1
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Fan X, Sun H. Exploring Agrobacterium-mediated genetic transformation methods and its applications in Lilium. PLANT METHODS 2024; 20:120. [PMID: 39123215 PMCID: PMC11313100 DOI: 10.1186/s13007-024-01246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024]
Abstract
As a typical bulb flower, lily is widely cultivated worldwide because of its high ornamental, medicinal and edible value. Although breeding efforts evolved over the last 10000 years, there are still many problems in the face of increasing consumer demand. The approach of biotechnological methods would help to solve this problem and incorporate traits impossible by conventional breeding. Target traits are dormancy, development, color, floral fragrance and resistances against various biotic and abiotic stresses, so as to improve the quality of bulbs and cut flowers in planting, cultivation, postharvest, plant protection and marketing. Genetic transformation technology is an important method for varietal improvement and has become the foundation and core of plant functional genomics research, greatly assisting various plant improvement programs. However, achieving stable and efficient genetic transformation of lily has been difficult worldwide. Many gene function verification studies depend on the use of model plants, which greatly limits the pace of directed breeding and germplasm improvement in lily. Although significant progress has been made in the development and optimization of genetic transformation systems, shortcomings remain. Agrobacterium-mediated genetic transformation has been widely used in lily. However, severe genotypic dependence is the main bottleneck limiting the genetic transformation of lily. This review will summarizes the research progress in the genetic transformation of lily over the past 30 years to generate the material including a section how genome engineering using stable genetic transformation system, and give an overview about recent and future applications of lily transformation. The information provided in this paper includes ideas for optimizing and improving the efficiency of existing genetic transformation methods and for innovation, provides technical support for mining and identifying regulatory genes for key traits, and lays a foundation for genetic improvement and innovative germplasm development in lily.
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Affiliation(s)
- Xinyue Fan
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, 110866, China.
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2
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Azizi-Dargahlou S, Pouresmaeil M. Agrobacterium tumefaciens-Mediated Plant Transformation: A Review. Mol Biotechnol 2024; 66:1563-1580. [PMID: 37340198 DOI: 10.1007/s12033-023-00788-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Agrobacterium tumefaciens-mediated plant transformation is the most dominant technique for the transformation of plants. It is used to transform monocotyledonous and dicotyledonous plants. A. tumefaciens apply for stable and transient transformation, random and targeted integration of foreign genes, as well as genome editing of plants. The Advantages of this method include cheapness, uncomplicated operation, high reproducibility, a low copy number of integrated transgenes, and the possibility of transferring larger DNA fragments. Engineered endonucleases such as CRISPR/Cas9 systems, TALENs, and ZFNs can be delivered with this method. Nowadays, Agrobacterium-mediated transformation is used for the Knock in, Knock down, and Knock out of genes. The transformation effectiveness of this method is not always desirable. Researchers applied various strategies to improve the effectiveness of this method. Here, a general overview of the characteristics and mechanism of gene transfer with Agrobacterium is presented. Advantages, updated data on the factors involved in optimizing this method, and other useful materials that lead to maximum exploitation as well as overcoming obstacles of this method are discussed. Moreover, the application of this method in the generation of genetically edited plants is stated. This review can help researchers to establish a rapid and highly effective Agrobacterium-mediated transformation protocol for any plant species.
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Affiliation(s)
| | - Mahin Pouresmaeil
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
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3
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Liu P, Panda K, Edwards SA, Swanson R, Yi H, Pandesha P, Hung YH, Klaas G, Ye X, Collins MV, Renken KN, Gilbertson LA, Veena V, Hancock CN, Slotkin RK. Transposase-assisted target-site integration for efficient plant genome engineering. Nature 2024; 631:593-600. [PMID: 38926583 PMCID: PMC11254759 DOI: 10.1038/s41586-024-07613-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone, and this inefficiency hampers genome-editing approaches to develop improved crops1,2. Often considered to be genome 'parasites', transposable elements (TEs) evolved to insert their DNA seamlessly into genomes3-5. Eukaryotic TEs select their site of insertion based on preferences for chromatin contexts, which differ for each TE type6-9. Here we developed a genome engineering tool that controls the TE insertion site and cargo delivered, taking advantage of the natural ability of the TE to precisely excise and insert into the genome. Inspired by CRISPR-associated transposases that target transposition in a programmable manner in bacteria10-12, we fused the rice Pong transposase protein to the Cas9 or Cas12a programmable nucleases. We demonstrated sequence-specific targeted insertion (guided by the CRISPR gRNA) of enhancer elements, an open reading frame and a gene expression cassette into the genome of the model plant Arabidopsis. We then translated this system into soybean-a major global crop in need of targeted insertion technology. We have engineered a TE 'parasite' into a usable and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Seth A Edwards
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Ryan Swanson
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Hochul Yi
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Pratheek Pandesha
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University, St Louis, MO, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Gerald Klaas
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Xudong Ye
- Bayer Crop Science, St Louis, MO, USA
| | | | | | | | - Veena Veena
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | | | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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4
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Tabara M, Matsumoto A, Kibayashi Y, Takeda A, Motomura K. Straightforward and affordable agroinfiltration with RUBY accelerates RNA silencing research. PLANT MOLECULAR BIOLOGY 2024; 114:61. [PMID: 38764076 PMCID: PMC11102880 DOI: 10.1007/s11103-024-01463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Transient expression and induction of RNA silencing by agroinfiltration is a fundamental method in plant RNA biology. Here, we introduce a new reporter assay using RUBY, which encodes three key enzymes of the betalain biosynthesis pathway, as a polycistronic mRNA. The red pigmentation conferred by betalains allows visual confirmation of gene expression or silencing levels without tissue disruption, and the silencing levels can be quantitatively measured by absorbance in as little as a few minutes. Infiltration of RUBY in combination with p19, a well-known RNA silencing suppressor, induced a fivefold higher accumulation of betalains at 7 days post infiltration compared to infiltration of RUBY alone. We demonstrated that co-infiltration of RUBY with two RNA silencing inducers, targeting either CYP76AD1 or glycosyltransferase within the RUBY construct, effectively reduces RUBY mRNA and betalain levels, indicating successful RNA silencing. Therefore, compared to conventional reporter assays for RNA silencing, the RUBY-based assay provides a simple and rapid method for quantitative analysis without the need for specialized equipment, making it useful for a wide range of RNA silencing studies.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Ayumi Matsumoto
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yuriko Kibayashi
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Atsushi Takeda
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kazuki Motomura
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
- Japanese Science and Technology Agency, PRESTO, Kawaguchi, Saitama, 332-0012, Japan.
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5
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Vu TV, Nguyen NT, Kim J, Hong JC, Kim J. Prime editing: Mechanism insight and recent applications in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:19-36. [PMID: 37794706 PMCID: PMC10754014 DOI: 10.1111/pbi.14188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.
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Affiliation(s)
- Tien V. Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
- Nulla Bio Inc.JinjuKorea
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6
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Iida E, Kuriyama K, Tabara M, Takeda A, Suzuki N, Moriyama H, Fukuhara T. Structural features of T-DNA that induce transcriptional gene silencing during agroinfiltration. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:289-299. [PMID: 38434119 PMCID: PMC10905568 DOI: 10.5511/plantbiotechnology.23.0719a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 03/05/2024]
Abstract
Agrobacterium tumefaciens (Rhizobium radiobacter) is used for the transient expression of foreign genes by the agroinfiltration method, but the introduction of foreign genes often induces transcriptional and/or post-transcriptional gene silencing (TGS and/or PTGS). In this study, we characterized the structural features of T-DNA that induce TGS during agroinfiltration. When A. tumefaciens cells harboring an empty T-DNA plasmid containing the cauliflower mosaic virus (CaMV) 35S promoter were infiltrated into the leaves of Nicotiana benthamiana line 16c with a GFP gene over-expressed under the control of the same promoter, no small interfering RNAs (siRNAs) were derived from the GFP sequence. However, siRNAs derived from the CaMV 35S promoter were detected, indicating that TGS against the GFP gene was induced. When the GFP gene was inserted into the T-DNA plasmid, PTGS against the GFP gene was induced whereas TGS against the CaMV 35S promoter was suppressed. We also showed the importance of terminator sequences in T-DNA for gene silencing. Therefore, depending on the combination of promoter, terminator and coding sequences on T-DNA and the host nuclear genome, either or both TGS and/or PTGS could be induced by agroinfiltration. Furthermore, we showed the possible involvement of three siRNA-producing Dicers (DCL2, DCL3 and DCL4) in the induction of TGS by the co-agroinfiltration method. Especially, DCL2 was probably the most important among them in the initial step of TGS induction. These results are valuable for controlling gene expression by agroinfiltration.
