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Kaneko A, Inoue K, Kojima K, Kandori H, Sudo Y. Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering. Biophys Rev 2017; 9:861-876. [PMID: 29178082 DOI: 10.1007/s12551-017-0335-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Technological progress has enabled the successful application of functional conversion to a variety of biological molecules, such as nucleotides and proteins. Such studies have revealed the functionally essential elements of these engineered molecules, which are difficult to characterize at the level of an individual molecule. The functional conversion of biological molecules has also provided a strategy for their rational and atomistic design. The engineered molecules can be used in studies to improve our understanding of their biological functions and to develop protein-based tools. In this review, we introduce the functional conversion of membrane-embedded photoreceptive retinylidene proteins (also called rhodopsins) and discuss these proteins mainly on the basis of results obtained from our own studies. This information provides insights into the molecular mechanism of light-induced protein functions and their use in optogenetics, a technology which involves the use of light to control biological activities.
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Affiliation(s)
- Akimasa Kaneko
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Yuki Sudo
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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Draft Genome Sequence of Rubricoccus marinus SG-29 T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes. GENOME ANNOUNCEMENTS 2017; 5:5/38/e00990-17. [PMID: 28935744 PMCID: PMC5609423 DOI: 10.1128/genomea.00990-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Rubricoccus marinus SG-29T, a bacterium isolated from the western North Pacific Ocean. R. marinus SG-29T possesses two different types of rhodopsin genes and belongs to the family Rhodothermaceae, with which halophilic, thermophilic, and marine bacteria are associated.
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