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Lee H, Depuydt S, Shin K, De Saeger J, Han T, Park J. Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga Ulva australis (Chlorophyta). PLANTS (BASEL, SWITZERLAND) 2024; 13:266. [PMID: 38256819 PMCID: PMC10820934 DOI: 10.3390/plants13020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/06/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Macroalgal growth and yield are key to sustainable aquaculture. Although light and water turbulence are two important factors that affect algal productivity, research on their interaction is limited. Therefore, in this study, we investigated the effects of different wavelengths of light and the presence or absence of water turbulence on the growth of the green macroalga Ulva australis. Water turbulence was found to enhance the growth of U. australis irrespective of photosynthetic performance, but only in blue light cultures. The quantum dose of blue light required to induce 50% growth promotion was 1.02 mol m-2, which is comparable to the reported values for cryptochrome-mediated effects in other macroalgae. The combined effect of blue light and water turbulence led to the accumulation of photosynthesis-related proteins that support plastid differentiation and facilitate efficient photosynthesis and growth. Our findings thus highlight the potential of harnessing blue light and water turbulence to maximise macroalgal cultivation for sustainable and profitable algal aquaculture.
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Affiliation(s)
- Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
| | - Stephen Depuydt
- Erasmus Brussels University of Applied Sciences and Arts, Nijverheidskaai 170, 1070 Brussels, Belgium
| | - Kisik Shin
- Water Environmental Engineering Research Division, National Institute of Environmental Research (NIER), 42, Hwangyeong-ro, Incheon 22689, Republic of Korea
| | - Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
| | - Taejun Han
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, B-9000 Gent, Belgium
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, B-9000 Gent, Belgium
- Center for Environmental and Energy Research, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
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Guan G, Lin J, Nie D. Swimming Mode of Two Interacting Squirmers under Gravity in a Narrow Vertical Channel. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1564. [PMID: 36359654 PMCID: PMC9689807 DOI: 10.3390/e24111564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The swimming mode of two interacting squirmers under gravity in a narrow vertical channel is simulated numerically using the lattice Boltzmann method (LBM) in the range of self-propelling strength 0.1 ≤ α ≤ 1.1 and swimming type −5 ≤ β ≤ 5. The results showed that there exist five typical swimming patterns for individual squirmers, i.e., steady upward rising (SUR), oscillation across the channel (OAC), oscillation near the wall (ONW), steady upward rising with small-amplitude oscillation (SURO), and vertical motion along the sidewall (VMS). The parametric space (α, β) illustrated the interactions on each pattern. In particular, the range of oscillation angle for ONW is from 19.8° to 32.4° as α varies from 0.3 to 0.7. Moreover, the swimming modes of two interacting squirmers combine the two squirmers’ independent swimming patterns. On the other hand, the pullers (β < 0) attract with each other at the initial stage, resulting in a low-pressure region between them and making the two pullers gradually move closer and finally make contact, while the result for the pushers (β > 0) is the opposite. After the squirmers’ interaction, the squirmer orientation and pressure distribution determine subsequent squirmer swimming patterns. Two pushers separate quickly, while there will be a more extended interaction period before the two pullers are entirely separated.
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Affiliation(s)
- Geng Guan
- State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou 310027, China
| | - Jianzhong Lin
- Zhejiang Provincial Engineering Research Center for the Safety of Pressure Vessel and Pipeline, Ningbo University, Ningbo 315211, China
| | - Deming Nie
- Institute of Fluid Mechanics, China Jiliang University, Hangzhou 310018, China
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Chen Z, Zhu J, Du M, Chen Z, Liu Q, Zhu H, Lei A, Wang J. A Synthetic Biology Perspective on the Bioengineering Tools for an Industrial Microalga: Euglena gracilis. Front Bioeng Biotechnol 2022; 10:882391. [PMID: 35464731 PMCID: PMC9020809 DOI: 10.3389/fbioe.2022.882391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Euglena is a genus of single-celled eukaryotes that show both plant- and animal-like characteristics. Euglena gracilis, a model species, is of great academic interest for studying endosymbiosis and chloroplast development. As an industrial species, E. gracilis is also of primary biotechnological and economic importance as high value-added food, medicine, and cosmetic and high-quality feedstock for jet-fuel production because of its cells containing many high-value products, such as vitamins, amino acids, pigments, unsaturated fatty acids, and carbohydrate paramylon, as metabolites. For more than half a century, E. gracilis has been used as an industrial biotechnology platform for fundamental biology research, mainly exploring relevant physiological and biochemical method studies. Although many researchers focused on genetic engineering tools for E. gracilis in recent years, little progress has been achieved because of the lack of high-quality genome information and efficient techniques for genetic operation. This article reviewed the progress of the genetic transformation of E. gracilis, including methods for the delivery of exogenous materials and other advanced biotechnological tools for E. gracilis, such as CRISPR and RNA interference. We hope to provide a reference to improve the research in functional genomics and synthetic biology of Euglena.
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Affiliation(s)
- Zhenfan Chen
- College of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jiayi Zhu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ming Du
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zixi Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Hui Zhu
- College of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Jiangxin Wang,
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Molecular Cross-Talk between Gravity- and Light-Sensing Mechanisms in Euglena gracilis. Int J Mol Sci 2022; 23:ijms23052776. [PMID: 35269918 PMCID: PMC8911436 DOI: 10.3390/ijms23052776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Euglena gracilis is a photosynthetic flagellate. To acquire a suitable position in its surrounding aquatic environment, it exploits light and gravity primarily as environmental cues. Several physiological studies have indicated a fine-tuned relationship between gravity sensing (gravitaxis) and light sensing in E. gracilis. However, the underlying molecular mechanism is largely unknown. The photoreceptor photoactivated adenylyl cyclase (PAC) has been studied for over a decade. Nevertheless, no direct/indirect interaction partner (upstream/downstream) has been reported for PAC. It has been shown that a specific protein, kinase A (PKA), showed to be involved in phototaxis and gravitaxis. The current study reports the localization of the specific PKA and its relationship with PAC.
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Fujisawa T, Masuda S, Takeuchi S, Tahara T. Femtosecond Time-Resolved Absorption Study of Signaling State of a BLUF Protein PixD from the Cyanobacterium Synechocystis: Hydrogen-Bond Rearrangement Completes during Forward Proton-Coupled Electron Transfer. J Phys Chem B 2021; 125:12154-12165. [PMID: 34726926 DOI: 10.1021/acs.jpcb.1c05957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond time-resolved absorption measurements were carried out for the dark and signaling states of a BLUF (Blue Light Using FAD) protein, PixD, from the cyanobacterium Synechocystis. When the dark state was excited, FAD semiquinone radical (FADH•) was produced from the S1 state, and FADH• led to the signaling state. On the other hand, photoexcitation of the signaling state generated FADH• and FAD anion radical (FAD•-), and they decayed back to the original signaling state. In both cases, FADH• was formed and decayed with a proton-coupled electron transfer (PCET) via the hydrogen-bond network that involves FAD, Gln50, and Tyr8, and hence the kinetics of FADH• directly reflects the hydrogen-bond structure in the FAD-binding sites. It was found that the formation rate of FADH• was significantly different between the dark and signaling states, whereas the decay rate was the same. This indicates that the hydrogen-bond network of FAD-Gln50-Tyr8 in the dark and signaling states is initially different but it becomes indistinguishable after FADH• is formed, implying that the FAD-Gln50-Tyr8 hydrogen-bond network is rearranged during the PCET to generate FADH•. The present results best agree with the model in which the Gln tautomerizes without rotation in the signaling-state formation.
