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Ulrich NJ, Shen G, Bryant DA, Miller SR. Ecological diversification of a cyanobacterium through divergence of its novel chlorophyll d-based light-harvesting system. Curr Biol 2024; 34:2972-2979.e4. [PMID: 38851184 DOI: 10.1016/j.cub.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
The evolution of novel traits can have important consequences for biological diversification. Novelties such as new structures are associated with changes in both genotype and phenotype that often lead to changes in ecological function.1,2 New ecological opportunities provided by a novel trait can trigger subsequent trait modification or niche partitioning3; however, the underlying mechanisms of novel trait diversification are still poorly understood. Here, we report that the innovation of a new chlorophyll (Chl) pigment, Chl d, by the cyanobacterium Acaryochloris marina was followed by the functional divergence of its light-harvesting complex. We identified three major photosynthetic spectral types based on Chl fluorescence properties for a collection of A. marina laboratory strains for which genome sequence data are available,4,5 with shorter- and longer-wavelength types more recently derived from an ancestral intermediate phenotype. Members of the different spectral types exhibited extensive variation in the Chl-binding proteins as well as the Chl energy levels of their photosynthetic complexes. This spectral-type divergence is associated with differences in the wavelength dependence of both growth rate and photosynthetic oxygen evolution. We conclude that the divergence of the light-harvesting apparatus has consequently impacted A. marina ecological diversification through specialization on different far-red photons for photosynthesis.
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Affiliation(s)
- Nikea J Ulrich
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 406 Althouse Lab, University Park, PA 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 406 Althouse Lab, University Park, PA 16802, USA
| | - Scott R Miller
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA.
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2
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Yang Y, Zhou GJ, Li Z, Sun J, Wong AST, Ko VCC, Wu RSS, Lai KP. Effects of benzophenone-3 and its metabolites on the marine diatom Chaetoceros neogracilis: Underlying mechanisms and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171371. [PMID: 38432364 DOI: 10.1016/j.scitotenv.2024.171371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
The wide application of benzophenones (BPs), such as benzophenone-3 (BP3), as an ingredient in sunscreens, cosmetics, coatings, and plastics, has led to their global contamination in aquatic environments. Using the marine diatom Chaetoceros neogracilis as a model, this study assessed the toxic effects and mechanisms of BP3 and its two major metabolites (BP8 and BP1). The results showed that BP3 exhibited higher toxicity on C. neogracilis than BP8 and BP1, with their 72-h median effective concentrations being 0.4, 0.8 and 4 mg/L, respectively. Photosynthesis efficiencies were significantly reduced after exposure to environmentally relevant concentrations of the three benzophenones, while cell viability, membrane integrity, membrane potential, and metabolic activities could be further impaired at their higher concentrations. Comparative transcriptomic analysis, followed by gene ontology and KEGG pathway enrichment analyses unraveled that all the three tested benzophenones disrupted photosynthesis and nitrogen metabolism of the diatom through alteration of similar pathways. The toxic effect of BP3 was also attributable to its unique inhibitory effects on eukaryotic ribosome biosynthesis and DNA replication. Taken together, our findings underscore that benzophenones may pose a significant threat to photosynthesis, oxygen production, primary productivity, carbon fixation, and the nitrogen cycle of diatom in coastal waters worldwide.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong
| | - Guang-Jie Zhou
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, PR China
| | - Ziying Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Shenzhen Academy of Metrology & Quality Inspection, Shenzhen 518055, PR China
| | - Jiaji Sun
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | | | - Vincent Chi Chiu Ko
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong
| | - Rudolf Shiu Sun Wu
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong; Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong
| | - Keng Po Lai
- Key Laboratory of Environmental Pollution and Integrative Omics, Education Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, Guilin, PR China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong.
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3
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Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol 2023; 12:3215-3228. [PMID: 37857380 PMCID: PMC10661051 DOI: 10.1021/acssynbio.3c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Indexed: 10/21/2023]
Abstract
While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom Phaeodactylum tricornutum, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 P. tricornutum promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels.
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Affiliation(s)
- Erin A. Garza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | - Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, California 92037, United States
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4
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Pajot A, Lavaud J, Carrier G, Garnier M, Saint-Jean B, Rabilloud N, Baroukh C, Bérard JB, Bernard O, Marchal L, Nicolau E. The Fucoxanthin Chlorophyll a/c-Binding Protein in Tisochrysis lutea: Influence of Nitrogen and Light on Fucoxanthin and Chlorophyll a/c-Binding Protein Gene Expression and Fucoxanthin Synthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:830069. [PMID: 35251102 PMCID: PMC8891753 DOI: 10.3389/fpls.2022.830069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/20/2022] [Indexed: 06/13/2023]
Abstract
We observed differences in lhc classification in Chromista. We proposed a classification of the lhcf family with two groups specific to haptophytes, one specific to diatoms, and one specific to seaweeds. Identification and characterization of the Fucoxanthin and Chlorophyll a/c-binding Protein (FCP) of the haptophyte microalgae Tisochrysis lutea were performed by similarity analysis. The FCP family contains 52 lhc genes in T. lutea. FCP pigment binding site candidates were characterized on Lhcf protein monomers of T. lutea, which possesses at least nine chlorophylls and five fucoxanthin molecules, on average, per monomer. The expression of T. lutea lhc genes was assessed during turbidostat and chemostat experiments, one with constant light (CL) and changing nitrogen phases, the second with a 12 h:12 h sinusoidal photoperiod and changing nitrogen phases. RNA-seq analysis revealed a dynamic decrease in the expression of lhc genes with nitrogen depletion. We observed that T. lutea lhcx2 was only expressed at night, suggesting that its role is to protect \cells from return of light after prolonged darkness exposure.
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Affiliation(s)
- Anne Pajot
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | - Johann Lavaud
- LEMAR-Laboratoire des Sciences de l’Environnement Marin, UMR 6539, CNRS/Univ Brest/Ifremer/IRD, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Plouzané, France
| | - Gregory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | - Matthieu Garnier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | - Noémie Rabilloud
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | - Caroline Baroukh
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
| | | | - Olivier Bernard
- Université Côte d’Azur, Biocore, INRIA, CNRS, Sorbonne Université (LOV, UMR 7093), Sophia-Antipolis, France
| | | | - Elodie Nicolau
- IFREMER, Physiology and Biotechnology of Algae Laboratory, Nantes, France
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5
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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6
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Kadono T, Tomaru Y, Suzuki K, Yamada K, Adachi M. The possibility of using marine diatom-infecting viral promoters for the engineering of marine diatoms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110475. [PMID: 32540005 DOI: 10.1016/j.plantsci.2020.110475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/26/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Marine diatoms constitute a major group of unicellular photosynthetic eukaryotes. Diatoms are widely applicable for both basic studies and applied studies. Molecular tools and techniques have been developed for diatom research. Among these tools, several endogenous gene promoters (e.g., the fucoxanthin chlorophyll a/c-binding protein gene promoter) have become available for expressing transgenes in diatoms. Gene promoters that drive transgene expression at a high level are very important for the metabolic engineering of diatoms. Various marine diatom-infecting viruses (DIVs), including both DNA viruses and RNA viruses, have recently been isolated, and their genome sequences have been characterized. Promoters from viruses that infect plants and mammals are widely used as constitutive promoters to achieve high expression of transgenes. Thus, we recently investigated the activity of promoters derived from marine DIVs in the marine diatom, Phaeodactylum tricornutum. We discuss novel viral promoters that will be useful for the future metabolic engineering of diatoms.
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Affiliation(s)
- Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Kengo Suzuki
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Koji Yamada
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan.
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7
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Kong L, Price NM. Identification of copper-regulated proteins in an oceanic diatom,Thalassiosira oceanica1005. Metallomics 2020; 12:1106-1117. [DOI: 10.1039/d0mt00033g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Plastocyanin-dependent diatoms adjust cellular metabolism to cope with chronic Cu deficiency.
