1
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Xu W, Li S, Bock R, Zhang J. A heat-inducible expression system for external control of gene expression in plastids. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:960-969. [PMID: 38059318 PMCID: PMC10955493 DOI: 10.1111/pbi.14238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/17/2023] [Accepted: 11/04/2023] [Indexed: 12/08/2023]
Abstract
Inducible expression systems can overcome the trade-off between high-level transgene expression and its pleiotropic effects on plant growth. In addition, they can facilitate the expression of biochemical pathways that produce toxic metabolites. Although a few inducible expression systems for the control of transgene expression in plastids have been developed, they all depend on chemical inducers and/or nuclear transgenes. Here we report a temperature-inducible expression system for plastids that is based on the bacteriophage λ leftward and rightward promoters (pL/pR) and the temperature-sensitive repressor cI857. We show that the expression of green fluorescent protein (GFP) in plastids can be efficiently repressed by cI857 under normal growth conditions, and becomes induced over time upon exposure to elevated temperatures in a light-dependent process. We further demonstrate that by introducing into plastids an expression system based on the bacteriophage T7 RNA polymerase, the temperature-dependent accumulation of GFP increased further and was ~24 times higher than expression driven by the pL/pR promoter alone, reaching ~0.48% of the total soluble protein. In conclusion, our heat-inducible expression system provides a new tool for the external control of plastid (trans) gene expression that is cost-effective and does not depend on chemical inducers.
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Affiliation(s)
- Wenbo Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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2
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Tanwar N, Arya SS, Rookes JE, Cahill DM, Lenka SK, Bansal KC. Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops. Crit Rev Biotechnol 2023; 43:1001-1018. [PMID: 35815847 DOI: 10.1080/07388551.2022.2092717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.
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Affiliation(s)
- Neha Tanwar
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sagar S Arya
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - James E Rookes
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sangram K Lenka
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- Gujarat Biotechnology University, Gujarat, India
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3
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Chung KP, Loiacono FV, Neupert J, Wu M, Bock R. An RNA thermometer in the chloroplast genome of Chlamydomonas facilitates temperature-controlled gene expression. Nucleic Acids Res 2023; 51:11386-11400. [PMID: 37855670 PMCID: PMC10639063 DOI: 10.1093/nar/gkad816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
Riboregulators such as riboswitches and RNA thermometers provide simple, protein-independent tools to control gene expression at the post-transcriptional level. In bacteria, RNA thermometers regulate protein synthesis in response to temperature shifts. Thermometers outside of the bacterial world are rare, and in organellar genomes, no RNA thermometers have been identified to date. Here we report the discovery of an RNA thermometer in a chloroplast gene of the unicellular green alga Chlamydomonas reinhardtii. The thermometer, residing in the 5' untranslated region of the psaA messenger RNA forms a hairpin-type secondary structure that masks the Shine-Dalgarno sequence at 25°C. At 40°C, melting of the secondary structure increases accessibility of the Shine-Dalgarno sequence to initiating ribosomes, thus enhancing protein synthesis. By targeted nucleotide substitutions and transfer of the thermometer into Escherichia coli, we show that the secondary structure is necessary and sufficient to confer the thermometer properties. We also demonstrate that the thermometer provides a valuable tool for inducible transgene expression from the Chlamydomonas plastid genome, in that a simple temperature shift of the algal culture can greatly increase recombinant protein yields.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - F Vanessa Loiacono
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mengting Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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4
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Bulle M, Sheri V, Aileni M, Zhang B. Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3448. [PMID: 37836188 PMCID: PMC10574609 DOI: 10.3390/plants12193448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad 500030, India
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Mahender Aileni
- Department of Biotechnology, Telangana University, Dichpally, Nizamabad 503322, India;
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
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5
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Wang Y, Demirer GS. Synthetic biology for plant genetic engineering and molecular farming. Trends Biotechnol 2023; 41:1182-1198. [PMID: 37012119 DOI: 10.1016/j.tibtech.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Many efforts have been put into engineering plants to improve crop yields and stress tolerance and boost the bioproduction of valuable molecules. Yet, our capabilities are still limited due to the lack of well-characterized genetic building blocks and resources for precise manipulation and given the inherently challenging properties of plant tissues. Advancements in plant synthetic biology can overcome these bottlenecks and release the full potential of engineered plants. In this review, we first discuss the recently developed plant synthetic elements from single parts to advanced circuits, software, and hardware tools expediting the engineering cycle. Next, we survey the advancements in plant biotechnology enabled by these recent resources. We conclude the review with outstanding challenges and future directions of plant synthetic biology.
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Affiliation(s)
- Yunqing Wang
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Legen J, Dühnen S, Gauert A, Götz M, Schmitz-Linneweber C. A CRR2-Dependent sRNA Sequence Supports Papillomavirus Vaccine Expression in Tobacco Chloroplasts. Metabolites 2023; 13:metabo13030315. [PMID: 36984756 PMCID: PMC10054877 DOI: 10.3390/metabo13030315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction: Human papillomavirus (HPV) infection is the leading cause of cervical cancer, and vaccination with HPV L1 capsid proteins has been successful in controlling it. However, vaccination coverage is not universal, particularly in developing countries, where 80% of all cervical cancer cases occur. Cost-effective vaccination could be achieved by expressing the L1 protein in plants. Various efforts have been made to produce the L1 protein in plants, including attempts to express it in chloroplasts for high-yield performance. However, manipulating chloroplast gene expression requires complex and difficult-to-control expression elements. In recent years, a family of nuclear-encoded, chloroplast-targeted RNA-binding proteins, the pentatricopeptide repeat (PPR) proteins, were described as key regulators of chloroplast gene expression. For example, PPR proteins are used by plants to stabilize and translate chloroplast mRNAs. Objectives: To demonstrate that a PPR target site can be used to drive HPV L1 expression in chloroplasts. Methods: To test our hypothesis, we used biolistic chloroplast transformation to establish tobacco lines that express two variants of the HPV L1 protein under the control of the target site of the PPR protein CHLORORESPIRATORY REDUCTION2 (CRR2). The transgenes were inserted into a dicistronic operon driven by the plastid rRNA promoter. To determine the effectiveness of the PPR target site for the expression of the HPV L1 protein in the chloroplasts, we analyzed the accumulation of the transgenic mRNA and its processing, as well as the accumulation of the L1 protein in the transgenic lines. Results: We established homoplastomic lines carrying either the HPV18 L1 protein or an HPV16B Enterotoxin::L1 fusion protein. The latter line showed severe growth retardation and pigment loss, suggesting that the fusion protein is toxic to the chloroplasts. Despite the presence of dicistronic mRNAs, we observed very little accumulation of monocistronic transgenic mRNA and no significant increase in CRR2-associated small RNAs. Although both lines expressed the L1 protein, quantification using an external standard suggested that the amounts were low. Conclusions: Our results suggest that PPR binding sites can be used to drive vaccine expression in plant chloroplasts; however, the factors that modulate the effectiveness of target gene expression remain unclear. The identification of dozens of PPR binding sites through small RNA sequencing expands the set of expression elements available for high-value protein production in chloroplasts.