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Affiliation(s)
- Emi Iida
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Atsushi Takeda
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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7
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Neelakandan AK, Kabahuma M, Yang Q, Lopez M, Wisser RJ, Balint-Kurti P, Lauter N. Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104. G3 (BETHESDA, MD.) 2023; 13:jkad166. [PMID: 37523773 PMCID: PMC10542558 DOI: 10.1093/g3journal/jkad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
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Affiliation(s)
| | - Mercy Kabahuma
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Miriam Lopez
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L’Institut Agro, Montpellier 34000, France
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Plant Science Research Unit, USDA-ARS, Raleigh, NC 27695, USA
| | - Nick Lauter
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
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8
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Yugay YA, Sorokina MR, Grigorchuk VP, Rusapetova TV, Silant’ev VE, Egorova AE, Adedibu PA, Kudinova OD, Vasyutkina EA, Ivanov VV, Karabtsov AA, Mashtalyar DV, Degtyarenko AI, Grishchenko OV, Kumeiko VV, Bulgakov VP, Shkryl YN. Biosynthesis of Functional Silver Nanoparticles Using Callus and Hairy Root Cultures of Aristolochia manshuriensis. J Funct Biomater 2023; 14:451. [PMID: 37754865 PMCID: PMC10532211 DOI: 10.3390/jfb14090451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
This study delves into the novel utilization of Aristolochia manshuriensis cultured cells for extracellular silver nanoparticles (AgNPs) synthesis without the need for additional substances. The presence of elemental silver has been verified using energy-dispersive X-ray spectroscopy, while distinct surface plasmon resonance peaks were revealed by UV-Vis spectra. Transmission and scanning electron microscopy indicated that the AgNPs, ranging in size from 10 to 40 nm, exhibited a spherical morphology. Fourier-transform infrared analysis validated the abilty of A. manshuriensis extract components to serve as both reducing and capping agents for metal ions. In the context of cytotoxicity on embryonic fibroblast (NIH 3T3) and mouse neuroblastoma (N2A) cells, AgNPs demonstrated varying effects. Specifically, nanoparticles derived from callus cultures exhibited an IC50 of 2.8 µg/mL, effectively inhibiting N2A growth, whereas AgNPs sourced from hairy roots only achieved this only at concentrations of 50 µg/mL and above. Notably, all studied AgNPs' treatment-induced cytotoxicity in fibroblast cells, yielding IC50 values ranging from 7.2 to 36.3 µg/mL. Furthermore, the findings unveiled the efficacy of the synthesized AgNPs against pathogenic microorganisms impacting both plants and animals, including Agrobacterium rhizogenes, A. tumefaciens, Bacillus subtilis, and Escherichia coli. These findings underscore the effectiveness of biotechnological methodologies in offering advanced and enhanced green nanotechnology alternatives for generating nanoparticles with applications in combating cancer and infectious disorders.
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Affiliation(s)
- Yulia A. Yugay
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Maria R. Sorokina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Valeria P. Grigorchuk
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Tatiana V. Rusapetova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Vladimir E. Silant’ev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok 690922, Russia; (V.E.S.); (V.V.K.)
- Institute of Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia;
| | - Anna E. Egorova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow 111123, Russia;
| | - Peter A. Adedibu
- School of Advanced Engineering Studies “Institute of Biotechnology, Bioengineering and Food Systems”, Far Eastern Federal University, Vladivostok 690922, Russia;
| | - Olesya D. Kudinova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Elena A. Vasyutkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Vladimir V. Ivanov
- Far Eastern Geological Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; (V.V.I.); (A.A.K.)
| | - Alexander A. Karabtsov
- Far Eastern Geological Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; (V.V.I.); (A.A.K.)
| | - Dmitriy V. Mashtalyar
- Institute of Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia;
| | - Anton I. Degtyarenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Olga V. Grishchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Vadim V. Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok 690922, Russia; (V.E.S.); (V.V.K.)
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690041, Russia
| | - Victor P. Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
| | - Yury N. Shkryl
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (Y.A.Y.); (M.R.S.); (V.P.G.); (T.V.R.); (O.D.K.); (E.A.V.); (A.I.D.); (O.V.G.); (V.P.B.)
- School of Advanced Engineering Studies “Institute of Biotechnology, Bioengineering and Food Systems”, Far Eastern Federal University, Vladivostok 690922, Russia;
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9
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KhokharVoytas A, Shahbaz M, Maqsood MF, Zulfiqar U, Naz N, Iqbal UZ, Sara M, Aqeel M, Khalid N, Noman A, Zulfiqar F, Al Syaad KM, AlShaqhaa MA. Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change. Funct Integr Genomics 2023; 23:283. [PMID: 37642792 DOI: 10.1007/s10142-023-01202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Enhancing the resilience of plants to abiotic stresses, such as drought, salinity, heat, and cold, is crucial for ensuring global food security challenge in the context of climate change. The adverse effects of climate change, characterized by rising temperatures, shifting rainfall patterns, and increased frequency of extreme weather events, pose significant threats to agricultural systems worldwide. Genetic modification strategies offer promising approaches to develop crops with improved abiotic stress tolerance. This review article provides a comprehensive overview of various genetic modification techniques employed to enhance plant resilience. These strategies include the introduction of stress-responsive genes, transcription factors, and regulatory elements to enhance stress signaling pathways. Additionally, the manipulation of hormone signaling pathways, osmoprotectant accumulation, and antioxidant defense mechanisms is discussed. The use of genome editing tools, such as CRISPR-Cas9, for precise modification of target genes related to stress tolerance is also explored. Furthermore, the challenges and future prospects of genetic modification for abiotic stress tolerance are highlighted. Understanding and harnessing the potential of genetic modification strategies can contribute to the development of resilient crop varieties capable of withstanding adverse environmental conditions caused by climate change, thereby ensuring sustainable agricultural productivity and food security.
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Affiliation(s)
| | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, Pakistan.
| | | | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Usama Zafar Iqbal
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Maheen Sara
- Department of Nutritional Sciences, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Sialkot, Pakistan
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Khalid M Al Syaad
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
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10
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Ma H, Liu N, Sun X, Zhu M, Mao T, Huang S, Meng X, Li H, Wang M, Liang H. Establishment of an efficient transformation system and its application in regulatory mechanism analysis of biological macromolecules in tea plants. Int J Biol Macromol 2023:125372. [PMID: 37321436 DOI: 10.1016/j.ijbiomac.2023.125372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
Tea (Camellia sinensis), one of the most important beverage crops originated from China and is now cultivated worldwide, provides numerous secondary metabolites that account for its health benefits and rich flavor. However, the lack of an efficient and reliable genetic transformation system has seriously hindered the gene function investigation and precise breeding of C. sinensis. In this study, we established a highly efficient, labor-saving, and cost-effective Agrobacterium rhizogenes-mediated hairy roots genetic transformation system for C. sinensis, which can be used for gene overexpression and genome editing. The established transformation system was simple to operate, bypassing tissue culture and antibiotic screening, and only took two months to complete. We used this system to conduct function analysis of transcription factor CsMYB73 and found that CsMYB73 negatively regulates L-theanine synthesis in tea plant. Additionally, callus formation was successfully induced using transgenic roots, and the transgenic callus exhibited normal chlorophyll production, enabling the study of the corresponding biological functions. Furthermore, this genetic transformation system was effective for multiple C. sinensis varieties and other woody plant species. By overcoming technical obstacles such as low efficiency, long experimental periods, and high costs, this genetic transformation will be a valuable tool for routine gene investigation and precise breeding in tea plants.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, China.
| | - Ningge Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Mengling Zhu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Tingfeng Mao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Xinyue Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Hangfei Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Min Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Huiling Liang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
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11
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Zhao J, Meng X, Zhang Z, Wang M, Nie F, Liu Q. OsLPR5 Encoding Ferroxidase Positively Regulates the Tolerance to Salt Stress in Rice. Int J Mol Sci 2023; 24:ijms24098115. [PMID: 37175822 PMCID: PMC10179522 DOI: 10.3390/ijms24098115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Salinity is a major abiotic stress that harms rice growth and productivity. Low phosphate roots (LPRs) play a central role in Pi deficiency-mediated inhibition of primary root growth and have ferroxidase activity. However, the function of LPRs in salt stress response and tolerance in plants remains largely unknown. Here, we reported that the OsLPR5 was induced by NaCl stress and positively regulates the tolerance to salt stress in rice. Under NaCl stress, overexpression of OsLPR5 led to increased ferroxidase activity, more green leaves, higher levels of chlorophyll and lower MDA contents compared with the WT. In addition, OsLPR5 could promote the accumulation of cell osmotic adjustment substances and promote ROS-scavenging enzyme activities. Conversely, the mutant lpr5 had a lower ferroxidase activity and suffered severe damage under salt stress. Moreover, knock out of OsLPR5 caused excessive Na+ levels and Na+/K+ ratios. Taken together, our results exemplify a new molecular link between ferroxidase and salt stress tolerance in rice.
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Affiliation(s)
- Juan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Xin Meng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhaonian Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Mei Wang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fanhao Nie
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
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12
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Vega M, Quintero-Corrales C, Mastretta-Yanes A, Casas A, López-Hilario V, Wegier A. Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico. Ecol Evol 2023; 13:e9838. [PMID: 36911302 PMCID: PMC9994486 DOI: 10.1002/ece3.9838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 03/14/2023] Open
Abstract
Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.
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Affiliation(s)
- Melania Vega
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico.,Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Christian Quintero-Corrales
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico.,Departamento de Botánica Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO) Ciudad de México Mexico.,Consejo Nacional de Ciencia y Tecnología (CONACYT) Programa de Investigadores e Investigadoras por México Ciudad de México Mexico
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad Universidad Nacional Autónoma de México Morelia Mexico
| | | | - Ana Wegier
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
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13
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Wang X, Chen S, Zhang H, Luo P, Zhou F, Zeng B, Xu J, Fan C. Agrobacterium-mediated genetic transformation of the most widely cultivated superior clone Eucalyptus urophylla × E. grandis DH32-29 in Southern China. FRONTIERS IN PLANT SCIENCE 2023; 13:1011245. [PMID: 36733602 PMCID: PMC9886895 DOI: 10.3389/fpls.2022.1011245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 06/18/2023]
Abstract
Eucalyptus, as an economically important species for wood and paper industries, remains a challenge to genetic improvement by transgenic technology owing to the deficiency of a highly efficient and stable genetic transformation system, especially in cultivated superior clones. Eucalyptus urophylla × E. grandis clone DH32-29 is most widely planted in southern China, but it is relatively recalcitrant to adventitious bud regeneration, which blocks the establishment of a genetic transformation system. Here, an efficient adventitious bud regeneration and transformation system of Eucalyptus was established using E. urophylla × E. grandis DH32-29 as material. The in vitro leaves from microshoots that were subcultured for 20-25 days were immersed into liquid Woody Plant Medium supplemented with 0.02 mg·L-1 α-naphthaleneacetic acid (NAA) and 0.24 mg·L-1 forchlorfenuron [callus-inducing medium (CIM)]. After 15 days, explants were transferred to a medium containing 0.10 mg·L-1 NAA and 0.50 mg·L-1 6-benzyladenine (shoot-inducing medium, SIM) for adventitious bud induction. The highest regeneration efficiency of adventitious buds was 76.5%. Moreover, an Agrobacterium tumefaciens-mediated genetic transformation system was optimized. The leaves were precultured for 7 days and infected for 30 min with A. tumefaciens strain EHA105 grown to a bacterial density of 0.3 (OD600). After 72 h of cocultivation in the dark, leaves were transferred to CIM supplemented with 100 mg·L-1 cefotaxime (Cef), 100 mg·L-1 timentin, and 15 mg·L-1 kanamycin (Kan) for 15 days to induce calluses. Then, the explants were transferred to SIM supplemented with the same concentration of antibiotics, and the fresh medium was replaced every 15 days until resistant adventitious buds appeared. After inducing roots in root-inducing medium supplemented with 200 mg·L-1 Cef and 75 mg·L-1 Kan, completely transgenic plants were obtained. Using the aforementioned method, the transformation frequency can reach 1.9%. This provides a powerful approach for genetic improvement of E. urophylla × E. grandis DH32-29 and gene function analysis in Eucalyptus.
