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Zhang D, Boch J. Development of TALE-adenine base editors in plants. Plant Biotechnol J 2024; 22:1067-1077. [PMID: 37997697 PMCID: PMC11022790 DOI: 10.1111/pbi.14246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/10/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Base editors enable precise nucleotide changes at targeted genomic loci without requiring double-stranded DNA breaks or repair templates. TALE-adenine base editors (TALE-ABEs) are genome editing tools, composed of a DNA-binding domain from transcription activator-like effectors (TALEs), an engineered adenosine deaminase (TadA8e), and a cytosine deaminase domain (DddA), that allow A•T-to-G•C editing in human mitochondrial DNA. However, the editing ability of TALE-ABEs in plants apart from chloroplast DNA has not been described, so far, and the functional role how DddA enhances TadA8e is still unclear. We tested a series of TALE-ABEs with different deaminase fusion architectures in Nicotiana benthamiana and rice. The results indicate that the double-stranded DNA-specific cytosine deaminase DddA can boost the activities of single-stranded DNA-specific deaminases (TadA8e or APOBEC3A) on double-stranded DNA. We analysed A•T-to-G•C editing efficiencies in a β-glucuronidase reporter system and showed precise adenine editing in genomic regions with high product purity in rice protoplasts. Furthermore, we have successfully regenerated rice plants with A•T-to-G•C mutations in the chloroplast genome using TALE-ABE. Consequently, TALE-adenine base editors provide alternatives for crop improvement and gene therapy by editing nuclear or organellar genomes.
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Affiliation(s)
- Dingbo Zhang
- Institute of Plant GeneticsLeibniz Universität HannoverHannoverGermany
| | - Jens Boch
- Institute of Plant GeneticsLeibniz Universität HannoverHannoverGermany
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2
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Zhang D, Pries V, Boch J. Targeted C•G-to-T•A base editing with TALE-cytosine deaminases in plants. BMC Biol 2024; 22:99. [PMID: 38679734 PMCID: PMC11057107 DOI: 10.1186/s12915-024-01895-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND TALE-derived DddA-based cytosine base editors (TALE-DdCBEs) can perform efficient base editing of mitochondria and chloroplast genomes. They use transcription activator-like effector (TALE) arrays as programmable DNA-binding domains and a split version of the double-strand DNA cytidine deaminase (DddA) to catalyze C•G-to-T•A editing. This technology has not been optimized for use in plant cells. RESULTS To systematically investigate TALE-DdCBE architectures and editing rules, we established a β-glucuronidase reporter for transient assays in Nicotiana benthamiana. We show that TALE-DdCBEs function with distinct spacer lengths between the DNA-binding sites of their two TALE parts. Compared to canonical DddA, TALE-DdCBEs containing evolved DddA variants (DddA6 or DddA11) showed a significant improvement in editing efficiency in Nicotiana benthamiana and rice. Moreover, TALE-DdCBEs containing DddA11 have broader sequence compatibility for non-TC target editing. We have successfully regenerated rice with C•G-to-T•A conversions in their chloroplast genome, as well as N. benthamiana with C•G-to-T•A editing in the nuclear genome using TALE-DdCBE. We also found that the spontaneous assembly of split DddA halves can cause undesired editing by TALE-DdCBEs in plants. CONCLUSIONS Altogether, our results refined the targeting scope of TALE-DdCBEs and successfully applied them to target the chloroplast and nuclear genomes. Our study expands the base editing toolbox in plants and further defines parameters to optimize TALE-DdCBEs for high-fidelity crop improvement.
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Affiliation(s)
- Dingbo Zhang
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Vanessa Pries
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Jens Boch
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany.
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Costa J, Pothier JF, Bosis E, Boch J, Kölliker R, Koebnik R. A Community-Curated DokuWiki Resource on Diagnostics, Diversity, Pathogenicity, and Genetic Control of Xanthomonads. Mol Plant Microbe Interact 2024; 37:347-353. [PMID: 38114082 DOI: 10.1094/mpmi-11-23-0184-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, including static content and rapid obsolescence. To address these challenges, we have developed a Web-based knowledge platform dedicated to xanthomonads, inspired by the concept of living systematic reviews. This platform offers a dynamic resource that encompasses bacterial virulence factors, plant resistance genes, and tools for diagnostics and genetic diversity studies. Our goal is to facilitate access for newcomers to the field, provide continuing education opportunities for students, assist plant protection services with diagnostics, provide valuable information to breeders on sources of resistance and breeding targets, and offer comprehensive expert knowledge to other stakeholders interested in plant-pathogenic xanthomonads. This resource is available for queries and updates at https://euroxanth.ipn.pt. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Joana Costa
- University of Coimbra, Centre for Functional Ecology-Science for People & the Planet, Associate Laboratory TERRA, Department of Life Sciences, Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Wei J, Brophy B, Cole SA, Leath S, Oback B, Boch J, Wells DN, Laible G. Production of light-coloured, low heat-absorbing Holstein Friesian cattle by precise embryo-mediated genome editing. Reprod Fertil Dev 2023; 36:112-123. [PMID: 38064192 DOI: 10.1071/rd23163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
CONTEXT Genome editing enables the introduction of beneficial sequence variants into the genomes of animals with high genetic merit in a single generation. This can be achieved by introducing variants into primary cells followed by producing a live animal from these cells by somatic cell nuclear transfer cloning. The latter step is associated with low efficiencies and developmental problems due to incorrect reprogramming of the donor cells, causing animal welfare concerns. Direct editing of fertilised one-cell embryos could circumvent this issue and might better integrate with genetic improvement strategies implemented by the industry. METHODS In vitro fertilised zygotes were injected with TALEN editors and repair template to introduce a known coat colour dilution mutation in the PMEL gene. Embryo biopsies of injected embryos were screened by polymerase chain reaction and sequencing for intended biallelic edits before transferring verified embryos into recipients for development to term. Calves were genotyped and their coats scanned with visible and hyperspectral cameras to assess thermal energy absorption. KEY RESULTS Multiple non-mosaic calves with precision edited genotypes were produced, including calves from high genetic merit parents. Compared to controls, the edited calves showed a strong coat colour dilution which was associated with lower thermal energy absorbance. CONCLUSIONS Although biopsy screening was not absolutely accurate, non-mosaic, precisely edited calves can be readily produced by embryo-mediated editing. The lighter coat colouring caused by the PMEL mutation can lower radiative heat gain which might help to reduce heat stress. IMPLICATIONS The study validates putative causative sequence variants to rapidly adapt grazing cattle to changing environmental conditions.
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Affiliation(s)
- Jingwei Wei
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Brigid Brophy
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Sally-Ann Cole
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Shane Leath
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Björn Oback
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand; and School of Sciences, University of Waikato, Hamilton, New Zealand; and Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - David N Wells
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Götz Laible
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand; and Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
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Erkes A, Grove RP, Žarković M, Krautwurst S, Koebnik R, Morgan RD, Wilson GG, Hölzer M, Marz M, Boch J, Grau J. Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing. BMC Genomics 2023; 24:151. [PMID: 36973643 PMCID: PMC10045945 DOI: 10.1186/s12864-023-09228-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. RESULTS Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. CONCLUSIONS Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - René P Grove
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Milena Žarković
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Sebastian Krautwurst
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34090, Montpellier, France
| | | | | | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Manja Marz
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
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Costa J, Pothier JF, Boch J, Stefani E, Koebnik R. Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management. Microorganisms 2022; 11:microorganisms11010006. [PMID: 36677298 PMCID: PMC9861534 DOI: 10.3390/microorganisms11010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Present, emerging or re-emerging plant diseases due to infection by bacteria of the Lysobacteraceae (syn: Xanthomonadaceae) family are continually challenging food security and cause significant losses to the economies of European countries each year [...].
