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Yang X, Liu Z, Zhang Y, Shi X, Wu Z. Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution. BIOLOGY 2024; 13:579. [PMID: 39194517 DOI: 10.3390/biology13080579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024]
Abstract
Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.
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Affiliation(s)
- Xiaohong Yang
- Guangzhou Marine Geological Survey, Guangzhou 511458, China
| | - Zijian Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yanwen Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xinguo Shi
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Zhen Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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2
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Cooney EC, Jacobson DM, Wolfe GV, Bright KJ, Saldarriaga JF, Keeling PJ, Leander BS, Strom SL. Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata. J Eukaryot Microbiol 2024:e13050. [PMID: 39019843 DOI: 10.1111/jeu.13050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/19/2024]
Abstract
Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gordon V Wolfe
- Department of Biological Sciences, California State University, Chico, Chico, California, USA
| | - Kelley J Bright
- Shannon Point Marine Center, Western Washington University, Anacortes, USA
| | - Juan F Saldarriaga
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne L Strom
- Shannon Point Marine Center, Western Washington University, Anacortes, USA
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3
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Cooney EC, Holt CC, Hehenberger E, Adams JA, Leander BS, Keeling PJ. Investigation of heterotrophs reveals new insights in dinoflagellate evolution. Mol Phylogenet Evol 2024; 196:108086. [PMID: 38677354 DOI: 10.1016/j.ympev.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Jayd A Adams
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Brian S Leander
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, 4200 - 6270, University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
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Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
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5
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Zepernick BN, Chase EE, Denison ER, Gilbert NE, Truchon AR, Frenken T, Cody WR, Martin RM, Chaffin JD, Bullerjahn GS, McKay RML, Wilhelm SW. Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms. THE ISME JOURNAL 2024; 18:wrad015. [PMID: 38366077 PMCID: PMC10939406 DOI: 10.1093/ismejo/wrad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007-2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly "ice-free" state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019-2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.
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Affiliation(s)
- Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Emily E Chase
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Elizabeth R Denison
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Naomi E Gilbert
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
- Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Alexander R Truchon
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Thijs Frenken
- HAS University of Applied Sciences, 5223 DE ‘s-Hertogenbosch, The Netherlands
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9C 1A2, Canada
| | - William R Cody
- Aquatic Taxonomy Specialists, Malinta, OH 43535, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Justin D Chaffin
- Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put-In-Bay, OH 43456, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9C 1A2, Canada
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
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6
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Sunda WG, Marchetti A. Proton-pumping rhodopsins promote the growth and survival of phytoplankton in a highly variable ocean. THE ISME JOURNAL 2024; 18:wrae079. [PMID: 38696358 PMCID: PMC11104272 DOI: 10.1093/ismejo/wrae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Affiliation(s)
- William G Sunda
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Adrian Marchetti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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7
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Sharma N, Shekhar P, Kumar V, Kaur H, Jayasena V. Microbial pigments: Sources, current status, future challenges in cosmetics and therapeutic applications. J Basic Microbiol 2024; 64:4-21. [PMID: 37861279 DOI: 10.1002/jobm.202300214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Color serves as the initial attraction and offers a pleasing aspect. While synthetic colorants have been popular for many years, their adverse environmental and health effects cannot be overlooked. This necessitates the search for natural colorants, especially microbial colorants, which have proven and more effective. Pigment-producing microorganisms offer substantial benefits. Natural colors improve product marketability and bestow additional benefits, including antioxidant, antiaging, anticancer, antiviral, antimicrobial, and antitumor properties. This review covers the various types of microbial pigments, the methods to enhance their production, and their cosmetic and therapeutic applications. We also address the challenges faced during the commercial production of microbial pigments and propose potential solutions.
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Affiliation(s)
- Nitin Sharma
- Chandigarh Group of Colleges, Landran, Mohali, Punjab, India
| | | | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Harpreet Kaur
- Chandigarh Group of Colleges, Landran, Mohali, Punjab, India
| | - Vijay Jayasena
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
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8
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Béjà O, Inoue K. Iron-limitation light switch. Nat Microbiol 2023; 8:1942-1943. [PMID: 37857820 DOI: 10.1038/s41564-023-01491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Affiliation(s)
- Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.
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9
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Strauss J, Deng L, Gao S, Toseland A, Bachy C, Zhang C, Kirkham A, Hopes A, Utting R, Joest EF, Tagliabue A, Löw C, Worden AZ, Nagel G, Mock T. Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans. Nat Microbiol 2023; 8:2050-2066. [PMID: 37845316 PMCID: PMC10627834 DOI: 10.1038/s41564-023-01498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Microbial rhodopsins are photoreceptor proteins that convert light into biological signals or energy. Proteins of the xanthorhodopsin family are common in eukaryotic photosynthetic plankton including diatoms. However, their biological role in these organisms remains elusive. Here we report on a xanthorhodopsin variant (FcR1) isolated from the polar diatom Fragilariopsis cylindrus. Applying a combination of biophysical, biochemical and reverse genetics approaches, we demonstrate that FcR1 is a plastid-localized proton pump which binds the chromophore retinal and is activated by green light. Enhanced growth of a Thalassiora pseudonana gain-of-function mutant expressing FcR1 under iron limitation shows that the xanthorhodopsin proton pump supports growth when chlorophyll-based photosynthesis is iron-limited. The abundance of xanthorhodopsin transcripts in natural diatom communities of the surface oceans is anticorrelated with the availability of dissolved iron. Thus, we propose that these proton pumps convey a fitness advantage in regions where phytoplankton growth is limited by the availability of dissolved iron.
