Sumario:
The International Journal of Developmental Biology
Linking Development, Stem Cells and Cancer Research
Euskal Herriko Unibertsitateko Argitalpen Zerbitzua / Servicio Editorial de la Universidad del País Vasco / University of the Basque Country Press
Volume 57 - Numbers 6/7/8 (2013) - Special Issue Editor-in-Chief: Juan Aréchaga
MORE INFORMATION [Abstract - FullText / FullText Open Access]
ISSN: 0214-6282 / ISSN-e: 1696-3547 www.intjdevbiol.com
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Special Issue: PLANT TRANSGENESIS
Guest Editors: Mieke Van Lijsebettens and Geert Angenon
CONTENTS + ABSTRACTS
Preface
Thirty years of transgenic research in plants
Mieke Van Lijsebettens and Geert Angenon
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 445-447
Agrobacterium tumefaciens – the gate to plant transgenesis
Fundamental discoveries and simple recombination between circular plasmid DNAs led to widespread use of Agrobacterium tumefaciens as a generalized vector for plant genetic engineering
Patricia Zambryski
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 449-452
From the tumor-inducing principle to plant biotechnology and its importance for society
Geert Angenon, Mieke Van Lijsebettensand Marc Van Montagu
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 453-460
Transgenic plants: from first successes to future applications
Mieke Van Lijsebettens, Geert Angenon and Marc De Block
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 461-465
The roles of bacterial and host plant factors in Agrobacterium-mediated genetic transformation
Benoît Lacroix and Vitaly Citovsky
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 467-481
Higher plant transformation: principles and molecular tools
Sylvester Anami, Elizabeth Njuguna, Griet Coussens, Stijn Aesaert and Mieke Van Lijsebettens
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 483-494
Genetic transformation of major cereal crops
Qing Ji, Xing Xu and Kan Wang
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 495-508
Transgenic technology in basic research
Transgenes and their contributions to epigenetic research
Peter Meyer
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 509-515
High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system
Mieko Higuchi-Takeuchi, Masaki Mori and Minami Matsui
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 517-523
From jellyfish to biosensors: the use of fluorescent proteins in plants
Ute Voss, Antoine Larrieu and Darren M. Wells
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 525-533
Fluorescent protein marker lines in maize: generation and applications
Qingyu Wu, Anding Luo, Tara Zadrozny, Anne Sylvester and Dave Jackson
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 535-543
The use of fluorescence-activated cell sorting in studying plant development and environmental responses
Anthony D. Carter, Roxanna Bonyadi and Miriam L. Gifford
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 545-552
The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function
Christoph Strotbek, Stefan Krinninger and Wolfgang Frank
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 553-564
Biotechnological applications
Engineering metabolic pathways in plants by multigene transformation
Uxue Zorrilla-López, Gemma Masip, Gemma Arjó, Chao Bai, Raviraj Banakar, Ludovic Bassie, Judit Berman, Gemma Farré, Bruna Miralpeix, Eduard Pérez-Massot, Maite Sabalza, Georgina Sanahuja, Evangelia Vamvaka, Richard M. Twyman, Paul Christou, Changfu Zhu and Teresa Capell
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 565-576
Transformation of leguminous plants to study symbiotic interactions
Anelia Iantcheva, Kirankumar S. Mysore and Pascal Ratet
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 577-586
Role of plant expression systems in antibody production for passive immunization
Vikram Virdi and Ann Depicker
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 587-593
Biotechnology of nutrient uptake and assimilation in plants
Damar L. López-Arredondo, Marco A. Leyva-González, Fulgencio Alatorre-Cobos and Luis Herrera-Estrella
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 595-610
Transfer of knowledge about flowering and vegetative propagation from model species to bulbous plants
Hendrika A.C.F. Leeggangers, Natalia Moreno-Pachon, Henk Gude and Richard G.H. Immink
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 611-620
Advances in transgene technology
Directed genome engineering for genome optimization
Kathleen D’Halluin and Rene Ruiter
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 621-627
Gene targeting in plants: 25 years later
Holger Puchta and Friedrich Fauser
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 629-637
From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes
Ira Marton, Arik Honig, Ayelet Omid, Noam De Costa, Elena Marhevka, Barry Cohen, Amir Zuker and Alexander Vainstein
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 639-650
Engineered plant minichromosomes
Andreas Houben, Michael F. Mette, Chee H. Teo, Inna Lermontova and Ingo Schubert
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 651-657
Transformation of the mitochondrial genome
Véronique Larosa and Claire Remacle
EHU/UPV/UBC - The International Journal of Developmental Biology (2013) 57: 659-665
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ABSTRACTS
Preface
EHU/UPV/UBC - The International Journal of Developmental Biology 57: 445-447 (2013)
doi: 10.1387/ijdb.130062mv / © UBC Press (www.a360grados.net)
Thirty years of transgenic research in plants
Mieke Van Lijsebettens and Geert Angenon
Ghent and Brussels
Abstract: In 1983, the first transgenic tissues and plants were generated by means of disarmed Agrobacterium tumefaciens strains, in which the oncogenes had been replaced by antibiotic resistance markers. Hence, this Special Issue of The International Journal of Developmental Biology celebrates 30 years of transgenic research in plants! Eminent scientists working in the field of plant transformation or plant biotechnology have contributed to this publication and reviewed the state-of-the-art of their particular subdomain or summarized the importance of transgenic research in the discovery of new mechanisms and the establishment of an entirely new field, such as epigenetics.
