Mini‐synplastomes for plastid genetic engineering
Abstract
Summary In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design–build–test of a novel synthetic genome structure that does not disturb the native plastome: the ‘mini‐synplastome’. The mini‐synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini‐synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non‐integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini‐synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker‐free plastid engineering, and provide an unparalleled platform for one‐step metabolic engineering in plants.
- Authors:
-
- Department of Food Science University of Tennessee Knoxville TN USA, Center for Agricultural Synthetic Biology University of Tennessee Institute of Agriculture Knoxville TN USA
- Center for Agricultural Synthetic Biology University of Tennessee Institute of Agriculture Knoxville TN USA, Department of Plant Sciences University of Tennessee Knoxville TN USA
- Department of Plant Sciences University of Tennessee Knoxville TN USA
- Department of Basic and Translational Sciences School of Dental Medicine University of Pennsylvania Philadelphia PA USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1827240
- Alternate Identifier(s):
- OSTI ID: 1827242
- Resource Type:
- Published Article
- Journal Name:
- Plant Biotechnology Journal
- Additional Journal Information:
- Journal Name: Plant Biotechnology Journal Journal Volume: 20 Journal Issue: 2; Journal ID: ISSN 1467-7644
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Occhialini, Alessandro, Pfotenhauer, Alexander C., Li, Li, Harbison, Stacee A., Lail, Andrew J., Burris, Jason N., Piasecki, Cristiano, Piatek, Agnieszka A., Daniell, Henry, Stewart, Jr, C. Neal, and Lenaghan, Scott C.. Mini‐synplastomes for plastid genetic engineering. United Kingdom: N. p., 2021.
Web. doi:10.1111/pbi.13717.
Occhialini, Alessandro, Pfotenhauer, Alexander C., Li, Li, Harbison, Stacee A., Lail, Andrew J., Burris, Jason N., Piasecki, Cristiano, Piatek, Agnieszka A., Daniell, Henry, Stewart, Jr, C. Neal, & Lenaghan, Scott C.. Mini‐synplastomes for plastid genetic engineering. United Kingdom. https://doi.org/10.1111/pbi.13717
Occhialini, Alessandro, Pfotenhauer, Alexander C., Li, Li, Harbison, Stacee A., Lail, Andrew J., Burris, Jason N., Piasecki, Cristiano, Piatek, Agnieszka A., Daniell, Henry, Stewart, Jr, C. Neal, and Lenaghan, Scott C.. Sun .
"Mini‐synplastomes for plastid genetic engineering". United Kingdom. https://doi.org/10.1111/pbi.13717.
@article{osti_1827240,
title = {Mini‐synplastomes for plastid genetic engineering},
author = {Occhialini, Alessandro and Pfotenhauer, Alexander C. and Li, Li and Harbison, Stacee A. and Lail, Andrew J. and Burris, Jason N. and Piasecki, Cristiano and Piatek, Agnieszka A. and Daniell, Henry and Stewart, Jr, C. Neal and Lenaghan, Scott C.},
abstractNote = {Summary In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design–build–test of a novel synthetic genome structure that does not disturb the native plastome: the ‘mini‐synplastome’. The mini‐synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini‐synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non‐integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini‐synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker‐free plastid engineering, and provide an unparalleled platform for one‐step metabolic engineering in plants.},
doi = {10.1111/pbi.13717},
journal = {Plant Biotechnology Journal},
number = 2,
volume = 20,
place = {United Kingdom},
year = {2021},
month = {10}
}
https://doi.org/10.1111/pbi.13717
Works referenced in this record:
Minicircular plastid DNA in the dinoflagellate Amphidinium operculatum
journal, February 2000
- Barbrook, A. C.; Howe, C. J.
- Molecular and General Genetics MGG, Vol. 263, Issue 1
Required sequence elements for chloroplast DNA replication activity in vitro and in electroporated chloroplasts
journal, January 2004
- Lugo, Samantha K.; Kunnimalaiyaan, Muthusamy; Singh, Narendra K.
- Plant Science, Vol. 166, Issue 1
An episomal vector system for plastid transformation in higher plants
journal, November 2015
- Min, Sung Ran; Davarpanah, Seyed Javad; Jung, Seo Hee
- Plant Biotechnology Reports, Vol. 9, Issue 6
Affordable oral health care: dental biofilm disruption using chloroplast made enzymes with chewing gum delivery
journal, June 2021
- Singh, Rahul; Ren, Zhi; Shi, Yao
- Plant Biotechnology Journal, Vol. 19, Issue 10
High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene.
journal, February 1993
- Svab, Z.; Maliga, P.
