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Albarracín VH, Kraiselburd I, Bamann C, Wood PG, Bamberg E, Farias ME, Gärtner W. Functional Green-Tuned Proteorhodopsin from Modern Stromatolites. PLoS One 2016; 11:e0154962. [PMID: 27187791 PMCID: PMC4871484 DOI: 10.1371/journal.pone.0154962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/21/2016] [Indexed: 11/18/2022] Open
Abstract
The sequenced genome of the poly-extremophile Exiguobacterium sp. S17, isolated from modern stromatolites at Laguna Socompa (3,570 m), a High-Altitude Andean Lake (HAAL) in Argentinean Puna revealed a putative proteorhodopsin-encoding gene. The HAAL area is exposed to the highest UV irradiation on Earth, making the microbial community living in the stromatolites test cases for survival strategies under extreme conditions. The heterologous expressed protein E17R from Exiguobacterium (248 amino acids, 85% sequence identity to its ortholog ESR from E. sibiricum) was assembled with retinal displaying an absorbance maximum at 524 nm, which makes it a member of the green-absorbing PR-subfamily. Titration down to low pH values (eventually causing partial protein denaturation) indicated a pK value between two and three. Global fitting of data from laser flash-induced absorption changes gave evidence for an early red-shifted intermediate (its formation being below the experimental resolution) that decayed (τ1 = 3.5 μs) into another red-shifted intermediate. This species decayed in a two-step process (τ2 = 84 μs, τ3 = 11 ms), to which the initial state of E17-PR was reformed with a kinetics of 2 ms. Proton transport capability of the HAAL protein was determined by BLM measurements. Additional blue light irradiation reduced the proton current, clearly identifying a blue light absorbing, M-like intermediate. The apparent absence of this intermediate is explained by closely matching formation and decay kinetics.
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Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET. Av. Belgrano y Pasaje Caseros. 4000- S. M. de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, 4000, S. M. de Tucumán, Argentina
- * E-mail: (VHA); (WG)
| | - Ivana Kraiselburd
- Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas (FBIOYF - UNR), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Christian Bamann
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Phillip G. Wood
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - María Eugenia Farias
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D-45470 Mülheim, Germany
- * E-mail: (VHA); (WG)
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Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree. Appl Environ Microbiol 2016; 82:2854-2861. [PMID: 26944845 DOI: 10.1128/aem.00483-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.
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Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Front Microbiol 2016; 7:211. [PMID: 26941731 PMCID: PMC4766312 DOI: 10.3389/fmicb.2016.00211] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/08/2016] [Indexed: 11/13/2022] Open
Abstract
Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.
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Affiliation(s)
- Charlotte D. Vavourakis
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
- Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of HydrobiologyČeské Budějovice, Czech Republic
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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Real-time kinetics of electrogenic Na(+) transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95. Sci Rep 2016; 6:21397. [PMID: 26864904 PMCID: PMC4749991 DOI: 10.1038/srep21397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/08/2016] [Indexed: 12/14/2022] Open
Abstract
Discovery of the light-driven sodium-motive pump Na+-rhodopsin (NaR) has initiated studies of the molecular mechanism of this novel membrane-linked energy transducer. In this paper, we investigated the photocycle of NaR from the marine flavobacterium Dokdonia sp. PRO95 and identified electrogenic and Na+-dependent steps of this cycle. We found that the NaR photocycle is composed of at least four steps: NaR519 + hv → K585 → (L450↔M495) → O585 → NaR519. The third step is the only step that depends on the Na+ concentration inside right-side-out NaR-containing proteoliposomes, indicating that this step is coupled with Na+ binding to NaR. For steps 2, 3, and 4, the values of the rate constants are 4×104 s–1, 4.7 × 103 M–1 s–1, and 150 s–1, respectively. These steps contributed 15, 15, and 70% of the total membrane electric potential (Δψ ~ 200 mV) generated by a single turnover of NaR incorporated into liposomes and attached to phospholipid-impregnated collodion film. On the basis of these observations, a mechanism of light-driven Na+ pumping by NaR is suggested.
