1
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Krasley A, Li E, Galeana JM, Bulumulla C, Beyene AG, Demirer GS. Carbon Nanomaterial Fluorescent Probes and Their Biological Applications. Chem Rev 2024; 124:3085-3185. [PMID: 38478064 PMCID: PMC10979413 DOI: 10.1021/acs.chemrev.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Fluorescent carbon nanomaterials have broadly useful chemical and photophysical attributes that are conducive to applications in biology. In this review, we focus on materials whose photophysics allow for the use of these materials in biomedical and environmental applications, with emphasis on imaging, biosensing, and cargo delivery. The review focuses primarily on graphitic carbon nanomaterials including graphene and its derivatives, carbon nanotubes, as well as carbon dots and carbon nanohoops. Recent advances in and future prospects of these fields are discussed at depth, and where appropriate, references to reviews pertaining to older literature are provided.
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Affiliation(s)
- Andrew
T. Krasley
- Janelia
Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Eugene Li
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Boulevard, Pasadena, California 91125, United States
| | - Jesus M. Galeana
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Boulevard, Pasadena, California 91125, United States
| | - Chandima Bulumulla
- Janelia
Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Abraham G. Beyene
- Janelia
Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Gozde S. Demirer
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Boulevard, Pasadena, California 91125, United States
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2
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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3
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Wang Y, Demirer GS. Synthetic biology for plant genetic engineering and molecular farming. Trends Biotechnol 2023; 41:1182-1198. [PMID: 37012119 DOI: 10.1016/j.tibtech.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Many efforts have been put into engineering plants to improve crop yields and stress tolerance and boost the bioproduction of valuable molecules. Yet, our capabilities are still limited due to the lack of well-characterized genetic building blocks and resources for precise manipulation and given the inherently challenging properties of plant tissues. Advancements in plant synthetic biology can overcome these bottlenecks and release the full potential of engineered plants. In this review, we first discuss the recently developed plant synthetic elements from single parts to advanced circuits, software, and hardware tools expediting the engineering cycle. Next, we survey the advancements in plant biotechnology enabled by these recent resources. We conclude the review with outstanding challenges and future directions of plant synthetic biology.
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Affiliation(s)
- Yunqing Wang
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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4
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Demirer GS, Gibson DJ, Yue X, Pan K, Elishav E, Khandal H, Horev G, Tarkowská D, Cantó-Pastor A, Kong S, Manzano C, Maloof JN, Savaldi-Goldstein S, Brady SM. Phosphate deprivation-induced changes in tomato are mediated by an interaction between brassinosteroid signaling and zinc. New Phytol 2023. [PMID: 37306070 DOI: 10.1111/nph.19007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023]
Abstract
Inorganic phosphate (Pi) is a necessary macronutrient for basic biological processes. Plants modulate their root system architecture (RSA) and cellular processes to adapt to Pi deprivation albeit with a growth penalty. Excess application of Pi fertilizer, on the contrary, leads to eutrophication and has a negative environmental impact. We compared RSA, root hair elongation, acid phosphatase activity, metal ion accumulation, and brassinosteroid hormone levels of Solanum lycopersicum (tomato) and Solanum pennellii, which is a wild relative of tomato, under Pi sufficiency and deficiency conditions to understand the molecular mechanism of Pi deprivation response in tomato. We showed that S. pennellii is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc overaccumulation. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.
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Affiliation(s)
- Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Donald J Gibson
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Xiaoyan Yue
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kelly Pan
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Eshel Elishav
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Hitaishi Khandal
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Guy Horev
- Lorey I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Olomouc, CZ-78371, Czech Republic
| | - Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Shuyao Kong
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Concepcion Manzano
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Julin N Maloof
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
| | | | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, 95616, USA
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5
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Legendre M, Demirer GS. Improving crop genetic transformation to feed the world. Trends Biotechnol 2023; 41:264-266. [PMID: 36513544 DOI: 10.1016/j.tibtech.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Food security is threatened by rising global population and effects of climate change. Most of our calories come from a few crops that are difficult to improve. Lowe et al. developed a plant transformation approach enabling crop genetic engineering that could provide a route to a future with greater food security.