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Affiliation(s)
- Liangliang Kong
- Department of Biology
- McGill University
- Montréal
- Canada
- College of Marine Life Sciences
| | - Neil M. Price
- Department of Biology
- McGill University
- Montréal
- Canada
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8
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Büchel C. Light harvesting complexes in chlorophyll c-containing algae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148027. [PMID: 31153887 DOI: 10.1016/j.bbabio.2019.05.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/30/2022]
Abstract
Besides the so-called 'green lineage' of eukaryotic photosynthetic organisms that include vascular plants, a huge variety of different algal groups exist that also harvest light by means of membrane intrinsic light harvesting proteins (Lhc). The main taxa of these algae are the Cryptophytes, Haptophytes, Dinophytes, Chromeridae and the Heterokonts, the latter including diatoms, brown algae, Xanthophyceae and Eustigmatophyceae amongst others. Despite the similarity in Lhc proteins between vascular plants and these algae, pigmentation is significantly different since no Chl b is bound, but often replaced by Chl c, and a large diversity in carotenoids functioning in light harvesting and/or photoprotection is present. Due to the presence of Chl c in most of the taxa the name 'Chl c-containing organisms' has become common, however, Chl b-less is more precise since some harbour Lhc proteins that only bind one type of Chl, Chl a. In recent years huge progress has been made about the occurrence and function of Lhc in diatoms, so-called fucoxanthin chlorophyll proteins (FCP), where also the first molecular structure became available recently. In addition, especially energy transfer amongst the unusual pigments bound was intensively studied in many of these groups. This review summarises the present knowledge about the molecular structure, the arrangement of the different Lhc in complexes, the excitation energy transfer abilities and the involvement in photoprotection of the different Lhc systems in the so-called Chl c-containing organisms. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.
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Affiliation(s)
- Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany.
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9
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Nagao R, Ueno Y, Akita F, Suzuki T, Dohmae N, Akimoto S, Shen JR. Biochemical characterization of photosystem I complexes having different subunit compositions of fucoxanthin chlorophyll a/c-binding proteins in the diatom Chaetoceros gracilis. PHOTOSYNTHESIS RESEARCH 2019; 140:141-149. [PMID: 30187302 DOI: 10.1007/s11120-018-0576-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Diatoms are dominant phytoplankton in aquatic environments and have unique light-harvesting apparatus, fucoxanthin chlorophyll a/c-binding protein (FCP). Diatom photosystem I (PSI) interacts with specific FCPs (FCPI); however, it remains unclear how PSI cores receive excitation energy from FCPI. To analyze the energy transfer dynamics, it is necessary to isolate both PSI cores and PSI-FCPI complexes. In this study, we prepared three PSI complexes, which are PSI-FCPI membrane fragments, detergent-solubilized PSI-FCPI supercomplexes and PSI core-like complexes, from the marine centric diatom, Chaetoceros gracilis, and examined their biochemical properties. Both the PSI-FCPI membrane fragments and supercomplexes showed similar subunit compositions including FCPI, whereas the PSI complexes were devoid of most FCPI subunits. The purity and homogeneity of the two detergent-solubilized PSI preparations were verified by clear-native PAGE and electron microscopy. The difference of pigment contents among the three PSI samples was shown by absorption spectra at 77 K. The intensity in the whole spectrum of PSI-FCPI membranes was much higher than those of the other two complexes, while the spectral shape of PSI complexes was similar to that of cyanobacterial PSI core complexes. 77-K fluorescence spectra of the three PSI preparations exhibited different spectral shapes, especially peak positions and band widths. Based on these observations, we discuss the merits of three PSI preparations for evaluating excitation energy dynamics in diatom PSI-FCPI complexes.
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Affiliation(s)
- Ryo Nagao
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama, 700-8530, Japan.
| | - Yoshifumi Ueno
- Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama, 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama, 700-8530, Japan.
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10
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Slattery SS, Diamond A, Wang H, Therrien JA, Lant JT, Jazey T, Lee K, Klassen Z, Desgagné-Penix I, Karas BJ, Edgell DR. An Expanded Plasmid-Based Genetic Toolbox Enables Cas9 Genome Editing and Stable Maintenance of Synthetic Pathways in Phaeodactylum tricornutum. ACS Synth Biol 2018; 7:328-338. [PMID: 29298053 DOI: 10.1021/acssynbio.7b00191] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the completion of the genome sequence, and development of an efficient conjugation-based transformation system allowing the introduction of stable episomes, Phaeodactylum tricornutum has become an ideal platform for the study of diatom biology and synthetic biology applications. The development of plasmid-based genetic tools is the next step to improve manipulation of this species. Here, we report the identification of endogenous P. tricornutum promoters and terminators allowing selective expression of antibiotic resistance markers from stably replicating plasmids in P. tricornutum. Significantly, we developed a protocol for sequential conjugation of plasmids from Escherichia coli to P. tricornutum and demonstrated simultaneous replication of two plasmids in P. tricornutum. We developed a simple and robust conjugative system for Cas9 editing that yielded up to 60% editing efficiency of the urease gene. Finally, we constructed a plasmid encoding eight genes involved in vanillin biosynthesis that was propagated in P. tricornutum over four months with no evidence of rearrangements, with whole-plasmid sequencing indicating that the majority of mutations occurred after plasmid assembly and initial conjugation rather than during long-term propagation. The plasmid-based tools described here will facilitate investigation of the basic biology of P. tricornutum and enable synthetic biology applications.
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Affiliation(s)
- Samuel S. Slattery
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Andrew Diamond
- Department
of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada
| | - Helen Wang
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Jasmine A. Therrien
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Designer Microbes Inc., 700 Collip
Circle, London ON N6G 4X8, Canada
| | - Jeremy T. Lant
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Teah Jazey
- Designer Microbes Inc., 700 Collip
Circle, London ON N6G 4X8, Canada
| | - Kyle Lee
- Designer Microbes Inc., 700 Collip
Circle, London ON N6G 4X8, Canada
| | - Zachary Klassen
- Designer Microbes Inc., 700 Collip
Circle, London ON N6G 4X8, Canada
| | - Isabel Desgagné-Penix
- Department
of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada
- Plant
Biology Research Group, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada
| | - Bogumil J. Karas
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Designer Microbes Inc., 700 Collip
Circle, London ON N6G 4X8, Canada
| | - David R. Edgell
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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11
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Li Y, Zhuang S, Wu Y, Ren H, Chen F, Lin X, Wang K, Beardall J, Gao K. Ocean acidification modulates expression of genes and physiological performance of a marine diatom. PLoS One 2017; 12:e0170970. [PMID: 28192486 PMCID: PMC5305191 DOI: 10.1371/journal.pone.0170970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/13/2017] [Indexed: 12/03/2022] Open
Abstract
Ocean Acidification (OA) is known to affect various aspects of physiological performances of diatoms, but little is known about the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum, the expression of key genes associated with photosynthetic light harvesting as well as those encoding Rubisco, carbonic anhydrase, NADH dehydrogenase and nitrite reductase, are modulated by OA (1000 μatm, pHnbs 7.83). Growth and photosynthetic carbon fixation were enhanced by elevated CO2. OA treatment decreased the expression of β-carbonic anhydrase (β-ca), which functions in balancing intracellular carbonate chemistry and the CO2 concentrating mechanism (CCM). The expression of the genes encoding fucoxanthin chlorophyll a/c protein (lhcf type (fcp)), mitochondrial ATP synthase (mtATP), ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene (rbcl) and NADH dehydrogenase subunit 2 (ndh2), were down-regulated during the first four days (< 8 generations) after the cells were transferred from LC (cells grown under ambient air condition; 390 μatm; pHnbs 8.19) to OA conditions, with no significant difference between LC and HC treatments with the time elapsed. The expression of nitrite reductase (nir) was up-regulated by the OA treatment. Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expression patterns. It appeared that the enhanced photosynthetic and growth rates under OA could be attributed to stimulated nitrogen assimilation, increased CO2 availability or saved energy from down-regulation of the CCM and consequently lowered cost of protein synthesis versus that of non-nitrogenous cell components.