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Affiliation(s)
- Julia Legen
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Sara Dühnen
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Anton Gauert
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Michael Götz
- BioEnergy GmbH, Dietersberg 1, 92334 Berching, Germany
| | - Christian Schmitz-Linneweber
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
- Correspondence: ; Tel.: +49-20-2093-49700
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7
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Wang W, An X, Yan K, Li Q. Construction and Application of Orthogonal T7 Expression System in Eukaryote: An Overview. Adv Biol (Weinh) 2023; 7:e2200218. [PMID: 36464626 DOI: 10.1002/adbi.202200218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The T7 system is an orthogonal transcription-system, which is characterized by simplicity, higher efficiency, and higher processivity, and it is used for protein or mRNA synthesis in various biological-systems. In comparison with prokaryotes, the construction of the T7 expression system is still on-going in eukaryotes, but it shows greatly applicable prospects. In the present paper, development of T7 expression system construction in eukaryotes is reviewed, including its construction in animal (mammalian cells, trypanosomatid protozoa, Xenopus oocytes, zebrafish), plant, and microorganism and its application in vaccine production and gene therapy. In addition, the innate challenges of T7 expression system construction in eukaryote and its potential application in vaccine production and gene therapy are discussed.
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Affiliation(s)
- Wenya Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xiaoyan An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Kun Yan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Qiang Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
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8
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Mellor SB, Behrendorff JBYH, Ipsen JØ, Crocoll C, Laursen T, Gillam EMJ, Pribil M. Exploiting photosynthesis-driven P450 activity to produce indican in tobacco chloroplasts. FRONTIERS IN PLANT SCIENCE 2023; 13:1049177. [PMID: 36743583 PMCID: PMC9890960 DOI: 10.3389/fpls.2022.1049177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 05/28/2023]
Abstract
Photosynthetic organelles offer attractive features for engineering small molecule bioproduction by their ability to convert solar energy into chemical energy required for metabolism. The possibility to couple biochemical production directly to photosynthetic assimilation as a source of energy and substrates has intrigued metabolic engineers. Specifically, the chemical diversity found in plants often relies on cytochrome P450-mediated hydroxylations that depend on reductant supply for catalysis and which often lead to metabolic bottlenecks for heterologous production of complex molecules. By directing P450 enzymes to plant chloroplasts one can elegantly deal with such redox prerequisites. In this study, we explore the capacity of the plant photosynthetic machinery to drive P450-dependent formation of the indigo precursor indoxyl-β-D-glucoside (indican) by targeting an engineered indican biosynthetic pathway to tobacco (Nicotiana benthamiana) chloroplasts. We show that both native and engineered variants belonging to the human CYP2 family are catalytically active in chloroplasts when driven by photosynthetic reducing power and optimize construct designs to improve productivity. However, while increasing supply of tryptophan leads to an increase in indole accumulation, it does not improve indican productivity, suggesting that P450 activity limits overall productivity. Co-expression of different redox partners also does not improve productivity, indicating that supply of reducing power is not a bottleneck. Finally, in vitro kinetic measurements showed that the different redox partners were efficiently reduced by photosystem I but plant ferredoxin provided the highest light-dependent P450 activity. This study demonstrates the inherent ability of photosynthesis to support P450-dependent metabolic pathways. Plants and photosynthetic microbes are therefore uniquely suited for engineering P450-dependent metabolic pathways regardless of enzyme origin. Our findings have implications for metabolic engineering in photosynthetic hosts for production of high-value chemicals or drug metabolites for pharmacological studies.
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Affiliation(s)
- Silas B. Mellor
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - James B. Y. H. Behrendorff
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johan Ø. Ipsen
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Tomas Laursen
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Mathias Pribil
- Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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9
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Expression strategies for the efficient synthesis of antimicrobial peptides in plastids. Nat Commun 2022; 13:5856. [PMID: 36195597 PMCID: PMC9532397 DOI: 10.1038/s41467-022-33516-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial peptides (AMPs) kill microbes or inhibit their growth and are promising next-generation antibiotics. Harnessing their full potential as antimicrobial agents will require methods for cost-effective large-scale production and purification. Here, we explore the possibility to exploit the high protein synthesis capacity of the chloroplast to produce AMPs in plants. Generating a large series of 29 sets of transplastomic tobacco plants expressing nine different AMPs as fusion proteins, we show that high-level constitutive AMP expression results in deleterious plant phenotypes. However, by utilizing inducible expression and fusions to the cleavable carrier protein SUMO, the cytotoxic effects of AMPs and fused AMPs are alleviated and plants with wild-type-like phenotypes are obtained. Importantly, purified AMP fusion proteins display antimicrobial activity independently of proteolytic removal of the carrier. Our work provides expression strategies for the synthesis of toxic polypeptides in chloroplasts, and establishes transplastomic plants as efficient production platform for antimicrobial peptides.
