DOCSLIB.ORG

Folding and Assembly of Proteorhodopsin

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Folding and Assembly of Proteorhodopsin doi:10.1016/j.jmb.2007.11.030 J. Mol. Biol. (2008) 376,35–41 Available online at www.sciencedirect.com Folding and Assembly of Proteorhodopsin Adriana L. Klyszejko1†, Sarika Shastri2†, Stefania A. Mari3, Helmut Grubmüller4, Daniel J. Muller1⁎ and Clemens Glaubitz2 1Biotechnology Center, Proteorhodopsins (PRs), the recently discovered light-driven proton University of Technology pumps, play a major role in supplying energy for microbial organisms of Dresden, Germany oceans. In contrast to PR, rhodopsins found in Archaea and Eukarya are structurally well characterized. Using single-molecule microscopy and 2Institute of Biophysical spectroscopy, we observed the oligomeric assembly of native PR molecules Chemistry and Center for and detected their folding in the membrane. PR showed unfolding patterns Biomolecular Magnetic identical with those of bacteriorhodopsin and halorhodopsin, indicating Resonance, Goethe University that PR folds similarly to archaeal rhodopsins. Surprisingly, PR predomi- Frankfurt, Germany nantly assembles into hexameric oligomers, with a smaller fraction 3Institute of General assembling into pentamers. Within these oligomers, PR arranged into Physiology and Biological radial assemblies. We suggest that this structural assembly of PR may have Chemistry, University functional implications. of Milan, Italy © 2007 Elsevier Ltd. All rights reserved. 4Max-Planck-Institute of Biophysical Chemistry, Göttingen, Germany Received 5 October 2007; accepted 9 November 2007 Available online 19 November 2007 Keywords: membrane protein folding; oligomeric state; hexamer; high- Edited by W. Baumeister resolution atomic force microscopy; single-molecule force spectroscopy Introduction brane α-helices surrounding the light-sensitive retinal. However, the oligomeric assembly of rho- Rhodopsins occur in Archaea, Bacteria, and dopsins in Archaea and Eukarya differs and ranges Eukarya. Using a chromophore, rhodopsins sense from monomeric, to dimeric, to trimeric forms, which supposedly have structural and functional light of certain wavelengths. In Archaea, this 1,3,4 captured light is employed to pump protons or origins. chloride ions across the membrane and to create an The recent discovery of rhodopsins in bacteria electrochemical gradient, which powers cellular [proteorhodopsin (PR)] came after the sequence analysis of a cloned genome region from a marine machineries. Other archaeal rhodopsins sense light 5 for phototaxis.1 In vertebrates, rhodopsins function bacterium of the uncultivated SAR86 clade. Sub- primarily as sensory proteins and account for sequent DNA screening of microorganisms from vision.2 Archaeal and eukaryal rhodopsins show different oceans revealed a very large diversity of PR common structural motifs; they are embedded in belonging to divergent clades of the Alphaproteo- 6–11 the membrane bilayer and have seven transmem- bacteria and Gammaproteobacteria classes. Two related PR families that absorb light with different absorption maxima, ≈525 nm (green) and ≈490 nm *Corresponding author. E-mail address: (blue), were found, and their distribution was [email protected]. shown to be stratified with water depth. A single † A.K. and S.S. contributed equally to this work. amino acid at position 105 functions as a spectral Abbreviations used: AFM, atomic force microscopy; PR, tuning switch and seems to account for most of the proteorhodopsin; SMFS, single-molecule force spectral difference between green-absorbing PRs spectroscopy; F–D, force–distance; DOPC, and blue-absorbing PRs.10 The phototrophy con- 1,2-dioleolyl-sn-glycero-3-phosphocholine. ferred by PR can provide critical amounts of energy 0022-2836/$ - see front matter © 2007 Elsevier Ltd. All rights reserved. 