Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family

Ji Hye Yun; Mio Ohki; Jae Hyun Park; Naito Ishimoto; Ayana Sato-Tomita; Wonbin Lee; Zeyu Jin; Jeremy R.H. Tame; Naoya Shibayama; Sam Yong Park; Weontae Lee

doi:10.1126/sciadv.aay2042

Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family

Ji Hye Yun, Mio Ohki, Jae Hyun Park, Naito Ishimoto, Ayana Sato-Tomita, Wonbin Lee, Zeyu Jin, Jeremy R.H. Tame, Naoya Shibayama, Sam Yong Park, Weontae Lee

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium Nonlabens marinus, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys¹⁰⁵, Ser⁶⁰, Gln²²⁴, and Phe⁹⁰—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.

Original language	English
Article number	eaay2042
Journal	Science Advances
Volume	6
Issue number	6
DOIs	https://doi.org/10.1126/sciadv.aay2042
Publication status	Published - 2020 Feb 7

Bibliographical note

Funding Information:
We thank all staff members at the NW12A beamline station at the Photon Factory for assistance with data collection. Funding: This work was supported by the Research Program (NRF-20171A2B2008483, 2019M3A9F6021810 to W.L. and NRF-20161A6A3A04010213 to J.-H.Y.) through the National Research Foundation of Korea and the Platform Project for Supporting Drug Discovery and Life Science Research (BINDS) from AMED under grant number JP18am0101076 (to S.-Y.P.), JSPS KAKENHI grant number JP19H05779 (to S.-Y.P.), and Takeda Science Foundation (to S.-Y.P.). The work was supported in part by Brain Korea 21 (BK21) PLUS program. J.-H.P. and Wonbin Lee are fellowship awardees of the BK21 PLUS program.

Publisher Copyright:
Copyright © 2020 The Authors, some rights reserved;

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title = "Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family",

abstract = "A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium Nonlabens marinus, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys105, Ser60, Gln224, and Phe90—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.",

author = "Yun, {Ji Hye} and Mio Ohki and Park, {Jae Hyun} and Naito Ishimoto and Ayana Sato-Tomita and Wonbin Lee and Zeyu Jin and Tame, {Jeremy R.H.} and Naoya Shibayama and Park, {Sam Yong} and Weontae Lee",

note = "Funding Information: We thank all staff members at the NW12A beamline station at the Photon Factory for assistance with data collection. Funding: This work was supported by the Research Program (NRF-20171A2B2008483, 2019M3A9F6021810 to W.L. and NRF-20161A6A3A04010213 to J.-H.Y.) through the National Research Foundation of Korea and the Platform Project for Supporting Drug Discovery and Life Science Research (BINDS) from AMED under grant number JP18am0101076 (to S.-Y.P.), JSPS KAKENHI grant number JP19H05779 (to S.-Y.P.), and Takeda Science Foundation (to S.-Y.P.). The work was supported in part by Brain Korea 21 (BK21) PLUS program. J.-H.P. and Wonbin Lee are fellowship awardees of the BK21 PLUS program. Publisher Copyright: Copyright {\textcopyright} 2020 The Authors, some rights reserved;",

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doi = "10.1126/sciadv.aay2042",

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AU - Yun, Ji Hye

AU - Ohki, Mio

AU - Park, Jae Hyun

AU - Ishimoto, Naito

AU - Sato-Tomita, Ayana

AU - Lee, Wonbin

AU - Jin, Zeyu

AU - Tame, Jeremy R.H.

AU - Shibayama, Naoya

AU - Park, Sam Yong

AU - Lee, Weontae

N1 - Funding Information: We thank all staff members at the NW12A beamline station at the Photon Factory for assistance with data collection. Funding: This work was supported by the Research Program (NRF-20171A2B2008483, 2019M3A9F6021810 to W.L. and NRF-20161A6A3A04010213 to J.-H.Y.) through the National Research Foundation of Korea and the Platform Project for Supporting Drug Discovery and Life Science Research (BINDS) from AMED under grant number JP18am0101076 (to S.-Y.P.), JSPS KAKENHI grant number JP19H05779 (to S.-Y.P.), and Takeda Science Foundation (to S.-Y.P.). The work was supported in part by Brain Korea 21 (BK21) PLUS program. J.-H.P. and Wonbin Lee are fellowship awardees of the BK21 PLUS program. Publisher Copyright: Copyright © 2020 The Authors, some rights reserved;

PY - 2020/2/7

Y1 - 2020/2/7

N2 - A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium Nonlabens marinus, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys105, Ser60, Gln224, and Phe90—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.

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Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family

Abstract

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