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Affiliation(s)
- Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Shanshan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Haonan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ping Luo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Fangping Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Bingshan Zeng
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Jianmin Xu
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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14
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Park I, Seo YS, Mannaa M. Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential. Front Microbiol 2023; 14:1163832. [PMID: 37213524 PMCID: PMC10196466 DOI: 10.3389/fmicb.2023.1163832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.
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Affiliation(s)
- Inmyoung Park
- School of Food and Culinary Arts, Youngsan University, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- *Correspondence: Young-Su Seo
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
- Mohamed Mannaa
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15
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Selma S, Gianoglio S, Uranga M, Vázquez‐Vilar M, Espinosa‐Ruiz A, Drapal M, Fraser PD, Daròs J, Orzáez D. Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1550-1564. [PMID: 35822533 PMCID: PMC9541417 DOI: 10.1111/tpj.15906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/07/2022] [Indexed: 05/11/2023]
Abstract
Programmable transcriptional regulators based on CRISPR architecture are promising tools for the induction of plant gene expression. In plants, CRISPR gene activation is effective with respect to modulating development processes, such as the flowering time or customizing biochemical composition. The most widely used method for delivering CRISPR components into the plant is Agrobacterium tumefaciens-mediated genetic transformation, either transient or stable. However, as a result of their versatility and their ability to move, virus-derived systems have emerged as an interesting alternative for supplying the CRISPR components to the plant, in particular guide RNA (gRNA), which represents the variable component in CRISPR strategies. In the present study, we describe a Potato virus X-derived vector that, upon agroinfection in Nicotiana benthamiana, serves as a vehicle for delivery of gRNAs, producing highly specific virus-induced gene activation. The system works in combination with a N. benthamiana transgenic line carrying the remaining complementary CRISPR gene activation components, specifically the dCasEV2.1 cassette, which has been shown previously to mediate strong programmable transcriptional activation in plants. Using an easily scalable, non-invasive spraying method, we show that gRNA-mediated activation programs move locally and systemically, generating a strong activation response in different target genes. Furthermore, by activating three different endogenous MYB transcription factors, we demonstrate that this Potato virus X-based virus-induced gene reprogramming strategy results in program-specific metabolic fingerprints in N. benthamiana leaves characterized by distinctive phenylpropanoid-enriched metabolite profiles.
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Affiliation(s)
- Sara Selma
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Silvia Gianoglio
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Mireia Uranga
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Marta Vázquez‐Vilar
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Ana Espinosa‐Ruiz
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | | | | | - José‐Antonio Daròs
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Diego Orzáez
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
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16
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Tiwari M, Mishra AK, Chakrabarty D. Agrobacterium-mediated gene transfer: recent advancements and layered immunity in plants. PLANTA 2022; 256:37. [PMID: 35819629 PMCID: PMC9274631 DOI: 10.1007/s00425-022-03951-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/19/2022] [Indexed: 05/15/2023]
Abstract
Plant responds to Agrobacterium via three-layered immunity that determines its susceptibility or resistance to Agrobacterium infection. Agrobacterium tumefaciens is a soil-borne Gram-negative bacterium that causes crown gall disease in plants. The remarkable feat of interkingdom gene transfer has been extensively utilised in plant biotechnology to transform plant as well as non-host systems. In the past two decades, the molecular mode of the pathogenesis of A. tumefaciens has been extensively studied. Agrobacterium has also been utilised as a premier model to understand the defence response of plants during plant-Agrobacterium interaction. Nonetheless, the threat of Agrobacterium-mediated crown gall disease persists and is associated with a huge loss of plant vigour in agriculture. Understanding the molecular dialogues between these two interkingdom species might provide a cure for crown gall disease. Plants respond to A. tumefaciens by mounting a three-layered immune response, which is manipulated by Agrobacterium via its virulence effector proteins. Comparative studies on plant defence proteins versus the counter-defence of Agrobacterium have shed light on plant susceptibility and tolerance. It is possible to manipulate a plant's immune system to overcome the crown gall disease and increase its competence via A. tumefaciens-mediated transformation. This review summarises the recent advances in the molecular mode of Agrobacterium pathogenesis as well as the three-layered immune response of plants against Agrobacterium infection.
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Affiliation(s)
- Madhu Tiwari
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Debasis Chakrabarty
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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17
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Induction of AmpC-Mediated β-Lactam Resistance Requires a Single Lytic Transglycosylase in Agrobacterium tumefaciens. Appl Environ Microbiol 2022; 88:e0033322. [PMID: 35638841 PMCID: PMC9238390 DOI: 10.1128/aem.00333-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The remarkable ability of Agrobacterium tumefaciens to transfer DNA to plant cells has allowed the generation of important transgenic crops. One challenge of A. tumefaciens-mediated transformation is eliminating the bacteria after plant transformation to prevent detrimental effects to plants and the release of engineered bacteria to the environment. Here, we use a reverse-genetics approach to identify genes involved in ampicillin resistance, with the goal of utilizing these antibiotic-sensitive strains for plant transformations. We show that treating A. tumefaciens C58 with ampicillin led to increased β-lactamase production, a response dependent on the broad-spectrum β-lactamase AmpC and its transcription factor, AmpR. Loss of the putative ampD orthologue atu2113 led to constitutive production of AmpC-dependent β-lactamase activity and ampicillin resistance. Finally, one cell wall remodeling enzyme, MltB3, was necessary for the AmpC-dependent β-lactamase activity, and its loss elicited ampicillin and carbenicillin sensitivity in the A. tumefaciens C58 and GV3101 strains. Furthermore, GV3101 ΔmltB3 transforms plants with efficiency comparable to that of the wild type but can be cleared with sublethal concentrations of ampicillin. The functional characterization of the genes involved in the inducible ampicillin resistance pathway of A. tumefaciens constitutes a major step forward in efforts to reduce the intrinsic antibiotic resistance of this bacterium. IMPORTANCE Agrobacterium tumefaciens, a significant biotechnological tool for production of transgenic plant lines, is highly resistant to a wide variety of antibiotics, posing challenges for various applications. One challenge is the efficient elimination of A. tumefaciens from transformed plant tissue without using levels of antibiotics that are toxic to the plants. Here, we present the functional characterization of genes involved in β-lactam resistance in A. tumefaciens. Knowledge about proteins that promote or inhibit β-lactam resistance will enable the development of strains to improve the efficiency of Agrobacterium-mediated plant genetic transformations. Effective removal of Agrobacterium from transformed plant tissue has the potential to maximize crop yield and food production, improving the outlook for global food security.
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18
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Zhao J, Liu X, Wang M, Xie L, Wu Z, Yu J, Wang Y, Zhang Z, Jia Y, Liu Q. The miR528-D3 Module Regulates Plant Height in Rice by Modulating the Gibberellin and Abscisic Acid Metabolisms. RICE (NEW YORK, N.Y.) 2022; 15:27. [PMID: 35596029 PMCID: PMC9123139 DOI: 10.1186/s12284-022-00575-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/13/2022] [Indexed: 05/02/2023]
Abstract
Plant height, as one of the important agronomic traits of rice, is closely related to yield. In recent years, plant height-related genes have been characterized and identified, among which the DWARF3 (D3) gene is one of the target genes of miR528, and regulates rice plant height and tillering mainly by affecting strigolactone (SL) signal transduction. However, it remains unknown whether the miR528 and D3 interaction functions in controlling plant height, and the underlying regulatory mechanism in rice. In this study, we found that the plant height, internode length, and cell length of internodes of d3 mutants and miR528-overexpressing (OE-miR528) lines were greatly shorter than WT, D3-overexpressing (OE-D3), and miR528 target mimicry (OE-MIM528) transgenic plants. Knockout of D3 gene (d3 mutants) or miR528-overexpressing (OE-miR528) triggers a substantial reduction of gibberellin (GA) content, but a significant increase of abscisic acid (ABA) accumulation than in WT. The d3 and OE-miR528 transgenic plants were much more sensitive to GA, but less sensitive to ABA than WT. Moreover, the expression level of GA biosynthesis-related key genes, including OsCPS1, OsCPS2, OsKO2 and OsKAO was remarkably higher in OE-D3 plants, while the NECD2 expression, a key gene involved in ABA biosynthesis, was significantly higher in d3 mutants than in WT and OE-D3 plants. The results indicate that the miR528-D3 module negatively regulates plant height in rice by modulating the GA and ABA homeostasis, thereby further affecting the elongation of internodes, and resulting in lower plant height, which adds a new regulatory role to the D3-mediated plant height controlling in rice.
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Affiliation(s)
- Juan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Xing Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Mei Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Lingjuan Xie
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Zhengxin Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Jiuming Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Yuchen Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Zhiqiao Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Yufang Jia
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China.