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Affiliation(s)
- Tomotsumi Fujisawa
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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Agrobacterium tumefaciens-Mediated Nuclear Transformation of a Biotechnologically Important Microalga- Euglena gracilis. Int J Mol Sci 2021; 22:ijms22126299. [PMID: 34208268 PMCID: PMC8230907 DOI: 10.3390/ijms22126299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/30/2022] Open
Abstract
Euglena gracilis (E. gracilis) is an attractive organism due to its evolutionary history and substantial potential to produce biochemicals of commercial importance. This study describes the establishment of an optimized protocol for the genetic transformation of E. gracilis mediated by Agrobacterium (A. tumefaciens). E. gracilis was found to be highly sensitive to hygromycin and zeocin, thus offering a set of resistance marker genes for the selection of transformants. A. tumefaciens-mediated transformation (ATMT) yielded hygromycin-resistant cells. However, hygromycin-resistant cells hosting the gus gene (encoding β-glucuronidase (GUS)) were found to be GUS-negative, indicating that the gus gene had explicitly been silenced. To circumvent transgene silencing, GUS was expressed from the nuclear genome as transcriptional fusions with the hygromycin resistance gene (hptII) (encoding hygromycin phosphotransferase II) with the foot and mouth disease virus (FMDV)-derived 2A self-cleaving sequence placed between the coding sequences. ATMT of Euglena with the hptII-2A–gus gene yielded hygromycin-resistant, GUS-positive cells. The transformation was verified by PCR amplification of the T-DNA region genes, determination of GUS activity, and indirect immunofluorescence assays. Cocultivation factors optimization revealed that a higher number of transformants was obtained when A. tumefaciens LBA4404 (A600 = 1.0) and E. gracilis (A750 = 2.0) cultures were cocultured for 48 h at 19 °C in an organic medium (pH 6.5) containing 50 µM acetosyringone. Transformation efficiency of 8.26 ± 4.9% was achieved under the optimized cocultivation parameters. The molecular toolkits and method presented here can be used to bioengineer E. gracilis for producing high-value products and fundamental studies.
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Tamaki S, Tanno Y, Kato S, Ozasa K, Wakazaki M, Sato M, Toyooka K, Maoka T, Ishikawa T, Maeda M, Shinomura T. Carotenoid accumulation in the eyespot apparatus required for phototaxis is independent of chloroplast development in Euglena gracilis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110564. [PMID: 32771165 DOI: 10.1016/j.plantsci.2020.110564] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Euglena gracilis exhibits photomovements in response to various light stimuli, such as phototactic and photophobic responses. Our recent study revealed that carotenoids in the eyespot apparatus are required for triggering phototaxis in this alga. However, the role of chloroplasts in eyespot formation is not understood. Here, we isolated carotenoid-less (cl) strains of E. gracilis from cells silenced gene expression of phytoene synthase (EgcrtB). Unlike WT, the culture colors of cl1, cl3, and the non-photosynthetic mutant SM-ZK were orange, while that of cl4 was white. Electron microscope observations showed that SM-ZK, cl1, and cl3 had no developed chloroplast and formed a normal eyespot apparatus, similar to that of WT, but this was not the case for cl4. Carotenoids detected in WT were diadinoxanthin, neoxanthin, and β-carotene. However, the most abundant species of SM-ZK, cl1, and cl3 was zeaxanthin, and there was no diadinoxanthin or neoxanthin. Photomovement analysis showed that SM-ZK, cl1, and cl3 exhibited negative phototactic and photophobic responses, similar to those of WT, whereas cl4 lacked negative phototaxis. Taken together, the formation of the eyespot apparatus required for phototaxis is independent of chloroplast development in E. gracilis, suggesting that this property is different from other photosynthetic flagellates.
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Affiliation(s)
- Shun Tamaki
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan
| | - Yuri Tanno
- Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan
| | - Shota Kato
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan
| | - Kazunari Ozasa
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mayumi Wakazaki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mayuko Sato
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kiminori Toyooka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takashi Maoka
- Research Institute for Production Development, 15 Shimogamomorimoto-cho, Sakyo-ku, Kyoto, 606-0805, Japan
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomoko Shinomura
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan; Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan.
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8
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Kato S, Ozasa K, Maeda M, Tanno Y, Tamaki S, Higuchi‐Takeuchi M, Numata K, Kodama Y, Sato M, Toyooka K, Shinomura T. Carotenoids in the eyespot apparatus are required for triggering phototaxis in Euglena gracilis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1091-1102. [PMID: 31630463 PMCID: PMC7155050 DOI: 10.1111/tpj.14576] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/08/2019] [Indexed: 06/02/2023]
Abstract
Carotenoids are the most universal and most widespread pigments in nature. They have played pivotal roles in the evolution of photosensing mechanisms in microbes and of vision in animals. Several groups of phytoflagellates developed a photoreceptive organelle called the eyespot apparatus (EA) consisting of two separable components: the eyespot, a cluster of carotenoid-rich globules that acts as a reflector device, and actual photoreceptors for photobehaviors. Unlike other algal eyespots, the eyespot of Euglenophyta lacks reflective properties and is generally considered to act as a shading device for the photoreceptor (paraflagellar body, PFB) for major photomovements. However, the function of the eyespot of Euglenophyta has not yet been fully proven. Here, we report that the blocking carotenoid biosynthesis in Euglena gracilis by suppressing the phytoene synthase gene (crtB) caused a defect in eyespot function resulting in a loss of phototaxis. Raman spectroscopy and transmission electron microscopy suggested that EgcrtB-suppressed cells formed eyespot globules but had a defect in the accumulation of carotenoids in those packets. Motion analysis revealed the loss of phototaxis in EgcrtB-suppressed cells: a defect in the initiation of turning movements immediately after a change in light direction, rather than a defect in the termination of cell turning at the appropriate position due to a loss of the shading effect on the PFB. This study revealed that carotenoids are essential for light perception by the EA for the initiation of phototactic movement by E. gracilis, suggesting one possible photosensory role of carotenoids in the EA for the phototaxis.