36 Proteorhodopsin Assembly not only for respiration and maintenance but also Results and Discussions for active growth of marine bacterioplankton in their natural environment.12 This potential to complement their chemotropic lifestyle by photo- Two-dimensional PR crystals show larger unit trophy has evolutionarily favored these oceanophi- cell size than bacteriorhodopsin lic microbial organisms and the wide oceanographic – distribution of PR genes.6,13 15 PRs overproduced in AFM imaging of reconstituted PR membranes in Escherichia coli have further established that PR buffer solution (Fig. 1a) showed crystalline (*) and functions as a light-driven proton pump with the densely packed (**) regions. At high resolution, the potential to generate energy for cell growth and surface of the two-dimensional PR crystals revealed maintenance.5,9,16 donut-like structures arranged in a hexagonal lattice PR is a light-driven proton pump like bacterior- of 8.8±0.7 nm (mean±SD; n=30) side length (Fig. hodopsin from archaeabacteria.1,17 In contrast to 1b), which agrees well with the low-resolution PR, the structure–function relationship of bacter- electron microscopy analysis of the same crystals.22 iorhodopsin and its homologues, the light-driven These donut-like structures featured pronounced chloride pump halorhodopsin18 and sensory protrusions extending 0.9±0.3 nm (n=50) above the rhodopsin,3 has been studied at molecular resolu- lipid surface. In comparison, the hexagonal lattice of tion. So far, the only structural insights available for bacteriorhodopsin trimers in native purple mem- PR have been revealed from spectroscopic studies brane patches shows a side length of ≈6.2 nm24 with and modeling.19,20 Recent low-resolution structural single bacteriorhodopsin molecules protruding data revealed from two-dimensionally crystallized between ≈0.5 and 0.8 nm from the lipid bilayer.25 PR suggested a hexagonal lattice constant of The hexagonal unit cell of the purple membrane ≈8.7 nm,21 showing a symmetric ringlike arrange- lattice covers an area of 16.64 nm2, hosting three ment.22 Initial solid-state NMR studies focused on bacteriorhodopsin molecules. In contrast, the area the characterization of retinal and Schiff base.23 covered by the unit cell of the hexagonal PR lattice is Here, we show high-resolution atomic force micro- 33.53 nm2. It was suggested that the secondary scopy (AFM) topographs of green PR reconstituted structures of PR and bacteriorhodopsin are very into the lipid bilayer. These topographs show similar.19 Thus, the unit cell of the PR lattice would oligomers of PRs assembled in a two-dimensional provide sufficient space to accommodate up to six lattice and densely packed in the membrane. PR molecules instead of three as observed for Single-molecule force spectroscopy (SMFS) shows bacteriorhodopsin. Recent calculations suggested PRs to unfold via similar structural intermediates ≈24,000 PR molecules per SAR86 cell.26 Packed as observed for bacteriorhodopsin and halorhodop- into a densely packed crystalline lattice, such as sin. This suggests that all three rhodopsins have observed for purple membrane, this would make a almost identical folding and three-dimensional 600-nm-diameter flat circular patch covering a structures. significant portion of a cell surface. Therefore, the Fig. 1. AFM of two-dimensionally crystallized and densely packed PR membranes. (a) Survey showing crystalline (*) and densely packed (**) patches of PRs embedded in the lipid (DOPC) bilayer. The lipid bilayer protruded 4.5±0.5 nm (n=10) from the support, the crystals protruded 7.1±0.5 nm (n=10), and the densely packed PRs protruded 6.3±0.5 nm (n=10). (b) High-resolution