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Affiliation(s)
- Jan Strauss
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
- German Maritime Centre, Hamburg, Germany.
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, France
| | - Chong Zhang
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Amy Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Utting
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Eike F Joest
- Department of Biology, Biocenter, University of Würzburg, Wuerzburg, Germany
| | | | - Christian Löw
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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Andrew SM, Moreno CM, Plumb K, Hassanzadeh B, Gomez-Consarnau L, Smith SN, Schofield O, Yoshizawa S, Fujiwara T, Sunda WG, Hopkinson BM, Septer AN, Marchetti A. Widespread use of proton-pumping rhodopsin in Antarctic phytoplankton. Proc Natl Acad Sci U S A 2023; 120:e2307638120. [PMID: 37722052 PMCID: PMC10523587 DOI: 10.1073/pnas.2307638120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/13/2023] [Indexed: 09/20/2023] Open
Abstract
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.
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Affiliation(s)
- Sarah M. Andrew
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Carly M. Moreno
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Kaylie Plumb
- Department of Marine Sciences, University of Georgia, Athens, GA30602
| | - Babak Hassanzadeh
- Department of Biological Sciences, University of Southern California, Log Angeles, CA90089
| | - Laura Gomez-Consarnau
- Department of Biological Sciences, University of Southern California, Log Angeles, CA90089
- Departamento de Oceanografía Biológica, Centro de Investigación Científca y de Educación Superior de Ensenada, Ensenada, Baja California22860, Mexico
| | - Stephanie N. Smith
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Oscar Schofield
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ08901
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
| | - Takayoshi Fujiwara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
| | - William G. Sunda
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | | | - Alecia N. Septer
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Adrian Marchetti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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11
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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12
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Ghosh M, Misra R, Bhattacharya S, Majhi K, Jung KH, Sheves M. Retinal-Carotenoid Interactions in a Sodium-Ion-Pumping Rhodopsin: Implications on Oligomerization and Thermal Stability. J Phys Chem B 2023; 127:2128-2137. [PMID: 36857147 PMCID: PMC10026069 DOI: 10.1021/acs.jpcb.2c07502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Microbial rhodopsin (also called retinal protein)-carotenoid conjugates represent a unique class of light-harvesting (LH) complexes, but their specific interactions and LH properties are not completely elucidated as only few rhodopsins are known to bind carotenoids. Here, we report a natural sodium-ion (Na+)-pumping Nonlabens (Donghaeana) dokdonensis rhodopsin (DDR2) binding with a carotenoid salinixanthin (Sal) to form a thermally stable rhodopsin-carotenoid complex. Different spectroscopic studies were employed to monitor the retinal-carotenoid interaction as well as the thermal stability of the protein, while size-exclusion chromatography (SEC) and homology modeling are performed to understand the protein oligomerization process. In analogy with that of another Na+-pumping protein Krokinobacter eikastus rhodopsin 2 (KR2), we propose that DDR2 (studied concentration range: 2 × 10-6 to 4 × 10-5 M) remains mainly as a pentamer at room temperature and neutral pH, while heating above 55 °C partially converted it into a thermally less stable oligomeric form of the protein. This process is affected by both the pH and concentration. At high concentrations (4 × 10-5 to 2 × 10-4 M), the protein adopts a pentamer form reflected in the excitonic circular dichroism (CD) spectrum. In the presence of Sal, the thermal stability of DDR2 is increased significantly, and the pigment is stable even at 85 °C. The results presented could have implications in designing stable rhodopsin-carotenoid antenna complexes.
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Affiliation(s)
- Mihir Ghosh
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ramprasad Misra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sudeshna Bhattacharya
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Koushik Majhi
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, South Korea
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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Westermann M, Hoischen C, Wöhlbrand L, Rabus R, Rhiel E. Light and prey influence the abundances of two rhodopsins in the dinoflagellate Oxyrrhis marina. PROTOPLASMA 2023; 260:529-544. [PMID: 35871098 PMCID: PMC9931815 DOI: 10.1007/s00709-022-01795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Antisera were raised against the C-terminal amino acid sequences of the two rhodopsins ADY17806 and AEA49880 of Oxyrrhis marina. The antisera and affinity-purified antibodies thereof were used in western immunoblotting experiments of total cell protein fractions from cultures grown either in darkness or in white, red, green, or blue light. Furthermore, the rhodopsin abundances were profiled in cultures fed with yeast or the prasinophyte Pyramimonas grossii. The immunosignals of ADY17806 and AEA49880 were similar when O. marina was grown in white, green, or blue light. Signal intensities were lower under conditions of red light and lowest in darkness. Higher amounts were registered for both rhodopsins when O. marina was fed with yeast compared to P. grossii. Furthermore, total cell protein of cultures of O. marina grown under all cultivation conditions was separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, followed by tryptic in-gel digestion and mass spectrometric analysis of the 25-kDa protein bands. The rhodopsin ADY17809 was detected in all samples of the light quality experiments and in 14 of the 16 samples of the prey quality experiments. The rhodopsin ABV22427 was not detected in one sample of the light quality experiments. It was detected in 15 of the 16 samples of the prey quality experiments. Peptide fragments of the other rhodopsins were detected less often, and no clear distribution pattern was evident with respect to the applied light quality or offered prey, indicating that none of them was exclusively formed under a distinct light regime or when feeding on yeast or the prasinophyte. Fluorescence light microscopy using the affinity-purified antibodies revealed significant labeling of the cell periphery and cell internal structures, which resembled vacuoles, tiny vesicles, and rather compact structures. Immunolabeling electron microscopy strengthened these results and showed that the cytoplasmic membrane, putative lysosome membranes, membranes encircling the food vacuole, and birefringent bodies became labeled.