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Affiliation(s)
- Shota Kato
- Plant Molecular and Cellular Biology LaboratoryDepartment of BiosciencesSchool of Science and EngineeringTeikyo University1‐1 ToyosatodaiUtsunomiyaTochigi320‐8551Japan
- Laboratory of Complex BiologyCenter for Plant Aging ResearchInstitute for Basic ScienceDGISTDaegu42988Republic of Korea
| | - Kazunari Ozasa
- Bioengineering LaboratoryCluster for Pioneering ResearchRIKEN2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Mizuo Maeda
- Bioengineering LaboratoryCluster for Pioneering ResearchRIKEN2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Yuri Tanno
- Plant Molecular and Cellular Biology LaboratoryDivision of Integrated Science and EngineeringGraduate School of Science and EngineeringTeikyo University Graduate Schools1‐1 ToyosatodaiUtsunomiyaTochigi320‐8551Japan
| | - Shun Tamaki
- Plant Molecular and Cellular Biology LaboratoryDepartment of BiosciencesSchool of Science and EngineeringTeikyo University1‐1 ToyosatodaiUtsunomiyaTochigi320‐8551Japan
| | - Mieko Higuchi‐Takeuchi
- Biomacromolecules Research TeamCenter for Sustainable Resource ScienceRIKEN2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Keiji Numata
- Biomacromolecules Research TeamCenter for Sustainable Resource ScienceRIKEN2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Yutaka Kodama
- Center for Bioscience Research and EducationUtsunomiya UniversityUtsunomiyaTochigi321‐8505Japan
| | - Mayuko Sato
- Center for Sustainable Resource ScienceRIKEN1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
| | - Kiminori Toyooka
- Center for Sustainable Resource ScienceRIKEN1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
| | - Tomoko Shinomura
- Plant Molecular and Cellular Biology LaboratoryDepartment of BiosciencesSchool of Science and EngineeringTeikyo University1‐1 ToyosatodaiUtsunomiyaTochigi320‐8551Japan
- Plant Molecular and Cellular Biology LaboratoryDivision of Integrated Science and EngineeringGraduate School of Science and EngineeringTeikyo University Graduate Schools1‐1 ToyosatodaiUtsunomiyaTochigi320‐8551Japan
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Krüger J, Richter P, Stoltze J, Strauch SM, Krüger M, Daiker V, Prasad B, Sonnewald S, Reid S, Lebert M. Changes of Gene Expression in Euglena gracilis Obtained During the 29 th DLR Parabolic Flight Campaign. Sci Rep 2019; 9:14260. [PMID: 31582787 PMCID: PMC6776534 DOI: 10.1038/s41598-019-50611-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/02/2019] [Indexed: 01/14/2023] Open
Abstract
Parabolic flight maneuvers of Novespace's Airbus A310 ZERO-G produce subsequent phases of hypergravity (about 20 s), microgravity (about 22 s) and another 20 s hypergravity on experiments located in the experiment area of the aircraft. The 29th DLR parabolic flight campaign consisted of four consecutive flight days with thirty-one parabolas each day. Euglena gracilis cells were fixed with TRIzol during different acceleration conditions at the first and the last parabola of each flight. Samples were collected and analyzed with microarrays for one-color gene expression analysis. The data indicate significant changes in gene expression in E. gracilis within short time. Hierarchical clustering shows that changes induced by the different accelerations yield reproducible effects at independent flight days. Transcription differed between the first and last parabolas indicating adaptation effects in the course of the flight. Different gene groups were found to be affected in different phases of the parabolic flight, among others, genes involved in signal transduction, calcium signaling, transport mechanisms, metabolic pathways, and stress-response as well as membrane and cytoskeletal proteins. In addition, transcripts of other areas, e.g., DNA and protein modification, were altered. The study contributes to the understanding of short-term effects of microgravity and different accelerations on cells at a molecular level.
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Affiliation(s)
- Julia Krüger
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Peter Richter
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Julia Stoltze
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Sebastian M Strauch
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
- Postgraduate Program in Health and Environment, University of Joinville Region, Rua Paulo Malschitzki, 10 - Zona Industrial Norte, Joinville, SC, CEP 89219-710, Brazil
| | - Marcus Krüger
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto von Guericke University Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Viktor Daiker
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Binod Prasad
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Sophia Sonnewald
- Biochemistry Division, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Stephen Reid
- Biochemistry Division, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Michael Lebert
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany.
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Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc 2019; 94:1701-1721. [PMID: 31095885 DOI: 10.1111/brv.12523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/23/2023]
Abstract
Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.
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Affiliation(s)
- Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Lucia Hadariová
- Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), 252 50, Vestec, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University in Prague, 128 44, Prague, Czech Republic
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Carlos E Estraño
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia
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Gissibl A, Sun A, Care A, Nevalainen H, Sunna A. Bioproducts From Euglena gracilis: Synthesis and Applications. Front Bioeng Biotechnol 2019; 7:108. [PMID: 31157220 PMCID: PMC6530250 DOI: 10.3389/fbioe.2019.00108] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/29/2019] [Indexed: 11/24/2022] Open
Abstract
In recent years, the versatile phototrophic protist Euglena gracilis has emerged as an interesting candidate for application-driven research and commercialisation, as it is an excellent source of dietary protein, pro(vitamins), lipids, and the β-1,3-glucan paramylon only found in euglenoids. From these, paramylon is already marketed as an immunostimulatory agent in nutraceuticals. Bioproducts from E. gracilis can be produced under various cultivation conditions discussed in this review, and their yields are relatively high when compared with those achieved in microalgal systems. Future challenges include achieving the economy of large-scale cultivation. Recent insights into the complex metabolism of E. gracilis have highlighted unique metabolic pathways, which could provide new leads for product enhancement by genetic modification of the organism. Also, development of molecular tools for strain improvement are emerging rapidly, making E. gracilis a noteworthy challenger for microalgae such as Chlorella spp. and their products currently on the market.
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Affiliation(s)
- Alexander Gissibl
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
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13
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Faggionato D, Serb JM. Strategy to Identify and Test Putative Light-Sensitive Non-Opsin G-Protein-Coupled Receptors: A Case Study. THE BIOLOGICAL BULLETIN 2017; 233:70-82. [PMID: 29182499 DOI: 10.1086/694842] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The rise of high-throughput RNA sequencing (RNA-seq) and de novo transcriptome assembly has had a transformative impact on how we identify and study genes in the phototransduction cascade of non-model organisms. But the advantage provided by the nearly automated annotation of RNA-seq transcriptomes may at the same time hinder the possibility for gene discovery and the discovery of new gene functions. For example, standard functional annotation based on domain homology to known protein families can only confirm group membership, not identify the emergence of new biochemical function. In this study, we show the importance of developing a strategy that circumvents the limitations of semiautomated annotation and apply this workflow to photosensitivity as a means to discover non-opsin photoreceptors. We hypothesize that non-opsin G-protein-coupled receptor (GPCR) proteins may have chromophore-binding lysines in locations that differ from opsin. Here, we provide the first case study describing non-opsin light-sensitive GPCRs based on tissue-specific RNA-seq data of the common bay scallop Argopecten irradians (Lamarck, 1819). Using a combination of sequence analysis and three-dimensional protein modeling, we identified two candidate proteins. We tested their photochemical properties and provide evidence showing that these two proteins incorporate 11-cis and/or all-trans retinal and react to light photochemically. Based on this case study, we demonstrate that there is potential for the discovery of new light-sensitive GPCRs, and we have developed a workflow that starts from RNA-seq assemblies to the discovery of new non-opsin, GPCR-based photopigments.