Keywords: Plant Transgenesis
Agrobacterium tumefaciens – the gate to plant transgenesis ---------------------
EHU/UPV/UBC - The International Journal of Developmental Biology 57: 449-452 (2013)
doi: 10.1387/ijdb.130190pz / © UBC Press (www.a360grados.net)
Fundamental discoveries and simple recombination between circular plasmid DNAs led to widespread use of Agrobacterium tumefaciens as a generalized vector for plant genetic engineering
Patricia Zambryski
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
Abstract: Fundamental research aimed to determine the limits of the Agrobacterium transfer DNA (T-DNA) element that stably inserted into plant nuclear DNA to cause crown gall tumor formation. The T-DNA borders were discovered to be exceedingly precise, revealing that T-DNA insertion into the plant genome was reproducible and exact. Deletion of the internal regions of the T-DNA, to remove the tumor forming genes, while retaining the T-DNA borders, resulted again in efficient DNA transfer to plant cells, but now such cells were capable of completely normal growth and differentiation. Thus, the internal region of the T-DNA was not needed for DNA transfer, and one could envisage insertion of any DNA of interest in between the T-DNA borders. Thus began plant genetic engineering.
Keywords: plant transformation, genetic engineering, tumor forming gene, crown gall, T-DNA border
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 453-460 (2013)
doi: 10.1387/ijdb.130295ga / © UBC Press (www.a360grados.net)
From the tumor-inducing principle to plant biotechnology and its importance for society
Geert Angenon 1, Mieke Van Lijsebettens 2,3 and Marc Van Montagu 2,3,4
1. Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel, Brussels
2. Department of Plant Systems Biology, VIB, Gent
3. Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent
4. Institute of Plant Biotechnology Outreach (IPBO), Gent, Belgium
Abstract: This dialogue was held between the Guest Editors of the Special Issue on “Plant Transgenesis” of the Int. J. Dev. Biol. and Marc Van Montagu. Research in the group of Marc Van Montagu and Jeff Schell in the 1970s was essential to reveal how the phytopathogenic bacterium Agrobacterium tumefaciens transfers DNA to host plants to cause crown gall disease. Knowledge of the molecular mechanism underlying gene transfer, subsequently led to the development of plant transgene technology, an indispensable tool in fundamental plant research and plant improvement. In the early 1980s, Marc Van Montagu founded a start-up company, Plant Genetic Systems, which successfully developed insect-resistant plants, herbicide-tolerant plants and a hybrid seed production system based on nuclear male sterility. Even before the first transgenic plant had been produced, Marc Van Montagu realized that the less developed countries might benefit most from plant biotechnology and throughout his subsequent career, this remained a focus of his efforts. After becoming emeritus professor, he founded the Institute of Plant Biotechnology Outreach (IPBO), which aims to raise awareness of the major role that plant biotechnology can play in sustainable agricultural systems, especially in less developed countries. Marc Van Montagu has been honored with many prizes and awards, the most recent being the prestigious World Food Prize 2013. In this paper, we look to the past and present of plant biotechnology and to the promises this technology holds for the future, on the basis of the personal perspective of Marc Van Montagu.