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Kwon YM, Kim S, Jung K, Kim S. Diversity and functional analysis of light-driven pumping rhodopsins in marine Flavobacteria. Microbiologyopen 2015; 5:212-23. [PMID: 26663527 PMCID: PMC4831467 DOI: 10.1002/mbo3.321] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 12/13/2022] Open
Abstract
The aims of this study are the description of diversity for proteorhodopsin (PR)-containing flavobacteria in marine environments, the finding of novel photoreceptive membrane proteins, and the elucidation of the effect of light on the growth of three rhodopsin genes containing flavobacterium. We investigated novel sodium ion rhodopsin (NaR) and halorhodopsin (HR) genes from PR-containing flavobacteria that were previously isolated from diverse aquatic sites, mainly from tidal flat sediment (62.5%). In 16 PR-containing isolates, three new types of genes were found. Among these three isolates, one (Nonlabens sp. YIK11 isolated from sediment) contained both the NaR and chloride ion rhodopsin (ClR) - HR type of gene. The sequences showed that the DTE (proton pump), NDQ (sodium ion pump) and NTQ (chloride ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR) were well conserved. Phylogenetic analysis indicated that three NaR and one ClR grouped within the same clade, as previously reported. Illumination of cell suspensions showed the change in proton pump activity, supporting that one or more rhodopsins are functional. The qRT-PCR study revealed that three rhodopsin genes, especially NaR, are highly induced when they are incubated in the presence of light or in the absence of sufficient nutrients. The expression levels of the DTE, NDQ, and NTQ motif-containing rhodopsin genes in YIK11 correlate positively with illumination, but negatively with nutrient levels. Based on those results, we concluded that light has a positive impact on the relative expression levels of the three rhodopsin genes in the flavobacterium, Nonlabens sp. YIK11, but with no apparent positive impact on growth. Consequently, light did not stimulate the growth of YIK11 as determined by cell numbers in a nutrient-limited or -enriched medium, although it contains and induces three rhodopsins.
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Affiliation(s)
- Yong Min Kwon
- Marine Biotechnology Research CenterKorea Institute of Ocean Science & Technology787 HaeanroAnsan426‐744Korea
| | - So‐Young Kim
- Department of Life Science and Institute of Biological ScienceSogang University35 Baekbeom‐RoMapo‐GuSeoul121‐742Korea
| | - Kwang‐Hwan Jung
- Department of Life Science and Institute of Biological ScienceSogang University35 Baekbeom‐RoMapo‐GuSeoul121‐742Korea
| | - Sang‐Jin Kim
- Marine Biotechnology Research CenterKorea Institute of Ocean Science & Technology787 HaeanroAnsan426‐744Korea
- Marine Biodiversity Institute of KoreaSeocheon325‐902Korea
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Gushchin I, Shevchenko V, Polovinkin V, Borshchevskiy V, Buslaev P, Bamberg E, Gordeliy V. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 2015; 283:1232-8. [DOI: 10.1111/febs.13585] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/22/2015] [Accepted: 10/30/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
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Kwon SK, Lee HG, Kwak MJ, Kim JF. Genome sequence of the marine flavobacterium Croceitalea dokdonensis DOKDO 023 that contains proton- and sodium-pumping rhodopsins. Mar Genomics 2015; 26:1-3. [PMID: 26631417 DOI: 10.1016/j.margen.2015.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 11/21/2015] [Accepted: 11/21/2015] [Indexed: 11/19/2022]
Abstract
Bacteroidetes are considered as efficient degraders of the high-molecular-weight particulate organic matter that is present in the marine environment. Here, we report the first genome sequence of the genus Croceitalea that belongs to Flavobacteriia. Gratifying the reputation, the genome of Croceitalea dokdonensis DOKDO 023 encodes many hydrolytic enzymes for utilizing biopolymers, mainly polysaccharides and proteins. The genome also harbors two genes for microbial rhodopsins, proteorhodopsin and a recently discovered sodium pump. This research provides a genetic basis for better understanding of Croceitalea, as well as insights into the strategies adapted by a rhodopsin-containing photoheterotroph to thrive in the marine environment.