- Proceedings of the National Academy of Sciences, Vol. 90, Issue 3
Validation of leaf enzymes in the detergent and textile industries: launching of a new platform technology
journal, February 2019
- Kumari, Uma; Singh, Rahul; Ray, Tui
- Plant Biotechnology Journal, Vol. 17, Issue 6
Marker rescue from the Nicotiana tabacum plastid genome using a plastid/Escherichia coli shuttle vector
journal, January 1995
- Staub, J. M.; Maliga, P.
- Molecular and General Genetics MGG, Vol. 249, Issue 1
Multiple pathways for Cre/lox-mediated recombination in plastids: Cre/lox-mediated recombination in plastids
journal, July 2001
- Hajdukiewicz, Peter T. J.; Gilbertson, Larry; Staub, Jeffrey M.
- The Plant Journal, Vol. 27, Issue 2
Generation, analysis, and transformation of macro-chloroplast Potato (Solanum tuberosum) lines for chloroplast biotechnology
journal, December 2020
- Occhialini, Alessandro; Pfotenhauer, Alexander C.; Frazier, Taylor P.
- Scientific Reports, Vol. 10, Issue 1
Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes
journal, March 2006
- Daniell, Henry; Lee, Seung-Bum; Grevich, Justin
- Theoretical and Applied Genetics, Vol. 112, Issue 8
MoChlo: A Versatile, Modular Cloning Toolbox for Chloroplast Biotechnology
journal, January 2019
- Occhialini, Alessandro; Piatek, Agnieszka A.; Pfotenhauer, Alexander C.
- Plant Physiology, Vol. 179, Issue 3
Electron microscopic localization of replication origins in Oenothera chloroplast DNA
journal, March 1992
- Chiu, Wan-Ling; Sears, Barbara B.
- Molecular and General Genetics MGG, Vol. 232, Issue 1
The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression
journal, September 1986
- Shinozaki, K.; Ohme, M.; Tanaka, M.
- The EMBO Journal, Vol. 5, Issue 9
Compartmentalized Metabolic Engineering for Artemisinin Biosynthesis and Effective Malaria Treatment by Oral Delivery of Plant Cells
journal, November 2016
- Malhotra, Karan; Subramaniyan, Mayavan; Rawat, Khushboo
- Molecular Plant, Vol. 9, Issue 11
Determining the transgene containment level provided by chloroplast transformation
journal, April 2007
- Ruf, S.; Karcher, D.; Bock, R.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 17
Generation of marker-free plastid transformants using a transiently cointegrated selection gene
journal, January 2004
- Klaus, Sebastian M. J.; Huang, Fong-Chin; Golds, Timothy J.
- Nature Biotechnology, Vol. 22, Issue 2
Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation
journal, July 2016
- Kwon, Kwang-Chul; Chan, Hui-Ting; León, Ileana R.
- Plant Physiology, Vol. 172, Issue 1
Characterization of the Pea Chloroplast DNA OriA Region
journal, November 1993
- Nielsen, Brent L.; Lu, Zhun; Tewari, Krishna K.
- Plasmid, Vol. 30, Issue 3
Enhancements and modifications of primer design program Primer3
journal, March 2007
- Koressaar, T.; Remm, M.
- Bioinformatics, Vol. 23, Issue 10
First plant-made biologic approved
journal, June 2012
- Fox, Jeffrey L.
- Nature Biotechnology, Vol. 30, Issue 6
Evolution of the chloroplast genome
journal, January 2003
- Howe, Christopher J.; Barbrook, Adrian C.; Koumandou, V. Lila
- Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 358, Issue 1429
Exceptional transmission of plastids and mitochondria from the transplastomic pollen parent and its impact on transgene containment
journal, April 2007
- Svab, Z.; Maliga, P.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 17
The remarkable chloroplast genome of dinoflagellates
journal, February 2008
- Howe, C. J.; Nisbet, R. E. R.; Barbrook, A. C.
- Journal of Experimental Botany, Vol. 59, Issue 5
Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants
journal, January 2009
- Gray, Benjamin N.; Ahner, Beth A.; Hanson, Maureen R.
- Transgenic Research, Vol. 18, Issue 4
Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis
journal, December 1983
- Norrander, Jan; Kempe, Tomas; Messing, Joachim
- Gene, Vol. 26, Issue 1
The Copy Number of Chloroplast Gene Minicircles Changes Dramatically with Growth Phase in the Dinoflagellate Amphidinium operculatum
journal, January 2007
- Koumandou, V. L.; Howe, Christopher J.