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Affiliation(s)
- Martin Westermann
- Electron Microscopy Center of the Jena University Hospital, Friedrich-Schiller-University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University Oldenburg, P.O.B. 2503, 26129, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University Oldenburg, P.O.B. 2503, 26129, Oldenburg, Germany
| | - Erhard Rhiel
- Plankton Ecology, Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University Oldenburg, P.O.B. 2503, 26129, Oldenburg, Germany.
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14
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Otsuka K, Seike T, Toya Y, Ishii J, Hirono-Hara Y, Hara KY, Matsuda F. Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli. J Biosci Bioeng 2022; 134:484-490. [PMID: 36171161 DOI: 10.1016/j.jbiosc.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/29/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022]
Abstract
A light-driven ATP regeneration system using rhodopsin has been utilized as a method to improve the production of useful substances by microorganisms. To enable the industrial use of this system, the proton pumping rate of rhodopsin needs to be enhanced. Nonetheless, a method for this enhancement has not been established. In this study, we attempted to develop an evolutionary engineering method to improve the proton-pumping activity of rhodopsins. We first introduced random mutations into delta-rhodopsin (dR) from Haloterrigena turkmenica using error-prone PCR to generate approximately 7000 Escherichia coli strains carrying the mutant dR genes. Rhodopsin-expressing E. coli with enhanced proton pumping activity have significantly increased survival rates in prolonged saline water. Considering this, we enriched the mutant E. coli cells with higher proton pumping rates by selecting populations able to survive starvation under 50 μmol m-2 s-1 at 37 °C. As a result, we successfully identified two strains, in which proton pumping activity was enhanced two-fold by heterologous expression in E. coli in comparison to wild-type strains. The combined approach of survival testing using saline water and evolutionary engineering methods used in this study will contribute greatly to the discovery of a novel rhodopsin with improved proton pumping activity. This will facilitate the utilization of rhodopsin in industrial applications.
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Affiliation(s)
- Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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15
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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16
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Rhiel E, Hoischen C, Westermann M. Rhodopsins build up the birefringent bodies of the dinoflagellate Oxyrrhis marina. PROTOPLASMA 2022; 259:1047-1060. [PMID: 34738175 PMCID: PMC9184458 DOI: 10.1007/s00709-021-01717-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The ultrastructure of the birefringent bodies of the dinoflagellate Oxyrrhis marina was investigated by transmission electron microscopy. Ultrathin sectioning revealed that the bodies consist of highly ordered and densely packed lamellae, which show a regular striation along their longitudinal axis. A lattice distance of 6.1 nm was measured for the densely packed lamellae by FFT (Fast Fourier Transformation) analysis. In addition, a rather faint and oblique running striation was registered. Lamellae sectioned rather oblique or almost close to the surface show a honeycombed structure with a periodicity of 7.2-7.8 nm. Freeze-fracture transmission electron microscopy revealed that the lamellae are composed of highly ordered, crystalline arrays of particles. Here, FFT analysis resulted in lattice distances of 7.0-7.6 nm. Freeze-fracture transmission electron microscopy further revealed that the bodies remained intact after cell rupture followed by ascending flotation of the membrane fractions on discontinuous sucrose gradients. The birefringent bodies most likely are formed by evaginations of membranes, which separate the cytoplasm from the food vacuoles. Distinct, slightly reddish-colored areas, which resembled the birefringent bodies with respect to size and morphology, were registered by bright field light microscopy within Oxyrrhis marina cells. An absorbance maximum at 540 nm was registered for these areas, indicating that they are composed of rhodopsins. This was finally proven by immuno-transmission electron microscopy, as antisera directed against the C-terminal amino acid sequences of the rhodopsins AEA49880 and ADY17806 intensely immunolabeled the birefringent bodies of Oxyrrhis marina.
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Affiliation(s)
- Erhard Rhiel
- Plankton Ecology, Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, D-26129, Oldenburg, Germany.
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, D-07745, Jena, Germany
| | - Martin Westermann
- Electron Microscopy Center at the Jena University Hospital, Friedrich-Schiller-University Jena, Ziegelmühlenweg 1, D-07743, Jena, Germany
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17
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Effiong K, Hu J, Xu C, Zhang Y, Yu S, Tang T, Huang Y, Lu Y, Li W, Zeng J, Xiao X. 3-Indoleacrylic acid from canola straw as a promising antialgal agent - Inhibition effect and mechanism on bloom-forming Prorocentrum donghaiense. MARINE POLLUTION BULLETIN 2022; 178:113657. [PMID: 35452911 DOI: 10.1016/j.marpolbul.2022.113657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Harmful algal blooms (HABs) have induced severe damage worldwide. A novel high-efficient antialgal natural chemical, 3-indoleacrylic acid (3-IDC) with a 5-day half-maximal inhibitory concentration (IC50, 5d), was discovered from canola straw, and its algal inhibition mechanism was investigated. Adverse effects were observed on the growth of P. donghaiense with 3-IDC addition, following an increase in reactive oxygen species (ROS) production. 3-IDC also hindered the photosynthetic mechanism of P. donghaiense cells. Transcriptional results showed 3-IDC inhibiting the functions of all the nutrient assimilating genes, down-regulated ribulose-1,5-bisphosphate carboxylase/oxygenase II, and cytochrome f genes. The expression of heat shock protein (HSP) 70 and 90 and rhodopsin genes were also suppressed. The binding affinity of investigated receptors was observed. The conformational changes induced by the spatial microstructural alteration through 3-IDC may further contribute to the perturbation of those enzyme catalytic activities. The present results provide new insights on controlling HABs using 3-IDC.
