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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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Del Toro F, Sun H, Robinson C, Jiménez Á, Covielles E, Higuera T, Aguilar E, Tenllado F, Canto T. In planta vs viral expression of HCPro affects its binding of nonplant 21-22 nucleotide small RNAs, but not its preference for 5'-terminal adenines, or its effects on small RNA methylation. THE NEW PHYTOLOGIST 2022; 233:2266-2281. [PMID: 34942019 DOI: 10.1111/nph.17935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Previous studies have found a correlation between the abilities of PVX vector-expressed HCPro variants to bind small RNAs (sRNAs), and to suppress silencing. Moreover, HCPro preferred to bind viral sRNAs of 21-22 nucleotides (nt) containing 5'-terminal adenines. This would require such viral sRNAs to have either different access to the suppressor than those of plant sequences, or different molecular properties. To investigate this preference further, we have used suppressor-competent or suppressor-deficient HCPro variants, expressed from either T-DNAs or potyvirus constructs. Then, the sRNAs generated in plants and associated with the purified HCPro variants were characterized. Marked differences were observed in the ratios of sRNAs of plant vs nonplant origin that bound to suppressor-competent HCPro, depending on the mode of its expression. Regardless of the means of expression, HCPro retained the same preference among the nonplant sRNAs of 21-22 nt for those with 5'-terminal adenines. Relative methylation levels of individual sRNAs were assessed, and the nonplant sRNAs were found to be significantly less methylated in the presence of the suppressor. Targeted binding of sRNAs based on size, 5'-terminal sequence and origin, together with affecting their methylation, could explain how HCPro counteracts silencing.
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Affiliation(s)
- Francisco Del Toro
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Hao Sun
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Carmen Robinson
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Álvaro Jiménez
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Eva Covielles
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Tomás Higuera
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Emmanuel Aguilar
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Francisco Tenllado
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Tomás Canto
- Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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Dormatey R, Sun C, Ali K, Fiaz S, Xu D, Calderón-Urrea A, Bi Z, Zhang J, Bai J. ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review. PeerJ 2021; 9:e11809. [PMID: 34395075 PMCID: PMC8323600 DOI: 10.7717/peerj.11809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/27/2021] [Indexed: 12/14/2022] Open
Abstract
Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes.
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Affiliation(s)
- Richard Dormatey
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Chao Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Kazim Ali
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Derong Xu
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Alejandro Calderón-Urrea
- Department of Biology, College of Science and Mathematics, California State University, Fresno, CA, USA
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Junlian Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Landzhou, China
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Debler JW, Henares BM, Lee RC. Agroinfiltration for transient gene expression and characterisation of fungal pathogen effectors in cool-season grain legume hosts. PLANT CELL REPORTS 2021; 40:805-818. [PMID: 33811500 PMCID: PMC8058004 DOI: 10.1007/s00299-021-02671-y] [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: 07/20/2020] [Accepted: 01/30/2021] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Modified pEAQ-HT-DEST1 vectors were used for agroinfiltration in legumes. We demonstrate protein expression and export in pea, lentil, and faba bean; however, the method for chickpea was not successful. Agroinfiltration is a valuable research method for investigating virulence and avirulence effector proteins from pathogens and pests, where heterologous effector proteins are transiently expressed in plant leaves and hypersensitive necrosis responses and other effector functions can be assessed. Nicotiana benthamiana is widely used for agroinfiltration and the characterisation of broad-spectrum effectors. The method has also been used in other plant species including field pea, but not yet developed for chickpea, lentil, or faba bean. Here, we have modified the pEAQ-HT-DEST1 vector for expression of 6 × histidine-tagged green-fluorescent protein (GFP) and the known necrosis-inducing broad-spectrum effector necrosis and ethylene-inducing peptide (Nep1)-like protein (NLP). Modified pEAQ-based vectors were adapted to encode signal peptide sequences for apoplast targeting of expressed proteins. We used confocal microscopy to assess the level of GFP expression in agroinfiltrated leaves. While at 3 days after infiltration in N. benthamiana, GFP was expressed at a relatively high level, expression in field pea and faba bean at the same time point was relatively low. In lentil, an expression level of GFP similar to field pea and faba bean at 3 days was only observed after 5 days. Chickpea leaf cells were transformed at low frequency and agroinfiltration was concluded to not be successful for chickpea. We concluded that the pEAQ vector is suitable for testing host-specific effectors in field pea, lentil, and faba bean, but low transformation efficiency limits the utility of the method for chickpea.
