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Kadono T, Kira N, Suzuki K, Iwata O, Ohama T, Okada S, Nishimura T, Akakabe M, Tsuda M, Adachi M. Effect of an Introduced Phytoene Synthase Gene Expression on Carotenoid Biosynthesis in the Marine Diatom Phaeodactylum tricornutum. Mar Drugs 2015; 13:5334-57. [PMID: 26308005 PMCID: PMC4557025 DOI: 10.3390/md13085334] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/11/2015] [Indexed: 11/16/2022] Open
Abstract
Carotenoids exert beneficial effects on human health through their excellent antioxidant activity. To increase carotenoid productivity in the marine Pennales Phaeodactylum tricornutum, we genetically engineered the phytoene synthase gene (psy) to improve expression because RNA-sequencing analysis has suggested that the expression level of psy is lower than other enzyme-encoding genes that are involved in the carotenoid biosynthetic pathway. We isolated psy from P. tricornutum, and this gene was fused with the enhanced green fluorescent protein gene to detect psy expression. After transformation using the microparticle bombardment technique, we obtained several P. tricornutum transformants and confirmed psy expression in their plastids. We investigated the amounts of PSY mRNA and carotenoids, such as fucoxanthin and β-carotene, at different growth phases. The introduction of psy increased the fucoxanthin content of a transformants by approximately 1.45-fold relative to the levels in the wild-type diatom. However, some transformants failed to show a significant increase in the carotenoid content relative to that of the wild-type diatom. We also found that the amount of PSY mRNA at log phase might contribute to the increase in carotenoids in the transformants at stationary phase.
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Affiliation(s)
- Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
| | - Nozomu Kira
- The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan.
| | - Kengo Suzuki
- Euglena Co., Ltd., 4th Floor, Yokohama Leading Venture Plaza, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
| | - Osamu Iwata
- Euglena Co., Ltd., 4th Floor, Yokohama Leading Venture Plaza, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kami, Kochi 782-8502, Japan.
| | - Shigeru Okada
- Department of Aquatic Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Tomohiro Nishimura
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
| | - Mai Akakabe
- Synthetic Organic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Masashi Tsuda
- Science Research Center, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 783-8506, Japan.
- Center for Advanced Marine Core Research, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
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Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens. PLoS One 2015; 10:e0132693. [PMID: 26167858 PMCID: PMC4500500 DOI: 10.1371/journal.pone.0132693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 06/17/2015] [Indexed: 11/19/2022] Open
Abstract
Plant-targeted pCB302 plasmids containing sequences encoding gfp fusions with a microtubule-binding domain; gfp with the fimbrin actin-binding domain 2; and gfp with AtRACK1C from Arabidopsis thaliana, all harbored in Agrobacterium tumefaciens, were used to assay heterologous expression on three different clades of the photosynthetic dinoflagellate, Symbiodinium. Accessibility to the resistant cell wall and through the plasma membrane of these dinoflagellates was gained after brief but vigorous shaking in the presence of glass beads and polyethylene glycol. A resistance gene to the herbicide Basta allowed appropriate selection of the cells expressing the hybrid proteins, which showed a characteristic green fluorescence, although they appeared to lose their photosynthetic pigments and did not further divide. Cell GFP expression frequency measured as green fluorescence emission yielded 839 per every 106 cells for Symbiodinium kawagutii, followed by 640 and 460 per every 106 cells for Symbiodinium microadriaticum and Symbiodinium sp. Mf11, respectively. Genomic PCR with specific primers amplified the AtRACK1C and gfp sequences after selection in all clades, thus revealing their presence in the cells. RT-PCR from RNA of S. kawagutii co-incubated with A. tumefaciens harboring each of the three vectors with their respective constructs, amplified products corresponding to the heterologous gfp sequence while no products were obtained from three distinct negative controls. The reported procedure shows that mild abrasion followed by co-incubation with A. tumefaciens harboring heterologous plasmids with CaMV35S and nos promoters can lead to expression of the encoded proteins into the Symbiodinium cells in culture. Despite the obvious drawbacks of the procedure, this is an important first step towards a stable transformation of Symbiodinium.
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Cloning and characterization of farnesyl pyrophosphate synthase from the highly branched isoprenoid producing diatom Rhizosolenia setigera. Sci Rep 2015; 5:10246. [PMID: 25996801 PMCID: PMC4440519 DOI: 10.1038/srep10246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/07/2015] [Indexed: 12/24/2022] Open
Abstract
The diatom Rhizosolenia setigera Brightwell produces highly branched isoprenoid (HBI) hydrocarbons that are ubiquitously present in marine environments. The hydrocarbon composition of R. setigera varies between C25 and C30 HBIs depending on the life cycle stage with regard to auxosporulation. To better understand how these hydrocarbons are biosynthesized, we characterized the farnesyl pyrophosphate (FPP) synthase (FPPS) enzyme of R. setigera. An isolated 1465-bp cDNA clone contained an open reading frame spanning 1299-bp encoding a protein with 432 amino acid residues. Expression of the RsFPPS cDNA coding region in Escherichia coli produced a protein that exhibited FPPS activity in vitro. A reduction in HBI content from diatoms treated with an FPPS inhibitor, risedronate, suggested that RsFPPS supplies precursors for HBI biosynthesis. Product analysis by gas chromatography-mass spectrometry also revealed that RsFPPS produced small amounts of the cis-isomers of geranyl pyrophosphate and FPP, candidate precursors for the cis-isomers of HBIs previously characterized. Furthermore, RsFPPS gene expression at various life stages of R. setigera in relation to auxosporulation were also analyzed. Herein, we present data on the possible role of RsFPPS in HBI biosynthesis, and it is to our knowledge the first instance that an FPPS was cloned and characterized from a diatom.
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Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM. Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes. Genome Biol Evol 2015; 7:1728-42. [PMID: 25994931 PMCID: PMC4494062 DOI: 10.1093/gbe/evv095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The internal compartmentation of eukaryotic cells not only allows separation of biochemical processes but it also creates the requirement for systems that can selectively transport proteins across the membrane boundaries. Although most proteins function in a single subcellular compartment, many are able to enter two or more compartments, a phenomenon known as dual or multiple targeting. The aminoacyl-tRNA synthetases (aaRSs), which catalyze the ligation of tRNAs to their cognate amino acids, are particularly prone to functioning in multiple subcellular compartments. They are essential for translation, so they are required in every compartment where translation takes place. In diatoms, there are three such compartments, the plastid, the mitochondrion, and the cytosol. In cryptophytes, translation also takes place in the periplastid compartment (PPC), which is the reduced cytoplasm of the plastid’s red algal ancestor and which retains a reduced red algal nucleus. We searched the organelle and nuclear genomes of the cryptophyte Guillardia theta and the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana for aaRS genes and found an insufficient number of genes to provide each compartment with a complete set of aaRSs. We therefore inferred, with support from localization predictions, that many aaRSs are dual targeted. We tested four of the predicted dual targeted aaRSs with green fluorescent protein fusion localizations in P. tricornutum and found evidence for dual targeting to the mitochondrion and plastid in P. tricornutum and G. theta, and indications for dual targeting to the PPC and cytosol in G. theta. This is the first report of dual targeting in diatoms or cryptophytes.