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Key Words
- Bta-RHO, bovine rhodopsin
- EL, extracellular loop
- FPKM, fragments per kilobase of exon per million fragments mapped
- GO, gene ontology
- GPCR, G-protein-coupled receptor
- Gr, gustatory receptor
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- TM, transmembrane helix
- Tpa-OPNGq1, Todarodes pacificus, rhodopsin
- mRNA, messenger RNA
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14
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Becker I, Strauch SM, Hauslage J, Lebert M. Long term stability of Oligo (dT) 25 magnetic beads for the expression analysis of Euglena gracilis for long term space projects. LIFE SCIENCES IN SPACE RESEARCH 2017; 13:12-18. [PMID: 28554505 DOI: 10.1016/j.lssr.2017.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/18/2017] [Indexed: 06/07/2023]
Abstract
The unicellular freshwater flagellate Euglena gracilis has a highly developed sensory system. The cells use different stimuli such as light and gravity to orient themselves in the surrounding medium to find areas for optimal growth. Due to the ability to produce oxygen and consume carbon dioxide, Euglena is a suitable candidate for life support systems. Participation in a long-term space experiment would allow for the analysis of changes and adaptations to the new environment, and this could bring new insights into the mechanism of perception of gravity and the associated signal transduction chain. For a molecular analysis of transcription patterns, an automated system is necessary, capable of performing all steps from taking a sample, processing it and generating data. One of the developmental steps is to find long-term stable reagents and materials and test them for stability at higher-than-recommended temperature conditions during extended storage time. We investigated the usability of magnetic beads in an Euglena specific lysis buffer after addition of the RNA stabilizer Dithiothreitol over 360 days and the lysis buffer with the stabilizer alone over 455 days at the expected storage temperature of 19 °C. We can claim that the stability is not impaired at all after an incubation period of over one year. This might be an interesting result for researchers who have to work under non-standard lab conditions, as in biological or medicinal fieldwork.
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Affiliation(s)
- Ina Becker
- Department of Cell Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstrasse 5, Erlangen 91058, Germany.
| | - Sebastian M Strauch
- Department of Cell Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstrasse 5, Erlangen 91058, Germany.
| | - Jens Hauslage
- German Aerospace Centre (DLR), Institute of Aerospace Medicine, Linder Höhe, Cologne 51147, Germany.
| | - Michael Lebert
- Department of Cell Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstrasse 5, Erlangen 91058, Germany.
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Lam AT, Samuel-Gama KG, Griffin J, Loeun M, Gerber LC, Hossain Z, Cira NJ, Lee SA, Riedel-Kruse IH. Device and programming abstractions for spatiotemporal control of active micro-particle swarms. LAB ON A CHIP 2017; 17:1442-1451. [PMID: 28322404 DOI: 10.1039/c7lc00131b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility. These device and programming concepts will enhance our capabilities for manipulating natural and synthetic swarms, with future applications for on-chip processing, diagnostics, education, and research on collective behaviors.
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Affiliation(s)
- Amy T Lam
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Karina G Samuel-Gama
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Jonathan Griffin
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Matthew Loeun
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Lukas C Gerber
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Zahid Hossain
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Nate J Cira
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Seung Ah Lee
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
| | - Ingmar H Riedel-Kruse
- Stanford University, 318 Campus Drive, Clark Center Room E350A, Stanford, CA 94305, USA.
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16
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Ozasa K, Won J, Song S, Tamaki S, Ishikawa T, Maeda M. Temporal change of photophobic step-up responses of Euglena gracilis investigated through motion analysis. PLoS One 2017; 12:e0172813. [PMID: 28234984 PMCID: PMC5325543 DOI: 10.1371/journal.pone.0172813] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/09/2017] [Indexed: 11/28/2022] Open
Abstract
The adaptation to a strong light is one of the essential characteristics of green algae, yet lacking relatively the information about the photophobic responses of Eukaryotic microalgae. We investigated the photophobic step-up responses of Euglena gracilis over a time course of several hours with alternated repetition of blue-light pulse illumination and spatially patterned blue-light illumination. Four distinctive photophobic motions in response to strong blue light were identified in a trace image analysis, namely on-site rotation, running and tumbling, continuous circular swimming, and unaffected straightforward swimming. The cells cultured in autotrophic conditions under weak light showed mainly the on-site rotation response at the beginning of blue-light illumination, but they acquired more blue-light tolerant responses of running and tumbling, circular swimming, or straightforward swimming. The efficiency of escaping from a blue-light illuminated area improved markedly with the development of these photophobic motions. Time constant of 3.0 h was deduced for the evolution of photophobic responses of E. gracilis. The nutrient-rich metabolic status of the cells resulting from photosynthesis during the experiments, i.e., the accumulation of photosynthesized nutrient products in balance between formation and consumption, was the main factor responsible for the development of photophobic responses. The reduction-oxidation status in and around E. gracilis cells did not affect their photophobic responses significantly, unlike the case of photophobic responses and phototaxis of Chlamydomonas reinhardtii cells. This study shows that the evolution of photophobic motion type of E. gracilis is dominated mainly by the nutrient metabolic status of the cells. The fact suggests that the nutrient-rich cells have a higher threshold for switching the flagellar motion from straightforward swimming to rotation under a strong light.
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Affiliation(s)
| | - June Won
- Department of Mechanical Convergence Engineering, Hanyang University, Seongdong-gu, Seoul, Korea
| | - Simon Song
- Department of Mechanical Convergence Engineering, Hanyang University, Seongdong-gu, Seoul, Korea
- Institute of Nano Science and Technology, Hanyang University, Seongdong-gu, Seoul, Korea
| | - Shun Tamaki
- Department of Applied Bioscience and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Takahiro Ishikawa
- Department of Applied Bioscience and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Mizuo Maeda
- Bioengineering Lab, RIKEN, Wako, Saitama, Japan
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17
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Häder DP, Iseki M. Photomovement in Euglena. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:207-235. [DOI: 10.1007/978-3-319-54910-1_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Porter ML. Beyond the Eye: Molecular Evolution of Extraocular Photoreception. Integr Comp Biol 2016; 56:842-852. [DOI: 10.1093/icb/icw052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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Fang-Yen C, Alkema MJ, Samuel ADT. Illuminating neural circuits and behaviour in Caenorhabditis elegans with optogenetics. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140212. [PMID: 26240427 DOI: 10.1098/rstb.2014.0212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The development of optogenetics, a family of methods for using light to control neural activity via light-sensitive proteins, has provided a powerful new set of tools for neurobiology. These techniques have been particularly fruitful for dissecting neural circuits and behaviour in the compact and transparent roundworm Caenorhabditis elegans. Researchers have used optogenetic reagents to manipulate numerous excitable cell types in the worm, from sensory neurons, to interneurons, to motor neurons and muscles. Here, we show how optogenetics applied to this transparent roundworm has contributed to our understanding of neural circuits.