Keywords: Agrobacterium tumefaciens, crown gall, genetically modified plants, plant genetic engineering, Ti plasmid, World Food Prize
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 461-465 (2013)
doi: 10.1387/ijdb.130063mv / © UBC Press (www.a360grados.net)
Transgenic plants: from first successes to future applications
Mieke Van Lijsebettens 1,2, Geert Angenon 3 and Marc De Block 4
1. Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
2. Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
3. Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
4. Bayer CropScience NV, Innovation Center, 9052 Gent, Belgium
Abstract: This dialogue was held between the Guest Editors of the Special Issue on “Plant Transgenesis” of the Int. J. Dev. Biol. and Marc De Block. He was one of the first scientists worldwide to obtain transgenic plants transformed with the chimeric selectable marker genes encoding neomycin phosphotransferase and bialaphos that confer resistance against the antibiotic kanamycin and the herbicide Basta®/glufosinate, respectively at the Department of Genetics of Ghent University and, later on, at the spin-off company, Plant Genetic Systems. Today, these two genes are still the most frequently utilized markers in transgene technology. Marc De Block chose to work on the improvement of crops in an industrial environment to help realize the production of superior seeds or products. He was part of the team that developed the male sterility/restorer system in canola (Brassica napus var. napus) that led to the first hybrid lines to be commercialized as successful products of transgene technology. In more than 30 years of research, he developed transformation procedures for numerous crops, designed histochemical, biochemical and physiological assays to monitor plant performance, and made original and innovative contributions to plant biology. Presently, he considers transgenic research part of the toolbox for plant improvement and essential for basic plant research.
Keywords: neomycin phosphotransferase II gene (nptII), bialaphos resistance gene (bar), ribonuclease gene (barnase), canola, tobacco, potato, cotton
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 467-481 (2013)
doi: 10.1387/ijdb.130199bl / © UBC Press (www.a360grados.net)
The roles of bacterial and host plant factors in Agrobacterium-mediated genetic transformation
Benoît Lacroix and Vitaly Citovsky
Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA
Abstract: The genetic transformation of plants mediated by Agrobacterium tumefaciens represents an essential tool for both fundamental and applied research in plant biology. For a successful infection, culminating in the integration of its transferred DNA (T-DNA) into the host genome, Agrobacterium relies on multiple interactions with host-plant factors. Extensive studies have unraveled many of such interactions at all major steps of the infection process: activation of the bacterial virulence genes, cell-cell contact and macromolecular translocation from Agrobacterium to host cell cytoplasm, intracellular transit of T-DNA and associated proteins (T-complex) to the host cell nucleus, disassembly of the T-complex, T-DNA integration, and expression of the transferred genes. During all these processes, Agrobacterium has evolved to control and even utilize several pathways of host-plant defense response. Studies of these Agrobacterium-host interactions substantially enhance our understanding of many fundamental cellular biological processes and allow improvements in the use of Agrobacterium as a gene transfer tool for biotechnology.
Keywords: Agrobacterium, genetic transformation, macromolecular transport, T-DNA expression
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 483-494 (2013)
doi: 10.1387/ijdb.130232mv / © UBC Press (www.a360grados.net)
Higher plant transformation: principles and molecular tools
Sylvester Anami 1, Elizabeth Njuguna 2,3, Griet Coussens 2,3, Stijn Aesaert 2,3 and Mieke Van Lijsebettens 2,3
1. Laboratory of Plant Genetics and Systems Biology, Department of Pure and Applied Sciences, Technical University of Mombasa, Mombasa, Kenya
2. Department of Plant Systems Biology, VIB, Gent, Belgium
3. Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
Abstract: In higher plants, genetic transformation, which is part of the toolbox for the study of living organisms, had been reported only 30 years ago, boosting basic plant biology research, generating superior crops, and leading to the new discipline of plant biotechnology. Here, we review its principles and the corresponding molecular tools. In vitro regeneration, through somatic embryogenesis or organogenesis, is discussed because they are prerequisites for the subsequent Agrobacterium tumefaciens-mediated transferred (T)-DNA or direct DNA transfer methods to produce transgenic plants. Important molecular components of the T-DNA are examined, such as selectable marker genes that allow the selection of transformed cells in tissue cultures and are used to follow the gene of interest in the next generations, and reporter genes that have been developed to visualize promoter activities, protein localizations, and protein-protein interactions. Genes of interest are assembled with promoters and termination signals in Escherichia coli by means of GATEWAY-derived binary vectors that represent the current versatile cloning tools. Finally, future promising developments in transgene technology are considered.
Keywords: Agrobacterium tumefaciens, T-DNA, transgene, plant transformation, somatic embryogenesis, organogenesis
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 495-508 (2013)
doi: 10.1387/ijdb.130244kw / © UBC Press (www.a360grados.net)
Genetic transformation of major cereal crops
Qing Ji, Xing Xu and Kan Wang
Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, Iowa, USA
Abstract: Of the more than 50,000 edible plant species in the world, at least 10,000 species are cereal grains. Three major cereal crops, rice (Oryza sativa), maize (Zea mays), and wheat (Triticum sp.), provide two-thirds of the world’s food energy intake. Although crop yields have improved tremendously thanks to technological advances in the past 50 years, population increases and climate changes continue to threaten the sustainability of current crop productions. Whereas conventional and marker-assisted breeding programs continue to play a major role in crop improvement, genetic engineering has drawn an intense worldwide interest from the scientific community. In the past decade, genetic transformation technologies have revolutionized agricultural practices and millions of hectares of biotech crops have been cultured. Because of its unique ability to insert well-characterized gene sequences into the plant genome, genetic engineering can also provide effective tools to address fundamental biological questions. This technology is expected to continue to be an indispensable approach for both basic and applied research. Here, we overview briefly the development of the genetic transformation in the top seven cereals, namely maize, rice, wheat, barley (Hordeum vulgare), sorghum (Sorghum sp.), oat (Avena sativa), and millets. The advantages and disadvantages of the two major transformation methods, Agrobacterium tumefaciens-mediated and biolistic methods, are also discussed.
