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Kumar P, Babu K, Singh A, Singh D, Nalli A, Mukul S, Roy A, Mazeed M, Raman B, Kruparani S, Siddiqi I, Sankaranarayanan R. Distinct localization of chiral proofreaders resolves organellar translation conflict in plants. Proc Natl Acad Sci U S A 2023; 120:e2219292120. [PMID: 37276405 PMCID: PMC10268278 DOI: 10.1073/pnas.2219292120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.
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Affiliation(s)
- Pradeep Kumar
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Kandhalu Sagadevan Dinesh Babu
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Avinash Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Dipesh Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Aswan Nalli
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shivapura Jagadeesha Mukul
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Ankit Roy
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Mohd Mazeed
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Bakthisaran Raman
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shobha P. Kruparani
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Imran Siddiqi
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
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Guihur A, Bourgine B, Rebeaud ME, Goloubinoff P. Design of an Arabidopsis thaliana reporter line to detect heat-sensing and signaling mutants. PLANT METHODS 2023; 19:56. [PMID: 37291595 DOI: 10.1186/s13007-023-01033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/28/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Global warming is a major challenge for plant survival and growth. Understanding the molecular mechanisms by which higher plants sense and adapt to upsurges in the ambient temperature is essential for developing strategies to enhance plant tolerance to heat stress. Here, we designed a heat-responsive Arabidopsis thaliana reporter line that allows an in-depth investigation of the mechanisms underlying the accumulation of protective heat-shock proteins (HSPs) in response to high temperature. METHODS A transgenic Arabidopsis thaliana reporter line named "Heat-Inducible Bioluminescence And Toxicity" (HIBAT) was designed to express from a conditional heat-inducible promoter, a fusion gene encoding for nanoluciferase and D-amino acid oxidase, whose expression is toxic in the presence of D-valine. HIBAT seedlings were exposed to different heat treatments in presence or absence of D-valine and analyzed for survival rate, bioluminescence and HSP gene expression. RESULTS Whereas at 22 °C, HIBAT seedlings grew unaffected by D-valine, and all survived iterative heat treatments without D-valine, 98% died following heat treatments on D-valine. The HSP17.3B promoter was highly specific to heat as it remained unresponsive to various plant hormones, Flagellin, H2O2, osmotic stress and high salt. RNAseq analysis of heat-treated HIBAT seedlings showed a strong correlation with expression profiles of two wild type lines, confirming that HIBAT does not significantly differ from its Col-0 parent. Using HIBAT, a forward genetic screen revealed candidate loss-of-function mutants, apparently defective either at accumulating HSPs at high temperature or at repressing HSP accumulation at non-heat-shock temperatures. CONCLUSION HIBAT is a valuable candidate tool to identify Arabidopsis mutants defective in the response to high temperature stress. It opens new avenues for future research on the regulation of HSP expression and for understanding the mechanisms of plant acquired thermotolerance.
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Affiliation(s)
- Anthony Guihur
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Baptiste Bourgine
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Mathieu E Rebeaud
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.
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Recent Advances in Antibiotic-Free Markers; Novel Technologies to Enhance Safe Human Food Production in the World. Mol Biotechnol 2022:10.1007/s12033-022-00609-7. [DOI: 10.1007/s12033-022-00609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
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Marker-Free Transplastomic Plants by Excision of Plastid Marker Genes Using Directly Repeated DNA Sequences. Methods Mol Biol 2021. [PMID: 34028764 DOI: 10.1007/978-1-0716-1472-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Excision of marker genes using DNA direct repeats makes use of the efficient native homologous recombination pathway present in the plastids of algae and plants. The method is simple, efficient, and widely applicable to plants and green algae. Marker excision frequency is dependent on the length and number of directly repeated sequences. When two repeats are used a repeat size of greater than 600 bp promotes efficient excision of the marker gene. A wide variety of sequences can be used to make the direct repeats. Only a single round of transformation is required and there is no requirement to introduce site-specific recombinases by retransformation or sexual crosses. Selection is used to maintain the marker and ensure homoplasmy of transgenic plastid genomes (plastomes). Release of selection allows the accumulation of marker-free plastomes generated by marker excision, which is a spontaneous and unidirectional process. Cytoplasmic sorting allows the segregation of cells with marker-free transgenic plastids. The marker-free shoots resulting from direct repeat mediated excision of marker genes have been isolated by vegetative propagation of shoots in the T0 generation. Alternatively, accumulation of marker-free plastomes during growth, development and flowering of T0 plants allows for the collection of seeds that give rise to a high proportion of marker-free T1 seedlings. The procedure enables precise plastome engineering involving insertion of transgenes, point mutations and deletion of genes without the inclusion of any extraneous DNA. The simplicity and convenience of direct repeat excision facilitates its widespread use to isolate marker-free crops.