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Affiliation(s)
- Joana Costa
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, 3000-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Emilio Stefani
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34394 Montpellier, France
- Correspondence: ; Tel.: +33-467-416228
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Heinemann D, Zabic M, Terakawa M, Boch J. Correction to: Laser‑based molecular delivery and its applications in plant science. Plant Methods 2022; 18:104. [PMID: 36002859 PMCID: PMC9404571 DOI: 10.1186/s13007-022-00936-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Dag Heinemann
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany.
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167, Hannover, Germany.
| | - Miroslav Zabic
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Mitsuhiro Terakawa
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Jens Boch
- Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Wei J, Brophy B, Cole SA, Moormann J, Boch J, Laible G. Cytoplasmic Injection of Zygotes to Genome Edit Naturally Occurring Sequence Variants Into Bovine Embryos. Front Genet 2022; 13:925913. [PMID: 35899192 PMCID: PMC9310181 DOI: 10.3389/fgene.2022.925913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
Genome editing provides opportunities to improve current cattle breeding strategies through targeted introduction of natural sequence variants, accelerating genetic gain. This can be achieved by harnessing homology-directed repair mechanisms following editor-induced cleavage of the genome in the presence of a repair template. Introducing the genome editors into zygotes and editing in embryos has the advantage of uncompromised development into live animals and alignment with contemporary embryo-based improvement practices. In our study, we investigated the potential to introduce sequence variants, known from the pre-melanosomal protein 17 (PMEL) and prolactin receptor (PRLR) genes, and produce non-mosaic, edited embryos, completely converted into the precision genotype. Injection of gRNA/Cas9 editors into bovine zygotes to introduce a 3 bp deletion variant into the PMEL gene produced up to 11% fully converted embryos. The conversion rate was increased to up to 48% with the use of TALEN but only when delivered by plasmid. Testing three gRNA/Cas9 editors in the context of several known PRLR sequence variants, different repair template designs and delivery as DNA, RNA or ribonucleoprotein achieved full conversion rates up to 8%. Furthermore, we developed a biopsy-based screening strategy for non-mosaic embryos which has the potential for exclusively producing non-mosaic animals with intended precision edits.
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Affiliation(s)
- Jingwei Wei
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Brigid Brophy
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Sally-Ann Cole
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Jannis Moormann
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Gӧtz Laible
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
- *Correspondence: Gӧtz Laible,
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Heinemann D, Zabic M, Terakawa M, Boch J. Laser-based molecular delivery and its applications in plant science. Plant Methods 2022; 18:82. [PMID: 35690858 PMCID: PMC9188231 DOI: 10.1186/s13007-022-00908-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 05/14/2023]
Abstract
Lasers enable modification of living and non-living matter with submicron precision in a contact-free manner which has raised the interest of researchers for decades. Accordingly, laser technologies have drawn interest across disciplines. They have been established as a valuable tool to permeabilize cellular membranes for molecular delivery in a process termed photoinjection. Laser-based molecular delivery was first reported in 1984, when normal kidney cells were successfully transfected with a frequency-multiplied Nd:YAG laser. Due to the rapid development of optical technologies, far more sophisticated laser platforms have become available. In particular, near infrared femtosecond (NIR fs) laser sources enable an increasing progress of laser-based molecular delivery procedures and opened up multiple variations and applications of this technique.This review is intended to provide a plant science audience with the physical principles as well as the application potentials of laser-based molecular delivery. The historical origins and technical development of laser-based molecular delivery are summarized and the principle physical processes involved in these approaches and their implications for practical use are introduced. Successful cases of laser-based molecular delivery in plant science will be reviewed in detail, and the specific hurdles that plant materials pose will be discussed. Finally, we will give an outlook on current limitations and possible future applications of laser-based molecular delivery in the field of plant science.
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Affiliation(s)
- Dag Heinemann
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany.
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167, Hannover, Germany.
| | - Miroslav Zabic
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Mitsuhiro Terakawa
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Jens Boch
- Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Assou J, Zhang D, Roth KDR, Steinke S, Hust M, Reinard T, Winkelmann T, Boch J. Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9. Plant J 2022; 109:649-663. [PMID: 34784073 DOI: 10.1111/tpj.15584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 05/21/2023]
Abstract
Food allergies are a major health issue worldwide. Modern breeding techniques such as genome editing via CRISPR/Cas9 have the potential to mitigate this by targeting allergens in plants. This study addressed the major allergen Bra j I, a seed storage protein of the 2S albumin class, in the allotetraploid brown mustard (Brassica juncea). Cotyledon explants of an Indian gene bank accession (CR2664) and the German variety Terratop were transformed using Agrobacterium tumefaciens harboring binary vectors with multiple single guide RNAs to induce either large deletions or frameshift mutations in both Bra j I homoeologs. A total of 49 T0 lines were obtained with up to 3.8% transformation efficiency. Four lines had large deletions of 566 up to 790 bp in the Bra j IB allele. Among 18 Terratop T0 lines, nine carried indels in the targeted regions. From 16 analyzed CR2664 T0 lines, 14 held indels and three had all four Bra j I alleles mutated. The majority of the CRISPR/Cas9-induced mutations were heritable to T1 progenies. In some edited lines, seed formation and viability were reduced and seeds showed a precocious development of the embryo leading to a rupture of the testa already in the siliques. Immunoblotting using newly developed Bra j I-specific antibodies revealed the amount of Bra j I protein to be reduced or absent in seed extracts of selected lines. Removing an allergenic determinant from mustard is an important first step towards the development of safer food crops.
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Affiliation(s)
- Juvenal Assou
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Dingbo Zhang
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Kristian D R Roth
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Reinard
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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Skoppek CI, Punt W, Heinrichs M, Ordon F, Wehner G, Boch J, Streubel J. The barley HvSTP13GR mutant triggers resistance against biotrophic fungi. Mol Plant Pathol 2022; 23:278-290. [PMID: 34816582 PMCID: PMC8743016 DOI: 10.1111/mpp.13161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 05/29/2023]
Abstract
High-yielding and stress-resistant crops are essential to ensure future food supply. Barley is an important crop to feed livestock and to produce malt, but the annual yield is threatened by pathogen infections. Pathogens can trigger an altered sugar partitioning in the host plant, which possibly leads to an advantage for the pathogen. Hampering these processes represents a promising strategy to potentially increase resistance. We analysed the response of the barley monosaccharide transporter HvSTP13 towards biotic stress and its potential use for plant protection. The expression of HvSTP13 increased on bacterial and fungal pathogen-associated molecular pattern (PAMP) application, suggesting a PAMP-triggered signalling that converged on the transcriptional induction of the gene. Promoter studies indicate a region that is probably targeted by transcription factors downstream of PAMP-triggered immunity pathways. We confirmed that the nonfunctional HvSTP13GR variant confers resistance against an economically relevant biotrophic rust fungus in barley. Our experimental setup provides basal prerequisites to further decode the role of HvSTP13 in response to biological stress. Moreover, in line with other studies, our experiments indicate that the alteration of sugar partitioning pathways, in a host-pathogen interaction, is a promising approach to achieve broad and durable resistance in plants.
