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Andreou AI, Nakayama N. Mobius Assembly. Methods Mol Biol 2020; 2205:201-218. [PMID: 32809201 DOI: 10.1007/978-1-0716-0908-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mobius Assembly is a versatile and user-friendly DNA Assembly method, which facilitates rapid and simple generation of DNA constructs. Mobius Assembly combines high cloning capacity and vector toolkit simplicity to streamline combinatorial assemblies. It is a two-level hierarchical modular cloning system that enables quadruple assembly augmentation. It adopts the 4 bp standard overhangs defined by Phytobricks to promote standard part sharing, and it can be made compatible with different chassis. Furthermore, Mobius Assembly reduces domestication requirements and uses chromogenic proteins to facilitate the identification of positive assemblies.
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Affiliation(s)
- Andreas I Andreou
- SyntheSys Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Naomi Nakayama
- SyntheSys Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
- Department of Bioengineering, Imperial College London, London, UK.
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102
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Feike D, Korolev AV, Soumpourou E, Murakami E, Reid D, Breakspear A, Rogers C, Radutoiu S, Stougaard J, Harwood WA, Oldroyd GED, Miller J. Characterizing standard genetic parts and establishing common principles for engineering legume and cereal roots. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2234-2245. [PMID: 31022324 PMCID: PMC6835126 DOI: 10.1111/pbi.13135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 04/18/2019] [Indexed: 05/20/2023]
Abstract
Plant synthetic biology and cereal engineering depend on the controlled expression of transgenes of interest. Most engineering in plant species to date has relied heavily on the use of a few, well-established constitutive promoters to achieve high levels of expression; however, the levels of transgene expression can also be influenced by the use of codon optimization, intron-mediated enhancement and varying terminator sequences. Most of these alternative approaches for regulating transgene expression have only been tested in small-scale experiments, typically testing a single gene of interest. It is therefore difficult to interpret the relative importance of these approaches and to design engineering strategies that are likely to succeed in different plant species, particularly if engineering multigenic traits where the expression of each transgene needs to be precisely regulated. Here, we present data on the characterization of 46 promoters and 10 terminators in Medicago truncatula, Lotus japonicus, Nicotiana benthamiana and Hordeum vulgare, as well as the effects of codon optimization and intron-mediated enhancement on the expression of two transgenes in H. vulgare. We have identified a core set of promoters and terminators of relevance to researchers engineering novel traits in plant roots. In addition, we have shown that combining codon optimization and intron-mediated enhancement increases transgene expression and protein levels in barley. Based on our study, we recommend a core set of promoters and terminators for broad use and also propose a general set of principles and guidelines for those engineering cereal species.
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Affiliation(s)
- Doreen Feike
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
EMBL HeidelbergMeyerhofstraße 169117HeidelbergGermany
| | | | - Eleni Soumpourou
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - Eiichi Murakami
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Present address:
GRA&GREEN Inc., Incubation Center 106Nagoya UniversityFuro‐cho, Chikusa‐kuNagoya464‐0814Japan
| | - Dugald Reid
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Christian Rogers
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - Simona Radutoiu
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Giles E. D. Oldroyd
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - J. Benjamin Miller
- John Innes CentreNorwich Research ParkNorwichUK
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
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103
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Good News for Nuclear Transgene Expression in Chlamydomonas. Cells 2019; 8:cells8121534. [PMID: 31795196 PMCID: PMC6952782 DOI: 10.3390/cells8121534] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Chlamydomonas reinhardtii is a well-established model system for basic research questions ranging from photosynthesis and organelle biogenesis, to the biology of cilia and basal bodies, to channelrhodopsins and photoreceptors. More recently, Chlamydomonas has also been recognized as a suitable host for the production of high-value chemicals and high-value recombinant proteins. However, basic and applied research have suffered from the inefficient expression of nuclear transgenes. The combined efforts of the Chlamydomonas community over the past decades have provided insights into the mechanisms underlying this phenomenon and have resulted in mutant strains defective in some silencing mechanisms. Moreover, many insights have been gained into the parameters that affect nuclear transgene expression, like promoters, introns, codon usage, or terminators. Here I critically review these insights and try to integrate them into design suggestions for the construction of nuclear transgenes that are to be expressed at high levels.
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104
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Bernabé‐Orts JM, Casas‐Rodrigo I, Minguet EG, Landolfi V, Garcia‐Carpintero V, Gianoglio S, Vázquez‐Vilar M, Granell A, Orzaez D. Assessment of Cas12a-mediated gene editing efficiency in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1971-1984. [PMID: 30950179 PMCID: PMC6737022 DOI: 10.1111/pbi.13113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/19/2019] [Accepted: 03/20/2019] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas12a editing system opens new possibilities for plant genome engineering. To obtain a comparative assessment of RNA-guided endonuclease (RGEN) types in plants, we adapted the CRISPR/Cas12a system to the GoldenBraid (GB) modular cloning platform and compared the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described GB-assembled Streptococcus pyogenes Cas9 (SpCas9) constructs in eight Nicotiana benthamiana loci using transient expression. All three nucleases showed drastic target-dependent differences in efficiency, with LbCas12 producing higher mutagenesis rates in five of the eight loci assayed, as estimated with the T7E1 endonuclease assay. Attempts to engineer crRNA direct repeat (DR) had little effect improving on-target efficiency for AsCas12a and resulted deleterious in the case of LbCas12a. To complete the assessment of Cas12a activity, we carried out genome editing experiments in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, we also resequenced Cas12a-free segregating T2 lines to assess possible off-target effects. Our results showed that the mutagenesis footprint of Cas12a is enriched in deletions of -10 to -2 nucleotides and included in some instances complex rearrangements in the surroundings of the target sites. We found no evidence of off-target mutations neither in related sequences nor somewhere else in the genome. Collectively, this study shows that LbCas12a is a viable alternative to SpCas9 for plant genome engineering.
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Affiliation(s)
- Joan Miquel Bernabé‐Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Iván Casas‐Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
- Present address:
Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule (ETH) ZurichBaselSwitzerland
| | - Eugenio G. Minguet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Viola Landolfi
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Victor Garcia‐Carpintero
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Silvia Gianoglio
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Marta Vázquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
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105
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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106
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Tonfack LB, Hussey SG, Veale A, Myburg AA, Mizrachi E. Analysis of Orthologous SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) Promotor Activity in Herbaceous and Woody Angiosperms. Int J Mol Sci 2019; 20:E4623. [PMID: 31540430 PMCID: PMC6770381 DOI: 10.3390/ijms20184623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) is a master regulator of fibre secondary wall deposition in Arabidopsis thaliana (Arabidopsis), with homologs in other angiosperms and gymnosperms. However, it is poorly understood to what extent the fibre-specific regulation of the SND1 promoter, and that of its orthologs, is conserved between diverged herbaceous and woody lineages. We performed a reciprocal reporter gene analysis of orthologous SND1 promoters from Arabidopsis (AthSND1), Eucalyptus grandis (EgrNAC61) and Populus alba × P. grandidentata (PagWND1A) relative to secondary cell wall-specific Cellulose Synthase4 (CesA4) and CesA7 promoters, in both a non-woody (Arabidopsis) and a woody (poplar) system. β-glucuronidase (GUS) reporter analysis in Arabidopsis showed that the SND1 promoter was active in vascular tissues as previously reported and showed interfascicular and xylary fibre-specific expression in inflorescence stems, while reporter constructs of the woody plant-derived promoters were partial to the (pro)cambium-phloem and protoxylem. In transgenic P. tremula × P. alba plants, all three orthologous SND1 promoters expressed the GUS reporter similarly and preferentially in developing secondary xylem, ray parenchyma and cork cambium. Ours is the first study to reciprocally test orthologous SND1 promoter specificity in herbaceous and woody species, revealing diverged regulatory functions in the herbaceous system.