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Affiliation(s)
- Yahe Li
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shufang Zhuang
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yaping Wu
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Honglin Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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12
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Chu L, Ewe D, Río Bártulos C, Kroth PG, Gruber A. Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum. PeerJ 2016; 4:e2344. [PMID: 27635322 PMCID: PMC5012323 DOI: 10.7717/peerj.2344] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/19/2016] [Indexed: 02/06/2023] Open
Abstract
An essential prerequisite for a controlled transgene expression is the choice of a suitable promoter. In the model diatom Phaeodactylum tricornutum, the most commonly used promoters for trans-gene expression are the light dependent lhcf1 promoters (derived from two endogenous genes encoding fucoxanthin chlorophyll a/c binding proteins) and the nitrate dependent nr promoter (derived from the endogenous nitrate reductase gene). In this study, we investigated the time dependent expression of the green fluorescent protein (GFP) reporter under control of the nitrate reductase promoter in independently genetically transformed P. tricornutum cell lines following induction of expression by change of the nitrogen source in the medium via flow cytometry, microscopy and western blotting. In all investigated cell lines, GFP fluorescence started to increase 1 h after change of the medium, the fastest increase rates were observed between 2 and 3 h. Fluorescence continued to increase slightly for up to 7 h even after transfer of the cells to ammonium medium. The subsequent decrease of GFP fluorescence was much slower than the increase, probably due to the stability of GFP. The investigation of several cell lines transformed with nr based constructs revealed that, also in the absence of nitrate, the promoter may show residual activity. Furthermore, we observed a strong variation of gene expression between independent cell lines, emphasising the importance of a thorough characterisation of genetically modified cell lines and their individual expression patterns.
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Affiliation(s)
- Lili Chu
- Fachbereich Biologie, Universität Konstanz , Konstanz , Germany
| | - Daniela Ewe
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany; Current affiliation: Centre Algatech, Institute of Microbiology, The Czech Academy of Science, Třeboň, Czech Republic
| | | | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz , Konstanz , Germany
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz , Konstanz , Germany
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13
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Barka F, Angstenberger M, Ahrendt T, Lorenzen W, Bode HB, Büchel C. Identification of a triacylglycerol lipase in the diatom Phaeodactylum tricornutum. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:239-48. [DOI: 10.1016/j.bbalip.2015.12.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 12/17/2015] [Accepted: 12/29/2015] [Indexed: 11/30/2022]
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14
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Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum. Sci Rep 2015; 5:18708. [PMID: 26692124 PMCID: PMC4686930 DOI: 10.1038/srep18708] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/24/2015] [Indexed: 01/27/2023] Open
Abstract
Viruses are considered key players in phytoplankton population control in oceans. However, mechanisms that control viral gene expression in prominent microalgae such as diatoms remain largely unknown. In this study, potential promoter regions isolated from several marine diatom-infecting viruses (DIVs) were linked to the egfp reporter gene and transformed into the Pennales diatom Phaeodactylum tricornutum. We analysed their activity in cells grown under different conditions. Compared to diatom endogenous promoters, novel DIV promoter (ClP1) mediated a significantly higher degree of reporter transcription and translation. Stable expression levels were observed in transformants grown under both light and dark conditions, and high levels of expression were reported in cells in the stationary phase compared to the exponential phase of growth. Conserved motifs in the sequence of DIV promoters were also found. These results allow the identification of novel regulatory regions that drive DIV gene expression and further examinations of the mechanisms that control virus-mediated bloom control in diatoms. Moreover, the identified ClP1 promoter can serve as a novel tool for metabolic engineering of diatoms. This is the first report describing a promoter of DIVs that may be of use in basic and applied diatom research.
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15
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Russo MT, Annunziata R, Sanges R, Ferrante MI, Falciatore A. The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion. Mar Genomics 2015; 24 Pt 1:69-79. [PMID: 26117181 DOI: 10.1016/j.margen.2015.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/31/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5'-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study.
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Affiliation(s)
| | - Rossella Annunziata
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France.
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16
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Weyman PD, Beeri K, Lefebvre SC, Rivera J, McCarthy JK, Heuberger AL, Peers G, Allen AE, Dupont CL. Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:460-70. [PMID: 25302562 DOI: 10.1111/pbi.12254] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 07/22/2014] [Accepted: 08/06/2014] [Indexed: 05/21/2023]
Abstract
Diatoms are unicellular photosynthetic algae with promise for green production of fuels and other chemicals. Recent genome-editing techniques have greatly improved the potential of many eukaryotic genetic systems, including diatoms, to enable knowledge-based studies and bioengineering. Using a new technique, transcription activator-like effector nucleases (TALENs), the gene encoding the urease enzyme in the model diatom, Phaeodactylum tricornutum, was targeted for interruption. The knockout cassette was identified within the urease gene by PCR and Southern blot analyses of genomic DNA. The lack of urease protein was confirmed by Western blot analyses in mutant cell lines that were unable to grow on urea as the sole nitrogen source. Untargeted metabolomic analysis revealed a build-up of urea, arginine and ornithine in the urease knockout lines. All three intermediate metabolites are upstream of the urease reaction within the urea cycle, suggesting a disruption of the cycle despite urea production. Numerous high carbon metabolites were enriched in the mutant, implying a breakdown of cellular C and N repartitioning. The presented method improves the molecular toolkit for diatoms and clarifies the role of urease in the urea cycle.
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Affiliation(s)
- Philip D Weyman
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, CA, USA
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17
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Ifuku K, Yan D, Miyahara M, Inoue-Kashino N, Yamamoto YY, Kashino Y. A stable and efficient nuclear transformation system for the diatom Chaetoceros gracilis. PHOTOSYNTHESIS RESEARCH 2015; 123:203-11. [PMID: 25297896 DOI: 10.1007/s11120-014-0048-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 05/23/2023]
Abstract
Chaetoceros gracilis belongs to the centric diatoms, and has recently been used in basic research on photosynthesis. In addition, it has been commercially used in fisheries and is also attracting interest as a feedstock for biofuels production and biorefinery. In this study, we developed an efficient genetic transformation system for C. gracilis. The diatom cells were transformed via multi-pulse electroporation using plasmids containing various promoters to drive expression of the nourseothricin acetyltransferase gene (nat) as a selectable marker. The transformation efficiency reached ~400 positive transgenic clones per 10(8) recipient cells, which is the first example of successful transformation with electroporation in a centric diatom species. We further produced two expression vectors: the vector pCgLhcr5p contains the light-dependent promoter of a fucoxanthin chlorophyll a/c binding protein gene and the vector pCgNRp contains the inducible promoter of a nitrate reductase gene to drive the expression of introduced genes. In both vectors, an acetyl-CoA acetyltransferase promoter drives nat gene expression for antibiotic selection. Stable integration and expression of reporter genes, such as the firefly luciferase and green fluorescent protein Azami-Green genes, were observed in transformed C. gracilis cells. This efficient and stable transformation system for C. gracilis will enable both functional analysis of diatom-specific genes and strain improvement for further biotechnological applications.