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Affiliation(s)
- Caroline Ines Skoppek
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
| | - Wilko Punt
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
- Present address:
Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Marleen Heinrichs
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
- Present address:
Department of Cellular BiochemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Frank Ordon
- Institute for Resistance Research and Stress ToleranceJulius Kühn Institute – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Gwendolin Wehner
- Institute for Resistance Research and Stress ToleranceJulius Kühn Institute – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Jens Boch
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
| | - Jana Streubel
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
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Becker S, Mücke S, Grau J, Boch J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2387-2400. [PMID: 35150566 PMCID: PMC8887545 DOI: 10.1093/nar/gkac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins with a programmable DNA-binding domain, which turned them into exceptional tools for biotechnology. TALEs contain a central array of consecutive 34 amino acid long repeats to bind DNA in a simple one-repeat-to-one-nucleotide manner. However, a few naturally occurring aberrant repeat variants break this strict binding mechanism, allowing for the recognition of an additional sequence with a −1 nucleotide frameshift. The limits and implications of this extended TALE binding mode are largely unexplored. Here, we analyse the complete diversity of natural and artificially engineered aberrant repeats for their impact on the DNA binding of TALEs. Surprisingly, TALEs with several aberrant repeats can loop out multiple repeats simultaneously without losing DNA-binding capacity. We also characterized members of the only natural TALE class harbouring two aberrant repeats and confirmed that their target is the major virulence factor OsSWEET13 from rice. In an aberrant TALE repeat, the position and nature of the amino acid sequence strongly influence its function. We explored the tolerance of TALE repeats towards alterations further and demonstrate that inserts as large as GFP can be tolerated without disrupting DNA binding. This illustrates the extraordinary DNA-binding capacity of TALEs and opens new uses in biotechnology.
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Affiliation(s)
- Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jens Boch
- To whom correspondence should be addressed. Tel: +49 511 762 4082; Fax: +49 511 762 4088;
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13
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. Epigenetic features improve TALE target prediction. BMC Genomics 2021; 22:914. [PMID: 34965853 PMCID: PMC8717664 DOI: 10.1186/s12864-021-08210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. Results To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets. Conclusions Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08210-z).
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Stefanie Mücke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
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14
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Costa J, Pothier JF, Boch J, Stefani E, Jacques M, Catara V, Koebnik R. Integrating science on Xanthomonadaceae for sustainable plant disease management in Europe. Mol Plant Pathol 2021; 22:1461-1463. [PMID: 34755430 PMCID: PMC8578814 DOI: 10.1111/mpp.13150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 05/27/2023]
Affiliation(s)
- Joana Costa
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
- Laboratory for PhytopathologyInstituto Pedro NunesCoimbraPortugal
| | - Joël F. Pothier
- Institute for Natural Resource SciencesEnvironmental Genomics and Systems Biology Research GroupZurich University of Applied SciencesWädenswilSwitzerland
| | - Jens Boch
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHannoverGermany
| | - Emilio Stefani
- Department of Life SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
| | | | - Vittoria Catara
- Department of Agriculture, Food and EnvironmentUniversity of CataniaCataniaItaly
| | - Ralf Koebnik
- Plant Health Institute of MontpellierUniversity of Montpellier, CIRAD, INRAE, Institut AgroIRDMontpellierFrance
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15
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Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:35-54. [PMID: 34435370 DOI: 10.1111/nyas.14675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
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Affiliation(s)
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, and the Joint BioEnergy Institute, Davis, California
| | - Daniel Voytas
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Feng Zhang
- College of Biological Sciences, University of Minnesota, St. Paul, Minnesota
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ayumu Takatsuka
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Steven E Jacobsen
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Department of Molecular, Cell and Developmental Biology; and Howard Hughes Medical Institute, University of California, Los Angeles, California
| | - Seiichi Toki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, and College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York, and Plant Breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Trevor Weiss
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, Iowa
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina
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16
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLoS Comput Biol 2019; 15:e1007206. [PMID: 31295249 PMCID: PMC6650089 DOI: 10.1371/journal.pcbi.1007206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/23/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria secrete transcription activator-like effectors (TALEs) into host cells, where they act as transcriptional activators on plant target genes to support bacterial virulence. TALEs have a unique modular DNA-binding domain composed of tandem repeats. Two amino acids within each tandem repeat, termed repeat-variable diresidues, bind to contiguous nucleotides on the DNA sequence and determine target specificity. In this paper, we propose a novel approach for TALE target prediction to identify potential virulence targets. Our approach accounts for recent findings concerning TALE targeting, including frame-shift binding by repeats of aberrant lengths, and the flexible strand orientation of target boxes relative to the transcription start of the downstream target gene. The computational model can account for dependencies between adjacent RVD positions. Model parameters are learned from the wealth of quantitative data that have been generated over the last years. We benchmark the novel approach, termed PrediTALE, using RNA-seq data after Xanthomonas infection in rice, and find an overall improvement of prediction performance compared with previous approaches. Using PrediTALE, we are able to predict several novel putative virulence targets. However, we also observe that no target genes are predicted by any prediction tool for several TALEs, which we term orphan TALEs for this reason. We postulate that one explanation for orphan TALEs are incomplete gene annotations and, hence, propose to replace promoterome-wide by genome-wide scans for target boxes. We demonstrate that known targets from promoterome-wide scans may be recovered by genome-wide scans, whereas the latter, combined with RNA-seq data, are able to detect putative targets independent of existing gene annotations. Diseases caused by plant-pathogenic Xanthomonas bacteria are a serious threat for many important crop plants including rice. Efficiently protecting plants from these pathogens requires a deeper understanding of infection strategies. For many Xanthomonas strains, such infection strategies depend on a special class of effector proteins, termed transcription activator-like effectors (TALEs). TALEs may specifically activate genes of the host plant and, by this means, re-program the plant cell for the benefit of the pathogen. Target sequences and, consequently, target genes of a specific TALE may be predicted computationally from its amino acids. Here, we propose a novel approach for TALE target prediction that makes use of several insights into TALE biology but also of broad experimental data gained over the last years. We demonstrate that this approach yields a higher prediction accuracy than previous approaches. We further postulate that a strategy change from a restricted search only considering promoters of annotated genes to a broad genome-wide search is feasible and yields novel targets including previously neglected protein-coding genes but also non-coding RNAs of possibly regulatory function.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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17
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Mücke S, Reschke M, Erkes A, Schwietzer CA, Becker S, Streubel J, Morgan RD, Wilson GG, Grau J, Boch J. Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs. Front Plant Sci 2019; 10:162. [PMID: 30858855 PMCID: PMC6397873 DOI: 10.3389/fpls.2019.00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/29/2019] [Indexed: 05/12/2023]
Abstract
Rice-pathogenic Xanthomonas oryzae bacteria cause severe harvest loss and challenge a stable food supply. The pathogen virulence relies strongly on bacterial TALE (transcription activator-like effector) proteins that function as transcriptional activators inside the plant cell. To understand the plant targets of TALEs, we determined the genome sequences of the Indian X. oryzae pv. oryzae (Xoo) type strain ICMP 3125T and the strain PXO142 from the Philippines. Their complete TALE repertoire was analyzed and genome-wide TALE targets in rice were characterized. Integrating computational target predictions and rice transcriptomics data, we were able to verify 12 specifically induced target rice genes. The TALEs of the Xoo strains were reconstructed and expressed in a TALE-free Xoo strain to attribute specific induced genes to individual TALEs. Using reporter assays, we could show that individual TALEs act directly on their target promoters. In particular, we show that TALE classes assigned by AnnoTALE reflect common target genes, and that TALE classes of Xoo and the related pathogen X. oryzae pv. oryzicola share more common target genes than previously believed. Taken together, we establish a detailed picture of TALE-induced plant processes that significantly expands our understanding of X. oryzae virulence strategies and will facilitate the development of novel resistances to overcome this important rice disease.
