A Unique Clade of Light-Driven Proton-Pumping Rhodopsins
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UNIVERSITY of CALIFORNIA, SAN DIEGO The
UNIVERSITY OF CALIFORNIA, SAN DIEGO The Transporter-Opsin-G protein-coupled receptor (TOG) Superfamily A Thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Biology by Daniel Choi Yee Committee in charge: Professor Milton H. Saier Jr., Chair Professor Yunde Zhao Professor Lin Chao 2014 The Thesis of Daniel Yee is approved and it is acceptable in quality and form for publication on microfilm and electronically: _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Chair University of California, San Diego 2014 iii DEDICATION This thesis is dedicated to my parents, my family, and my mentor, Dr. Saier. It is only with their help and perseverance that I have been able to complete it. iv TABLE OF CONTENTS Signature Page ............................................................................................................... iii Dedication ...................................................................................................................... iv Table of Contents ........................................................................................................... v List of Abbreviations ..................................................................................................... vi List of Supplemental Files ............................................................................................ vii List of -
Maria Barthmes, Andre Bazzone, Ulrich Thomas, Andrea Brüggemann, Michael George, Niels Fertig, Alison Obergrussberger
Label-free analysis of Na+/Ca2+- exchanger (NCX) isolated from iPSC-derived cardiomyocytes Maria Barthmes, Andre Bazzone, Ulrich Thomas, Andrea Brüggemann, Michael George, Niels Fertig, Alison Obergrussberger Nanion Technologies GmbH, Ganghoferstr. 70A, 80339 Munich, Germany, contact: [email protected] Abstract Measuring NCX activity in human iPSC derived The Sodium-Calcium Exchangers (NCX) play an To drive the progress in pharmacological NCX cardiomyocytes important role in the cellular calcium research, new methods to measure NCX Human iPSC derived cardiomyocytes are being with high fluidic speed, the cells detached homeostasis under physiological and function are needed. At the current time, investigated as a model for cardiac safety again, but a sheet of the cell membrane pathological conditions. NCX has been of functional investigation of NCX range from assessment. To measure native NCX in these remains on the sensor. NCX currents can be interest as a pharmacological target for many patch-clamp, calcium flux assays, Langendorff- cardiomyocytes a cell based assay was evoked in these sheets. For a higher NCX signal years, in particular because clinical trials perfused hearts to studies in whole animals. We developed. Cardiomyocytes were detached female cardiomyocytes were used. This method involving inhibitors of the sodium-proton have developed an electrophysiological from the culture dish and added to the lipid enables the efficient investigation of the isolated exchanger, NHE, have delivered mixed results. method to investigate NCX function which is coated SSM sensor. Where the cell connected cardiac NCX current in a native membrane. Inhibition of the reversed mode of NCX is based on the solid supported membrane (SSM) with the lipid layer. -
Early-Stage Dynamics of Chloride Ion–Pumping Rhodopsin Revealed by a Femtosecond X-Ray Laser
Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser Ji-Hye Yuna,1, Xuanxuan Lib,c,1, Jianing Yued, Jae-Hyun Parka, Zeyu Jina, Chufeng Lie, Hao Hue, Yingchen Shib,c, Suraj Pandeyf, Sergio Carbajog, Sébastien Boutetg, Mark S. Hunterg, Mengning Liangg, Raymond G. Sierrag, Thomas J. Laneg, Liang Zhoud, Uwe Weierstalle, Nadia A. Zatsepine,h, Mio Ohkii, Jeremy R. H. Tamei, Sam-Yong Parki, John C. H. Spencee, Wenkai Zhangd, Marius Schmidtf,2, Weontae Leea,2, and Haiguang Liub,d,2 aDepartment of Biochemistry, College of Life Sciences and Biotechnology, Yonsei University, Seodaemun-gu, 120-749 Seoul, South Korea; bComplex Systems Division, Beijing Computational Science Research Center, Haidian, 100193 Beijing, People’s Republic of China; cDepartment of Engineering Physics, Tsinghua University, 100086 Beijing, People’s Republic of China; dDepartment of Physics, Beijing Normal University, Haidian, 100875 Beijing, People’s Republic of China; eDepartment of Physics, Arizona State University, Tempe, AZ 85287; fPhysics Department, University of Wisconsin, Milwaukee, Milwaukee, WI 53201; gLinac Coherent Light Source, Stanford Linear Accelerator Center National Accelerator Laboratory, Menlo Park, CA 94025; hDepartment of Chemistry and Physics, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; and iDrug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 230-0045 Yokohama, Japan Edited by Nicholas K. Sauter, Lawrence Berkeley National Laboratory, Berkeley, CA, and accepted by Editorial Board Member Axel T. Brunger February 21, 2021 (received for review September 30, 2020) Chloride ion–pumping rhodopsin (ClR) in some marine bacteria uti- an acceptor aspartate (13–15). -