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Affiliation(s)
- Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan,
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18
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Büchel C. Evolution and function of light harvesting proteins. JOURNAL OF PLANT PHYSIOLOGY 2015; 172:62-75. [PMID: 25240794 DOI: 10.1016/j.jplph.2014.04.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/11/2014] [Accepted: 04/14/2014] [Indexed: 05/10/2023]
Abstract
Photosynthetic eukaryotes exhibit very different light-harvesting proteins, but all contain membrane-intrinsic light-harvesting complexes (Lhcs), either as additional or sole antennae. Lhcs non-covalently bind chlorophyll a and in most cases another Chl, as well as very different carotenoids, depending on the taxon. The proteins fall into two major groups: The well-defined Lhca/b group of proteins binds typically Chl b and lutein, and the group is present in the 'green lineage'. The other group consists of Lhcr/Lhcf, Lhcz and Lhcx/LhcSR proteins. The former are found in the so-called Chromalveolates, where they mostly bind Chl c and carotenoids very efficient in excitation energy transfer, and in their red algae ancestors. Lhcx/LhcSR are present in most Chromalveolates and in some members of the green lineage as well. Lhcs function in light harvesting, but also in photoprotection, and they influence the organisation of the thylakoid membrane. The different functions of the Lhc subfamilies are discussed in the light of their evolution.
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Affiliation(s)
- Claudia Büchel
- Goethe University Frankfurt, Institute of Molecular Biosciences, Max von Laue Str. 9, 60438 Frankfurt, Germany.
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19
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Evidence of functional trimeric chlorophyll a/c-peridinin proteins in the dinoflagellate Symbiodinium. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1904-1912. [DOI: 10.1016/j.bbabio.2014.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/07/2014] [Accepted: 07/24/2014] [Indexed: 12/17/2022]
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20
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Willis A, Eason-Hubbard M, Hodson O, Maheswari U, Bowler C, Wetherbee R. Adhesion molecules from the diatom Phaeodactylum tricornutum (Bacillariophyceae): genomic identification by amino-acid profiling and in vivo analysis. JOURNAL OF PHYCOLOGY 2014; 50:837-849. [PMID: 26988639 DOI: 10.1111/jpy.12214] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/22/2014] [Indexed: 06/05/2023]
Abstract
Cell adhesion molecules (CAMs) are important in prokaryotes and eukaryotes for cell-cell and cell-substratum interactions. The characteristics of adhesive proteins in the model diatom Phaeodactylum tricornutum were investigated by bioinformatic analysis and in vivo characterization. Bioinformatic analysis of the protein coding potential of the P. tricornutum genome used an amino-acid profile that we developed as a new system to identify uncharacterized or novel CAMs. Putative diatom CAMs were identified and seven were characterized in vivo, by generation of transgenic diatom lines overexpressing genes encoding C-terminal yellow fluorescent protein (YFP) fusion proteins. Three of these selected genes encode proteins with weak similarity to characterized proteins, a c-type lectin and two fasciclins, whereas the others are novel. The resultant cell lines were investigated for alterations in their adhesive ability. Whole cell-substratum adhesion strength was measured in a fully turbulent flow chamber, while atomic force microscopy was used to quantify the relative frequency of adhesion, as well as the length and strength of single molecules in the secreted mucilage. Finally, quartz crystal microbalance analysis characterized the visco-elastic properties and interaction of the mucilage-substratum interface. These combined studies revealed a range of phenotypes affecting adhesion, and led to the identification of candidate proteins involved in diatom adhesion. In summary, our study has for the first time combined bioinformatics and molecular physiological studies to provide new insights into diatom adhesive molecules.
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Affiliation(s)
- Anusuya Willis
- School of Botany, The University of Melbourne, Parkville, 3010, Victoria, Australia
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm 75230, Paris Cedex 05, France
| | - Maeve Eason-Hubbard
- School of Botany, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Oliver Hodson
- School of Botany, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Uma Maheswari
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm 75230, Paris Cedex 05, France
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm 75230, Paris Cedex 05, France
| | - Richard Wetherbee
- School of Botany, The University of Melbourne, Parkville, 3010, Victoria, Australia
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21
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Nagao R, Yokono M, Teshigahara A, Akimoto S, Tomo T. Light-Harvesting Ability of the Fucoxanthin Chlorophyll a/c-Binding Protein Associated with Photosystem II from the Diatom Chaetoceros gracilis As Revealed by Picosecond Time-Resolved Fluorescence Spectroscopy. J Phys Chem B 2014; 118:5093-100. [DOI: 10.1021/jp502035y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ryo Nagao
- Division
of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Makio Yokono
- Molecular
Photoscience Research Center, Kobe University, Kobe 657-8501, Japan
| | | | - Seiji Akimoto
- Molecular
Photoscience Research Center, Kobe University, Kobe 657-8501, Japan
- Graduate
School of Science, Kobe University, Kobe 657-8501, Japan
- JST, CREST, Kobe 657-8501, Japan
| | - Tatsuya Tomo
- Department
of Biology, Faculty of Science, Tokyo University of Science, Kagurazaka
1-3, Shinjuku-ku, Tokyo 162-8601, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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22
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Rhiel E, Marquardt J, Eppard M, Mörschel E, Krumbein WE. The Light Harvesting System of the DiatomCyclotella cryptica. Isolation and Characterization of the Main Light Harvesting Complex and Evidence for the Existence of Minor Pigment Proteins*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1997.tb00617.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Structure and Functional Heterogeneity of Fucoxanthin-Chlorophyll Proteins in Diatoms. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Nagao R, Tomo T, Noguchi E, Suzuki T, Okumura A, Narikawa R, Enami I, Ikeuchi M. Proteases are associated with a minor fucoxanthin chlorophyll a/c-binding protein from the diatom, Chaetoceros gracilis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2110-7. [DOI: 10.1016/j.bbabio.2012.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
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25
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Bertrand M. Carotenoid biosynthesis in diatoms. PHOTOSYNTHESIS RESEARCH 2010; 106:89-102. [PMID: 20734232 DOI: 10.1007/s11120-010-9589-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 07/24/2010] [Indexed: 05/20/2023]
Abstract
Diatoms are ubiquitous and constitute an important group of the phytoplankton community having a major contribution to the total marine primary production. These microalgae exhibit a characteristic golden-brown colour due to a high amount of the xanthophyll fucoxanthin that plays a major role in the light-harvesting complex of photosystems. In the water column, diatoms are exposed to light intensities that vary quickly from lower to higher values. Xanthophyll cycles prevent photodestruction of the cells in excessive light intensities. In diatoms, the diadinoxanthin-diatoxanthin cycle is the most important short-term photoprotective mechanism. If the biosynthetic pathways of chloroplast pigments have been extensively studied in higher plants and green algae, the research on carotenoid biosynthesis in diatoms is still in its infancy. In this study, the data on the biosynthetic pathway of diatom carotenoids are reviewed. The early steps occur through the 2-C-methyl-D: -erythritol 4-phosphate (MEP) pathway. Then a hypothetical pathway is suggested from dimethylallyl diphosphate (DMAPP) and isopentenyl pyrophosphate (IPP). Most of the enzymes of the pathway have not been so far isolated from diatoms, but candidate genes for each of them were identified using protein similarity searches of genomic data.
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Affiliation(s)
- Martine Bertrand
- MiMeTox, National Institute for Marine Sciences and Techniques, CNAM, BP 324, 50103 Cherbourg-Octeville Cedex, France.
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26
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Busch A, Hippler M. The structure and function of eukaryotic photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:864-77. [PMID: 20920463 DOI: 10.1016/j.bbabio.2010.09.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/20/2010] [Accepted: 09/28/2010] [Indexed: 12/27/2022]
Abstract
Eukaryotic photosystem I consists of two functional moieties: the photosystem I core, harboring the components for the light-driven charge separation and the subsequent electron transfer, and the peripheral light-harvesting complex (LHCI). While the photosystem I-core remained highly conserved throughout the evolution, with the exception of the oxidizing side of photosystem I, the LHCI complex shows a high degree of variability in size, subunits composition and bound pigments, which is due to the large variety of different habitats photosynthetic organisms dwell in. Besides summarizing the most current knowledge on the photosystem I-core structure, we will discuss the composition and structure of the LHCI complex from different eukaryotic organisms, both from the red and the green clade. Furthermore, mechanistic insights into electron transfer between the donor and acceptor side of photosystem I and its soluble electron transfer carrier proteins will be given. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.