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Affiliation(s)
- Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia-Alice Schwietzer
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Jana Streubel
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | | | | | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
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18
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Abstract
Transcription activator-like effectors (TALEs) are secreted by plant–pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid (AA) tandem repeats, where AA 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs. Here, we study the evolution of TALEs from the level of RVDs determining target specificity down to the level of DNA sequence with focus on rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains. We observe that codon pairs coding for individual RVDs are conserved to a similar degree as the flanking repeat sequence. We find strong indications that TALEs may evolve 1) by base substitutions in codon pairs coding for RVDs, 2) by recombination of N-terminal or C-terminal regions of existing TALEs, or 3) by deletion of individual TALE repeats, and we propose possible mechanisms. We find indications that the reassortment of TALE genes in clusters is mediated by an integron-like mechanism in Xoc. We finally study the effect of the presence/absence and evolutionary modifications of TALEs on transcriptional activation of putative target genes in rice, and find that even single RVD swaps may lead to considerable differences in activation. This correlation allowed a refined prediction of TALE targets, which is the crucial step to decipher their virulence activity.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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Streubel J, Baum H, Grau J, Stuttmann J, Boch J. Correction: Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0175653. [PMID: 28384283 PMCID: PMC5383322 DOI: 10.1371/journal.pone.0175653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0173580.].
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20
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Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
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Affiliation(s)
- Jana Streubel
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
| | - Heidi Baum
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute of Computer Science, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Johannes Stuttman
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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21
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Blanvillain‐Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, Meynard D, Portefaix M, Cunnac S, Guiderdoni E, Boch J, Koebnik R. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. Plant Biotechnol J 2017; 15:306-317. [PMID: 27539813 PMCID: PMC5316920 DOI: 10.1111/pbi.12613] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 05/04/2023]
Abstract
As a key virulence strategy to cause bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of the OsSWEET14 promoter through stable expression of TALE-nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.
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Affiliation(s)
- Servane Blanvillain‐Baufumé
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
- Present address: LabEx CeMEBUniversité de MontpellierMontpellierFrance
| | - Maik Reschke
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Montserrat Solé
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Sustainable Agro Solutions S.A.Almacelles (Lleida)Spain
| | - Florence Auguy
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Hinda Doucoure
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Donaldo Meynard
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Murielle Portefaix
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Sébastien Cunnac
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Emmanuel Guiderdoni
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Jens Boch
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Ralf Koebnik
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
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Volohonsky G, Hopp AK, Saenger M, Soichot J, Scholze H, Boch J, Blandin SA, Marois E. Transgenic Expression of the Anti-parasitic Factor TEP1 in the Malaria Mosquito Anopheles gambiae. PLoS Pathog 2017; 13:e1006113. [PMID: 28095489 PMCID: PMC5240933 DOI: 10.1371/journal.ppat.1006113] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/06/2016] [Indexed: 12/18/2022] Open
Abstract
Mosquitoes genetically engineered to be resistant to Plasmodium parasites represent a promising novel approach in the fight against malaria. The insect immune system itself is a source of anti-parasitic genes potentially exploitable for transgenic designs. The Anopheles gambiae thioester containing protein 1 (TEP1) is a potent anti-parasitic protein. TEP1 is secreted and circulates in the mosquito hemolymph, where its activated cleaved form binds and eliminates malaria parasites. Here we investigated whether TEP1 can be used to create malaria resistant mosquitoes. Using a GFP reporter transgene, we determined that the fat body is the main site of TEP1 expression. We generated transgenic mosquitoes that express TEP1r, a potent refractory allele of TEP1, in the fat body and examined the activity of the transgenic protein in wild-type or TEP1 mutant genetic backgrounds. Transgenic TEP1r rescued loss-of-function mutations, but did not increase parasite resistance in the presence of a wild-type susceptible allele. Consistent with previous reports, TEP1 protein expressed from the transgene in the fat body was taken up by hemocytes upon a challenge with injected bacteria. Furthermore, although maturation of transgenic TEP1 into the cleaved form was impaired in one of the TEP1 mutant lines, it was still sufficient to reduce parasite numbers and induce parasite melanization. We also report here the first use of Transcription Activator Like Effectors (TALEs) in Anopheles gambiae to stimulate expression of endogenous TEP1. We found that artificial elevation of TEP1 expression remains moderate in vivo and that enhancement of endogenous TEP1 expression did not result in increased resistance to Plasmodium. Taken together, our results reveal the difficulty of artificially influencing TEP1-mediated Plasmodium resistance, and contribute to further our understanding of the molecular mechanisms underlying mosquito resistance to Plasmodium parasites.
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Affiliation(s)
- Gloria Volohonsky
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
- * E-mail: (GV); (EM)
| | - Ann-Katrin Hopp
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Mélanie Saenger
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Julien Soichot
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Heidi Scholze
- Martin-Luther Universität Halle-Wittenberg, Institut für Genetik, Halle (Saale), Germany
| | - Jens Boch
- Martin-Luther Universität Halle-Wittenberg, Institut für Genetik, Halle (Saale), Germany
| | - Stéphanie A. Blandin
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Eric Marois
- Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
- * E-mail: (GV); (EM)
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Ordon J, Gantner J, Kemna J, Schwalgun L, Reschke M, Streubel J, Boch J, Stuttmann J. Generation of chromosomal deletions in dicotyledonous plants employing a user-friendly genome editing toolkit. Plant J 2017; 89:155-168. [PMID: 27579989 DOI: 10.1111/tpj.13319] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 05/20/2023]
Abstract
Genome editing facilitated by Cas9-based RNA-guided nucleases (RGNs) is becoming an increasingly important and popular technique for reverse genetics in both model and non-model species. So far, RGNs were mainly applied for the induction of point mutations, and one major challenge consists in the detection of genome-edited individuals from a mutagenized population. Also, point mutations are not appropriate for functional dissection of non-coding DNA. Here, the multiplexing capacity of a newly developed genome editing toolkit was exploited for the induction of inheritable chromosomal deletions at six different loci in Nicotiana benthamiana and Arabidopsis. In both species, the preferential formation of small deletions was observed, suggesting reduced efficiency with increasing deletion size. Importantly, small deletions (<100 bp) were detected at high frequencies in N. benthamiana T0 and Arabidopsis T2 populations. Thus, targeting of small deletions by paired nucleases represents a simple approach for the generation of mutant alleles segregating as size polymorphisms in subsequent generations. Phenotypically selected deletions of up to 120 kb occurred at low frequencies in Arabidopsis, suggesting larger population sizes for the discovery of valuable alleles from addressing gene clusters or non-coding DNA for deletion by programmable nucleases.
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Affiliation(s)
- Jana Ordon
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Johannes Gantner
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jan Kemna
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Lennart Schwalgun
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Maik Reschke
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jana Streubel
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Johannes Stuttmann
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
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Hutin M, Césari S, Chalvon V, Michel C, Tran TT, Boch J, Koebnik R, Szurek B, Kroj T. Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance to bacterial blight and bacterial leaf streak diseases. Plant J 2016; 88:43-55. [PMID: 27289079 DOI: 10.1111/tpj.13231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
Bacterial blight (BB) and bacterial leaf streak (BLS) are important diseases in Oryza sativa caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively. In both bacteria, transcription activator-like (TAL) effectors are major virulence determinants that act by transactivating host genes downstream of effector-binding elements (EBEs) bound in a sequence-specific manner. Resistance to Xoo is mostly related to the action of TAL effectors, either by polymorphisms that prevent the induction of susceptibility (S) genes or by executor (R) genes with EBEs embedded in their promoter, and that induce cell death and resistance. For Xoc, no resistance sources are known in rice. Here, we investigated whether the recognition of effectors by nucleotide binding and leucine-rich repeat domain immune receptors (NLRs), the most widespread resistance mechanism in plants, is also able to stop BB and BLS. In one instance, transgenic rice lines harboring the AVR1-CO39 effector gene from the rice blast fungus Magnaporthe oryzae, under the control of an inducible promoter, were challenged with transgenic Xoo and Xoc strains carrying a TAL effector designed to transactivate the inducible promoter. This induced AVR1-CO39 expression and triggered BB and BLS resistance when the corresponding Pi-CO39 resistance locus was present. In a second example, the transactivation of an auto-active NLR by Xoo-delivered designer TAL effectors resulted in BB resistance, demonstrating that NLR-triggered immune responses efficiently control Xoo. This forms the foundation for future BB and BLS disease control strategies, whereupon endogenous TAL effectors will target synthetic promoter regions of Avr or NLR executor genes.