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Affiliation(s)
- Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 120-749, Republic of Korea
| | - Hyun Gwon Lee
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 120-749, Republic of Korea
| | - Min-Jung Kwak
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 120-749, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 120-749, Republic of Korea.
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Boeuf D, Audic S, Brillet-Guéguen L, Caron C, Jeanthon C. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav080. [PMID: 26286928 PMCID: PMC4539915 DOI: 10.1093/database/bav080] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/25/2015] [Indexed: 11/12/2022]
Abstract
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr.
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Affiliation(s)
- Dominique Boeuf
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group, CNRS, UMR 7144, Team Evolution des Protistes et Ecosystèmes Pélagiques and
| | | | - Christophe Caron
- CNRS, UPMC, FR2424, ABiMS, Station Biologique de Roscoff, F-29680 Roscoff, France
| | - Christian Jeanthon
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group,
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Inoue K, Kato Y, Kandori H. Light-driven ion-translocating rhodopsins in marine bacteria. Trends Microbiol 2015; 23:91-8. [PMID: 25432080 DOI: 10.1016/j.tim.2014.10.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/14/2014] [Accepted: 10/27/2014] [Indexed: 12/25/2022]
Abstract
Microbial rhodopsins are the photoreceptive membrane proteins found in diverse microorganisms from within Archaea, Eubacteria, and eukaryotes. They have a hep-tahelical transmembrane structure that binds to an all-trans retinal chromophore. Since 2000, thousands of proteorhodopsins, genes of light-driven proton pump rhodopsins, have been identified from various species of marine bacteria. This suggests that they are used for the conversion of light into chemical energy, contribut-ing to carbon circulation related to ATP synthesis in the ocean. Furthermore, novel types of rhodopsin (sodium and chloride pumps) have recently been discovered. Here, we review recent progress in our understanding of ion-transporting rhodopsins of marine bacteria, based mainly on biophysical and biochemical research.
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da Silva GFZ, Goblirsch BR, Tsai AL, Spudich JL. Cation-Specific Conformations in a Dual-Function Ion-Pumping Microbial Rhodopsin. Biochemistry 2015; 54:3950-9. [PMID: 26037033 DOI: 10.1021/bi501386d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A recently discovered rhodopsin ion pump (DeNaR, also known as KR2) in the marine bacterium Dokdonia eikasta uses light to pump protons or sodium ions from the cell depending on the ionic composition of the medium. In cells suspended in a KCl solution, DeNaR functions as a light-driven proton pump, whereas in a NaCl solution, DeNaR conducts light-driven sodium ion pumping, a novel activity within the rhodopsin family. These two distinct functions raise the questions of whether the conformations of the protein differ in the presence of K(+) or Na(+) and whether the helical movements that result in the canonical E → C conformational change in other microbial rhodopsins are conserved in DeNaR. Visible absorption maxima of DeNaR in its unphotolyzed (dark) state show an 8 nm difference between Na(+) and K(+) in decyl maltopyranoside micelles, indicating an influence of the cations on the retinylidene photoactive site. In addition, electronic paramagnetic resonance (EPR) spectra of the dark states reveal repositioning of helices F and G when K(+) is replaced with Na(+). Furthermore, the conformational changes assessed by EPR spin-spin dipolar coupling show that the light-induced transmembrane helix movements are very similar to those found in bacteriorhodopsin but are altered by the presence of Na(+), resulting in a new feature, the clockwise rotation of helix F. The results establish the first observation of a cation switch controlling the conformations of a microbial rhodopsin and indicate specific interactions of Na(+) with the half-channels of DeNaR to open an appropriate path for ion translocation.