Keywords: Agrobacterium tumefaciens, biolistic gun, cereal, genetic transformation
Transgenic technology in basic research -----------------------------
EHU/UPV/UBC - The International Journal of Developmental Biology 57: 509-515 (2013)
doi: 10.1387/ijdb.120254pm / © UBC Press (www.a360grados.net)
Transgenes and their contributions to epigenetic research
Peter Meyer
Center for Plant Sciences, University of Leeds, UK
Abstract: Shortly after gene transfer technologies had been established for different plant species, the first reports emerged about transgenes showing unexpected segregation patterns due to unstable expression. Initially, the erratic expression behavior of transgenes was considered a nuisance that impeded the impact and efficiency of a new technology. With the investigation of transgene silencing effects, however, it soon became clear that transgenes had helped us in a rather unexpected way to identify novel molecular pathways that were highly relevant to plant development and evolution. This article gives an account of a journey that started with the analysis of transgene-related silencing events and that led to the discovery of a new molecular world of small RNAs and epigenetic marks that regulate plant gene expression and adaptation to environmental changes.
Keywords: epigenetics, gene silencing, DNA methylation, small RNAs
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 517-523 (2013)
doi: 10.1387/ijdb.130176mm / © UBC Press (www.a360grados.net)
High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system
Mieko Higuchi-Takeuchi 1, Masaki Mori 2 and Minami Matsui 1,3
1. RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
2. Disease Resistance Crops Research and Development Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
3. Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
Abstract: Mutant populations are indispensable tools for investigating plant gene functions. Gain-of-function technology is one of the approaches used for the systematic production of mutant resources and activation tagging is a well-established method to generate gain-of-function mutants in plants. As an alternative approach for the systematic generation of a gain-of-function mutant population, we developed the Full-length cDNA OvereXpressor (FOX)-hunting system in which full-length cDNAs (fl-cDNAs) are overexpressed in plants to quickly identify candidate genes. The FOX-hunting system was used for high-throughput analysis of rice (Oryza sativa) genes heterologously expressed in Arabidopsis thaliana (rice FOX Arabidopsis lines). A large screening to identify and characterize rice genes with rice FOX Arabidopsis lines revealed that one of the isolated genes, BROAD-SPECTRUM RESISTANCE 1 (BSR1) conferred multiple or broad-spectrum disease resistance in both a dicotyledonous and monocotyledonous plant. We found that expression of rice fl-cDNAs without a homolog in Arabidopsis affected morphological traits. In addition, overexpression of homologous genes of rice and Arabidopsis led to a similar phenotype. Thus, we conclude that the FOX-hunting system is an excellent heterologous system and offers a new tool with which to explore gene function in rice.
Keywords: full-length cDNA, rice, Arabidopsis, gain-of-function
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 525-533 (2013)
doi: 10.1387/ijdb.130208dw / © UBC Press (www.a360grados.net)
From jellyfish to biosensors: the use of fluorescent proteins in plants
Ute Voss 1, Antoine Larrieu 1,2 and Darren M. Wells 1
1. Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, UK
2. Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Lyon, France.
Abstract: The milestone discovery of green fluorescent protein (GFP) from the jellyfish Aequorea victoria, its optimisation for efficient use in plantae, and subsequent improvements in techniques for fluorescent detection and quantification have changed plant molecular biology research dramatically. Using fluorescent protein tags allows the temporal and spatial monitoring of dynamic expression patterns at tissue, cellular and subcellular scales. Genetically-encoded fluorescence has become the basis for applications such as cell-type specific transcriptomics, monitoring cell fate and identity during development of individual organs or embryos, and visualising protein-protein interactions in vivo. In this article, we will give an overview of currently available fluorescent proteins, their applications in plant research, the techniques used to analyse them and, using the recent development of an auxin sensor as an example, discuss the design principles and prospects for the next generation of fluorescent plant biosensors.