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Affiliation(s)
- Mathilde Hutin
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Stella Césari
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Véronique Chalvon
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Corinne Michel
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Tuan Tu Tran
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06099, Germany
| | - Ralf Koebnik
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Boris Szurek
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France.
| | - Thomas Kroj
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
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Affiliation(s)
- Sebastian Becker
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
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26
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Geissler R, Hauber I, Funk N, Richter A, Behrens M, Renner I, Chemnitz J, Hofmann-Sieber H, Baum H, van Lunzen J, Boch J, Hauber J, Behrens SE. Patient-adapted, specific activation of HIV-1 by customized TAL effectors (TALEs), a proof of principle study. Virology 2015; 486:248-54. [PMID: 26474371 DOI: 10.1016/j.virol.2015.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 07/30/2015] [Accepted: 09/24/2015] [Indexed: 11/15/2022]
Abstract
The major obstacle to cure infections with human immunodeficiency virus (HIV-1) is integrated proviral genomes, which are not eliminated by antiretroviral therapies (ART). Treatment approaches with latency-reversing agents (LRAs) aim at inducing provirus expression to tag latently-infected cells for clearance through viral cytopathic effects or cytotoxic T cell (CTL) responses. However, the currently tested LRAs reveal evident drawbacks as gene expression is globally induced and viral outgrowth is insecure. Here, we present transcription activator-like effector (TALE) proteins as potent tools to activate HIV-1 specifically. The large variety of circulating HIV-1 strains and, accordingly, integrated proviruses was addressed by the programmable DNA-specificity of TALEs. Using customized engineered TALEs, a substantial transcription activation and viral outgrowth was achieved with cells obtained from different HIV-1 patients. Our data suggest that TALEs may be useful tools in future strategies aimed at removing HIV-1 reservoirs.
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Affiliation(s)
- Rene Geissler
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Ilona Hauber
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nancy Funk
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Annekatrin Richter
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Martina Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Ivonne Renner
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Jan Chemnitz
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Helga Hofmann-Sieber
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Heidi Baum
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Jan van Lunzen
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg, Hamburg, Germany; University Medical Center Hamburg-Eppendorf, Infectious Diseases Unit, Hamburg, Germany
| | - Jens Boch
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany
| | - Joachim Hauber
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg, Hamburg, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Halle/Saale, Germany.
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27
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Keyes D, Moore J, Nguyen P, Hasgavei T, Boch J, Kondrat K. 121 Good to Great: Strategies That Result in Successful Scholarly Publications in Emergency Medicine Programs. Ann Emerg Med 2015. [DOI: 10.1016/j.annemergmed.2015.07.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Abstract
Transcription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant–pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.
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29
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Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero ÁL, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A. Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PLoS One 2013; 8:e79704. [PMID: 24278159 PMCID: PMC3838355 DOI: 10.1371/journal.pone.0079704] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/24/2013] [Indexed: 11/24/2022] Open
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
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Affiliation(s)
- Mario L. Arrieta-Ortiz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Luis M. Rodríguez-R
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | | | - Lucie Poulin
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Ana C. Díaz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathalia Arias Rojas
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Cesar Trujillo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | | | - Rebecca Bart
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jens Boch
- Department of Genetics, Martin Luther University, Halle-Wittenberg, Germany
| | - Tristan Boureau
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Armelle Darrasse
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Perrine David
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Paula Fontanilla
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Lionel Gagnevin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Fabien Guérin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Marie-Agnès Jacques
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Pierre Lefeuvre
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Cesar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Edgar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathaly Montenegro
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Alejandra Muñoz Bodnar
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Juan F. Ortiz Quiñones
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniela Osorio
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Carolina Pardo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Prabhu B. Patil
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Stéphane Poussier
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
| | - Olivier Pruvost
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Isabelle Robène-Soustrade
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Robert P. Ryan
- College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Javier Tabima
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Oscar G. Urrego Morales
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Christian Vernière
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Valérie Verdier
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Boris Szurek
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Camilo López
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ralf Koebnik
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Adriana Bernal
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- * E-mail:
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Streubel J, Pesce C, Hutin M, Koebnik R, Boch J, Szurek B. Five phylogenetically close rice SWEET genes confer TAL effector-mediated susceptibility to Xanthomonas oryzae pv. oryzae. New Phytol 2013; 200:808-819. [PMID: 23879865 DOI: 10.1111/nph.12411] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/03/2013] [Indexed: 05/03/2023]
Abstract
Bacterial plant-pathogenic Xanthomonas strains translocate transcription activator-like (TAL) effectors into plant cells to function as specific transcription factors. Only a few plant target genes of TAL effectors have been identified, so far. Three plant SWEET genes encoding putative sugar transporters are known to be induced by TAL effectors from rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo). We predict and validate that expression of OsSWEET14 is induced by a novel TAL effector, Tal5, from an African Xoo strain. Artificial TAL effectors (ArtTALs) were constructed to individually target 20 SWEET orthologs in rice. They were used as designer virulence factors to study which rice SWEET genes can support Xoo virulence. The Tal5 target box differs from those of the already known TAL effectors TalC, AvrXa7 and PthXo3, which also induce expression of OsSWEET14, suggesting evolutionary convergence on key targets. ArtTALs efficiently complemented an Xoo talC mutant, demonstrating that specific induction of OsSWEET14 is the key target of TalC. ArtTALs that specifically target individual members of the rice SWEET family revealed three known and two novel SWEET genes to support bacterial virulence. Our results demonstrate that five phylogenetically close SWEET proteins, which presumably act as sucrose transporters, can support Xoo virulence.