- Protist, Vol. 158, Issue 1
A faster Rubisco with potential to increase photosynthesis in crops
journal, September 2014
- Lin, Myat T.; Occhialini, Alessandro; Andralojc, P. John
- Nature, Vol. 513, Issue 7519
Electron microscopic localization of the chloroplast DNA replicative origins in Chlamydomonas reinhardu
journal, January 1984
- Waddell, Jody; Wang, Xun-Ming; Wu, Madeline
- Nucleic Acids Research, Vol. 12, Issue 9
Containment of herbicide resistance through genetic engineering of the chloroplast genome
journal, April 1998
- Daniell, Henry; Datta, Rina; Varma, Sam
- Nature Biotechnology, Vol. 16, Issue 4
Pea chloroplast topoisomerase I: purification, characterization, and role in replication
journal, January 1988
- Nielsen, Brent L.; Tewari, K. K.
- Plant Molecular Biology, Vol. 11, Issue 1
Primer3—new capabilities and interfaces
journal, June 2012
- Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu
- Nucleic Acids Research, Vol. 40, Issue 15
Fine mapping of replication origins (oriA and oriB) in Nicotiana tabacum chloroplast DNA
journal, September 1997
- Kunnimalaiyaan, M.; Nielsen, B. L.
- Nucleic Acids Research, Vol. 25, Issue 18
The fate of extrachromosomal DNAs in the progeny of plastid-transformed tobacco plants
journal, November 2015
- Min, Sung Ran; Jung, Seo Hee; Liu, Jang R.
- Plant Biotechnology Reports, Vol. 9, Issue 6
Cold chain and virus‐free chloroplast‐made booster vaccine to confer immunity against different poliovirus serotypes
journal, June 2016
- Chan, Hui‐Ting; Xiao, Yuhong; Weldon, William C.
- Plant Biotechnology Journal, Vol. 14, Issue 11
Overexpression of the Bacillus thuringiensis (Bt) Cry2Aa2 protein in chloroplasts confers resistance to plants against susceptible and Bt-resistant insects
journal, March 1999
- Kota, M.; Daniell, H.; Varma, S.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 5
Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids
journal, February 2015
- Zhang, Jiang; Khan, Sher Afzal; Hasse, Claudia
- Science, Vol. 347, Issue 6225
Efficient elimination of selectable marker genes from the plastid genome by the CRE-lox site-specific recombination system: CRE-mediated marker gene excision in plastids
journal, July 2001
- Corneille, Sylvie; Lutz, Kerry; Svab, Zora
- The Plant Journal, Vol. 27, Issue 2
Cold chain and virus‐free oral polio booster vaccine made in lettuce chloroplasts confers protection against all three poliovirus serotypes
journal, January 2019
- Daniell, Henry; Rai, Vineeta; Xiao, Yuhong
- Plant Biotechnology Journal, Vol. 17, Issue 7
Cloning and delimiting one chloroplast DNA replicative origin of Chlamydomonas
journal, January 1984
- Wang, Xun-Ming; Chang, C. H.; Waddell, Jody
- Nucleic Acids Research, Vol. 12, Issue 9
Autoluminescent Plants
journal, November 2010
- Krichevsky, Alexander; Meyers, Benjamin; Vainstein, Alexander
- PLoS ONE, Vol. 5, Issue 11
Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons
journal, February 2013
- Lu, Y.; Rijzaani, H.; Karcher, D.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 8
Localization of replication origins in pea chloroplast DNA.
journal, March 1988
- Meeker, R.; Nielsen, B.; Tewari, K. K.
- Molecular and Cellular Biology, Vol. 8, Issue 3
Chloroplast DNA replication in vitro : site-specific initiation from preferred templates
journal, January 1988
- Carrillo, Nestor; Bogorad, Lawrence
- Nucleic Acids Research, Vol. 16, Issue 12
Seamless editing of the chloroplast genome in plants
journal, July 2016
- Martin Avila, Elena; Gisby, Martin F.; Day, Anil
- BMC Plant Biology, Vol. 16, Issue 1
The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression
journal, February 2010
- Ruhlman, Tracey; Verma, Dheeraj; Samson, Nalapalli
- Plant Physiology, Vol. 152, Issue 4
Chloroplast genomes: diversity, evolution, and applications in genetic engineering
journal, June 2016
- Daniell, Henry; Lin, Choun-Sea; Yu, Ming
- Genome Biology, Vol. 17, Issue 1
Stable expression of a biodegradable protein-based polymer in tobacco chloroplasts
journal, January 2000
- Guda, C.; Lee, S. -B.; Daniell, H.