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Li S, Chang L, Zhang J. Advancing organelle genome transformation and editing for crop improvement. PLANT COMMUNICATIONS 2021; 2:100141. [PMID: 33898977 PMCID: PMC8060728 DOI: 10.1016/j.xplc.2021.100141] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/15/2020] [Accepted: 01/01/2021] [Indexed: 05/05/2023]
Abstract
Plant cells contain three organelles that harbor DNA: the nucleus, plastids, and mitochondria. Plastid transformation has emerged as an attractive platform for the generation of transgenic plants, also referred to as transplastomic plants. Plastid genomes have been genetically engineered to improve crop yield, nutritional quality, and resistance to abiotic and biotic stresses, as well as for recombinant protein production. Despite many promising proof-of-concept applications, transplastomic plants have not been commercialized to date. Sequence-specific nuclease technologies are widely used to precisely modify nuclear genomes, but these tools have not been applied to edit organelle genomes because the efficient homologous recombination system in plastids facilitates plastid genome editing. Unlike plastid transformation, successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group, but not successful to date. However, stepwise progress has been made in modifying mitochondrial genes and their transcripts, thus enabling the study of their functions. Here, we provide an overview of advances in organelle transformation and genome editing for crop improvement, and we discuss the bottlenecks and future development of these technologies.
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Affiliation(s)
- Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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Esland L, Larrea-Alvarez M, Purton S. Selectable Markers and Reporter Genes for Engineering the Chloroplast of Chlamydomonas reinhardtii. BIOLOGY 2018; 7:E46. [PMID: 30309004 PMCID: PMC6315944 DOI: 10.3390/biology7040046] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 02/07/2023]
Abstract
Chlamydomonas reinhardtii is a model alga of increasing interest as a cell factory for the production of valuable compounds, including therapeutic proteins and bioactive metabolites. Expression of foreign genes in the chloroplast is particularly advantageous as: (i) accumulation of product in this sub-cellular compartment minimises potential toxicity to the rest of the cell; (ii) genes can integrate at specific loci of the chloroplast genome (plastome) by homologous recombination; (iii) the high ploidy of the plastome and the high-level expression of chloroplast genes can be exploited to achieve levels of recombinant protein as high as 5% total cell protein; (iv) the lack of any gene silencing mechanisms in the chloroplast ensures stable expression of transgenes. However, the generation of C. reinhardtii chloroplast transformants requires efficient methods of selection, and ideally methods for subsequent marker removal. Additionally, the use of reporter genes is critical to achieving a comprehensive understanding of gene expression, thereby informing experimental design for recombinant applications. This review discusses currently available selection and reporter systems for chloroplast engineering in C. reinhardtii, as well as those used for chloroplast engineering in higher plants and other microalgae, and looks to the future in terms of possible new markers and reporters that will further advance the C. reinhardtii chloroplast as an expression platform.
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Affiliation(s)
- Lola Esland
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Marco Larrea-Alvarez
- School of Biological Sciences and Engineering, Yachay-Tech University, Hacienda San José, Urcuquí-Imbabura 100650, Ecuador.