topography showing the hexagonal lattice (a=8.8±0.7 nm) of donut-shaped oligomers formed by PRs. (c) Calculated diffraction pattern of (b) documents spots (red circles), suggesting a lateral resolution of ≈1.5 nm. (d) Correlation average of (b). The symmetrized average showed a 9% deviation from 6-fold symmetry. AFM topographs recorded in buffer solution exhibit a full gray level corresponding to a vertical scale of 20 nm (a) and 2 nm (b and d). Proteorhodopsin Assembly 37 half packing density of PR would cover twice the The oligomeric assembly of PR area of the cell membrane. Hence, the enhanced size of the PR donuts leads to the question whether they High-resolution AFM of the noncrystalline areas reflect the oligomeric state of trimers, tetramers, of the reconstituted membrane patches showed pentamers, or hexamers. densely packed PR oligomers (Fig. 2a). The highest Most of the donut-shaped molecules observed in protrusions of these oligomers extended 1.3±0.2 nm the high-resolution AFM images (N90%) of the (n=50) from the surface of the lipid bilayer. The crystalline PR patches showed the same diameter majority of oligomers (N90%) observed were circu- (Fig. 1b). The donuts showed an average diameter of lar, with their protrusions being equally distributed 4.3±0.3 nm (n=83) and, in most cases, six protru- at the outer circle diameter. Surprisingly, indivi- sions, which became clearly visible after correlation dual oligomers exhibited either six (Fig. 2b) or five averaging (Fig. 1d). In contrast, some donut-like (Fig. 2c) protrusions, thus showing either 6- or 5-fold shapes exhibited smaller diameters (Fig. 1b, com- symmetries. In rare cases, incomplete oligomers pare circles) and less than six protrusions. However, missed a single subunit or more (Fig. 2, dotted from these topographs, it could not be unambigu- ellipse). The surface area occupied by a PR molecule ously answered how many PR molecules have ≈2×3 nm2 matches that observed for bacterio- established the protrusions. rhodopsin25 and halorhodopsin.27 This suggested Fig. 2. High-resolution AFM of densely packed PR oligomers. (a) PR molecules
Load more

Recommended publications
  • POSTER LIST (Alphabetical by Author)
    POSTER LIST (alphabetical by author) First author Poster Title Session or General Archibald, Kevin Modeling the impact of zooplankton diel vertical migration on General the carbon export flux of the biological pump Arroyo, Mar CO2 System Dynamics in the Dalton Polynya, East Antarctica Polar Bif, Mariana Using cruises and Bio-Argo floats data to estimate dissolved Time-series organic carbon in the Northeast Pacific Ocean Bochdansky, Net carbon remineralization (defined here as CO2 release) of Microzooplankton Alexander stable isotope-labeled phytoplankton measured in the mesopelagic environment with a newly designed deep-sea incubator Bociu, Ioana Initial DECK analysis of the carbon cycle in GFDL's CM4 Time-series contribution to CMIP6 Boyd, Philip A web- based Best Practice Guide to design marine multiple General driver experiments Buchanan, Marine nitrogen fixers crucial for dust-driven strengthening of Phytoplankton/models Pearse the biological carbon pump Busecke, Julius How important are forced changes in the equatorial current General system for the extent of tropical oxygen minimum zones? Cael, B.B. A metabolic model of biogeochemistry Phytoplankton/models Campbell, Mesozooplankton are not herbivores: The importance of Microzooplankton Robert microzooplankton in mesozooplankton diets and in arctic and *C. Ashjian, sub-arctic trophic linkages presenting Chappell, P. Both dissolved iron and coastal water additions to Southern Polar Dreux Drake Passage waters stimulate similar growth responses and shifts in diatom community composition.