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Affiliation(s)
- Gillian H Gile
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Moog
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Uwe-G Maier
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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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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Vinayak V, Manoylov KM, Gateau H, Blanckaert V, Hérault J, Pencréac'h G, Marchand J, Gordon R, Schoefs B. Diatom milking: a review and new approaches. Mar Drugs 2015; 13:2629-65. [PMID: 25939034 PMCID: PMC4446598 DOI: 10.3390/md13052629] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
The rise of human populations and the growth of cities contribute to the depletion of natural resources, increase their cost, and create potential climatic changes. To overcome difficulties in supplying populations and reducing the resource cost, a search for alternative pharmaceutical, nanotechnology, and energy sources has begun. Among the alternative sources, microalgae are the most promising because they use carbon dioxide (CO2) to produce biomass and/or valuable compounds. Once produced, the biomass is ordinarily harvested and processed (downstream program). Drying, grinding, and extraction steps are destructive to the microalgal biomass that then needs to be renewed. The extraction and purification processes generate organic wastes and require substantial energy inputs. Altogether, it is urgent to develop alternative downstream processes. Among the possibilities, milking invokes the concept that the extraction should not kill the algal cells. Therefore, it does not require growing the algae anew. In this review, we discuss research on milking of diatoms. The main themes are (a) development of alternative methods to extract and harvest high added value compounds; (b) design of photobioreactors;
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Affiliation(s)
- Vandana Vinayak
- Department of Criminology & Forensic Science, School of Applied Sciences, Dr. H.S. Gour University (Central University), Sagar Madhya Pradesh, India.
| | - Kalina M Manoylov
- Department of Biological & Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA.
| | - Hélène Gateau
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Vincent Blanckaert
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Josiane Hérault
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Gaëlle Pencréac'h
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Justine Marchand
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Richard Gordon
- Gulf Specimen Aquarium & Marine Laboratory, Panacea, FL 32346, USA.
- Mott Center for Human Growth and Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI 48201, USA.
| | - Benoît Schoefs
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
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Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison III CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD. Designer diatom episomes delivered by bacterial conjugation. Nat Commun 2015; 6:6925. [PMID: 25897682 PMCID: PMC4411287 DOI: 10.1038/ncomms7925] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/13/2015] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.
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Affiliation(s)
- Bogumil J. Karas
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Rachel E. Diner
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, USA
| | - Stephane C. Lefebvre
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Jeff McQuaid
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Alex P.R. Phillips
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Chari M. Noddings
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - John K. Brunson
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Ruben E. Valas
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Thomas J. Deerinck
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California 92093, USA
| | - Jelena Jablanovic
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Jeroen T.F. Gillard
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Karen Beeri
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California 92093, USA
| | - John I. Glass
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Clyde A. Hutchison III
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Hamilton O. Smith
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - J. Craig Venter
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, USA
| | - Christopher L. Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Philip D. Weyman
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, USA
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58
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Shih CH, Chen HY, Lee HC, Tsai HJ. Purple chromoprotein gene serves as a new selection marker for transgenesis of the microalga Nannochloropsis oculata. PLoS One 2015; 10:e0120780. [PMID: 25793255 PMCID: PMC4368691 DOI: 10.1371/journal.pone.0120780] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/03/2015] [Indexed: 12/20/2022] Open
Abstract
Among the methods used to screen transgenic microalgae, antibiotics selection has raised environmental and food safety concerns, while the observation of fluorescence proteins could be influenced by the endogenous fluorescence of host chloroplasts. As an alternative, this study isolated the purple chromoprotein (CP) from Stichodacyla haddoni (shCP). A plasmid in which shCP cDNA is driven by a heat-inducible promoter was linearized and electroporated into 2.5×108 protoplasts of Nannochloropsis oculata. Following regeneration and cultivation on an f/2 medium plate for two weeks, we observed 26 colonies that displayed a slightly dark green coloration. After individually subculturing and performing five hours of heat shock at 42°C, a dark brown color was mosaically displayed in five of these colonies, indicating that both untransformed and transformed cells were mixed together in each colony. To obtain a uniform expression of shCP throughout the whole colony, we continuously isolated each transformed cell that exhibited brown coloration and subcultured it on a fresh plate, resulting in the generation of five transgenic lines of N. oculata which stably harbored the shCP gene for at least 22 months, as confirmed by PCR detection and observation by the naked eye. As shown by Western blot, exogenous shCP protein was expressed in these transgenic microalgae. Since shCP protein is biodegradable and originates from a marine organism, both environmental and food safety concerns have been eliminated, making this novel shCP reporter gene a simple, but effective and ecologically safe, marker for screening and isolating transgenic microalgae.
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Affiliation(s)
- Chen-Han Shih
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Yin Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Hung-Chieh Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
| | - Huai-Jen Tsai
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
- * E-mail:
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Buhmann MT, Poulsen N, Klemm J, Kennedy MR, Sherrill CD, Kröger N. A tyrosine-rich cell surface protein in the diatom Amphora coffeaeformis identified through transcriptome analysis and genetic transformation. PLoS One 2014; 9:e110369. [PMID: 25372470 PMCID: PMC4220933 DOI: 10.1371/journal.pone.0110369] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
Diatoms are single-celled eukaryotic microalgae that are ubiquitously found in almost all aquatic ecosystems, and are characterized by their intricately structured SiO2 (silica)-based cell walls. Diatoms with a benthic life style are capable of attaching to any natural or man-made submerged surface, thus contributing substantially to both microbial biofilm communities and economic losses through biofouling. Surface attachment of diatoms is mediated by a carbohydrate- and protein- based glue, yet no protein involved in diatom underwater adhesion has been identified so far. In the present work, we have generated a normalized transcriptome database from the model adhesion diatom Amphora coffeaeformis. Using an unconventional bioinformatics analysis we have identified five proteins that exhibit unique amino acid sequences resembling the amino acid composition of the tyrosine-rich adhesion proteins from mussel footpads. Establishing the first method for the molecular genetic transformation of A. coffeaeformis has enabled investigations into the function of one of these proteins, AC3362, through expression as YFP fusion protein. Biochemical analysis and imaging by fluorescence microscopy revealed that AC3362 is not involved in adhesion, but rather plays a role in biosynthesis and/or structural stability of the cell wall. The methods established in the present study have paved the way for further molecular studies on the mechanisms of underwater adhesion and biological silica formation in the diatom A. coffeaeformis.
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Affiliation(s)
- Matthias T. Buhmann
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Jennifer Klemm
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Matthew R. Kennedy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - C. David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nils Kröger
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Department of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
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Development of a nuclear transformation system for Oleaginous Green Alga Lobosphaera (Parietochloris) incisa and genetic complementation of a mutant strain, deficient in arachidonic acid biosynthesis. PLoS One 2014; 9:e105223. [PMID: 25133787 PMCID: PMC4136796 DOI: 10.1371/journal.pone.0105223] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/19/2014] [Indexed: 11/30/2022] Open
Abstract
Microalgae are considered a promising source for various high value products, such as carotenoids, ω-3 and ω-6 polyunsaturated fatty acids (PUFA). The unicellular green alga Lobosphaera (Parietochloris) incisa is an outstanding candidate for the efficient phototrophic production of arachidonic acid (AA), an essential ω-6 PUFA for infant brain development and a widely used ingredient in the baby formula industry. Although phototrophic production of such algal products has not yet been established, estimated costs are considered to be 2–5 times higher than competing heterotrophic production costs. This alga accumulates unprecedented amounts of AA within triacylglycerols and the molecular pathway of AA biosynthesis in L. incisa has been previously elucidated. Thus, progress in transformation and metabolic engineering of this high value alga could be exploited for increasing the efficient production of AA at competitive prices. We describe here the first successful transformation of L. incisa using the ble gene as a selection marker, under the control of the endogenous RBCS promoter. Furthermore, we have succeeded in the functional complementation of the L. incisa mutant strain P127, containing a mutated, inactive version of the delta-5 (Δ5) fatty acid desaturase gene. A copy of the functional Δ5 desaturase gene, linked to the ble selection marker, was transformed into the P127 mutant. The resulting transformants selected for zeocine resistant, had AA biosynthesis partially restored, indicating the functional complementation of the mutant strain with the wild-type gene. The results of this study present a platform for the successful genetic engineering of L. incisa and its long-chain PUFA metabolism.
