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Phototrophy by antenna-containing rhodopsin pumps in aquatic environments

  • Balashov, S. P. et al. Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science 309, 2061–2064 (2005).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Imasheva, E. S., Balashov, S. P., Choi, A. R., Jung, K.-H. & Lanyi, J. K. Reconstitution of Gloeobacter violaceus rhodopsin with a light-harvesting carotenoid antenna. Biochemistry 48, 10948–10955 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fuhrman, J. A., Schwalbach, M. S. & Stingl, U. Proteorhodopsins: an array of physiological roles? Nat. Rev. Microbiol. 6, 488–494 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Vollmers, J. et al. Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS ONE 8, e63422 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bertsova, Y. V., Arutyunyan, A. M. & Bogachev, A. V. Na+-translocating rhodopsin from Dokdonia sp. PRO95 does not contain carotenoid antenna. Biochem. Mosc. 81, 414–419 (2016).

    Article 
    CAS 

    Google Scholar 

  • Misra, R., Eliash, T., Sudo, Y. & Sheves, M. Retinal–salinixanthin interactions in a thermophilic rhodopsin. J. Phys. Chem. B 123, 10–20 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Béjà, O. et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 1902–1906 (2000).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. Nature 411, 786–789 (2001).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Atamna-Ismaeel, N. et al. Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME J. 2, 656–662 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Frigaard, N.-U., Martinez, A., Mincer, T. J. & DeLong, E. F. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439, 847–850 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Finkel, O. M., Béjà, O. & Belkin, S. Global abundance of microbial rhodopsins. ISME J. 7, 448–451 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gómez-Consarnau, L. et al. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Sci. Adv. 5, eaaw8855 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • DeLong, E. F. & Béjà, O. The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol. 8, e1000359 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Munson-McGee, J. H. et al. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 612, 764–770 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, W.-W., Sineshchekov, O. A., Spudich, E. N. & Spudich, J. L. Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin. J. Biol. Chem. 278, 33985–33991 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Man, D. Diversification and spectral tuning in marine proteorhodopsins. EMBO J. 22, 1725–1731 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lanyi, J. K. & Balashov, S. P. in Halophiles and Hypersaline Environments (eds. Ventosa, A., Oren, A. & Ma, Y.) 319–340 (Springer, 2011).

  • Balashov, S. P. et al. Reconstitution of Gloeobacter rhodopsin with echinenone: role of the 4-keto group. Biochemistry 49, 9792–9799 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kopejtka, K. et al. A bacterium from a mountain lake harvests light using both proton-pumping xanthorhodopsins and bacteriochlorophyll-based photosystems. Proc. Natl Acad. Sci. USA 119, e2211018119 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pushkarev, A. & Béjà, O. Functional metagenomic screen reveals new and diverse microbial rhodopsins. ISME J. 10, 2331–2335 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pushkarev, A. et al. A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Nature 558, 595–599 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Chazan, A. et al. Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea. Environ. Microbiol. 24, 110–121 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Inoue, K. et al. A light-driven sodium ion pump in marine bacteria. Nat. Commun. 4, 1678 (2013).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Bhosale, P. & Bernstein, P. S. Microbial xanthophylls. Appl. Microbiol. Biotechnol. 68, 445–455 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Demmig-Adams, B., Polutchko, S. K. & Adams, W. W. Structure–function–environment relationship of the isomers zeaxanthin and lutein. Photochem 2, 308–325 (2022).

    Article 

    Google Scholar 

  • Barreiro C. & Barredo J. L. Microbial Carotenoids: Methods and Protocols (Humana Press, 2018).

  • Ram, S., Mitra, M., Shah, F., Tirkey, S. R. & Mishra, S. Bacteria as an alternate biofactory for carotenoid production: a review of its applications, opportunities and challenges. J. Funct. Foods 67, 103867 (2020).

    Article 
    CAS 

    Google Scholar 

  • Shibata, M. et al. Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. Sci. Rep. 8, 8262 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Luecke, H. et al. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc. Natl Acad. Sci. USA 105, 16561–16565 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chuon, K. et al. Assembly of natively synthesized dual chromophores into functional actinorhodopsin. Front. Microbiol. 12, 652328 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yoshizawa, S., Kawanabe, A., Ito, H., Kandori, H. & Kogure, K. Diversity and functional analysis of proteorhodopsin in marine Flavobacteria. Environ. Microbiol. 14, 1240–1248 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ahmed, F. et al. Profiling of carotenoids and antioxidant capacity of microalgae from subtropical coastal and brackish waters. Food Chem. 165, 300–306 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Shihoya, W. et al. Crystal structure of heliorhodopsin. Nature 574, 132–136 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Kishi, K. E. et al. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell 185, 672–689.e23 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Balashov, S. P., Imasheva, E. S., Wang, J. M. & Lanyi, J. K. Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin. Biophys. J. 95, 2402–2414 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lakowicz, J. R. (ed.) in Principles of Fluorescence Spectroscopy 27–61 (Springer, 2006).

  • Dana, J. et al. Testing the fate of nascent holes in CdSe nanocrystals with sub-10 fs pump–probe spectroscopy. Nanoscale 13, 1982–1987 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Polívka, T. et al. Femtosecond carotenoid to retinal energy transfer in xanthorhodopsin. Biophys. J. 96, 2268–2277 (2009).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Iyer, E. S. S., Gdor, I., Eliash, T., Sheves, M. & Ruhman, S. Efficient femtosecond energy transfer from carotenoid to retinal in Gloeobacter rhodopsin–salinixanthin complex. J. Phys. Chem. B 119, 2345–2349 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Doi, S., Tsukamoto, T., Yoshizawa, S. & Sudo, Y. An inhibitory role of Arg-84 in anion channelrhodopsin-2 expressed in Escherichia coli. Sci. Rep. 7, 41879 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nagiri, C. et al. Crystal structure of human endothelin ETB receptor in complex with peptide inverse agonist IRL2500. Commun. Biol. 2, 236 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data processing for microcrystals. Acta Crystallogr. D Struct. Biol. 74, 441–449 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine.Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3.eLife 7, e42166 (2018).

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

  • Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article 
    PubMed 

    Google Scholar 

  • Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yamashita, K., Palmer, C. M., Burnley, T. & Murshudov, G. N. Cryo-EM single-particle structure refinement and map calculation using Servalcat. Acta Crystallogr. D Struct. Biol. 77, 1282–1291 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Inoue, K. et al. Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design. Commun. Biol. 4, 362 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083.e21 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen, I.-M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sunagawa, S. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196–1199 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wickham, H. in ggplot2 (eds Gentleman, R., Hornik, K. & Parmigiani, G.) 189–201 (Springer, 2016).

  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 


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