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10
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Yang S, Deng Y, Li S. Advances in plastid transformation for metabolic engineering in higher plants. ABIOTECH 2022; 3:224-232. [PMID: 36313931 PMCID: PMC9590572 DOI: 10.1007/s42994-022-00083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/09/2022] [Indexed: 03/12/2023]
Abstract
The plastid (chloroplast) genome of higher plants is an appealing target for metabolic engineering via genetic transformation. Although the bacterial-type plastid genome is small compared with the nuclear genome, it can accommodate large quantities of foreign genes that precisely integrate through homologous recombination. Engineering complex metabolic pathways in plants often requires simultaneous and concerted expression of multiple transgenes, the possibility of stacking several transgenes in synthetic operons makes the transplastomic approach amazing. The potential for extraordinarily high-level transgene expression, absence of epigenetic gene silencing and transgene containment due to the exclusion of plastids from pollen transmission in most angiosperm species further add to the attractiveness of plastid transformation technology. This minireview describes recent advances in expanding the toolboxes for plastid genome engineering, and highlights selected high-value metabolites produced using transplastomic plants, including artemisinin, astaxanthin and paclitaxel.
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Affiliation(s)
- Sheng Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yi Deng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
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11
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Zhang M, Liu G, Zhang Y, Chen T, Feng S, Cai R, Lu C. The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes. Int J Mol Sci 2022; 23:ijms23115903. [PMID: 35682583 PMCID: PMC9180208 DOI: 10.3390/ijms23115903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2′-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.
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Affiliation(s)
- Minmin Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China;
| | - Yunlong Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Ting Chen
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Shanshan Feng
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Rujie Cai
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
| | - Changrui Lu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
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12
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Latif S, Gottschamel J, Syed T, Younus I, Gull K, Sameeullah M, Batool N, Lössl AG, Mariz F, Müller M, Mirza B, Waheed MT. Inducible expression of human papillomavirus-16 L1 capsomeres in the plastomes of Nicotiana tabacum: Transplastomic plants develop normal flowers and pollen. Biotechnol Appl Biochem 2022; 69:596-611. [PMID: 33650709 DOI: 10.1002/bab.2136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/24/2021] [Indexed: 12/20/2022]
Abstract
Human papillomavirus type-16 (HPV-16) is the major HPV type involved in causing cervical cancer among women. The disease burden is high in developing and underdeveloped countries. Previously, the constitutive expression of HPV-16 L1 protein led to male sterility in transplastomic tobacco plants. Here, the HPV-16 L1 gene was expressed in chloroplasts of Nicotiana tabacum under the control of an ethanol-inducible promoter, trans-activated by nucleus-derived signal peptide. Plants containing nuclear component were transformed with transformation vector pEXP-T7-L1 by biolistic gun. The transformation and homoplasmic status of transformed plants was verified by polymerase chain reaction and Southern blotting, respectively. Protein was induced by spraying 5% ethanol for 7 consecutive days. The correct folding of L1 protein was confirmed by antigen-capture ELISA using a conformation-specific antibody. The L1 protein accumulated up to 3 μg/g of fresh plant material. The L1 protein was further purified using affinity chromatography. All transplastomic plants developed normal flowers and produced viable seeds upon self-pollination. Pollens also showed completely normal structure under light microscope and scanning electron microscopy. These data confirm the use of the inducible expression as plant-safe approach for expressing transgenes in plants, especially those genes that cause detrimental effects on plant growth and morphology.
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Affiliation(s)
- Sara Latif
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Johanna Gottschamel
- Department of Applied Plant Science and Plant Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tahira Syed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iqra Younus
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, , Oxford Road, Manchester, United Kingdom
| | - Kehkshan Gull
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Sameeullah
- Innovative Food Technologies Development Application and Research Centre, Faculty of Engineering, Bolu Abant Izzet Baysal University, Golkoye Campus, Bolu, Turkey
| | - Neelam Batool
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Andreas Günter Lössl
- Department of Applied Plant Science and Plant Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Filipe Mariz
- Tumorvirus-specific Vaccination Strategies, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Martin Müller
- Tumorvirus-specific Vaccination Strategies, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Lahore College for Women University, Lahore, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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13
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Bock R. Transplastomic approaches for metabolic engineering. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102185. [PMID: 35183927 DOI: 10.1016/j.pbi.2022.102185] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The plastid (chloroplast) genome of seed plants represents an attractive target of metabolic pathway engineering by genetic transformation. Although the plastid genome is relatively small, it can accommodate large amounts of foreign DNA that precisely integrates via homologous recombination, and is largely excluded from pollen transmission due to the maternal mode of plastid inheritance. Since the engineering of metabolic pathways often requires the expression of multiple transgenes, the possibility to conveniently stack transgenes in synthetic operons makes the transplastomic technology particularly appealing in the area of metabolic engineering. Absence of epigenetic gene silencing mechanisms from plastids and the possibility to achieve high transgene expression levels further add to the attractiveness of plastid genome transformation. This review focuses on engineering principles and available tools for the transplastomic expression of enzymes and pathways, and highlights selected recent applications in metabolic engineering.
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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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14
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Frusciante S, Demurtas OC, Sulli M, Mini P, Aprea G, Diretto G, Karcher D, Bock R, Giuliano G. Heterologous expression of Bixa orellana cleavage dioxygenase 4-3 drives crocin but not bixin biosynthesis. PLANT PHYSIOLOGY 2022; 188:1469-1482. [PMID: 34919714 PMCID: PMC8896647 DOI: 10.1093/plphys/kiab583] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2021] [Indexed: 06/07/2023]
Abstract
Annatto (Bixa orellana) is a perennial shrub native to the Americas, and bixin, derived from its seeds, is a methoxylated apocarotenoid used as a food and cosmetic colorant. Two previous reports claimed to have isolated the carotenoid cleavage dioxygenase (CCD) responsible for the production of the putative precursor of bixin, the C24 apocarotenal bixin dialdehyde. We re-assessed the activity of six Bixa CCDs and found that none of them produced substantial amounts of bixin dialdehyde in Escherichia coli. Unexpectedly, BoCCD4-3 cleaved different carotenoids (lycopene, β-carotene, and zeaxanthin) to yield the C20 apocarotenal crocetin dialdehyde, the known precursor of crocins, which are glycosylated apocarotenoids accumulated in saffron stigmas. BoCCD4-3 lacks a recognizable transit peptide but localized to plastids, the main site of carotenoid accumulation in plant cells. Expression of BoCCD4-3 in Nicotiana benthamiana leaves (transient expression), tobacco (Nicotiana tabacum) leaves (chloroplast transformation, under the control of a synthetic riboswitch), and in conjunction with a saffron crocetin glycosyl transferase, in tomato (Solanum lycopersicum) fruits (nuclear transformation) led to high levels of crocin accumulation, reaching the highest levels (>100 µg/g dry weight) in tomato fruits, which also showed a crocin profile similar to that found in saffron, with highly glycosylated crocins as major compounds. Thus, while the bixin biosynthesis pathway remains unresolved, BoCCD4-3 can be used for the metabolic engineering of crocins in a wide range of different plant tissues.