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Affiliation(s)
- Libert B Tonfack
- Plant Physiology and Improvement Unit, Laboratory of Biotechnology and Environment, Department of Plant Biology, University of Yaoundé I, Yaoundé 0812, Cameroon.
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Adri Veale
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
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107
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Lin D, O'Callaghan CA. MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme. Nucleic Acids Res 2019; 46:e113. [PMID: 29986052 PMCID: PMC6212791 DOI: 10.1093/nar/gky596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 06/27/2018] [Indexed: 01/05/2023] Open
Abstract
Efficient DNA assembly is of great value in biological research and biotechnology. Type IIS restriction enzyme-based assembly systems allow assembly of multiple DNA fragments in a one-pot reaction. However, large DNA fragments can only be assembled by alternating use of two or more type IIS restriction enzymes in a multi-step approach. Here, we present MetClo, a DNA assembly method that uses only a single type IIS restriction enzyme for hierarchical DNA assembly. The method is based on in vivo methylation-mediated on/off switching of type IIS restriction enzyme recognition sites that overlap with site-specific methylase recognition sequences. We have developed practical MetClo systems for the type IIS enzymes BsaI, BpiI and LguI, and demonstrated hierarchical assembly of large DNA fragments up to 218 kb. The MetClo approach substantially reduces the need to remove internal restriction sites from components to be assembled. The use of a single type IIS enzyme throughout the different stages of DNA assembly allows novel and powerful design schemes for rapid large-scale hierarchical DNA assembly. The BsaI-based MetClo system is backward-compatible with component libraries of most of the existing type IIS restriction enzyme-based assembly systems, and has potential to become a standard for modular DNA assembly.
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Affiliation(s)
- Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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108
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Kautsar SA, Suarez Duran HG, Blin K, Osbourn A, Medema MH. plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res 2019; 45:W55-W63. [PMID: 28453650 PMCID: PMC5570173 DOI: 10.1093/nar/gkx305] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery. The plantiSMASH web server, precalculated results and source code are freely available from http://plantismash.secondarymetabolites.org.
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Affiliation(s)
- Satria A Kautsar
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands.,Teknik Informatika, Universitas Lampung, Jln. Sumantri Brojonegoro No. 01, Lampung 35141, Indonesia
| | | | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
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109
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Page MT, Parry MA, Carmo‐Silva E. A high-throughput transient expression system for rice. PLANT, CELL & ENVIRONMENT 2019; 42:2057-2064. [PMID: 30938460 PMCID: PMC6618034 DOI: 10.1111/pce.13542] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 05/18/2023]
Abstract
Rice is an important global crop and represents a vital source of calories for many food insecure regions. Efforts to improve this crop by improving yield, nutritional content, stress tolerance, or resilience to climate change are certain to include biotechnological approaches, which rely on the expression of transgenes in planta. The throughput and cost of currently available transgenic expression systems is frequently incompatible with modern, high-throughput molecular cloning methods. Here, we present a protocol for isolating high yields of green rice protoplasts and for PEG-mediated transformation of isolated protoplasts. Factors affecting transformation efficiency were investigated, and the resulting protocol is fast, cheap, robust, high-throughput, and does not require specialist equipment. When coupled to a high-throughput modular cloning system such as Golden Gate, this transient expression system provides a valuable resource to help break the "design-build-test" bottleneck by permitting the rapid screening of large numbers of transgenic expression cassettes prior to stable plant transformation. We used this system to rapidly assess the expression level, subcellular localisation, and protein aggregation pattern of nine single-gene expression cassettes, which represent the essential component parts of the β-cyanobacterial carboxysome.
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Affiliation(s)
- Mike T. Page
- Lancaster Environment CentreLancaster UniversityLancasterUK
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110
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Liu CW, Breakspear A, Stacey N, Findlay K, Nakashima J, Ramakrishnan K, Liu M, Xie F, Endre G, de Carvalho-Niebel F, Oldroyd GED, Udvardi MK, Fournier J, Murray JD. A protein complex required for polar growth of rhizobial infection threads. Nat Commun 2019; 10:2848. [PMID: 31253759 PMCID: PMC6599036 DOI: 10.1038/s41467-019-10029-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
During root nodule symbiosis, intracellular accommodation of rhizobia by legumes is a prerequisite for nitrogen fixation. For many legumes, rhizobial colonization initiates in root hairs through transcellular infection threads. In Medicago truncatula, VAPYRIN (VPY) and a putative E3 ligase LUMPY INFECTIONS (LIN) are required for infection thread development but their cellular and molecular roles are obscure. Here we show that LIN and its homolog LIN-LIKE interact with VPY and VPY-LIKE in a subcellular complex localized to puncta both at the tip of the growing infection thread and at the nuclear periphery in root hairs and that the punctate accumulation of VPY is positively regulated by LIN. We also show that an otherwise nuclear and cytoplasmic exocyst subunit, EXO70H4, systematically co-localizes with VPY and LIN during rhizobial infection. Genetic analysis shows that defective rhizobial infection in exo70h4 is similar to that in vpy and lin. Our results indicate that VPY, LIN and EXO70H4 are part of the symbiosis-specific machinery required for polar growth of infection threads.
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Affiliation(s)
- Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicola Stacey
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim Findlay
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jin Nakashima
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | | | - Miaoxia Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gabriella Endre
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
| | | | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Michael K Udvardi
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Joëlle Fournier
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France.