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Affiliation(s)
- Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia
| | - Bernadette M Henares
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia
| | - Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia.
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Thompson MG, Moore WM, Hummel NFC, Pearson AN, Barnum CR, Scheller HV, Shih PM. Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology. BIODESIGN RESEARCH 2020; 2020:8189219. [PMID: 37849895 PMCID: PMC10530663 DOI: 10.34133/2020/8189219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/26/2020] [Indexed: 10/19/2023] Open
Abstract
Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - William M. Moore
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Niklas F. C. Hummel
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Collin R. Barnum
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
- Genome Center, University of California-Davis, Davis, CA, USA
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Abstract
Epigenetic changes influence gene expression and contribute to the modulation of biological processes in response to the environment. Transgenerational epigenetic changes in gene expression have been described in many eukaryotes. However, plants appear to have a stronger propensity for inheriting novel epialleles. This mini-review discusses how plant traits, such as meristematic growth, totipotency, and incomplete epigenetic erasure in gametes promote epiallele inheritance. Additionally, we highlight how plant biology may be inherently tailored to reap the benefits of epigenetic metastability. Importantly, environmentally triggered small RNA expression and subsequent epigenetic changes may allow immobile plants to adapt themselves, and possibly their progeny, to thrive in local environments. The change of epigenetic states through the passage of generations has ramifications for evolution in the natural and agricultural world. In populations containing little genetic diversity, such as elite crop germplasm or habitually self-reproducing species, epigenetics may provide an important source of heritable phenotypic variation. Basic understanding of the processes that direct epigenetic shifts in the genome may allow for breeding or bioengineering for improved plant traits that do not require changes to DNA sequence.
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Affiliation(s)
- Mark A A Minow
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada.,Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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Broad RC, Bonneau JP, Beasley JT, Roden S, Philips JG, Baumann U, Hellens RP, Johnson AAT. Genome-wide identification and characterization of the GDP-L-galactose phosphorylase gene family in bread wheat. BMC PLANT BIOLOGY 2019; 19:515. [PMID: 31771507 PMCID: PMC6878703 DOI: 10.1186/s12870-019-2123-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway-the dominant ascorbate biosynthetic pathway in plants-and is a promising gene candidate for increasing ascorbate in crops. In addition to transcriptional regulation, GGP production is regulated at the translational level through an upstream open reading frame (uORF) in the long 5'-untranslated region (5'UTR). The GGP genes have yet to be identified in bread wheat (Triticum aestivum L.), one of the most important food grain sources for humans. RESULTS Bread wheat chromosomal groups 4 and 5 were found to each contain three homoeologous TaGGP genes on the A, B, and D subgenomes (TaGGP2-A/B/D and TaGGP1-A/B/D, respectively) and a highly conserved uORF was present in the long 5'UTR of all six genes. Phylogenetic analyses demonstrated that the TaGGP genes separate into two distinct groups and identified a duplication event of the GGP gene in the ancestor of the Brachypodium/Triticeae lineage. A microsynteny analysis revealed that the TaGGP1 and TaGGP2 subchromosomal regions have no shared synteny suggesting that TaGGP2 may have been duplicated via a transposable element. The two groups of TaGGP genes have distinct expression patterns with the TaGGP1 homoeologs broadly expressed across different tissues and developmental stages and the TaGGP2 homoeologs highly expressed in anthers. Transient transformation of the TaGGP coding sequences in Nicotiana benthamiana leaf tissue increased ascorbate concentrations more than five-fold, confirming their functional role in ascorbate biosynthesis in planta. CONCLUSIONS We have identified six TaGGP genes in the bread wheat genome, each with a highly conserved uORF. Phylogenetic and microsynteny analyses highlight that a transposable element may have been responsible for the duplication and specialized expression of GGP2 in anthers in the Brachypodium/Triticeae lineage. Transient transformation of the TaGGP coding sequences in N. benthamiana demonstrated their activity in planta. The six TaGGP genes and uORFs identified in this study provide a valuable genetic resource for increasing ascorbate concentrations in bread wheat.