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Affiliation(s)
- Sarah Frusciante
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Olivia Costantina Demurtas
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Paola Mini
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
| | - Daniel Karcher
- 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
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, 00123 Roma, Italy
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15
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Cesarino I. Going red but not mad: efficient astaxanthin production in tobacco without yield penalty. PLANT PHYSIOLOGY 2022; 188:35-37. [PMID: 35051289 PMCID: PMC8774826 DOI: 10.1093/plphys/kiab482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, 370, 05508-020, São Paulo, Brazil
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16
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Agrawal S, Karcher D, Ruf S, Erban A, Hertle AP, Kopka J, Bock R. Riboswitch-mediated inducible expression of an astaxanthin biosynthetic operon in plastids. PLANT PHYSIOLOGY 2022; 188:637-652. [PMID: 34623449 PMCID: PMC8774745 DOI: 10.1093/plphys/kiab428] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/06/2021] [Indexed: 06/01/2023]
Abstract
The high-value carotenoid astaxanthin (3,3'-dihydroxy-β,β-carotene-4,4'-dione) is one of the most potent antioxidants in nature. In addition to its large-scale use in fish farming, the pigment has applications as a food supplement and an active ingredient in cosmetics and in pharmaceuticals for the treatment of diseases linked to reactive oxygen species. The biochemical pathway for astaxanthin synthesis has been introduced into seed plants, which do not naturally synthesize this pigment, by nuclear and plastid engineering. The highest accumulation rates have been achieved in transplastomic plants, but massive production of astaxanthin has resulted in severe growth retardation. What limits astaxanthin accumulation levels and what causes the mutant phenotype is unknown. Here, we addressed these questions by making astaxanthin synthesis in tobacco (Nicotiana tabacum) plastids inducible by a synthetic riboswitch. We show that, already in the uninduced state, astaxanthin accumulates to similarly high levels as in transplastomic plants expressing the pathway constitutively. Importantly, the inducible plants displayed wild-type-like growth properties and riboswitch induction resulted in a further increase in astaxanthin accumulation. Our data suggest that the mutant phenotype associated with constitutive astaxanthin synthesis is due to massive metabolite turnover, and indicate that astaxanthin accumulation is limited by the sequestration capacity of the plastid.
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Affiliation(s)
- Shreya Agrawal
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alexander P Hertle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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17
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Molina-Hidalgo FJ, Vazquez-Vilar M, D'Andrea L, Demurtas OC, Fraser P, Giuliano G, Bock R, Orzáez D, Goossens A. Engineering Metabolism in Nicotiana Species: A Promising Future. Trends Biotechnol 2021; 39:901-913. [PMID: 33341279 DOI: 10.1016/j.tibtech.2020.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Lucio D'Andrea
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Olivia C Demurtas
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, London, UK
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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18
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Zhang Y, Ding W, Wang Z, Zhao H, Shi S. Development of Host-Orthogonal Genetic Systems for Synthetic Biology. Adv Biol (Weinh) 2021; 5:e2000252. [PMID: 33729696 DOI: 10.1002/adbi.202000252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/18/2020] [Indexed: 12/17/2022]
Abstract
The construction of a host-orthogonal genetic system can not only minimize the impact of host-specific nuances on fine-tuning of gene expression, but also expand cellular functions such as in vivo continuous evolution of genes based on an error-prone DNA polymerase. It represents an emerging powerful approach for making biology easier to engineer. In this review, the recent advances are described on the design of genetic systems that can be stably inherited in the host cells and are responsible for important biological processes including DNA replication, RNA transcription, protein translation, and gene regulation. Their applications in synthetic biology are summarized and the future challenges and opportunities are discussed in developing such systems.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.,Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, P. R. China
| | - Zhihui Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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19
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Abstract
Expression of transgenes from the plastid genome offers a number of attractions to biotechnologists, with the potential to attain very high protein accumulation levels arguably being the most attractive one. High-level transgene expression is of particular importance in resistance engineering (e.g., for expression of insecticidal proteins) and molecular farming (e.g., for expression of pharmaceutical proteins and industrial enzymes). Over the past decades, the production of many commercially valuable proteins in chloroplast-transgenic (transplastomic) plants has been attempted, including pharmaceutical proteins (e.g., subunit vaccines and protein antibiotics) and industrial enzymes. Although in some cases, spectacularly high foreign protein accumulation levels have been obtained, expression levels were disappointingly poor in other cases. In this review, I summarize our current knowledge about the factors influencing the efficiency of plastid transgene expression, and highlight possible optimization strategies to alleviate problems with poor expression levels. I also discuss available techniques for inducible expression of chloroplast transgenes.
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20
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Patron NJ. Beyond natural: synthetic expansions of botanical form and function. THE NEW PHYTOLOGIST 2020; 227:295-310. [PMID: 32239523 PMCID: PMC7383487 DOI: 10.1111/nph.16562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 05/05/2023]
Abstract
Powered by developments that enabled genome-scale investigations, systems biology emerged as a field aiming to understand how phenotypes emerge from network functions. These advances fuelled a new engineering discipline focussed on synthetic reconstructions of complex biological systems with the goal of predictable rational design and control. Initially, progress in the nascent field of synthetic biology was slow due to the ad hoc nature of molecular biology methods such as cloning. The application of engineering principles such as standardisation, together with several key technical advances, enabled a revolution in the speed and accuracy of genetic manipulation. Combined with mathematical and statistical modelling, this has improved the predictability of engineering biological systems of which nonlinearity and stochasticity are intrinsic features leading to remarkable achievements in biotechnology as well as novel insights into biological function. In the past decade, there has been slow but steady progress in establishing foundations for synthetic biology in plant systems. Recently, this has enabled model-informed rational design to be successfully applied to the engineering of plant gene regulation and metabolism. Synthetic biology is now poised to transform the potential of plant biotechnology. However, reaching full potential will require conscious adjustments to the skillsets and mind sets of plant scientists.