| | - Saul Purton
- Institute of Structural & Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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El Hajj M, Hamdan MFB, Avila EM, Day A. Rescue of Deletion Mutants to Isolate Plastid Transformants in Higher Plants. Methods Mol Biol 2018; 1829:325-339. [PMID: 29987732 DOI: 10.1007/978-1-4939-8654-5_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Plastid transformation is an attractive alternative to nuclear transformation enabling manipulation of native plastid genes and the insertion of foreign genes into plastids for applications in agriculture and industrial biotechnology. Transformation is achieved using dominant positive selection markers that confer resistance to antibiotics. The very high copy number of plastid DNA means that a prolonged selection step is required to obtain a uniform population of transgenic plastid genomes. Repair of mutant plastid genes with the corresponding functional allele allows selection based on restoration of the wild type phenotype. The use of deletion rather than point mutants avoids spontaneous reversion back to wild type. Combining antibiotic resistance markers with native plastid genes speeds up the attainment of homoplasmy and allows early transfer of transplastomic lines to soil where antibiotic selection is replaced by selection for photoautotrophic growth. Here we describe our method using the wild type rbcL gene as a plastid transformation marker to restore pigmentation and photosynthesis to a pale green heterotrophic rbcL mutant.
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Affiliation(s)
- Mohammad El Hajj
- School of Biological Sciences, The University of Manchester, Manchester, UK
| | | | - Elena Martin Avila
- School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Anil Day
- School of Biological Sciences, The University of Manchester, Manchester, UK.
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Yurina NP, Sharapova LS, Odintsova MS. Structure of Plastid Genomes of Photosynthetic Eukaryotes. BIOCHEMISTRY (MOSCOW) 2017; 82:678-691. [PMID: 28601077 DOI: 10.1134/s0006297917060049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review presents current views on the plastid genomes of higher plants and summarizes data on the size, structural organization, gene content, and other features of plastid DNAs. Special emphasis is placed on the properties of organization of land plant plastid genomes (nucleoids) that distinguish them from bacterial genomes. The prospects of genetic engineering of chloroplast genomes are discussed.
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Affiliation(s)
- N P Yurina
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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Tabatabaei I, Ruf S, Bock R. A bifunctional aminoglycoside acetyltransferase/phosphotransferase conferring tobramycin resistance provides an efficient selectable marker for plastid transformation. PLANT MOLECULAR BIOLOGY 2017; 93:269-281. [PMID: 27858324 PMCID: PMC5306187 DOI: 10.1007/s11103-016-0560-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/10/2016] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE A new selectable marker gene for stable transformation of the plastid genome was developed that is similarly efficient as the aadA, and produces no background of spontaneous resistance mutants. More than 25 years after its development for Chlamydomonas and tobacco, the transformation of the chloroplast genome still represents a challenging technology that is available only in a handful of species. The vast majority of chloroplast transformation experiments conducted thus far have relied on a single selectable marker gene, the spectinomycin resistance gene aadA. Although a few alternative markers have been reported, the aadA has remained unrivalled in efficiency and is, therefore, nearly exclusively used. The development of new marker genes for plastid transformation is of crucial importance to all efforts towards extending the species range of the technology as well as to those applications in basic research, biotechnology and synthetic biology that involve the multistep engineering of plastid genomes. Here, we have tested a bifunctional resistance gene for its suitability as a selectable marker for chloroplast transformation. The bacterial enzyme aminoglycoside acetyltransferase(6')-Ie/aminoglycoside phosphotransferase(2″)-Ia possesses an N-terminal acetyltransferase domain and a C-terminal phosphotransferase domain that can act synergistically and detoxify aminoglycoside antibiotics highly efficiently. We report that, in combination with selection for resistance to the aminoglycoside tobramycin, the aac(6')-Ie/aph(2″)-Ia gene represents an efficient marker for plastid transformation in that it produces similar numbers of transplastomic lines as the spectinomycin resistance gene aadA. Importantly, no spontaneous antibiotic resistance mutants appear under tobramycin selection.