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Affiliation(s)
- Kokoette Effiong
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Jing Hu
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Caicai Xu
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Yiyi Zhang
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Shumiao Yu
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Tao Tang
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Yuzhou Huang
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China
| | - Yongliang Lu
- China National Rice Research Institute, Hangzhou 310012, People's Republic of China
| | - Wei Li
- Academy of Agriculture and Forestry, Qinghai University, Xining 810016, People's Republic of China
| | - Jiangning Zeng
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, People's Republic of China
| | - Xi Xiao
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, People's Republic of China.
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18
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Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng 2022; 72:227-236. [PMID: 35346842 DOI: 10.1016/j.ymben.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
In microbial fermentative production, ATP regeneration, while crucial for cellular processes, conflicts with efficient target chemical production because ATP regeneration exhausts essential carbon sources also required for target chemical biosynthesis. To wrestle with this dilemma, we harnessed the power of microbial rhodopsins with light-driven proton pumping activity to supplement with ATP, thereby facilitating the bioproduction of various chemicals. We first demonstrated a photo-driven ATP supply and redistribution of metabolic carbon flows to target chemical synthesis by installing already-known delta rhodopsin (dR) in Escherichia coli. In addition, we identified novel rhodopsins with higher proton pumping activities than dR, and created an engineered cell for in vivo self-supply of the rhodopsin-activator, all-trans-retinal. Our concept exploiting the light-powering ATP supplier offers a potential increase in carbon use efficiency for microbial productions through metabolic reprogramming.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hidenobu Hirayama
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
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19
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Govorunova EG, Sineshchekov OA, Spudich JL. Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships. Front Cell Neurosci 2022; 15:800313. [PMID: 35140589 PMCID: PMC8818676 DOI: 10.3389/fncel.2021.800313] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) from phototactic algae have become widely used as genetically encoded molecular tools to control cell membrane potential with light. Recent advances in polynucleotide sequencing, especially in environmental samples, have led to identification of hundreds of channelrhodopsin homologs in many phylogenetic lineages, including non-photosynthetic protists. Only a few CCRs and ACRs have been characterized in detail, but there are indications that ion channel function has evolved within the rhodopsin superfamily by convergent routes. The diversity of channelrhodopsins provides an exceptional platform for the study of structure-function evolution in membrane proteins. Here we review the current state of channelrhodopsin research and outline perspectives for its further development.
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20
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Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol 2022; 2501:1-52. [PMID: 35857221 DOI: 10.1007/978-1-0716-2329-9_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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21
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Sprecher BN, Zhang H, Park G, Lin S. Isolation from a fish kill and transcriptomic characterization of Gyrodinium jinhaense off Long Island Sound. HARMFUL ALGAE 2021; 110:102136. [PMID: 34887013 DOI: 10.1016/j.hal.2021.102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
First found in Korean coastal water, the dinoflagellate Gyrodinium jinhaense is a recently established species with unclear global distribution and unexplored genomic characteristics. From a laboratory fish mortality event off Long Island Sound, USA, we isolated a dinoflagellate, and by microscopic and molecular (18S rRNA gene; >99% identical) analyses found that it resembles G. jinhaense, hence named G. jinhaense strain AP17. Towards developing a genetic database for this dinoflagellate, a transcriptome of this species was sequenced using RNA-seq, producing 6 Gbp of data that was assembled into over 70,000 unigenes. The assembled transcriptome GC content was approximately 56% and the total Benchmarking Universal Single-Copy Orthologs for Eukaryota and Alveolata databases were approximately 50% and 57%, respectfully. Genes involved in grazing, energy generation, genome architecture, and protein synthesis, processing, and degradation were highly represented in the transcriptome. Moreover, fragments of polyketide synthase and saxitoxin genes were found but saxitoxins were not detected in high performance liquid chromatography measurements. With the first reported transcriptome for the Gyrodinium genus, this study will serve as a baseline for future Gyrodinium genomics and toxicological studies.
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Affiliation(s)
- Brittany N Sprecher
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States; Current Address - University of Konstanz, Universitätsstraße 10, 78462 Konstanz, Germany.
| | - Huan Zhang
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States
| | - Gihong Park
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States
| | - Senjie Lin
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States.
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22
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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23
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Abstract
Microbial rhodopsins are diverse photoreceptive proteins containing a retinal chromophore and are found in all domains of cellular life and are even encoded in genomes of viruses. These rhodopsins make up two families: type 1 rhodopsins and the recently discovered heliorhodopsins. These families have seven transmembrane helices with similar structures but opposing membrane orientation. Microbial rhodopsins participate in a portfolio of light-driven energy and sensory transduction processes. In this review we present data collected over the last two decades about these rhodopsins and describe their diversity, functions, and biological and ecological roles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan;
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan;
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
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24
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Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity.