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Lerche K, Hallmann A. Stable nuclear transformation of Pandorina morum. BMC Biotechnol 2014; 14:65. [PMID: 25031031 PMCID: PMC4115218 DOI: 10.1186/1472-6750-14-65] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/11/2014] [Indexed: 12/04/2022] Open
Abstract
Background Volvocine green algae like Pandorina morum represent one of the most recent inventions of multicellularity diverged from their unicellular relatives. The 8–16 celled P. morum alga and its close multicellular relatives constitute a model lineage for research into cellular differentiation, morphogenesis and epithelial folding, sexual reproduction and evolution of multicellularity. Pandorina is the largest and most complex organism in the volvocine lineage that still exhibits isogamous sexual reproduction. So far, molecular-biological investigations in P. morum were constricted due to the absence of methods for transformation of this species, which is a prerequisite for introduction of reporter genes and (modified) genes of interest. Results Stable nuclear transformation of P. morum was achieved using chimeric constructs with a selectable marker, a reporter gene, promoters and upstream and downstream flanking sequences from heterologous sources. DNA was introduced into the cells by particle bombardment with plasmid-coated gold particles. The aminoglycoside 3′-phosphotransferase VIII (aphVIII) gene of Streptomyces rimosus under control of an artificial, heterologous promoter was used as the selectable marker. The artificial promoter contained a tandem arrangement of the promoter of both the heat shock protein 70A (hsp70A) and the ribulose-1,5-bisphosphat-carboxylase/-oxygenase S3 (rbcS3) gene of Volvox carteri. Due to the expression of aphVIII, transformants gained up to 333-fold higher resistance to paromomycin in comparison to the parent wild-type strain. The heterologous luciferase (gluc) gene of Gaussia princeps, which was previously genetically engineered to match the nuclear codon usage of Chlamydomonas reinhardtii, was used as a co-transformed, unselectable reporter gene. The expression of the co-bombarded gluc gene in transformants and the induction of gluc by heat shock were demonstrated through bioluminescence assays. Conclusion Stable nuclear transformation of P. morum using the particle bombardment technique is now feasible. Functional expression of heterologous genes is achieved using heterologous flanking sequences from Volvox carteri and Chlamydomonas reinhardtii. The aphVIII gene of the actinobacterium S. rimosus can be used as a selectable marker for transformation experiments in the green alga P. morum. The gluc gene of the marine copepod G. princeps, expressed under control of heterologous promoter elements, represents a suitable reporter gene for monitoring gene expression or for other applications in P. morum.
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Affiliation(s)
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany.
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Surveillance of C-allocation in microalgal cells. Metabolites 2014; 4:453-64. [PMID: 24957036 PMCID: PMC4101516 DOI: 10.3390/metabo4020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 11/16/2022] Open
Abstract
When microalgae are exposed to changing environmental conditions, e.g., light-dark cycles or oscillations in nutrient availability (CO2, nitrogen, phosphate or silicate) they respond with metabolic changes in the carbon allocation pattern. Short time regulations in the time range of few seconds to minutes can be mirrored best by mass spectroscopy based metabolomics. However, these snap shots do not reflect the alterations in the carbon flow to the cellular macromolecules like protein, carbohydrate or lipid. In this review it is shown how the combination of FTIR spectroscopy and Chla-in-vivo-fluorescence based electron transport rates can reveal changes in the metabolic flux rates of carbon during a shift of the environmental conditions. The review will demonstrate in which time range FTIR spectroscopy can deliver significant information and how FTIR spectroscopy data can synergistically support metabolome analysis by mass-spectroscopy.
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Profiling of polar lipids in marine oleaginous diatom Fistulifera solaris JPCC DA0580: prediction of the potential mechanism for eicosapentaenoic acid-incorporation into triacylglycerol. Mar Drugs 2014; 12:3218-30. [PMID: 24879545 PMCID: PMC4071573 DOI: 10.3390/md12063218] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/03/2023] Open
Abstract
The marine oleaginous diatom Fistulifera solaris JPCC DA0580 is a candidate for biodiesel production because of its high lipid productivity. However, the substantial eicosapentaenoic acid (EPA) content in this strain would affect the biodiesel quality. On the other hand, EPA is also known as the essential health supplement for humans. EPAs are mainly incorporated into glycerolipids in the microalgal cell instead of the presence as free fatty acids. Therefore, the understanding of the EPA biosynthesis including the incorporation of the EPA into glycerolipids especially triacylglycerol (TAG) is fundamental for regulating EPA content for different purposes. In this study, in order to identify the biosynthesis pathway for the EPA-containing TAG species, a lipidomic characterization of the EPA-enriched polar lipids was performed by using direct infusion electrospray ionization (ESI)-Q-TRAP-MS and MS/MS analyses. The determination of the fatty acid positional distribution showed that the sn-2 position of all the chloroplast lipids and part of phosphatidylcholine (PC) species was occupied by C16 fatty acids. This result suggested the critical role of the chloroplast on the lipid synthesis in F. solaris. Furthermore, the exclusive presence of C18 fatty acids in PC highly indicated the biosynthesis of EPA on PC. Finally, the PC-based acyl-editing and head group exchange processes were proposed to be essential for the incorporation of EPA into TAG and chloroplast lipids.
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64
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Veyel D, Erban A, Fehrle I, Kopka J, Schroda M. Rationales and approaches for studying metabolism in eukaryotic microalgae. Metabolites 2014; 4:184-217. [PMID: 24957022 PMCID: PMC4101502 DOI: 10.3390/metabo4020184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 11/16/2022] Open
Abstract
The generation of efficient production strains is essential for the use of eukaryotic microalgae for biofuel production. Systems biology approaches including metabolite profiling on promising microalgal strains, will provide a better understanding of their metabolic networks, which is crucial for metabolic engineering efforts. Chlamydomonas reinhardtii represents a suited model system for this purpose. We give an overview to genetically amenable microalgal strains with the potential for biofuel production and provide a critical review of currently used protocols for metabolite profiling on Chlamydomonas. We provide our own experimental data to underpin the validity of the conclusions drawn.
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Affiliation(s)
- Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Ines Fehrle
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Technical University of Kaiserslautern, Paul-Ehrlich-Str. 23, D-67663 Kaiserslautern, Germany.
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Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD. Assembly of eukaryotic algal chromosomes in yeast. J Biol Eng 2013; 7:30. [PMID: 24325901 PMCID: PMC4029449 DOI: 10.1186/1754-1611-7-30] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synthetic genomic approaches offer unique opportunities to use powerful yeast and Escherichia coli genetic systems to assemble and modify chromosome-sized molecules before returning the modified DNA to the target host. For example, the entire 1 Mb Mycoplasma mycoides chromosome can be stably maintained and manipulated in yeast before being transplanted back into recipient cells. We have previously demonstrated that cloning in yeast of large (> ~ 150 kb), high G + C (55%) prokaryotic DNA fragments was improved by addition of yeast replication origins every ~100 kb. Conversely, low G + C DNA is stable (up to at least 1.8 Mb) without adding supplemental yeast origins. It has not been previously tested whether addition of yeast replication origins similarly improves the yeast-based cloning of large (>150 kb) eukaryotic DNA with moderate G + C content. The model diatom Phaeodactylum tricornutum has an average G + C content of 48% and a 27.4 Mb genome sequence that has been assembled into chromosome-sized scaffolds making it an ideal test case for assembly and maintenance of eukaryotic chromosomes in yeast. RESULTS We present a modified chromosome assembly technique in which eukaryotic chromosomes as large as ~500 kb can be assembled from cloned ~100 kb fragments. We used this technique to clone fragments spanning P. tricornutum chromosomes 25 and 26 and to assemble these fragments into single, chromosome-sized molecules. We found that addition of yeast replication origins improved the cloning, assembly, and maintenance of the large chromosomes in yeast. Furthermore, purification of the fragments to be assembled by electroelution greatly increased assembly efficiency. CONCLUSIONS Entire eukaryotic chromosomes can be successfully cloned, maintained, and manipulated in yeast. These results highlight the improvement in assembly and maintenance afforded by including yeast replication origins in eukaryotic DNA with moderate G + C content (48%). They also highlight the increased efficiency of assembly that can be achieved by purifying fragments before assembly.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Philip D Weyman
- Department of Synthetic Biology and Bioenergy, J, Craig Venter Institute, 10355 Science Center Dr,, San Diego, CA 92121, USA.