Keywords: fluorescent protein, transgenic plant, biosensor, DII-VENUS, confocal microscopy
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 535-543 (2013)
doi: 10.1387/ijdb.130240qw / © UBC Press (www.a360grados.net)
Fluorescent protein marker lines in maize: generation and applications
Qingyu Wu 1, Anding Luo 2, Tara Zadrozny 1, Anne Sylvester 2 and Dave Jackson 1
1. Cold Spring Harbor Laboratory, NY
2. Department of Molecular Biology, University of Wyoming,Wyoming, USA
Abstract: Fluorescent proteins (FP) have significantly impacted the way that we study plants in the past two decades. In the post-genomics era, these FP tools are in higher demand by plant scientists for studying the dynamics of protein localization, function, and interactions, and to translate sequence information to biological knowledge that can benefit humans. Although FP tools have been widely used in the model plant Arabidopsis, few FP resources have been developed for maize, one of the most important food crops worldwide, and an ideal species for genetic and developmental biology research. In an effort to provide the maize and cereals research communities with a comprehensive set of FP resources for different purposes of study, we generated more than 100 stable transformed maize FP marker lines, which mark most compartments in maize cells with different FPs. Additionally, we are generating driver and reporter lines, based on the principle of the pOp-LhG4 transactivation system, allowing specific expression or mis-expression of any gene of interest to precisely study protein functions. These marker lines can be used not only for static protein localization studies, but will be useful for studying protein dynamics and interactions using kinetic microscopy methods, such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), and fluorescence resonance energy transfer (FRET). All of the constructs and maize marker lines are publicly available through our website, http://maize.jcvi.org/cellgenomics/index.php
Keywords: fluorescent protein, FRET, maize, pOp, LhG4
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 545 - 552 (2013)
doi: 10.1387/ijdb.130195mg / © UBC Press (www.a360grados.net)
The use of fluorescence-activated cell sorting in studying plant development and environmental responses
Anthony D. Carter 1,2, Roxanna Bonyadi 1 and Miriam L. Gifford 1,2
1. School of Life Sciences and 2. Warwick Systems Biology Centre, University of Warwick, Coventry, UK
Abstract: Fluorescence-Activated Cell Sorting (FACS) is a powerful tool that enables plant growth and development to be studied at the cellular level. Flow cytometry is used to isolate subpopulations of cells, such as those of specific cell types, or cells at particular developmental stages that have been marked with fluorescent proteins. Transgenic technology has given us the ability to generate plants that express fluorescent proteins, not just constitutively in particular cell types, but also dynamically in response to endogenous or external factors. By processing such transgenic lines with FACS, it is possible to isolate distinct populations of cells in a wide range of likely response states for further analysis. This is particularly useful for investigating biological mechanisms in plants because the control of growth and development is manifest at the cell type level. Furthermore, the specificity of the resulting data enables fine modelling of the transcriptional networks that exert systems-level control of the transcriptome; hence key regulators of responses and processes in the plant can be identified. In this review, the current state of the art for FACS methods in plants is explored by means of case studies of research in which cell sorting allowed us to make significant new discoveries.
Keywords: cell sorting, cell specificity, plant root, fluorescent reporter, Arabidopsis
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 553-564 (2013)
doi: 10.1387/ijdb.130189wf / © UBC Press (www.a360grados.net)
The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function
Christoph Strotbek, Stefan Krinninger and Wolfgang Frank
Ludwig-Maximilians-University Munich (LMU), Faculty of Biology, Department Biology I,Plant Molecular Cell Biology, LMU Biocenter, Germany
Abstract: To comprehensively understand the major processes in plant biology, it is necessary to study a diverse set of species that represent the complexity of plants. This research will help to comprehend common conserved mechanisms and principles, as well as to elucidate those mechanisms that are specific to a particular plant clade. Thereby, we will gain knowledge about the invention and loss of mechanisms and their biological impact causing the distinct specifications throughout the plant kingdom. Since the establishment of transgenic plants, these studies concentrate on the elucidation of gene functions applying an increasing repertoire of molecular techniques. In the last two decades, the moss Physcomitrella patens joined the estab-lished set of plant models based on its evolutionary position bridging unicellular algae and vascular plants and a number of specific features alleviating gene function analysis. Here, we want to provide an overview of the specific features of P. patens making it an interesting model for many research fields in plant biology, to present the major achievements in P. patens genetic engineering, and to introduce common techniques to scientists who intend to use P. patens as a model in their research activities.