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Affiliation(s)
- Nicola J. Patron
- Engineering BiologyEarlham InstituteNorwich Research Park, NorwichNorfolkNR4 7UZUK
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21
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Shanidze N, Lenkeit F, Hartig JS, Funck D. A Theophylline-Responsive Riboswitch Regulates Expression of Nuclear-Encoded Genes. PLANT PHYSIOLOGY 2020; 182:123-135. [PMID: 31704721 PMCID: PMC6945857 DOI: 10.1104/pp.19.00625] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/25/2019] [Indexed: 05/27/2023]
Abstract
Riboswitches are small cis-regulatory RNA elements that regulate gene expression by conformational changes in response to ligand binding. Synthetic riboswitches have been engineered as versatile and innovative tools for gene regulation by external application of their ligand in prokaryotes and eukaryotes. In plants, synthetic riboswitches were used to regulate gene expression in plastids, but the application of synthetic riboswitches for the regulation of nuclear-encoded genes in planta remains to be explored. Here, we characterize the properties of a theophylline-responsive synthetic aptazyme for control of nuclear-encoded transgenes in Arabidopsis (Arabidopsis thaliana). Activation of the aptazyme, inserted in the 3' UTR of the target gene, resulted in rapid self-cleavage and subsequent decay of the mRNA. This riboswitch allowed reversible, theophylline-dependent down-regulation of the GFP reporter gene in a dose- and time-dependent manner. Insertion of the riboswitch into the ONE HELIX PROTEIN1 gene allowed complementation of ohp1 mutants and induction of the mutant phenotype by theophylline. GFP and ONE HELIX PROTEIN1 transcript levels were downregulated by up to 90%, and GFP protein levels by 95%. These results establish artificial riboswitches as tools for externally controlled gene expression in synthetic biology in plants or functional crop design.
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Affiliation(s)
- Nana Shanidze
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Felina Lenkeit
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany
| | - Dietmar Funck
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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22
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Saba K, Gottschamel J, Younus I, Syed T, Gull K, Lössl AG, Mirza B, Waheed MT. Chloroplast-based inducible expression of ESAT-6 antigen for development of a plant-based vaccine against tuberculosis. J Biotechnol 2019; 305:1-10. [PMID: 31454508 DOI: 10.1016/j.jbiotec.2019.08.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis causes tuberculosis in humans. The major disease burden of tuberculosis lies in developing countries. Lack of an effective vaccine for adults is one of the major hurdles for controlling this deadly disease. In the present study, 6 kDa early secretory antigenic target (ESAT-6) of M. tuberculosis was inducibly expressed in chloroplasts of Nicotiana tabacum. The expression of ESAT-6 in chloroplasts was controlled by T7 promoter that was activated by nuclear-generated signal peptide. Tobacco plants, containing nuclear component, were transformed via biolistic bombardment with pEXP-T7-ESAT-6 obtained by Gateway® cloning. Transformation and homoplasmic status of transplastomic plants was confirmed by polymerase chain reaction and Southern blotting. Plants were induced for protein expression by spraying with 5% ethanol for 1 day, 3 days, 7 days and 10 days. ESAT-6 protein was detected by immunoblot analysis and maximum protein was obtained for 10 days induced plants that was estimated to accumulate up to 1.2% of total soluble fraction of protein. Transplastomic plants showed completely normal morphology. Transplastomic and untransformed plants became slightly chlorotic upon prolonged exposure to ethanol until 10 days. Taken together, this data could help in the development of an antigen-based subunit vaccine against tuberculosis.
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Affiliation(s)
- Kiran Saba
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Johanna Gottschamel
- University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Iqra Younus
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Tahira Syed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Kehkshan Gull
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Andreas Günter Lössl
- University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan.
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23
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Rojas M, Yu Q, Williams-Carrier R, Maliga P, Barkan A. Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes. NATURE PLANTS 2019; 5:505-511. [PMID: 31036912 DOI: 10.1038/s41477-019-0412-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/22/2019] [Indexed: 05/08/2023]
Abstract
The engineering of plant genomes presents exciting opportunities to modify agronomic traits and to produce high-value products in plants. Expression of foreign proteins from transgenes in the chloroplast genome offers advantages that include the capacity for prodigious protein output, the lack of transgene silencing and the ability to express multicomponent pathways from polycistronic mRNA. However, there remains a need for robust methods to regulate plastid transgene expression. We designed orthogonal activators that boost the expression of chloroplast transgenes harbouring cognate cis-elements. Our system exploits the programmable RNA sequence specificity of pentatricopeptide repeat proteins and their native functions as activators of chloroplast gene expression. When expressed from nuclear transgenes, the engineered proteins stimulate the expression of plastid transgenes by up to ~40-fold, with maximal protein abundance approaching that of Rubisco. This strategy provides a means to regulate and optimize the expression of foreign genes in chloroplasts and to avoid deleterious effects of their products on plant growth.
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Affiliation(s)
- Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Qiguo Yu
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | | | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
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24
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Boehm CR, Bock R. Recent Advances and Current Challenges in Synthetic Biology of the Plastid Genetic System and Metabolism. PLANT PHYSIOLOGY 2019; 179:794-802. [PMID: 30181342 PMCID: PMC6393795 DOI: 10.1104/pp.18.00767] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/27/2018] [Indexed: 05/05/2023]
Abstract
Building on recombinant DNA technology, leaps in synthesis, assembly, and analysis of DNA have revolutionized genetics and molecular biology over the past two decades (Kosuri and Church, 2014). These technological advances have accelerated the emergence of synthetic biology as a new discipline (Cameron et al., 2014). Synthetic biology is characterized by efforts targeted at the modification of existing and the design of novel biological systems based on principles adopted from information technology and engineering (Andrianantoandro et al., 2006; Khalil and Collins, 2010). As in more traditional engineering disciplines such as mechanical, electrical and civil engineering, synthetic biologists utilize abstraction, decoupling and standardization to make the design of biological systems more efficient and scalable. To facilitate the management of complexity, synthetic biology relies on an abstraction hierarchy composed of multiple levels (Endy, 2005): DNA as genetic material, "parts" as elements of DNA encoding basic biological functions (e.g. promoter, ribosome-binding site, terminator sequence), "devices" as any combination of parts implementing a human-defined function, and "systems" as any combination of devices fulfilling a predefined purpose. Parts are designated to perform predictable and modular functions in the context of higher-level devices or systems, which are successively refined through a cycle of designing, building, and testing.