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Affiliation(s)
- Jana Streubel
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Céline Pesce
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
- Earth and Life Institute, Applied Microbiology Phytopathology, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Mathilde Hutin
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Ralf Koebnik
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Boris Szurek
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
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Abstract
SUMMARY Transcription activator-like effector nucleases (TALENs) have become an accepted tool for targeted mutagenesis, but undesired off-targets remain an important issue. We present TALENoffer, a novel tool for the genome-wide prediction of TALEN off-targets. We show that TALENoffer successfully predicts known off-targets of engineered TALENs and yields a competitive runtime, scanning complete mammalian genomes within a few minutes. AVAILABILITY TALENoffer is available as a command line program from http://www.jstacs.de/index.php/TALENoffer and as a Galaxy server at http://galaxy.informatik.uni-halle.de. CONTACT grau@informatik.uni-halle.de
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Affiliation(s)
- Jan Grau
- Institute of Computer Science and Department of Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, D-06099 Halle (Saale), Germany
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Grau J, Wolf A, Reschke M, Bonas U, Posch S, Boch J. Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol 2013; 9:e1002962. [PMID: 23526890 PMCID: PMC3597551 DOI: 10.1371/journal.pcbi.1002962] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
Transcription activator-like (TAL) effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen. The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues (RVDs) that determine DNA binding specificity. In this paper, we present TALgetter, a new approach for predicting TAL effector target sites based on a statistical model. In contrast to previous approaches, the parameters of TALgetter are estimated from training data computationally. We demonstrate that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite. We study the binding specificities estimated by TALgetter and approve that different RVDs are differently important for transcriptional activation. In subsequent studies, the predictions of TALgetter indicate a previously unreported positional preference of TAL effector target sites relative to the transcription start site. In addition, several TAL effectors are predicted to bind to the TATA-box, which might constitute one general mode of transcriptional activation by TAL effectors. Scrutinizing the predicted target sites of TALgetter, we propose several novel TAL effector virulence targets in rice and sweet orange. TAL-mediated induction of the candidates is supported by gene expression microarrays. Validity of these targets is also supported by functional analogy to known TAL effector targets, by an over-representation of TAL effector targets with similar function, or by a biological function related to pathogen infection. Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors. TALgetter is implemented as part of the open-source Java library Jstacs, and is freely available as a web-application and a command line program.
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Affiliation(s)
- Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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Nau-Wagner G, Opper D, Rolbetzki A, Boch J, Kempf B, Hoffmann T, Bremer E. Genetic control of osmoadaptive glycine betaine synthesis in Bacillus subtilis through the choline-sensing and glycine betaine-responsive GbsR repressor. J Bacteriol 2012; 194:2703-14. [PMID: 22408163 PMCID: PMC3347207 DOI: 10.1128/jb.06642-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 02/27/2012] [Indexed: 11/20/2022] Open
Abstract
Synthesis of the compatible solute glycine betaine confers a considerable degree of osmotic stress tolerance to Bacillus subtilis. This osmoprotectant is produced through the uptake of the precursor choline via the osmotically inducible OpuB and OpuC ABC transporters and a subsequent two-step oxidation process by the GbsB and GbsA enzymes. We characterized a regulatory protein, GbsR, controlling the transcription of both the structural genes for the glycine betaine biosynthetic enzymes (gbsAB) and those for the choline-specific OpuB transporter (opuB) but not of that for the promiscuous OpuC transporter. GbsR acts genetically as a repressor and functions as an intracellular choline sensor. Spectroscopic analysis of the purified GbsR protein showed that it binds the inducer choline with an apparent K(D) (equilibrium dissociation constant) of approximately 165 μM. Based on the X-ray structure of a protein (Mj223) from Methanococcus jannaschii, a homology model for GbsR was derived. Inspection of this GbsR in silico model revealed a possible ligand-binding pocket for choline resembling those of known choline-binding sites present in solute receptors of microbial ABC transporters, e.g., that of the OpuBC ligand-binding protein of the OpuB ABC transporter. GbsR was not only needed to control gbsAB and opuB expression in response to choline availability but also required to genetically tune down glycine betaine production once cellular adjustment to high osmolarity has been achieved. The GbsR regulatory protein from B. subtilis thus records and integrates cellular and environmental signals for both the onset and the repression of the synthesis of the osmoprotectant glycine betaine.
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Affiliation(s)
- Gabriele Nau-Wagner
- Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Marburg, Germany
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Yu Y, Streubel J, Balzergue S, Champion A, Boch J, Koebnik R, Feng J, Verdier V, Szurek B. Colonization of rice leaf blades by an African strain of Xanthomonas oryzae pv. oryzae depends on a new TAL effector that induces the rice nodulin-3 Os11N3 gene. Mol Plant Microbe Interact 2011; 24:1102-13. [PMID: 21679014 DOI: 10.1094/mpmi-11-10-0254] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
African strains of Xanthomonas oryzae pv. oryzae contain fewer TAL effectors than Asian strains, and their contribution to pathogenicity is unknown. Systematic mutagenesis of tal genes was used to decipher the contribution of each of the eight TAL effector paralogs to pathogenicity of African X. oryzae pv. oryzae BAI3. A strain mutated in talC was severely affected in the production of disease symptoms. Analysis of growth in planta upon leaf-clip inoculation showed that mutant bacteria multiplied only at the site of inoculation at the apex of the leaf, suggesting a requirement for talC during colonization of vascular tissues. Such tissue-specific effect of a tal mutant is a novel phenotype, which has not yet been characterized in other xanthomonads. Microarray experiments comparing the host response of rice leaves challenged with BAI3(R) vs. BAI3(R)ΔtalC were performed to identify genes targeted by TalC. A total of 120 upregulated and 21 downregulated genes were identified, among them Os11N3, which is a member of the MtN3/saliva family. Based on semiquantitative reverse transcription-polymerase chain reaction and β-glucuronidase reporter assays, we show that Os11N3 is directly upregulated by TalC and identify a TalC DNA target box within the Os11N3 upstream sequence.
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Affiliation(s)
- Yanhua Yu
- Laboratoire Genome et Developpement des Plantes, Montpellier, France
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Geiβler R, Scholze H, Hahn S, Streubel J, Bonas U, Behrens SE, Boch J. Transcriptional activators of human genes with programmable DNA-specificity. PLoS One 2011; 6:e19509. [PMID: 21625585 PMCID: PMC3098229 DOI: 10.1371/journal.pone.0019509] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/30/2011] [Indexed: 02/07/2023] Open
Abstract
TAL (transcription activator-like) effectors are translocated by Xanthomonas bacteria into plant cells where they activate transcription of target genes. DNA target sequence recognition occurs in a unique mode involving a central domain of tandem repeats. Each repeat recognizes a single base pair in a contiguous DNA sequence and a pair of adjacent hypervariable amino acid residues per repeat specifies which base is bound. Rearranging the repeats allows the design of novel TAL proteins with predictable DNA-recognition specificities. TAL protein-based transcriptional activation in plant cells is mediated by a C-terminal activation domain (AD). Here, we created synthetic TAL proteins with designed repeat compositions using a novel modular cloning strategy termed “Golden TAL Technology”. Newly programmed TAL proteins were not only functional in plant cells, but also in human cells and activated targeted expression of exogenous as well as endogenous genes. Transcriptional activation in different human cell lines was markedly improved by replacing the TAL-AD with the VP16-AD of herpes simplex virus. The creation of TAL proteins with potentially any desired DNA-recognition specificity allows their versatile use in biotechnology.
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Affiliation(s)
- René Geiβler
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Scholze
- Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Simone Hahn
- Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Jana Streubel
- Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Ulla Bonas
- Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Sven-Erik Behrens
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (JB); (S-EB)
| | - Jens Boch
- Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (JB); (S-EB)
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37
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Abstract
TAL effectors are important virulence factors of bacterial plant pathogenic Xanthomonas, which infect a wide variety of plants including valuable crops like pepper, rice, and citrus. TAL proteins are translocated via the bacterial type III secretion system into host cells and induce transcription of plant genes by binding to target gene promoters. Members of the TAL effector family differ mainly in their central domain of tandemly arranged repeats of typically 34 amino acids each with hypervariable di-amino acids at positions 12 and 13. We recently showed that target DNA-recognition specificity of TAL effectors is encoded in a modular and clearly predictable mode. The repeats of TAL effectors feature a surprising one repeat-to-one-bp correlation with different repeat types exhibiting a different DNA base pair specificity. Accordingly, we predicted DNA specificities of TAL effectors and generated artificial TAL proteins with novel DNA recognition specificities. We describe here novel artificial TALs and discuss implications for the DNA recognition specificity. The unique TAL-DNA binding domain allows design of proteins with potentially any given DNA recognition specificity enabling many uses for biotechnology.