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Affiliation(s)
- Mark Legendre
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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6
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Abstract
In this issue of Developmental Cell, Hernández-Coronado et al. present genetic and pharmacological evidence that reveals the central role of plant glutamate receptor-like proteins (GLRs) in the tradeoff between wounding-triggered regeneration and defense, offering new strategies to improve plant regeneration.
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Affiliation(s)
- Chao Bian
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
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7
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Gonzalez-Grandio E, Demirer GS, Jackson CT, Yang D, Ebert S, Molawi K, Keller H, Landry MP. Correction to: Carbon nanotube biocompatibility in plants is determined by their surface chemistry. J Nanobiotechnology 2022; 20:81. [PMID: 35177081 PMCID: PMC8851704 DOI: 10.1186/s12951-022-01302-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Eduardo Gonzalez-Grandio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.,Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Christopher T Jackson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Sophia Ebert
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Kian Molawi
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Harald Keller
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute (IGI), Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA. .,Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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8
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Park J, Demirer GS, Cheung LS. Toolboxes for plant systems biology research. Curr Opin Biotechnol 2022; 75:102692. [PMID: 35144172 DOI: 10.1016/j.copbio.2022.102692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
The terms 'systems' and 'synthetic biology' are often used together, with most scientists striding between the two fields rather than adhering to a single side. Often too, scientists want to understand a system to inform the design of gene circuits that could endow it with new functions. However, this does not need to be the progression of research, as synthetic constructs can help improve our understanding of a system. Here, we review synthetic biology tool kits with the potential to overcome pleiotropic effects, compensatory mechanisms, and redundancy in plants. Combined with -omics techniques, these tools could reveal novel insights on plant growth and development, an aim that has gained renewed urgency given the impact of climate change on crop productivity.
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Affiliation(s)
- Jihyun Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA; Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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9
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Zhang H, Goh NS, Wang JW, Pinals RL, González-Grandío E, Demirer GS, Butrus S, Fakra SC, Del Rio Flores A, Zhai R, Zhao B, Park SJ, Landry MP. Nanoparticle cellular internalization is not required for RNA delivery to mature plant leaves. Nat Nanotechnol 2022. [PMID: 34811553 DOI: 10.1101/2021.03.17.435888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Rapidly growing interest in the nanoparticle-mediated delivery of DNA and RNA to plants requires a better understanding of how nanoparticles and their cargoes translocate in plant tissues and into plant cells. However, little is known about how the size and shape of nanoparticles influence transport in plants and the delivery efficiency of their cargoes, limiting the development of nanotechnology in plant systems. In this study we employed non-biolistically delivered DNA-modified gold nanoparticles (AuNPs) of various sizes (5-20 nm) and shapes (spheres and rods) to systematically investigate their transport following infiltration into Nicotiana benthamiana leaves. Generally, smaller AuNPs demonstrated more rapid, higher and longer-lasting levels of association with plant cell walls compared with larger AuNPs. We observed internalization of rod-shaped but not spherical AuNPs into plant cells, yet, surprisingly, 10 nm spherical AuNPs functionalized with small-interfering RNA (siRNA) were the most efficient at siRNA delivery and inducing gene silencing in mature plant leaves. These results indicate the importance of nanoparticle size in efficient biomolecule delivery and, counterintuitively, demonstrate that efficient cargo delivery is possible and potentially optimal in the absence of nanoparticle cellular internalization. Overall, our results highlight nanoparticle features of importance for transport within plant tissues, providing a mechanistic overview of how nanoparticles can be designed to achieve efficacious biocargo delivery for future developments in plant nanobiotechnology.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- College of Chemistry and Materials Science, Jinan University, Guangzhou, China
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey W Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Bin Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, China
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Zhang H, Goh NS, Wang JW, Pinals RL, González-Grandío E, Demirer GS, Butrus S, Fakra SC, Del Rio Flores A, Zhai R, Zhao B, Park SJ, Landry MP. Nanoparticle cellular internalization is not required for RNA delivery to mature plant leaves. Nat Nanotechnol 2022; 17:197-205. [PMID: 34811553 PMCID: PMC10519342 DOI: 10.1038/s41565-021-01018-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