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Schellenberger Costa B, Sachse M, Jungandreas A, Bartulos CR, Gruber A, Jakob T, Kroth PG, Wilhelm C. Aureochrome 1a is involved in the photoacclimation of the diatom Phaeodactylum tricornutum. PLoS One 2013; 8:e74451. [PMID: 24073211 PMCID: PMC3779222 DOI: 10.1371/journal.pone.0074451] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/01/2013] [Indexed: 01/22/2023] Open
Abstract
Aureochromes constitute a family of blue light (BL) receptors which are found exclusively in heterokont algae such as diatoms (Bacillariophyceae) and yellow-green algae (Xanthophyceae). Previous studies on the diatom Phaeodactylum tricornutum indicate that the formation of a high light acclimated phenotype is mediated by the absorption of BL and that aureochromes might play an important role in this process. P. tricornutum possesses four genes encoding aureochromes. In this study we confirm the nuclear localisation of the PtAUREO1a, 1b and 2 proteins. Furthermore we studied the physiology of light quality acclimation in genetically transformed P. tricornutum cell lines with reduced expression of the aureochrome 1a gene. The results demonstrate that the AUREO1a protein has a distinct function in light acclimation. However, rather unexpectedly AUREO1a seems to repress high light acclimation which resulted in a state of ‘hyper’ high light acclimation in aureo1a silenced strains. This was indicated by characteristic changes of several photosynthetic parameters, including increased maximum photosynthesis rates, decreased chlorophyll a contents per cell and increased values of non-photochemical quenching in AUREO1a silenced strains compared to wild type cultures. Strikingly, AUREO1a silenced strains exhibited phenotypic differences compared to wild type cells during cultivation under BL as well as under red light (RL) conditions. Therefore, AUREO1a might influence the RL signalling process, suggesting an interaction of AUREO1a with RL perception pathways.
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Affiliation(s)
| | - Matthias Sachse
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | | | | | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - Torsten Jakob
- Institut für Biologie, Universität Leipzig, Leipzig, Germany
| | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
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Poulsen N, Scheffel A, Sheppard VC, Chesley PM, Kröger N. Pentalysine clusters mediate silica targeting of silaffins in Thalassiosira pseudonana. J Biol Chem 2013; 288:20100-9. [PMID: 23720751 DOI: 10.1074/jbc.m113.469379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biological formation of inorganic materials (biomineralization) often occurs in specialized intracellular vesicles. Prominent examples are diatoms, a group of single-celled eukaryotic microalgae that produce their SiO2 (silica)-based cell walls within intracellular silica deposition vesicles (SDVs). SDVs contain protein-based organic matrices that control silica formation, resulting in species specifically nanopatterned biosilica, an organic-inorganic composite material. So far no information is available regarding the molecular mechanisms of SDV biogenesis. Here we have investigated by fluorescence microscopy and subcellular membrane fractionation the intracellular transport of silaffin Sil3. Silaffins are a group of phosphoproteins constituting the main components of the organic matrix of diatom biosilica. We demonstrate that the N-terminal signal peptide of Sil3 mediates import into a specific subregion of the endoplasmic reticulum. Additional segments from the mature part of Sil3 are required to reach post-endoplasmic reticulum compartments. Further transport of Sil3 and incorporation into the biosilica (silica targeting) require protein segments that contain a high density of modified lysine residues and phosphoserines. Silica targeting of Sil3 is not dependent on a particular peptide sequence, yet a lysine-rich 12-14-amino acid peptide motif (pentalysine cluster), which is conserved in all silaffins, strongly promotes silica targeting. The results of the present work provide the first insight into the molecular mechanisms for biogenesis of mineral-forming vesicles from an eukaryotic organism.
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The central carbon and energy metabolism of marine diatoms. Metabolites 2013; 3:325-46. [PMID: 24957995 PMCID: PMC3901268 DOI: 10.3390/metabo3020325] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 01/27/2023] Open
Abstract
Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.
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69
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Vila M, Díaz-Santos E, de la Vega M, Rodríguez H, Vargas A, León R. Promoter trapping in microalgae using the antibiotic paromomycin as selective agent. Mar Drugs 2012; 10:2749-65. [PMID: 23211713 PMCID: PMC3528124 DOI: 10.3390/md10122749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/12/2012] [Accepted: 11/15/2012] [Indexed: 11/16/2022] Open
Abstract
The lack of highly active endogenous promoters to drive the expression of transgenes is one of the main drawbacks to achieving efficient transformation of many microalgal species. Using the model chlorophyte Chlamydomonas reinhardtii and the paromomycin resistance APHVIII gene from Streptomyces rimosus as a marker, we have demonstrated that random insertion of the promoterless marker gene and subsequent isolation of the most robust transformants allows for the identification of novel strong promoter sequences in microalgae. Digestion of the genomic DNA with an enzyme that has a unique restriction site inside the marker gene and a high number of target sites in the genome of the microalga, followed by inverse PCR, allows for easy determination of the genomic region, which precedes the APHVIII marker gene. In most of the transformants analyzed, the marker gene is inserted in intragenic regions and its expression relies on its adequate insertion in frame with native genes. As an example, one of the new promoters identified was used to direct the expression of the APHVIII marker gene in C. reinhardtii, showing high transformation efficiencies.
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Affiliation(s)
- Marta Vila
- Biochemistry Laboratory, Experimental Sciences Faculty, University of Huelva, Huelva 27071, Spain
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Distribution of the SELMA translocon in secondary plastids of red algal origin and predicted uncoupling of ubiquitin-dependent translocation from degradation. EUKARYOTIC CELL 2012; 11:1472-81. [PMID: 23042132 DOI: 10.1128/ec.00183-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein import into complex plastids of red algal origin is a multistep process including translocons of different evolutionary origins. The symbiont-derived ERAD-like machinery (SELMA), shown to be of red algal origin, is proposed to be the transport system for preprotein import across the periplastidal membrane of heterokontophytes, haptophytes, cryptophytes, and apicomplexans. In contrast to the canonical endoplasmic reticulum-associated degradation (ERAD) system, SELMA translocation is suggested to be uncoupled from proteasomal degradation. We investigated the distribution of known and newly identified SELMA components in organisms with complex plastids of red algal origin by intensive data mining, thereby defining a set of core components present in all examined organisms. These include putative pore-forming components, a ubiquitylation machinery, as well as a Cdc48 complex. Furthermore, the set of known 20S proteasomal components in the periplastidal compartment (PPC) of diatoms was expanded. These newly identified putative SELMA components, as well as proteasomal subunits, were in vivo localized as PPC proteins in the diatom Phaeodactylum tricornutum. The presented data allow us to speculate about the specific features of SELMA translocation in contrast to the canonical ERAD system, especially the uncoupling of translocation from degradation.