Keywords: Physcomitrella patens, genetic engineering, gene function analysis, reverse genetics, homologous recombination
Biotechnological applications ------------------------------
EHU/UPV/UBC - The International Journal of Developmental Biology 57: 565-576 (2013)
doi: 10.1387/ijdb.130162pc / © UBC Press (www.a360grados.net)
Engineering metabolic pathways in plants by multigene transformation
Uxue Zorrilla-López 1, Gemma Masip 1, Gemma Arjó 2, Chao Bai 1, Raviraj Banakar 1, Ludovic Bassie 1, Judit Berman 1, Gemma Farré 1, Bruna Miralpeix 1, Eduard Pérez-Massot 1, Maite Sabalza 1, Georgina Sanahuja 1, Evangelia Vamvaka 1, Richard M. Twyman 3, Paul Christou 1,4, Changfu Zhu 1 and Teresa Capell 1
1. Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain
2. Department of Medicine, Institute of Biomedical Research (IRB), University of Lleida, Lleida, Spain
3. School of Life Sciences, University of Warwick, Coventry, UK
4. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
Abstract: Metabolic engineering in plants can be used to increase the abundance of specific valuable metabolites, but single-point interventions generally do not improve the yields of target metabolites unless that product is immediately downstream of the intervention point and there is a plentiful supply of precursors. In many cases, an intervention is necessary at an early bottleneck, sometimes the first committed step in the pathway, but is often only successful in shifting the bottleneck downstream, sometimes also causing the accumulation of an undesirable metabolic intermediate. Occasionally it has been possible to induce multiple genes in a pathway by controlling the expression of a key regulator, such as a transcription factor, but this strategy is only possible if such master regulators exist and can be identified. A more robust approach is the simultaneous expression of multiple genes in the pathway, preferably representing every critical enzymatic step, therefore removing all bottlenecks and ensuring completely unrestricted metabolic flux. This approach requires the transfer of multiple enzyme-encoding genes to the recipient plant, which is achieved most efficiently if all genes are transferred at the same time. Here we review the state of the art in multigene transformation as applied to metabolic engineering in plants, highlighting some of the most significant recent advances in the field.
Keywords: direct DNA transfer, multigene transformation, metabolic pathway, genetic engineering
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 577-586 (2013)
doi: 10.1387/ijdb.130239pr / © UBC Press (www.a360grados.net)
Transformation of leguminous plants to study symbiotic interactions
Anelia Iantcheva 1, Kirankumar S. Mysore 2 and Pascal Ratet 3
1. AgroBioInstitute, Sofia, Bulgaria
2. Plant Biology Division, The Samuel Roberts Noble Foundation, OK, USA
3. Institut des Sciences Végétales, Centre National de Recherche Scientifique, Gif sur Yvette, France
Abstract: Legume plants are important in agriculture because they represent an important source of protein for human and animal consumption. This high protein content results from their capacity to use atmospheric nitrogen for their nutrition as a consequence of their symbiotic interaction with rhizobia. Understanding this interaction at the molecular level is a prerequisite for its better use in agriculture and for the long term objective of its transfer to other crops. Agrobacterium-mediated transformation is a tool of choice for studying this interaction and for unraveling the function of the different genes discovered through classical genetic approaches. However, legume plants are often recalcitrant to regeneration and transformation. This paper describes the technology developments (regeneration, transformation, insertion mutagenesis) related to Agrobacterium transformations that were established in the legume plants, as well as different examples of the technology developments or gene discoveries resulting from these studies.
Keywords: legume plant, agrobacterium, rhizobium, transformation, symbiosis
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 587-593 (2013)
doi: 10.1387/ijdb.130266ad / © UBC Press (www.a360grados.net)
Role of plant expression systems in antibody production for passive immunization
Vikram Virdi and Ann Depicker
Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
Abstract: Passive immunization is a method to achieve immediate protection against infectious agents by administering pathogen-specific antibodies. It has proven to be lifesaving for many acute infections, and it is now also used for cancer treatment. Passive immunization therapies, however, are extremely expensive because they require large amounts of specific antibodies that are produced predominantly in mammalian expression systems. The cost for manufacturing plant-made antibodies is estimated to be comparatively low since plant production systems require relatively less capital investments. In addition, they are not prone to mammalian pathogens, which also eases downstream processing along with making it a safe expression system. Moreover, some of the recent developments in transient expression have enabled rapid, cGMP (current Good Manufacturing Practices) compliant manufacturing of antibodies. Whether lower production costs will be reflected in a lower market price for purified antibodies will be known when more plant-produced antibodies come to the market. Promisingly, the current mo-lecular techniques in the field of in planta expression have enabled high-level production of a variety of antibodies in different plant organs, like roots/tubers/fruits, leaves and seeds, of a va-riety of plants, like potato, tobacco, maize, rice, tomato and pea, providing a very wide range of possible plant-based passive immunization therapies. For instance, the production of antibodies in edible tissues would allow for a unique, convenient, needle-less, oral passive immunization at the gastric mucosal surface. The technological advances, together with the innate capacity of plant tissues to assemble complex antibodies, will enable carving a niche in the antibody market. This non-exhaustive review aims to shed light on the role of plants as a flexible expression system for passive immunotherapy, which we envisage to progress alongside the conventional production platforms to manufacture specialized antibodies.