Abstract
Rapidly growing interest in the nanoparticle-mediated delivery of DNA and RNA to plants requires a better understanding of how nanoparticles and their cargoes translocate in plant tissues and into plant cells. However, little is known about how the size and shape of nanoparticles influence transport in plants and the delivery efficiency of their cargoes, limiting the development of nanotechnology in plant systems. In this study we employed non-biolistically delivered DNA-modified gold nanoparticles (AuNPs) of various sizes (5-20 nm) and shapes (spheres and rods) to systematically investigate their transport following infiltration into Nicotiana benthamiana leaves. Generally, smaller AuNPs demonstrated more rapid, higher and longer-lasting levels of association with plant cell walls compared with larger AuNPs. We observed internalization of rod-shaped but not spherical AuNPs into plant cells, yet, surprisingly, 10 nm spherical AuNPs functionalized with small-interfering RNA (siRNA) were the most efficient at siRNA delivery and inducing gene silencing in mature plant leaves. These results indicate the importance of nanoparticle size in efficient biomolecule delivery and, counterintuitively, demonstrate that efficient cargo delivery is possible and potentially optimal in the absence of nanoparticle cellular internalization. Overall, our results highlight nanoparticle features of importance for transport within plant tissues, providing a mechanistic overview of how nanoparticles can be designed to achieve efficacious biocargo delivery for future developments in plant nanobiotechnology.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- College of Chemistry and Materials Science, Jinan University, Guangzhou, China
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey W Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Bin Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, China
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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11
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González-Grandío E, Demirer GS, Ma W, Brady S, Landry MP. A Ratiometric Dual Color Luciferase Reporter for Fast Characterization of Transcriptional Regulatory Elements in Plants. ACS Synth Biol 2021; 10:2763-2766. [PMID: 34520169 PMCID: PMC10503406 DOI: 10.1021/acssynbio.1c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant synthetic biology requires precise characterization of genetic elements to construct complex genetic circuits that can improve plant traits or confer them with new characteristics. Transcriptional reporter assays are essential to quantify the effect of gene expression regulator elements. Additionally, transcriptional reporter systems are a key tool in understanding control of gene expression in biology. In this work, we construct and characterize a dual color luciferase ratiometric reporter system that possesses several advantages over currently used reporters. It is ratiometric, thus reducing variability and increasing consistency between experiments; it is fast, as both reporters can be measured at the same time in a single reaction, and it is less expensive to perform than current dual luciferase reporter assays. We have validated our system quantifying the transcriptional capability of a panel of promoters and terminators commonly used in synthetic biology with a broad range of expression magnitudes, and in a biologically relevant system, nitrate response.
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Affiliation(s)
- Eduardo González-Grandío
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Gozde S Demirer
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Wenhe Ma
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Siobhan Brady
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Markita P Landry
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
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12
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Zhang H, Cao Y, Xu D, Goh NS, Demirer GS, Cestellos-Blanco S, Chen Y, Landry MP, Yang P. Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown. Nano Lett 2021; 21:5859-5866. [PMID: 34152779 PMCID: PMC10539026 DOI: 10.1021/acs.nanolett.1c01792] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium-mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.
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Affiliation(s)
- Huan Zhang
- Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou, Guangdong 510632, People's Republic of China
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yuhong Cao
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Yuan Chen
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, and Department of Plant and Microbial Biology, University of California Berkeley, Albany, California 94710, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg BioHub, San Francisco, California 94158, United States
| | - Peidong Yang
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, United States
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13
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Zhang H, Cao Y, Xu D, Goh NS, Demirer GS, Cestellos-Blanco S, Chen Y, Landry MP, Yang P. Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown. Nano Lett 2021. [PMID: 34152779 DOI: 10.1101/2021.03.17.435890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium-mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.