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25
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Kikuchi M, Kojima K, Nakao S, Yoshizawa S, Kawanishi S, Shibukawa A, Kikukawa T, Sudo Y. Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization. Sci Rep 2021; 11:14765. [PMID: 34285294 PMCID: PMC8292405 DOI: 10.1038/s41598-021-94181-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an Escherichia coli expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate Oxyrrhis marina (O. marina rhodopsin-2, OmR2) that can be expressed in E. coli cells. E. coli cells harboring the OmR2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified OmR2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-trans retinal chromophore, (2) the possession of the deprotonated counterion (pKa = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of OmR2 expressed in E. coli cells could build a basis for understanding and utilizing eukaryotic rhodopsins.
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Affiliation(s)
- Masuzu Kikuchi
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Shin Nakao
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Shiho Kawanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, GI-CoRE, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan. .,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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26
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Abstract
Rhodopsins, most of which are proton pumps generating transmembrane electrochemical proton gradients, span all three domains of life, are abundant in the biosphere, and could play a crucial role in the early evolution of life on earth. Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins, rhodopsins from unicellular eukaryotes have not been well characterized. To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach, we performed a structural and functional analysis of the light-driven proton pump LR (Mac) from the pathogenic fungus Leptosphaeria maculans. The first high-resolution structure of fungi rhodopsin and its functional properties reveal the striking similarity of its membrane part to archaeal but not to bacterial rhodopsins. We show that an unusually long N-terminal region stabilizes the protein through direct interaction with its extracellular loop (ECL2). We compare to our knowledge all available structures and sequences of outward light-driven proton pumps and show that eukaryotic and archaeal proton pumps, most likely, share a common ancestor. Zabelskii et al. present a structural and functional analysis of the lightdriven proton pump LR (Mac) from the fungus Leptosphaeria maculans. Their findings indicate that the archaeal ancestry of eukaryotic type 1 rhodopsins, and that the archaeal host of the proto-mitochondrial endosymbiont was capable of light-driven proton pumping.
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27
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Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
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28
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Labarre A, López-Escardó D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R, Massana R. Comparative genomics reveals new functional insights in uncultured MAST species. THE ISME JOURNAL 2021; 15:1767-1781. [PMID: 33452482 PMCID: PMC8163842 DOI: 10.1038/s41396-020-00885-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.
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Affiliation(s)
- Aurelie Labarre
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain.
| | - David López-Escardó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Francisco Latorre
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, UK
| | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Corinne Cruaud
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de biologie François-Jacob, Genoscope, Evry, France
| | | | - Olivier Jaillon
- Metabolic Genomics, Institut de Biologie François Jacob, Genoscope, CEA, CNRS, Univ Evry, Université Paris Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Ghent, Belgium
| | - Patrick Wincker
- Metabolic Genomics, Institut de Biologie François Jacob, Genoscope, CEA, CNRS, Univ Evry, Université Paris Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Paris, France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain.
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29
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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30
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Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nat Microbiol 2021; 6:173-186. [PMID: 33398100 DOI: 10.1038/s41564-020-00814-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023]
Abstract
Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
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31
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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32
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Rhiel E, Westermann M, Steiniger F, Hoischen C. The proteorhodopsins of the dinoflagellate Oxyrrhis marina: ultrastructure and localization by immunofluorescence light microscopy and immunoelectron microscopy. PROTOPLASMA 2020; 257:1531-1541. [PMID: 32617685 PMCID: PMC8285334 DOI: 10.1007/s00709-020-01530-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/24/2020] [Indexed: 05/26/2023]
Abstract
At least 7 proteorhodopsin sequences of Oxyrrhis marina were recently proven in bands obtained by sucrose density gradient centrifugation, and MS analyses revealed that the bands consisted almost of pure, native proteorhodopsins (Rhiel et al. 2020). The proteorhodopsin fractions, i.e., bands B2, B3, and B4 were subjected to transmission electron microscopy. Negative staining revealed that band B2 consisted most likely of monomeric/oligomeric proteorhodopsins with particle dimensions of about 6 nm. Negative staining, freeze-fracture, and cryo-transmission electron microscopy revealed that bands B3 and B4 consisted of vesicular, sheet-like, and cup-shaped structures which all seemed to be composed of protein. Frequently, ring-like protein aggregates were registered at higher magnifications. They measured about 4 nm in diameter with a tiny hole of 1.5 nm in the middle. The bands B2, B3, and B4 were pooled and used to raise an antiserum. Immunoelectron microscopy resulted in intense labeling of the isolated structures. Immunofluorescence light microscopy of formaldehyde-fixed Oxyrrhis cells resulted in intense labeling of the cell periphery. Some cell internal structures became labeled, too. Immunoelectron microscopy of freeze-fractured cells revealed that most likely the membranes of the amphiesmal vesicles were labeled at the cell periphery, while the cell internal label seemed to originate from the food vacuoles.
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Affiliation(s)
- Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111, Oldenburg, Germany.
- Planktology, ICBM, Carl von Ossietzky University Oldenburg, P. O. B. 2503, 26129, Oldenburg, Germany.
| | - Martin Westermann
- Electron Microscopy Center at the Jena University Hospital, Friedrich-Schiller-University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Frank Steiniger
- Electron Microscopy Center at the Jena University Hospital, Friedrich-Schiller-University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leipniz Institute on Aging, Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
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33
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Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol 2020; 18:56. [PMID: 32448240 PMCID: PMC7245778 DOI: 10.1186/s12915-020-00782-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.