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Affiliation(s)
- Heidi Scholze
- Department of Genetics, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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Scholze H, Boch J. TAL effectors are remote controls for gene activation. Curr Opin Microbiol 2011; 14:47-53. [PMID: 21215685 DOI: 10.1016/j.mib.2010.12.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 12/21/2022]
Abstract
TAL (transcription activator-like) effectors constitute a novel class of DNA-binding proteins with predictable specificity. They are employed by Gram-negative plant-pathogenic bacteria of the genus Xanthomonas which translocate a cocktail of different effector proteins via a type III secretion system (T3SS) into plant cells where they serve as virulence determinants. Inside the plant cell, TALs localize to the nucleus, bind to target promoters, and induce expression of plant genes. DNA-binding specificity of TALs is determined by a central domain of tandem repeats. Each repeat confers recognition of one base pair (bp) in the DNA. Rearrangement of repeat modules allows design of proteins with desired DNA-binding specificities. Here, we summarize how TAL specificity is encoded, first structural data and first data on site-specific TAL nucleases.
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Affiliation(s)
- Heidi Scholze
- Department of Genetics, Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
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Römer P, Recht S, Strauß T, Elsaesser J, Schornack S, Boch J, Wang S, Lahaye T. Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. New Phytol 2010; 187:1048-1057. [PMID: 20345643 DOI: 10.1111/j.1469-8137.2010.03217.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
*Plant pathogenic bacteria of the genus Xanthomonas inject transcription activator-like effector (TALe) proteins that bind to and activate host promoters, thereby promoting disease or inducing plant defense. TALes bind to corresponding UPT (up-regulated by TALe) promoter boxes via tandemly arranged 34/35-amino acid repeats. Recent studies uncovered the TALe code in which two amino acid residues of each repeat define specific pairing to UPT boxes. *Here we employed the TALe code to predict potential UPT boxes in TALe-induced host promoters and analyzed these via beta-glucuronidase (GUS) reporter and electrophoretic mobility shift assays (EMSA). *We demonstrate that the Xa13, OsTFX1 and Os11N3 promoters from rice are induced directly by the Xanthomonas oryzae pv. oryzae TALes PthXo1, PthXo6 and AvrXa7, respectively. We identified and functionally validated a UPT box in the corresponding rice target promoter for each TALe and show that box mutations suppress TALe-mediated promoter activation. Finally, EMSA demonstrate that code-predicted UPT boxes interact specifically with corresponding TALes. *Our findings show that variations in the UPT boxes of different rice accessions correlate with susceptibility or resistance of these accessions to the bacterial blight pathogen.
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Affiliation(s)
- Patrick Römer
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Sabine Recht
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Tina Strauß
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Janett Elsaesser
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Sebastian Schornack
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Jens Boch
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Thomas Lahaye
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
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Abstract
Xanthomonads are bacterial plant pathogens that cause diseases on many plant species, including important crops. Key to pathogenicity of most Xanthomonas pathovars is a Hrp-type III secretion (T3S) system that translocates effector proteins into plant cells. Within the eukaryotic cell, the effectors are thought to perform a variety of tasks to support bacterial virulence, proliferation, and dissemination. We are only beginning to understand the host targets of different effectors. The largest effector family found in Xanthomonas spp. is the AvrBs3/PthA or TAL (transcription activator-like) family. TAL effectors act as transcriptional activators in the plant cell nucleus. Specificity of TAL effectors is determined by a novel modular DNA-binding domain. Here, we describe the discovery of TAL effectors and their structure, activity, and host targets.
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Affiliation(s)
- Jens Boch
- Department of Genetics, Martin-Luther-University Halle-Wittenberg, D-06099 Halle (Saale), Germany.
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Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 2009; 326:1509-12. [PMID: 19933107 DOI: 10.1126/science.1178811] [Citation(s) in RCA: 1729] [Impact Index Per Article: 115.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The pathogenicity of many bacteria depends on the injection of effector proteins via type III secretion into eukaryotic cells in order to manipulate cellular processes. TAL (transcription activator-like) effectors from plant pathogenic Xanthomonas are important virulence factors that act as transcriptional activators in the plant cell nucleus, where they directly bind to DNA via a central domain of tandem repeats. Here, we show how target DNA specificity of TAL effectors is encoded. Two hypervariable amino acid residues in each repeat recognize one base pair in the target DNA. Recognition sequences of TAL effectors were predicted and experimentally confirmed. The modular protein architecture enabled the construction of artificial effectors with new specificities. Our study describes the functionality of a distinct type of DNA binding domain and allows the design of DNA binding domains for biotechnology.
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Affiliation(s)
- Jens Boch
- Department of Genetics, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, D-06099 Halle (Saale) Germany.
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Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 2006; 24:1385-91. [PMID: 17057704 DOI: 10.1038/nbt1243] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 08/04/2006] [Indexed: 11/09/2022]
Abstract
Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.
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Affiliation(s)
- Andrea Krause
- Laboratory of General Microbiology, University of Bremen, PO Box 330440, D-28334 Bremen, Germany
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Landgraf A, Weingart H, Tsiamis G, Boch J. Different versions of Pseudomonas syringae pv. tomato DC3000 exist due to the activity of an effector transposon. Mol Plant Pathol 2006; 7:355-364. [PMID: 20507452 DOI: 10.1111/j.1364-3703.2006.00343.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
SUMMARY The plant pathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 is a key model organism to study plant-pathogen interactions. We realized that two versions of this strain, which carry plasmids of different sizes, exist in our strain collections. The difference was located to a 9.4-kb deletion within the larger of the two endogenous plasmids encompassing the partitioning genes parA and parB and a putative mobile element encoding the type III effector hopAM1-2 (formerly avrPpiB2). Both plasmid variants are lost in similar frequency, indicating that the partitioning genes are not essential for stability of the plasmid. In addition, the deletion derivative strain DC3001 exhibited the same virulence towards Arabidopsis as strain DC3000. The deletion site in DC3001 is located immediately adjacent to a putative transposon that carries the effector hopX1 (formerly avrPphE), suggesting that the deletion originated from an aberrant transposition event of this element. By tagging the hopX1 transposon with an antibiotic resistance cassette on a suicide plasmid it was shown that the element is functional and produces a target site duplication of 5 bp. The plasmid also integrated into the chromosome in several cases, possibly mediated by one-ended transposition of the hopX1 transposon. This is the first report that describes an active effector-transposon. Comparison of DC3000 strains from several sources revealed that strains exist with differences in the endogenous plasmid composition.
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Affiliation(s)
- Angelika Landgraf
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06099 Halle (Saale), Germany
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de Torres M, Mansfield JW, Grabov N, Brown IR, Ammouneh H, Tsiamis G, Forsyth A, Robatzek S, Grant M, Boch J. Pseudomonas syringae effector AvrPtoB suppresses basal defence in Arabidopsis. Plant J 2006; 47:368-82. [PMID: 16792692 DOI: 10.1111/j.1365-313x.2006.02798.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The virulence and avirulence activities of members of the Pseudomonas syringae HopAB family of effectors and AvrPto were examined in bean, tomato and Arabidopsis. Proteins were delivered by the RW60 strain of P. syringae pv. phaseolicola. RW60 causes a hypersensitive reaction (HR) in bean and tomato but is restricted without the HR in Arabidopsis. Dual avirulence and virulence functions in tomato and bean, respectively, were identified in virPphA homologues but only avrPtoB strongly enhanced virulence to Arabidopsis, overcoming basal defences operating against RW60. Virulence activity in both bean and Arabidopsis required regions of the C-terminus of the AvrPtoB protein, whereas elicitation of the rapid HR in tomato, with the matching Pto resistance gene, did not. The effect of AvrPtoB on Arabidopsis was accession-specific; most obvious in Wassilewskija (Ws-3), intermediate in Columbia and not detectable in Niedersenz (Nd-1) after inoculation with RW60 + avrPtoB. Analysis of crosses between Ws-3 and Nd-1 indicated co-segregation for the AvrPtoB virulence function with the absence of the Nd-1 FLS2 gene which mediates recognition of bacterial flagellin. In planta expression of AvrPtoB did not prevent the HR activated by P. syringae pv. tomato DC3000 + avrB, avrRpm1, avrRps4 or avrRpt2, but suppressed cell wall alterations, including callose deposition, characteristic of basal defence and was associated with reprogramming of the plant's transcriptional response. The success or failure of AvrPtoB in suppressing basal defences in Nd-1 depended on the timing of exposure of plant cells to the effector and the flagellin flg22 peptide.