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Affiliation(s)
- Iman Tabatabaei
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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Daniell H, Chan HT, Pasoreck EK. Vaccination via Chloroplast Genetics: Affordable Protein Drugs for the Prevention and Treatment of Inherited or Infectious Human Diseases. Annu Rev Genet 2016; 50:595-618. [PMID: 27893966 PMCID: PMC5496655 DOI: 10.1146/annurev-genet-120215-035349] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plastid-made biopharmaceuticals treat major metabolic or genetic disorders, including Alzheimer's, diabetes, hypertension, hemophilia, and retinopathy. Booster vaccines made in chloroplasts prevent global infectious diseases, such as tuberculosis, malaria, cholera, and polio, and biological threats, such as anthrax and plague. Recent advances in this field include commercial-scale production of human therapeutic proteins in FDA-approved cGMP facilities, development of tags to deliver protein drugs to targeted human cells or tissues, methods to deliver precise doses, and long-term stability of protein drugs at ambient temperature, maintaining their efficacy. Codon optimization utilizing valuable information from sequenced chloroplast genomes enhanced expression of eukaryotic human or viral genes in chloroplasts and offered unique insights into translation in chloroplasts. Support from major biopharmaceutical companies, development of hydroponic production systems, and evaluation by regulatory agencies, including the CDC, FDA, and USDA, augur well for advancing this novel concept to the clinic and revolutionizing affordable healthcare.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Hui-Ting Chan
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Elise K Pasoreck
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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Ahmad N, Michoux F, Lössl AG, Nixon PJ. Challenges and perspectives in commercializing plastid transformation technology. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5945-5960. [PMID: 27697788 DOI: 10.1093/jxb/erw360] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plastid transformation has emerged as an alternative platform to generate transgenic plants. Attractive features of this technology include specific integration of transgenes-either individually or as operons-into the plastid genome through homologous recombination, the potential for high-level protein expression, and transgene containment because of the maternal inheritance of plastids. Several issues associated with nuclear transformation such as gene silencing, variable gene expression due to the Mendelian laws of inheritance, and epigenetic regulation have not been observed in the plastid genome. Plastid transformation has been successfully used for the production of therapeutics, vaccines, antigens, and commercial enzymes, and for engineering various agronomic traits including resistance to biotic and abiotic stresses. However, these demonstrations have usually focused on model systems such as tobacco, and the technology per se has not yet reached the market. Technical factors limiting this technology include the lack of efficient protocols for the transformation of cereals, poor transgene expression in non-green plastids, a limited number of selection markers, and the lengthy procedures required to recover fully segregated plants. This article discusses the technology of transforming the plastid genome, the positive and negative features compared with nuclear transformation, and the current challenges that need to be addressed for successful commercialization.
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Affiliation(s)
- Niaz Ahmad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Franck Michoux
- Alkion Biopharma SAS, 4 rue Pierre Fontaine, 91058 Evry, France
| | - Andreas G Lössl
- Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College, South Kensington Campus, London SW7 2AZ, UK
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Martin Avila E, Gisby MF, Day A. Seamless editing of the chloroplast genome in plants. BMC PLANT BIOLOGY 2016; 16:168. [PMID: 27474038 PMCID: PMC4966725 DOI: 10.1186/s12870-016-0857-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/20/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Gene editing technologies enable the precise insertion of favourable mutations and performance enhancing trait genes into chromosomes whilst excluding all excess DNA from modified genomes. The technology gives rise to a new class of biotech crops which is likely to have widespread applications in agriculture. Despite progress in the nucleus, the seamless insertions of point mutations and non-selectable foreign genes into the organelle genomes of crops have not been described. The chloroplast genome is an attractive target to improve photosynthesis and crop performance. Current chloroplast genome engineering technologies for introducing point mutations into native chloroplast genes leave DNA scars, such as the target sites for recombination enzymes. Seamless editing methods to modify chloroplast genes need to address reversal of site-directed point mutations by template mediated repair with the vast excess of wild type chloroplast genomes that are present early in the transformation process. RESULTS Using tobacco, we developed an efficient two-step method to edit a chloroplast gene by replacing the wild type sequence with a transient intermediate. This was resolved to the final edited gene by recombination between imperfect direct repeats. Six out of 11 transplastomic plants isolated contained the desired intermediate and at the second step this was resolved to the edited chloroplast gene in five of six plants tested. Maintenance of a single base deletion mutation in an imperfect direct repeat of the native chloroplast rbcL gene showed the limited influence of biased repair back to the wild type sequence. The deletion caused a frameshift, which replaced the five C-terminal amino acids of the Rubisco large subunit with 16 alternative residues resulting in a ~30-fold reduction in its accumulation. We monitored the process in vivo by engineering an overlapping gusA gene downstream of the edited rbcL gene. Translational coupling between the overlapping rbcL and gusA genes resulted in relatively high GUS accumulation (~0.5 % of leaf protein). CONCLUSIONS Editing chloroplast genomes using transient imperfect direct repeats provides an efficient method for introducing point mutations into chloroplast genes. Moreover, we describe the first synthetic operon allowing expression of a downstream overlapping gene by translational coupling in chloroplasts. Overlapping genes provide a new mechanism for co-ordinating the translation of foreign proteins in chloroplasts.
