The permeability ratio PK/PNa of 23 makes H. catenoides KCR1 (HcKCR1) a powerful hyperpolarizing tool to suppress excitable cell firing upon illumination, demonstrated here in mouse cortical neurons. HcKCR1 enables optogenetic control of K+ gradients, which is promising for the study and potential treatment of potassium channelopathies such as epilepsy, Parkinson's disease and long-QT syndrome and other cardiac arrhythmias.
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Affiliation(s)
- Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Yueyang Gou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- The Cain Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Yumei Wang
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Mingshan Xue
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- The Cain Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
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16
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Wang F, Ding P, Liang X, Ding X, Brandt CB, Sjöstedt E, Zhu J, Bolund S, Zhang L, de Rooij LPMH, Luo L, Wei Y, Zhao W, Lv Z, Haskó J, Li R, Qin Q, Jia Y, Wu W, Yuan Y, Pu M, Wang H, Wu A, Xie L, Liu P, Chen F, Herold J, Kalucka J, Karlsson M, Zhang X, Helmig RB, Fagerberg L, Lindskog C, Pontén F, Uhlen M, Bolund L, Jessen N, Jiang H, Xu X, Yang H, Carmeliet P, Mulder J, Chen D, Lin L, Luo Y. Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nat Commun 2022; 13:3620. [PMID: 35750885 DOI: 10.1038/s41467-022-31388-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-β, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia. Pigs are important large animal models for biomedical research. Here, the authors construct a single-cell landscape of pig tissues, unravelling the phenotypic heterogeneity of blood endothelial cells in adipose tissues and the evolutionally conserved regulons of microglia in brains.
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17
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Xu J, Koizumi N, Morimoto YV, Ozuru R, Masuzawa T, Nakamura S. Light dependent synthesis of a nucleotide second messenger controls the motility of a spirochete bacterium. Sci Rep 2022; 12:6825. [PMID: 35474318 DOI: 10.1038/s41598-022-10556-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleotide second messengers are universally crucial factors for the signal transduction of various organisms. In prokaryotes, cyclic nucleotide messengers are involved in the bacterial life cycle and in functions such as virulence and biofilm formation, mainly via gene regulation. Here, we show that the swimming motility of the soil bacterium Leptospira kobayashii is rapidly modulated by light stimulation. Analysis of a loss-of-photoresponsivity mutant obtained by transposon random mutagenesis identified the novel sensory gene, and its expression in Escherichia coli through codon optimization elucidated the light-dependent synthesis of cyclic adenosine monophosphate (cAMP). GFP labeling showed the localization of the photoresponsive enzyme at the cell poles where flagellar motors reside. These findings suggest a new role for cAMP in rapidly controlling the flagella-dependent motility of Leptospira and highlight the global distribution of the newly discovered photoactivated cyclase among diverse microbial species.
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18
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Rockwell NC, Moreno MV, Martin SS, Lagarias JC. Protein-chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes. Photochem Photobiol Sci 2022; 21:471-491. [PMID: 35411484 PMCID: PMC9609751 DOI: 10.1007/s43630-022-00213-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Photoreceptors in the phytochrome superfamily use 15,16-photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties. Canonical phytochromes include master regulators of plant growth and development in which light signals trigger interconversion between a red-absorbing 15Z dark-adapted state and a metastable, far-red-absorbing 15E photoproduct state. Distantly related cyanobacteriochromes (CBCRs) carry out a diverse range of photoregulatory functions in cyanobacteria and exhibit considerable spectral diversity. One widespread CBCR subfamily typically exhibits a red-absorbing 15Z dark-adapted state similar to that of phytochrome that gives rise to a distinct green-absorbing 15E photoproduct. This red/green CBCR subfamily also includes red-inactive examples that fail to undergo photoconversion, providing an opportunity to study protein-chromophore interactions that either promote photoisomerization or block it. In this work, we identified a conserved lineage of red-inactive CBCRs. This enabled us to identify three substitutions sufficient to block photoisomerization in photoactive red/green CBCRs. The resulting red-inactive variants faithfully replicated the fluorescence and circular dichroism properties of naturally occurring examples. Converse substitutions restored photoconversion in naturally red-inactive CBCRs. This work thus identifies protein-chromophore interactions that control the fate of the excited-state population in red/green cyanobacteriochromes.
