More Like this

1. Widespread use of proton-pumping rhodopsin in Antarctic phytoplankton

   https://doi.org/10.1073/pnas.2307638120  

   Andrew, Sarah M.; Moreno, Carly M.; Plumb, Kaylie; Hassanzadeh, Babak; Gomez-Consarnau, Laura; Smith, Stephanie N.; Schofield, Oscar; Yoshizawa, Susumu; Fujiwara, Takayoshi; Sunda, William G.; et al (September 2023, Proceedings of the National Academy of Sciences)

   Photosynthetic carbon (C) fixation by phytoplankton in the Southern Ocean (SO) plays a critical role in regulating air–sea exchange of carbon dioxide and thus global climate. In the SO, photosynthesis (PS) is often constrained by low iron, low temperatures, and low but highly variable light intensities. Recently, proton-pumping rhodopsins (PPRs) were identified in marine phytoplankton, providing an alternate iron-free, light-driven source of cellular energy. These proteins pump protons across cellular membranes through light absorption by the chromophore retinal, and the resulting pH energy gradient can then be used for active membrane transport or for synthesis of adenosine triphosphate. Here, we show that PPR is pervasive in Antarctic phytoplankton, especially in iron-limited regions. In a model SO diatom, we found that it was localized to the vacuolar membrane, making the vacuole a putative alternative phototrophic organelle for light-driven production of cellular energy. Unlike photosynthetic C fixation, which decreases substantially at colder temperatures, the proton transport activity of PPR was unaffected by decreasing temperature. Cellular PPR levels in cultured SO diatoms increased with decreasing iron concentrations and energy production from PPR photochemistry could substantially augment that of PS, especially under high light intensities, where PS is often photoinhibited. PPR gene expression and high retinal concentrations in phytoplankton in SO waters support its widespread use in polar environments. PPRs are an important adaptation of SO phytoplankton to growth and survival in their cold, iron-limited, and variable light environment. 

   more » « less
2. Chromophore hydrolysis and release from photoactivated rhodopsin in native membranes

   https://doi.org/10.1073/pnas.2213911119  

   Hong, John D.; Salom, David; Kochman, Michał Andrzej; Kubas, Adam; Kiser, Philip D.; Palczewski, Krzysztof (November 2022, Proceedings of the National Academy of Sciences)

   For sustained vision, photoactivated rhodopsin (Rho*) must undergo hydrolysis and release of all- trans -retinal, producing substrate for the visual cycle and apo-opsin available for regeneration with 11- cis -retinal. The kinetics of this hydrolysis has yet to be described for rhodopsin in its native membrane environment. We developed a method consisting of simultaneous denaturation and chromophore trapping by isopropanol/borohydride, followed by exhaustive protein digestion, complete extraction, and liquid chromatography–mass spectrometry. Using our method, we tracked Rho* hydrolysis, the subsequent formation of N -retinylidene-phosphatidylethanolamine ( N -ret-PE) adducts with the released all- trans -retinal, and the reduction of all- trans -retinal to all- trans -retinol. We found that hydrolysis occurred faster in native membranes than in detergent micelles typically used to study membrane proteins. The activation energy of the hydrolysis in native membranes was determined to be 17.7 ± 2.4 kcal/mol. Our data support the interpretation that metarhodopsin II, the signaling state of rhodopsin, is the primary species undergoing hydrolysis and release of its all- trans -retinal. In the absence of NADPH, free all- trans -retinal reacts with phosphatidylethanolamine (PE), forming a substantial amount of N -ret-PE (∼40% of total all- trans -retinal at physiological pH), at a rate that is an order of magnitude faster than Rho* hydrolysis. However, N -ret-PE formation was highly attenuated by NADPH-dependent reduction of all- trans -retinal to all- trans -retinol. Neither N -ret-PE formation nor all- trans -retinal reduction affected the rate of hydrolysis of Rho*. Our study provides a comprehensive picture of the hydrolysis of Rho* and the release of all- trans -retinal and its reentry into the visual cycle, a process in which alteration can lead to severe retinopathies. 

   more » « less
3. Rhodopsin Activation in Lipid Membranes Based on Solid-State NMR Spectroscopy

   https://doi.org/10.1007/978-3-642-35943-9_788-2  

   Perera, S. M..; Xu, X.; Molugu, T. R.; Struts, A. V.; Brown, M. F. (January 2020, Encyclopedia of Biophysics)

   Roberts, G. C.; Watts, A. (Ed.)
4. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

   https://doi.org/10.1007/s41061-022-00374-w  

   Pedraza-González, Laura; Barneschi, Leonardo; Padula, Daniele; De Vico, Luca; Olivucci, Massimo (March 2022, Topics in Current Chemistry)

   Abstract In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that arereproducibleby any user,accurateandreliableso as to replicate experimental trends. Furthermore, the code isefficientin terms of necessary computing resources and time, andscalablein terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties. 

   more » « less
5. In Situ Structural Studies of Anabaena Sensory Rhodopsin in the E. coli Membrane

   https://doi.org/10.1016/j.bpj.2015.02.018  

   Ward, Meaghan E.; Wang, Shenlin; Munro, Rachel; Ritz, Emily; Hung, Ivan; Gor’kov, Peter L.; Jiang, Yunjiang; Liang, Hongjun; Brown, Leonid S.; Ladizhansky, Vladimir (April 2015, Biophysical Journal)