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Affiliation(s)
- Elena Martin Avila
- Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT UK
- Present address: Research School of Biology, The Australian National University, Acton, ACT 2601 Australia
| | - Martin F. Gisby
- Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT UK
| | - Anil Day
- Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT UK
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Li Y, Wang R, Hu Z, Li H, Lu S, Zhang J, Lin Y, Zhou F. Expression of a Codon-Optimized dsdA Gene in Tobacco Plastids and Rice Nucleus Confers D-Serine Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:640. [PMID: 27242842 PMCID: PMC4863892 DOI: 10.3389/fpls.2016.00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
D-serine is toxic to plants. D-serine ammonia lyase, which is encoded by the dsdA gene, can attenuate this toxicity with high specificity. In the present study, we explored the function of codon-optimized dsdA with tobacco plastids and rice nuclear transformation system. It was shown that dsdA gene was site-specifically integrated into the tobacco plastid genome and displayed a high level of expression. Genetic analysis of the progenies showed that dsdA gene is maternally inherited and confers sufficient D-serine resistance in tobacco. The effective screening concentrations of D-serine for seed germination, callus regeneration and foliar spray were 10, 30, and 75 mM, respectively. In addition, calluses from homozygous transgenic rice lines also showed significant tolerance to D-serine (up to 75 mM). Our study proves the feasibility of using dsdA gene as a selectable marker in both plastid and nuclear transformation systems.
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Bellucci M, De Marchis F, Ferradini N, Pompa A, Veronesi F, Rosellini D. A mutant Synechococcus gene encoding glutamate 1-semialdehyde aminotransferase confers gabaculine resistance when expressed in tobacco plastids. PLANT CELL REPORTS 2015; 34:2127-36. [PMID: 26265112 DOI: 10.1007/s00299-015-1856-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/20/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE A mutant glutamate 1-semialdehyde aminotransferase gene from the Synechococcus , inserted into tobacco plastid DNA by means of particle bombardment and antibiotic selection, conferred gabaculine resistance allowing to attain homoplasmy. Many plant species are recalcitrant to plastid genome transformation. New selections systems may help to overcome this limitation and to extend the application of this technology. A mutant hemL gene from the photosynthetic cyanobacterium Synechococcus, encoding a gabaculine-insensitive glutamate 1-semialdehyde aminotransferase (GSA), is an efficient selectable marker gene for nuclear transformation of tobacco, alfalfa and durum wheat. Since GSA functions in the plastid, we introduced the mutant hemL gene into the tobacco plastid genome along with the conventional antibiotic resistance aadA gene, in the attempt to develop a new selection system for plastome transformation. Although we were unable to directly regenerate gabaculine resistant transplastomic plants, we demonstrated the functionality of hemL in tobacco plastids by using gabaculine selection in the second and third rounds of in vitro selection that permitted to obtain the homoplasmic state in transgenic plants. Thus, the mutant hemL gene functions as a secondary selection marker in tobacco plastids. Our results encourage further attempts to test gabaculine resistant GSA for plastome transformation of crop plants in which gabaculine has stronger regeneration-inhibiting effects with respect to tobacco.
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Affiliation(s)
- Michele Bellucci
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128, Perugia, Italy
| | - Francesca De Marchis
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128, Perugia, Italy
| | - Nicoletta Ferradini
- Department of Agricultural Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Andrea Pompa
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128, Perugia, Italy
| | - Fabio Veronesi
- Department of Agricultural Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Daniele Rosellini
- Department of Agricultural Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
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15
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Jin S, Daniell H. The Engineered Chloroplast Genome Just Got Smarter. TRENDS IN PLANT SCIENCE 2015; 20:622-640. [PMID: 26440432 PMCID: PMC4606472 DOI: 10.1016/j.tplants.2015.07.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/18/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Chloroplasts are known to sustain life on earth by providing food, fuel, and oxygen through the process of photosynthesis. However, the chloroplast genome has also been smartly engineered to confer valuable agronomic traits and/or serve as bioreactors for the production of industrial enzymes, biopharmaceuticals, bioproducts, or vaccines. The recent breakthrough in hyperexpression of biopharmaceuticals in edible leaves has facilitated progression to clinical studies by major pharmaceutical companies. This review critically evaluates progress in developing new tools to enhance or simplify expression of targeted genes in chloroplasts. These tools hold the promise to further the development of novel fuels and products, enhance the photosynthetic process, and increase our understanding of retrograde signaling and cellular processes.