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Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
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19
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Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell 2022; 185:672-689.e23. [PMID: 35114111 PMCID: PMC7612760 DOI: 10.1016/j.cell.2022.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
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Affiliation(s)
- Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Elina Thadhani
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Takashi Nagata
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masae Konno
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Sean Quirin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tyler Benster
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tomoko Uemura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma, Kanazawa, Japan; High-Speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan; RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Palo Alto, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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20
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Govorunova EG, Sineshchekov OA, Spudich JL. Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships. Front Cell Neurosci 2022; 15:800313. [PMID: 35140589 PMCID: PMC8818676 DOI: 10.3389/fncel.2021.800313] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) from phototactic algae have become widely used as genetically encoded molecular tools to control cell membrane potential with light. Recent advances in polynucleotide sequencing, especially in environmental samples, have led to identification of hundreds of channelrhodopsin homologs in many phylogenetic lineages, including non-photosynthetic protists. Only a few CCRs and ACRs have been characterized in detail, but there are indications that ion channel function has evolved within the rhodopsin superfamily by convergent routes. The diversity of channelrhodopsins provides an exceptional platform for the study of structure-function evolution in membrane proteins. Here we review the current state of channelrhodopsin research and outline perspectives for its further development.
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21
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Balandin T, Volkov D, Alekseev A, Kovalev K, Bratanov D, Gordeliy V. E. coli Expression and Purification of Microbial and Viral Rhodopsins. Methods Mol Biol 2022; 2501:109-124. [PMID: 35857225 DOI: 10.1007/978-1-0716-2329-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial rhodopsins have become an indispensable tool for neurobiology. Of thousands of identified microbial rhodopsins, a minute fraction has been studied so far and they have shown remarkable functional diversity suggesting more great promises that this large family holds. Effective production of recombinant microbial and viral rhodopsins is a prerequisite for the success of functional and structural studies of these proteins. Escherichia coli (E. coli) are suitable for high yield expression of many of microbial and viral rhodopsins and they facilitate rapid exploration of this large protein family.
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Affiliation(s)
- Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Kirill Kovalev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Dmitry Bratanov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
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22
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Bulzu PA, Kavagutti VS, Chiriac MC, Vavourakis CD, Inoue K, Kandori H, Andrei AS, Ghai R. Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. mSphere 2021; 6:e0066121. [PMID: 34817235 DOI: 10.1128/mSphere.00661-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rhodopsins are light-activated proteins displaying an enormous versatility of function as cation/anion pumps or sensing environmental stimuli and are widely distributed across all domains of life. Even with wide sequence divergence and uncertain evolutionary linkages between microbial (type 1) and animal (type 2) rhodopsins, the membrane orientation of the core structural scaffold of both was presumed universal. This was recently amended through the discovery of heliorhodopsins (HeRs; type 3), that, in contrast to known rhodopsins, display an inverted membrane topology and yet retain similarities in sequence, structure, and the light-activated response. While no ion-pumping activity has been demonstrated for HeRs and multiple crystal structures are available, fundamental questions regarding their cellular and ecological function or even their taxonomic distribution remain unresolved. Here, we investigated HeR function and distribution using genomic/metagenomic data with protein domain fusions, contextual genomic information, and gene coexpression analysis with strand-specific metatranscriptomics. We bring to resolution the debated monoderm/diderm occurrence patterns and show that HeRs are restricted to monoderms. Moreover, we provide compelling evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla. In addition, we also describe two novel putative signal-transducing domains fused to some HeRs. We posit that HeRs likely function as generalized light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. Their role as sensory rhodopsins is corroborated by their photocycle dynamics and their presence/function in monoderms is likely connected to the higher sensitivity of these organisms to light-induced damage. IMPORTANCE Heliorhodopsins are enigmatic, novel rhodopsins with a membrane orientation that is opposite to all known rhodopsins. However, their cellular and ecological functions are unknown, and even their taxonomic distribution remains a subject of debate. We provide evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla boundaries. In support of this, we also identify two novel putative signal transducing domains in HeRs that are fused with them. We also observe linkages of HeRs to genes involved in mitigation of light-induced oxidative stress and increased carbon and nitrogen metabolism. Finally, we synthesize these findings into a framework that connects HeRs with the cellular response to light in monoderms, activating light-induced oxidative stress defenses along with carbon/nitrogen metabolic circuitries. These findings are consistent with the evolutionary, taxonomic, structural, and genomic data available so far.