    [Show full text]
  • Ecosystem Structure and Dynamics in the North Pacific Subtropical Gyre
    Ecosystems DOI: 10.1007/s10021-017-0117-0 Ó 2017 The Author(s). This article is published with open access at Springerlink.com 20th Anniversary Paper Ecosystem Structure and Dynamics in the North Pacific Subtropical Gyre: New Views of an Old Ocean David M. Karl1,2* and Matthew J. Church1,2,3 1Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaii at Manoa, 1950 East-West Rd., Honolulu, Hawaii 96822, USA; 2School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA; 3Present address: Flathead Lake Biological Station, University of Montana, Polson, MT 59860, USA ABSTRACT The North Pacific Subtropical Gyre (NPSG) is one of community with a relatively stable plankton com- the largest biomes on Earth. It has a semi-enclosed munity structure and relatively low variability in key surface area of about 2 9 107 km2 and mean depth of microbiological rates and processes. Now, after nearly nearly 5 km and includes a broad range of habitats three decades of observations and experimentation from warm, light-saturated, nutrient-starved surface we present a new view of this old ocean, one that waters to the cold, nutrient-rich abyss. Microorgan- highlights temporal variability in ecosystem pro- isms are found throughout the water column and are cesses across a broad range of scales from diel to vertically stratified by their genetically determined decadal and beyond. Our revised paradigm is built on metabolic capabilities that establish physiological the strength of high-quality time-series observations, tolerances to temperature, light, pressure, as well as on insights from the application of state-of-the-art organic and inorganic growth substrates.
    [Show full text]
  • Proteorhodopsin Phototrophy in the Ocean
    letters to nature 17. Schatz, J. F. & Simmons, G. Thermal conductivity of Earth materials at high temperatures. J. Geophys. an H+-ATPase4. Similar rhodopsin-mediated, light-driven proton Res. 77, 6966±6983 (1972). pumping, formerly thought to exist only in halophilic archaea, has 18. Holt, J. B. Thermal diffusivity of olivine. Earth Planet. Sci. Lett. 27, 404±408 (1975). 1 19. Seipold, U. Temperature dependence of thermal transport properties of crystalline rocks±general law. been discovered in an uncultivated marine bacterium of the Tectonophysics 291, 161±171 (1998). `SAR86' phylogenetic group5. This ®nding suggested that a pre- 20. Hofmeister, A. M. Mantle values of thermal conductivity and the geotherm from phonon lifetimes. viously unrecognized phototrophic pathway may occur in the Science 283, 1699±1706 (1999). 21. Klemens, P. G. Thermal conductivity and lattice vibrational modes. Solid State Phys. 7, 1±98 (1958). ocean's photic zone; however, all earlier data are based solely on 22. Bouhifd, M. A., Andrault, D., Fiquet, G. & Richet, P.Thermal expansion of forsterite up to the melting recombinant DNA and in vitro biochemical analyses, and this point. Geophys. Res. Lett. 23, 134±1136 (1996). phenomenon has not yet been observed in the sea. 23. Vauchez, A., Barruol, G. & Tommasi,A. Why do continents break up parallel to ancient orogenic belts? To test whether rhodopsin-like molecules form photoactive Terra Nova 9, 62±66 (1997). 24. Tommasi, A. & Vauchez, A. Continental rifting parallel to ancient collisional belts: An effect of the proteins in native marine bacteria, we analysed membrane prepara- mechanical anisotropy of the lithospheric mantle.
    [Show full text]
  • Proteorhodopsin Variability and Distribution in the North Pacific
    The ISME Journal (2018) 12:1047–1060 https://doi.org/10.1038/s41396-018-0074-4 ARTICLE Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre 1 2 1 2,3 1 Daniel K. Olson ● Susumu Yoshizawa ● Dominique Boeuf ● Wataru Iwasaki ● Edward F. DeLong Received: 30 August 2017 / Revised: 21 November 2017 / Accepted: 5 December 2017 / Published online: 23 February 2018 © The Author(s) 2018. This article is published with open access Abstract Proteorhodopsin is a light-activated retinal-containing proton pump found in many marine bacteria. These photoproteins are globally distributed in the ocean’s photic zone and are capable of generating a proton motive force across the cell membrane. We investigated the phylogenetic diversity, distribution, and abundance of proteorhodopsin encoding genes in free-living bacterioplankton in the North Pacific Subtropical Gyre, leveraging a gene catalog derived from metagenomic samples from the ocean’s surface to 1000 m depth. Proteorhodopsin genes were identified at all depths sampled, but were most abundant at depths shallower than 200 m. The majority of proteorhodopsin gene sequences (60.9%) belonged to members of the SAR11 lineage, with remaining sequences distributed among other diverse taxa. We observed variations in the conserved residues fi 1234567890();,: involved in ion pumping and spectral tuning, and biochemically con rmed four different proton pumping proteorhodopsin motifs, including one unique to deep-water SAR11. We also identified a new group of putative proteorhodopsins having unknown function. Our results reveal a broad organismal and unexpected depth distribution for different proteorhodopsin types, as well as substantial within-taxon variability. These data provide a framework for exploring the ecological relevance of proteorhodopsins and their spatiotemporal variation and function in heterotrophic bacteria in the open ocean.