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Affiliation(s)
- Christian R Boehm
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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25
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Occhialini A, Piatek AA, Pfotenhauer AC, Frazier TP, Stewart CN, Lenaghan SC. MoChlo: A Versatile, Modular Cloning Toolbox for Chloroplast Biotechnology. PLANT PHYSIOLOGY 2019; 179:943-957. [PMID: 30679266 PMCID: PMC6393787 DOI: 10.1104/pp.18.01220] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/16/2019] [Indexed: 05/19/2023]
Abstract
Plant synthetic biology is a rapidly evolving field with new tools constantly emerging to drive innovation. Of particular interest is the application of synthetic biology to chloroplast biotechnology to generate plants capable of producing new metabolites, vaccines, biofuels, and high-value chemicals. Progress made in the assembly of large DNA molecules, composing multiple transcriptional units, has significantly aided in the ability to rapidly construct novel vectors for genetic engineering. In particular, Golden Gate assembly has provided a facile molecular tool for standardized assembly of synthetic genetic elements into larger DNA constructs. In this work, a complete modular chloroplast cloning system, MoChlo, was developed and validated for fast and flexible chloroplast engineering in plants. A library of 128 standardized chloroplast-specific parts (47 promoters, 38 5' untranslated regions [5'UTRs], nine promoter:5'UTR fusions, 10 3'UTRs, 14 genes of interest, and 10 chloroplast-specific destination vectors) were mined from the literature and modified for use in MoChlo assembly, along with chloroplast-specific destination vectors. The strategy was validated by assembling synthetic operons of various sizes and determining the efficiency of assembly. This method was successfully used to generate chloroplast transformation vectors containing up to seven transcriptional units in a single vector (∼10.6-kb synthetic operon). To enable researchers with limited resources to engage in chloroplast biotechnology, and to accelerate progress in the field, the entire kit, as described, is available through Addgene at minimal cost. Thus, the MoChlo kit represents a valuable tool for fast and flexible design of heterologous metabolic pathways for plastid metabolic engineering.
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Affiliation(s)
- Alessandro Occhialini
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996
- Center for Agricultural Synthetic Biology, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996
| | - Agnieszka A Piatek
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Alexander C Pfotenhauer
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996
- Center for Agricultural Synthetic Biology, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996
| | - Taylor P Frazier
- Center for Agricultural Synthetic Biology, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
- Elo Life Systems, Durham, North Carolina 27709
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996
- Center for Agricultural Synthetic Biology, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996
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26
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Wang W, Li Y, Wang Y, Shi C, Li C, Li Q, Linhardt RJ. Bacteriophage T7 transcription system: an enabling tool in synthetic biology. Biotechnol Adv 2018; 36:2129-2137. [DOI: 10.1016/j.biotechadv.2018.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
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Young R, Purton S. CITRIC: cold-inducible translational readthrough in the chloroplast of Chlamydomonas reinhardtii using a novel temperature-sensitive transfer RNA. Microb Cell Fact 2018; 17:186. [PMID: 30474564 PMCID: PMC6260665 DOI: 10.1186/s12934-018-1033-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023] Open
Abstract
Background The chloroplast of eukaryotic microalgae such as Chlamydomonas reinhardtii is a potential platform for metabolic engineering and the production of recombinant proteins. In industrial biotechnology, inducible expression is often used so that the translation or function of the heterologous protein does not interfere with biomass accumulation during the growth stage. However, the existing systems used in bacterial or fungal platforms do not transfer well to the microalgal chloroplast. We sought to develop a simple inducible expression system for the microalgal chloroplast, exploiting an unused stop codon (TGA) in the plastid genome. We have previously shown that this codon can be translated as tryptophan when we introduce into the chloroplast genome a trnWUCA gene encoding a plastidial transfer RNA with a modified anticodon sequence, UCA. Results A mutated version of our trnWUCA gene was developed that encodes a temperature-sensitive variant of the tRNA. This allows transgenes that have been modified to contain one or more internal TGA codons to be translated differentially according to the culture temperature, with a gradient of recombinant protein accumulation from 35 °C (low/off) to 15 °C (high). We have named this the CITRIC system, an acronym for cold-inducible translational readthrough in chloroplasts. The exact induction behaviour can be tailored by altering the number of TGA codons within the transgene. Conclusions CITRIC adds to the suite of genetic engineering tools available for the microalgal chloroplast, allowing a greater degree of control over the timing of heterologous protein expression. It could also be used as a heat-repressible system for studying the function of essential native genes in the chloroplast. The genetic components of CITRIC are entirely plastid-based, so no engineering of the nuclear genome is required. Electronic supplementary material The online version of this article (10.1186/s12934-018-1033-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosanna Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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Schindel HS, Piatek AA, Stewart CN, Lenaghan SC. The plastid genome as a chassis for synthetic biology-enabled metabolic engineering: players in gene expression. PLANT CELL REPORTS 2018; 37:1419-1429. [PMID: 30039465 DOI: 10.1007/s00299-018-2323-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/10/2018] [Indexed: 05/21/2023]
Abstract
Owing to its small size, prokaryotic-like molecular genetics, and potential for very high transgene expression, the plastid genome (plastome) is an attractive plant synthetic biology chassis for metabolic engineering. The plastome exists as a homogenous, compact, multicopy genome within multiple-specialized differentiated plastid compartments. Because of this multiplicity, transgenes can be highly expressed. For coordinated gene expression, it is the prokaryotic molecular genetics that is an especially attractive feature. Multiple genes in a metabolic pathway can be expressed in a series of operons, which are regulated at the transcriptional and translational levels with cross talk from the plant's nuclear genome. Key features of each regulatory level are reviewed, as well as some examples of plastome-enabled metabolic engineering. We also speculate about the transformative future of plastid-based synthetic biology to enable metabolic engineering in plants as well as the problems that must be solved before routine plastome-enabled synthetic circuits can be installed.