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Affiliation(s)
- Huan Zhang
- Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou, Guangdong 510632, People's Republic of China
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yuhong Cao
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Yuan Chen
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, and Department of Plant and Microbial Biology, University of California Berkeley, Albany, California 94710, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg BioHub, San Francisco, California 94158, United States
| | - Peidong Yang
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, United States
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14
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Demirer GS, Silva TN, Jackson CT, Thomas JB, W Ehrhardt D, Rhee SY, Mortimer JC, Landry MP. Nanotechnology to advance CRISPR-Cas genetic engineering of plants. Nat Nanotechnol 2021; 16:243-250. [PMID: 33712738 PMCID: PMC10461802 DOI: 10.1038/s41565-021-00854-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/14/2021] [Indexed: 05/05/2023]
Abstract
CRISPR-Cas genetic engineering of plants holds tremendous potential for providing food security, battling biotic and abiotic crop stresses caused by climate change, and for environmental remediation and sustainability. Since the discovery of CRISPR-Cas technology, its usefulness has been demonstrated widely, including for genome editing in plants. Despite the revolutionary nature of genome-editing tools and the notable progress that these tools have enabled in plant genetic engineering, there remain many challenges for CRISPR applications in plant biotechnology. Nanomaterials could address some of the most critical challenges of CRISPR genome editing in plants through improvements in cargo delivery, species independence, germline transformation and gene editing efficiency. This Perspective identifies major barriers preventing CRISPR-mediated plant genetic engineering from reaching its full potential, and discusses ways that nanoparticle technologies can lower or eliminate these barriers. We also describe advances that are needed in nanotechnology to facilitate and accelerate plant genome editing. Timely advancement of the application of CRISPR technologies in plant engineering is crucial for our ability to feed and sustain the growing human population under a changing global climate.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Department of Plant Biology and Genome Center, University of California, Davis, CA, USA.
| | - Tallyta N Silva
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher T Jackson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Jason B Thomas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia.
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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15
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Demirer GS, Landry MP. Efficient Transient Gene Knock-down in Tobacco Plants Using Carbon Nanocarriers. Bio Protoc 2021; 11:e3897. [PMID: 33732771 DOI: 10.21769/bioprotoc.3897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/27/2022] Open
Abstract
Gene knock-down in plants is a useful approach to study genotype-phenotype relationships, render disease resistance to crops, and enable efficient biosynthesis of molecules in plants. Small interfering RNA (siRNA)-mediated gene silencing is one of the most common ways to achieve gene knock-down in plants. Traditionally, siRNA is delivered into intact plant cells by coding the siRNA sequences into DNA vectors, which are then delivered through viral and/or bacterial methods. In this protocol, we provide an alternative direct delivery method of siRNA molecules into intact plant cells for efficient transient gene knock-down in model tobacco plant, Nicotiana benthamiana, leaves. Our approach uses one dimensional carbon-based nanomaterials, single-walled carbon nanotubes (SWNTs), to deliver siRNA, and does not rely on viral/bacterial delivery. The distinct advantages of our method are i) there is no need for DNA coding of siRNA sequences, ii) this abiotic method could work in a broader range of plant species than biotic methods, and iii) there are fewer regulatory complications when using abiotic delivery methods, whereby gene silencing is transient without permanent modification of the plant genome. Graphic abstract.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA.,Innovative Genomics Institute, Berkeley, CA 94702, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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16
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Zhang H, Zhang H, Demirer GS, González-Grandío E, Fan C, Landry MP. Engineering DNA nanostructures for siRNA delivery in plants. Nat Protoc 2020; 15:3064-3087. [PMID: 32807907 PMCID: PMC10493160 DOI: 10.1038/s41596-020-0370-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Targeted downregulation of select endogenous plant genes is known to confer disease or pest resistance in crops and is routinely accomplished via transgenic modification of plants for constitutive gene silencing. An attractive alternative to the use of transgenics or pesticides in agriculture is the use of a 'green' alternative known as RNAi, which involves the delivery of siRNAs that downregulate endogenous genes to confer resistance. However, siRNA is a molecule that is highly susceptible to enzymatic degradation and is difficult to deliver across the lignin-rich and multi-layered plant cell wall that poses the dominant physical barrier to biomolecule delivery in plants. We have demonstrated that DNA nanostructures can be utilized as a cargo carrier for direct siRNA delivery and gene silencing in mature plants. The size, shape, compactness and stiffness of the DNA nanostructure affect both internalization into plant cells and subsequent gene silencing efficiency. Herein, we provide a detailed protocol that can be readily adopted with standard biology benchtop equipment to generate geometrically optimized DNA nanostructures for transgene-free and force-independent siRNA delivery and gene silencing in mature plants. We further discuss how such DNA nanostructures can be rationally designed to efficiently enter plant cells and deliver cargoes to mature plants, and provide guidance for DNA nanostructure characterization, storage and use. The protocol described herein can be completed in 4 d.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Honglu Zhang