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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111
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Myburg AA, Hussey SG, Wang JP, Street NR, Mizrachi E. Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks. FRONTIERS IN PLANT SCIENCE 2019; 10:775. [PMID: 31281326 PMCID: PMC6597874 DOI: 10.3389/fpls.2019.00775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
Fast-growing forest plantations are sustainable feedstocks of plant biomass that can serve as alternatives to fossil carbon resources for materials, chemicals, and energy. Their ability to efficiently harvest light energy and carbon from the atmosphere and sequester this into metabolic precursors for lignocellulosic biopolymers and a wide range of plant specialized metabolites make them excellent biochemical production platforms and living biorefineries. Their large sizes have facilitated multi-omics analyses and systems modeling of key biological processes such as lignin biosynthesis in trees. High-throughput 'omics' approaches have also been applied in segregating tree populations where genetic variation creates abundant genetic perturbations of system components allowing construction of systems genetics models linking genes and pathways to complex trait variation. With this information in hand, it is now possible to start using synthetic biology and genome editing techniques in a bioengineering approach based on a deeper understanding and rational design of biological parts, devices, and integrated systems. However, the complexity of the biology and interacting components will require investment in big data informatics, machine learning, and intuitive visualization to fully explore multi-dimensional patterns and identify emergent properties of biological systems. Predictive systems models could be tested rapidly through high-throughput synthetic biology approaches and multigene editing. Such a bioengineering paradigm, together with accelerated genomic breeding, will be crucial for the development of a new generation of woody biorefinery crops.
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Affiliation(s)
- Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, South Africa
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Nathaniel R. Street
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, South Africa
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112
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Nandan A, Siddiqui NA, Kumar P. Assessment of environmental and ergonomic hazard associated to printing and photocopying: a review. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:1187-1211. [PMID: 30350125 DOI: 10.1007/s10653-018-0205-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
"Knowledge is power" and distribution of knowledge is fueled by printing and photocopying industry. Even as printing and photocopying industry have revolutionized the availability of documents and perceptible image quickly at extremely inexpensive and affordable cost, the boon of its revolution has turned into a bane by irresponsible, uncontrolled and extensive use, causing irreversible degradation to not only ecosystem by continuous release of ozone and other volatile organic compounds (VOCs) but also the health of workers occupationally exposed to it. Indoor ozone level due to emission from different photocopying equipment's increases drastically and the condition of other air quality parameters are not different. This situation is particularly sedate in extremely sensitive educational and research industry where sharing of knowledge is extremely important to meet the demands. This work is an attempt to catalogue all the environmental as well as health impacts of printing or photocopying. It has been observed that printing/photocopying operation is a significant factor contributing to indoor air quality degradation, which includes increase in concentration of ozone, VOCs, semi-volatile organic compounds (SVOCs) and heavy metals such as cadmium, selenium, arsenic, zinc, nickel, and other pollutants from photocopy machines. The outcome of this study will empower the manufactures with information regarding ozone and other significant emission, so that their impact can be reduced.
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Affiliation(s)
- Abhishek Nandan
- University of Petroleum and Energy Studies, Dehradun, India.
| | - N A Siddiqui
- University of Petroleum and Energy Studies, Dehradun, India
| | - Pankaj Kumar
- University of Petroleum and Energy Studies, Dehradun, India
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113
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Courville KJ, Frantzeskakis L, Gul S, Haeger N, Kellner R, Heßler N, Day B, Usadel B, Gupta YK, van Esse HP, Brachmann A, Kemen E, Feldbrügge M, Göhre V. Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors. THE NEW PHYTOLOGIST 2019; 222:1474-1492. [PMID: 30663769 DOI: 10.1111/nph.15692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 05/25/2023]
Abstract
Biotrophic fungal plant pathogens can balance their virulence and form intricate relationships with their hosts. Sometimes, this leads to systemic host colonization over long time scales without macroscopic symptoms. However, how plant-pathogenic endophytes manage to establish their sustained systemic infection remains largely unknown. Here, we present a genomic and transcriptomic analysis of Thecaphora thlaspeos. This relative of the well studied grass smut Ustilago maydis is the only smut fungus adapted to Brassicaceae hosts. Its ability to overwinter with perennial hosts and its systemic plant infection including roots are unique characteristics among smut fungi. The T. thlaspeos genome was assembled to the chromosome level. It is a typical smut genome in terms of size and genome characteristics. In silico prediction of candidate effector genes revealed common smut effector proteins and unique members. For three candidates, we have functionally demonstrated effector activity. One of these, TtTue1, suggests a potential link to cold acclimation. On the plant side, we found evidence for a typical immune response as it is present in other infection systems, despite the absence of any macroscopic symptoms during infection. Our findings suggest that T. thlaspeos distinctly balances its virulence during biotrophic growth ultimately allowing for long-lived infection of its perennial hosts.
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Affiliation(s)
- Kaitlyn J Courville
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Lamprinos Frantzeskakis
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Summia Gul
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Natalie Haeger
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Ronny Kellner
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Natascha Heßler
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Brad Day
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824-6254, USA
| | - Björn Usadel
- Unit of Botany and Molecular Genetics, Institute for Biology I, BioSC, RWTH Aachen University, 52074, Aachen, Germany
| | | | | | - Andreas Brachmann
- Faculty of Biology, Genetics, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Vera Göhre
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr. 1, Düsseldorf, 40225, Germany
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114
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Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R, Endy D. Opening options for material transfer. Nat Biotechnol 2019; 36:923-927. [PMID: 30307930 PMCID: PMC6871013 DOI: 10.1038/nbt.4263] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Open Material Transfer Agreement is a material-transfer agreement that enables broader sharing and use of biological materials by biotechnology practitioners working within the practical realities of technology transfer.
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Affiliation(s)
- Linda Kahl
- BioBricks Foundation, San Francisco, California, USA
| | - Jennifer Molloy
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - David Grewal
- BioBricks Foundation, San Francisco, California, USA.,Yale Law School, New Haven, Connecticut, USA
| | - Richard Johnson
- BioBricks Foundation, San Francisco, California, USA.,Global Helix, Washington, DC, USA
| | - Drew Endy
- BioBricks Foundation, San Francisco, California, USA.,Department of Bioengineering, Stanford University, Stanford, California, USA
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115
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Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. THE NEW PHYTOLOGIST 2019; 222:628-640. [PMID: 30521109 DOI: 10.1111/nph.15625] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 09/20/2018] [Indexed: 06/09/2023]
Abstract
High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Ariel Cerda
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomás Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Anthony West
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Fernán Federici
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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116
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Raitskin O, Schudoma C, West A, Patron NJ. Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering. PLoS One 2019; 14:e0211598. [PMID: 30811422 PMCID: PMC6392405 DOI: 10.1371/journal.pone.0211598] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/16/2019] [Indexed: 12/26/2022] Open
Abstract
Molecular tools adapted from bacterial CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) systems for adaptive immunity have become widely used for plant genome engineering, both to investigate gene functions and to engineer desirable traits. A number of different Cas (CRISPR-associated) nucleases are now used but, as most studies performed to date have engineered different targets using a variety of plant species and molecular tools, it has been difficult to draw conclusions about the comparative performance of different nucleases. Due to the time and effort required to regenerate engineered plants, efficiency is critical. In addition, there have been several reports of mutations at sequences with less than perfect identity to the target. While in some plant species it is possible to remove these so-called 'off-targets' by backcrossing to a parental line, the specificity of genome engineering tools is important when targeting specific members of closely-related gene families, especially when recent paralogues are co-located in the genome and unlikely to segregate. Specificity is also important for species that take years to reach sexual maturity or that are clonally propagated. Here, we directly compare the efficiency and specificity of Cas nucleases from different bacterial species together with engineered variants of Cas9. We find that the nucleotide content of the target correlates with efficiency and that Cas9 from Staphylococcus aureus (SaCas9) is comparatively most efficient at inducing mutations. We also demonstrate that 'high-fidelity' variants of Cas9 can reduce off-target mutations in plants. We present these molecular tools as standardised DNA parts to facilitate their re-use.