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Affiliation(s)
- Andreas Busch
- Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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27
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Gildenhoff N, Herz J, Gundermann K, Büchel C, Wachtveitl J. The excitation energy transfer in the trimeric fucoxanthin–chlorophyll protein from Cyclotella meneghiniana analyzed by polarized transient absorption spectroscopy. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Joshi-Deo J, Schmidt M, Gruber A, Weisheit W, Mittag M, Kroth PG, Büchel C. Characterization of a trimeric light-harvesting complex in the diatom Phaeodactylum tricornutum built of FcpA and FcpE proteins. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3079-87. [PMID: 20478968 PMCID: PMC2892152 DOI: 10.1093/jxb/erq136] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 04/23/2010] [Accepted: 04/23/2010] [Indexed: 05/25/2023]
Abstract
Fucoxanthin chlorophyll proteins (Fcps), the light-harvesting antennas of heterokont algae, are encoded by a multigene family and are highly similar with respect to their molecular masses as well as to their pigmentation, making it difficult to purify single Fcps. In this study, a hexa-histidine tag was genetically added to the C-terminus of the FcpA protein of the pennate diatom Phaeodactylum tricornutum. A transgenic strain expressing the recombinant His-tagged FcpA protein in addition to the endogenous wild type Fcps was created. This strategy allowed, for the first time, the purification of a specific, stable trimeric Fcp complex. In addition, a pool of various trimeric Fcps was also purified from the wild-type cells using sucrose density gradient ultracentrifugation and gel filtration. In both the His-tagged and the wild-type Fcps, excitation energy coupling between fucoxanthin and chlorophyll a was intact and the existence of a chlorophyll a/fucoxanthin excitonic dimer was demonstrated using circular dichroism spectroscopy. Mass spectrometric analyses of the trimeric His-tagged complex indicated that it is composed of FcpA and FcpE polypeptides. It is confirmed here that a trimer is the basic organizational unit of Fcps in P. tricornutum. From circular dichroism spectra, it is proposed that the organization of the pigments on the polypeptide backbone of Fcps is a conserved feature in the case of chlorophyll a/c containing algae.
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Affiliation(s)
- Jidnyasa Joshi-Deo
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University, Siesmayerstrasse 70, D-60323 Frankfurt am Main, Germany
| | - Matthias Schmidt
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University, Siesmayerstrasse 70, D-60323 Frankfurt am Main, Germany
| | - Ansgar Gruber
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Wolfram Weisheit
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Peter G. Kroth
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University, Siesmayerstrasse 70, D-60323 Frankfurt am Main, Germany
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29
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Park S, Jung G, Hwang YS, Jin E. Dynamic response of the transcriptome of a psychrophilic diatom, Chaetoceros neogracile, to high irradiance. PLANTA 2010; 231:349-360. [PMID: 19924439 DOI: 10.1007/s00425-009-1044-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 10/19/2009] [Indexed: 05/28/2023]
Abstract
Large-scale RNA profiling revealed that high irradiance differentially regulated 577 out of 1,439 non-redundant genes of the Antarctic marine diatom Chaetoceros neogracile, represented on a custom cDNA chip, during 6 h of treatment. Among genes that were up- or down-regulated more than twofold within 30 min of treatment (310/1,439), about half displayed an acclimatory response during 6 h under high light. Expression of the remaining non-acclimatory genes also rapidly returned to initial levels within 30 min following a shift to low irradiance. High light altered expression of most of the photosynthesis genes (48/70), in contrast to genes in other functional categories. In addition, opposite response patterns were provoked in genes encoding fucoxanthin chlorophyll a/c binding protein (FCP), the main component of the diatom light-harvesting complex; high irradiance caused a decrease in expression of most FCP genes, but drove the rapid and specific up-regulation of ten others. C. neogracile responded very promptly to a change in light intensity by rapidly adjusting the transcript levels of FCP genes up-regulated by high light, and these dynamic adjustments coincided well with diatoxanthin (Dtx) levels formed by the xanthophyll cycle under the same conditions. The observation that the non-photochemical quenching (NPQ) capacity of this polar diatom was highly dependent on Dtx, which could bind to FCP and trigger NPQ, suggests that the up-regulated FCP gene products may participate in a photoprotective process as Dtx-binding proteins.
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Affiliation(s)
- Seunghye Park
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
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30
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Identification of a specific fucoxanthin-chlorophyll protein in the light harvesting complex of photosystem I in the diatom Cyclotella meneghiniana. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:905-12. [DOI: 10.1016/j.bbabio.2009.04.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/30/2009] [Accepted: 04/20/2009] [Indexed: 11/17/2022]
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31
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Gillard J, Devos V, Huysman MJJ, De Veylder L, D'Hondt S, Martens C, Vanormelingen P, Vannerum K, Sabbe K, Chepurnov VA, Inzé D, Vuylsteke M, Vyverman W. Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta. PLANT PHYSIOLOGY 2008; 148:1394-411. [PMID: 18820084 PMCID: PMC2577256 DOI: 10.1104/pp.108.122176] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 09/18/2008] [Indexed: 05/18/2023]
Abstract
Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated.
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Affiliation(s)
- Jeroen Gillard
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, B-9000 Gent, Belgium.
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Veith T, Büchel C. The monomeric photosystem I-complex of the diatom Phaeodactylum tricornutum binds specific fucoxanthin chlorophyll proteins (FCPs) as light-harvesting complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1428-35. [PMID: 18028870 DOI: 10.1016/j.bbabio.2007.09.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 09/11/2007] [Accepted: 09/17/2007] [Indexed: 11/18/2022]
Abstract
A photosystem I (PSI)-fucoxanthin chlorophyll protein (FCP) complex with a chlorophyll a/P700 ratio of approximately 200:1 was isolated from the diatom Phaeodactylum tricornutum. Spectroscopic analysis proved that the more tightly bound FCP functions as a light-harvesting complex, actively transferring light energy from its accessory pigments chlorophyll c and fucoxanthin to the PSI core. Using an antibody against all FCP polypeptides of Cyclotella cryptica it could be shown that the polypeptides of the major FCP fraction differ from the FCPs found in the PSI fraction. Since these FCPs are tightly bound to PSI, active in energy transfer, and not found in the main FCP fraction, we suppose them to be PSI specific. Blue Native-PAGE, gel filtration and first electron microscopy studies of the PSI-FCP sample revealed a monomeric complex comparable in size and shape to the PSI-LHCI complex of green algae.
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Affiliation(s)
- Thomas Veith
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University, Siesmayerstrasse 70, D-60323 Frankfurt am Main, Germany
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Siaut M, Heijde M, Mangogna M, Montsant A, Coesel S, Allen A, Manfredonia A, Falciatore A, Bowler C. Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 2007; 406:23-35. [PMID: 17658702 DOI: 10.1016/j.gene.2007.05.022] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 04/20/2007] [Accepted: 05/18/2007] [Indexed: 11/16/2022]
Abstract
Research into diatom biology has now entered the post-genomics era, following the recent completion of the Thalassiosira pseudonana and Phaeodactylum tricornutum whole genome sequences and the establishment of Expressed Sequence Tag (EST) databases. The thorough exploitation of these resources will require the development of molecular tools to analyze and modulate the function of diatom genes in vivo. Towards this objective, we report here the identification of several reference genes that can be used as internal standards for gene expression studies by quantitative real-time PCR (qRT-PCR) in P. tricornutum cells grown over a diel cycle. In addition, we describe a series of diatom expression vectors based on Invitrogen Gateway technology for high-throughput protein tagging and overexpression studies in P. tricornutum. We demonstrate the utility of the diatom Destination vectors for determining the subcellular localization of a protein of interest and for immunodetection. The availability of these new resources significantly enriches the molecular toolbox for P. tricornutum and provides the diatom research community with well defined high-throughput methods for the analysis of diatom genes and proteins in vivo.