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71
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Wang B, Wang J, Zhang W, Meldrum DR. Application of synthetic biology in cyanobacteria and algae. Front Microbiol 2012; 3:344. [PMID: 23049529 PMCID: PMC3446811 DOI: 10.3389/fmicb.2012.00344] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO2 and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed.
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Affiliation(s)
- Bo Wang
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University Tempe, AZ, USA ; Biological Design Graduate Program, Arizona State University Tempe, AZ, USA
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Hempel F, Maier UG. An engineered diatom acting like a plasma cell secreting human IgG antibodies with high efficiency. Microb Cell Fact 2012; 11:126. [PMID: 22970838 PMCID: PMC3503769 DOI: 10.1186/1475-2859-11-126] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although there are many different expression systems for recombinant production of pharmaceutical proteins, many of these suffer from drawbacks such as yield, cost, complexity of purification, and possible contamination with human pathogens. Microalgae have enormous potential for diverse biotechnological applications and currently attract much attention in the biofuel sector. Still underestimated, though, is the idea of using microalgae as solar-fueled expression system for the production of recombinant proteins. RESULTS In this study, we show for the first time that completely assembled and functional human IgG antibodies can not only be expressed to high levels in algal systems, but also secreted very efficiently into the culture medium. We engineered the diatom Phaeodactylum tricornutum to synthesize and secrete a human IgG antibody against the Hepatitis B Virus surface protein. As the diatom P. tricornutum is not known to naturally secrete many endogenous proteins, the secreted antibodies are already very pure making extensive purification steps redundant and production extremely cost efficient. CONCLUSIONS Microalgae combine rapid growth rates with all the advantages of eukaryotic expression systems, and offer great potential for solar-powered, low cost production of pharmaceutical proteins.
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Affiliation(s)
- Franziska Hempel
- LOEWE Center for Synthetic Microbiology-SYNMIKRO, Hans-Meerwein-Strasse, Marburg D-35032, Germany.
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73
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Jinkerson RE, Radakovits R, Posewitz MC. Genomic insights from the oleaginous model alga Nannochloropsis gaditana. Bioengineered 2012; 4:37-43. [PMID: 22922732 PMCID: PMC3566019 DOI: 10.4161/bioe.21880] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nannochloropsis species have emerged as leading phototrophic microorganisms for the production of biofuels. Several isolates produce large quantities of triacylglycerols, grow rapidly, and can be cultivated at industrial scales. Recently, the mitochondrial, plastid and nuclear genomes of Nannochloropsis gaditana were sequenced. Genomic interrogation revealed several key features that likely facilitate the oleaginous phenotype observed in Nannochloropsis, including an over-representation of genes involved in lipid biosynthesis. Here we present additional analyses on gene orientation, vitamin B12 requiring enzymes, the acetyl-CoA metabolic node, and codon usage in N. gaditana. Nuclear genome transformation methods are established with exogenous DNA integration occurring via either random incorporation or by homologous recombination, making Nannochloropsis amenable to both forward and reverse genetic engineering. Completion of a draft genomic sequence, establishment of transformation techniques, and robust outdoor growth properties have positioned Nannochloropsis as a new model alga with significant potential for further development into an integrated photons-to-fuel production platform.
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Affiliation(s)
- Robert E Jinkerson
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, USA
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Maumus F, Rabinowicz P, Bowler C, Rivarola M. Stemming epigenetics in marine stramenopiles. Curr Genomics 2012; 12:357-70. [PMID: 22294878 PMCID: PMC3145265 DOI: 10.2174/138920211796429727] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 05/24/2011] [Accepted: 06/17/2011] [Indexed: 12/27/2022] Open
Abstract
Epigenetics include DNA methylation, the modification of histone tails that affect chromatin states, and small RNAs that are involved in the setting and maintenance of chromatin modifications. Marine stramenopiles (MAS), which are a diverse assemblage of algae that acquired photosynthesis from secondary endosymbiosis, include single-celled organisms such as diatoms as well as multicellular forms such as brown algae. The recent publication of two diatom genomes that diverged ~90 million years ago (mya), as well as the one of a brown algae that diverged from diatoms ~250 Mya, provide a great system of related, yet diverged set of organisms to compare epigenetic marks and their relationships. For example, putative DNA methyltransferase homologues were found in diatoms while none could be identified in the brown algal genome. On the other hand, no canonical DICER-like protein was found in diatoms in contrast to what is observed in brown algae. A key interest relies in understanding the adaptive nature of epigenetics and its inheritability. In contrast to yeast that lack DNA methylation, homogeneous cultures of diatoms constitute an attractive system to study epigenetic changes in response to environmental conditions such as nutrient-rich to nutrient-poor transitions which is especially relevant because of their ecological importance. P. tricornutum is also of outstanding interest because it is observed as three different morphotypes and thus constitutes a simple and promising model for the study of the epigenetic phenomena that accompany cellular differentiation. In this review we focus on the insights obtained from MAS comparative genomics and epigenomic analyses.
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Affiliation(s)
- Florian Maumus
- Unité de Recherche en Génomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France
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Lavaud J, Materna AC, Sturm S, Vugrinec S, Kroth PG. Silencing of the violaxanthin de-epoxidase gene in the diatom Phaeodactylum tricornutum reduces diatoxanthin synthesis and non-photochemical quenching. PLoS One 2012; 7:e36806. [PMID: 22629333 PMCID: PMC3356336 DOI: 10.1371/journal.pone.0036806] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 04/13/2012] [Indexed: 11/19/2022] Open
Abstract
Diatoms are a major group of primary producers ubiquitous in all aquatic ecosystems. To protect themselves from photooxidative damage in a fluctuating light climate potentially punctuated with regular excess light exposures, diatoms have developed several photoprotective mechanisms. The xanthophyll cycle (XC) dependent non-photochemical chlorophyll fluorescence quenching (NPQ) is one of the most important photoprotective processes that rapidly regulate photosynthesis in diatoms. NPQ depends on the conversion of diadinoxanthin (DD) into diatoxanthin (DT) by the violaxanthin de-epoxidase (VDE), also called DD de-epoxidase (DDE). To study the role of DDE in controlling NPQ, we generated transformants of P. tricornutum in which the gene (Vde/Dde) encoding for DDE was silenced. RNA interference was induced by genetic transformation of the cells with plasmids containing either short (198 bp) or long (523 bp) antisense (AS) fragments or, alternatively, with a plasmid mediating the expression of a self-complementary hairpin-like construct (inverted repeat, IR). The silencing approaches generated diatom transformants with a phenotype clearly distinguishable from wildtype (WT) cells, i.e. a lower degree as well as slower kinetics of both DD de-epoxidation and NPQ induction. Real-time PCR based quantification of Dde transcripts revealed differences in transcript levels between AS transformants and WT cells but also between AS and IR transformants, suggesting the possible presence of two different gene silencing mediating mechanisms. This was confirmed by the differential effect of the light intensity on the respective silencing efficiency of both types of transformants. The characterization of the transformants strengthened some of the specific features of the XC and NPQ and confirmed the most recent mechanistic model of the DT/NPQ relationship in diatoms.
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Affiliation(s)
- Johann Lavaud
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
- UMR7266 ‘LIENSs,’ CNRS/University of La Rochelle, Institute for Coastal and Environmental Research, La Rochelle, France
| | - Arne C. Materna
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - Sabine Sturm
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
- * E-mail:
| | - Sascha Vugrinec
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
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Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC. Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana. Nat Commun 2012; 3:686. [PMID: 22353717 PMCID: PMC3293424 DOI: 10.1038/ncomms1688] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/17/2012] [Indexed: 11/09/2022] Open
Abstract
The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.
