101
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Polka JK, Hays SG, Silver PA. Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a024018. [PMID: 27270297 DOI: 10.1101/cshperspect.a024018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses.
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Affiliation(s)
- Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Stephanie G Hays
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
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102
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Lyndby NH, Kühl M, Wangpraseurt D. Heat generation and light scattering of green fluorescent protein-like pigments in coral tissue. Sci Rep 2016; 6:26599. [PMID: 27225857 PMCID: PMC4880895 DOI: 10.1038/srep26599] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022] Open
Abstract
Green fluorescent protein (GFP)-like pigments have been proposed to have beneficial effects on coral photobiology. Here, we investigated the relationships between green fluorescence, coral heating and tissue optics for the massive coral Dipsastraea sp. (previously Favia sp.). We used microsensors to measure tissue scalar irradiance and temperature along with hyperspectral imaging and combined imaging of variable chlorophyll fluorescence and green fluorescence. Green fluorescence correlated positively with coral heating and scalar irradiance enhancement at the tissue surface. Coral tissue heating saturated for maximal levels of green fluorescence. The action spectrum of coral surface heating revealed that heating was highest under red (peaking at 680 nm) irradiance. Scalar irradiance enhancement in coral tissue was highest when illuminated with blue light, but up to 62% (for the case of highest green fluorescence) of this photon enhancement was due to green fluorescence emission. We suggest that GFP-like pigments scatter the incident radiation, which enhances light absorption and heating of the coral. However, heating saturates, because intense light scattering reduces the vertical penetration depth through the tissue eventually leading to reduced light absorption at high fluorescent pigment density. We conclude that fluorescent pigments can have a central role in modulating coral light absorption and heating.
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Affiliation(s)
- Niclas H Lyndby
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark.,Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, New South Wales 2007, Australia
| | - Daniel Wangpraseurt
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark.,Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, New South Wales 2007, Australia
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103
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Aihara Y, Takahashi S, Minagawa J. Heat Induction of Cyclic Electron Flow around Photosystem I in the Symbiotic Dinoflagellate Symbiodinium. PLANT PHYSIOLOGY 2016; 171:522-9. [PMID: 26951432 PMCID: PMC4854689 DOI: 10.1104/pp.15.01886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/07/2016] [Indexed: 05/05/2023]
Abstract
Increases in seawater temperature impair photosynthesis (photoinhibition) in the symbiotic dinoflagellate Symbiodinium within cnidarian hosts, such as corals and sea anemones, and may destroy their symbiotic relationship. Although the degree of photoinhibition in Symbiodinium under heat stress differs among strains, the differences in their responses to increased temperatures, including cyclic electron flow (CEF), which sustains photoprotective thermal energy dissipation, have not been investigated. Here, we examined CEF in cultured Symbiodinium cells or those in an endosymbiotic relationship within a cnidarian host. The light-dependent reduction of the primary electron donor photosystem I, i.e. P700(+), was enhanced in any Symbiodinium cell by increasing temperatures, indicating CEF was induced by heat, which was accompanied by thermal energy dissipation activation. The critical temperatures for inducing CEF were different among Symbiodinium strains. The clade A strains with greater susceptibility to photoinhibition, OTcH-1 and Y106, exhibited higher CEF activities under moderate heat stress than a more phototolerant clade B strain Mf1.05b, suggesting that the observed CEF induction was not a preventive measure but a stress response in Symbiodinium.
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Affiliation(s)
- Yusuke Aihara
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan (Y.A., S.T., J.M.); andDepartment of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan (S.T., J.M.)
| | - Shunichi Takahashi
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan (Y.A., S.T., J.M.); andDepartment of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan (S.T., J.M.)
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan (Y.A., S.T., J.M.); andDepartment of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan (S.T., J.M.)
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104
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Rodriguez IB, Lin S, Ho J, Ho TY. Effects of Trace Metal Concentrations on the Growth of the Coral Endosymbiont Symbiodinium kawagutii. Front Microbiol 2016; 7:82. [PMID: 26903964 PMCID: PMC4744903 DOI: 10.3389/fmicb.2016.00082] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
Symbiodinium is an indispensable endosymbiont in corals and the most important primary producer in coral reef ecosystems. During the past decades, coral bleaching attributed to the disruption of the symbiosis has frequently occurred resulting in reduction of coral reef coverage globally. Growth and proliferation of corals require some specific trace metals that are essential components of pertinent biochemical processes, such as in photosynthetic systems and electron transport chains. In addition, trace metals are vital in the survival of corals against oxidative stress because these metals serve as enzymatic cofactors in antioxidative defense mechanisms. The basic knowledge about trace metal requirements of Symbiodinium is lacking. Here we show that the requirement of Symbiodinium kawagutii for antioxidant-associated trace metals exhibits the following order: Fe >> Cu/Zn/Mn >> Ni. In growth media with Cu, Zn, Mn, and varying Fe concentrations, we observed that Cu, Zn, and Mn cellular quotas were inversely related to Fe concentrations. In the absence of Cu, Zn, and Mn, growth rates increased with increasing inorganic Fe concentrations up to 1250 pM, indicating the relatively high Fe requirement for Symbiodinium growth and potential functional complementarity of these metals. These results demonstrate the relative importance of trace metals to sustain Symbiodinium growth and a potential metal inter replacement strategy in Symbiodinium to ensure survival of coral reefs in an oligotrophic and stressful environment.