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Affiliation(s)
- Magali Siaut
- Laboratory of Cell Signalling, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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Brakemann T, Schlörmann W, Marquardt J, Nolte M, Rhiel E. Association of Fucoxanthin Chlorophyll a/c-binding Polypeptides with Photosystems and Phosphorylation in the Centric Diatom Cyclotella cryptica. Protist 2006; 157:463-75. [PMID: 16904939 DOI: 10.1016/j.protis.2006.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 07/02/2006] [Indexed: 10/24/2022]
Abstract
Solubilization of thylakoid membranes of Cyclotella cryptica with dodecyl-beta maltoside followed by sucrose density gradient centrifugation or deriphate polyacrylamide gel electrophoresis resulted in the isolation of pigment protein complexes. These complexes were characterized by absorption and fluorescence spectroscopy, sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western immunoblotting using antisera against fucoxanthin chlorophyll a/c-binding proteins and the reaction center protein D2 of photosystem II. Sucrose density gradient centrifugation yielded four bands. Band 1 consisted of free pigments with minor amounts of fucoxanthin chlorophyll a/c-binding proteins. Bands 2, 3, and 4 represented a major fucoxanthin chlorophyll a/c-binding protein fraction, photosystem II, and photosystem I, respectively. Deriphate polyacrylamide gel electrophoresis gave rise to five bands, representing photosystem I, photosystem II, two fucoxanthin chlorophyll a/c-binding protein complexes, and a band mostly consisting of free pigments. In the Western immunoblotting experiments, the specific association of two fucoxanthin chlorophyll a/c-binding proteins, Fcp2 and Fcp4, to the photosystems could be demonstrated. In vivo experiments using antibodies against phosphothreonine residues and in vitro studies using [gamma-32P]ATP showed that fucoxanthin chlorophyll a/c binding-proteins of 22 kDa became phosphorylated.
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Affiliation(s)
- Tanja Brakemann
- Geomikrobiologie, ICBM, Carl-von-Ossietzky-Universität Oldenburg, POB. 2503, 26129 Oldenburg, Germany
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35
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Wilhelm C, Büchel C, Fisahn J, Goss R, Jakob T, Laroche J, Lavaud J, Lohr M, Riebesell U, Stehfest K, Valentin K, Kroth PG. The regulation of carbon and nutrient assimilation in diatoms is significantly different from green algae. Protist 2006; 157:91-124. [PMID: 16621693 DOI: 10.1016/j.protis.2006.02.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christian Wilhelm
- Department of Plant Physiology, Institute of Biology I, University of Leipzig, Johannisallee 23, 04103 Leipzig, Germany.
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36
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Harada H, Nakatsuma D, Ishida M, Matsuda Y. Regulation of the expression of intracellular beta-carbonic anhydrase in response to CO2 and light in the marine diatom Phaeodactylum tricornutum. PLANT PHYSIOLOGY 2005; 139:1041-50. [PMID: 16169965 PMCID: PMC1256016 DOI: 10.1104/pp.105.065185] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 07/09/2005] [Accepted: 07/27/2005] [Indexed: 05/04/2023]
Abstract
Cells of the marine diatom Phaeodactylum tricornutum Bohlin (UTEX 642) grown in 5% CO(2) were transferred to air-level CO(2) in the light or dark and allowed to acclimate to air. No accumulation of the transcript of the P. tricornutum beta-carbonic anhydrase 1 (ptca1) was detected in 5% CO(2)-grown cells, but ptca1 mRNA accumulated and reached a peak after 6 h acclimation to air but decreased over the next 18 h. A similar accumulation time course was observed in cells air-acclimated in the dark, except that levels of mRNA were <50% those in the light. These results suggest that air-level [CO(2)] is required to trigger the transcription of ptca1 and that light affects the extent of acclimation. During acclimation to air for 120 h in the light, levels of ptca1 mRNA exhibited a periodic oscillation with a cycle of about 24 h, which, however, was not reflected in protein accumulation levels. A 5'-upstream region from the transcription-start site toward -1,292 bp of ptca1 was cloned by inverse polymerase chain reaction, and 5'-truncations were carried out on this fragment. The truncated promoter regions were fused with the beta-glucuronidase gene (uidA) and introduced into P. tricornutum. The promoter fragments, truncated at positions -1,292, -824, -484, -225, and -70 bp, conferred on transformants clear CO(2)-responsive beta-glucuronidase expressions. In contrast, the CO(2)-responsive regulation was severely impaired or completely abolished by truncations, respectively, at position -50 or -30 bp. These results indicate that critical cis-elements required for CO(2)-responsive transcription of ptca1 may be located between -70 and -30 bp relative to the transcription start site.
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Affiliation(s)
- Hisashi Harada
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan
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37
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Guglielmi G, Lavaud J, Rousseau B, Etienne AL, Houmard J, Ruban AV. The light-harvesting antenna of the diatom Phaeodactylum tricornutum. Evidence for a diadinoxanthin-binding subcomplex. FEBS J 2005; 272:4339-48. [PMID: 16128804 DOI: 10.1111/j.1742-4658.2005.04846.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diatoms differ from higher plants by their antenna system, in terms of both polypeptide and pigment contents. A rapid isolation procedure was designed for the membrane-intrinsic light harvesting complexes (LHC) of the diatom Phaeodactylum tricornutum to establish whether different LHC subcomplexes exist, as well to determine an uneven distribution between them of pigments and polypeptides. Two distinct fractions were separated that contain functional oligomeric complexes. The major and more stable complex ( approximately 75% of total polypeptides) carries most of the chlorophyll a, and almost only one type of carotenoid, fucoxanthin. The minor complex, carrying approximately 10-15% of the total antenna chlorophyll and only a little chlorophyll c, is highly enriched in diadinoxanthin, the main xanthophyll cycle carotenoid. The two complexes also differ in their polypeptide composition, suggesting specialized functions within the antenna. The diadinoxanthin-enriched complex could be where the de-epoxidation of diadinoxanthin into diatoxanthin mostly occurs.
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Affiliation(s)
- Gérard Guglielmi
- Organismes Photosynthétiques et Environnement, CNRS, Département de Biologie, Ecole Normale Supérieure, Paris, France.
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38
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Michels AK, Wedel N, Kroth PG. Diatom plastids possess a phosphoribulokinase with an altered regulation and no oxidative pentose phosphate pathway. PLANT PHYSIOLOGY 2005; 137:911-20. [PMID: 15734914 PMCID: PMC1065392 DOI: 10.1104/pp.104.055285] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 12/01/2004] [Accepted: 12/04/2004] [Indexed: 05/18/2023]
Abstract
The chloroplast enzyme phosphoribulokinase (PRK; EC 2.7.1.19) is part of the Calvin cycle (reductive pentose phosphate pathway) responsible for CO(2) fixation in photosynthetic organisms. In green algae and vascular plants, this enzyme is light regulated via reversible reduction by reduced thioredoxin. We have sequenced and characterized the gene of the PRK from the marine diatom Odontella sinensis and found that the enzyme has the conserved cysteine residues necessary for thioredoxin-dependent regulation. Analysis of enzymatic activity of partially purified diatom enzyme and of purified protein obtained by native overexpression in Escherichia coli, however, revealed that under natural redox conditions the diatom enzyme is generally active. Treatment of the enzyme with strong oxidants results in inhibition of the enzyme, which is reversible by subsequent incubation with reducing agents. We determined the redox midpoint potentials of the regulatory cysteine in the PRK from O. sinensis in comparison to the respective spinach (Spinacia oleracea) enzyme and found a more positive redox potential for the diatom PRK, indicating that in vivo this enzyme might not be regulated by thioredoxin. We also demonstrate that in protease-treated diatom plastids, activities of enzymes of the oxidative pentose phosphate pathway are not detectable, thus reducing the need for a tight regulation of the Calvin cycle in diatoms. We discuss our results in the context of rearrangements of the subcellular compartmentation of metabolic pathways due to the peculiar evolution of diatoms by secondary endocytobiosis.