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Affiliation(s)
- Randor Radakovits
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA
- These authors contributed equally to this work
| | - Robert E. Jinkerson
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA
- These authors contributed equally to this work
| | | | - Hongseok Tae
- Data Analysis Core, Virginia Bioinformatics Institute, Virginia Tech, 1 Washington Street, Blacksburg, Virginia 24060, USA
| | - Robert E. Settlage
- Data Analysis Core, Virginia Bioinformatics Institute, Virginia Tech, 1 Washington Street, Blacksburg, Virginia 24060, USA
| | - Jeffrey L. Boore
- Genome Project Solutions, 1024 Promenade Street, Hercules, California 94547, USA
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA
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Hempel F, Lau J, Klingl A, Maier UG. Algae as protein factories: expression of a human antibody and the respective antigen in the diatom Phaeodactylum tricornutum. PLoS One 2011; 6:e28424. [PMID: 22164289 PMCID: PMC3229587 DOI: 10.1371/journal.pone.0028424] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 11/08/2011] [Indexed: 12/29/2022] Open
Abstract
Microalgae are thought to offer great potential as expression system for various industrial, therapeutic and diagnostic recombinant proteins as they combine high growth rates with all benefits of eukaryotic expression systems. Moreover, microalgae exhibit a phototrophic lifestyle like land plants, hence protein expression is fuelled by photosynthesis, which is CO2-neutral and involves only low production costs. So far, however, research on algal bioreactors for recombinant protein expression is very rare calling for further investigations in this highly promising field. In this study, we present data on the expression of a monoclonal human IgG antibody against the Hepatitis B surface protein and the respective antigen in the diatom Phaeodactylum tricornutum. Antibodies are fully-assembled and functional and accumulate to 8.7% of total soluble protein, which complies with 21 mg antibody per gram algal dry weight. The Hepatitis B surface protein is functional as well and is recognized by algae-produced and commercial antibodies.
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Affiliation(s)
- Franziska Hempel
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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78
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High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. Proc Natl Acad Sci U S A 2011; 108:21265-9. [PMID: 22123974 DOI: 10.1073/pnas.1105861108] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for Nannochloropsis sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that Nannochloropsis is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology.
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79
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Hempel F, Bozarth AS, Lindenkamp N, Klingl A, Zauner S, Linne U, Steinbüchel A, Maier UG. Microalgae as bioreactors for bioplastic production. Microb Cell Fact 2011; 10:81. [PMID: 22004563 PMCID: PMC3214846 DOI: 10.1186/1475-2859-10-81] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/17/2011] [Indexed: 11/21/2022] Open
Abstract
Background Poly-3-hydroxybutyrate (PHB) is a polyester with thermoplastic properties that is naturally occurring and produced by such bacteria as Ralstonia eutropha H16 and Bacillus megaterium. In contrast to currently utilized plastics and most synthetic polymers, PHB is biodegradable, and its production is not dependent on fossil resources making this bioplastic interesting for various industrial applications. Results In this study, we report on introducing the bacterial PHB pathway of R. eutropha H16 into the diatom Phaeodactylum tricornutum, thereby demonstrating for the first time that PHB production is feasible in a microalgal system. Expression of the bacterial enzymes was sufficient to result in PHB levels of up to 10.6% of algal dry weight. The bioplastic accumulated in granule-like structures in the cytosol of the cells, as shown by light and electron microscopy. Conclusions Our studies demonstrate the great potential of microalgae like the diatom P. tricornutum to serve as solar-powered expression factories and reveal great advantages compared to plant based production systems.
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Affiliation(s)
- Franziska Hempel
- LOEWE Research Centre for Synthetic Microbiology, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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80
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A single peroxisomal targeting signal mediates matrix protein import in diatoms. PLoS One 2011; 6:e25316. [PMID: 21966495 PMCID: PMC3178647 DOI: 10.1371/journal.pone.0025316] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/31/2011] [Indexed: 12/04/2022] Open
Abstract
Peroxisomes are single membrane bound compartments. They are thought to be present in almost all eukaryotic cells, although the bulk of our knowledge about peroxisomes has been generated from only a handful of model organisms. Peroxisomal matrix proteins are synthesized cytosolically and posttranslationally imported into the peroxisomal matrix. The import is generally thought to be mediated by two different targeting signals. These are respectively recognized by the two import receptor proteins Pex5 and Pex7, which facilitate transport across the peroxisomal membrane. Here, we show the first in vivo localization studies of peroxisomes in a representative organism of the ecologically relevant group of diatoms using fluorescence and transmission electron microscopy. By expression of various homologous and heterologous fusion proteins we demonstrate that targeting of Phaeodactylum tricornutum peroxisomal matrix proteins is mediated only by PTS1 targeting signals, also for proteins that are in other systems imported via a PTS2 mode of action. Additional in silico analyses suggest this surprising finding may also apply to further diatoms. Our data suggest that loss of the PTS2 peroxisomal import signal is not reserved to Caenorhabditis elegans as a single exception, but has also occurred in evolutionary divergent organisms. Obviously, targeting switching from PTS2 to PTS1 across different major eukaryotic groups might have occurred for different reasons. Thus, our findings question the widespread assumption that import of peroxisomal matrix proteins is generally mediated by two different targeting signals. Our results implicate that there apparently must have been an event causing the loss of one targeting signal even in the group of diatoms. Different possibilities are discussed that indicate multiple reasons for the detected targeting switching from PTS2 to PTS1.
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81
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Gong Y, Hu H, Gao Y, Xu X, Gao H. Microalgae as platforms for production of recombinant proteins and valuable compounds: progress and prospects. J Ind Microbiol Biotechnol 2011; 38:1879-90. [PMID: 21882013 DOI: 10.1007/s10295-011-1032-6] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/19/2011] [Indexed: 12/19/2022]
Abstract
Over the last few years microalgae have gained increasing interest as a natural source of valuable compounds and as bioreactors for recombinant protein production. Natural high-value compounds including pigments, long-chain polyunsaturated fatty acids, and polysaccharides, which have a wide range of applications in the food, feed, cosmetics, and pharmaceutical industries, are currently produced with nontransgenic microalgae. However, transgenic microalgae can be used as bioreactors for the production of therapeutic and industrially relevant recombinant proteins. This technology shows great promise to simplify the production process and significantly decrease the production costs. To date, a variety of recombinant proteins have been produced experimentally from the nuclear or chloroplast genome of transgenic Chlamydomonas reinhardtii. These include monoclonal antibodies, vaccines, hormones, pharmaceutical proteins, and others. In this review, we outline recent progress in the production of recombinant proteins with transgenic microalgae as bioreactors, methods for genetic transformation of microalgae, and strategies for highly efficient expression of heterologous genes. In particular, we highlight the importance of maximizing the value of transgenic microalgae through producing recombinant proteins together with recovery of natural high-value compounds. Finally, we outline some important issues that need to be addressed before commercial-scale production of high-value recombinant proteins and compounds from transgenic microalgae can be realized.
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Affiliation(s)
- Yangmin Gong
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, Hubei, China
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82
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Huang A, He L, Wang G. Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics 2011; 12:337. [PMID: 21718527 PMCID: PMC3141676 DOI: 10.1186/1471-2164-12-337] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 06/30/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. RESULTS A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on. CONCLUSIONS Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.