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Affiliation(s)
- Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark J Alkema
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Aravinthan D T Samuel
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
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20
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Oakley TH, Speiser DI. How Complexity Originates: The Evolution of Animal Eyes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-110512-135907] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106;
| | - Daniel I. Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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21
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O’Neill EC, Trick M, Henrissat B, Field RA. Euglena in time: Evolution, control of central metabolic processes and multi-domain proteins in carbohydrate and natural product biochemistry. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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22
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Affiliation(s)
| | - Suely L Gomes
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
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23
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Hegemann P. Photoactivated cyclases: In memoriam Masakatsu Watanabe. Photochem Photobiol Sci 2015; 14:1781-6. [DOI: 10.1039/c5pp00233h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In memoriamMasakatsu Watanabe.
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Affiliation(s)
- Peter Hegemann
- Institute of Biology
- Experimental Biophysics
- Humboldt-Universität zu Berlin
- 10115 Berlin
- Germany
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24
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Fujisawa T, Takeuchi S, Masuda S, Tahara T. Signaling-State Formation Mechanism of a BLUF Protein PapB from the Purple Bacterium Rhodopseudomonas palustris Studied by Femtosecond Time-Resolved Absorption Spectroscopy. J Phys Chem B 2014; 118:14761-73. [PMID: 25406769 DOI: 10.1021/jp5076252] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the signaling-state formation of a BLUF (blue light using FAD) protein, PapB, from the purple bacterium Rhodopseudomonas palustris, using femtosecond time-resolved absorption spectroscopy. Upon photoexcitation of the dark state, FADH(•) (neutral flavin semiquinone FADH radical) was observed as the intermediate before the formation of the signaling state. The kinetic analysis based on singular value decomposition showed that FADH(•) mediates the signaling-state formation, showing that PapB is the second example of FADH(•)-mediated formation of the signaling state after Slr1694 (M. Gauden et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10895-10900). The mechanism of the signaling-state formation is discussed on the basis of the comparison between femtosecond time-resolved absorption spectra of the dark state and those obtained by exciting the signaling state. FADH(•) was observed also with excitation of the signaling state, and surprisingly, the kinetics of FADH(•) was indistinguishable from the case of exciting the dark state. This result suggests that the hydrogen bond environment in the signaling state is realized before the formation of FADH(•) in the photocycle of PapB.
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Affiliation(s)
- Tomotsumi Fujisawa
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, and Earth-Life Science Institute, Tokyo Institute of Technology , Yokohama 226-8501, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
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25
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ten Hagen B, Kümmel F, Wittkowski R, Takagi D, Löwen H, Bechinger C. Gravitaxis of asymmetric self-propelled colloidal particles. Nat Commun 2014; 5:4829. [DOI: 10.1038/ncomms5829] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 07/09/2014] [Indexed: 01/25/2023] Open
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26
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Lee WM, An YJ. Evidence of three-level trophic transfer of quantum dots in an aquatic food chain by using bioimaging. Nanotoxicology 2014; 9:407-12. [PMID: 25119416 DOI: 10.3109/17435390.2014.948517] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this study, we demonstrated the three-level trophic transfer of quantum dots (QDs) within the aquatic food chain. Using bioimaging, we observed QD transfer from protozoa (Astasia longa) to zooplankton (Moina macrocopa) to fish (Danio rerio). Bioimaging is an effective tool that can improve our understanding of the delivery of nanomaterials in vivo. Measurement with an intravital multiphoton laser scanning microscope visually proved the transfer of QDs from the first to the second and the second to the third levels. As QDs may be passed from lower organisms to humans via the food chain, our findings have implications for the safety of their use.
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Affiliation(s)
- Woo-Mi Lee
- Department of Environmental Health Science, Konkuk University , 1 Hwayang-dong, Gwangjin-gu, Seoul , Korea
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27
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Ooka H, Ishii T, Hashimoto K, Nakamura R. Light-induced cell aggregation of Euglena gracilis towards economically feasible biofuel production. RSC Adv 2014. [DOI: 10.1039/c4ra02101k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Using the photoresponse of the green algae Euglena gracilis, we demonstrate a novel and economically feasible method for cell aggregation.
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Affiliation(s)
- Hideshi Ooka
- Department of Applied Chemistry
- The University of Tokyo
- Tokyo 113-8656, Japan
| | - Takumi Ishii
- Department of Applied Chemistry
- The University of Tokyo
- Tokyo 113-8656, Japan
| | - Kazuhito Hashimoto
- Department of Applied Chemistry
- The University of Tokyo
- Tokyo 113-8656, Japan
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198, Japan
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28
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Nasir A, Strauch SM, Becker I, Sperling A, Schuster M, Richter PR, Weißkopf M, Ntefidou M, Daiker V, An YA, Li XY, Liu YD, Lebert M. The influence of microgravity on Euglena gracilis as studied on Shenzhou 8. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16 Suppl 1:113-119. [PMID: 23926886 DOI: 10.1111/plb.12067] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023]
Abstract
The German Aerospace Center (DLR) enabled German participation in the joint space campaign on the unmanned Shenzhou 8 spacecraft in November 2011. In this report, the effect of microgravity on Euglena gracilis cells is described. Custom-made dual compartment cell fixation units (containing cells in one chamber and fixative - RNA lysis buffer - in another one) were enclosed in a small container and placed in the Simbox incubator, which is an experiment support system. Cells were fixed by injecting them with fixative at different time intervals. In addition to stationary experiment slots, Simbox provides a 1 g reference centrifuge. Cell fixation units were mounted in microgravity and 1 g reference positions of Simbox. Two Simbox incubators were used, one for space flight and the other as ground reference. Cells were fixed soon after launch and shortly before return of the spaceship. Due to technical problems, only early in-flight samples (about 40 min after launch microgravity and corresponding 1 g reference) were fully mixed with fixative, therefore only data from those samples are presented. Transcription of several genes involved in signal transduction, oxidative stress defence, cell cycle regulation and heat shock responses was investigated with quantitative PCR. The data indicate that Euglena cells suffer stress upon short-term exposure to microgravity; various stress-induced genes were up-regulated. Of 32 tested genes, 18 were up-regulated, one down-regulated and the rest remained unaltered. These findings are in a good agreement with results from other research groups using other organisms.
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Affiliation(s)
- A Nasir
- Department of Biology, Cell Biology Division, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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29
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Proteomic signatures implicate cAMP in light and temperature responses in Arabidopsis thaliana. J Proteomics 2013; 83:47-59. [PMID: 23517717 DOI: 10.1016/j.jprot.2013.02.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/23/2022]
Abstract
UNLABELLED The second messenger 3'-5'-cyclic adenosine monophosphate (cAMP) and adenylyl cyclases (ACs), enzymes that catalyse the formation of cAMP from ATP, are increasingly recognized as important signaling molecules in a number of physiological responses in higher plants. Here we used proteomics to identify cAMP-dependent protein signatures in Arabidopsis thaliana and identify a number of differentially expressed proteins with a role in light- and temperature-dependent responses, notably photosystem II subunit P-1, plasma membrane associated cation-binding protein and chaperonin 60 β. Based on these proteomics results we conclude that, much like in cyanobacteria, algae and fungi, cAMP may have a role in light signaling and the regulation of photosynthesis as well as responses to temperature and we speculate that ACs could act as light and/or temperature sensors in higher plants. BIOLOGICAL SIGNIFICANCE This current study is significant since it presents the first proteomic response to cAMP, a novel and key second messenger in plants. It will be relevant to researchers in plant physiology and in particular those with an interest in second messengers and their role in biotic and abiotic stress responses.