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Affiliation(s)
- Oleg Raitskin
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Anthony West
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Nicola J. Patron
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
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117
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Hussey SG, Grima-Pettenati J, Myburg AA, Mizrachi E, Brady SM, Yoshikuni Y, Deutsch S. A Standardized Synthetic Eucalyptus Transcription Factor and Promoter Panel for Re-engineering Secondary Cell Wall Regulation in Biomass and Bioenergy Crops. ACS Synth Biol 2019; 8:463-465. [PMID: 30605615 DOI: 10.1021/acssynbio.8b00440] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Re-engineering of transcriptional networks regulating secondary cell wall formation may allow the improvement of plant biomass in widely grown plantation crops such as Eucalyptus. However, there is currently a scarcity of freely available standardized biological parts (e.g., Phytobricks) compatible with Type IIS assembly approaches from forest trees, and there is a need to accelerate transcriptional network inference in nonmodel biomass crops. Here we describe the design and synthesis of a versatile three-panel biological parts collection of 221 secondary cell wall-related Eucalyptus grandis transcription factor coding sequences and 65 promoters that are compatible with GATEWAY, Golden Gate, MoClo, and GoldenBraid DNA assembly methods and generally conform to accepted Phytobrick syntaxes. This freely available resource is intended to accelerate synthetic biology applications in multiple plant biomass crops and enable reconstruction of secondary cell wall transcriptional networks using high-throughput assays such as DNA affinity purification sequencing (DAP-seq) and enhanced yeast one-hybrid (eY1H) screening.
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Affiliation(s)
- Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria 0002, South Africa
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse, UPS, CNRS, BP 42617, F-31326 Castanet-Tolosan, France
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria 0002, South Africa
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, United States
| | - Yasuo Yoshikuni
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Samuel Deutsch
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
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118
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Navarro FJ, Baulcombe DC. miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii. ACS Synth Biol 2019; 8:358-370. [PMID: 30624905 DOI: 10.1021/acssynbio.8b00393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.
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Affiliation(s)
- Francisco J. Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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119
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Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, Asyraf Md Hatta M, Athiyannan N, Cheema J, Yu G, Kangara N, Ghosh S, Szabo LJ, Poland J, Bariana H, Jones JDG, Bentley AR, Ayliffe M, Olson E, Xu SS, Steffenson BJ, Lagudah E, Wulff BBH. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol 2019; 37:139-143. [PMID: 30718880 DOI: 10.1038/s41587-018-0007-9] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 12/12/2018] [Indexed: 01/17/2023]
Abstract
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.
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Affiliation(s)
- Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Kumar Gaurav
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sutha Chandramohan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jacob Enk
- Arbor Biosciences, Ann Arbor, MI, USA
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Narinder Singh
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, UK.,Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Naveenkumar Athiyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Les J Szabo
- US Department of Agriculture, Agriculture Research Service, Cereal Disease Laboratory, St. Paul, MN, USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Harbans Bariana
- The University of Sydney Plant Breeding Institute, Cobbitty, New South Wales, Australia
| | | | | | - Mick Ayliffe
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Eric Olson
- Michigan State University, East Lansing, MI, USA
| | - Steven S Xu
- US Department of Agriculture, Agriculture Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
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120
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Jan J. Lyczakowski. THE NEW PHYTOLOGIST 2019; 221:1195-1196. [PMID: 30644582 DOI: 10.1111/nph.15483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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121
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Gerasymenko I, Sheludko Y, Fräbel S, Staniek A, Warzecha H. Combinatorial biosynthesis of small molecules in plants: Engineering strategies and tools. Methods Enzymol 2019; 617:413-442. [PMID: 30784411 DOI: 10.1016/bs.mie.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biosynthetic capacity of plants, rooted in a near inexhaustible supply of photosynthetic energy and founded upon an intricate matrix of metabolic networks, makes them versatile chemists producing myriad specialized compounds. Along with tremendous success in elucidation of several plant biosynthetic routes, their reestablishment in heterologous hosts has been a hallmark of recent bioengineering endeavors. However, current efforts in the field are, in the main, aimed at grafting the pathways to fermentable recipient organisms, like bacteria or yeast. Conversely, while harboring orthologous metabolic trails, select plant species now emerge as viable vehicles for mobilization and engineering of complex biosynthetic pathways. Their distinctive features, like intricate cell compartmentalization and formation of specialized production and storage structures on tissue and organ level, make plants an especially promising chassis for the manufacture of considerable amounts of high-value natural small molecules. Inspired by the fundamental tenets of synthetic biology, capitalizing on the versatility of the transient plant transformation system, and drawing on the unique compartmentation of plant cells, we explore combinatorial approaches affording production of natural and new-to-nature, bespoke chemicals of potential importance. Here, we focus on the transient engineering of P450 monooxygenases, alone or in concert with other orthogonal catalysts, like tryptophan halogenases.
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Affiliation(s)
- Iryna Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Yuriy Sheludko
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sabine Fräbel
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Agata Staniek
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany.
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122
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Xu F, Wang K, Yuan W, Xu W, Liu S, Kronzucker HJ, Chen G, Miao R, Zhang M, Ding M, Xiao L, Kai L, Zhang J, Zhu Y. Overexpression of rice aquaporin OsPIP1;2 improves yield by enhancing mesophyll CO2 conductance and phloem sucrose transport. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:671-681. [PMID: 30535321 PMCID: PMC6322580 DOI: 10.1093/jxb/ery386] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/13/2018] [Indexed: 05/19/2023]
Abstract
Aquaporins are involved in CO2 transport from the leaf intercellular air space to the chloroplast, which contributes to CO2 assimilation. However, the mechanism of CO2 transport by rice (Oryza sativa L.) aquaporins is unknown. Here, we investigated the function of the aquaporin OsPIP1;2 in CO2 diffusion-associated photosynthesis and phloem sucrose transport. Moreover, the grain yield of rice lines overexpressing OsPIP1;2 was determined. OsPIP1;2 was localized to the plasma membrane and the relative expression of OsPIP1;2 was approximately 5-fold higher in leaves in the presence of an elevated CO2 concentration. Overexpression of OsPIP1;2 increased mesophyll conductance by approximately 150% compared with wild-type (WT) rice. The OsPIP1;2-overexpressing lines had higher biomass than the WT, possibly due to increased phloem sucrose transport. In addition, the grain yield of OsPIP1;2-overexpressing lines was approximately 25% higher than that of the WT in three-season field experiments, due to the increased numbers of effective tillers and spikelets per panicle. Our results suggest that OsPIP1;2 modulates rice growth and grain yield by facilitating leaf CO2 diffusion, which increases both the net CO2 assimilation rate and sucrose transport.