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Affiliation(s)
- Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Yuanyuan Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, 4067, Australia
| | - David W Burt
- UQ Genomics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Pan J, Zhou Z, Béjà O, Cai M, Yang Y, Liu Y, Gu JD, Li M. Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota. MICROBIOME 2020; 8:43. [PMID: 32234071 PMCID: PMC7110647 DOI: 10.1186/s40168-020-00820-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. RESULTS In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. CONCLUSIONS The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. Video abstract.
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Affiliation(s)
- Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Rhiel E, Nguyen T, Wöhlbrand L, Rabus R. A simple protocol for the isolation of proteorhodopsins of the dinoflagellate Oxyrrhis marina. J Basic Microbiol 2020; 60:351-361. [PMID: 31960981 DOI: 10.1002/jobm.201900594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/19/2019] [Accepted: 01/07/2020] [Indexed: 11/05/2022]
Abstract
For the first time, native proteorhodopsins of the marine dinoflagellate Oxyrrhis marina were isolated. Total cell membrane fractions were minced in a bead beater and solubilized with the detergent Triton X-100. Subsequent sucrose density gradient centrifugation resulted in three or four red-colored bands. Nonsolubilized, but still red colored, membranes sedimented at the bottom. For each of these bands, absorbance maxima were registered at approximately 514-516 nm with shoulders toward shorter wavelengths (470-490 nm). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the uppermost band represented free retinal chromophore, as it contained no protein. The other bands were almost pure proteorhodopsin fractions as the banding patterns showed one major protein of 25 kDa. Tryptic, in-gel digestion of the 25 kDa proteins and of faint protein bands above and below 25 kDa was followed by mass spectrometry, confirming these protein bands to consist, nearly exclusively, proteorhodopsins. Only single peptides of few other proteins were detected. In total, at least seven predicted proteorhodopsin protein sequences were experimentally verified.
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Affiliation(s)
- Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Tien Nguyen
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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36
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Sprecher BN, Zhang H, Lin S. Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina. Microorganisms 2020; 8:E126. [PMID: 31963386 PMCID: PMC7022241 DOI: 10.3390/microorganisms8010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The lack of a robust gene transformation tool that allows proper expression of foreign genes and functional testing for the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of the fundamental biology in this ecologically important and evolutionarily unique lineage of microeukaryotes. Here, we report the development of a dinoflagellate expression vector containing various DNA elements from phylogenetically separate dinoflagellate lineages, an electroporation protocol, and successful expression of introduced genes in an early branching dinoflagellate, Oxyrrhis marina. This protocol, involving the use of Lonza's Nucleofector and a codon-optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments for O. marina. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.
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Affiliation(s)
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
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López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I. Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190088. [PMID: 31587642 PMCID: PMC6792448 DOI: 10.1098/rstb.2019.0088] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Fajardo C, Amil-Ruiz F, Fuentes-Almagro C, De Donato M, Martinez-Rodriguez G, Escobar-Niño A, Carrasco R, Mancera JM, Fernandez-Acero FJ. An “omic” approach to Pyrocystis lunula: New insights related with this bioluminescent dinoflagellate. J Proteomics 2019; 209:103502. [DOI: 10.1016/j.jprot.2019.103502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
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Misra R, Hirshfeld A, Sheves M. Molecular mechanism for thermal denaturation of thermophilic rhodopsin. Chem Sci 2019; 10:7365-7374. [PMID: 31489158 PMCID: PMC6713869 DOI: 10.1039/c9sc00855a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding the factors affecting the stability and function of proteins at the molecular level is of fundamental importance. In spite of their use in bioelectronics and optogenetics, factors influencing thermal stability of microbial rhodopsins, a class of photoreceptor protein ubiquitous in nature are not yet well-understood. Here we report on the molecular mechanism for thermal denaturation of microbial retinal proteins, including, a highly thermostable protein, thermophilic rhodopsin (TR). External stimuli-dependent thermal denaturation of TR, the proton pumping rhodopsin of Thermus thermophilus bacterium, and other microbial rhodopsins are spectroscopically studied to decipher the common factors guiding their thermal stability. The thermal denaturation process of the studied proteins is light-catalyzed and the apo-protein is thermally less stable than the corresponding retinal-covalently bound opsin. In addition, changes in structure of the retinal chromophore affect the thermal stability of TR. Our results indicate that the hydrolysis of the retinal protonated Schiff base (PSB) is the rate-determining step for denaturation of the TR as well as other retinal proteins. Unusually high thermal stability of TR multilayers, in which PSB hydrolysis is restricted due to lack of bulk water, strongly supports this proposal. Our results also show that the protonation state of the PSB counter-ion does not affect the thermal stability of the studied proteins. Thermal photo-bleaching of an artificial TR pigment derived from non-isomerizable trans-locked retinal suggests, rather counterintuitively, that the photoinduced retinal trans-cis isomerization is not a pre-requisite for light catalyzed thermal denaturation of TR. Protein conformation alteration triggered by light-induced retinal excited state formation is likely to facilitate the PSB hydrolysis.
