The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
CryoRhodopsins: a comprehensive characterization of a group of microbial rhodopsins from cold environments
Open accessPreprint — published as 10.1126/sciadv.adv1015 · Paper page
Abstract
Microbial rhodopsins are omnipresent on Earth, however the vast majority of them remain uncharacterized. Here we describe a new rhodopsin group from cold-adapted organisms and cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). Our data suggest that CryoRs have dual functionality switching between inward transmembrane proton translocation and photosensory activity, both of which can be modulated with UV light. CryoR1 exhibits two subpopulations in the ground state, which upon light activation lead to transient photocurrents of opposing polarities. A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face of its members. Combining single-particle cryo-electron microscopy and X-ray crystallography with the rhodopsin activation by light, we demonstrate that the arginine stabilizes a UV-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the newly identified group and demonstrate principles of the adaptation of these rhodopsins to low temperatures.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Flagged first, then by citations
Research works printed but not linked: 82
- 2022, The Evolutionary Kaleidoscope of Rhodopsins, mSystems, 7, e00405
- 10.1146/annurev-biochem-101910-144233 · DOI
- 10.1126/science.289.5486.1902 · DOI
- 10.1038/s41586-018-0225-9 · DOI
- 10.1038/nn1525 · DOI
- 10.1038/s41593-022-01094-6 · DOI
- 10.1126/sciadv.add7729 · DOI
- 10.1126/science.aaa7484 · DOI
- 10.1038/newbio233149a0 · DOI
- 2019, Unique structure and function of viral rhodopsins, Nat. Commun, 10, 4939, 10.1038/s41467-019-12718-0 · DOI
- 2020, Viral rhodopsins 1 are an unique family of light-gated cation channels, Nat. Commun, 11, 5707, 10.1038/s41467-020-19457-7 · DOI
- 2015, A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor, Biochim. Biophys. Acta BBA - Bioenerg, 1847, 1518, 10.1016/j.bbabio.2015.08.003 · DOI
- 2023, Mirror proteorhodopsins, Commun. Chem, 6, 1
- Marín, M. del C.,, 2023, Biophysical characterization of microbial rhodopsins with DSE motif, Biophys. Physicobiology, 20, e201023
- 2023, Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota, ISME J, 17, 1063, 10.1038/s41396-023-01412-1 · DOI
- 10.1038/s42003-021-02156-4 · DOI
- Montero-Calasanz, M. del C., 2020, Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments, Bioinformatics, 36, 1668, 10.1093/bioinformatics/btz840 · DOI
- Shibata, M. et al. Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. Sci. Rep. 8, (2018). · DOI
- 10.1073/pnas.86.23.9228 · DOI
- 1992, Aspartic acid 85 in bacteriorhodopsin functions both as proton acceptor and negative counterion to the Schiff base, J. Biol. Chem, 267, 25730, 10.1016/S0021-9258(18)35668-0 · DOI
- 10.1126/sciadv.1603187 · DOI
- 2021, The Voltage Dependent Sidedness of the Reprotonation of the Retinal Schiff Base Determines the Unique Inward Pumping of Xenorhodopsin, Angew. Chem. Int. Ed, 60, 23010, 10.1002/anie.202103882 · DOI
- 1977, Studies on the Retinal-Protein Interaction in Bacteriorhodopsin, Eur. J. Biochem, 76, 499, 10.1111/j.1432-1033.1977.tb11620.x · DOI
- 2017, Ultrafast Photoinduced Deactivation Dynamics of Proteorhodopsin, J. Phys. Chem. Lett, 8, 512, 10.1021/acs.jpclett.6b02975 · DOI
- 10.1021/bi901634p · DOI
- 1985, The transport activity of the light-driven chloride pump halorhodopsin is regulated by green and blue light, Biochim. Biophys. Acta BBA - Biomembr, 819, 195, 10.1016/0005-2736(85)90174-9 · DOI
- 10.1016/0014-5793(77)80115-4 · DOI
- 10.1038/ncomms2689 · DOI
- 10.1016/S0006-3495(03)74934-0 · DOI
- 10.1021/bi048318h · DOI
- 2007, Photoisomerization in Proteorhodopsin Mutant D97N†, Photochem. Photobiol, 83, 226
- 10.1016/j.bpj.2012.04.034 · DOI