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Affiliation(s)
- Feiyun Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences and Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ke Wang
- College of Life Sciences and Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Yuan
- College of Life Sciences and Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weifeng Xu
- College of Life Sciences and Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang Liu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Herbert J Kronzucker
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC, Australia
| | - Guanglei Chen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Rui Miao
- College of Life Sciences and Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maoxing Zhang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Ming Ding
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Liang Xiao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and the State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Yiyong Zhu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
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123
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Mann DGJ, Bevan SA, Harvey AJ, Leffert-Sorenson RA. The Use of an Automated Platform to Assemble Multigenic Constructs for Plant Transformation. Methods Mol Biol 2019; 1864:19-35. [PMID: 30415326 DOI: 10.1007/978-1-4939-8778-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Compared to traditional means, modern DNA assembly methods allow cloning of large, multigenic vectors for plant transformation in rapid fashion. These methods are often robust and efficient and can assemble multiple DNA fragments into a single vector in one reaction. Here we describe the use of an automated DNA assembly platform for the generation of complex, multigenic T-DNA binary vectors using a hierarchical Golden Gate cloning strategy. These DNA constructs contained diverse DNA elements for the expression of multiple genes for trait stacking in the crop of interest. This platform streamlines the DNA assembly and validation process through high-efficiency cloning methods, integrated automation equipment, and increased throughput. The implementation of this platform removes bottlenecks for routine molecular biology and opens new possibilities for downstream experimental idea testing.
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Affiliation(s)
- David G J Mann
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA.
| | - Scott A Bevan
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Anthony J Harvey
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
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124
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Nadzieja M, Stougaard J, Reid D. A Toolkit for High Resolution Imaging of Cell Division and Phytohormone Signaling in Legume Roots and Root Nodules. FRONTIERS IN PLANT SCIENCE 2019; 10:1000. [PMID: 31428118 PMCID: PMC6688427 DOI: 10.3389/fpls.2019.01000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 05/22/2023]
Abstract
Legume plants benefit from a nitrogen-fixing symbiosis in association with rhizobia hosted in specialized root nodules. Formation of root nodules is initiated by de novo organogenesis and coordinated infection of these developing lateral root organs by rhizobia. Both bacterial infection and nodule organogenesis involve cell cycle activation and regulation by auxin and cytokinin is tightly integrated in the process. To characterize the hormone dynamics and cell division patterns with cellular resolution during nodulation, sensitive and specific sensors suited for imaging of multicellular tissues are required. Here we report a modular toolkit, optimized in the model legume Lotus japonicus, for use in legume roots and root nodules. This toolkit includes synthetic transcriptional reporters for auxin and cytokinin, auxin accumulation sensors and cell cycle progression markers optimized for fluorescent and bright field microscopy. The developed vectors allow for efficient one-step assembly of multiple units using the GoldenGate cloning system. Applied together with a fluorescence-compatible clearing approach, these reporters improve imaging depth and facilitate fluorescence examination in legume roots. We additionally evaluate the utility of the dynamic gravitropic root response in altering the timing and location of auxin accumulation and nodule emergence. We show that alteration of auxin distribution in roots allows for preferential nodule emergence at the outer side of the bend corresponding to a region of high auxin signaling capacity. The presented tools and procedures open new possibilities for comparative mutant studies and for developing a more comprehensive understanding of legume-rhizobia interactions.
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125
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D'Adamo S, Schiano di Visconte G, Lowe G, Szaub‐Newton J, Beacham T, Landels A, Allen MJ, Spicer A, Matthijs M. Engineering the unicellular alga Phaeodactylum tricornutum for high-value plant triterpenoid production. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:75-87. [PMID: 29754445 PMCID: PMC6330534 DOI: 10.1111/pbi.12948] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 05/23/2023]
Abstract
Plant triterpenoids constitute a diverse class of organic compounds that play a major role in development, plant defence and environmental interaction. Several triterpenes have demonstrated potential as pharmaceuticals. One example is betulin, which has shown promise as a pharmaceutical precursor for the treatment of certain cancers and HIV. Major challenges for triterpenoid commercialization include their low production levels and their cost-effective purification from the complex mixtures present in their natural hosts. Therefore, attempts to produce these compounds in industrially relevant microbial systems such as bacteria and yeasts have attracted great interest. Here, we report the production of the triterpenes betulin and its precursor lupeol in the photosynthetic diatom Phaeodactylum tricornutum, a unicellular eukaryotic alga. This was achieved by introducing three plant enzymes in the microalga: a Lotus japonicus oxidosqualene cyclase and a Medicago truncatula cytochrome P450 along with its native reductase. The introduction of the L. japonicus oxidosqualene cyclase perturbed the mRNA expression levels of the native mevalonate and sterol biosynthesis pathway. The best performing strains were selected and grown in a 550-L pilot-scale photobioreactor facility. To our knowledge, this is the most extensive pathway engineering undertaken in a diatom and the first time that a sapogenin has been artificially produced in a microalga, demonstrating the feasibility of the photo-bio-production of more complex high-value, metabolites in microalgae.
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Affiliation(s)
- Sarah D'Adamo
- Eden LaboratoryAlgenuityStewartbyUK
- Wageningen Universiteit en ResearchcentrumBioprocess EngineeringWageningenThe Netherlands
| | | | | | | | | | - Andrew Landels
- PML: Plymouth Marine LaboratoryPlymouthUK
- Rothamsted ResearchHarpendenUK
| | - Michael J. Allen
- PML: Plymouth Marine LaboratoryPlymouthUK
- BiosciencesCollege of Life and Environmental SciencesUniversity of ExeterExeterUK
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126
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South PF, Cavanagh AP, Lopez-Calcagno PE, Raines CA, Ort DR. Optimizing photorespiration for improved crop productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1217-1230. [PMID: 30126060 DOI: 10.1111/jipb.12709] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 05/24/2023]
Abstract
In C3 plants, photorespiration is an energy-expensive process, including the oxygenation of ribulose-1,5-bisphosphate (RuBP) by ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the ensuing multi-organellar photorespiratory pathway required to recycle the toxic byproducts and recapture a portion of the fixed carbon. Photorespiration significantly impacts crop productivity through reducing yields in C3 crops by as much as 50% under severe conditions. Thus, reducing the flux through, or improving the efficiency of photorespiration has the potential of large improvements in C3 crop productivity. Here, we review an array of approaches intended to engineer photorespiration in a range of plant systems with the goal of increasing crop productivity. Approaches include optimizing flux through the native photorespiratory pathway, installing non-native alternative photorespiratory pathways, and lowering or even eliminating Rubisco-catalyzed oxygenation of RuBP to reduce substrate entrance into the photorespiratory cycle. Some proposed designs have been successful at the proof of concept level. A plant systems-engineering approach, based on new opportunities available from synthetic biology to implement in silico designs, holds promise for further progress toward delivering more productive crops to farmer's fields.