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Affiliation(s)
- Shuangxia Jin
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA; National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Bock R. Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:211-41. [PMID: 25494465 DOI: 10.1146/annurev-arplant-050213-040212] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany;
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17
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Monselise EBI, Levkovitz A, Kost D. Ultraviolet radiation induces stress in etiolated Landoltia punctata, as evidenced by the presence of alanine, a universal stress signal: a ¹⁵N NMR study. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:101-107. [PMID: 24889211 DOI: 10.1111/plb.12198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 06/03/2023]
Abstract
Analysis with (15) N NMR revealed that alanine, a universal cellular stress signal, accumulates in etiolated duckweed plants exposed to 15-min pulsed UV light, but not in the absence of UV irradiation. The addition of 10 mm vitamin C, a radical scavenger, reduced alanine levels to zero, indicating the involvement of free radicals. Free D-alanine was detected in (15) N NMR analysis of the chiral amino acid content, using D-tartaric acid as solvent. The accumulation of D-alanine under stress conditions presents a new perspective on the biochemical processes taking place in prokaryote and eukaryote cells.
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Affiliation(s)
- E B-I Monselise
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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18
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Suarez JV, Banks S, Thomas PG, Day A. A new F131V mutation in Chlamydomonas phytoene desaturase locates a cluster of norflurazon resistance mutations near the FAD-binding site in 3D protein models. PLoS One 2014; 9:e99894. [PMID: 24936791 PMCID: PMC4061028 DOI: 10.1371/journal.pone.0099894] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
The green alga Chlamydomonas reinhardtii provides a tractable genetic model to study herbicide mode of action using forward genetics. The herbicide norflurazon inhibits phytoene desaturase, which is required for carotenoid synthesis. Locating amino acid substitutions in mutant phytoene desaturases conferring norflurazon resistance provides a genetic approach to map the herbicide binding site. We isolated a UV-induced mutant able to grow in very high concentrations of norflurazon (150 µM). The phytoene desaturase gene in the mutant strain contained the first resistance mutation to be localised to the dinucleotide-binding Rossmann-likedomain. A highly conserved phenylalanine amino acid at position 131 of the 564 amino acid precursor protein was changed to a valine in the mutant protein. F131, and two other amino acids whose substitution confers norflurazon resistance in homologous phytoene desaturase proteins, map to distant regions in the primary sequence of the C. reinhardtii protein (V472, L505) but in tertiary models these residues cluster together to a region close to the predicted FAD binding site. The mutant gene allowed direct 5 µM norflurazon based selection of transformants, which were tolerant to other bleaching herbicides including fluridone, flurtamone, and diflufenican but were more sensitive to beflubutamid than wild type cells. Norflurazon resistance and beflubutamid sensitivity allow either positive or negative selection against transformants expressing the mutant phytoene desaturase gene.
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Affiliation(s)
- Julio V. Suarez
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Stephen Banks
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | | | - Anil Day
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
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Bock R. Genetic engineering of the chloroplast: novel tools and new applications. Curr Opin Biotechnol 2013; 26:7-13. [PMID: 24679252 DOI: 10.1016/j.copbio.2013.06.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
Abstract
The plastid genome represents an attractive target of genetic engineering in crop plants. Plastid transgenes often give high expression levels, can be stacked in operons and are largely excluded from pollen transmission. Recent research has greatly expanded our toolbox for plastid genome engineering and many new proof-of-principle applications have highlighted the enormous potential of the transplastomic technology in both crop improvement and the development of plants as bioreactors for the sustainable and cost-effective production of biopharmaceuticals, enzymes and raw materials for the chemical industry. This review describes recent technological advances with plastid transformation in seed plants. It focuses on novel tools for plastid genome engineering and transgene expression and summarizes progress with harnessing the potential of plastid transformation in biotechnology.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany.
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