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Sathishkumar R, Kumar SR, Hema J, Baskar V. Green Biotechnology: A Brief Update on Plastid Genome Engineering. ADVANCES IN PLANT TRANSGENICS: METHODS AND APPLICATIONS 2019. [PMCID: PMC7120283 DOI: 10.1007/978-981-13-9624-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plant genetic engineering has become an inevitable tool in the molecular breeding of crops. Significant progress has been made in the generation of novel plastid transformation vectors and optimized transformation protocols. There are several advantages of plastid genome engineering over conventional nuclear transformation. Some of the advantages include multigene engineering by expression of biosynthetic pathway genes as operons, extremely high-level expression of protein accumulation, lack of transgene silencing, etc. Transgene containment owing to maternal inheritance is another important advantage of plastid genome engineering. Chloroplast genome modification usually results in alteration of several thousand plastid genome copies in a cell. Several therapeutic proteins, edible vaccines, antimicrobial peptides, and industrially important enzymes have been successfully expressed in chloroplasts so far. Here, we critically recapitulate the latest developments in plastid genome engineering. Latest advancements in plastid genome sequencing are briefed. In addition, advancement of extending the toolbox for plastid engineering for selected applications in the area of molecular farming and production of industrially important enzyme is briefed.
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Affiliation(s)
- Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
| | | | - Jagadeesan Hema
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu India
| | - Venkidasamy Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
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Quispe-Huamanquispe DG, Gheysen G, Kreuze JF. Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs. FRONTIERS IN PLANT SCIENCE 2017; 8:2015. [PMID: 29225610 PMCID: PMC5705623 DOI: 10.3389/fpls.2017.02015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/13/2017] [Indexed: 05/04/2023]
Abstract
Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals. In plants, one well-studied example of HGT is the transfer of the tumor-inducing genes (T-DNAs) from some Agrobacterium species into their host plant genomes. Evidence of T-DNAs from Agrobacterium spp. into plant genomes, and their subsequent maintenance in the germline, has been reported in Nicotiana, Linaria and, more recently, in Ipomoea species. The transferred genes do not produce the usual disease phenotype, and appear to have a role in evolution of these plants. In this paper, we review previous reported cases of HGT from Agrobacterium, including the transfer of T-DNA regions from Agrobacterium spp. to the sweetpotato [Ipomoea batatas (L.) Lam.] genome which is, to date, the sole documented example of a naturally-occurring incidence of HGT from Agrobacterium to a domesticated crop plant. We also discuss the possible evolutionary impact of T-DNA acquisition on plants.
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Affiliation(s)
- Dora G. Quispe-Huamanquispe
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
- International Potato Center (CIP), Lima, Peru
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Jan F. Kreuze
- International Potato Center (CIP), Lima, Peru
- *Correspondence: Jan F. Kreuze,
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Martínez F, Arif A, Nebauer SG, Bueso E, Ali R, Montesinos C, Brunaud V, Muñoz-Bertomeu J, Serrano R. A fungal transcription factor gene is expressed in plants from its own promoter and improves drought tolerance. PLANTA 2015; 242:39-52. [PMID: 25809153 DOI: 10.1007/s00425-015-2285-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/16/2015] [Indexed: 06/04/2023]
Abstract
MAIN CONCLUSION A fungal gene encoding a transcription factor is expressed from its own promoter in Arabidopsis phloem and improves drought tolerance by reducing transpiration and increasing osmotic potential. Horizontal gene transfer from unrelated organisms has occurred in the course of plant evolution, suggesting that some foreign genes may be useful to plants. The CtHSR1 gene, previously isolated from the halophytic yeast Candida tropicalis, encodes a heat-shock transcription factor-related protein. CtHSR1, with expression driven by its own promoter or by the Arabidopsis UBQ10 promoter, was introduced into the model plant Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation and the resulting transgenic plants were more tolerant to drought than controls. Fusions of the CtHSR1 promoter with β-glucuronidase reporter gene indicated that this fungal promoter drives expression to phloem tissues. A chimera of CtHSR1 and green fluorescence protein is localized at the cell nucleus. The physiological mechanism of drought tolerance in transgenic plants is based on reduced transpiration (which correlates with decreased opening of stomata and increased levels of jasmonic acid) and increased osmotic potential (which correlates with increased proline accumulation). Transcriptomic analysis indicates that the CtHSR1 transgenic plants overexpressed a hundred of genes, including many relevant to stress defense such as LOX4 (involved in jasmonic acid synthesis) and P5CS1 (involved in proline biosynthesis). The promoters of the induced genes were enriched in upstream activating sequences for water stress induction. These results demonstrate that genes from unrelated organisms can have functional expression in plants from its own promoter and expand the possibilities of useful transgenes for plant biotechnology.
