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Selvakesavan RK, Nuc M, Kolarčik V, Krajewski P, Franklin G. Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures. Sci Data 2024; 11:42. [PMID: 38184679 PMCID: PMC10771467 DOI: 10.1038/s41597-023-02878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
Hypericum is a large genus that includes more than 500 species of pharmacological, ecological and conservation value. Although latest advances in sequencing technologies were extremely exploited for generating and assembling genomes of many living organisms, annotated whole genome sequence data is not publicly available for any of the Hypericum species so far. Bioavailability of secondary metabolites varies for different tissues and the data derived from different cultures will be a valuable tool for comparative studies. Here, we report the single molecule real-time sequencing (SMRT) data sets of Hypericum perforatum L. plantlets and cell suspension cultures for the first time. Sequencing data from cell suspension cultures yielded more than 33,000 high-quality transcripts from 20 Gb of raw data, while more than 55,000 high-quality transcripts were obtained from 35 Gb of raw data from plantlets. This dataset is a valuable tool for comparative transcriptomic analysis and will help to understand the unknown biosynthetic pathways of high medicinal value in the Hypericum genus.
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Affiliation(s)
- Rajendran K Selvakesavan
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
- Department of Biotechnology, PSGR Krishnammal College for Women, Coimbatore, 641004, India
| | - Maria Nuc
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-041 54, Košice, Slovakia
| | - Paweł Krajewski
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Arya SS, Mahto BK, Sengar MS, Rookes JE, Cahill DM, Lenka SK. Metabolic Engineering of Rice Cells with Vanillin Synthase Gene (VpVAN) to Produce Vanillin. Mol Biotechnol 2022; 64:861-872. [PMID: 35192168 DOI: 10.1007/s12033-022-00470-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/12/2022] [Indexed: 11/29/2022]
Abstract
Vanillin production by metabolic engineering of proprietary microbial strains has gained impetus due to increasing consumer demand for naturally derived products. Here, we demonstrate the use of rice cell cultures metabolically engineered with vanillin synthase gene (VpVAN) as a plant-based alternative to microbial vanillin production systems. VpVAN catalyzes the signature step to convert ferulic acid into vanillin in Vanilla planifolia. As ferulic acid is a phenylpropanoid pathway intermediate in plant cells, rice calli cells are ideal platform for in vivo vanillin synthesis due to the availability of its precursor. In this study, rice calli derived from embryonic rice cells were metabolically engineered with a codon-optimized VpVAN gene using Agrobacterium-mediated transformation. The putative transformants were selected based on their proliferation on herbicide-supplemented N6D medium. Expression of the transgenes were confirmed through a β-glucuronidase (GUS) reporter assay and polymerase chain reaction (PCR) analysis provided evidence of genetic transformation. The semiquantitative RT-PCR and real-time (RT)-qPCR revealed expression of VpVAN in six transgenic calli lines. High-performance liquid chromatography identified the biosynthesis of vanillin in transgenic calli lines, with the highest yielding line producing 544.72 (± 102.50) μg of vanillin-g fresh calli. This work serves as a proof-of-concept to produce vanillin using metabolically engineered rice cell cultures.
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Affiliation(s)
- Sagar S Arya
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India.,School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, 3216, Australia
| | - Binod K Mahto
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India.,University Department of Botany, Ranchi University, Ranchi, Jharkhand, 834008, India
| | - Meenu S Sengar
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India
| | - James E Rookes
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, 3216, Australia
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, 3216, Australia
| | - Sangram K Lenka
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India.
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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. NATURE NANOTECHNOLOGY 2022. [PMID: 34811553 DOI: 10.1101/2021.03.17.435888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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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. NATURE NANOTECHNOLOGY 2022; 17:197-205. [PMID: 34811553 PMCID: PMC10519342 DOI: 10.1038/s41565-021-01018-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [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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