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Affiliation(s)
- Giordano F Z da Silva
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
| | - Brandon R Goblirsch
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
| | - Ah-Lim Tsai
- ‡Department of Internal Medicine, Division of Hematology, University of Texas Medical School, Houston, Texas 77030, United States
| | - John L Spudich
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
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Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6. Enzyme Microb Technol 2015; 77:29-37. [PMID: 26138397 DOI: 10.1016/j.enzmictec.2015.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 11/22/2022]
Abstract
The γ-carotenoids, such as myxol and saproxanthin, have a high potential to be utilized in nutraceutical and pharmaceutical industries for their neuro-protective and antioxidant effects. CrtD is involved in the production of γ-carotenoids by desaturating the C3'-C4' position of 1'-OH-γ-carotenoid. We determined the crystal structure of CrtD from Nonlabens dokdonensis DSW-6 (NdCrtD), the first structure of CrtD family enzymes. The NdCrtD structure was composed of two distinct domains, an FAD-binding domain and a substrate-binding domain, and the substrate-binding domain can be divided into two subdomains, a Rossmann fold-like subdomain and a lid subdomain. Although the FAD-binding domain showed a structure similar to canonical FAD-containing enzymes, the substrate-binding domain exhibited a novel structure to constitute a long and hydrophobic tunnel with a length of ∼40 Å. The molecular docking-simulation reveals that the tunnel provides an appropriate substrate-binding site for the carotenoid such as 1'-OH-γ-carotene with a length of ∼35 Å. We could predict residues related to recognize the 1'-hydroxyl group and to stabilize the hydrophobic end without hydroxyl group. Moreover, we suggest that the flexible entrance loop may undergo an open-closed formational change during the binding of the substrate.
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Bertsova YV, Bogachev AV, Skulachev VP. Proteorhodopsin from Dokdonia sp. PRO95 is a light-driven Na+-pump. BIOCHEMISTRY (MOSCOW) 2015; 80:449-54. [DOI: 10.1134/s0006297915040082] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Gushchin I, Shevchenko V, Polovinkin V, Kovalev K, Alekseev A, Round E, Borshchevskiy V, Balandin T, Popov A, Gensch T, Fahlke C, Bamann C, Willbold D, Büldt G, Bamberg E, Gordeliy V. Crystal structure of a light-driven sodium pump. Nat Struct Mol Biol 2015; 22:390-5. [PMID: 25849142 DOI: 10.1038/nsmb.3002] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/09/2015] [Indexed: 11/09/2022]
Abstract
Recently, the first known light-driven sodium pumps, from the microbial rhodopsin family, were discovered. We have solved the structure of one of them, Krokinobacter eikastus rhodopsin 2 (KR2), in the monomeric blue state and in two pentameric red states, at resolutions of 1.45 Å and 2.2 and 2.8 Å, respectively. The structures reveal the ion-translocation pathway and show that the sodium ion is bound outside the protein at the oligomerization interface, that the ion-release cavity is capped by a unique N-terminal α-helix and that the ion-uptake cavity is unexpectedly large and open to the surface. Obstruction of the cavity with the mutation G263F imparts KR2 with the ability to pump potassium. These results pave the way for the understanding and rational design of cation pumps with new specific properties valuable for optogenetics.
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Affiliation(s)
- Ivan Gushchin
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Vitaly Shevchenko
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany. [3] Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Polovinkin
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Kirill Kovalev
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Alexey Alekseev
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Valentin Borshchevskiy
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | | | - Thomas Gensch
- ICS, ICS-4, Cellular Biophysics, Research Center Jülich, Jülich, Germany
| | - Christoph Fahlke
- ICS, ICS-4, Cellular Biophysics, Research Center Jülich, Jülich, Germany
| | | | - Dieter Willbold
- 1] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany. [2] Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Georg Büldt
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] ICS, ICS-5, Molecular Biophysics, Research Center Jülich, Jülich, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
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64
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Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark. Curr Opin Microbiol 2015; 25:33-9. [PMID: 25863027 DOI: 10.1016/j.mib.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/07/2015] [Accepted: 03/16/2015] [Indexed: 11/24/2022]
Abstract
Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of -omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant functional genes in the sunlit ocean.