Optogenetics and Its Application in Neural Degeneration and Regeneration
3/13/2018 Optogenetics and its application in neural degeneration and regeneration Neural Regen Res. 2017 Aug; 12(8): 1197–1209. PMCID: PMC5607808 doi: 10.4103/1673-5374.213532 Optogenetics and its application in neural degeneration and regeneration Josue D. Ordaz,1,2,3 Wei Wu,1,2,3 and Xiao-Ming Xu, M.D., Ph.D.1,2,3,4,* 1 Spinal Cord and Brain Injury Research Group, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA 2 Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA 3 Goodman Campbell Brain and Spine, Indianapolis, Indiana, USA 4 Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA * Correspondence to: Xiao-Ming Xu, [email protected]. Author contributions: JDO wrote the paper. JDO and WW were responsible for making figures and edited the paper. XMX reviewed and edited the paper. All authors participated in the conception of this study and approved the final version of this paper. Accepted 2017 Jul 11. Copyright : © Neural Regeneration Research This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms. Abstract Neural degeneration and regeneration are important topics in neurological diseases. There are limited options for therapeutic interventions in neurological diseases that provide simultaneous spatial and temporal control of neurons. This drawback increases side effects due to non-specific targeting. -
Xenorhodopsins, an Enigmatic New Class of Microbial Rhodopsins Horizontally Transferred Between Archaea and Bacteria
UC San Diego UC San Diego Previously Published Works Title Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria Permalink https://escholarship.org/uc/item/8rg5f54b Journal Biology Direct, 6(1) ISSN 1745-6150 Authors Ugalde, Juan A Podell, Sheila Narasingarao, Priya et al. Publication Date 2011-10-10 DOI http://dx.doi.org/10.1186/1745-6150-6-52 Supplemental Material https://escholarship.org/uc/item/8rg5f54b#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Ugalde et al. Biology Direct 2011, 6:52 http://www.biology-direct.com/content/6/1/52 DISCOVERYNOTES Open Access Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria Juan A Ugalde1, Sheila Podell1, Priya Narasingarao1 and Eric E Allen1,2* Abstract Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats. Reviewers: This article was reviewed by Dr. Michael Galperin and Dr. Rob Knight. Findings disseminated photoreceptor and photosensory activities Microbial rhodopsins are a widespread family of photo- across large evolutionary distances [1]. -
Microbial Rhodopsins on Leaf Surfaces of Terrestrial Plants
Environmental Microbiology (2011) doi:10.1111/j.1462-2920.2011.02554.x Microbial rhodopsins on leaf surfaces of terrestrial plantsemi_2554 1..7 Nof Atamna-Ismaeel,1‡ Omri M. Finkel,4‡ soybean (Glycine max), Arabidopsis (Arabidopsis Fabian Glaser,2 Itai Sharon,1,3† Ron Schneider,4 thaliana), clover (Trifolium repens) and rice (Oryza Anton F. Post,5 John L. Spudich,6 sativa). Our findings, for the first time describing Christian von Mering,7 Julia A. Vorholt,8 David Iluz,9 microbial rhodopsins from non-aquatic habitats, Oded Béjà1* and Shimshon Belkin4** point towards the potential coexistence of microbial 1Faculty of Biology, 2Bioinformatics Knowledge Unit, rhodopsin-based phototrophy and plant chlorophyll- Lorry I. Lokey Interdisciplinary Center for Life Sciences based photosynthesis, with the different pigments and Engineering, 3Faculty of Computer Science, absorbing non-overlapping fractions of the light Technion – Israel Institute of Technology, Haifa 32000, spectrum. Israel. 4Department of Plant and Environmental Sciences, Introduction Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel. Solar radiation is the main source of energy for both 5Josephine Bay Paul Center for Comparative Molecular marine and terrestrial organisms, with terrestrial plants Biology and Evolution, Marine Biology Laboratory, and aquatic phytoplankton performing an equivalent Woods Hole, MA 02543, USA. ecological function as chlorophyll-based photosynthetic 6Center for Membrane Biology, Department of primary producers (Field et al., 1998). Marine surface Biochemistry and Molecular Biology, The University of waters are now known to harbour an additional type of Texas Medical School, Houston, TX 77030, USA. phototrophy; several lineages of bacteria and archaea 7Faculty of Science, Institute of Molecular Life Sciences utilize rhodopsins (Béjà et al., 2000; 2001; de la Torre and Swiss Institute of Bioinformatics, University of et al., 2003; Balashov et al., 2005; Giovannoni et al., Zurich, 8057 Zurich, Switzerland. -