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Affiliation(s)
- Ramprasad Misra
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Amiram Hirshfeld
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
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40
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Gómez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B, Arístegui J, Fuhrman JA, Gasol JM, Sañudo-Wilhelmy SA. Microbial rhodopsins are major contributors to the solar energy captured in the sea. SCIENCE ADVANCES 2019; 5:eaaw8855. [PMID: 31457093 PMCID: PMC6685716 DOI: 10.1126/sciadv.aaw8855] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/28/2019] [Indexed: 05/19/2023]
Abstract
All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to that of chlorophyll-a. We further show that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a-based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism. This suggests that proteorhodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean.
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Affiliation(s)
- Laura Gómez-Consarnau
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - John A. Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Biological Sciences, University of Western Australia, 25 Stirling Highway, Crawley, WA 6009, Australia
| | - Naomi M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lynda S. Cutter
- Department of Earth Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, 422 Siming Nanlu, 361005 Xiamen, China
| | - Brian Seegers
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas de Gran Canaria, Spain
| | - Jed A. Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Josep M. Gasol
- Institut de Ciències del Mar-CSIC, ES-08003 Barcelona, Catalonia, Spain
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
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Critical light-related gene expression varies in two different strains of the dinoflagellate Karlodinium veneficum in response to the light spectrum and light intensity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 194:76-83. [PMID: 30933874 DOI: 10.1016/j.jphotobiol.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 11/20/2022]
Abstract
The toxic dinoflagellate Karlodinium veneficum is widely distributed in cosmopolitan estuaries and is responsible for massive fish mortality worldwide. Intraspecific biodiversity is important for the spread to various habitats, interspecific competition to dominate a population, and bloom formation and density maintenance. Strategies for light adaptation may help determine the ecological niches of different ecotypes. However, the mechanism of phenotypic biodiversity is still unclear. In this study, intraspecific differences in genetic regulatory mechanisms in response to varied light intensities and qualities were comparatively researched on two different strains isolated from coastal areas of the East China Sea, namely, GM2 and GM3. In GM2, the expression of genes in the Calvin cycle, namely, rbcL and SBPase, and a light-related gene that correlated with cellular motility, rhodopsin, were significantly inhibited under high light intensities. Thus, this strain was adapted to low light. In contrast, the gene expression levels were promoted by high light conditions in GM3. These upregulated genes in the GM3 strain probably compensated for the negative effects on the maximum quantum yields of PSII (Fv/Fm) under high light stress, which inhibited both strains, enabling GM3 to maintain a constant growth rate. Thus, this strain was adapted to high light. Compared with white light, monochromatic blue light had negative effects on Fv/Fm and the relative electron transfer rate (ETR) in both strains. Under blue light, gene expression levels of rbcL and SBPase in GM2 were inhibited; in contrast, the levels of these genes, especially rbcL, were promoted in GM3. rbcL was significantly upregulated in the blue light groups. Monochromatic red light promoted rhodopsin gene expression in the two strains in a similar manner. These intraspecific diverse responses to light play important roles in the motor characteristics, diel vertical migration, interspecific relationships and photosynthetic or phagotrophic activities of K. veneficum and can determine the population distribution, population maintenance and bloom formation.
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Misra R, Eliash T, Sudo Y, Sheves M. Retinal-Salinixanthin Interactions in a Thermophilic Rhodopsin. J Phys Chem B 2018; 123:10-20. [PMID: 30525616 DOI: 10.1021/acs.jpcb.8b06795] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In microbial rhodopsins (also called retinal proteins), the retinal chromophore is used for harvesting light. A carotenoid molecule has been reported to complement the retinal as light harvesting antenna in bacterial retinal proteins, although examples are scarce. In this paper, we present the formation of a novel antenna complex between thermophilic rhodopsin (TR) and the carotenoid salinixanthin (Sal). The complex formation and its structure were studied using UV-visible absorption as well as circular dichroism (CD) spectroscopies. Our studies indicate that the complex is formed in both the trimeric and monomeric forms of TR. CD spectroscopy suggests that excitonic coupling takes place between retinal and Sal. The binding of Sal with artificial TR pigments derived from synthetic retinal analogues further supports the contribution of the retinal chromophore to the CD spectrum. These studies further support the possibility of interaction between the 4-keto ring of the Sal and the retinal in TR-Sal complexes. Temperature-dependent CD spectra indicate that the positive band (ca. 482 nm) of the bisignate CD spectra of the studied complexes originates from the contribution of excitonic coupling and induced chirality of Sal in the protein binding site. The presence of a relatively smaller glycine residue in the vicinity of the retinal chromophore in TR is proposed to be crucial for binding with Sal. The results are expected to shed light on the mechanism of retinal-carotenoid interactions in other biological systems.