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65
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Using total internal reflection fluorescence microscopy to visualize rhodopsin-containing cells. Appl Environ Microbiol 2015; 81:3442-50. [PMID: 25769822 DOI: 10.1128/aem.00230-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/04/2015] [Indexed: 01/03/2023] Open
Abstract
Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low-comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls-these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria. Escherichia coli cells were engineered to produce lycopene, β-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing E. coli. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in E. coli and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.
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66
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Zhang Y, Liu J, Tang K, Yu M, Coenye T, Zhang XH. Genome analysis of Flaviramulus ichthyoenteri Th78(T) in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine. BMC Genomics 2015; 16:38. [PMID: 25652846 PMCID: PMC4324048 DOI: 10.1186/s12864-015-1275-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/22/2015] [Indexed: 12/04/2022] Open
Abstract
Background Intestinal microbes play significant roles in fish and can be possibly used as probiotics in aquaculture. In our previous study, Flaviramulus ichthyoenteri Th78T, a novel species in the family Flavobacteriaceae, was isolated from fish intestine and showed strong quorum quenching (QQ) ability. To identify the QQ enzymes in Th78T and explore the potential roles of Th78T in fish intestine, we sequenced the genome of Th78T and performed extensive genomic analysis. Results An N-acyl homoserine lactonase FiaL belonging to the metallo-β-lactamase superfamily was identified and the QQ activity of heterologously expressed FiaL was confirmed in vitro. FiaL has relatively little similarity to the known lactonases (25.2 ~ 27.9% identity in amino acid sequence). Various digestive enzymes including alginate lyases and lipases can be produced by Th78T, and enzymes essential for production of B vitamins such as biotin, riboflavin and folate are predicted. Genes encoding sialic acid lyases, sialidases, sulfatases and fucosidases, which contribute to utilization of mucus, are present in the genome. In addition, genes related to response to different stresses and gliding motility were also identified. Comparative genome analysis shows that Th78T has more specific genes involved in carbohydrate transport and metabolism compared to other two isolates in Flavobacteriaceae, both isolated from sediments. Conclusions The genome of Th78T exhibits evident advantages for this bacterium to survive in the fish intestine, including production of QQ enzyme, utilization of various nutrients available in the intestine as well as the ability to produce digestive enzymes and vitamins, which also provides an application prospect of Th78T to be used as a probiotic in aquaculture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1275-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China.
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China.
| | - Kaihao Tang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China.
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China.
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, 9000, Gent, Belgium.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China.
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67
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Balashov SP, Imasheva ES, Dioumaev A, Wang JM, Jung KH, Lanyi JK. Light-driven Na(+) pump from Gillisia limnaea: a high-affinity Na(+) binding site is formed transiently in the photocycle. Biochemistry 2014; 53:7549-61. [PMID: 25375769 PMCID: PMC4263435 DOI: 10.1021/bi501064n] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/17/2014] [Indexed: 02/06/2023]
Abstract
A group of microbial retinal proteins most closely related to the proton pump xanthorhodopsin has a novel sequence motif and a novel function. Instead of, or in addition to, proton transport, they perform light-driven sodium ion transport, as reported for one representative of this group (KR2) from Krokinobacter. In this paper, we examine a similar protein, GLR from Gillisia limnaea, expressed in Escherichia coli, which shares some properties with KR2 but transports only Na(+). The absorption spectrum of GLR is insensitive to Na(+) at concentrations of ≤3 M. However, very low concentrations of Na(+) cause profound differences in the decay and rise time of photocycle intermediates, consistent with a switch from a "Na(+)-independent" to a "Na(+)-dependent" photocycle (or photocycle branch) at ∼60 μM Na(+). The rates of photocycle steps in the latter, but not the former, are linearly dependent on Na(+) concentration. This suggests that a high-affinity Na(+) binding site is created transiently after photoexcitation, and entry of Na(+) from the bulk to this site redirects the course of events in the remainder of the cycle. A greater concentration of Na(+) is needed for switching the reaction path at lower pH. The data suggest therefore competition between H(+) and Na(+) to determine the two alternative pathways. The idea that a Na(+) binding site can be created at the Schiff base counterion is supported by the finding that upon perturbation of this region in the D251E mutant, Na(+) binds without photoexcitation. Binding of Na(+) to the mutant shifts the chromophore maximum to the red like that of H(+), which occurs in the photocycle of the wild type.
