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For: Flores-Uribe J, Hevroni G, Ghai R, Pushkarev A, Inoue K, Kandori H, Béjà O. Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity. Environ Microbiol Rep 2019;11:419-424. [PMID: 30618066 DOI: 10.1111/1758-2229.12730] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/27/2018] [Accepted: 12/27/2018] [Indexed: 06/09/2023]
Number Cited by Other Article(s)
1
Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024;15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]  Open
2
Palombo R, Barneschi L, Pedraza-González L, Yang X, Olivucci M. Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin. Phys Chem Chem Phys 2024;26:10343-10356. [PMID: 38501246 DOI: 10.1039/d4cp00193a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
3
Singh M, Hashimoto M, Katayama K, Furutani Y, Kandori H. Internal Proton Transfer in the Activation of Heliorhodopsin. J Mol Biol 2024;436:168273. [PMID: 37709010 DOI: 10.1016/j.jmb.2023.168273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
4
Chiba Y, Tsujimura M, Saito K, Ishikita H. pH-Dependent Binding and Releasing Mechanism of Acetate in the Inner Water Cavity of Heliorhodopsin. Biochemistry 2023;62:2363-2370. [PMID: 37471424 PMCID: PMC10434121 DOI: 10.1021/acs.biochem.3c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/28/2023] [Indexed: 07/22/2023]
5
Nakasone Y, Kawasaki Y, Konno M, Inoue K, Terazima M. Time-resolved detection of light-induced conformational changes of heliorhodopsin. Phys Chem Chem Phys 2023;25:12833-12840. [PMID: 37165904 DOI: 10.1039/d3cp00711a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
6
Ganapathy S, Meng X, Mossel D, Jagt M, Brinks D. Expanding the family of genetically encoded voltage indicators with a candidate Heliorhodopsin exhibiting near-infrared fluorescence. J Biol Chem 2023;299:104771. [PMID: 37127067 DOI: 10.1016/j.jbc.2023.104771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023]  Open
7
Suzuki S, Kumagai S, Nagashima T, Yamazaki T, Okitsu T, Wada A, Naito A, Katayama K, Inoue K, Kandori H, Kawamura I. Characterization of retinal chromophore and protonated Schiff base in Thermoplasmatales archaeon heliorhodopsin using solid-state NMR spectroscopy. Biophys Chem 2023;296:106991. [PMID: 36905840 DOI: 10.1016/j.bpc.2023.106991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
8
Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023;25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
9
He S, Linz AM, Stevens SLR, Tran PQ, Moya-Flores F, Oyserman BO, Dwulit-Smith JR, Forest KT, McMahon KD. Diversity, distribution, and expression of opsin genes in freshwater lakes. Mol Ecol 2023;32:2798-2817. [PMID: 36799010 DOI: 10.1111/mec.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
10
Tsujimura M, Chiba Y, Saito K, Ishikita H. Proton transfer and conformational changes along the hydrogen bond network in heliorhodopsin. Commun Biol 2022;5:1336. [PMID: 36474019 PMCID: PMC9726877 DOI: 10.1038/s42003-022-04311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]  Open
11
Iniesto M, Moreira D, Benzerara K, Reboul G, Bertolino P, Tavera R, López‐García P. Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient. LIMNOLOGY AND OCEANOGRAPHY 2022;67:2718-2733. [PMID: 37064594 PMCID: PMC10087431 DOI: 10.1002/lno.12233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/12/2022] [Accepted: 09/04/2022] [Indexed: 06/19/2023]
12
Low pH structure of heliorhodopsin reveals chloride binding site and intramolecular signaling pathway. Sci Rep 2022;12:13955. [PMID: 35977989 PMCID: PMC9385722 DOI: 10.1038/s41598-022-17716-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022]  Open
13
Chazan A, Rozenberg A, Mannen K, Nagata T, Tahan R, Yaish S, Larom S, Inoue K, Béjà O, Pushkarev A. Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea. Environ Microbiol 2022;24:110-121. [PMID: 34984789 DOI: 10.1111/1462-2920.15890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 12/26/2021] [Indexed: 12/25/2022]
14
Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. mSphere 2021;6:e0066121. [PMID: 34817235 PMCID: PMC8612252 DOI: 10.1128/msphere.00661-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
15
Nagata T, Inoue K. Rhodopsins at a glance. J Cell Sci 2021;134:273540. [PMID: 34821363 DOI: 10.1242/jcs.258989] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
16
Rozenberg A, Inoue K, Kandori H, Béjà O. Microbial Rhodopsins: The Last Two Decades. Annu Rev Microbiol 2021;75:427-447. [PMID: 34343014 DOI: 10.1146/annurev-micro-031721-020452] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
17
Urui T, Mizuno M, Otomo A, Kandori H, Mizutani Y. Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates. J Phys Chem B 2021;125:7155-7162. [PMID: 34167296 DOI: 10.1021/acs.jpcb.1c04010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
Hashimoto M, Katayama K, Furutani Y, Kandori H. Zinc Binding to Heliorhodopsin. J Phys Chem Lett 2020;11:8604-8609. [PMID: 32940480 DOI: 10.1021/acs.jpclett.0c02383] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
19
Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Büldt G, Gordeliy V. High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A 2020;117:4131-4141. [PMID: 32034096 PMCID: PMC7049168 DOI: 10.1073/pnas.1915888117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
20
Shihoya W, Inoue K, Singh M, Konno M, Hososhima S, Yamashita K, Ikeda K, Higuchi A, Izume T, Okazaki S, Hashimoto M, Mizutori R, Tomida S, Yamauchi Y, Abe-Yoshizumi R, Katayama K, Tsunoda SP, Shibata M, Furutani Y, Pushkarev A, Béjà O, Uchihashi T, Kandori H, Nureki O. Crystal structure of heliorhodopsin. Nature 2019;574:132-136. [DOI: 10.1038/s41586-019-1604-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 08/20/2019] [Indexed: 11/10/2022]
21
Gómez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B, Arístegui J, Fuhrman JA, Gasol JM, Sañudo-Wilhelmy SA. Microbial rhodopsins are major contributors to the solar energy captured in the sea. SCIENCE ADVANCES 2019;5:eaaw8855. [PMID: 31457093 PMCID: PMC6685716 DOI: 10.1126/sciadv.aaw8855] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/28/2019] [Indexed: 05/19/2023]
22
Shibukawa A, Kojima K, Nakajima Y, Nishimura Y, Yoshizawa S, Sudo Y. Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12. Biochemistry 2019;58:2934-2943. [DOI: 10.1021/acs.biochem.9b00257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
23
Pedraza-González L, De Vico L, del Carmen Marín M, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019;15:3134-3152. [PMID: 30916955 PMCID: PMC7141608 DOI: 10.1021/acs.jctc.9b00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
24
Bulzu PA, Andrei AŞ, Salcher MM, Mehrshad M, Inoue K, Kandori H, Beja O, Ghai R, Banciu HL. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019;4:1129-1137. [DOI: 10.1038/s41564-019-0404-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/08/2019] [Indexed: 11/09/2022]
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