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Affiliation(s)
- Paul F South
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture/Agricultural Research Service, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - Christine A Raines
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
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127
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Timoneda A, Sheehan H, Feng T, Lopez-Nieves S, Maeda HA, Brockington S. Redirecting Primary Metabolism to Boost Production of Tyrosine-Derived Specialised Metabolites in Planta. Sci Rep 2018; 8:17256. [PMID: 30467357 PMCID: PMC6250739 DOI: 10.1038/s41598-018-33742-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 10/05/2018] [Indexed: 11/13/2022] Open
Abstract
L-Tyrosine-derived specialized metabolites perform many important functions in plants, and have valuable applications in human health and nutrition. A necessary step in the overproduction of specialised tyrosine-derived metabolites in planta is the manipulation of primary metabolism to enhance the availability of tyrosine. Here, we utilise a naturally occurring de-regulated isoform of the key enzyme, arogenate dehydrogenase, to re-engineer the interface of primary and specialised metabolism, to boost the production of tyrosine-derived pigments in a heterologous plant host. Through manipulation of tyrosine availability, we report a 7-fold increase in the production of tyrosine-derived betalain pigments, with an upper range of 855 mg·kg-1·FW, which compare favourably to many in vitro and commercial sources of betalain pigments. Since the most common plant pathway for tyrosine synthesis occurs via arogenate, the de-regulated arogenate dehydrogenase isoform is a promising route for enhanced production of tyrosine-derived pharmaceuticals in diverse plant hosts.
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Affiliation(s)
- Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hester Sheehan
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Samuel Lopez-Nieves
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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128
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Smith-Moore CM, Grunden AM. Bacteria and archaea as the sources of traits for enhanced plant phenotypes. Biotechnol Adv 2018; 36:1900-1916. [DOI: 10.1016/j.biotechadv.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
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129
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Abstract
Population growth, climate change, and dwindling finite resources are amongst the major challenges which are facing the planet. Requirements for food, materials, water, and energy will soon exceed capacity. Green biotechnology, fueled by recent plant synthetic biology breakthroughs, may offer solutions. This review summarizes current progress towards robust and predictable engineering of plants. I then discuss applications from the lab and field, with a focus on bioenergy, biomaterials, and medicine.
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Affiliation(s)
- Jenny C Mortimer
- 1 Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,2 Joint BioEnergy Institute, Emeryville, CA 94608, USA
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130
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Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Lauersen KJ, Pérez-Pérez ME, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich LD, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire SD. Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth Biol 2018; 7:2074-2086. [PMID: 30165733 DOI: 10.1021/acssynbio.8b00251] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microalgae are regarded as promising organisms to develop innovative concepts based on their photosynthetic capacity that offers more sustainable production than heterotrophic hosts. However, to realize their potential as green cell factories, a major challenge is to make microalgae easier to engineer. A promising approach for rapid and predictable genetic manipulation is to use standardized synthetic biology tools and workflows. To this end we have developed a Modular Cloning toolkit for the green microalga Chlamydomonas reinhardtii. It is based on Golden Gate cloning with standard syntax, and comprises 119 openly distributed genetic parts, most of which have been functionally validated in several strains. It contains promoters, UTRs, terminators, tags, reporters, antibiotic resistance genes, and introns cloned in various positions to allow maximum modularity. The toolkit enables rapid building of engineered cells for both fundamental research and algal biotechnology. This work will make Chlamydomonas the next chassis for sustainable synthetic biology.
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Affiliation(s)
- Pierre Crozet
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | | | - Felix Willmund
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Kamil Bakowski
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kyle J. Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Maria-Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - Pascaline Auroy
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues Cadarache, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Susana Sauret-Gueto
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Justus Niemeyer
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Benjamin Spaniol
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Jasmine Theis
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Raphael Trösch
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Lisa-Desiree Westrich
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Baier
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Department of Physics, Bielefeld University, Bielefeld, 33615, Germany
| | - Felix de Carpentier
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Mathieu Cassarini
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Antoine Danon
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Julien Henri
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Christophe H. Marchand
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Marcello de Mia
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Kevin Sarkissian
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Gilles Peltier
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues Cadarache, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - José-Luis Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - Olaf Kruse
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Poul-Erik Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Schroda
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Stéphane D. Lemaire
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
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131
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Shih PM. Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:84-91. [PMID: 29907312 PMCID: PMC6005202 DOI: 10.1016/j.plantsci.2018.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/28/2018] [Accepted: 03/10/2018] [Indexed: 05/23/2023]
Abstract
Humans have domesticated many plant species as indispensable sources of food, materials, and medicines. The dawning era of synthetic biology represents a means to further refine, redesign, and engineer crops to meet various societal and industrial needs. Current and future endeavors will utilize plants as the foundation of a bio-based economy through the photosynthetic production of carbohydrate feedstocks for the microbial fermentation of biofuels and bioproducts, with the end goal of decreasing our dependence on petrochemicals. As our technological capabilities improve, metabolic engineering efforts may expand the utility of plants beyond sugar feedstocks through the direct production of target compounds, including pharmaceuticals, renewable fuels, and commodity chemicals. However, relatively little work has been done to fully realize the potential in redirecting central carbon metabolism in plants for the engineering of novel bioproducts. Although our ability to rationally engineer and manipulate plant metabolism is in its infancy, I highlight some of the opportunities and challenges in applying synthetic biology towards engineering plant primary metabolism.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA, 94720, United States; Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, United States.
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132
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Kassaw TK, Donayre-Torres AJ, Antunes MS, Morey KJ, Medford JI. Engineering synthetic regulatory circuits in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:13-22. [PMID: 29907304 DOI: 10.1016/j.plantsci.2018.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/05/2018] [Accepted: 04/07/2018] [Indexed: 05/21/2023]
Abstract
Plant synthetic biology is a rapidly emerging field that aims to engineer genetic circuits to function in plants with the same reliability and precision as electronic circuits. These circuits can be used to program predictable plant behavior, producing novel traits to improve crop plant productivity, enable biosensors, and serve as platforms to synthesize chemicals and complex biomolecules. Herein we introduce the importance of developing orthogonal plant parts and the need for quantitative part characterization for mathematical modeling of complex circuits. In particular, transfer functions are important when designing electronic-like genetic controls such as toggle switches, positive/negative feedback loops, and Boolean logic gates. We then discuss potential constraints and challenges in synthetic regulatory circuit design and integration when using plants. Finally, we highlight current and potential plant synthetic regulatory circuit applications.
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Affiliation(s)
- Tessema K Kassaw
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Alberto J Donayre-Torres
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Mauricio S Antunes
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Kevin J Morey
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - June I Medford
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA.