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Affiliation(s)
- Sergei P. Balashov
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Eleonora S. Imasheva
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Andrei
K. Dioumaev
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Jennifer M. Wang
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Kwang-Hwan Jung
- Department
of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, Korea
| | - Janos K. Lanyi
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
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68
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A marine inducible prophage vB_CibM-P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354. Sci Rep 2014; 4:7118. [PMID: 25406510 PMCID: PMC4236739 DOI: 10.1038/srep07118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/30/2014] [Indexed: 12/01/2022] Open
Abstract
A prophage vB_CibM-P1 was induced by mitomycin C from the epipelagic strain Citromicrobium bathyomarinum JL354, a member of the alpha-IV subcluster of marine aerobic anoxygenic phototrophic bacteria (AAPB). The induced bacteriophage vB_CibM-P1 had Myoviridae-like morphology and polyhedral heads (approximately capsid 60–100 nm) with tail fibers. The vB_CibM-P1 genome is ~38 kb in size, with 66.0% GC content. The genome contains 58 proposed open reading frames that are involved in integration, DNA packaging, morphogenesis and bacterial lysis. VB_CibM-P1 is a temperate phage that can be directly induced in hosts. In response to mitomycin C induction, virus-like particles can increase to 7 × 109 per ml, while host cells decrease an order of magnitude. The vB_CibM-P1 bacteriophage is the first inducible prophage from AAPB.
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69
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Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01165-14. [PMID: 25395639 PMCID: PMC4241665 DOI: 10.1128/genomea.01165-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here, we present the draft genome sequences of six carotenoid producers affiliated with Nonlabens spp. isolated from marine environments in both the northern and southern parts of Japan. The genomic information will help to elucidate the function and evolution of carotenoid synthetic gene clusters not only in the genus Nonlabens but also in the family Flavobacteriaceae.
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70
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Gorriti MF, Dias GM, Chimetto LA, Trindade-Silva AE, Silva BS, Mesquita MMA, Gregoracci GB, Farias ME, Thompson CC, Thompson FL. Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake. BMC Genomics 2014; 15:473. [PMID: 24927949 PMCID: PMC4094778 DOI: 10.1186/1471-2164-15-473] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 06/06/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. We obtained three novel conspecific Salinivibrio strains closely related to S. costicola, from Socompa Lake, a high altitude hypersaline Andean lake (approx. 3,570 meters above the sea level). RESULTS The three novel Salinivibrio spp. were extremely resistant to arsenic (up to 200 mM HAsO42-), NaCl (up to 15%), and UV-B radiation (19 KJ/m2, corresponding to 240 minutes of exposure) by means of phenotypic tests. Our subsequent draft genome ionsequencing and RAST-based genome annotation revealed the presence of genes related to arsenic, NaCl, and UV radiation resistance. The three novel Salinivibrio genomes also had the xanthorhodopsin gene cluster phylogenetically related to Marinobacter and Spiribacter. The genomic taxonomy analysis, including multilocus sequence analysis, average amino acid identity, and genome-to-genome distance revealed that the three novel strains belong to a new Salinivibrio species. CONCLUSIONS Arsenic resistance genes, genes involved in DNA repair, resistance to extreme environmental conditions and the possible light-based energy production, may represent important attributes of the novel salinivibrios, allowing these microbes to thrive in the Socompa Lake.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fabiano L Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil.