S42003-021-01878-9.Pdf
ARTICLE https://doi.org/10.1038/s42003-021-01878-9 OPEN Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design ✉ Keiichi Inoue 1,2,3,4,5,11 , Masayuki Karasuyama5,6,11, Ryoko Nakamura3, Masae Konno3, Daichi Yamada3, Kentaro Mannen1, Takashi Nagata1,5, Yu Inatsu6, Hiromu Yawo 1, Kei Yura 7,8,9, Oded Béjà10, ✉ Hideki Kandori 2,3,4 & Ichiro Takeuchi 2,4,6 Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is 1234567890():,; introduced for screening rhodopsins that are likely to be red-shifted from representative rhodopsins in the same subfamily. Among 3,022 ion-pumping rhodopsins that were sug- gested by a protein BLAST search in several protein databases, the ML-based method selected 65 candidate rhodopsins. The wavelengths of 39 of them were able to be experi- mentally determined by expressing proteins with the Escherichia coli system, and 32 (82%, p = 7.025 × 10−5) actually showed red-shift gains. In addition, four showed red-shift gains >20 nm, and two were found to have desirable ion-transporting properties, indicating that they would be potentially useful in optogenetics. These findings suggest that data-driven ML-based approaches play effective roles in the experimental design of rhodopsin and other photobiological studies. (141/150 words). 1 The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan. 2 RIKEN Center for Advanced Intelligence Project, Tokyo, Japan. 3 Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan. -
Lokiarchaeota Archaeon Schizorhodopsin-2 (Laszr2) Is an Inward Proton Pump Displaying a Characteristic Feature of Acid-Induced S
www.nature.com/scientificreports OPEN Lokiarchaeota archaeon schizorhodopsin‑2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid‑induced spectral blue‑shift Keiichi Kojima1,5, Susumu Yoshizawa2,5, Masumi Hasegawa2, Masaki Nakama1, Marie Kurihara1, Takashi Kikukawa3,4 & Yuki Sudo1,2* The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identifed as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all‑trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schif base of the retinal chromophore (Lys188, pKa = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pKa = 3.7). The fash‑photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M‑decay, the Schif base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid‑induced spectral ‘blue‑shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red‑shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid‑induced spectral shift. Sunlight provides a fundamental source for organisms, including humans. Many organisms possess a variety of photoreceptor proteins that can capture sunlight. -
Genome Sequence of Halobacterium Species NRC-1
Genome sequence of Halobacterium species NRC-1 Wailap Victor Nga,b, Sean P. Kennedyc, Gregory G. Mahairasa,b, Brian Berquistc, Min Pana,b, Hem Dutt Shuklac, Stephen R. Laskya,b, Nitin S. Baligac, Vesteinn Thorssona,b, Jennifer Sbrognac, Steven Swartzella, Douglas Weirc, John Halla, Timothy A. Dahla,b, Russell Weltia,b, Young Ah Gooa,b, Brent Leithausera, Kim Kellera, Randy Cruza, Michael J. Dansond, David W. Houghd, Deborah G. Maddocksd, Peter E. Jablonskie, Mark P. Krebsf, Christine M. Angevinef, Heather Dalef, Thomas A. Isenbargerf, Ronald F. Peckf, Mechthild Pohlschroderg, John L. Spudichh, Kwang-Hwan Jungh, Maqsudul Alami, Tracey Freitasi, Shaobin Houi, Charles J. Danielsj, Patrick P. Dennisk, Arina D. Omerk, Holger Ebhardtk, Todd M. Lowel, Ping Liangm, Monica Rileym, Leroy Hooda,b,n, and Shiladitya DasSarmac,n aDepartment of Molecular Biotechnology, University of Washington, Seattle, WA 98195; cDepartment of Microbiology, University of Massachusetts, Amherst, MA 01003; dCentre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom; eDepartment of Biological Sciences, Northern Illinois University, DeKalb, IL 60115; fDepartment of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706; gDepartment of Biology, University of Pennsylvania, Philadelphia, PA 19104; hDepartment of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030; iDepartment of Microbiology, University of Hawaii, Honolulu, HI 96822; jDepartment of Microbiology, Ohio State University, Columbus, OH 43210; kDepartment of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada V6T 1Z3; lDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305; mMarine Biological Laboratory, Woods Hole, MA 02543; and bInstitute for Systems Biology, Seattle, WA 98105 Contributed by Leroy Hood, July 20, 2000 We report the complete sequence of an extreme halophile, in size (8–11). -