    [Show full text]
  • Seasonality of Archaeal Proteorhodopsin and Associated Marine Group Iib Ecotypes (Ca
    The ISME Journal (2021) 15:1302–1316 https://doi.org/10.1038/s41396-020-00851-4 ARTICLE Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea 1,5 1 2 3 4 Olivier Pereira ● Corentin Hochart ● Dominique Boeuf ● Jean Christophe Auguet ● Didier Debroas ● Pierre E. Galand 1 Received: 23 July 2020 / Revised: 9 November 2020 / Accepted: 18 November 2020 / Published online: 7 December 2020 © The Author(s), under exclusive licence to International Society for Microbial Ecology 2020 Abstract The Archaea Marine Group II (MGII) is widespread in the world’s ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group’s metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs’ seasonality revealed 1234567890();,: 1234567890();,: a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight’s energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group.
    [Show full text]
  • Diel Vertical Migration in Marine Dinoflagellates Jephson, Therese
    Diel vertical migration in marine dinoflagellates Jephson, Therese 2012 Link to publication Citation for published version (APA): Jephson, T. (2012). Diel vertical migration in marine dinoflagellates. Department of Biology, Lund University. Total number of authors: 1 General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Diel vertical migration in marine dinoflagellates Therese Jephson AKADEMISK AVHANDLING som för avläggande av filosofie doktorsexamen vid naturvetenskapliga fakulteten, Lunds universitet kommer att offentligen försvaras i Blå Hallen, Ekologihuset, Sölvegatan 37, Lund, torsdagen den 15 november 2012 kl 9:30 Fakultetens opponent: Associate Professor Tammi L. Richardson, Dept. of Marine Science Program and Biological Sciences University of South Carolina, USA Avhandlingen kommer att försvaras på engelska Dissertation Lund 2012 List of papers This thesis is based on the following papers, referred to in the text by their roman numerals: I.