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72
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Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc Natl Acad Sci U S A 2014; 111:6732-7. [PMID: 24706784 DOI: 10.1073/pnas.1403051111] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-activated, ion-pumping rhodopsins are broadly distributed among many different bacteria and archaea inhabiting the photic zone of aquatic environments. Bacterial proton- or sodium-translocating rhodopsins can convert light energy into a chemiosmotic force that can be converted into cellular biochemical energy, and thus represent a widespread alternative form of photoheterotrophy. Here we report that the genome of the marine flavobacterium Nonlabens marinus S1-08(T) encodes three different types of rhodopsins: Nonlabens marinus rhodopsin 1 (NM-R1), Nonlabens marinus rhodopsin 2 (NM-R2), and Nonlabens marinus rhodopsin 3 (NM-R3). Our functional analysis demonstrated that NM-R1 and NM-R2 are light-driven outward-translocating H(+) and Na(+) pumps, respectively. Functional analyses further revealed that the light-activated NM-R3 rhodopsin pumps Cl(-) ions into the cell, representing the first chloride-pumping rhodopsin uncovered in a marine bacterium. Phylogenetic analysis revealed that NM-R3 belongs to a distinct phylogenetic lineage quite distant from archaeal inward Cl(-)-pumping rhodopsins like halorhodopsin, suggesting that different types of chloride-pumping rhodopsins have evolved independently within marine bacterial lineages. Taken together, our data suggest that similar to haloarchaea, a considerable variety of rhodopsin types with different ion specificities have evolved in marine bacteria, with individual marine strains containing as many as three functionally different rhodopsins.
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 771] [Impact Index Per Article: 77.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent. ISME JOURNAL 2013; 7:2206-13. [PMID: 23788334 PMCID: PMC3806269 DOI: 10.1038/ismej.2013.97] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/15/2013] [Accepted: 05/16/2013] [Indexed: 12/27/2022]
Abstract
Proteorhodopsins (PRs) are commonly found in marine prokaryotes and allow microbes to use light as an energy source. In recent studies, it was reported that PR stimulates growth and survival under nutrient-limited conditions. In this study, we tested the effect of nutrient and salinity stress on the extremely psychrophilic sea-ice bacterial species Psychroflexus torquis, which possesses PR. We demonstrated for the first time that light-stimulated growth occurs under conditions of salinity stress rather than nutrient limitation and that elevated salinity is related to increased growth yields, PR levels and associated proton-pumping activity. PR abundance in P. torquis also is post-transcriptionally regulated by both light and salinity and thus could represent an adaptation to its sea-ice habitat. Our findings extend the existing paradigm that light provides an energy source for marine prokaryotes under stress conditions other than nutrient limitation.
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75
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Brown LS. Eubacterial rhodopsins - unique photosensors and diverse ion pumps. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:553-61. [PMID: 23748216 DOI: 10.1016/j.bbabio.2013.05.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Since the discovery of proteorhodopsins, the ubiquitous marine light-driven proton pumps of eubacteria, a large number of other eubacterial rhodopsins with diverse structures and functions have been characterized. Here, we review the body of knowledge accumulated on the four major groups of eubacterial rhodopsins, with the focus on their biophysical characterization. We discuss advances and controversies on the unique eubacterial sensory rhodopsins (as represented by Anabaena sensory rhodopsin), proton-pumping proteorhodopsins and xanthorhodopsins, as well as novel non-proton ion pumps. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario N1G 2W1, Canada.
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76
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Inoue K, Ono H, Abe-Yoshizumi R, Yoshizawa S, Ito H, Kogure K, Kandori H. A light-driven sodium ion pump in marine bacteria. Nat Commun 2013; 4:1678. [DOI: 10.1038/ncomms2689] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/01/2013] [Indexed: 11/09/2022] Open
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