Keywords: molecular farming, in leaf production, in seed production, plantibodies, disruptive technology
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 595-610 (2013)
doi: 10.1387/ijdb.130268lh / © UBC Press (www.a360grados.net)
Biotechnology of nutrient uptake and assimilation in plants
Damar L. López-Arredondo 1, Marco A. Leyva-González 1, Fulgencio Alatorre-Cobos 2 and Luis Herrera-Estrella 2
1. StelaGenomics México
2. Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
Abstract: Plants require a complex balance of mineral nutrients to reproduce successfully. Because the availability of many of these nutrients in the soil is compromised by several factors, such as soil pH, cation presence, and microbial activity, crop plants depend directly on nutrients applied as fertilizers to achieve high yields. However, the excessive use of fertilizers is a major environmental concern due to nutrient leaching that causes water eutrophication and promotes toxic algae blooms. This situation generates the urgent need for crop plants with increased nutrient use efficiency and better-designed fertilization schemes. The plant biology revolution triggered by the development of efficient gene transfer systems for plant cells together with the more recent development of next-generation DNA and RNA sequencing and other omics platforms have advanced considerably our understanding on the molecular basis of plant nutrition and how plants respond to nutritional stress. To date, genes encoding sensors, transcription factors, transporters, and metabolic enzymes have been identified as potential candidates to improve nutrient use efficiency. In addition, the study of other genetic resources, such as bacteria and fungi, allows the identification of alternative mechanisms of nutrient assimilation, which are potentially applicable in plants. Although significant progress in this respect has been achieved by conventional breeding, in this review we focus on the biotechnological approaches reported to date aimed at boosting the use of the three most limiting nutrients in the majority of arable lands: nitrogen, phosphorus, and iron.
Keywords: plant nutrition, macronutrients, grain yield, gene overexpression, bacterial gene, biotechnology
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 611-620 (2013)
doi: 10.1387/ijdb.130238ri / © UBC Press (www.a360grados.net)
Transfer of knowledge about flowering and vegetative propagation from model species to bulbous plants
Hendrika A.C.F. Leeggangers 1, Natalia Moreno-Pachon 1, Henk Gude 2 and Richard G.H. Immink 1
1. Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen
2. Flower Bulbs, Applied Plant Research, Wageningen University & Research Centre, Lisse, The Netherlands.
Abstract: The extensive characterization of plant genes and genome sequences summed to the continuous development of biotechnology tools, has played a major role in understanding biological processes in plant model species. The challenge for the near future is to generate methods and pipelines for an efficient transfer of this knowledge to economically important crops and other plant species. In the case of flower bulbs, which are economically very important for the ornamental industry, flowering time control and vegetative propagation constitute the most relevant processes for agronomical improvements. Those processes have been reasonably studied in reference species, making them excellent candidates for translational investigations in bulbous plant species. The approaches that can be taken for the transfer of biological knowledge from model to non-model species can be roughly categorized as “bottom-up” or “top-down”. The former approach usually goes from individual genes to systems, also known as a “gene-by-gene” approach. It assumes conservation of molecular pathways and therefore makes use of sequence homology searches to identify candidate genes. ”Top-down” methodologies go from systems to genes, and are e.g. based on large scale transcriptome profiling via heterologous microarrays or RNA sequencing, followed by the identification of associations between phenotypes, genes, and gene expression patterns and levels. In this review, examples of the various knowledge-transfer approaches are provided and pros and cons are discussed. Due to the latest developments in transgenic research and next generation sequencing and the emerging of systems biology as a matured research field, transfer of knowledge concerning flowering time and vegetative propagation capacity in bulbous species are now within sight.
Keywords: bulbous plant, flowering time control, vegetative propagation, gene regulation
Advances in transgene technology ----------------------------------------
EHU/UPV/UBC - The International Journal of Developmental Biology 57: 621-627 (2013)
doi: 10.1387/ijdb.130217kd / © UBC Press (www.a360grados.net)
Directed genome engineering for genome optimization
Kathleen D’Halluin and Rene Ruiter
Bayer CropScience N.V., Gent, Belgium
Abstract: The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmis-sion of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.
