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Misra R, Das I, Dér A, Steinbach G, Shim JG, Busse W, Jung KH, Zimányi L, Sheves M. Impact of protein-chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues. Chem Sci 2023; 14:9951-9958. [PMID: 37736621 PMCID: PMC10510653 DOI: 10.1039/d3sc02961a] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
The function of microbial as well as mammalian retinal proteins (aka rhodopsins) is associated with a photocycle initiated by light excitation of the retinal chromophore of the protein, covalently bound through a protonated Schiff base linkage. Although electrostatics controls chemical reactions of many organic molecules, attempt to understand its role in controlling excited state reactivity of rhodopsins and, thereby, their photocycle is scarce. Here, we investigate the effect of highly conserved tryptophan residues, between which the all-trans retinal chromophore of the protein is sandwiched in microbial rhodopsins, on the charge distribution along the retinal excited state, quantum yield and nature of the light-induced photocycle and absorption properties of Gloeobacter rhodopsin (GR). Replacement of these tryptophan residues by non-aromatic leucine (W222L and W122L) or phenylalanine (W222F) does not significantly affect the absorption maximum of the protein, while all the mutants showed higher sensitivity to photobleaching, compared to wild-type GR. Flash photolysis studies revealed lower quantum yield of trans-cis photoisomerization in W222L as well as W222F mutants relative to wild-type. The photocycle kinetics are also controlled by these tryptophan residues, resulting in altered accumulation and lifetime of the intermediates in the W222L and W222F mutants. We propose that protein-retinal interactions facilitated by conserved tryptophan residues are crucial for achieving high quantum yield of the light-induced retinal isomerization, and affect the thermal retinal re-isomerization to the resting state.
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Affiliation(s)
- Ramprasad Misra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Gábor Steinbach
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
- Cellular Imaging Laboratory, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University Seoul 04107 South Korea
| | - Wayne Busse
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin Berlin 10115 Germany
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University Seoul 04107 South Korea
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
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Setiawati A, Jeong S, Brillian AI, Lee SH, Shim JG, Jung KH, Shin K. Fabrication of a Tailored, Hybrid Extracellular Matrix Composite. Macromol Biosci 2022; 22:e2200106. [PMID: 35765216 DOI: 10.1002/mabi.202200106] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/24/2022] [Indexed: 11/10/2022]
Abstract
The extracellular matrix (ECM) is a network of connective fibers that supports cells living in their surroundings. Native ECM, generated by the secretory products of each tissue's resident cells, has a unique architecture with different protein composition depending on the tissue. Therefore, it is very difficult to artificially design in vivo architecture in tissue engineering. In this study, we fabricated a hybrid ECM scaffold from the basic structure of fibroblast-derived cellular ECMs by adding major ECM components of fibronectin (FN) and collagen (COL I) externally. It was confirmed that while maintaining the basic structure of the native ECM, major protein components can be regulated. Then, decellularization was performed to prepare hybrid ECM scaffolds with various protein compositions and we demonstrated that a liver-mimicking fibronectin (FN)-rich hybrid ECM promoted successful settling of H4IIE rat hepatoma cells. We believe that our method holds promise for the fabrication of scaffolds that provide a tailored cellular microenvironment for specific organs and serve as novel pathways for the replacement or regeneration of specific organ tissues. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Agustina Setiawati
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea.,Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea.,Faculty of Pharmacy, Paingan, Maguwoharjo, Depok, Sanata Dharma University, Sleman, Yogyakarta, 55284, Indonesia
| | - Sungwoo Jeong
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Albertus Ivan Brillian
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Sang Ho Lee
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Jin-Gon Shim
- Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
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Shim JG, Kang NR, Chuon K, Cho SG, Meas S, Jung KH. Mutational analyses identify a single amino acid critical for color tuning in proteorhodopsins. FEBS Lett 2022; 596:784-795. [PMID: 35090057 DOI: 10.1002/1873-3468.14297] [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: 10/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/08/2022]
Abstract
Microbial rhodopsins are light-activated proteins that contain seven transmembrane alpha-helices. Spectral tuning in microbial rhodopsins is a useful optogenetic tool. In this study, we report a new site that controls spectral tuning. In the proteorhodopsins ISR34 and ISR36, a single amino-acid substitution at Cys189 caused an absorption maximum shift of 44 nm, indicating spectral tuning at a specific site. Comparison of single amino acid substitutions was conducted using photochemical and photobiological approaches. The maximum absorption for red-shift was measured for mutations at positions 189 and 105 in ISR34, both residues being equally important. Structural changes resulting from amino acid substitutions are related to pKa values, pumping activity, and spectral tuning.