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Affiliation(s)
- Aiyou Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, China
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83
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Felsner G, Sommer MS, Gruenheit N, Hempel F, Moog D, Zauner S, Martin W, Maier UG. ERAD components in organisms with complex red plastids suggest recruitment of a preexisting protein transport pathway for the periplastid membrane. Genome Biol Evol 2010; 3:140-50. [PMID: 21081314 PMCID: PMC3045029 DOI: 10.1093/gbe/evq074] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The plastids of cryptophytes, haptophytes, and heterokontophytes (stramenopiles) (together once known as chromists) are surrounded by four membranes, reflecting the origin of these plastids through secondary endosymbiosis. They share this trait with apicomplexans, which are alveolates, the plastids of which have been suggested to stem from the same secondary symbiotic event and therefore form a phylogenetic clade, the chromalveolates. The chromists are quantitatively the most important eukaryotic contributors to primary production in marine ecosystems. The mechanisms of protein import across their four plastid membranes are still poorly understood. Components of an endoplasmic reticulum-associated degradation (ERAD) machinery in cryptophytes, partially encoded by the reduced genome of the secondary symbiont (the nucleomorph), are implicated in protein transport across the second outermost plastid membrane. Here, we show that the haptophyte Emiliania huxleyi, like cryptophytes, stramenopiles, and apicomplexans, possesses a nuclear-encoded symbiont-specific ERAD machinery (SELMA, symbiont-specific ERAD-like machinery) in addition to the host ERAD system, with targeting signals that are able to direct green fluorescent protein or yellow fluorescent protein to the predicted cellular localization in transformed cells of the stramenopile Phaeodactylum tricornutum. Phylogenies of the duplicated ERAD factors reveal that all SELMA components trace back to a red algal origin. In contrast, the host copies of cryptophytes and haptophytes associate with the green lineage to the exclusion of stramenopiles and alveolates. Although all chromalveolates with four membrane-bound plastids possess the SELMA system, this has apparently not arisen in a single endosymbiotic event. Thus, our data do not support the chromalveolate hypothesis.
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Affiliation(s)
- Gregor Felsner
- Department of Cell Biology, Philipps University of Marburg, Marburg, Germany
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84
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Jiroutová K, Kořený L, Bowler C, Oborník M. A gene in the process of endosymbiotic transfer. PLoS One 2010; 5:e13234. [PMID: 20949086 PMCID: PMC2950852 DOI: 10.1371/journal.pone.0013234] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 09/13/2010] [Indexed: 12/02/2022] Open
Abstract
Background The endosymbiotic birth of organelles is accompanied by massive transfer of endosymbiont genes to the eukaryotic host nucleus. In the centric diatom Thalassiosira pseudonana the Psb28 protein is encoded in the plastid genome while a second version is nuclear-encoded and possesses a bipartite N-terminal presequence necessary to target the protein into the diatom complex plastid. Thus it can represent a gene captured during endosymbiotic gene transfer. Methodology/Principal Findings To specify the origin of nuclear- and plastid-encoded Psb28 in T. pseudonana we have performed extensive phylogenetic analyses of both mentioned genes. We have also experimentally tested the intracellular location of the nuclear-encoded Psb28 protein (nuPsb28) through transformation of the diatom Phaeodactylum tricornutum with the gene in question fused to EYFP. Conclusions/Significance We show here that both versions of the psb28 gene in T. pseudonana are transcribed. We also provide experimental evidence for successful targeting of the nuPsb28 fused with EYFP to the diatom complex plastid. Extensive phylogenetic analyses demonstrate that nucleotide composition of the analyzed genes deeply influences the tree topology and that appropriate methods designed to deal with a compositional bias of the sequences and the long branch attraction artefact (LBA) need to be used to overcome this obstacle. We propose that nuclear psb28 in T. pseudonana is a duplicate of a plastid localized version, and that it has been transferred from its endosymbiont.
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Affiliation(s)
- Kateřina Jiroutová
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Luděk Kořený
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, Ecole Normale Supérieure, Paris, France
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
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85
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Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, De Martino A, Heijde M, Kaas R, La Roche J, Lopez PJ, Martin-Jézéquel V, Meichenin A, Mock T, Schnitzler Parker M, Vardi A, Armbrust EV, Weissenbach J, Katinka M, Bowler C. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol 2010; 11:R85. [PMID: 20738856 PMCID: PMC2945787 DOI: 10.1186/gb-2010-11-8-r85] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 05/11/2010] [Accepted: 08/25/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. RESULTS We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. CONCLUSIONS The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
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Affiliation(s)
- Uma Maheswari
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Current address: EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamel Jabbari
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Jean-Louis Petit
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Betina M Porcel
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Andrew E Allen
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Current address: J Craig Venter Institute, 11149 N. Torrey Pines Rd, Suite 220, La Jolla, CA 92037, USA
| | - Jean-Paul Cadoret
- Physiologie et Biotechnologie des Algues, IFREMER, BP 21105, 44311 Nantes, France
| | - Alessandra De Martino
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Marc Heijde
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, BP 21105, 44311 Nantes, France
| | - Julie La Roche
- Marine Biogeochemistry, IFM-GEOMAR Leibniz-Institut für Meereswissenschaften, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Pascal J Lopez
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Véronique Martin-Jézéquel
- Université de Nantes, EA 2160, Laboratoire 'Mer, Molécule, Santé', Faculté des Sciences et Techniques, 2 rue de la Houssinière, 44322, BP 92208, 44322 Nantes Cedex 3, France
| | - Agnès Meichenin
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Thomas Mock
- School of Oceanography, University of Washington, 616 NE Northlake Place, Seattle, WA 98105, USA
- University of East Anglia, School of Environmental Sciences, Norwich Research Park, Norwich NR4 7TJ, UK
| | | | - Assaf Vardi
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - E Virginia Armbrust
- School of Oceanography, University of Washington, 616 NE Northlake Place, Seattle, WA 98105, USA
| | - Jean Weissenbach
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Michaël Katinka
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
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Radakovits R, Jinkerson RE, Darzins A, Posewitz MC. Genetic engineering of algae for enhanced biofuel production. EUKARYOTIC CELL 2010; 9:486-501. [PMID: 20139239 PMCID: PMC2863401 DOI: 10.1128/ec.00364-09] [Citation(s) in RCA: 517] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
There are currently intensive global research efforts aimed at increasing and modifying the accumulation of lipids, alcohols, hydrocarbons, polysaccharides, and other energy storage compounds in photosynthetic organisms, yeast, and bacteria through genetic engineering. Many improvements have been realized, including increased lipid and carbohydrate production, improved H(2) yields, and the diversion of central metabolic intermediates into fungible biofuels. Photosynthetic microorganisms are attracting considerable interest within these efforts due to their relatively high photosynthetic conversion efficiencies, diverse metabolic capabilities, superior growth rates, and ability to store or secrete energy-rich hydrocarbons. Relative to cyanobacteria, eukaryotic microalgae possess several unique metabolic attributes of relevance to biofuel production, including the accumulation of significant quantities of triacylglycerol; the synthesis of storage starch (amylopectin and amylose), which is similar to that found in higher plants; and the ability to efficiently couple photosynthetic electron transport to H(2) production. Although the application of genetic engineering to improve energy production phenotypes in eukaryotic microalgae is in its infancy, significant advances in the development of genetic manipulation tools have recently been achieved with microalgal model systems and are being used to manipulate central carbon metabolism in these organisms. It is likely that many of these advances can be extended to industrially relevant organisms. This review is focused on potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes.