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Affiliation(s)
- Ramprasad Misra
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Tamar Eliash
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical sciences , Okayama University , Kita-Ku, Okayama 700-8530 , Japan
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
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Faramarzi S, Feng J, Mertz B. Allosteric Effects of the Proton Donor on the Microbial Proton Pump Proteorhodopsin. Biophys J 2018; 115:1240-1250. [PMID: 30219284 DOI: 10.1016/j.bpj.2018.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 11/17/2022] Open
Abstract
Proteorhodopsin (PR) is a microbial proton pump that is ubiquitous in marine environments and may play an important role in the oceanic carbon cycle. Photoisomerization of the retinal chromophore in PR leads to a series of proton transfers between specific acidic amino acid residues and the Schiff base of retinal, culminating in a proton motive force to facilitate ATP synthesis. The proton donor in a similar retinal protein, bacteriorhodopsin, acts as a latch to allow the influx of bulk water. However, it is unclear if the proton donor in PR, E108, utilizes the same latch mechanism to become internally hydrated. Here, we used molecular dynamics simulations to model the changes in internal hydration of the blue variant of PR during photoactivation with the proton donor in protonated and deprotonated states. We find that there is a stark contrast in the levels of internal hydration of the cytoplasmic half of PR based on the protonation state of E108. Instead of a latch mechanism, deprotonation of E108 acts as a gate, taking advantage of a nearby polar residue (S61) to promote the formation of a stable water wire from bulk cytoplasm to the retinal-binding pocket over hundreds of nanoseconds. No large-scale conformational changes occur in PR over the microsecond timescale. This subtle yet clear difference in the effect of deprotonation of the proton donor in PR may help explain why the photointermediates that involve the proton donor (i.e., M and N states) have timescales that are orders of magnitude different from the archaeal proton pump, bacteriorhodopsin. In general, our study highlights the importance of understanding how structural fluctuations lead to differences in the way that retinal proteins accomplish the same task.
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Affiliation(s)
- Sadegh Faramarzi
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Jun Feng
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Blake Mertz
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia.
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Abstract
While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry. Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.
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45
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Ranjan P, Kateriya S. Localization and dimer stability of a newly identified microbial rhodopsin from a polar, non-motile green algae. BMC Res Notes 2018; 11:65. [PMID: 29361974 PMCID: PMC5781313 DOI: 10.1186/s13104-018-3181-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The eukaryotic plasma membrane localized light-gated proton-pumping rhodopsins possesses great optogenetic applications for repolarization (silencing) of the neuronal activity simply by light illumination. Very few plasma membrane localized proton-pumping rhodopsins of a eukaryotic origin are known that have optogenetic potential. Our objective was to identify and characterize microbial rhodopsin of an eukaryotic origin that expresses on plasma membrane. The plasma membrane localized light-gated proton pump of an eukaryotic origin hold great promise to be used as an optogenetic tools for the neurobiology. RESULTS Here, we had characterized the cellular expression and membrane localization of a new rhodopsin in Antarctican algae Coccomyxa subellipsoidea. It is the first algal ion pumping rhodopsin that localizes to the plasma membrane of the eukaryotic cells. Coccomyxa subellipsoidea rhodopsin exists in the monomeric and dimeric state both the in vivo and in vitro. The dimeric form of the Coccomyxa subellipsoidea rhodopsin is resistant to heat and detergent denaturants.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nat Commun 2018; 9:310. [PMID: 29358710 PMCID: PMC5778133 DOI: 10.1038/s41467-017-02235-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/15/2017] [Indexed: 11/20/2022] Open
Abstract
Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology. The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.
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Vader A, Laughinghouse HD, Griffiths C, Jakobsen KS, Gabrielsen TM. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord. Environ Microbiol 2018; 20:890-902. [PMID: 29266690 DOI: 10.1111/1462-2920.14035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 11/21/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice.
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Affiliation(s)
- Anna Vader
- University Centre in Svalbard, Longyearbyen, Norway
| | | | | | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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Jana S, Eliash T, Jung KH, Sheves M. Retinal Binding to Apo-Gloeobacter Rhodopsin: The Role of pH and Retinal-Carotenoid Interaction. J Phys Chem B 2017; 121:10759-10769. [PMID: 29111729 DOI: 10.1021/acs.jpcb.7b07523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Over the past few decades, the structure, functions, properties, and molecular mechanisms of retinal proteins have been studied extensively. The newly studied retinal protein Gloeobacter rhodopsin (gR) acts as a light-driven proton pump, transferring a proton from the cytoplasmic region to the extracellular region of a cell following light absorption. It was previously shown that gR can bind the carotenoid salinixanthin (sal). In the present study, we report the effect of pH on the binding of retinal to the apo-protein of gR, in the presence and absence of sal, to form the gR pigment. We found that binding at different pH levels reflects the titration of two different protein residues, one at the lower pKa 3.5 and another at the higher pKa 8.4, that affect the pigment's formation. The maximum amount of pigment was formed at pH 5, both with and without the presence of sal. The introduction of sal accelerates the rate of pigment formation by a factor of 190. Furthermore, it is suggested that occupation of the binding site by the retinal chromophore induces protein conformational alterations which in turn affect the carotenoid conformation, which precedes the formation of the retinal-protein covalent bond. Our examination of synthetic retinal analogues in which the ring structure was modified revealed that, in the absence of sal, the retinal ring structure affects the rate of pigment formation and that the intact structure is needed for efficient pigment formation. However, the presence of sal abolishes this effect, and all-trans retinal and its modified ring analogues bind at a similar rate.
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Affiliation(s)
- Sankar Jana
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Tamar Eliash
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University , Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
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Strassert JFH, Karnkowska A, Hehenberger E, Del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME JOURNAL 2017; 12:304-308. [PMID: 28994824 DOI: 10.1038/ismej.2017.167] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/15/2017] [Accepted: 07/27/2017] [Indexed: 11/10/2022]
Abstract
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Karnkowska
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Kolisko
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabien Burki
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan Janouškovec
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Guy Leonard
- Biosciences, University of Exeter, Exeter, UK
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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