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Affiliation(s)
- Andreas K Michels
- Institute of Plant Biochemistry, University of Düsseldorf, 40225 Duesseldorf, Germany
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39
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Montsant A, Jabbari K, Maheswari U, Bowler C. Comparative genomics of the pennate diatom Phaeodactylum tricornutum. PLANT PHYSIOLOGY 2005; 137:500-13. [PMID: 15665249 PMCID: PMC1065351 DOI: 10.1104/pp.104.052829] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Revised: 11/24/2004] [Accepted: 11/25/2004] [Indexed: 05/04/2023]
Abstract
Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.
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Affiliation(s)
- Anton Montsant
- Laboratory of Cell Signalling, Stazione Zoologica Anton Dohrn, I-80121 Naples, Italy
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40
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Kroth PG. Protein transport into secondary plastids and the evolution of primary and secondary plastids. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 221:191-255. [PMID: 12455749 DOI: 10.1016/s0074-7696(02)21013-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chloroplasts are key organelles in algae and plants due to their photosynthetic abilities. They are thought to have evolved from prokaryotic cyanobacteria taken up by a eukaryotic host cell in a process termed primary endocytobiosis. In addition, a variety of organisms have evolved by subsequent secondary endocytobioses, in which a heterotrophic host cell engulfed a eukaryotic alga. Both processes dramatically enhanced the complexity of the resulting cells. Since the first version of the endosymbiotic theory was proposed more than 100 years ago, morphological, physiological, biochemical, and molecular data have been collected substantiating the emerging picture about the origin and the relationship of individual organisms with different primary or secondary chloroplast types. Depending on their origin, plastids in different lineages may have two, three, or four envelope membranes. The evolutionary success of endocytobioses depends, among other factors, on the specific exchange of molecules between the host and endosymbiont. This raises questions concerning how targeting of nucleus-encoded proteins into the different plastid types occurs and how these processes may have developed. Most studies of protein translocation into plastids have been performed on primary plastids, but in recent years more complex protein-translocation systems of secondary plastids have been investigated. Analyses of transport systems in different algal lineages with secondary plastids reveal that during evolution existing translocation machineries were recycled or recombined rather than being developed de novo. This review deals with current knowledge about the evolution and function of primary and secondary plastids and the respective protein-targeting systems.
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Affiliation(s)
- Peter G Kroth
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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41
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Durnford DG. Structure and Regulation of Algal Light-Harvesting Complex Genes. PHOTOSYNTHESIS IN ALGAE 2003. [DOI: 10.1007/978-94-007-1038-2_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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42
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Macpherson AN, Hiller RG. Light-Harvesting Systems in Chlorophyll c-Containing Algae. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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Lavaud J, Rousseau B, Etienne AL. In diatoms, a transthylakoid proton gradient alone is not sufficient to induce a non-photochemical fluorescence quenching. FEBS Lett 2002; 523:163-6. [PMID: 12123825 DOI: 10.1016/s0014-5793(02)02979-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-photochemical fluorescence quenching (NPQ) in diatoms is associated with a xanthophyll cycle involving diadinoxanthin (DD) and its de-epoxidized form, diatoxanthin (DT). In higher plants, an obligatory role of de-epoxidized xanthophylls in NPQ remains controversial and the presence of a transthylakoid proton gradient (DeltapH) alone may induce NPQ. We used inhibitors to alter the amplitude of DeltapH and/or DD de-epoxidation, and coupled NPQ. No DeltapH-dependent quenching was detected in the absence of DT. In diatoms, both DeltapH and DT are required for NPQ. The binding of DT to protonated antenna sites could be obligatory for energy dissipation.
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Affiliation(s)
- J Lavaud
- Laboratoire Organismes Photosynthétiques et Environnement, UMR CNRS 8543, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Cedex 05, Paris, France.
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Lavaud J, Rousseau B, van Gorkom HJ, Etienne AL. Influence of the diadinoxanthin pool size on photoprotection in the marine planktonic diatom Phaeodactylum tricornutum. PLANT PHYSIOLOGY 2002; 129:1398-406. [PMID: 12114593 PMCID: PMC166533 DOI: 10.1104/pp.002014] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2001] [Revised: 02/21/2002] [Accepted: 03/18/2002] [Indexed: 05/18/2023]
Abstract
The pool size of the xanthophyll cycle pigment diadinoxanthin (DD) in the diatom Phaeodactylum tricornutum depends on illumination conditions during culture. Intermittent light caused a doubling of the DD pool without significant change in other pigment contents and photosynthetic parameters, including the photosystem II (PSII) antenna size. On exposure to high-light intensity, extensive de-epoxidation of DD to diatoxanthin (DT) rapidly caused a very strong quenching of the maximum chlorophyll fluorescence yield (F(m), PSII reaction centers closed), which was fully reversed in the dark. The non-photochemical quenching of the minimum fluorescence yield (F(o), PSII centers open) decreased the quantum efficiency of PSII proportionally. For both F(m) and F(o), the non-photochemical quenching expressed as F/F' - 1 (with F' the quenched level) was proportional to the DT concentration. However, the quenching of F(o) relative to that of F(m) was much stronger than random quenching in a homogeneous antenna could explain, showing that the rate of photochemical excitation trapping was limited by energy transfer to the reaction center rather than by charge separation. The cells can increase not only the amount of DT they can produce, but also its efficiency in competing with the PSII reaction center for excitation. The combined effect allowed intermittent light grown cells to down-regulate PSII by 90% and virtually eliminated photoinhibition by saturating light. The unusually rapid and effective photoprotection by the xanthophyll cycle in diatoms may help to explain their dominance in turbulent waters.
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Affiliation(s)
- Johann Lavaud
- Laboratoire Organismes Photosynthétiques et Environnement, Unité Mixte de Recherche-Centre National de la Recherche Scientifique 8543, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex 05, France.
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45
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Scala S, Carels N, Falciatore A, Chiusano ML, Bowler C. Genome properties of the diatom Phaeodactylum tricornutum. PLANT PHYSIOLOGY 2002; 129:993-1002. [PMID: 12114555 PMCID: PMC166495 DOI: 10.1104/pp.010713] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2001] [Revised: 01/28/2002] [Accepted: 03/28/2002] [Indexed: 05/20/2023]
Abstract
Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about diatom cell biology or about their genome structure. For diatom researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species. Phaeodactylum tricornutum is an obvious candidate because of its ease of culture and because it can be genetically transformed. Therefore, we have examined its genome composition by the generation of approximately 1,000 expressed sequence tags. Although more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had high similarity with a range of genes defined functionally at the protein level. It is interesting that many of these sequences are more similar to animal rather than plant counterparts. Base composition at each codon position and GC content of the genome were compared with Arabidopsis, maize (Zea mays), and Chlamydomonas reinhardtii. It was found that distribution of GC within the coding sequences is as homogeneous in P. tricornutum as in Arabidopsis, but with a slightly higher GC content. Furthermore, we present evidence that the P. tricornutum genome is likely to be small (less than 20 Mb). Therefore, this combined information supports the development of this species as a model system for molecular-based studies of diatom biology. The nucleotide sequence data reported has been deposited in GenBank Nucleotide Sequence Database (dbEST section) under accession nos. BI306757 through BI307753.
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Affiliation(s)
- Simona Scala
- Laboratory of Molecular Plant Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Naples, Italy
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46
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Abstract
Diatoms are unicellular photosynthetic eukaryotes that contribute close to one quarter of global primary productivity. In spite of their ecological success in the world's oceans, very little information is available at the molecular level about their biology. Their most well-known characteristic is the ability to generate a highly ornamented silica cell wall, which made them very popular study organisms for microscopists in the last century. Recent advances, such as the development of a range of molecular tools, are now allowing the dissection of diatom biology, e.g., for understanding the molecular and cellular basis of bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. Making diatoms accessible to genomics technologies will potentiate greatly these efforts and may lead to the use of diatoms to construct submicrometer-scale silica structures for the nanotechnology industry.