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Abstract
Microbial rhodopsin is a ubiquitous membrane protein in unicellular microorganisms. Similar to animal rhodopsin, this protein consists of seven transmembrane helices and the chromophore retinal. However, unlike animal rhodopsin, microbial rhodopsin acts as not only a photosignal receptor but also a light-activated ion transporter and light-switchable enzyme. In this article, the third Cl- pump microbial rhodopsin will be introduced. The physiological importance of Cl- pumps has not been clarified. Despite this, their mechanisms, especially that of the first Cl- pump halorhodopsin (HR), have been studied to characterize them as model proteins for membrane anion transporters. The third Cl- pump defines a phylogenetic cluster distinct from other microbial rhodopsins. However, this Cl- pump conserves characteristic residues for not only the Cl- pump HR but also the H+ pump bacteriorhodopsin (BR). Reflecting close similarity to BR, the third Cl- pump begins to pump H+ outwardly after single amino acid replacement. This mutation activates several residues that have no roles in the original Cl- pump function but act as important H+ relay residues in the H+ pump mutant. Thus, the third Cl- pump might be the model protein for functional differentiation because this rhodopsin seems to be the Cl- pump occurring immediately after functional differentiation from the BR-type H+ pump.
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Affiliation(s)
- Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060–0810, Japan
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Zhou Y, Ding M, Nagel G, Konrad KR, Gao S. Advances and prospects of rhodopsin-based optogenetics in plant research. Plant Physiol 2021; 187:572-589. [PMID: 35237820 PMCID: PMC8491038 DOI: 10.1093/plphys/kiab338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
Microbial rhodopsins have advanced optogenetics since the discovery of channelrhodopsins almost two decades ago. During this time an abundance of microbial rhodopsins has been discovered, engineered, and improved for studies in neuroscience and other animal research fields. Optogenetic applications in plant research, however, lagged largely behind. Starting with light-regulated gene expression, optogenetics has slowly expanded into plant research. The recently established all-trans retinal production in plants now enables the use of many microbial opsins, bringing extra opportunities to plant research. In this review, we summarize the recent advances of rhodopsin-based plant optogenetics and provide a perspective for future use, combined with fluorescent sensors to monitor physiological parameters.
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Affiliation(s)
- Yang Zhou
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Meiqi Ding
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Georg Nagel
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Kai R. Konrad
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Shiqiang Gao
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
- Author for communication:
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25
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Abstract
Microbial rhodopsins are diverse photoreceptive proteins containing a retinal chromophore and are found in all domains of cellular life and are even encoded in genomes of viruses. These rhodopsins make up two families: type 1 rhodopsins and the recently discovered heliorhodopsins. These families have seven transmembrane helices with similar structures but opposing membrane orientation. Microbial rhodopsins participate in a portfolio of light-driven energy and sensory transduction processes. In this review we present data collected over the last two decades about these rhodopsins and describe their diversity, functions, and biological and ecological roles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan;
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan;
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
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26
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Sasaki S, Tamogami J, Nishiya K, Demura M, Kikukawa T. Replaceability of Schiff base proton donors in light-driven proton pump rhodopsins. J Biol Chem 2021; 297:101013. [PMID: 34329681 PMCID: PMC8387761 DOI: 10.1016/j.jbc.2021.101013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Many H+-pump rhodopsins conserve “H+ donor” residues in cytoplasmic (CP) half channels to quickly transport H+ from the CP medium to Schiff bases at the center of these proteins. For conventional H+ pumps, the donors are conserved as Asp or Glu but are replaced by Lys in the minority, such as Exiguobacterium sibiricum rhodopsin (ESR). In dark states, carboxyl donors are protonated, whereas the Lys donor is deprotonated. As a result, carboxyl donors first donate H+ to the Schiff bases and then capture the other H+ from the medium, whereas the Lys donor first captures H+ from the medium and then donates it to the Schiff base. Thus, carboxyl and Lys-type H+ pumps seem to have different mechanisms, which are probably optimized for their respective H+-transfer reactions. Here, we examined these differences via replacement of donor residues. For Asp-type deltarhodopsin (DR), the embedded Lys residue distorted the protein conformation and did not act as the H+ donor. In contrast, for Glu-type proteorhodopsin (PR) and ESR, the embedded residues functioned well as H+ donors. These differences were further examined by focusing on the activation volumes during the H+-transfer reactions. The results revealed essential differences between archaeal H+ pump (DR) and eubacterial H+ pumps PR and ESR. Archaeal DR requires significant hydration of the CP channel for the H+-transfer reactions; however, eubacterial PR and ESR require the swing-like motion of the donor residue rather than hydration. Given this common mechanism, donor residues might be replaceable between eubacterial PR and ESR.