    [Show full text]
  • Early Evolution of Purple Retinal Pigments on Earth and Implications
    International Journal of Early evolution of purple retinal pigments on Astrobiology Earth and implications for exoplanet cambridge.org/ija biosignatures Shiladitya DasSarma1 and Edward W. Schwieterman2,3,4,5 Review 1Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Marine and Environmental Technology, Baltimore, MD, USA; 2Department of Earth Sciences, University of California, Riverside, Cite this article: DasSarma S, Schwieterman CA, USA; 3NASA Postdoctoral Program Fellow, Universities Space Research Association, Columbia, MD, USA; EW (2018). Early evolution of purple retinal 4NASA Astrobiology Institute’s Alternative Earths and Virtual Planetary Laboratory Teams and 5Blue Marble Space pigments on Earth and implications for Institute of Science, Seattle, WA, USA exoplanet biosignatures. International Journal of Astrobiology 1–10. https://doi.org/10.1017/ S1473550418000423 Abstract Received: 20 June 2018 We propose that retinal-based phototrophy arose early in the evolution of life on Earth, pro- Revised: 4 September 2018 foundly impacting the development of photosynthesis and creating implications for the search Accepted: 10 September 2018 for life beyond our planet. While the early evolutionary history of phototrophy is largely in the realm of the unknown, the onset of oxygenic photosynthesis in primitive cyanobacteria sig- Key words: ’ ∼ Bacteriorhodopsin; biosignatures; carotenoids; nificantly altered the Earth s atmosphere by contributing to the rise of oxygen 2.3 billion chemiosmotic
    [Show full text]
  • Light-Stimulated Growth of Proteorhodopsin-Bearing Sea-Ice Psychrophile Psychroflexus Torquis Is Salinity Dependent
    The ISME Journal (2013) 7, 2206–2213 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 OPEN www.nature.com/ismej ORIGINAL ARTICLE Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent Shi Feng1, Shane M Powell1, Richard Wilson2 and John P Bowman1 1Food Safety Centre, School of Agriculture Science, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia and 2Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia Proteorhodopsins (PRs) are commonly found in marine prokaryotes and allow microbes to use light as an energy source. In recent studies, it was reported that PR stimulates growth and survival under nutrient-limited conditions. In this study, we tested the effect of nutrient and salinity stress on the extremely psychrophilic sea-ice bacterial species Psychroflexus torquis, which possesses PR. We demonstrated for the first time that light-stimulated growth occurs under conditions of salinity stress rather than nutrient limitation and that elevated salinity is related to increased growth yields, PR levels and associated proton-pumping activity. PR abundance in P. torquis also is post- transcriptionally regulated by both light and salinity and thus could represent an adaptation to its sea-ice habitat. Our findings extend the existing paradigm that light provides an energy source for marine prokaryotes under stress conditions other than nutrient limitation. The ISME Journal (2013) 7, 2206–2213; doi:10.1038/ismej.2013.97; published online 20 June 2013 Subject Category: Microbial ecology and functional diversity of natural habitats Keywords: post-transcriptional regulation; proteomics; proteorhodopsin; salinity stress; sea-ice Introduction then exhibited increased proton pumping (Be´ja` et al., 2000).
    [Show full text]
  • Diel, Daily, and Spatial Variation of Coral Reef Seawater Microbial Communities
    Diel, daily, and spatial variation of coral reef seawater microbial communities The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Weber, Laura, and Amy ApprillI, "Diel, daily, and spatial variation of coral reef seawater microbial communities." PloS one 15, 3 (March 2020): no.: e0229442 doi 10.1371/journal.pone.0229442 ©2020 Author(s) As Published 10.1371/journal.pone.0229442 Publisher PLOS Version Final published version Citable link https://hdl.handle.net/1721.1/124753 Terms of Use Creative Commons Attribution 4.0 International license Detailed Terms https://creativecommons.org/licenses/by/4.0/ RESEARCH ARTICLE Diel, daily, and spatial variation of coral reef seawater microbial communities 1,2 1 Laura WeberID , Amy ApprillID * 1 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America, 2 MIT-WHOI Joint PhD Program in Biological Oceanography, Woods Hole, MA, United States of America * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 a1111111111 Reef organisms influence microorganisms within the surrounding seawater, yet the spatial and temporal dynamics of seawater microbial communities located in proximity to corals are rarely investigated. To better understand reef seawater microbial community dynamics over time and space, we collected small-volume seawater samples during the day and night over a 72 hour period from three locations that differed in spatial distance from 5 Porites OPEN ACCESS astreoides coral colonies on a shallow reef in St. John, U.S. Virgin Islands: near-coral (sam- Citation: Weber L, Apprill A (2020) Diel, daily, and pled 5 cm horizontally from each colony), reef-depth (sampled 2 m above each colony) and spatial variation of coral reef seawater microbial communities.