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Affiliation(s)
- Heidi S Schindel
- Department of Food Science, University of Tennessee, 2600 River Dr., Knoxville, TN, 37996-4561, USA
| | - Agnieszka A Piatek
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA.
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, 2600 River Dr., Knoxville, TN, 37996-4561, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA.
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN, 37996, USA.
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Fuentes P, Armarego-Marriott T, Bock R. Plastid transformation and its application in metabolic engineering. Curr Opin Biotechnol 2018; 49:10-15. [DOI: 10.1016/j.copbio.2017.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/14/2017] [Accepted: 07/03/2017] [Indexed: 12/31/2022]
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Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C. Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation. FRONTIERS IN PLANT SCIENCE 2018; 9:1453. [PMID: 30337934 PMCID: PMC6180158 DOI: 10.3389/fpls.2018.01453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
Chloroplasts (and other plastids) harbor their own genetic material, with a bacterial-like gene-expression systems. Chloroplast RNA metabolism is complex and is predominantly mediated by nuclear-encoded RNA-binding proteins. In addition to these nuclear factors, the chloroplast-encoded intron maturase MatK has been suggested to perform as a splicing factor for a subset of chloroplast introns. MatK is essential for plant cell survival in tobacco, and thus null mutants have not yet been isolated. We therefore attempted to over-express MatK from a neutral site in the chloroplast, placing it under the control of a theophylline-inducible riboswitch. This ectopic insertion of MatK lead to a variegated cotyledons phenotype. The addition of the inducer theophylline exacerbated the phenotype in a concentration-dependent manner. The extent of variegation was further modulated by light, sucrose and spectinomycin, suggesting that the function of MatK is intertwined with photosynthesis and plastid translation. Inhibiting translation in the transplastomic lines has a profound effect on the accumulation of several chloroplast mRNAs, including the accumulation of an RNA antisense to rpl33, a gene coding for an essential chloroplast ribosomal protein. Our study further supports the idea that MatK expression needs to be tightly regulated to prevent detrimental effects and establishes another link between leaf variegation and chloroplast translation.
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Affiliation(s)
- Yujiao Qu
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Legen
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jürgen Arndt
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stephanie Henkel
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Galina Hoppe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Giovanna Ranzini
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M. Muino
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Weihe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gert Weber
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Joint Research Group Macromolecular Crystallography, Berlin, Germany
| | - Oren Ostersetzer
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Schmitz-Linneweber
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Christian Schmitz-Linneweber,
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Abstract
Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits.
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Affiliation(s)
- Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Ribo-attenuators: novel elements for reliable and modular riboswitch engineering. Sci Rep 2017; 7:4599. [PMID: 28676696 PMCID: PMC5496857 DOI: 10.1038/s41598-017-04093-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/09/2017] [Indexed: 11/09/2022] Open
Abstract
Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, thus increasing their reliability for a wide range of applications.
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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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Yang W, Sinha S. A novel method for predicting activity of cis-regulatory modules, based on a diverse training set. Bioinformatics 2016; 33:1-7. [PMID: 27609510 DOI: 10.1093/bioinformatics/btw552] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/26/2016] [Accepted: 08/17/2016] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION With the rapid emergence of technologies for locating cis-regulatory modules (CRMs) genome-wide, the next pressing challenge is to assign precise functions to each CRM, i.e. to determine the spatiotemporal domains or cell-types where it drives expression. A popular approach to this task is to model the typical k-mer composition of a set of CRMs known to drive a common expression pattern, and assign that pattern to other CRMs exhibiting a similar k-mer composition. This approach does not rely on prior knowledge of transcription factors relevant to the CRM or their binding motifs, and is thus more widely applicable than motif-based methods for predicting CRM activity, but is also prone to false positive predictions. RESULTS We present a novel strategy to improve the above-mentioned approach: to predict if a CRM drives a specific gene expression pattern, assess not only how similar the CRM is to other CRMs with similar activity but also to CRMs with distinct activities. We use a state-of-the-art statistical method to quantify a CRM's sequence similarity to many different training sets of CRMs, and employ a classification algorithm to integrate these similarity scores into a single prediction of the CRM's activity. This strategy is shown to significantly improve CRM activity prediction over current approaches. AVAILABILITY AND IMPLEMENTATION Our implementation of the new method, called IMMBoost, is freely available as source code, at https://github.com/weiyangedward/IMMBoost CONTACT: sinhas@illinois.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wei Yang
- Department of Computer Science, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, Urbana, IL, USA
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35
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Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
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Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
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Mehdizadeh Aghdam E, Hejazi MS, Barzegar A. Riboswitches: From living biosensors to novel targets of antibiotics. Gene 2016; 592:244-59. [PMID: 27432066 DOI: 10.1016/j.gene.2016.07.035] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/11/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
Riboswitches are generally located in 5'-UTR region of mRNAs and specifically bind small ligands. Following ligand binding, gene expression is controlled mostly by transcription termination, translation inhibition or mRNA degradation processes. More than 30 classes of known riboswitches have been identified by now. Most riboswitches consist of an aptamer domain and an expression platform. The aptamer domain of each class of riboswitch is a conserved structure and stabilizes specific structures of the expression platforms through binding to specific compounds. In this review, we are highlighting most aspects of riboswitch research including the novel riboswitch discoveries, routine methods for discovering and investigating riboswitches along with newly discovered classes and mechanistic principles of riboswitch-mediated gene expression control. Moreover, we will give an overview about the potential of riboswitches as therapeutic targets for antibiotic design and also their utilization as biosensors for molecular detection.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
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Gottschamel J, Lössl A, Ruf S, Wang Y, Skaugen M, Bock R, Clarke JL. Production of dengue virus envelope protein domain III-based antigens in tobacco chloroplasts using inducible and constitutive expression systems. PLANT MOLECULAR BIOLOGY 2016; 91:497-512. [PMID: 27116001 DOI: 10.1007/s11103-016-0484-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Dengue fever is a disease in many parts of the tropics and subtropics and about half the world's population is at risk of infection according to the World Health Organization. Dengue is caused by any of the four related dengue virus serotypes DEN-1, -2, -3 and -4, which are transmitted to people by Aedes aegypti mosquitoes. Currently there is only one vaccine (Dengvaxia(®)) available (limited to a few countries) on the market since 2015 after half a century's intensive efforts. Affordable and accessible vaccines against dengue are hence still urgently needed. The dengue envelop protein domain III (EDIII), which is capable of eliciting serotype-specific neutralizing antibodies, has become the focus for subunit vaccine development. To contribute to the development of an accessible and affordable dengue vaccine, in the current study we have used plant-based vaccine production systems to generate a dengue subunit vaccine candidate in tobacco. Chloroplast genome engineering was applied to express serotype-specific recombinant EDIII proteins in tobacco chloroplasts using both constitutive and ethanol-inducible expression systems. Expression of a tetravalent antigen fusion construct combining EDIII polypeptides from all four serotypes was also attempted. Transplastomic EDIII-expressing tobacco lines were obtained and homoplasmy was verified by Southern blot analysis. Northern blot analyses showed expression of EDIII antigen-encoding genes. EDIII protein accumulation levels varied for the different recombinant EDIII proteins and the different expression systems, and reached between 0.8 and 1.6 % of total cellular protein. Our study demonstrates the suitability of the chloroplast compartment as a production site for an EDIII-based vaccine candidate against dengue fever and presents a Gateway(®) plastid transformation vector for inducible transgene expression.