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Euglena-based neurocomputing with two-dimensional optical feedback on swimming cells in micro-aquariums. Appl Soft Comput 2013. [DOI: 10.1016/j.asoc.2012.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Gehring WJ. The evolution of vision. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 3:1-40. [DOI: 10.1002/wdev.96] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Mathes T, van Stokkum IHM, Stierl M, Kennis JTM. Redox modulation of flavin and tyrosine determines photoinduced proton-coupled electron transfer and photoactivation of BLUF photoreceptors. J Biol Chem 2012; 287:31725-38. [PMID: 22833672 DOI: 10.1074/jbc.m112.391896] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photoinduced electron transfer in biological systems, especially in proteins, is a highly intriguing matter. Its mechanistic details cannot be addressed by structural data obtained by crystallography alone because this provides only static information on a given redox system. In combination with transient spectroscopy and site-directed manipulation of the protein, however, a dynamic molecular picture of the ET process may be obtained. In BLUF (blue light sensors using FAD) photoreceptors, proton-coupled electron transfer between a tyrosine and the flavin cofactor is the key reaction to switch from a dark-adapted to a light-adapted state, which corresponds to the biological signaling state. Particularly puzzling is the fact that, although the various naturally occurring BLUF domains show little difference in the amino acid composition of the flavin binding pocket, the reaction rates of the forward reaction differ quite largely from a few ps up to several hundred ps. In this study, we modified the redox potential of the flavin/tyrosine redox pair by site-directed mutagenesis close to the flavin C2 carbonyl and fluorination of the tyrosine, respectively. We provide information on how changes in the redox potential of either reaction partner significantly influence photoinduced proton-coupled electron transfer. The altered redox potentials allowed us furthermore to experimentally describe an excited state charge transfer intermediately prior to electron transfer in the BLUF photocycle. Additionally, we show that the electron transfer rate directly correlates with the quantum yield of signaling state formation.
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Affiliation(s)
- Tilo Mathes
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.
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Christie JM, Gawthorne J, Young G, Fraser NJ, Roe AJ. LOV to BLUF: flavoprotein contributions to the optogenetic toolkit. MOLECULAR PLANT 2012; 5:533-44. [PMID: 22431563 DOI: 10.1093/mp/sss020] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Optogenetics is an emerging field that combines optical and genetic approaches to non-invasively interfere with cellular events with exquisite spatiotemporal control. Although it arose originally from neuroscience, optogenetics is widely applicable to the study of many different biological systems and the range of applications arising from this technology continues to increase. Moreover, the repertoire of light-sensitive proteins used for devising new optogenetic tools is rapidly expanding. Light, Oxygen, or Voltage sensing (LOV) and Blue-Light-Utilizing flavin adenine dinucleotide (FAD) (BLUF) domains represent new contributors to the optogenetic toolkit. These small (100-140-amino acids) flavoprotein modules are derived from plant and bacterial photoreceptors that respond to UV-A/blue light. In recent years, considerable progress has been made in uncovering the photoactivation mechanisms of both LOV and BLUF domains. This knowledge has been applied in the design of synthetic photoswitches and fluorescent reporters with applications in cell biology and biotechnology. In this review, we summarize the photochemical properties of LOV and BLUF photosensors and highlight some of the recent advances in how these flavoproteins are being employed to artificially regulate and image a variety of biological processes.
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Affiliation(s)
- John M Christie
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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Penzkofer A, Stierl M, Hegemann P, Kateriya S. Photo-dynamics of the BLUF domain containing soluble adenylate cyclase (nPAC) from the amoeboflagellate Naegleria gruberi NEG-M strain. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.05.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ozasa K, Lee J, Song S, Hara M, Maeda M. Two-dimensional optical feedback control of Euglena confined in closed-type microfluidic channels. LAB ON A CHIP 2011; 11:1933-1940. [PMID: 21491041 DOI: 10.1039/c0lc00719f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We examined two-dimensional (2D) optical feedback control of phototaxis flagellate Euglena cells confined in closed-type microfluidic channels (microaquariums), and demonstrated that the 2D optical feedback enables the control of the density and position of Euglena cells in microaquariums externally, flexibly, and dynamically. Using three types of feedback algorithms, the density of Euglena cells in a specified area can be controlled arbitrarily and dynamically, and more than 70% of the cells can be concentrated into a specified area. Separation of photo-sensitive/insensitive Euglena cells was also demonstrated. Moreover, Euglena-based neuro-computing has been achieved, where 16 imaginary neurons were defined as Euglena-activity levels in 16 individual areas in microaquariums. The study proves that 2D optical feedback control of photoreactive flagellate microbes is promising for microbial biology studies as well as applications such as microbe-based particle transportation in microfluidic channels or separation of photo-sensitive/insensitive microbes.
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Affiliation(s)
- Kazunari Ozasa
- RIKEN Advanced Science Institute, Hirosawa, Wako, Saitama, Japan.
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Mathes T, van Stokkum IHM, Bonetti C, Hegemann P, Kennis JTM. The Hydrogen-Bond Switch Reaction of the Blrb Bluf Domain of Rhodobacter sphaeroides. J Phys Chem B 2011; 115:7963-71. [DOI: 10.1021/jp201296m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tilo Mathes
- Institut für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Ivo H. M. van Stokkum
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Cosimo Bonetti
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T. M. Kennis
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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Daiker V, Häder DP, Richter PR, Lebert M. The involvement of a protein kinase in phototaxis and gravitaxis of Euglena gracilis. PLANTA 2011; 233:1055-1062. [PMID: 21286747 DOI: 10.1007/s00425-011-1364-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 01/14/2011] [Indexed: 05/30/2023]
Abstract
The unicellular flagellate Euglena gracilis shows positive phototaxis at low-light intensities (<10 W/m(2)) and a negative one at higher irradiances (>10 W/m(2)). Phototaxis is based on blue light-activated adenylyl cyclases, which produce cAMP upon irradiation. In the absence of light the cells swim upward in the water column (negative gravitaxis). The results of sounding rocket campaigns and of a large number of ground experiments led to the following model of signal perception and transduction in gravitaxis of E. gracilis: The body of the cell is heavier than the surrounding medium, sediments and thereby exerts a force onto the lower membrane. Upon deviation from a vertical swimming path mechano-sensitive ion channels are activated. Calcium is gated inwards which leads to an increase in the intracellular calcium concentration and causes a change of the membrane potential. After influx, calcium activates one of several calmodulins found in Euglena, which in turn activates an adenylyl cyclase (different from the one involved in phototaxis) to produce cAMP from ATP. One further element in the sensory transduction chain of both phototaxis and gravitaxis is a specific protein kinase A. We found five different protein kinases A in E. gracilis. The blockage of only one of these (PK.4, accession No. EU935859) by means of RNAi inhibited both phototaxis and gravitaxis, while inhibition of the other four affected neither phototaxis nor gravitaxis. It is assumed that cAMP directly activates this protein kinase A which may in turn phosphorylate a protein involved in the flagellar beating mechanism.