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Affiliation(s)
- Irene B Rodriguez
- Research Center for Environmental Changes, Academia Sinica Taipei, Taiwan
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China; Department of Marine Sciences, University of Connecticut, GrotonCT, USA
| | - Jiaxuan Ho
- Research Center for Environmental Changes, Academia SinicaTaipei, Taiwan; School of Marine Sciences and Engineering, Plymouth UniversityDevon, UK
| | - Tung-Yuan Ho
- Research Center for Environmental Changes, Academia Sinica Taipei, Taiwan
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105
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Jones R, Bessell-Browne P, Fisher R, Klonowski W, Slivkoff M. Assessing the impacts of sediments from dredging on corals. MARINE POLLUTION BULLETIN 2016; 102:9-29. [PMID: 26654296 DOI: 10.1016/j.marpolbul.2015.10.049] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
There is a need to develop water quality thresholds for dredging near coral reefs that can relate physical pressures to biological responses and define exposure conditions above which effects could occur. Water quality characteristics during dredging have, however, not been well described. Using information from several major dredging projects, we describe sediment particle sizes in the water column/seabed, suspended sediment concentrations at different temporal scales during natural and dredging-related turbidity events, and changes in light quantity/quality underneath plumes. These conditions differ considerably from those used in past laboratory studies of the effects of sediments on corals. The review also discusses other problems associated with using information from past studies for developing thresholds such as the existence of multiple different and inter-connected cause-effect pathways (which can confuse/confound interpretations), the use of sediment proxies, and the reliance on information from sediment traps to justify exposure regimes in sedimentation experiments.
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Affiliation(s)
- Ross Jones
- Australian Institute of Marine Science (AIMS), Perth, Australia; Western Australian Marine Science Institution, Perth, Australia.
| | - Pia Bessell-Browne
- Australian Institute of Marine Science (AIMS), Perth, Australia; Centre of Microscopy, Charaterisation and Analysis, The University of Western Australia, Perth, Australia; Western Australian Marine Science Institution, Perth, Australia
| | - Rebecca Fisher
- Australian Institute of Marine Science (AIMS), Perth, Australia; Curtin University, Bentley, Perth, Australia
| | - Wojciech Klonowski
- Curtin University, Bentley, Perth, Australia; In situ Marine Optics, Bibra Lake, Perth, Australia
| | - Matthew Slivkoff
- Curtin University, Bentley, Perth, Australia; In situ Marine Optics, Bibra Lake, Perth, Australia
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106
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Suggett DJ, Goyen S, Evenhuis C, Szabó M, Pettay DT, Warner ME, Ralph PJ. Functional diversity of photobiological traits within the genus Symbiodinium appears to be governed by the interaction of cell size with cladal designation. THE NEW PHYTOLOGIST 2015; 208:370-81. [PMID: 26017701 DOI: 10.1111/nph.13483] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/23/2015] [Indexed: 05/13/2023]
Abstract
Dinoflagellates of the genus Symbiodinium express broad diversity in both genetic identity (phylogeny) and photosynthetic function to presumably optimize ecological success across extreme light environments; however, whether differences in the primary photobiological characteristics that govern photosynthetic optimization are ultimately a function of phylogeny is entirely unresolved. We applied a novel fast repetition rate fluorometry approach to screen genetically distinct Symbiodinium types (n = 18) spanning five clades (A-D, F) for potential phylogenetic trends in factors modulating light absorption (effective cross-section, reaction center content) and utilization (photochemical vs dynamic nonphotochemical quenching; [1 - C] vs [1 - Q]) by photosystem II (PSII). The variability of PSII light absorption was independent of phylogenetic designation, but closely correlated with cell size across types, whereas PSII light utilization intriguingly followed one of three characteristic patterns: (1) similar reliance on [1 - C] and [1 - Q] or (2) preferential reliance on [1 - C] (mostly A, B types) vs (3) preferential reliance on [1 - Q] (mostly C, D, F types), and thus generally consistent with cladal designation. Our functional trait-based approach shows, for the first time, how Symbiodinium photosynthetic function is governed by the interplay between phylogenetically dependent and independent traits, and is potentially a means to reconcile complex biogeographic patterns of Symbiodinium phylogenetic diversity in nature.