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19
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Rosenthal E, Potnis N, Bull CT. Comparative Genomic Analysis of the Lettuce Bacterial Leaf Spot Pathogen, Xanthomonas hortorum pv. vitians, to Investigate Race Specificity. Front Microbiol 2022; 13:840311. [PMID: 35516433 PMCID: PMC9062649 DOI: 10.3389/fmicb.2022.840311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial leaf spot (BLS) of lettuce caused by Xanthomonas hortorum pv. vitians (Xhv) was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the Xhv strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen Xhv strains representing the three races, along with eight related Xanthomonas strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of Xhv strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the Xhv races. Genome sequences were mined for effector genes, which have been shown to be involved in race specificity in other systems. Two effectors identified in this study, xopAQ and the novel variant xopAF2, were revealed as possible mediators of a gene-for-gene interaction between Xhv race 1 and 3 strains and wild lettuce Lactuca serriola ARM-09-161-10-1. Transposase sequence identified downstream of xopAF2 and prophage sequence found nearby within Xhv race 1 and 3 insertion sequences suggest that this gene may have been acquired through phage-mediated gene transfer. No other factors were identified from these analyses that distinguish the Xhv races.
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Affiliation(s)
- Emma Rosenthal
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
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20
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Monreal-Escalante E, Ramos-Vega A, Angulo C, Bañuelos-Hernández B. Plant-Based Vaccines: Antigen Design, Diversity, and Strategies for High Level Production. Vaccines (Basel) 2022; 10:100. [PMID: 35062761 PMCID: PMC8782010 DOI: 10.3390/vaccines10010100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/25/2021] [Accepted: 01/01/2022] [Indexed: 12/18/2022] Open
Abstract
Vaccines for human use have conventionally been developed by the production of (1) microbial pathogens in eggs or mammalian cells that are then inactivated, or (2) by the production of pathogen proteins in mammalian and insect cells that are purified for vaccine formulation, as well as, more recently, (3) by using RNA or DNA fragments from pathogens. Another approach for recombinant antigen production in the last three decades has been the use of plants as biofactories. Only have few plant-produced vaccines been evaluated in clinical trials to fight against diseases, of which COVID-19 vaccines are the most recent to be FDA approved. In silico tools have accelerated vaccine design, which, combined with transitory antigen expression in plants, has led to the testing of promising prototypes in pre-clinical and clinical trials. Therefore, this review deals with a description of immunoinformatic tools and plant genetic engineering technologies used for antigen design (virus-like particles (VLP), subunit vaccines, VLP chimeras) and the main strategies for high antigen production levels. These key topics for plant-made vaccine development are discussed and perspectives are provided.
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Affiliation(s)
- Elizabeth Monreal-Escalante
- Immunology and Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, Instituto PoliItécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, BCS, Mexico; (A.R.-V.); (C.A.)
- CONACYT—Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, BCS, Mexico
| | - Abel Ramos-Vega
- Immunology and Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, Instituto PoliItécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, BCS, Mexico; (A.R.-V.); (C.A.)
| | - Carlos Angulo
- Immunology and Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, Instituto PoliItécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, BCS, Mexico; (A.R.-V.); (C.A.)
| | - Bernardo Bañuelos-Hernández
- Escuela de Veterinaria, Universidad De La Salle Bajío, Avenida Universidad 602, Lomas del Campestre, Leon 37150, GTO, Mexico
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21
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Lazra Y, Gandu B, Amar ID, Emanuel E, Cahan R. Effects of Atmospheric Plasma Corona Discharge on Agrobacterium tumefaciens Survival. Microorganisms 2021; 10:microorganisms10010032. [PMID: 35056481 PMCID: PMC8780683 DOI: 10.3390/microorganisms10010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Soil-borne pathogenic microorganisms are known to cause extensive crop losses. Agrobacterium tumefaciens, a member of the Proteobacteria, causes the neoplastic crown gall disease in plants. Plant protection is mainly based on toxic chemicals that are harmful to the environment. The use of cold atmospheric-pressure plasma is an attractive method for microbial eradication. Its antimicrobial mechanism includes the formation of large quantities of reactive oxygen species (ROS). The advantages of eradicating bacteria using cold plasma are not needed for chemicals, short treatment, and environmental temperatures. This study examined the impact of plasma corona discharge exposure on A. tumefaciens viability, membrane permeability, relative cell size, and ROS formation. The results showed that 90 s of plasma exposure led to a reduction by four orders of magnitude when the initial concentration was 1 × 107 CFU/mL and in a dry environment. When the initial concentration was 1 × 106 CFU/mL, 45 s of exposure resulted in total bacterial eradication. In a liquid environment, in an initial concentration of 2.02 × 106 CFU/mL, there was no complete bacterial eradication even at the most prolonged examined exposure (90 s). The influence of plasma treatment on the membrane permeability of A. tumefaciens, and their possible recovery, were analyzed using flow cytometer analysis using propidium iodide (PI). When the plasma-treated bacteria were suspended in Luria–Bertani (LB) (rich medium), the PI-positive count of the plasma-treated bacteria after two hours was 12 ± 3.9%. At the 24th hour, this percentage was only 1.74 ± 0.6%, as the control (0.7 ± 0.1%). These results may indicate the repair of the plasma-treated bacteria that were suspended in LB. At the 24th hour, the relative cell size of the treated bacteria shifted to the right, to ~3 × 104 forward side scatter (FSC), about 0.5-fold higher than the untreated cells. Measurement of the ROS showed that the intracellular fluorescence of the 90-s plasma-treated cells led to significant fluorescence formation of 32 relative fluorescence units (RFU)/cell (9 × 104 fold, compared to the nontreated cells). This study showed that cold plasma is a useful method for A. tumefaciens eradication. The eradication mechanism involves ROS generation, membrane permeability, and changes in cell size.
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Affiliation(s)
- Yulia Lazra
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel; (Y.L.); (B.G.); (I.D.A.); (E.E.)
| | - Bharath Gandu
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel; (Y.L.); (B.G.); (I.D.A.); (E.E.)
- Department of Environmental Studies, University of Delhi, New Delhi 110007, India
| | - Irina Dubrovin Amar
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel; (Y.L.); (B.G.); (I.D.A.); (E.E.)
| | - Efrat Emanuel
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel; (Y.L.); (B.G.); (I.D.A.); (E.E.)
| | - Rivka Cahan
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel; (Y.L.); (B.G.); (I.D.A.); (E.E.)
- Correspondence: ; Tel.: +972-54-774-0293
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22
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Castellano-Hinojosa A, Correa-Galeote D, Ramírez-Bahena MH, Tortosa G, González-López J, Bedmar EJ, Peix Á. Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870578 DOI: 10.1099/ijsem.0.005120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to 'A. deltaense' YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium. Whole genome average nucleotide identity and digital DNA-DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10-42 °C, pH 5.0-10.0 and with 0.0-0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium, for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain.,Department of Microbiology, Faculty of Pharmacy, University of Granada. Campus Cartuja, 18071-Granada, Spain
| | - David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | | | - Germán Tortosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | - Jesús González-López
- Department of Microbiology, Faculty of Pharmacy, University of Granada. Campus Cartuja, 18071-Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
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23
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Roushan MR, Shao S, Poledri I, Hooykaas PJJ, van Heusden GPH. Increased Agrobacterium-mediated transformation of Saccharomyces cerevisiae after deletion of the yeast ADA2 gene. Lett Appl Microbiol 2021; 74:228-237. [PMID: 34816457 PMCID: PMC9299121 DOI: 10.1111/lam.13605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/23/2022]
Abstract
Agrobacterium tumefaciens is the causative agent of crown gall disease and is widely used as a vector to create transgenic plants. Under laboratory conditions, the yeast Saccharomyces cerevisiae and other yeasts and fungi can also be transformed, and Agrobacterium-mediated transformation (AMT) is now considered the method of choice for genetic transformation of many fungi. Unlike plants, in S. cerevisiae, T-DNA is integrated preferentially by homologous recombination and integration by non-homologous recombination is very inefficient. Here we report that upon deletion of ADA2, encoding a component of the ADA and SAGA transcriptional adaptor/histone acetyltransferase complexes, the efficiency of AMT significantly increased regardless of whether integration of T-DNA was mediated by homologous or non-homologous recombination. This correlates with an increase in double-strand DNA breaks, the putative entry sites for T-DNA, in the genome of the ada2Δ deletion mutant, as visualized by the number of Rad52-GFP foci. Our observations may be useful to enhance the transformation of species that are difficult to transform.
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Affiliation(s)
- M R Roushan
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - S Shao
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - I Poledri
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - P J J Hooykaas
- Institute of Biology, Leiden University, Leiden, The Netherlands
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24
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Kaur M, Manchanda P, Kalia A, Ahmed FK, Nepovimova E, Kuca K, Abd-Elsalam KA. Agroinfiltration Mediated Scalable Transient Gene Expression in Genome Edited Crop Plants. Int J Mol Sci 2021; 22:10882. [PMID: 34639221 PMCID: PMC8509792 DOI: 10.3390/ijms221910882] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 02/07/2023] Open
Abstract
Agrobacterium-mediated transformation is one of the most commonly used genetic transformation method that involves transfer of foreign genes into target plants. Agroinfiltration, an Agrobacterium-based transient approach and the breakthrough discovery of CRISPR/Cas9 holds trending stature to perform targeted and efficient genome editing (GE). The predominant feature of agroinfiltration is the abolishment of Transfer-DNA (T-DNA) integration event to ensure fewer biosafety and regulatory issues besides showcasing the capability to perform transcription and translation efficiently, hence providing a large picture through pilot-scale experiment via transient approach. The direct delivery of recombinant agrobacteria through this approach carrying CRISPR/Cas cassette to knockout the expression of the target gene in the intercellular tissue spaces by physical or vacuum infiltration can simplify the targeted site modification. This review aims to provide information on Agrobacterium-mediated transformation and implementation of agroinfiltration with GE to widen the horizon of targeted genome editing before a stable genome editing approach. This will ease the screening of numerous functions of genes in different plant species with wider applicability in future.