- 2021, Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration, J. Phys. Chem. Lett, 12, 6284, 10.1021/acs.jpclett.1c01436 · DOI
- 2018, Origin of the Reactive and Nonreactive Excited States in the Primary Reaction of Rhodopsins: pH Dependence of Femtosecond Absorption of Light-Driven Sodium Ion Pump Rhodopsin KR2, J. Phys. Chem. B, 122, 4784, 10.1021/acs.jpcb.8b01934 · DOI
- 2022, A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins, Angew. Chem. Int. Ed, 61, e202111930, 10.1002/anie.202111930 · DOI
- 10.1126/science.7939680 · DOI
- 2010, Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch, Phys. Chem. Chem. Phys, 12, 3178, 10.1039/b918603d · DOI
- 10.1021/bi0355894 · DOI
- 10.1021/bi050438h · DOI
- 2012, Critical Role of Asp227 in the Photocycle of Proteorhodopsin, Biochemistry, 51, 5589, 10.1021/bi3003764 · DOI
- 2012, Anomalous pH Effect of Blue Proteorhodopsin, J. Phys. Chem. Lett, 3, 800, 10.1021/jz3000257 · DOI
- 10.1006/jmbi.1999.3027 · DOI
- 2022, True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins, Nat. Struct. Mol. Biol, 29, 440, 10.1038/s41594-022-00762-2 · DOI
- 2020, Structural insights into the mechanism of rhodopsin phosphodiesterase, Nat. Commun, 11, 5605, 10.1038/s41467-020-19376-7 · DOI
- 10.1126/sciadv.aav2671 · DOI
- 10.1038/s41467-020-16032-y · DOI
- 10.1101/2023.10.11.561842 · DOI · Paper page
- 2023, Mechanisms of inward transmembrane proton translocation, Nat. Struct. Mol. Biol, 30, 970, 10.1038/s41594-023-01020-9 · DOI
- 2002, Proteorhodopsin, a bR homolog from marine bacteria, acts as a light-driven, bidirectional proton pump, Biophys. J. V82, 1, 228a
- 2014, Proteorhodopsin, Biochim. Biophys. Acta BBA - Bioenerg, 1837, 614, 10.1016/j.bbabio.2013.09.010 · DOI
- 10.1016/S0022-2836(02)00696-4 · DOI
- 10.1021/ja5097946 · DOI
- 10.1098/rsif.2013.0197 · DOI
- 2023, Some aspects of using the fundamental properties of bacteriorhodopsin for recording, processing, and storage of optical information, J. Photochem. Photobiol. C Photochem. Rev, 56, 100620, 10.1016/j.jphotochemrev.2023.100620 · DOI
- 10.1038/nmeth.1766 · DOI
- 10.1038/s41467-021-24759-5 · DOI
- 10.1093/nar/gkh340 · DOI · Paper page
- 10.1093/nar/gkw256 · DOI
- 10.1093/NAR/GKAB301 · DOI
- 10.1093/molbev/mst010 · DOI · Paper page
- 10.1093/bioinformatics/bts565 · DOI · Paper page
- 2018, Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2, Sci. Rep, 8, 9316, 10.1038/s41598-018-27690-w · DOI
- 10.1016/j.pep.2005.01.016 · DOI
- 10.1038/s41467-020-14834-8 · DOI
- 2017, Connectivity pattern modifies excited state relaxation dynamics of fluorophore– photoswitch molecular dyads, Phys. Chem. Chem. Phys, 19, 4010, 10.1039/C6CP07112K · DOI
- 2015, Implementation and Evaluation of Data Analysis Strategies for Time-Resolved Optical Spectroscopy, Anal. Chem, 87, 2328, 10.1021/ac504348h · DOI
- 10.1038/nmeth.4169 · DOI · Paper page
- 2019, Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, Nat. Methods, 16, 1153, 10.1038/s41592-019-0575-8 · DOI
- 2018, Real-space refinement in PHENIX for cryo-EM and crystallography, Acta Crystallogr. Sect. Struct. Biol, 74, 531, 10.1107/S2059798318006551 · DOI
- 2018, New tools for the analysis and validation of cryo-EM maps and atomic models, Acta Crystallogr. Sect. Struct. Biol, 74, 814, 10.1107/S2059798318009324 · DOI
- 10.1107/S0907444910007493 · DOI · Paper page
- 10.1002/pro.3235 · DOI · Paper page
- 10.1002/jcc.20084 · DOI
- 10.1073/pnas.93.25.14532 · DOI
- 2015, In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF, Acta Crystallogr. D Biol. Crystallogr, 71, 15, 10.1107/S139900471401517X · DOI
- Engilberge, S. et al. The TR-icOS setup at the ESRF: time-resolved microsecond UV–Vis absorption spectroscopy on protein crystals. Acta Crystallogr. Sect. Struct. Biol. 80, (2024). · DOI
- 10.1107/S0907444909047337 · DOI · Paper page
- Tickle, I. J. , et al. STARANISO. Cambridge, United Kingdom: Global Phasing Ltd. (2018).