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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17
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Demirer GS, Zhang H, Goh NS, Pinals RL, Chang R, Landry MP. Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown. Sci Adv 2020; 6:eaaz0495. [PMID: 32637592 PMCID: PMC7314522 DOI: 10.1126/sciadv.aaz0495] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/08/2020] [Indexed: 05/19/2023]
Abstract
Posttranscriptional gene silencing (PTGS) is a powerful tool to understand and control plant metabolic pathways, which is central to plant biotechnology. PTGS is commonly accomplished through delivery of small interfering RNA (siRNA) into cells. Standard plant siRNA delivery methods (Agrobacterium and viruses) involve coding siRNA into DNA vectors and are only tractable for certain plant species. Here, we develop a nanotube-based platform for direct delivery of siRNA and show high silencing efficiency in intact plant cells. We demonstrate that nanotubes successfully deliver siRNA and silence endogenous genes, owing to effective intracellular delivery and nanotube-induced protection of siRNA from nuclease degradation. This study establishes that nanotubes could enable a myriad of plant biotechnology applications that rely on RNA delivery to intact cells.
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Affiliation(s)
- Gozde S. Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Natalie S. Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca L. Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94702, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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18
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Abstract
Biolistic delivery of biomolecular cargoes to plants with micron-scale projectiles is a well-established technique in plant biotechnology. However, the relatively large micron-scale biolistic projectiles can result in tissue damage, low regeneration efficiency, and create difficulties for the biolistic transformation of isomorphic small cells or subcellular target organelles (i.e., mitochondria and plastids). As an alternative to micron-sized carriers, nanomaterials provide a promising approach for biomolecule delivery to plants. While most studies exploring nanoscale biolistic carriers have been carried out in animal cells and tissues, which lack a cell wall, we can nonetheless extrapolate their utility for nanobiolistic delivery of biomolecules in plant targets. Specifically, nanobiolistics has shown promising results for use in animal systems, in which nanoscale projectiles yield lower levels of cell and tissue damage while maintaining similar transformation efficiencies as their micron-scale counterparts. In this chapter, we specifically discuss biolistic delivery of nanoparticles for plant genetic transformation purposes and identify the figures of merit requiring optimization for broad-scale implementation of nanobiolistics in plant genetic transformations.
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Affiliation(s)
- Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Demirer GS, Zhang H, Goh NS, González-Grandío E, Landry MP. Carbon nanotube-mediated DNA delivery without transgene integration in intact plants. Nat Protoc 2019; 14:2954-2971. [PMID: 31534231 PMCID: PMC10496593 DOI: 10.1038/s41596-019-0208-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/06/2019] [Indexed: 11/09/2022]
Abstract
Exogenous biomolecule delivery into plants is difficult because the plant cell wall poses a dominant transport barrier, thereby limiting the efficiency of plant genetic engineering. Traditional DNA delivery methods for plants suffer from host-species limitations, low transformation efficiencies, tissue damage, or unavoidable and uncontrolled DNA integration into the host genome. We have demonstrated efficient plasmid DNA delivery into intact plants of several species with functionalized high-aspect-ratio carbon nanotube (CNT) nanoparticles (NPs), enabling efficient DNA delivery into a variety of non-model plant species (arugula, wheat, and cotton) and resulting in high protein expression levels without transgene integration. Herein, we provide a protocol that can be implemented by plant biologists and adapted to produce functionalized single-walled CNTs (SWNTs) with surface chemistries optimized for delivery of plasmid DNA in a plant species-independent manner. This protocol describes how to prepare, construct, and optimize polyethylenimine (PEI)-functionalized SWNTs and perform plasmid DNA loading. The authors also provide guidance on material characterization, gene expression evaluation, and storage conditions. The entire protocol, from the covalent functionalization of SWNTs to expression quantification, can be completed in 5 d.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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20
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Wang JW, Grandio EG, Newkirk GM, Demirer GS, Butrus S, Giraldo JP, Landry MP. Nanoparticle-Mediated Genetic Engineering of Plants. Mol Plant 2019; 12:1037-1040. [PMID: 31283997 PMCID: PMC10461873 DOI: 10.1016/j.molp.2019.06.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 05/05/2023]
Affiliation(s)
- Jeffrey W Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Eduardo G Grandio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Gregory M Newkirk
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Salwan Butrus
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48103, USA
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute of Integrative Genome Biology (IIGB), Riverside, CA 92521, USA.