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Affiliation(s)
- Viktor Daiker
- Department of Biology, Cell Biology Division, Friedrich-Alexander University, Staudtstr. 5, 91058 Erlangen, Germany
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38
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Losi A, Gärtner W. Old Chromophores, New Photoactivation Paradigms, Trendy Applications: Flavins in Blue Light-Sensing Photoreceptors†. Photochem Photobiol 2011; 87:491-510. [DOI: 10.1111/j.1751-1097.2011.00913.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J, Jaeger KE. Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 2011; 90:23-40. [PMID: 21336931 DOI: 10.1007/s00253-011-3141-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 01/10/2023]
Abstract
Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.
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40
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Weissenberger S, Schultheis C, Liewald JF, Erbguth K, Nagel G, Gottschalk A. PACα--an optogenetic tool for in vivo manipulation of cellular cAMP levels, neurotransmitter release, and behavior in Caenorhabditis elegans. J Neurochem 2011; 116:616-25. [PMID: 21166803 DOI: 10.1111/j.1471-4159.2010.07148.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoactivated adenylyl cyclase α (PACα) was originally isolated from the flagellate Euglena gracilis. Following stimulation by blue light it causes a rapid increase in cAMP levels. In the present study, we expressed PACα in cholinergic neurons of Caenorhabditis elegans. Photoactivation led to a rise in swimming frequency, speed of locomotion, and a decrease in the number of backward locomotion episodes. The extent of the light-induced behavioral effects was dependent on the amount of PACα that was expressed. Furthermore, electrophysiological recordings from body wall muscle cells revealed an increase in miniature post-synaptic currents during light stimulation. We conclude that the observed effects were caused by cAMP synthesis because of photoactivation of pre-synaptic PACα which subsequently triggered acetylcholine release at the neuromuscular junction. Our results demonstrate that PACα can be used as an optogenetic tool in C. elegans for straightforward in vivo manipulation of intracellular cAMP levels by light, with good temporal control and high cell specificity. Thus, using PACα allows manipulation of neurotransmitter release and behavior by directly affecting intracellular signaling.
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Affiliation(s)
- Simone Weissenberger
- Department of Biochemistry, Chemistry, and Pharmacy, Institute of Biochemistry, Goethe-University, Frankfurt, Germany
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41
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Stierl M, Stumpf P, Udwari D, Gueta R, Hagedorn R, Losi A, Gärtner W, Petereit L, Efetova M, Schwarzel M, Oertner TG, Nagel G, Hegemann P. Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J Biol Chem 2011; 286:1181-8. [PMID: 21030594 PMCID: PMC3020725 DOI: 10.1074/jbc.m110.185496] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/26/2010] [Indexed: 11/06/2022] Open
Abstract
The recent success of channelrhodopsin in optogenetics has also caused increasing interest in enzymes that are directly activated by light. We have identified in the genome of the bacterium Beggiatoa a DNA sequence encoding an adenylyl cyclase directly linked to a BLUF (blue light receptor using FAD) type light sensor domain. In Escherichia coli and Xenopus oocytes, this photoactivated adenylyl cyclase (bPAC) showed cyclase activity that is low in darkness but increased 300-fold in the light. This enzymatic activity decays thermally within 20 s in parallel with the red-shifted BLUF photointermediate. bPAC is well expressed in pyramidal neurons and, in combination with cyclic nucleotide gated channels, causes efficient light-induced depolarization. In the Drosophila central nervous system, bPAC mediates light-dependent cAMP increase and behavioral changes in freely moving animals. bPAC seems a perfect optogenetic tool for light modulation of cAMP in neuronal cells and tissues and for studying cAMP-dependent processes in live animals.
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Affiliation(s)
- Manuela Stierl
- From the Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Patrick Stumpf
- the Department of Botany I, the University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Daniel Udwari
- the Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Ronnie Gueta
- the Department of Botany I, the University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Rolf Hagedorn
- From the Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Aba Losi
- the Department of Physics, University of Parma, 43121 Parma, Italy
| | - Wolfgang Gärtner
- the Max-Planck-Institute for Bioinorganic Chemistry, Postfach 1013 56, D-45410 Mülheim, Germany, and
| | - Linda Petereit
- the Department of Biology, Free University Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Marina Efetova
- the Department of Biology, Free University Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Martin Schwarzel
- the Department of Biology, Free University Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Thomas G. Oertner
- the Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Georg Nagel
- the Department of Botany I, the University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Peter Hegemann
- From the Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
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42
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Daiker V, Lebert M, Richter P, Häder DP. Molecular characterization of a calmodulin involved in the signal transduction chain of gravitaxis in Euglena gracilis. PLANTA 2010; 231:1229-1236. [PMID: 20213123 DOI: 10.1007/s00425-010-1126-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 02/10/2010] [Indexed: 05/28/2023]
Abstract
The unicellular flagellate Euglena gracilis shows a negative gravitactic behavior. This is based on physiological mechanisms which in the past have been indirectly assessed. Meanwhile, it was possible to isolate genes involved in the signal transduction chain of gravitaxis. The DNA sequences of five calmodulins were found in Euglena, one of which was only known in its protein structure (CaM.1); the other four are new. The biosynthesis of the corresponding proteins of CaM.1-CaM.5 was inhibited by means of RNA interference to determine their involvement in the gravitactic signal transduction chain. RNAi of CaM.1 inhibits free swimming of the cells and pronounced cell-form aberrations. The division of cells was also hampered. After recovery from RNAi the cell showed precise negative gravitaxis again. Blockage of CaM.3 to CaM. 5 did not impair gravitaxis. In contrast, the blockage of CaM.2 has only a transient and not pronounced influence on motility and cell form, but leads to a total loss of gravitactic orientation for more than 30 days. This indicates that CaM.2 is an element in the signal transduction chain of gravitaxis in E. gracilis. The results are discussed with regard to the current working model of gravitaxis in E. gracilis.
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Affiliation(s)
- Viktor Daiker
- Department of Biology, Plant Ecophysiology, Friedrich-Alexander University, Erlangen, Germany
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43
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Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 2010; 140:631-42. [PMID: 20211133 DOI: 10.1016/j.cell.2010.01.032] [Citation(s) in RCA: 341] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 11/17/2009] [Accepted: 01/15/2010] [Indexed: 12/18/2022]
Abstract
Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.