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Affiliation(s)
- Maninder Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Farah K. Ahmed
- Biotechnology English Program, Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital Hradec Kralove, 50005 Hradec Kralove, Czech Republic
| | - Kamel A. Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center (ARC), 9-Gamaa St., Giza 12619, Egypt;
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25
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Qian Y, Kong W, Lu T. Precise and reliable control of gene expression in Agrobacterium tumefaciens. Biotechnol Bioeng 2021; 118:3962-3972. [PMID: 34180537 DOI: 10.1002/bit.27872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Agrobacterium tumefaciens is a soil-borne bacterium that is known for its DNA delivery ability and widely exploited for plant transformation. Despite continued interest in improving the utility of the organism, the lack of well-characterized engineering tools limits the realization of its full potential. Here, we present a synthetic biology toolkit that enables precise and effective control of gene expression in A. tumefaciens. We constructed and characterized six inducible expression systems. Then, we optimized the one regulated by cumic acid through amplifier introduction and promoter engineering and evaluated its 15 cognate promoters. To establish fine-tunability, we constructed a series of spacers and a promoter library to systematically modulate both translational and transcriptional rates. We finally demonstrated the application of the tools by co-expressing genes with altered expression levels using a single signal. This study provides precise expression tools for A. tumefaciens, facilitating rational engineering of the bacterium for advanced plant biotechnological applications.
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Affiliation(s)
- Yuanchao Qian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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26
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Agrobacterium tumefaciens-Mediated Nuclear Transformation of a Biotechnologically Important Microalga- Euglena gracilis. Int J Mol Sci 2021; 22:ijms22126299. [PMID: 34208268 PMCID: PMC8230907 DOI: 10.3390/ijms22126299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/30/2022] Open
Abstract
Euglena gracilis (E. gracilis) is an attractive organism due to its evolutionary history and substantial potential to produce biochemicals of commercial importance. This study describes the establishment of an optimized protocol for the genetic transformation of E. gracilis mediated by Agrobacterium (A. tumefaciens). E. gracilis was found to be highly sensitive to hygromycin and zeocin, thus offering a set of resistance marker genes for the selection of transformants. A. tumefaciens-mediated transformation (ATMT) yielded hygromycin-resistant cells. However, hygromycin-resistant cells hosting the gus gene (encoding β-glucuronidase (GUS)) were found to be GUS-negative, indicating that the gus gene had explicitly been silenced. To circumvent transgene silencing, GUS was expressed from the nuclear genome as transcriptional fusions with the hygromycin resistance gene (hptII) (encoding hygromycin phosphotransferase II) with the foot and mouth disease virus (FMDV)-derived 2A self-cleaving sequence placed between the coding sequences. ATMT of Euglena with the hptII-2A–gus gene yielded hygromycin-resistant, GUS-positive cells. The transformation was verified by PCR amplification of the T-DNA region genes, determination of GUS activity, and indirect immunofluorescence assays. Cocultivation factors optimization revealed that a higher number of transformants was obtained when A. tumefaciens LBA4404 (A600 = 1.0) and E. gracilis (A750 = 2.0) cultures were cocultured for 48 h at 19 °C in an organic medium (pH 6.5) containing 50 µM acetosyringone. Transformation efficiency of 8.26 ± 4.9% was achieved under the optimized cocultivation parameters. The molecular toolkits and method presented here can be used to bioengineer E. gracilis for producing high-value products and fundamental studies.
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27
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Manera K, Kamal F, Burkinshaw B, Dong TG. Essential functions of chaperones and adaptors of protein secretion systems in Gram-negative bacteria. FEBS J 2021; 289:4704-4717. [PMID: 34092034 DOI: 10.1111/febs.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/18/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023]
Abstract
Equipped with a plethora of secreted toxic effectors, protein secretion systems are essential for bacteria to interact with and manipulate their neighboring environment to survive in host microbiota and other highly competitive communities. While effectors have received spotlight attention in secretion system studies, many require accessory chaperone and adaptor proteins for proper folding/unfolding and stability throughout the secretion process. Here, we review the functions of chaperones and adaptors of three protein secretions systems, type 3 secretion system (T3SS), type 4 secretion system (T4SS), and type 6 secretion system (T6SS), which are employed by many Gram-negative bacterial pathogens to deliver toxins to bacterial, plant, and mammalian host cells through direct contact. Since chaperone and adaptor functions of the T3SS and the T4SS are relatively well studied, we discuss in detail the methods of chaperone-facilitated effector secretion by the T6SS and highlight commonalities between the effector chaperone/adaptor proteins of these diverse secretion systems. While the chaperones and adaptors are generally referred to as accessory proteins as they are not directly involved in toxicities to target cells, they are nonetheless vital for the biological functions of the secretion systems. Future research on biochemical and structural properties of these chaperones will not only elucidate the mechanisms of chaperone-effector binding and release process but also facilitate custom design of cargo effectors to be translocated by these widespread secretion systems for biotechnological applications.
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Affiliation(s)
- Kevin Manera
- Department of Ecosystem and Public Health, University of Calgary, Canada
| | - Fatima Kamal
- Department of Ecosystem and Public Health, University of Calgary, Canada
| | | | - Tao G Dong
- Department of Ecosystem and Public Health, University of Calgary, Canada.,State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
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28
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Gutiérrez S, Lauersen KJ. Gene Delivery Technologies with Applications in Microalgal Genetic Engineering. BIOLOGY 2021; 10:265. [PMID: 33810286 PMCID: PMC8067306 DOI: 10.3390/biology10040265] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/28/2022]
Abstract
Microalgae and cyanobacteria are photosynthetic microbes that can be grown with the simple inputs of water, carbon dioxide, (sun)light, and trace elements. Their engineering holds the promise of tailored bio-molecule production using sustainable, environmentally friendly waste carbon inputs. Although algal engineering examples are beginning to show maturity, severe limitations remain in the transformation of multigene expression cassettes into model species and DNA delivery into non-model hosts. This review highlights common and emerging DNA delivery methods used for other organisms that may find future applications in algal engineering.
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Affiliation(s)
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
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29
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Li X, Yang Q, Peng L, Tu H, Lee LY, Gelvin SB, Pan SQ. Agrobacterium-delivered VirE2 interacts with host nucleoporin CG1 to facilitate the nuclear import of VirE2-coated T complex. Proc Natl Acad Sci U S A 2020; 117:26389-26397. [PMID: 33020260 PMCID: PMC7584991 DOI: 10.1073/pnas.2009645117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Agrobacterium tumefaciens is the causal agent of crown gall disease. The bacterium is capable of transferring a segment of single-stranded DNA (ssDNA) into recipient cells during the transformation process, and it has been widely used as a genetic modification tool for plants and nonplant organisms. Transferred DNA (T-DNA) has been proposed to be escorted by two virulence proteins, VirD2 and VirE2, as a nucleoprotein complex (T-complex) that targets the host nucleus. However, it is not clear how such a proposed large DNA-protein complex is delivered through the host nuclear pore in a natural setting. Here, we studied the natural nuclear import of the Agrobacterium-delivered ssDNA-binding protein VirE2 inside plant cells by using a split-GFP approach with a newly constructed T-DNA-free strain. Our results demonstrate that VirE2 is targeted into the host nucleus in a VirD2- and T-DNA-dependent manner. In contrast with VirD2 that binds to plant importin α for nuclear import, VirE2 directly interacts with the host nuclear pore complex component nucleoporin CG1 to facilitate its nuclear uptake and the transformation process. Our data suggest a cooperative nuclear import model in which T-DNA is guided to the host nuclear pore by VirD2 and passes through the pore with the assistance of interactions between VirE2 and host nucleoporin CG1. We hypothesize that this large linear nucleoprotein complex (T-complex) is targeted to the nucleus by a "head" guide from the VirD2-importin interaction and into the nucleus by a lateral assistance from the VirE2-nucleoporin interaction.
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Affiliation(s)
- Xiaoyang Li
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Qinghua Yang
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Ling Peng
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Haitao Tu
- School of Stomatology and Medicine, Foshan University, Foshan 528000, China
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Shen Q Pan
- Department of Biological Sciences, National University of Singapore, Singapore 117543;
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30
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F-Box Gene D5RF Is Regulated by Agrobacterium Virulence Protein VirD5 and Essential for Agrobacterium-Mediated Plant Transformation. Int J Mol Sci 2020; 21:ijms21186731. [PMID: 32937889 PMCID: PMC7555846 DOI: 10.3390/ijms21186731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/16/2022] Open
Abstract
We previously reported that the Agrobacterium virulence protein VirD5 possesses transcriptional activation activity, binds to a specific DNA element D5RE, and is required for Agrobacterium-mediated stable transformation, but not for transient transformation. However, direct evidence for a role of VirD5 in plant transcriptional regulation has been lacking. In this study, we found that the Arabidopsis gene D5RF (coding for VirD5 response F-box protein, At3G49480) is regulated by VirD5. D5RF has two alternative transcripts of 930 bp and 1594 bp that encode F-box proteins of 309 and 449 amino acids, designated as D5RF.1 and D5RF.2, respectively. D5RF.2 has a N-terminal extension of 140 amino acids compared to D5RF.1, and both of them are located in the plant cell nucleus. The promoter of the D5RF.1 contains two D5RE elements and can be activated by VirD5. The expression of D5RF is downregulated when the host plant is infected with virD5 deleted Agrobacterium. Similar to VirD5, D5RF also affects the stable but not transient transformation efficiency of Agrobacterium. Some pathogen-responsive genes are downregulated in the d5rf mutant. In conclusion, this study further confirmed Agrobacterium VirD5 as the plant transcription activator and identified Arabidopsis thalianaD5RF.1 as the first target gene of VirD5 in regulation.