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Affiliation(s)
- Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Na-Rae Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
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Cho SG, Shim JG, Choun K, Meas S, Kang KW, Kim JH, Cho HS, Jung KH. Discovery of a new light-driven Li +/Na +-pumping rhodopsin with DTG motif. J Photochem Photobiol B 2021; 223:112285. [PMID: 34411952 DOI: 10.1016/j.jphotobiol.2021.112285] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/31/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022]
Abstract
Microbial pumping rhodopsin is a seven-transmembrane retinal binding protein, which is light-driven ion pump with a functional key motif. Ion-pumping with the key motif and charged amino acids in the rhodopsin is biochemically important. The rhodopsins with DTG motif have been discovered in various eubacteria, and they function as H+ pump. Especially, the DTG motif rhodopsins transported H+ despite the replacement of a proton donor by Gly. We investigated Methylobacterium populi rhodopsin (MpR) in one of the DTG motif rhodopsin clades. To determine which ions the MpR transport, we tested with various monovalent ion solutions and determined that MpR transports Li+/Na+. By replacing the three negatively charged residues residues which are located in helix B, Glu32, Glu33, and Asp35, we concluded that the residues play a critical role in the transport of Li+/Na+. The MpR E33Q transported H+ in place of Li+/Na+, suggesting that Glu33 is a Li+/Na+ binding site on the cytoplasmic side. Gly93 in MpR was replaced by Asp to convert from the Li+/Na+ pump to the H+ pump, resulting in MpR G93D transporting H+. Dissociation constant (Kd) values of Na+ for MpR WT and E33Q were determined to be 4.0 and 72.5 mM, respectively. These results indicated the mechanism by which MpR E33Q transports H+. Up to now, various ion-pumping rhodopsins have been discovered, and Li+/Na+-pumping rhodopsins were only found in the NDQ motif in NaR. Here, we report a new light-driven Na+ pump MpR and have determined the important residues required for Li+/Na+-pumping different from previously known NaR.
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Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kimleng Choun
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea; Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Kun-Wook Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Ji-Hyun Kim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Hyun-Suk Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea.
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Chuon K, Kim SY, Meas S, Shim JG, Cho SG, Kang KW, Kim JH, Cho HS, Jung KH. Assembly of Natively Synthesized Dual Chromophores Into Functional Actinorhodopsin. Front Microbiol 2021; 12:652328. [PMID: 33995310 PMCID: PMC8113403 DOI: 10.3389/fmicb.2021.652328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 01/12/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Microbial rhodopsin is a simple solar energy-capturing molecule compared to the complex photosynthesis apparatus. Light-driven proton pumping across the cell membrane is a crucial mechanism underlying microbial energy production. Actinobacteria is one of the highly abundant bacterial phyla in freshwater habitats, and members of this lineage are considered to boost heterotrophic growth via phototrophy, as indicated by the presence of actino-opsin (ActR) genes in their genome. However, it is difficult to validate their function under laboratory settings because Actinobacteria are not consistently cultivable. Based on the published genome sequence of Candidatus aquiluna sp. strain IMCC13023, actinorhodopsin from the strain (ActR-13023) was isolated and characterized in this study. Notably, ActR-13023 assembled with natively synthesized carotenoid/retinal (used as a dual chromophore) and functioned as a light-driven outward proton pump. The ActR-13023 gene and putative genes involved in the chromophore (retinal/carotenoid) biosynthetic pathway were detected in the genome, indicating the functional expression ActR-13023 under natural conditions for the utilization of solar energy for proton translocation. Heterologous expressed ActR-13023 exhibited maximum absorption at 565 nm with practical proton pumping ability. Purified ActR-13023 could be reconstituted with actinobacterial carotenoids for additional light-harvesting. The existence of actinorhodopsin and its chromophore synthesis machinery in Actinobacteria indicates the inherent photo-energy conversion function of this microorganism. The assembly of ActR-13023 to its synthesized chromophores validated the microbial community's importance in the energy cycle.
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Affiliation(s)
- Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - So Young Kim
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Kun-Wook Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Ji-Hyun Kim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Hyun-Suk Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
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Pushkarev A, Hevroni G, Roitman S, Shim JG, Choi A, Jung KH, Béjà O. The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color. Front Microbiol 2018; 9:439. [PMID: 29593685 PMCID: PMC5859045 DOI: 10.3389/fmicb.2018.00439] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 11/16/2017] [Accepted: 02/26/2018] [Indexed: 11/20/2022] Open
Abstract
Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4–5 days that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions – green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students’ laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.
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Affiliation(s)
- Alina Pushkarev
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Gur Hevroni
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Ahreum Choi
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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