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute (IGI), Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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21
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Demirer GS, Zhang H, Matos JL, Goh NS, Cunningham FJ, Sung Y, Chang R, Aditham AJ, Chio L, Cho MJ, Staskawicz B, Landry MP. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. Nat Nanotechnol 2019; 14:456-464. [PMID: 30804481 PMCID: PMC10461892 DOI: 10.1038/s41565-019-0382-5] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/18/2019] [Indexed: 05/19/2023]
Abstract
Genetic engineering of plants is at the core of sustainability efforts, natural product synthesis and crop engineering. The plant cell wall is a barrier that limits the ease and throughput of exogenous biomolecule delivery to plants. Current delivery methods either suffer from host-range limitations, low transformation efficiencies, tissue damage or unavoidable DNA integration into the host genome. Here, we demonstrate efficient diffusion-based biomolecule delivery into intact plants of several species with pristine and chemically functionalized high aspect ratio nanomaterials. Efficient DNA delivery and strong protein expression without transgene integration is accomplished in Nicotiana benthamiana (Nb), Eruca sativa (arugula), Triticum aestivum (wheat) and Gossypium hirsutum (cotton) leaves and arugula protoplasts. We find that nanomaterials not only facilitate biomolecule transport into plant cells but also protect polynucleotides from nuclease degradation. Our work provides a tool for species-independent and passive delivery of genetic material, without transgene integration, into plant cells for diverse biotechnology applications.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Juliana L Matos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Younghun Sung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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22
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Zhang H, Demirer GS, Zhang H, Ye T, Goh NS, Aditham AJ, Cunningham FJ, Fan C, Landry MP. DNA nanostructures coordinate gene silencing in mature plants. Proc Natl Acad Sci U S A 2019; 116:7543-7548. [PMID: 30910954 PMCID: PMC6462094 DOI: 10.1073/pnas.1818290116] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Delivery of biomolecules to plants relies on Agrobacterium infection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene in Nicotiana benthamiana leaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Honglu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Tianzheng Ye
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Chinese Academy of Sciences Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720;
- Innovative Genomics Institute, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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23
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Cunningham FJ, Goh NS, Demirer GS, Matos JL, Landry MP. Nanoparticle-Mediated Delivery towards Advancing Plant Genetic Engineering. Trends Biotechnol 2018; 36:882-897. [PMID: 29703583 PMCID: PMC10461776 DOI: 10.1016/j.tibtech.2018.03.009] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/15/2022]
Abstract
Genetic engineering of plants has enhanced crop productivity in the face of climate change and a growing global population by conferring desirable genetic traits to agricultural crops. Efficient genetic transformation in plants remains a challenge due to the cell wall, a barrier to exogenous biomolecule delivery. Conventional delivery methods are inefficient, damaging to tissue, or are only effective in a limited number of plant species. Nanoparticles are promising materials for biomolecule delivery, owing to their ability to traverse plant cell walls without external force and highly tunable physicochemical properties for diverse cargo conjugation and broad host range applicability. With the advent of engineered nuclease biotechnologies, we discuss the potential of nanoparticles as an optimal platform to deliver biomolecules to plants for genetic engineering.