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Elfahmi E, Cahyani FM, Kristianti T, Suhandono S. Transformation of Amorphadiene Synthase and Antisilencing P19 Genes into Artemisia annua L. and its Effect on Antimalarial Artemisinin Production. Adv Pharm Bull 2020; 10:464-471. [PMID: 32665907 PMCID: PMC7335994 DOI: 10.34172/apb.2020.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/12/2020] [Accepted: 01/27/2020] [Indexed: 11/09/2022] Open
Abstract
Purpose: The low content of artemisinin related to the biosynthetic pathway is influenced by the role of certain enzymes in the formation of artemisinin. The regulation of genes involved in artemisinin biosynthesis through genetic engineering is a choice to enhance the content. This research aims to transform ads and p19 gene as an antisilencing into Artemisia annua and to see their effects on artemisinin production. Methods: The presence of p19 and ads genes was confirmed through polymerase chain reaction (PCR) products and sequencing analysis. The plasmids, which contain ads and/or p19 genes, were transformed into Agrobacterium tumefaciens, and then inserted into leaves and hairy roots of A. annua by vacuum and syringe infiltration methods. The successful transformation was checked through the GUS histochemical test and the PCR analysis. Artemisinin levels were measured using HPLC. Results: The percentages of the blue area on leaves by using vacuum and syringe infiltration method and on hairy roots were up to 98, 92.55%, and 99.00% respectively. The ads-p19 sample contained a higher level of artemisinin (0.18%) compared to other samples. Transformed hairy root with co-transformation of ads-p19 contained 0.095% artemisinin, where no artemisinin was found in the control hairy root. The transformation of ads and p19 genes into A. annua plant has been successfully done and could enhance the artemisinin content on the transformed leaves with ads-p19 up to 2.57 folds compared to the untransformed leaves, while for p19, cotransformed and ads were up to 2.25, 1.29, and 1.14 folds respectively. Conclusion: Antisilencing p19 gene could enhance the transformation efficiency of ads and artemisinin level in A. annua.
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Affiliation(s)
- Elfahmi Elfahmi
- School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia.,Biosciences and Biotechnology Research Center, Bandung Institute of Technology, Bandung, Indonesia
| | | | | | - Sony Suhandono
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia
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Delamuta JRM, Scherer AJ, Ribeiro RA, Hungria M. Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. Int J Syst Evol Microbiol 2020; 70:4233-4244. [PMID: 32568030 DOI: 10.1099/ijsem.0.004278] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Anderson José Scherer
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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Li X, Zhu T, Tu H, Pan SQ. Agrobacterium VirE3 Uses Its Two Tandem Domains at the C-Terminus to Retain Its Companion VirE2 on the Cytoplasmic Side of the Host Plasma Membrane. FRONTIERS IN PLANT SCIENCE 2020; 11:464. [PMID: 32373148 PMCID: PMC7187210 DOI: 10.3389/fpls.2020.00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/30/2020] [Indexed: 05/30/2023]
Abstract
Agrobacterium tumefaciens is the causal agent of crown gall disease in nature; in the laboratory the bacterium is widely used for plant genetic modification. The bacterium delivers a single-stranded transferred DNA (T-DNA) and a group of crucial virulence proteins into host cells. A putative T-complex is formed inside host cells that is composed of T-DNA and virulence proteins VirD2 and VirE2, which protect the foreign DNA from degradation and guide its way into the host nucleus. However, little is known about how the T-complex is assembled inside host cells. We combined the split-GFP and split-sfCherry labeling systems to study the interaction of Agrobacterium-delivered VirE2 and VirE3 in host cells. Our results indicated that VirE2 co-localized with VirE3 on the cytoplasmic side of the host cellular membrane upon the delivery. We identified and characterized two tandem domains at the VirE3 C-terminus that interacted with VirE2 in vitro. Deletion of these two domains abolished the VirE2 accumulation on the host plasma membrane and affected the transformation. Furthermore, the two VirE2-interacting domains of VirE3 exhibited different affinities with VirE2. Collectively, this study demonstrates that the anchorage protein VirE3 uses the two tandem VirE2-interacting domains to facilitate VirE2 protection for T-DNA at the cytoplasmic side of the host cell entrance.
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Affiliation(s)
- Xiaoyang Li
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Tingting Zhu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Haitao Tu
- School of Stomatology and Medicine, Foshan Institute of Molecular Bio-Engineering, Foshan University, Foshan, China
| | - Shen Q. Pan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Dawe RK. Charting the path to fully synthetic plant chromosomes. Exp Cell Res 2020; 390:111951. [PMID: 32151492 DOI: 10.1016/j.yexcr.2020.111951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.
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Affiliation(s)
- R Kelly Dawe
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Rukmana TI, Moran G, Méallet-Renault R, Ohtani M, Demura T, Yasukuni R, Hosokawa Y. Enzyme-Assisted Photoinjection of Megadalton Molecules into Intact Plant Cells Using Femtosecond Laser Amplifier. Sci Rep 2019; 9:17530. [PMID: 31772312 PMCID: PMC6879609 DOI: 10.1038/s41598-019-54124-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
Femtosecond laser photoporation has become a popular method to deliver various kinds of molecules such as genes, proteins, and fluorescent dyes into single mammalian cells. However, this method is not easily applied to plant cells because their cell wall and turgor pressure prevent the delivery, especially for larger molecules than the mesh size of the cell wall. This work is the first demonstration of the efficient photoinjection of megadalton molecules into a cytoplasm of an intact single plant cell by employing a femtosecond laser amplifier under moderate enzyme treatment conditions. The intense femtosecond laser pulse effectively formed a pore on the cell wall and membrane of Tobacco BY-2, and 2 MDa dextran molecules were introduced through the pore. Along with the pore formation, induced mechanical tensile stresses on BY-2 cells were considered to increase permeability of the cell membrane and enhance the uptake of large molecules. Moreover, the moderate enzyme treatment partially degraded the cell wall thereby facilitating the increase of the molecular introduction efficiency.
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Affiliation(s)
- Taufiq Indra Rukmana
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Gabriela Moran
- Université Paris-Sud, Université Paris-Saclay, Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, F-91405, Orsay, France
| | - Rachel Méallet-Renault
- Université Paris-Sud, Université Paris-Saclay, Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, F-91405, Orsay, France
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Ryohei Yasukuni
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan.
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
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Yu G, Wang J, Miao L, Xi M, Wang Q, Wang K. Optimization of Mature Embryo-Based Tissue Culture and Agrobacterium-Mediated Transformation in Model Grass Brachypodium distachyon. Int J Mol Sci 2019; 20:E5448. [PMID: 31683725 PMCID: PMC6862288 DOI: 10.3390/ijms20215448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Agrobacterium-mediated genetic transformation is well established in the model grass Brachypodium distachyon. However, most protocols employ immature embryos because of their better regenerative capacity. A major problem associated with the immature embryo system is that they are available only during a limited time window of growing plants. In this study, we have developed an optimized Agrobacterium-mediated genetic transformation protocol that utilizes mature embryos. We have adopted seed shearing and photoautotrophic rooting (PR) in callus induction and root regeneration, respectively, with evident significant improvement in these aspects. We have also revealed that the newly developed chemical inducer Fipexide (FPX) had the ability to induce callus, shoots, and roots. By comparison, we have demonstrated that FPX shows higher efficiency in shoot generation than other frequently used chemicals in our mature embryo-based system. In addition, we demonstrated that the age of embryogenetic callus severely affects the transformation efficiency (TE), with the seven-week-old embryogenetic callus having the highest TE reaching 52.6%, which is comparable with that in immature embryo transformation. The new methodologies reported here will advance the development and utilization of Brachypodium as a new model system for grass genomics.
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Affiliation(s)
- Guangrun Yu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Jianyong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China/Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Li Miao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China/Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Qiongli Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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37
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Yarra R, Jin L, Zhao Z, Cao H. Progress in Tissue Culture and Genetic Transformation of Oil Palm: An Overview. Int J Mol Sci 2019; 20:E5353. [PMID: 31661801 PMCID: PMC6862151 DOI: 10.3390/ijms20215353] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 11/24/2022] Open
Abstract
Oil palm (Elaeis guineensis, Jacq.) is a prominent vegetable-oil-yielding crop. Cultivating high-yielding oil palm with improved traits is a pre-requisite to meet the increasing demands of palm oil consumption. However, tissue culture and biotechnological approaches can resolve these concerns. Over the past three decades, significant research has been carried out to develop tissue culture and genetic transformation protocols for oil palm. Somatic embryogenesis is an efficient platform for the micropropagation of oil palm on a large scale. In addition, various genetic transformation techniques, including microprojectile bombardment, Agrobacterium tumefaciens mediated, Polyethylene glycol mediated mediated, and DNA microinjection, have been developed by optimizing various parameters for the efficient genetic transformation of oil palm. This review mainly emphasizes the methods established for in vitro propagation and genetic transformation of oil palm. Finally, we propose the application of the genome editing tool CRISPR/Cas9 to improve the various traits in this oil yielding crop.
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Affiliation(s)
- Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| | - Zhihao Zhao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
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Chandrasekaran M, Lee JM, Ye BM, Jung SM, Kim J, Kim JW, Chun SC. Isolation and Characterization of Avirulent and Virulent Strains of Agrobacterium tumefaciens from Rose Crown Gall in Selected Regions of South Korea. PLANTS (BASEL, SWITZERLAND) 2019; 8:E452. [PMID: 31731525 PMCID: PMC6918265 DOI: 10.3390/plants8110452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 01/22/2023]
Abstract
Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease in various hosts across kingdoms. In the present study, five regions (Wonju, Jincheon, Taean, Suncheon, and Kimhae) of South Korea were chosen to isolate A. tumefaciens strains on roses and assess their opine metabolism (agrocinopine, nopaline, and octopine) genes based on PCR amplification. These isolated strains were confirmed as Agrobacterium using morphological, biochemical, and 16S rDNA analyses; and pathogenicity tests, including the growth characteristics of the white colony appearance on ammonium sulfate glucose minimal media, enzyme activities, 16S rDNA sequence alignment, and pathogenicity on tomato (Solanum lycopersicum). Carbon utilization, biofilm formation, tumorigenicity, and motility assays were performed to demarcate opine metabolism genes. Of 87 isolates, 18 pathogenic isolates were affirmative for having opine plasmid genes. Most of these isolates showed the presence of an agrocinopine type of carbon utilization. Two isolates showed nopaline types. However, none of these isolates showed octopine metabolic genes. The objectives of the present study were to isolate and confirm virulent strains from rose crown galls grown in the different regions of Korea and characterize their physiology and opine types. This is the first report to describe the absence of the octopine type inciting the crown gall disease of rose in South Korea.