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Affiliation(s)
- Félix Martínez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Camino de Vera, 46022, Valencia, Spain
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Kovacova V, Zluvova J, Janousek B, Talianova M, Vyskot B. The evolutionary fate of the horizontally transferred agrobacterial mikimopine synthase gene in the genera Nicotiana and Linaria. PLoS One 2014; 9:e113872. [PMID: 25420106 PMCID: PMC4242671 DOI: 10.1371/journal.pone.0113872] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 10/31/2014] [Indexed: 11/19/2022] Open
Abstract
Few cases of spontaneously horizontally transferred bacterial genes into plant genomes have been described to date. The occurrence of horizontally transferred genes from the T-DNA of Agrobacterium rhizogenes into the plant genome has been reported in the genus Nicotiana and in the species Linaria vulgaris. Here we compare patterns of evolution in one of these genes (a gene encoding mikimopine synthase, mis) following three different events of horizontal gene transfer (HGT). As this gene plays an important role in Agrobacterium, and there are known cases showing that genes from pathogens can acquire plant protection function, we hypothesised that in at least some of the studied species we will find signs of selective pressures influencing mis sequence. The mikimopine synthase (mis) gene evolved in a different manner in the branch leading to Nicotiana tabacum and N. tomentosiformis, in the branch leading to N. glauca and in the genus Linaria. Our analyses of the genus Linaria suggest that the mis gene began to degenerate soon after the HGT. In contrast, in the case of N. glauca, the mis gene evolved under significant selective pressures. This suggests a possible role of mikimopine synthase in current N. glauca and its ancestor(s). In N. tabacum and N. tomentosiformis, the mis gene has a common frameshift mutation that disrupted its open reading frame. Interestingly, our results suggest that in spite of the frameshift, the mis gene could evolve under selective pressures. This sequence may still have some regulatory role at the RNA level as suggested by coverage of this sequence by small RNAs in N. tabacum.
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Affiliation(s)
- Viera Kovacova
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, Brno, Czech Republic
| | - Jitka Zluvova
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, Brno, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, Brno, Czech Republic
| | - Martina Talianova
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, Brno, Czech Republic
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Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, LockLear S, Concepcion GP, Purugganan MD. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol 2014; 31:793-803. [PMID: 24458431 PMCID: PMC3969568 DOI: 10.1093/molbev/msu051] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
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Affiliation(s)
- Jeanmaire Molina
- Department of Biology, Long Island University, Brooklyn
- Center for Genomics and Systems Biology, New York University
- *Corresponding author: E-mail: ;
| | - Khaled M. Hazzouri
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Daniel Nickrent
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Matthew Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Rachel S. Meyer
- Center for Genomics and Systems Biology, New York University
| | - Melissa M. Pentony
- Computational Genomics Core, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Pieter Pelser
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Julie Barcelona
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Samuel Alan Inovejas
- Electron Microscope Facility, St. Luke’s Medical Center, Quezon City, Philippines
| | - Iris Uy
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Wei Yuan
- Center for Genomics and Systems Biology, New York University
| | - Olivia Wilkins
- Center for Genomics and Systems Biology, New York University
| | | | | | - Gisela P. Concepcion
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Corresponding author: E-mail: ;
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Venkatesh J, Park SW. Plastid genetic engineering in Solanaceae. PROTOPLASMA 2012; 249:981-99. [PMID: 22395455 PMCID: PMC3459085 DOI: 10.1007/s00709-012-0391-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/21/2012] [Indexed: 05/23/2023]
Abstract
Plastid genetic engineering has come of age, becoming today an attractive alternative approach for the expression of foreign genes, as it offers several advantages over nuclear transformants. Significant progress has been made in plastid genetic engineering in tobacco and other Solanaceae plants, through the use of improved regeneration procedures and transformation vectors with efficient promoters and untranslated regions. Many genes encoding for industrially important proteins and vaccines, as well as genes conferring important agronomic traits, have been stably integrated and expressed in the plastid genome. Despite these advances, it remains a challenge to achieve marked levels of plastid transgene expression in non-green tissues. In this review, we summarize the basic requirements of plastid genetic engineering and discuss the current status, limitations, and the potential of plastid transformation for expanding future studies relating to Solanaceae plants.
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Affiliation(s)
- Jelli Venkatesh
- Department of Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701 Republic of Korea
| | - Se Won Park
- Department of Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701 Republic of Korea
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Christin PA, Edwards E, Besnard G, Boxall S, Gregory R, Kellogg E, Hartwell J, Osborne C. Adaptive Evolution of C4 Photosynthesis through Recurrent Lateral Gene Transfer. Curr Biol 2012; 22:445-9. [DOI: 10.1016/j.cub.2012.01.054] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/12/2012] [Accepted: 01/25/2012] [Indexed: 01/17/2023]
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