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133
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Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
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Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
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134
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Hernanz-Koers M, Gandía M, Garrigues S, Manzanares P, Yenush L, Orzaez D, Marcos JF. FungalBraid: A GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology. Fungal Genet Biol 2018; 116:51-61. [DOI: 10.1016/j.fgb.2018.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022]
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135
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Nadzieja M, Kelly S, Stougaard J, Reid D. Epidermal auxin biosynthesis facilitates rhizobial infection in Lotus japonicus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:101-111. [PMID: 29676826 DOI: 10.1111/tpj.13934] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/29/2018] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
Symbiotic nitrogen fixation in legumes requires nodule organogenesis to be coordinated with infection by rhizobia. The plant hormone auxin influences symbiotic infection, but the precise timing of auxin accumulation and the genetic network governing it remain unclear. We used a Lotus japonicus optimised variant of the DII-based auxin accumulation sensor and identified a rapid accumulation of auxin in the epidermis, specifically in the root hair cells. This auxin accumulation occurs in the infected root hairs during rhizobia invasion, while Nod factor application induces this response across a broader range of root hairs. Using the DR5 auxin responsive promoter, we demonstrate that activation of auxin signalling also occurs specifically in infected root hairs. Analysis of root hair transcriptome data identified induction of an auxin biosynthesis gene of the Tryptophan Amino-transferase Related (LjTar1) family following both bacteria inoculation and Nod factor treatment. Genetic analysis showed that both expression of the LjTar1 biosynthesis gene and the auxin response requires Nod factor perception, while common symbiotic pathway transcription factors are only partially required or act redundantly to initiate auxin accumulation. Using a chemical genetics approach, we confirmed that auxin biosynthesis has a functional role in promoting symbiotic infection events in the epidermis.
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Affiliation(s)
- Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
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136
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Gantner J, Ordon J, Ilse T, Kretschmer C, Gruetzner R, Löfke C, Dagdas Y, Bürstenbinder K, Marillonnet S, Stuttmann J. Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system. PLoS One 2018; 13:e0197185. [PMID: 29847550 PMCID: PMC5976141 DOI: 10.1371/journal.pone.0197185] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/27/2018] [Indexed: 11/21/2022] Open
Abstract
Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a "peripheral infrastructure" around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies.
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Affiliation(s)
- Johannes Gantner
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Theresa Ilse
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Ramona Gruetzner
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Christian Löfke
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
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137
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van Dolleweerd CJ, Kessans SA, Van de Bittner KC, Bustamante LY, Bundela R, Scott B, Nicholson MJ, Parker EJ. MIDAS: A Modular DNA Assembly System for Synthetic Biology. ACS Synth Biol 2018; 7:1018-1029. [PMID: 29620866 DOI: 10.1021/acssynbio.7b00363] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.
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Affiliation(s)
- Craig J. van Dolleweerd
- Protein Science & Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Sarah A. Kessans
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
| | - Kyle C. Van de Bittner
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Kelburn, Wellington 6012, New Zealand
| | - Leyla Y. Bustamante
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Kelburn, Wellington 6012, New Zealand
| | - Rudranuj Bundela
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Matthew J. Nicholson
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Kelburn, Wellington 6012, New Zealand
| | - Emily J. Parker
- Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8041, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Kelburn, Wellington 6012, New Zealand
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138
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Fräbel S, Wagner B, Krischke M, Schmidts V, Thiele CM, Staniek A, Warzecha H. Engineering of new-to-nature halogenated indigo precursors in plants. Metab Eng 2018; 46:20-27. [PMID: 29466700 DOI: 10.1016/j.ymben.2018.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/14/2017] [Accepted: 02/13/2018] [Indexed: 11/16/2022]
Abstract
Plants are versatile chemists producing a tremendous variety of specialized compounds. Here, we describe the engineering of entirely novel metabolic pathways in planta enabling generation of halogenated indigo precursors as non-natural plant products. Indican (indolyl-β-D-glucopyranoside) is a secondary metabolite characteristic of a number of dyers plants. Its deglucosylation and subsequent oxidative dimerization leads to the blue dye, indigo. Halogenated indican derivatives are commonly used as detection reagents in histochemical and molecular biology applications; their production, however, relies largely on chemical synthesis. To attain the de novo biosynthesis in a plant-based system devoid of indican, we employed a sequence of enzymes from diverse sources, including three microbial tryptophan halogenases substituting the amino acid at either C5, C6, or C7 of the indole moiety. Subsequent processing of the halotryptophan by bacterial tryptophanase TnaA in concert with a mutant of the human cytochrome P450 monooxygenase 2A6 and glycosylation of the resulting indoxyl derivatives by an endogenous tobacco glucosyltransferase yielded corresponding haloindican variants in transiently transformed Nicotiana benthamiana plants. Accumulation levels were highest when the 5-halogenase PyrH was utilized, reaching 0.93 ± 0.089 mg/g dry weight of 5-chloroindican. The identity of the latter was unambiguously confirmed by NMR analysis. Moreover, our combinatorial approach, facilitated by the modular assembly capabilities of the GoldenBraid cloning system and inspired by the unique compartmentation of plant cells, afforded testing a number of alternative subcellular localizations for pathway design. In consequence, chloroplasts were validated as functional biosynthetic venues for haloindican, with the requisite reducing augmentation of the halogenases as well as the cytochrome P450 monooxygenase fulfilled by catalytic systems native to the organelle. Thus, our study puts forward a viable alternative production platform for halogenated fine chemicals, eschewing reliance on fossil fuel resources and toxic chemicals. We further contend that in planta generation of halogenated indigoid precursors previously unknown to nature offers an extended view on and, indeed, pushes forward the established frontiers of biosynthetic capacity of plants.
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Affiliation(s)
- Sabine Fräbel
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Bastian Wagner
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Markus Krischke
- Lehrstuhl für Pharmazeutische Biologie, Julius-von-Sachs-Institut der Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Agata Staniek
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany.