- Plant Cell Reports, Vol. 19, Issue 3
Expression and assembly of largest foreign protein in chloroplasts: oral delivery of human FVIII made in lettuce chloroplasts robustly suppresses inhibitor formation in haemophilia A mice
journal, December 2017
- Kwon, Kwang-Chul; Sherman, Alexandra; Chang, Wan-Jung
- Plant Biotechnology Journal, Vol. 16, Issue 6
Novel plastid gene minicircles in the dinoflagellate Amphidinium operculatum
journal, April 2004
- Nisbet, R. Ellen R.; Koumandou, V. Lila; Barbrook, Adrian C.
- Gene, Vol. 331
Stable transformation of plastids in higher plants.
journal, November 1990
- Svab, Z.; Hajdukiewicz, P.; Maliga, P.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 21
Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors.
journal, January 1990
- Daniell, H.; Vivekananda, J.; Nielsen, B. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 1
A comparative approach to elucidate chloroplast genome replication
journal, January 2009
- Krishnan, Neeraja M.; Rao, Basuthkar J.
- BMC Genomics, Vol. 10, Issue 1
Release of Proteins from Intact Chloroplasts Induced by Reactive Oxygen Species during Biotic and Abiotic Stress
journal, June 2013
- Kwon, Kwang-Chul; Verma, Dheeraj; Jin, Shuangxia
- PLoS ONE, Vol. 8, Issue 6
Removal of antibiotic resistance genes from transgenic tobacco plastids
journal, November 2000
- Iamtham, Siriluck; Day, Anil
- Nature Biotechnology, Vol. 18, Issue 11
Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals
journal, January 2001
- Cosa, Brandy De; Moar, William; Lee, Seung-Bum
- Nature Biotechnology, Vol. 19, Issue 1
Functional analysis of plastid DNA replication origins in tobacco by targeted inactivation
journal, October 2002
- K. Mühlbauer, Stefan; Lössl, Andreas; Tzekova, Lilia
- The Plant Journal, Vol. 32, Issue 2
Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae
journal, May 2012
- Barbrook, Adrian C.; Dorrell, Richard G.; Burrows, Jennifer
- Plant Molecular Biology, Vol. 79, Issue 4-5
Investigational new drug enabling angiotensin oral-delivery studies to attenuate pulmonary hypertension
journal, March 2020
- Daniell, Henry; Mangu, Venkata; Yakubov, Bakhtiyor
- Biomaterials, Vol. 233
Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts
journal, January 2012
- Kumar, Shashi; Hahn, Frederick M.; Baidoo, Edward
- Metabolic Engineering, Vol. 14, Issue 1
Designer diatom episomes delivered by bacterial conjugation
journal, April 2015
- Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.
- Nature Communications, Vol. 6, Issue 1
Generation and characterization of soybean and marker-free tobacco plastid transformants over-expressing a bacterial 4-hydroxyphenylpyruvate dioxygenase which provides strong herbicide tolerance
journal, January 2007
- Dufourmantel, Nathalie; Dubald, Manuel; Matringe, Michel
- Plant Biotechnology Journal, Vol. 5, Issue 1
Transgenic tobacco plants with improved cyanobacterial Rubisco expression but no extra assembly factors grow at near wild-type rates if provided with elevated CO 2
journal, December 2015
- Occhialini, Alessandro; Lin, Myat T.; Andralojc, P. John
- The Plant Journal, Vol. 85, Issue 1
Extrachromosomal elements in tobacco plastids.
journal, August 1994
- Staub, J. M.; Maliga, P.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 16
Long-term evaluation of mucosal and systemic immunity and protection conferred by different polio booster vaccines
journal, September 2017
- Xiao, Yuhong; Daniell, Henry
- Vaccine, Vol. 35, Issue 40
High efficiency plastid transformation in potato and regulation of transgene expression in leaves and tubers by alternative 5′ and 3′ regulatory sequences
journal, May 2010
- Valkov, Vladimir T.; Gargano, Daniela; Manna, Carmela
- Transgenic Research, Vol. 20, Issue 1
Validation of leaf and microbial pectinases: commercial launching of a new platform technology
journal, February 2019
- Daniell, Henry; Ribeiro, Thuanne; Lin, Shina
- Plant Biotechnology Journal, Vol. 17, Issue 6
Oral delivery of novel human IGF-1 bioencapsulated in lettuce cells promotes musculoskeletal cell proliferation, differentiation and diabetic fracture healing
journal, March 2020
- Park, J.; Yan, G.; Kwon, K. -C.
- Biomaterials, Vol. 233