    [Show full text]
  • A Versatile Class of Microbial Rhodopsins
    J. Microbiol. Biotechnol. 2020. 30(5): 633–641 https://doi.org/10.4014/jmb.1912.12010 Review Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins Soon-Kyeong Kwon1*, Sung-Hoon Jun2, and Jihyun F. Kim3* 1Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea 2Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju 28119, Republic of Korea 3Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea Microbial rhodopsins are a superfamily of photoactive membrane proteins with the covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the ‘3 omega motif.’ This motif forms a stack of three non-consecutive aromatic amino acids that correlates with the B–C loop orientation and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodium- pumping rhodopsin, the NTQ motif-containing chloride-pumping
    [Show full text]
  • Spectroscopic and Photochemical Analysis of Proteorhodopsin Variants from the Surface of the Arctic Ocean
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 582 (2008) 1679–1684 Spectroscopic and photochemical analysis of proteorhodopsin variants from the surface of the Arctic Ocean Jae Yong Junga,1, Ah Reum Choia,1, Yoo Kyung Leeb, Hong Kum Leeb, Kwang-Hwan Junga,* a Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, Republic of Korea b Polar BioCenter, Korea Polar Research Institute, KORDI, Songdo Techno Park, Songdo-dong 7-50, Yeonsu-gu, Incheon 406-840, Republic of Korea Received 18 January 2008; revised 14 April 2008; accepted 15 April 2008 Available online 22 April 2008 Edited by Peter Brzezinski The absorption maxima of PR variants depend on the places Abstract Proteorhodopsin (PR), a retinal-containing seven transmembrane helix protein, functions as a light-driven proton and depth of the ocean where their hosts reside [3,5]. PR vari- pump. Using PCR, we isolated 18 PR variants originating from ants from the surface or from the deep ocean of the same place the surface of the Arctic Ocean. Their absorption maxima were (e.g., Hawaiian Pacific Ocean) have different absorption max- between 517 and 546 nm at pH 7. One of the isolates turned out ima being spectrally tuned to usable light in their environment to be identical to GPR (green light-absorbing proteorhodopsin) [3]. PR from Monterey Bay and HOT_0m have green absorp- from Monterey Bay. Interestingly, 10 isolates had replaced a tion maxima (525 nm), whereas PRs from the Antarctic Ocean tyrosine in the retinal-binding site (Tyr200 in GPR) with Asn.
    [Show full text]
  • The Origin of Phototrophy Reveals the Importance of Pri
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 1 December 2020 1 The Origin of Phototrophy Reveals the Importance of Pri- 2 ority Effects for Evolutionary Innovation 1 1 3 Anthony Burnetti ,William C. Ratcliff 1 4 Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, USA. 5 The history of life on Earth has been shaped by a series of major evolutionary innovations. 6 While some of these innovations occur repeatedly, some of the most important evolutionary 7 innovations (e.g., the origin of life itself, eukaryotes, or the genetic code) are evolutionary 8 singularities, arising just once in the history of life. This historical fact has often been in- 9 terpreted to mean that singularities are particularly difficult, low-probability evolutionary 10 events, thus making the long-term course of life on Earth highly contingent on their chance 11 appearances. Alternatively, singularities may arise from evolutionary priority effects, where 12 first-movers suppress subsequent independent origins. Here, we disentangle these hypothe- 13 ses by examining a distinctive innovation: phototrophy. The ability to use light to generate 14 metabolic energy evolved twice, preserving information about the origins of rare, transfor- 15 mative innovations that is lost when examining singular innovations. We show that the two 16 forms of phototrophy occupy opposite ends of several key trade-offs: efficiency of light cap- 17 ture vs. return on investment in protein infrastructure, dependence on limiting nutrients vs. 18 metabolic versatility, and complexity vs. simplicity. Our results suggest that the ‘dual singu- 19 larity’ of phototrophy exists due to evolutionary interactions between nascent phototrophs, 20 with phototrophic niche space too large for a first mover to fill all niches and fully suppress fu- 1 © 2020 by the author(s).
    [Show full text]