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Affiliation(s)
- Syogo Sasaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan.
| | - Koki Nishiya
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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27
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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part I. Acta Naturae 2021; 13:52-64. [PMID: 34707897 PMCID: PMC8526180 DOI: 10.32607/actanaturae.11414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed
manipulation of a cell’s biochemistry is a highly topical one. In the
case of electrically excitable cells, the aim of the manipulation is to control
the cells’ electrical activity, with the result being either excitation
with subsequent generation of an action potential or inhibition and suppression
of the excitatory currents. The techniques of electrical activity stimulation
are of particular significance in tackling the most challenging basic problem:
figuring out how the nervous system of higher multicellular organisms
functions. At this juncture, when neuroscience is gradually abandoning the
reductionist approach in favor of the direct investigation of complex neuronal
systems, minimally invasive methods for brain tissue stimulation are becoming
the basic element in the toolbox of those involved in the field. In this
review, we describe three approaches that are based on the delivery of
exogenous, genetically encoded molecules sensitive to external stimuli into the
nervous tissue. These approaches include optogenetics (Part I) as well as
chemogenetics and thermogenetics (Part II), which are significantly different
not only in the nature of the stimuli and structure of the appropriate effector
proteins, but also in the details of experimental applications. The latter
circumstance is an indication that these are rather complementary than
competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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28
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Kato T, Tsukamoto T, Demura M, Kikukawa T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J Biol Chem 2021; 296:100792. [PMID: 34019877 PMCID: PMC8219890 DOI: 10.1016/j.jbc.2021.100792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na+-pump rhodopsin. We triggered the transport cycle of Na+-pump rhodopsin using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions and elucidated the sequential formation of the Na+-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na+ concentration, indicating that Na+ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na+ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na+ release on the extracellular side. Thus, there is an irreversible switch in “accessibility” during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na+ transport.
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Affiliation(s)
- Tomoya Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
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29
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Abstract
Bacteria and fungi of the plant microbiota can be phytopathogens, parasites or symbionts that establish mutually advantageous relationships with plants. They are often rich in photoreceptors for UVA-Visible light, and in many cases, they exhibit light regulation of growth patterns, infectivity or virulence, reproductive traits, and production of pigments and of metabolites. In addition to the light-driven effects, often demonstrated via the generation of photoreceptor gene knock-outs, microbial photoreceptors can exert effects also in the dark. Interestingly, some fungi switch their attitude towards plants in dependence of illumination or dark conditions in as much as they may be symbiotic or pathogenic. This review summarizes the current knowledge about the roles of light and photoreceptors in plant-associated bacteria and fungi aiming at the identification of common traits and general working ideas. Still, reports on light-driven infection of plants are often restricted to the description of macroscopically observable phenomena, whereas detailed information on the molecular level, e.g., protein-protein interaction during signal transduction or induction mechanisms of infectivity/virulence initiation remains sparse. As it becomes apparent from still only few molecular studies, photoreceptors, often from the red- and the blue light sensitive groups interact and mutually modulate their individual effects. The topic is of great relevance, even in economic terms, referring to plant-pathogen or plant-symbionts interactions, considering the increasing usage of artificial illumination in greenhouses, the possible light-regulation of the synthesis of plant-growth stimulating substances or herbicides by certain symbionts, and the biocontrol of pests by selected fungi and bacteria in a sustainable agriculture.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103, Leipzig, Germany
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30
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Abstract
The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.
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Affiliation(s)
- Vincent R. Daria
- Research School of Physics, The Australian National University, Canberra, Australia
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | | | - Hans-A. Bachor
- Research School of Physics, The Australian National University, Canberra, Australia
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31
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Labarre A, López-Escardó D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R, Massana R. Comparative genomics reveals new functional insights in uncultured MAST species. ISME J 2021; 15:1767-81. [PMID: 33452482 DOI: 10.1038/s41396-020-00885-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.
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32
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Abstract
After first describing the issue contents (Biophysical Reviews-Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)-two major figures in Biophysical/Biochemical science from the last 100 years.
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Affiliation(s)
- Damien Hall
- Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, 466-8555 Japan
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33
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Abstract
Heliorhodopsin (HeR), a recently discovered new rhodopsin family, has an inverted membrane topology compared to animal and microbial rhodopsins, and no ion-transport activity. The slow photocycle of HeRs suggests a light-sensor function, although the function remains unknown. HeRs exhibit no specific binding of monovalent cations or anions. Despite this, ATR-FTIR spectroscopy in the present study demonstrates binding of Zn2+ to HeR from Thermoplasmatales archaeon (TaHeR). The biding of Zn2+ to 0.2 mM Kd is accompanied by helical structural perturbations without altering its color. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn2+-binding. Similar results were obtained for HeR 48C12. These findings suggest a possible modification of HeR function by Zn2+.
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Affiliation(s)
- Masanori Hashimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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34
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Abstract
This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bld. 8, Bethesda, MD, 20892-0830, USA.
- Institute for Protein Research, Osaka University, 3-1-Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
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