- 10.1107/S0907444909042589 · DOI
- 10.1107/S0907444910045749 · DOI · Paper page
- 10.1107/S0907444911001314 · DOI
- 10.1107/S0907444904019158 · DOI · Paper page
Metadata
- Authors
- Lamm, G. H. U., Marin, E., Alekseev, A., Schellbach, A. V., Stetsenko, A., Bourenkov, G., Borshchevskiy, V., Asido, M., Agthe, M., Engilberge, S., Rose, S. L., Caramello, N., Royant, A., Schneider, T. R., Bateman, A., Mager, T., Moser, T., Wachtveitl, J., Guskov, A., & Kovalev, K.
- Affiliations
- Goethe University Frankfurt (DE)
- University of Groningen (NL)
- Universitätsmedizin Göttingen (DE)
- Deutsches Elektronen-Synchrotron DESY (DE)
- Forschungszentrum Jülich (DE)
- Centre National de la Recherche Scientifique (FR)
- Universität Hamburg (DE)
- European Bioinformatics Institute (GB)
- German Primate Center (DE)
- Corresponding author
- Lamm, G.H.U.
- Marin, E.
- Alekseev, A.
- Wachtveitl, J.
- Guskov, A.
- Kovalev, K.
- ORCID
- Venue
- Science Advances
- Publisher
- openRxiv
- Published
- 2024-01-17
- Volume
- 11
- Issue
- 27
- Pages
- eadv1015-eadv1015
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC12227055
- OpenAlex
- W4412021670
- Cited by
- 7
- References
- 1
- Citations by year
- 2026: 4 · 2025: 3
- FWCI
- 2.75
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Science Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion)
- Desy publication database (The Deutsches Elektronen-Synchrotron) (submittedVersion, other-oa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, other-oa)
- Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by-nc-nd)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron)
- Funders
- Deutsche Forschungsgemeinschaft (EXC 2067, CRC1507, EXC 2067‐1, 390729940, EXC 2067/1390729940)
- Agence Nationale de la Recherche (UAR 3518 CNRS-CEA-UGA-EMBL, ANR-17-EURE-0003, ANR-17-EURE-, ANR-17, ANR-10, ANR-10-INBS-0005)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (184.034.014, OCENW.KLEIN.141)
- Centre National de la Recherche Scientifique (UAR 3518 CNRS-CEA-UGA-EMBL)
- French Infrastructure for Integrated Structural Biology (ANR-17-EURE-0003, ANR-10-INBS-0005, ANR-10-INBS-000502)
- HORIZON EUROPE Marie Sklodowska-Curie Actions (847543)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Physical Sciences › Materials Science › Materials Chemistry › Photochromic and Fluorescence Chemistry
- Keywords
- microbial rhodopsins, cold-adapted microorganisms, glaciers, photocycle, photoswitching, proton translocation, light-driven proton pump
- MeSH terms
- Arginine, Cold Temperature, Models, Molecular, Ultraviolet Rays, Crystallography, X-Ray, Cryoelectron Microscopy, Rhodopsins, Microbial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