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Affiliation(s)
- Lillian K Fritz-Laylin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Looser J, Schröder-Lang S, Hegemann P, Nagel G. Mechanistic insights in light-induced cAMP production by photoactivated adenylyl cyclase alpha (PACalpha). Biol Chem 2009; 390:1105-11. [PMID: 19747080 DOI: 10.1515/bc.2009.132] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The flagellate Euglena gracilis contains as photoreceptor complex a heterotetrameric light-sensitive adenylyl cyclase (AC), consisting of the flavoproteins PACalpha and PACbeta. Previously, we demonstrated the functional expression of PACalpha and PACbeta in oocytes from Xenopus laevis and of PACalpha in different animal cell types. Both yielded a blue light-induced increase of cellular [cAMP]. Here, we report that the action spectrum of PACalpha is flavoprotein-typical, with maxima at approximately 380 and approximately 470 nm. Mutational analysis of PACalpha yields a model for its structure and function. PACalpha shows a basal AC activity in the dark which is unaffected by mutating the conserved tyrosines in the two flavin-binding domains (F1, F2), Y60 in F1 and Y472 in F2. Y60 in F1 is, however, essential for photoactivation as light-stimulation of cyclase activity is completely lost in the F1 mutant Y60F. This effect does not occur in the respective mutation in F2 (Y472F). Mutating the two cyclase domains (C1, C2) indicated that C1 and C2 form a heterodimeric catalytic center as in mammalian class III cyclases. Interaction of C1 with C2 in the same molecule could be excluded as coexpression of non-functional C1 and C2 mutants restored light-induced cyclase activity. Our results strongly suggest an intermolecular dimerization of C1 and C2 domains on PACalpha for a functional enzyme.
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Affiliation(s)
- Jens Looser
- Universität Würzburg, Julius-von-Sachs-Institut, D-97082 Würzburg, Germany
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Abstract
Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present.
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Affiliation(s)
- Gáspár Jékely
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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Transduction mechanisms of photoreceptor signals in plant cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2009.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Shpakov AO, Pertseva MN. Chapter 4 Signaling Systems of Lower Eukaryotes and Their Evolution. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 269:151-282. [DOI: 10.1016/s1937-6448(08)01004-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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Gradinaru V, Thompson KR, Zhang F, Mogri M, Kay K, Schneider MB, Deisseroth K. Targeting and readout strategies for fast optical neural control in vitro and in vivo. J Neurosci 2007; 27:14231-8. [PMID: 18160630 PMCID: PMC6673457 DOI: 10.1523/jneurosci.3578-07.2007] [Citation(s) in RCA: 397] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/21/2007] [Accepted: 11/21/2007] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | - Feng Zhang
- Department of Bioengineering
- Department of Chemistry, and
| | | | | | - M. Bret Schneider
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305
| | - Karl Deisseroth
- Department of Bioengineering
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305
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49
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Lobban CS, Hallam SJ, Mukherjee P, Petrich JW. Photophysics and Multifunctionality of Hypericin-Like Pigments in Heterotrich Ciliates: A Phylogenetic Perspective. Photochem Photobiol 2007; 83:1074-94. [PMID: 17880503 DOI: 10.1111/j.1751-1097.2007.00191.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we review the literature and present some new data to examine the occurrence and photophysics of the diverse hypericin-like chromophores in heterotrichs, the photoresponses of the cells, the various roles of the pigments and the taxa that might be studied to advance our understanding of these pigments. Hypericin-like chromophores are known chemically and spectrally so far only from the stentorids and Fabrea, the latter now seen to be sister to stentorids in the phylogenetic tree. For three hypericin-like pigments, the structures are known but these probably do not account for all the colors seen in stentorids. At least eight physiological groups of Stentor exist depending on pigment color and presence/absence of zoochlorellae, and some species can be bleached, leading to many opportunities for comparison of pigment chemistry and cell behavior. Several different responses to light are exhibited among heterotrichs, sometimes by the same cell; in particular, cells with algal symbionts are photophilic in contrast to the well-studied sciaphilous (shade-loving) species. Hypericin-like pigments are involved in some well-known photophobic reactions but other pigments (rhodopsin and flavins) are also involved in photoresponses in heterotrichs and other protists. The best characterized role of hypericin-like pigments in heterotrichs is in photoresponses and they have at least twice evolved a role as photoreceptors. However, hypericin and hypericin-like pigments in diverse organisms more commonly serve as predator defense and the pigments are multifunctional in heterotrichs. A direct role for the pigments in UV protection is possible but evidence is equivocal. New observations are presented on a folliculinid from deep water, including physical characterization of its hypericin-like pigment and its phylogenetic position based on SSU rRNA sequences. The photophysics of hypericin and hypericin-like pigments is reviewed. Particular attention is given to how their excited-state properties are modified by the environment. Dramatic changes in excited-state behavior are observed as hypericin is moved from the homogeneous environment of organic solvents to the much more structured surroundings provided by the complexes it forms with proteins. Among these complexes, it is useful to consider the differences between environments where hypericin is not found naturally and those where it is, notably, for example, in heterotrichs. It is clear that interaction with a protein modifies the photophysics of hypericin and understanding the molecular basis of this interaction is one of the outstanding problems in elucidating the function of hypericin and hypericin-like chromophores.
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Shihira-Ishikawa I, Nakamura T, Higashi SI, Watanabe M. Distinct Responses of Chloroplasts to Blue and Green Laser Microbeam Irradiations in the Centric Diatom Pleurosira laevis. Photochem Photobiol 2007; 83:1101-9. [PMID: 17880505 DOI: 10.1111/j.1751-1097.2007.00167.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The centric diatom Pleurosira laevis is a large unicellular alga, in which ca 200 chloroplasts migrate toward the nuclear cytoplasm through the transvacuolar cytoplasmic strands in response to blue-light irradiation and, on the contrary, toward the cortical cytoplasm in response to green-light irradiation. We analyzed these light-induced chloroplast migrations using a scanning laser microbeam provided by a confocal microscope for intracellular irradiation. Spot irradiation of a blue laser microbeam induced rapid assemblage of chroloplasts into the nuclear cytoplasm regardless of the spot position and spot number. On the other hand, one or two spots of green laser microbeam induced chloroplast accumulation at the spots, although increasing spot numbers suppressed chloroplast accumulation at each spot. In our experimental condition, ca 1 min of blue-light irradiation was sufficient to stimulate movement, whereas green-light irradiation required uninterrupted and longer irradiation time (ca 15 min). Chloroplast assemblage induced by blue-light required extracellular Ca2+, and was inhibited by Ca2+ channel antagonists. Furthermore, higher efficiencies of chloroplast migration were obtained when a single beam spot was fragmented and scattered over wider area of plasma membrane. These observations suggested that blue-light induced a response at the plasma membrane, which subsequently activated Ca2+ permeable channels. This sequence of physiological events is identical to what was previously observed with chloroplast movement in response to mechanical stimulation. Furthermore, experiments with the cytoskeleton-disrupting agents, colchicine and cytochalasin D, indicated that blue-light-induced chloroplast movement required microtubules whereas the green-light-induced response to beam spot required actin filaments.
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