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Affiliation(s)
- Randor Radakovits
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
| | - Robert E. Jinkerson
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
| | - Al Darzins
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
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87
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Bullmann L, Haarmann R, Mirus O, Bredemeier R, Hempel F, Maier UG, Schleiff E. Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates. J Biol Chem 2009; 285:6848-56. [PMID: 20042599 DOI: 10.1074/jbc.m109.074807] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. They possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. Today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. In particular, how proteins cross the third outermost membrane has remained unexplained. We identified a protein in the third outermost membrane of the diatom Phaeodactylum tricornutum with properties comparable to those of the Omp85 family. We demonstrate that the targeting route of P. tricornutum Omp85 parallels that of the translocation channel of the outer envelope membrane of chloroplasts, Toc75. In addition, the electrophysiological properties are similar to those of the Omp85 proteins involved in protein translocation. This supports the hypothesis that P. tricornutum Omp85 is involved in precursor protein translocation, which would close a gap in the fundamental understanding of the evolutionary origin and function of protein import in secondary plastids.
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Affiliation(s)
- Lars Bullmann
- Cell Biology, Philipps-University Marburg, D-35032 Marburg, Germany
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88
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Lippmeier JC, Crawford KS, Owen CB, Rivas AA, Metz JG, Apt KE. Characterization of Both Polyunsaturated Fatty Acid Biosynthetic Pathways in Schizochytrium sp. Lipids 2009; 44:621-30. [DOI: 10.1007/s11745-009-3311-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 05/01/2009] [Indexed: 10/20/2022]
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89
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De Riso V, Raniello R, Maumus F, Rogato A, Bowler C, Falciatore A. Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res 2009; 37:e96. [PMID: 19487243 PMCID: PMC2724275 DOI: 10.1093/nar/gkp448] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Diatoms are a major but poorly understood phytoplankton group. The recent completion of two whole genome sequences has revealed that they contain unique combinations of genes, likely recruited during their history as secondary endosymbionts, as well as by horizontal gene transfer from bacteria. A major limitation for the study of diatom biology and gene function is the lack of tools to generate targeted gene knockout or knockdown mutants. In this work, we have assessed the possibility of triggering gene silencing in Phaeodactylum tricornutum using constructs containing either anti-sense or inverted repeat sequences of selected target genes. We report the successful silencing of a GUS reporter gene expressed in transgenic lines, as well as the knockdown of endogenous phytochrome (DPH1) and cryptochrome (CPF1) genes. To highlight the utility of the approach we also report the first phenotypic characterization of a diatom mutant (cpf1). Our data open the way for reverse genetics in diatoms and represent a major advance for understanding their biology and ecology. Initial molecular analyses reveal that targeted downregulation likely occurs through transcriptional and post-transcriptional gene silencing mechanisms. Interestingly, molecular players involved in RNA silencing in other eukaryotes are only poorly conserved in diatoms.
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Affiliation(s)
- Valentina De Riso
- Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
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90
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Abstract
Two genome sequences of diatoms, marine single-celled photosynthetic eukaryotes that often have ornate cell walls, give insights into their metabolic and signaling systems. The results of two published genome sequences from marine diatoms provide basic insights into how these remarkable organisms evolved to become one of the most successful groups of eukaryotic algae in the contemporary ocean.
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Affiliation(s)
- Assaf Vardi
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08540, USA
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91
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Cadoret JP, Bardor M, Lerouge P, Cabigliera M, Henriquez V, Carlier A. Les microalgues. Med Sci (Paris) 2008; 24:375-82. [DOI: 10.1051/medsci/2008244375] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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92
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Gould SB, Sommer MS, Hadfi K, Zauner S, Kroth PG, Maier UG. Protein targeting into the complex plastid of cryptophytes. J Mol Evol 2006; 62:674-81. [PMID: 16752208 DOI: 10.1007/s00239-005-0099-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 07/25/2005] [Indexed: 11/24/2022]
Abstract
The cryptophyte Guillardia theta harbors a plastid surrounded by four membranes. This turns protein targeting of nucleus-encoded endosymbiont localized proteins into quite a challenge, as the respective precursors have to pass either all four membranes to reach the plastid stroma or only the outermost two membranes to enter the periplastidal compartment. Therefore two sets of nuclear-encoded proteins imported into the endosymbiont can be distinguished and their topogenic signals may serve as good indicators for studying protein targeting and subsequent transport across the outermost membranes of the cryptophyte plastid. We isolated genes encoding enzymes involved in two different biochemical pathways, both of which are predicted to be localized inside the periplastidal compartment, and compared their topogenic signals to those of precursor proteins for the plastid stroma, which are encoded on either the nucleus or the nucleomorph. By this and exemplary in vitro and in vivo analyses of the topogenic signal of one protein localized in the periplastidal compartment, we present new data implicating the mechanism of targeting and transport of proteins to and across the outermost plastid membranes. Furthermore, we demonstrate that one single, but conserved amino acid is the triggering key for the discrimination between nucleus-encoded plastid and periplastidal proteins.
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Affiliation(s)
- Sven B Gould
- Cell Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, 35042, Marburg, Germany
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93
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Tanaka Y, Nakatsuma D, Harada H, Ishida M, Matsuda Y. Localization of soluble beta-carbonic anhydrase in the marine diatom Phaeodactylum tricornutum. Sorting to the chloroplast and cluster formation on the girdle lamellae. PLANT PHYSIOLOGY 2005; 138:207-17. [PMID: 15849303 PMCID: PMC1104176 DOI: 10.1104/pp.104.058982] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 02/20/2005] [Accepted: 02/21/2005] [Indexed: 05/19/2023]
Abstract
A beta-carbonic anhydrase (CA) in the marine diatom Phaeodactylum tricornutum (PtCA1) is encoded by the nuclear genome. This enzyme was previously found to be important for the operation of photosynthesis with a high affinity for dissolved inorganic carbon. A cDNA sequence that encodes PtCA1 (ptca1) was shown to possess a presequence of 138 bp (pre138), which encodes an N-terminal sequence of 46 amino acids (Pre46AA) that does not exist in the mature PtCA1. In this study, pre138 was ligated with the enhanced green fluorescent protein (GFP) gene (egfp), and introduced into P. tricornutum by microprojectile bombardment. Subsequently, the expressed Pre46AA-GFP fusion was shown to be localized in the chloroplast stroma, whereas the expressed GFP without Pre46AA was localized in the cytoplasm. Insertion of the DNA sequence, encoding a mature region of ptca1 (mptca1) between pre138 and egfp, resulted in the formation of particles with concentrated GFP fluorescence in the stroma of P. tricornutum. These particles, 0.3 to 3.0 mum in size, were shown to be distinct from the mitochondria and localized on the surface of the putative girdle lamella. The attachment of the initial one-half of the pre138 to the mptca1-egfp fusion caused the expressed GFP fusion to accumulate in areas surrounding the chloroplast, presumably due to the presence of the endoplasmic reticulum signal encoded by the initial half-sequence and to the absence of the chloroplast transit sequence. These results indicate that PtCA1 is targeted to the stroma by the bipartite sequences of Pre46AA and that the observed GFP particles are formed specifically in the stroma due to the function of the mptca1.
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Affiliation(s)
- Yuji Tanaka
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337 Hyogo, Japan
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94
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Affiliation(s)
- Arthur R Grossman
- The Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA.
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95
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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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96
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Abstract
Plant transformation has its roots in the research on Agrobacterium that was being undertaken in the early 1980s. The last two decades have seen significant developments in plant transformation technology, such that a large number of transgenic crop plants have now been released for commercial production. Advances in the technology have been due to development of a range of Agrobacterium-mediated and direct DNA delivery techniques, along with appropriate tissue culture techniques for regenerating whole plants from plant cells or tissues in a large number of species. In addition, parallel developments in molecular biology have greatly extended the range of investigations to which plant transformation technology can be applied. Research in plant transformation is concentrating now not so much on the introduction of DNA into plant cells, but rather more on the problems associated with stable integration and reliable expression of the DNA once it has been integrated.
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Affiliation(s)
- C A Newell
- Department of Plant Sciences, University of Cambridge, UK
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