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Affiliation(s)
- Murugesan Chandrasekaran
- Department of Food Science and Biotechnology, Sejong University, Gwangjin-gu, Seoul 05006, Korea;
| | - Jong Moon Lee
- Department of Environmental Health Science, Konkuk University, Gwangjin-gu, Seoul-143 701, Korea; (J.M.L.); (B.-M.Y.); (S.M.J.)
| | - Bee-Moon Ye
- Department of Environmental Health Science, Konkuk University, Gwangjin-gu, Seoul-143 701, Korea; (J.M.L.); (B.-M.Y.); (S.M.J.)
| | - So Mang Jung
- Department of Environmental Health Science, Konkuk University, Gwangjin-gu, Seoul-143 701, Korea; (J.M.L.); (B.-M.Y.); (S.M.J.)
| | - Jinwoo Kim
- Institute of Agriculture & Life Science and Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Jin-Won Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Korea;
| | - Se Chul Chun
- Department of Environmental Health Science, Konkuk University, Gwangjin-gu, Seoul-143 701, Korea; (J.M.L.); (B.-M.Y.); (S.M.J.)
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Zhao Q, Du Y, Wang H, Rogers HJ, Yu C, Liu W, Zhao M, Xie F. 5-Azacytidine promotes shoot regeneration during Agrobacterium-mediated soybean transformation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:40-50. [PMID: 31128562 DOI: 10.1016/j.plaphy.2019.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/07/2019] [Accepted: 05/14/2019] [Indexed: 05/27/2023]
Abstract
Agrobacterium-mediated soybean transformation has been greatly improved in recent years, however the transformation efficiency is still low and highly genotype-dependent when compared to other species. Here, we characterized seventeen soybean genotypes based on their genetic transformation efficiencies, i.e., high and low, during Agrobacterium-mediated transformation. To reveal the molecular basis of this transformation difference, we constructed a highly efficient transient transgene expression system using soybean cotyledon protoplasts and then assess the methylation levels of promoter and coding regions of an EYFP (enhanced yellow fluorescent protein) gene introduced into the protoplast cultures of various soybean genotypes using BSP (bisulfite sequencing PCR). Increased methylation was found to be associated with the considerably decreased transfection efficiency (as percentage of EYFP fluorescent protoplasts) in low-efficacy genotypes as compared with those in high-efficacy on three DAT (day after transfection). 5-Azacytidine (5-Azac), a demethylating reagent commonly applied in epigenetic researches, significantly improved the transient transfection efficiency and transgene expression level in low-efficiency genotypes. Furthermore, the shoot regeneration efficiency in low-efficiency genotypes was substantially increased by 5-Azac treatment in an Agrobacterium-mediated soybean transformation system. Taken together, we concluded that lower methylation level in transgene contributed to enhanced shoot regeneration in Agrobacterium-mediated soybean transformation.
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Affiliation(s)
- Qiang Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Yanli Du
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Hetong Wang
- College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Hilary J Rogers
- Cardiff University, School of Biosciences, Cardiff, CF10 3TL, UK.
| | - Cuimei Yu
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
| | - Mingzhe Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Futi Xie
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
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Zuniga-Soto E, Fitzpatrick DA, Doohan FM, Mullins E. Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. Sci Rep 2019; 9:10344. [PMID: 31316079 PMCID: PMC6637203 DOI: 10.1038/s41598-019-44648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
The ability to engineer plant genomes has been primarily driven by the soil bacterium Agrobacterium tumefaciens but recently the potential of alternative rhizobia such as Rhizobium etli and Ensifer adhaerens OV14, the latter of which supports Ensifer Mediated Transformation (EMT) has been reported. Surprisingly, a knowledge deficit exists in regards to understanding the whole genome processes underway in plant transforming bacteria, irrespective of the species. To begin to address the issue, we undertook a temporal RNAseq-based profiling study of E. adhaerens OV14 in the presence/absence of Arabidopsis thaliana tissues. Following co-cultivation with root tissues, 2333 differentially expressed genes (DEGs) were noted. Meta-analysis of the RNAseq data sets identified a clear shift from plasmid-derived gene expression to chromosomal-based transcription within the early stages of bacterium-plant co-cultivation. During this time, the number of differentially expressed prokaryotic genes increased steadily out to 7 days co-cultivation, a time at which optimum rates of transformation were observed. Gene ontology evaluations indicated a role for both chromosomal and plasmid-based gene families linked specifically with quorum sensing, flagellin production and biofilm formation in the process of EMT. Transcriptional evaluation of vir genes, housed on the pCAMBIA 5105 plasmid in E. adhaerens OV14 confirmed the ability of E. adhaerens OV14 to perceive and activate its transcriptome in response to the presence of 200 µM of acetosyringone. Significantly, this is the first study to characterise the whole transcriptomic response of a plant engineering bacterium in the presence of plant tissues and provides a novel insight into prokaryotic genetic processes that support T-DNA transfer.
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Affiliation(s)
- Evelyn Zuniga-Soto
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Fitzpatrick
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Fiona M Doohan
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland.
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Khemthong S, Nuonming P, Dokpikul T, Sukchawalit R, Mongkolsuk S. Regulation and function of the flavonoid-inducible efflux system, emrR-emrAB, in Agrobacterium tumefaciens C58. Appl Microbiol Biotechnol 2019; 103:5763-5780. [PMID: 31127355 DOI: 10.1007/s00253-019-09899-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 11/29/2022]
Abstract
The expression of the Agrobacterium tumefaciens emrAB operon, which encodes a membrane fusion protein and an inner membrane protein, is inducible by various flavonoids, including apigenin, genistein, luteolin, naringenin, and quercetin. Among these flavonoids, quercetin is the best inducer, followed by genistein. The emrR gene is divergently transcribed from the emrAB operon. The EmrR protein, which belongs to the TetR transcriptional regulator family, negatively regulates the expression of emrAB and of itself. Electrophoretic mobility shift assays and DNase I footprinting showed that EmrR binds directly at two EmrR-binding sites in the emrR-emrAB intergenic region and that quercetin inhibits the DNA-binding activity of EmrR. Promoter-lacZ fusion analyses and 5' rapid amplification of cDNA ends were performed to map the emrR and emrAB promoters. Compared with the wild-type strain, the emrA mutant strain exhibited similar levels of resistance to the tested antibiotics. In contrast, disruption of emrR conferred protection against nalidixic acid and novobiocin, but it rendered A. tumefaciens sensitive to tetracycline and erythromycin. The emrR mutation also destabilized the outer membrane of A. tumefaciens, resulting in increased sensitivity to SDS and low pH. These findings demonstrate that proper regulation of emrR-emrAB is required for free-living A. tumefaciens to survive in deleterious environments in which toxic compounds are present. Nonetheless, A. tumefaciens strains that lack emrR or emrA still have the ability to cause tumors when infecting Nicotiana benthamiana plants.
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Affiliation(s)
- Sasimaporn Khemthong
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Puttamas Nuonming
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Thanittra Dokpikul
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand.
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand.
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
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El Sarraf N, Gurel F, Tufan F, McGuffin LJ. Characterisation of HvVIP1 and expression profile analysis of stress response regulators in barley under Agrobacterium and Fusarium infections. PLoS One 2019; 14:e0218120. [PMID: 31199821 PMCID: PMC6570034 DOI: 10.1371/journal.pone.0218120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/27/2019] [Indexed: 01/23/2023] Open
Abstract
Arabidopsis thaliana's VirE2-Interacting Protein 1 (VIP1) interacts with Agrobacterium tumefaciens VirE2 protein and regulates stress responses and plant immunity signaling occurring downstream of the Mitogen-Activated Protein Kinase (MPK3) signal transduction pathway. In this study, a full-length cDNA of 972bp encoding HvVIP1 was obtained from barley (Hordeum vulgare L.) leaves. A corresponding 323 amino acid poly-peptide was shown to carry the conserved bZIP (Basic Leucine Zipper) domain within its 157th and 223rd amino acid residue. 13 non-synonymous SNPs were spotted within the HvVIP1 bZIP domain sequence when compared with AtVIP1. Moreover, minor differences in the bZIP domain locations and lengths were noted when comparing Arabidopsis thaliana and Hordeum vulgare VIP1 proteins through the 3D models, structural domain predictions and disorder prediction profiling. The expression of HvVIP1 was stable in barley tissues infected by pathogen (whether Agrobacterium tumefaciens or Fusarium culmorum), but was induced at specific time points. We found a strong correlation between the transcript accumulation of HvVIP1 and barley PR- genes HvPR1, HvPR4 and HvPR10, but not with HvPR3 and HvPR5, probably due to low induction of those particular genes. In addition, a gene encoding for a member of the barley MAPK family, HvMPK1, showed significantly higher expression after pathogenic infection of barley cells. Collectively, our results might suggest that early expression of PR genes upon infection in barley cells play a pivotal role in the Agrobacterium-resistance of this plant.