Cholinergic Interneuron Mediated Activation of G
CHOLINERGIC INTERNEURON MEDIATED ACTIVATION OF G- PROTEIN COUPLED RECEPTORS IN THE DORSAL STRIATUM by APHRODITI A. MAMALIGAS Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Neurosciences CASE WESTERN RESERVE UNIVERSITY August, 2018 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of Aphroditi A. Mamaligas Candidate for the degree of Doctor of Philosophy.* Thesis advisor: Christopher Ford, PhD Committee Chair: David Friel, PhD Committee Member: Lynn Landmesser, PhD Committee Member: Evan Deneris, PhD Date of Defense: May 23, 2018 *We also certify that written approval has been obtained for any proprietary material contained therein. 2 TABLE OF CONTENTS List of figures..........................................................................................................6 Acknowledgements................................................................................................8 List of abbreviations................................................................................................9 Abstract................................................................................................................12 Chapter 1..........................................................................................14 Introduction.............................................................................................15 Striatal microcircuitry.................................................................................16 Striatal -
Review Article a Protocell Design for Bioaccumulation Applications
Review article A protocell design for bioaccumulation applications Ian von Hegner ABSTRACT This article provides a review of specific example of recombinant cell and protocell technology, moving from what is presently known to suggesting how novel application of existing methodologies could be utilized to design a complex synthetic system in form of a self-sufficient light empowered protocell. A practical application of protocells using a primary example of desalination in water treatment is given, followed by a more general review regarding bioaccumulation and bio-diagnostics, outlining the possibilities associated with applications of protocells. The key hypothesis is that the inside- negative electrochemical membrane potential generated by Cl− pump activity via halorhodopsin could also be utilized to drive the accumulation of cations into a protocell. Thus, the functional expression of halorhodopsin could energize proton-coupled uptake of substances or metals through a selective cotransport channel for a number of applications in biotechnology, molecular medicine, and water biotechnology. Keywords: Protocells, membrane potential, polymersomes, molecular medicine. INTRODUCTION Between 4.0-3.5 billion years ago the first cell on Earth emerged. This first cell existed only a brief moment, and represented the beginning of life as we know it [Altermann et al., 2003]. Shortly after the abiogenesis this original cell split in two, and these two split again, and during a short geological time scale Earth was populated by unicellular organisms. That was the beginning of the history of life on this planet, and thus the beginning of the history of biology itself. Synthetic biology reflects the view that the best way to investigate the accuracy and limits of current biological knowledge and phenomena is to modify or engineer a different artificial version of a complex biological system and compare its functions with theoretical expectations [Solé et al., 2007]. -
A Versatile Class of Microbial Rhodopsins
J. Microbiol. Biotechnol. 2020. 30(5): 633–641 https://doi.org/10.4014/jmb.1912.12010 Review Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins Soon-Kyeong Kwon1*, Sung-Hoon Jun2, and Jihyun F. Kim3* 1Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea 2Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju 28119, Republic of Korea 3Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea Microbial rhodopsins are a superfamily of photoactive membrane proteins with the covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the ‘3 omega motif.’ This motif forms a stack of three non-consecutive aromatic amino acids that correlates with the B–C loop orientation and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodium- pumping rhodopsin, the NTQ motif-containing chloride-pumping