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Affiliation(s)
- Ronan C Broad
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Julien P Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Jesse T Beasley
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sally Roden
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Joshua G Philips
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Ute Baumann
- School of Agriculture, The University of Adelaide, Adelaide, South Australia, 5064, Australia
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Alexander A T Johnson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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Philips JG, Dumin W, Winefield C. Functional Characterization of the Grapevine γ-Glutamyl Transferase/Transpeptidase (E.C. 2.3.2.2) Gene Family Reveals a Single Functional Gene Whose Encoded Protein Product Is Not Located in Either the Vacuole or Apoplast. FRONTIERS IN PLANT SCIENCE 2019; 10:1402. [PMID: 31749820 PMCID: PMC6843540 DOI: 10.3389/fpls.2019.01402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 06/08/2023]
Abstract
γ-glutamyl transferases/transpeptidases (E.C. 2.3.2.2, GGTs) are involved in the catabolism of many compounds that are conjugated to glutathione (GSH), which have a variety of roles. GSH can act as storage and transport vehicle for reduced sulfur; it is involved in the detoxification of xenobiotics and also acts as a redox buffer by utilizing its thiol residue to protect against reactive oxygen species, which accumulate in response to biotic and abiotic stress. Furthermore, many distinctive flavor and aroma compounds in Sauvignon blanc wines originate from odorless C5- and C6-GSH conjugates or their GGT catabolized derivatives. These precursors are then processed into their volatile forms by yeast during fermentation. In many plant species, two or more isoforms of GGTs exist that target GSH-conjugates to either the apoplast or the vacuole. A bioinformatics approach identified multiple GGT candidates in grapevine (Vitis vinifera). However, only a single candidate, VvGGT3, has all the conserved residues needed for GGT activity. This is intriguing given the variety of roles of GSH and GGTs in plant cells. Characterization of VvGGT3 from cv. Sauvignon blanc was then undertaken. The VvGGT3 transcript is present in roots, leaves, inflorescences, and tendril and at equal abundance in the skin, pulp, and seed of mature berries and shows steady accumulation over the course of whole berry development. In addition, the VvGGT3 transcript in whole berries is upregulated upon Botrytis cinerea infection as well as mechanical damage to leaf tissue. VvGGT3-GFP fusion proteins transiently over-expressed in onion cells were used to study subcellular localization. To confirm VvGGT3 activity and localization in vivo, the fluorescent γ-glutamyl-7-amido-4-methylcoumarin substrate was added to Nicotiana benthamiana leaves transiently over-expressing VvGGT3. In combination, these results suggest that the functional VvGGT3 is associated with membrane-like structures. This is not consistent with its closely related functionally characterized GGTs from Arabidopsis, radish and garlic.
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Affiliation(s)
| | | | - Christopher Winefield
- Department of Wine Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
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Přibylová A, Čermák V, Tyč D, Fischer L. Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells. Epigenetics Chromatin 2019; 12:54. [PMID: 31511048 PMCID: PMC6737654 DOI: 10.1186/s13072-019-0299-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Methylation of cytosines is an evolutionarily conserved epigenetic mark that is essential for the control of chromatin activity in many taxa. It acts mainly repressively, causing transcriptional gene silencing. In plants, de novo DNA methylation is established mainly by RNA-directed DNA-methylation pathway. Even though the protein machinery involved is relatively well-described, the course of the initial phases remains covert. RESULTS We show the first detailed description of de novo DNA-methylation dynamics. Since prevalent plant model systems do not provide the possibility to collect homogenously responding material in time series with short intervals, we developed a convenient system based on tobacco BY-2 cell lines with inducible production of siRNAs (from an RNA hairpin) guiding the methylation machinery to the CaMV 35S promoter controlling GFP reporter. These lines responded very synchronously, and a high level of promoter-specific siRNAs triggered rapid promoter methylation with the first increase observed already 12 h after the induction. The previous presence of CG methylation in the promoter did not affect the methylation dynamics. The individual cytosine contexts reacted differently. CHH methylation peaked at about 80% in 2 days and then declined, whereas CG and CHG methylation needed more time with CHG reaching practically 100% after 10 days. Spreading of methylation was only minimal outside the target region in accordance with the absence of transitive siRNAs. The low and stable proportion of 24-nt siRNAs suggested that Pol IV was not involved in the initial phases. CONCLUSIONS Our results show that de novo DNA methylation is a rapid process initiated practically immediately with the appearance of promoter-specific siRNAs and independently of the prior presence of methylcytosines at the target locus. The methylation was precisely targeted, and its dynamics varied depending on the cytosine sequence context. The progressively increasing methylation resulted in a smooth, gradual inhibition of the promoter activity, which was entirely suppressed in 2 days.
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Affiliation(s)
- Adéla Přibylová
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Vojtěch Čermák
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Dimitrij Tyč
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic.
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