Keywords: DNA double strand break induction and repair, site-specific nuclease, genome editing, crop improvement
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 629-637 (2013)
doi: 10.1387/ijdb.130194hp / © UBC Press (www.a360grados.net)
Gene targeting in plants: 25 years later
Holger Puchta and Friedrich Fauser
Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
Abstract: Only five years after the initiation of transgenic research in plants, gene targeting (GT) was achieved for the first time in tobacco. Unfortunately, the frequency of targeted integration via homologous recombination (HR) was so low in comparison to random integration that GT could not be established as a feasible technique in higher plants. It took another 25 years and great effort to develop the knowledge and tools necessary to overcome this challenge, at least for some plant species. In some cases, the overexpression of proteins involved in HR or the use of negative selectable markers improved GT to a certain extent. An effective solution to this problem was developed in 1996, when a sequence-specific endonuclease was used to induce a double-strand break (DSB) at the target locus. Thus, GT frequencies were enhanced dramatically. Thereafter, the main limitation was the absence of tools needed to induce DSBs at specific sites in the genome. Such tools became available with the development of zinc finger nucleases (ZFNs), and a breakthrough was achieved in 2005 when ZFNs were used to target a marker gene in tobacco. Subsequently, endogenous loci were targeted in maize, tobacco and Arabidopsis. Recently, our toolbox for genetic engineering has expanded with the addition of more types of site-specific endonucleases, meganucleases, transcription activator-like effector nucleases (TALENs) and the CRISPR/Cas system. We assume that targeted genome modifica-tions will become routine in the near future in crop plants using these nucleases along with the newly developed in planta GT technique.
Keywords: plant biotechnology, gene technology, synthetic nucleases, transformation, double-strand break repair
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 639-650 (2013)
doi: 10.1387/ijdb.130205av / © UBC Press (www.a360grados.net)
From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes
Ira Marton 1, Arik Honig 1, Ayelet Omid 1, Noam De Costa 1, Elena Marhevka 1, Barry Cohen 1, Amir Zuker 1 and Alexander Vainstein 2
1. Danziger Innovations Ltd., Mishmar Hashiva Village, Beit Dagan, Israel
2. Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
Abstract: Researchers and biotechnologists require methods to accurately modify the genome of higher eukaryotic cells. Such modifications include, but are not limited to, site-specific mutagenesis, site-specific insertion of foreign DNA, and replacement and deletion of native sequences. Accurate genome modifications in plant species have been rather limited, with only a handful of plant species and genes being modified through the use of early genome-editing techniques. The development of rare-cutting restriction enzymes as a tool for the induction of site-specific genomic double-strand breaks and their introduction as a reliable tool for genome modification in animals, animal cells and human cell lines have paved the way for the adaptation of rare-cutting restriction enzymes to genome editing in plant cells. Indeed, the number of plant species and genes which have been successfully edited using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and engineered homing endonucleases is on the rise. In our review, we discuss the basics of rare-cutting restriction enzyme-mediated genome-editing technology with an emphasis on its application in plant species.
Keywords: genome editing, homing endonucleases, TALENs, viral vectors, ZFNs
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 651-657 (2013)
doi: 10.1387/ijdb.130144ah / © UBC Press (www.a360grados.net)
Engineered plant minichromosomes
Andreas Houben, Michael F. Mette, Chee H. Teo, Inna Lermontova and Ingo Schubert
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland OT Gatersleben, Germany
Abstract: Minichromosomes offer an enormous potential for plant breeding and biotechnology, because they may simultaneously transfer and stably express multiple genes. Segregating independently of their host chromosomes, they provide a platform for accelerating plant breeding. Minichromosomes can be established from cloned components in vivo (bottom up) or via engineering of natural chromosomes (top down). When they possess functional centromeres and telomeres, they should be stably inherited, but their meiotic transmission rate is below that of endogenous chromosomes. To achieve the customized generation and control the regular transmission of minichromosomes are important challenges for applied research in chromosome biology. Here, construction and biology of plant minichromosomes are compared with data available for yeast and animal systems.
Keywords: minichromosome, engineered chromosome, telomere seeding, vector, centromere
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EHU/UPV/UBC - The International Journal of Developmental Biology 57: 659-665 (2013)
doi: 10.1387/ijdb.130230cr / © UBC Press (www.a360grados.net)
Transformation of the mitochondrial genome
Véronique Larosa and Claire Remacle
Genetics of Microorganisms, Department of Life Sciences, Institute of Botany, University of Liege, Liege, Belgium
Abstract: Although mitochondrial transformation is highly desirable in mammals and plants, it is only possible in two unicellular organisms, the budding yeast Saccharomyces cerevisiae and the unicellular green alga Chlamydomonas reinhardtii. Here, we give an overview of the attempts made to transform mitochondria of mammals and plants and the possible reasons for their failure. This review briefly describes the mitochondrial transformation principles in yeast and describes in more detail the transformation and its applications in Chlamydomonas.
Keywords: mitochondria, transformation, Chlamydomonas, respiration, mutation
The International Journal of Developmental Biology
ISSN 1696-3547 (online) and 0214-6282 (print)
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