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139
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Plant secretory structures: more than just reaction bags. Curr Opin Biotechnol 2018; 49:73-79. [DOI: 10.1016/j.copbio.2017.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 12/20/2022]
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140
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Andreou AI, Nakayama N. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly. PLoS One 2018; 13:e0189892. [PMID: 29293531 PMCID: PMC5749717 DOI: 10.1371/journal.pone.0189892] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/04/2017] [Indexed: 11/26/2022] Open
Abstract
Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
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Affiliation(s)
- Andreas I. Andreou
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Naomi Nakayama
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Science at Extreme Condition, University of Edinburgh, Edinburgh, United Kingdom
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141
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de Lorenzo V, Schmidt M. Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol 2018; 40:170-180. [DOI: 10.1016/j.nbt.2017.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023]
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142
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Pérez-González A, Kniewel R, Veldhuizen M, Verma HK, Navarro-Rodríguez M, Rubio LM, Caro E. Adaptation of the GoldenBraid modular cloning system and creation of a toolkit for the expression of heterologous proteins in yeast mitochondria. BMC Biotechnol 2017; 17:80. [PMID: 29132331 PMCID: PMC5683533 DOI: 10.1186/s12896-017-0393-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions. Another advantage is that mitochondria are suitable organelles to host oxygen sensitive proteins as a low oxygen environment is created within the matrix during cellular respiration. RESULTS Here we describe the adaptation of a modular cloning system, GoldenBraid2.0, for the integration of assembled transcriptional units into two different sites of the yeast genome, yielding a high expression level. We have also generated a toolkit comprising various promoters, terminators and selection markers that facilitate the generation of multigenic constructs and allow the reconstruction of biosynthetic pathways within Saccharomyces cerevisiae. To facilitate the specific expression of recombinant proteins within the mitochondrial matrix, we have also included in the toolkit an array of mitochondrial targeting signals and tested their efficiency at different growth conditions. As a proof of concept, we show here the integration and expression of 14 bacterial nitrogen fixation (nif) genes, some of which are known to require specific metallocluster cofactors that contribute to their stability yet make these proteins highly sensitive to oxygen. For one of these genes, nifU, we show that optimal production of this protein is achieved through the use of the Su9 mitochondrial targeting pre-sequence and glycerol as a carbon source to sustain aerobic respiration. CONCLUSIONS We present here an adapted GoldenBraid2.0 system for modular cloning, genome integration and expression of recombinant proteins in yeast. We have produced a toolkit that includes inducible and constitutive promoters, mitochondrial targeting signals, terminators and selection markers to guarantee versatility in the design of recombinant transcriptional units. By testing the efficiency of the system with nitrogenase Nif proteins and different mitochondrial targeting pre-sequences and growth conditions, we have paved the way for future studies addressing the expression of heterologous proteins in yeast mitochondria.
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Affiliation(s)
- Ana Pérez-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Ryan Kniewel
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), 28040, Madrid, Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Hemant K Verma
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Mankind Research Centre, IMT Manesar, Gurgaon, Haryana, 122050, India
| | - Mónica Navarro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
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143
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Pasin F, Bedoya LC, Bernabé-Orts JM, Gallo A, Simón-Mateo C, Orzaez D, García JA. Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins. ACS Synth Biol 2017; 6:1962-1968. [PMID: 28657330 DOI: 10.1021/acssynbio.6b00354] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vectors, a set of mini binary T-DNA plasmids suitable for Type IIS restriction endonuclease- and overlap-based assembly methods. pLX vectors include replicons from compatible broad host range plasmids. Simultaneous usage of pBBR1- and RK2-based pLX vectors in a two-plasmid/one-Agrobacterium strain strategy allowed multigene delivery to plants. Adoption of pLX vectors will facilitate routine plant transformations and targeted mutagenesis, as well as complex part and circuit characterization.
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Affiliation(s)
- Fabio Pasin
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Leonor C. Bedoya
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Joan Miquel Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Araíz Gallo
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Carmen Simón-Mateo
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Camino de Vera s/n, 46022 Valencia, Spain
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145
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Vazquez-Vilar M, Quijano-Rubio A, Fernandez-Del-Carmen A, Sarrion-Perdigones A, Ochoa-Fernandez R, Ziarsolo P, Blanca J, Granell A, Orzaez D. GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Res 2017; 45:2196-2209. [PMID: 28053117 PMCID: PMC5389719 DOI: 10.1093/nar/gkw1326] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022] Open
Abstract
Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module.
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Affiliation(s)
- Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Asun Fernandez-Del-Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rocio Ochoa-Fernandez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Peio Ziarsolo
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - José Blanca
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
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146
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Owen C, Patron N, Huang A, Osbourn A. Harnessing plant metabolic diversity. Curr Opin Chem Biol 2017; 40:24-30. [PMID: 28527344 PMCID: PMC5693780 DOI: 10.1016/j.cbpa.2017.04.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/20/2017] [Indexed: 01/09/2023]
Abstract
Advances in DNA sequencing and synthesis technologies in the twenty-first century are now making it possible to build large-scale pipelines for engineering plant natural product pathways into heterologous production species using synthetic biology approaches. The ability to decode the chemical potential of plants by sequencing their transcriptomes and/or genomes and to then use this information as an instruction manual to make drugs and other high-value chemicals is opening up new routes to harness the vast chemical diversity of the Plant Kingdom. Here we describe recent progress in methods for pathway discovery, DNA synthesis and assembly, and expression of engineered pathways in heterologous hosts. We also highlight the importance of standardization and the challenges associated with dataset integration in the drive to build a systematic framework for effective harnessing of plant metabolic diversity.
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Affiliation(s)
- Charlie Owen
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nicola Patron
- Engineering Biology, the Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ancheng Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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147
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Phan HT, Ho TT, Chu HH, Vu TH, Gresch U, Conrad U. Neutralizing immune responses induced by oligomeric H5N1-hemagglutinins from plants. Vet Res 2017; 48:53. [PMID: 28931425 PMCID: PMC5607582 DOI: 10.1186/s13567-017-0458-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/18/2017] [Indexed: 12/20/2022] Open
Abstract
Plant-based transient expression is an alternative platform to produce hemagglutinin-based subunit vaccines. This production system provides not only fast and effective response in the context of a pandemic but also enables the supply of big volume vaccines at low cost. Crude plant extracts containing influenza hemagglutinin are considered to use as vaccine sources because of avoidance of related purification steps resulting in low cost production allowing veterinary applications. Highly immunogenic influenza hemagglutinins are urgently required to meet these pre-conditions. Here, we present a new and innovative way to generate functional H5 oligomers from avian flu hemagglutinin in planta by the specific interaction of S·Tag and S·Protein. A S·Tag was fused to H5 trimers and this construct was transiently co-expressed in planta with S·Protein-TPs which was multimerized by disulfide bonds via cysteine residues in tailpiece sequences (TP) of IgM antibody. Multimerized S·Protein-TPs serve as bridges/molecular docks to combine S·Tag-fused hemagglutinin trimers to form very large hemagglutinin H5 oligomers. H5 oligomers in the plant crude extract were highly active in hemagglutination resulting in high titers. Immunization of mice with two doses of plant crude extracts containing H5 oligomers after storage for 1 week at 4 °C caused strong immune responses and induced neutralizing specific humoral immune responses in mice. These results allow for the development of cheap influenza vaccines for veterinary application in future.
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Affiliation(s)
- Hoang Trong Phan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Institute of Biotechnology, Hanoi, Vietnam
| | - Thuong Thi Ho
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Institute of Biotechnology, Hanoi, Vietnam
| | | | | | - Ulrike Gresch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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148
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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149
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Abstract
GeneMill officially launched on 4th February 2016 and is an open access academic facility located at The University of Liverpool that has been established for the high-throughput construction and testing of synthetic DNA constructs. GeneMill provides end-to-end design, construction and phenotypic characterization of small to large gene constructs or genetic circuits/pathways for academic and industrial applications. Thus, GeneMill is equipping the scientific community with easy access to the validated tools required to explore the possibilities of Synthetic Biology.
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150
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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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