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Affiliation(s)
- Johanna Gottschamel
- NIBIO-Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, Norway
- BOKU-University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Andreas Lössl
- BOKU-University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Stephanie Ruf
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yanliang Wang
- NIBIO-Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, Norway
| | | | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Jihong Liu Clarke
- NIBIO-Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, Norway.
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Gnanasekaran T, Karcher D, Nielsen AZ, Martens HJ, Ruf S, Kroop X, Olsen CE, Motawie MS, Pribil M, Møller BL, Bock R, Jensen PE. Transfer of the cytochrome P450-dependent dhurrin pathway from Sorghum bicolor into Nicotiana tabacum chloroplasts for light-driven synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2495-506. [PMID: 26969746 PMCID: PMC4809297 DOI: 10.1093/jxb/erw067] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant chloroplasts are light-driven cell factories that have great potential to act as a chassis for metabolic engineering applications. Using plant chloroplasts, we demonstrate how photosynthetic reducing power can drive a metabolic pathway to synthesise a bio-active natural product. For this purpose, we stably engineered the dhurrin pathway from Sorghum bicolor into the chloroplasts of Nicotiana tabacum (tobacco). Dhurrin is a cyanogenic glucoside and its synthesis from the amino acid tyrosine is catalysed by two membrane-bound cytochrome P450 enzymes (CYP79A1 and CYP71E1) and a soluble glucosyltransferase (UGT85B1), and is dependent on electron transfer from a P450 oxidoreductase. The entire pathway was introduced into the chloroplast by integrating CYP79A1, CYP71E1, and UGT85B1 into a neutral site of the N. tabacum chloroplast genome. The two P450s and the UGT85B1 were functional when expressed in the chloroplasts and converted endogenous tyrosine into dhurrin using electrons derived directly from the photosynthetic electron transport chain, without the need for the presence of an NADPH-dependent P450 oxidoreductase. The dhurrin produced in the engineered plants amounted to 0.1-0.2% of leaf dry weight compared to 6% in sorghum. The results obtained pave the way for plant P450s involved in the synthesis of economically important compounds to be engineered into the thylakoid membrane of chloroplasts, and demonstrate that their full catalytic cycle can be driven directly by photosynthesis-derived electrons.
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Affiliation(s)
- Thiyagarajan Gnanasekaran
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Daniel Karcher
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Helle Juel Martens
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Stephanie Ruf
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Xenia Kroop
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Carl Erik Olsen
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Mohammed Saddik Motawie
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Poul Erik Jensen
- Copenhagen Plant Science Centre, Center for Synthetic Biology bioSYNergy, Villum Research Center "Plant Plasticity", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
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Warzecha H. Lights, P450, action! Metabolite formation in chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2123-5. [PMID: 27022183 PMCID: PMC4809302 DOI: 10.1093/jxb/erw114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 3-5, 64285 Darmstadt, Germany
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Doron L, Segal N, Shapira M. Transgene Expression in Microalgae-From Tools to Applications. FRONTIERS IN PLANT SCIENCE 2016; 7:505. [PMID: 27148328 PMCID: PMC4840263 DOI: 10.3389/fpls.2016.00505] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/29/2016] [Indexed: 05/17/2023]
Abstract
Microalgae comprise a biodiverse group of photosynthetic organisms that reside in water sources and sediments. The green microalgae Chlamydomonas reinhardtii was adopted as a useful model organism for studying various physiological systems. Its ability to grow under both photosynthetic and heterotrophic conditions allows efficient growth of non-photosynthetic mutants, making Chlamydomonas a useful genetic tool to study photosynthesis. In addition, this green alga can grow as haploid or diploid cells, similar to yeast, providing a powerful genetic system. As a result, easy and efficient transformation systems have been developed for Chlamydomonas, targeting both the chloroplast and nuclear genomes. Since microalgae comprise a rich repertoire of species that offer variable advantages for biotech and biomed industries, gene transfer technologies were further developed for many microalgae to allow for the expression of foreign proteins of interest. Expressing foreign genes in the chloroplast enables the targeting of foreign DNA to specific sites by homologous recombination. Chloroplast transformation also allows for the introduction of genes encoding several enzymes from a complex pathway, possibly as an operon. Expressing foreign proteins in the chloroplast can also be achieved by introducing the target gene into the nuclear genome, with the protein product bearing a targeting signal that directs import of the transgene-product into the chloroplast, like other endogenous chloroplast proteins. Integration of foreign genes into the nuclear genome is mostly random, resulting in large variability between different clones, such that extensive screening is required. The use of different selection modalities is also described, with special emphasis on the use of herbicides and metabolic markers which are considered to be friendly to the environment, as compared to drug-resistance genes that are commonly used. Finally, despite the development of a wide range of transformation tools and approaches, expression of foreign genes in microalgae suffers from low efficiency. Thus, novel tools have appeared in recent years to deal with this problem. Finally, while C. reinhardtii was traditionally used as a model organism for the development of transformation systems and their subsequent improvement, similar technologies can be adapted for other microalgae that may have higher biotechnological value.
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