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Affiliation(s)
- Angela Falciatore
- Laboratory of Molecular Plant Biology, Stazione Zoologica A. Dohrn, Villa Comunale, I-80121 Naples, Italy
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47
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Armbrust EV, Galindo HM. Rapid evolution of a sexual reproduction gene in centric diatoms of the genus Thalassiosira. Appl Environ Microbiol 2001; 67:3501-13. [PMID: 11472926 PMCID: PMC93050 DOI: 10.1128/aem.67.8.3501-3513.2001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sexual reproduction is commonly assumed to occur in the vast majority of diatoms due to the intimate association of this process with cell size control. Surprisingly, however, little is known about the impact of sexual events on diatom population dynamics. The Sig1 gene is strongly upregulated during sexual reproduction in the centric diatom Thalassiosira weissflogii and has been hypothesized to encode a protein involved in gamete recognition. In the present study, degenerate PCR primers were designed and used to amplify a portion of Sig1 from three closely related species in the cosmopolitan genus Thalassiosira, Thalassiosira oceanica, Thalassiosira guillardii, and Thalassiosira pseudonana. Identification of Sig1 in these three additional species facilitated development of this gene as a molecular marker for diatom sexual events. Examination of the new sequences indicated that multiple copies of Sig1 are probably present in the genome. Moreover, compared to the housekeeping gene beta-tubulin, the Sig1 genes of isolates of T. weissflogii collected from different regions of the Atlantic and Pacific oceans displayed high levels of divergence. The Sig1 genes of the four closely related Thalassiosira species also displayed high levels of sequence divergence compared to the levels observed with a second gene, Fcp, probably explaining why Sig1 could not be amplified from more distantly related species. The high levels of sequence divergence both within and between species suggest that Sig1 is rapidly evolving in a manner reminiscent of the manner observed in other genes that encode gamete recognition proteins. A simple model is presented for Sig1 evolution and the implications of such a rapidly evolving sexual reproduction gene for diatom speciation and population dynamics.
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Affiliation(s)
- E V Armbrust
- Marine Molecular Biotechnology Laboratory, School of Oceanography, University of Washington, Seattle, Washington 98195, USA.
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Marquardt J, Lutz B, Wans S, Rhiel E, Krumbein WE. The gene family coding for the light-harvesting polypeptides of Photosystem I of the red alga Galdieria sulphuraria. PHOTOSYNTHESIS RESEARCH 2001; 68:121-30. [PMID: 16228335 DOI: 10.1023/a:1011865415369] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recently [Marquardt et al. (2000) Gene 255: 257-265], we isolated a gene encoding a polypeptide of the light-harvesting complex of Photosystem I (LHC I) of the red alga Galdieria sulphuraria. By screening a G. sulphuraria cDNA library with a DNA probe coding for the conserved first transmembrane helix of this protein we isolated four additional genes coding for LHC I polypeptides. The deduced preproteins had calculated molecular masses of 24.6-25.6 kDa and isoelectric points of 8.09-9.82. N-terminal sequencing of a LHC I polypeptide isolated by gel electrophoresis allowed us to determine the cleavage site of the transit peptide of one of the deduced polypeptides. The mature protein has a calculated molecular mass of 20.6 kDa and an isoelectric point of 7.76. The genes were amplified from nuclear G. sulphuraria DNA by polymerase chain reaction (PCR) using oligonucleotides annealing in the regions of the start and stop codons as primers. All genomic sequences were 80-300 base pairs longer than the PCR products obtained from the respective cDNA clones, pointing to the existence of 1-5 introns per gene. The G. sulphuraria genes form a homogeneous gene family with overall pairwise amino acid identities of 46.0-56.6%. Homology to two diatom, one cryptophytic and two higher plant light-harvesting polypeptides was lower with pairwise identities of 21.1-34.1%. Only one diatom polypeptide showed a higher degree of identity of up to -39.3%.
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Affiliation(s)
- J Marquardt
- ICBM/Geomikrobiologie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26111, Oldenburg, Germany,
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Marquardt J, Wans S, Rhiel E, Randolf A, Krumbein WE. Intron-exon structure and gene copy number of a gene encoding for a membrane-intrinsic light-harvesting polypeptide of the red alga Galdieria sulphuraria. Gene 2000; 255:257-65. [PMID: 11024285 DOI: 10.1016/s0378-1119(00)00332-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genes for light-harvesting proteins (lhc genes) of higher plants are well examined. However, little is known about the corresponding genes of algae, although this knowledge might give valuable information about the evolution of photosynthetic antennae. In the case of rhodophytes only two cDNA sequences from a single organism, Porphyridium cruentum, have been published. Here we describe an additional sequence from another species, the thermo-acidophilic red alga Galdieria sulphuraria. For the first time also a genomic sequence for a red algal lhc gene is presented. From a cDNA library of G. sulphuraria we isolated a clone containing an open reading frame for a protein of 302 amino acids with a deduced molecular mass of 33.86kDa. It shares major structural features with eukaryotic light-harvesting polypeptides. A proposed cleavage site between transit peptide and mature protein gives rise to a transit peptide of 119 amino acids and a mature protein of 183 residues. Hydropathy analysis suggests that the mature protein consists of three transmembrane helices. Several amino acid residues supposed to bind chlorophyll a and chlorophyll b in higher plants are conserved. The protein shows up to 69% identity and 81% similarity to the Porphyridium polypeptides in the transmembrane helices 1 and 3. Using oligonucleotides annealing in the regions of the start and stop codons of the gene as primers, a DNA sequence was amplified from nuclear G. sulphuraria DNA by PCR. Compared with the cDNA clone, this sequence contains five additional intervening DNA strings of 50-74bp length. Four of them show typical features of spliceosomal introns with GT-AG borders, and the fifth differs by starting with GC. Three of the supposed introns are located in similar positions as introns of higher plant light-harvesting proteins. Southern blotting and hybridization experiments indicate that G. sulphuraria contains at least three copies of this gene.
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Affiliation(s)
- J Marquardt
- ICBM/Geomikrobiologie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26111, Oldenburg, Germany.
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De Martino A, Douady D, Quinet-Szely M, Rousseau B, Crépineau F, Apt K, Caron L. The light-harvesting antenna of brown algae: highly homologous proteins encoded by a multigene family. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:5540-9. [PMID: 10951213 DOI: 10.1046/j.1432-1327.2000.01616.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Accessory light-harvesting complexes (LHCFs) were isolated from the brown alga Laminaria saccharina. Complexes specifically associated with photosystem I or II are identical with each other with respect to molecular mass, isoelectric point and behavior on anion-exchange chromatography or non-denaturing isoelectric focusing. The purified complexes also have similar pigment composition and spectroscopic properties. It is concluded that LHC antennae associated with photosystem I or II cannot be distinguished biochemically. After screening of genomic and cDNA libraries produced from L. saccharina sporophytes, six lhcf genes were isolated. Sequence analysis of these lhcf genes showed a high level of homology between the encoded polypeptides. Comparisons with coding sequences of lhcf genes from Macrocystis pyrifera and expressed sequence tags from Laminaria digitata (two other Laminariales) indicated that these proteins are probably very similar in all brown algae. Another feature common to the lhcf genes characterized was the presence of an intron in the coding region corresponding to the plastid-targeting presequence. The sequence similarity extended to the 5' and 3' UTRs of several genes. In spite of the common origin of the chloroplasts, no light-regulating elements involved in the expression of the genes encoding the higher-plant light-harvesting proteins has been found in the UTRs.
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Affiliation(s)
- A De Martino
- Ecole Normale Superieure, CNRS UMR 8543, Paris, France
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