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Affiliation(s)
- Nadia El Sarraf
- Department of Agriculture and Food Engineering, University of Balamand, Koura, Lebanon
- * E-mail:
| | - Filiz Gurel
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Feyza Tufan
- Institute of Science, Program of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Liam J. McGuffin
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, United Kingdom
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Wang G, Zhao J, Wang X, Wang T, Zhuang Y, Chu J, Zhang S, Noorman HJ. Quantitative metabolomics and metabolic flux analysis reveal impact of altered trehalose metabolism on metabolic phenotypes of Penicillium chrysogenum in aerobic glucose-limited chemostats. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Sgro GG, Oka GU, Souza DP, Cenens W, Bayer-Santos E, Matsuyama BY, Bueno NF, dos Santos TR, Alvarez-Martinez CE, Salinas RK, Farah CS. Bacteria-Killing Type IV Secretion Systems. Front Microbiol 2019; 10:1078. [PMID: 31164878 PMCID: PMC6536674 DOI: 10.3389/fmicb.2019.01078] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria have been constantly competing for nutrients and space for billions of years. During this time, they have evolved many different molecular mechanisms by which to secrete proteinaceous effectors in order to manipulate and often kill rival bacterial and eukaryotic cells. These processes often employ large multimeric transmembrane nanomachines that have been classified as types I-IX secretion systems. One of the most evolutionarily versatile are the Type IV secretion systems (T4SSs), which have been shown to be able to secrete macromolecules directly into both eukaryotic and prokaryotic cells. Until recently, examples of T4SS-mediated macromolecule transfer from one bacterium to another was restricted to protein-DNA complexes during bacterial conjugation. This view changed when it was shown by our group that many Xanthomonas species carry a T4SS that is specialized to transfer toxic bacterial effectors into rival bacterial cells, resulting in cell death. This review will focus on this special subtype of T4SS by describing its distinguishing features, similar systems in other proteobacterial genomes, and the nature of the effectors secreted by these systems and their cognate inhibitors.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel U. Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Diorge P. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Y. Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia F. Bueno
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, University of Campinas (UNICAMP), Campinas, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Mohammed S, Samad AA, Rahmat Z. Agrobacterium-Mediated Transformation of Rice: Constraints and Possible Solutions. RICE SCIENCE 2019; 26:133-146. [DOI: 10.1016/j.rsci.2019.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Gang H, Liu G, Zhang M, Zhao Y, Jiang J, Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant. BMC Genomics 2019; 20:311. [PMID: 31014254 PMCID: PMC6480916 DOI: 10.1186/s12864-019-5636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/24/2019] [Indexed: 11/29/2022] Open
Abstract
Background Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch (Betula platyphylla × B. pendula) T-DNA mutant yl. Results We performed PacBio genome resequencing for yl and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and cause chromosomal translocation. We also found that these T-DNA were connected into tandem fragment regardless of direction before integrating into plant genome. In addition, the integration of T-DNA in yl genome also caused several chromosomal fragments deletion. We then summarized three cases for T-DNA integration model in the yl genome. (1) A T-DNA fragment is linked to the two ends of a double-stranded break (DSB); (2) Only one end of a T-DNA fragment is linked to a DSB; (3) A T-DNA fragment is linked to the ends of different DSBs. All the observations in the yl genome supported the DSB repair model. Conclusions In this study, we showed a comprehensive genome analysis of a T-DNA mutant and provide a new insight into T-DNA integration in plants. These findings would be helpful for the analysis of T-DNA mutants with special phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5636-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Manman Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Lee K, Eggenberger AL, Banakar R, McCaw ME, Zhu H, Main M, Kang M, Gelvin SB, Wang K. CRISPR/Cas9-mediated targeted T-DNA integration in rice. PLANT MOLECULAR BIOLOGY 2019; 99:317-328. [PMID: 30645710 DOI: 10.1007/s11103-018-00819-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 12/27/2018] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Combining with a CRISPR/Cas9 system, Agrobacterium-mediated transformation can lead to precise targeted T-DNA integration in the rice genome. Agrobacterium-mediated T-DNA integration into the plant genomes is random, which often causes variable transgene expression and insertional mutagenesis. Because T-DNA preferentially integrates into double-strand DNA breaks, we adapted a CRISPR/Cas9 system to demonstrate that targeted T-DNA integration can be achieved in the rice genome. Using a standard Agrobacterium binary vector, we constructed a T-DNA that contains a CRISPR/Cas9 system using SpCas9 and a gRNA targeting the exon of the rice AP2 domain-containing protein gene Os01g04020. The T-DNA also carried a red fluorescent protein and a hygromycin resistance (hptII) gene. One version of the vector had hptII expression driven by an OsAct2 promoter. In an effort to detect targeted T-DNA insertion events, we built another T-DNA with a promoterless hptII gene adjacent to the T-DNA right border such that integration of T-DNA into the targeted exon sequence in-frame with the hptII gene would allow hptII expression. Our results showed that these constructs could produce targeted T-DNA insertions with frequencies ranging between 4 and 5.3% of transgenic callus events, in addition to generating a high frequency (50-80%) of targeted indel mutations. Sequencing analyses showed that four out of five sequenced T-DNA/gDNA junctions carry a single copy of full-length T-DNA at the target site. Our results indicate that Agrobacterium-mediated transformation combined with a CRISPR/Cas9 system can efficiently generate targeted T-DNA insertions.
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MESH Headings
- Agrobacterium/genetics
- Base Sequence
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems/genetics
- DNA, Bacterial/genetics
- Exons
- Gene Editing
- Gene Expression Regulation, Plant/genetics
- Gene Frequency
- Gene Targeting
- Genes, Plant/genetics
- Genetic Vectors/genetics
- Genome, Plant/genetics
- INDEL Mutation
- Luminescent Proteins/genetics
- Mutagenesis, Insertional/methods
- Oryza/genetics
- Oryza/metabolism
- Plant Proteins/genetics
- Plants, Genetically Modified/genetics
- Promoter Regions, Genetic
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Sequence Analysis
- Red Fluorescent Protein
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Affiliation(s)
- Keunsub Lee
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Alan L Eggenberger
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Raviraj Banakar
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Morgan E McCaw
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Huilan Zhu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Plant Transformation Facility, Iowa State University, Ames, IA, 50011, USA
| | - Marcy Main
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Plant Transformation Facility, Iowa State University, Ames, IA, 50011, USA
| | - Minjeong Kang
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, 50011, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Kan Wang
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA.
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
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Kerpen L, Niccolini L, Licausi F, van Dongen JT, Weits DA. Hypoxic Conditions in Crown Galls Induce Plant Anaerobic Responses That Support Tumor Proliferation. FRONTIERS IN PLANT SCIENCE 2019; 10:56. [PMID: 30804956 PMCID: PMC6371838 DOI: 10.3389/fpls.2019.00056] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/16/2019] [Indexed: 05/21/2023]
Abstract
Agrobacterium tumefaciens infection of wounded plant tissues causes the formation of crown gall tumors. Upon infection, genes encoded on the A. tumefaciens tumor inducing plasmid are integrated in the plant genome to induce the biosynthesis of auxin and cytokinin, leading to uncontrolled cell division. Additional sequences present on the bacterial T-DNA encode for opine biosynthesis genes, which induce the production of opines that act as a unique carbon and nitrogen source for Agrobacterium. Crown galls therefore become a very strong sink for photosynthate. Here we found that the increased metabolic demand in crown galls causes an increase in oxygen consumption rate, which leads to a steep drop in the internal oxygen concentration. Consistent with this, plant hypoxia-responsive genes were found to be significantly upregulated in crown galls compared to uninfected stem tissue. Following this observation, we aimed at understanding whether the low-oxygen response pathway, mediated by group VII ethylene response factor (ERF-VII) transcription factors, plays a role in the development of crown galls. We found that quintuple knock-out mutants of all ERF-VII members, which are incapable of inducing the hypoxic response, show reduced crown gall symptoms. Conversely, mutant genotypes characterized by constitutively high levels of hypoxia-associated transcripts, displayed more severe crown gall symptoms. Based on these results, we concluded that uncontrolled cell proliferation of crown galls established hypoxic conditions, thereby requiring adequate anaerobic responses of the plant tissue to support tumor growth.
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Affiliation(s)
- Lucy Kerpen
- Institute of Biology I, RWTH Aachen University, Aachen, Germany
| | | | - Francesco Licausi
- Department of Biology, University of Pisa, Pisa, Italy
- Scuola Superiore Sant’Anna, Institute of Life Sciences, Pisa, Italy
| | | | - Daan A. Weits
- Institute of Biology I, RWTH Aachen University, Aachen, Germany
- Scuola Superiore Sant’Anna, Institute of Life Sciences, Pisa, Italy
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Sabzehzari M, Naghavi MR. Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants. Gene 2019; 682:13-24. [PMID: 30267812 DOI: 10.1016/j.gene.2018.09.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022]
Abstract
Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.
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Affiliation(s)
- M Sabzehzari
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran
| | - M R Naghavi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran.
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50
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Infection of Embryonic Callus with Agrobacterium Enables High-Speed Transformation of Maize. Int J Mol Sci 2019; 20:ijms20020279. [PMID: 30641963 PMCID: PMC6358778 DOI: 10.3390/ijms20020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/06/2019] [Accepted: 01/06/2019] [Indexed: 11/22/2022] Open
Abstract
Several approaches have recently been adopted to improve Agrobacterium-mediated transformation of maize; however, about eight months of in vitro culture are still required to isolate transgenic plants. Furthermore, genetic transformation of maize depends on immature embryos, which greatly increases costs. Here, we report a method that ensures the competency of an embryogenic callus secondary culture under laboratory conditions for Agrobacterium-mediated transformation. Moreover, pretreatment of the cell wall with a mixed lytic enzyme solution prior to Agrobacterium infection, significantly improved transformation efficiency and stability. Average stable transformation efficiency was approximately 30.39%, with peaks of 94.46%. Expression and phenotypic analysis of the Rsc reporter gene were tested in the T0 generation of transgenic plants. Using this system, we successfully regenerated transgenic maize plantlets within three months of the emergence of the embryogenic callus. Additionally, we reduced somaclonal variation accompanying prolonged culture of maize cells in the dedifferentiated state, thus facilitating the molecular breeding of maize.
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