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Affiliation(s)
- Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, USA; These authors contributed equally to this work
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, USA; These authors contributed equally to this work
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Juliana L Matos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute (IGI), Berkeley, CA 94720, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute (IGI), Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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24
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Beyene AG, Demirer GS, Landry MP. Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes. Curr Protoc Chem Biol 2016; 8:197-223. [PMID: 27622569 PMCID: PMC10539024 DOI: 10.1002/cpch.10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular recognition of biological analytes with optical nanosensors provides both spatial and temporal biochemical information. A recently developed sensing platform exploits near-infrared fluorescent single-wall carbon nanotubes combined with electrostatically pinned heteropolymers to yield a synthetic molecular recognition technique that is maximally transparent through biological matter. This molecular recognition technique is known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe, the specificity of a folded polymer toward an analyte does not arise from a pre-existing polymer-analyte chemical affinity. Rather, specificity is conferred through conformational changes undergone by a polymer that is pinned to the surface of a nanoparticle in the presence of an analyte and the subsequent modifications in fluorescence readout of the nanoparticles. The protocols in this article describe a novel single-molecule microscopy tool (near-infrared fluorescence and total internal reflection fluorescence [nIRF TIRF] hybrid microscope) to visualize the CoPhMoRe recognition process, enabling a better understanding of synthetic molecular recognition. We describe this requisite microscope for simultaneous single-molecule visualization of optical molecular recognition and signal transduction. We elaborate on the general procedures for synthesizing and identifying single-walled carbon nanotube-based sensors that employ CoPhMoRe via two biologically relevant examples of single-molecule recognition for the hormone estradiol and the neurotransmitter dopamine. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Abraham G Beyene
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California
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25
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Demirer GS, Okur AC, Kizilel S. Synthesis and design of biologically inspired biocompatible iron oxide nanoparticles for biomedical applications. J Mater Chem B 2015; 3:7831-7849. [PMID: 32262898 DOI: 10.1039/c5tb00931f] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During the last couple of decades considerable research efforts have been directed towards the synthesis and coating of iron oxide nanoparticles (IONPs) for biomedical applications. To address the current limitations, recent studies have focused on the design of new generation nanoparticle systems whose internalization and targeting capabilities have been improved through surface modifications. This review covers the most recent challenges and advances in the development of IONPs with enhanced quality, and biocompatibility for various applications in biotechnology and medicine.
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Affiliation(s)
- Gozde S Demirer
- Koc University, Chemical and Biological Engineering, Istanbul 34450, Turkey.
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Nazli C, Demirer GS, Yar Y, Acar HY, Kizilel S. Targeted delivery of doxorubicin into tumor cells via MMP-sensitive PEG hydrogel-coated magnetic iron oxide nanoparticles (MIONPs). Colloids Surf B Biointerfaces 2014; 122:674-683. [PMID: 25183059 DOI: 10.1016/j.colsurfb.2014.07.049] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 01/03/2023]
Abstract
Targeting tumors with nano-scale delivery systems shows promise to improve the therapeutic effects of chemotherapeutic drugs. However, the limited specificity of current nano-scale systems for cancer tissues prevents realization of their full clinical potential. Here, we demonstrate an effective approach to creating as targeted nanocarriers for drug delivery: MIONPs coated with integrin-targeted and matrix-metalloproteinase (MMP)-sensitive PEG hydrogel scaffolds. The functional PEG hydrogel coating has been designed for active loading as well as triggered intra-cellular release of the cancer therapeutic agent doxorubicin (DOX). Our study demonstrated that coated nanocarriers could be taken into cancer cells 11 times more efficiently than uncoated ones. Furthermore, confocal laser scanning microscopy images revealed that these targeted nanocarriers could efficiently deliver and release DOX into the nuclei of HeLa cells within 2h. Coating MIONPs with multifunctional PEG hydrogel could be a promising alternative to existing vehicles for targeted delivery of DOX into tumor tissue.
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Affiliation(s)
- Caner Nazli
- Koç University, Material Science and Engineering, Istanbul 34450, Turkey
| | - Gozde S Demirer
- Koç University, Chemical and Biological Engineering, Istanbul 34450, Turkey
| | - Yasemin Yar
- Koç University, Material Science and Engineering, Istanbul 34450, Turkey
| | - H Yagci Acar
- Koç University, Material Science and Engineering, Istanbul 34450, Turkey; Koç University, Chemistry Department, Istanbul 34450, Turkey
| | - Seda Kizilel
- Koç University, Material Science and Engineering, Istanbul 34450, Turkey; Koç University, Chemical and Biological Engineering, Istanbul 34450, Turkey.
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