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Affiliation(s)
- David J Suggett
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Broadway, 2007, NSW, Australia
| | - Samantha Goyen
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Broadway, 2007, NSW, Australia
| | - Chris Evenhuis
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Broadway, 2007, NSW, Australia
| | - Milán Szabó
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Broadway, 2007, NSW, Australia
| | - D Tye Pettay
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, 19958, USA
| | - Mark E Warner
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, 19958, USA
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Broadway, 2007, NSW, Australia
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107
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Jiang J, Zhang H, Lu X, Lu Y, Cuneo MJ, O'Neill HM, Urban V, Lo CS, Blankenship RE. Oligomerization state and pigment binding strength of the peridinin-Chl a-protein. FEBS Lett 2015; 589:2713-9. [PMID: 26241331 DOI: 10.1016/j.febslet.2015.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 11/28/2022]
Abstract
The peridinin-chlorophyll a-protein (PCP) is one of the major light harvesting complexes (LHCs) in photosynthetic dinoflagellates. We analyzed the oligomeric state of PCP isolated from the dinoflagellate Symbiodinium, which has received increasing attention in recent years because of its role in coral bleaching. Size-exclusion chromatography (SEC) and small angle neutron scattering (SANS) analysis indicated PCP exists as monomers. Native mass spectrometry (native MS) demonstrated two oligomeric states of PCP, with the monomeric PCP being dominant. The trimerization may not be necessary for PCP to function as a light-harvesting complex.
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Affiliation(s)
- Jing Jiang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xun Lu
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew J Cuneo
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh M O'Neill
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Volker Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Cynthia S Lo
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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108
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Light microenvironment and single-cell gradients of carbon fixation in tissues of symbiont-bearing corals. ISME JOURNAL 2015; 10:788-92. [PMID: 26241503 DOI: 10.1038/ismej.2015.133] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/23/2015] [Accepted: 07/01/2015] [Indexed: 11/08/2022]
Abstract
Recent coral optics studies have revealed the presence of steep light gradients and optical microniches in tissues of symbiont-bearing corals. Yet, it is unknown whether such resource stratification allows for physiological differences of Symbiodinium within coral tissues. Using a combination of stable isotope labelling and nanoscale secondary ion mass spectrometry, we investigated in hospite carbon fixation of individual Symbiodinium as a function of the local O2 and light microenvironment within the coral host determined with microsensors. We found that net carbon fixation rates of individual Symbiodinium cells differed on average about sixfold between upper and lower tissue layers of single coral polyps, whereas the light and O2 microenvironments differed ~15- and 2.5-fold, respectively, indicating differences in light utilisation efficiency along the light microgradient within the coral tissue. Our study suggests that the structure of coral tissues might be conceptually similar to photosynthetic biofilms, where steep physico-chemical gradients define form and function of the local microbial community.
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109
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Kuwahara VS, Taguchi S. Estimating the Diurnal Cycle and Daily Insolation of Ultraviolet and Photosynthetically Active Radiation at the Sea Surface. Photochem Photobiol 2015; 91:1103-11. [PMID: 26031560 DOI: 10.1111/php.12474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Abstract
Accurate determination of the diurnal variability and daily insolation of surface (0(+) ) and subsurface (0(-) ) irradiance are essential to estimate several physical, chemical and biological processes occurring at the surface layer of marine environments. Natural downwelling PAR and spectral UVR were examined on eight occasions at 0(+) and 0(-) to refine empirical models, particularly in the UVR spectrum. The diurnal variability in UVR and PAR were wavelength dependent and were modeled by a sinusoidal equation. The best fit for PAR at 0(+) and 0(-) was the sinusoid power of n = 2 and n = 2.5, respectively. In the UVR spectrum, sinusoids increased as wavelengths decreased ranging from n = 2-5. Higher n values in the UV-B spectrum suggest sharper increase/decrease near sunrise and sunset hours, ultimately reducing the final value of daily insolation at specified wavelengths. Calculated daily insolation of UV-B/(UV-A + PAR) ratio suggests that photoinhibition from exposure to UV-B occurs within a shorter biologically effective day length than PAR, and is high during summer and low during winter. These results suggest that biogeochemical calculations based on diurnal models of irradiance measurements would benefit from accurate solar noon references and wavelength specificity, particularly in the UVR spectrum.
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Affiliation(s)
- Victor S Kuwahara
- Graduate School of Engineering, Soka University, Hachioji-shi, Tokyo, Japan
| | - Satoru Taguchi
- Graduate School of Engineering, Soka University, Hachioji-shi, Tokyo, Japan
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110
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Temperature Effects on the Growth Rates and Photosynthetic Activities of Symbiodinium Cells. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3020368] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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