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Affiliation(s)
- Marta de Torres
- Division of Biology, Imperial College London, Wye Campus, Ashford, Kent TN25 5AH, UK
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Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 2005; 187:7254-66. [PMID: 16237009 PMCID: PMC1272972 DOI: 10.1128/jb.187.21.7254-7266.2005] [Citation(s) in RCA: 292] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
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Affiliation(s)
- Frank Thieme
- Martin-Luther-Universität, Institut für Genetik, Weinbergweg 10, D-06120 Halle (Saale), Germany
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Kay S, Boch J, Bonas U. Characterization of AvrBs3-like effectors from a Brassicaceae pathogen reveals virulence and avirulence activities and a protein with a novel repeat architecture. Mol Plant Microbe Interact 2005; 18:838-48. [PMID: 16134896 DOI: 10.1094/mpmi-18-0838] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Xanthomonas campestris pv. armoraciae strain 5 is a Brassicaceae pathogen that expresses three members of the highly related avrBs3 gene family of type III effectors. Here, we report on the isolation and characterization of these genes, designated hax2, hax3, and hax4 (homolog of avrBs3 in Xanthomonas). All three Hax proteins are translocated from Xanthomonas spp. into the plant cell via the type III secretion system. Hax3 and Hax4 show the typical structure of AvrBs3-like effectors and contain a repetitive region in their central part consisting of 34-amino-acid (aa) repeats. By contrast, the Hax2 repeat region is composed of 35-aa repeats that are characterized by an additional proline residue. Hax2, Hax3, and Hax4 contain 21.5, 11.5, and 14.5 repeats, respectively. Genetic studies revealed an additive effect of hax2, hax3, and hax4 on disease symptom formation of X. campestris pv. armoraciae strain 5 on radish. The contribution of individual genes to the aggressiveness of strain 5 is quantitatively different, with hax2 showing the strongest effect on the development of chlorosis and necrosis. In addition, hax3 and hax4, but not hax2, have a Bs4-dependent avirulence activity in tomato and in transgenic Nicotiana benthamiana expressing the Bs4 resistance gene.
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Affiliation(s)
- Sabine Kay
- Institute of Genetics, Martin Luther University Halle Wittenberg, D-06099 Halle, Saale, Germany
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Kabisch U, Landgraf A, Krause J, Bonas U, Boch J. Type III secretion chaperones ShcS1 and ShcO1 from Pseudomonas syringae pv. tomato DC3000 bind more than one effector. Microbiology (Reading) 2005; 151:269-280. [PMID: 15632444 DOI: 10.1099/mic.0.27491-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The hrp-type III secretion (TTS) system is a key pathogenicity factor of the plant pathogen Pseudomonas syringae pv. tomato DC3000 that translocates effector proteins into the cytosol of the eukaryotic host cell. The translocation of a subset of effectors is dependent on specific chaperones. In this study an operon encoding a TTS chaperone (ShcS1) and the truncated effector HopS1′ was characterized. Yeast two-hybrid analysis and pull-down assays demonstrated that these proteins interact. Using protein fusions to AvrRpt2 it was shown that ShcS1 facilitates the translocation of HopS1′, suggesting that ShcS1 is a TTS chaperone for HopS1′ and that amino acids 1 to 118 of HopS1′ are required for translocation. P. syringae pv. tomato DC3000 carries two shcS1 homologues, shcO1 and shcS2, which are located in different operons, and both operons include additional putative effector genes. Transcomplementation experiments showed that ShcS1 and ShcO1, but not ShcS2, can facilitate the translocation of HopS1′ : : AvrRpt2. To characterize the specificities of the putative chaperones, yeast two-hybrid interaction studies were performed between the three chaperones and putative target effectors. These experiments showed that both ShcS1 and ShcO1 bind to two different effectors, HopS1′ and HopO1-1, that share only 16 % amino acid sequence identity. Using gel filtration it was shown that ShcS1 forms homodimers, and this was confirmed by yeast two-hybrid experiments. In addition, ShcS1 is also able to form heterodimers with ShcO1. These data demonstrate that ShcS1 and ShcO1 are exceptional class IA TTS chaperones because they can bind more than one target effector.
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Affiliation(s)
- Ute Kabisch
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Angelika Landgraf
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Jana Krause
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Ulla Bonas
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Jens Boch
- Institute of Genetics, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
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Jackson RW, Mansfield JW, Ammouneh H, Dutton LC, Wharton B, Ortiz-Barredo A, Arnold DL, Tsiamis G, Sesma A, Butcher D, Boch J, Kim YJ, Martin GB, Tegli S, Murillo J, Vivian A. Location and activity of members of a family of virPphA homologues in pathovars of Pseudomonas syringae and P. savastanoi. Mol Plant Pathol 2002; 3:205-216. [PMID: 20569328 DOI: 10.1046/j.1364-3703.2002.00121.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Summary virPphA is a major determinant of the pathogenicity of Pseudomonas savastanoi pv. phaseolicola to Phaseolus bean. A family of homologues of virPphA was detected in pathovars of P. savastanoi and P. syringae. We examined the structure and activity of alleles designated virPphA, virPphA(Pgy), and virPphA(Psv) from P. savastanoi pathovars phaseolicola, glycinea, and savastanoi, respectively, and avrPtoB from P. syringae pv. tomato. Sequencing showed that the virPphA(Pgy) homologue had a 48-bp central deletion in the open reading frame (ORF) compared with virPphA and virPphA(Psv), but otherwise all three P. savastanoi alleles had > 98% identity at the DNA level. By contrast, AvrPtoB from P. syringae pv. tomato strain DC3000 was predicted to have only 51% amino acid similarity with VirPphA. All ORFs have an upstream hrp-box promoter indicating potential regulation by HrpL. Each cloned homologue was introduced into the P. savastanoi pv. phaseolicola strain RW60, which lacks a native plasmid carrying virPphA as part of a pathogenicity island (PAI), and which is not pathogenic on bean. The homologues all restored virulence, as measured by the development of water-soaked lesions in bean pods, and increased bacterial populations in leaves compared with RW60 alone. RW60 harbouring virPphA or virPphA(Psv) elicited a strong hypersensitive reaction (HR) in soybean cv. Osumi; the presence of avrPtoB caused a weak HR, but virPphA(Pgy) did not affect the null reaction observed in soybean with RW60 alone. A second effector gene, avrPphD, was detected on the genomic clones carrying virPphA(Pgy) and virPphA(Psv). avrPphD was also present in both P. savastanoi pv. phaseolicola and P. syringae pv. tomato, but elsewhere in their genomes. Comparison of the genomic locations of virPphA and other effectors found in the P. savastanoi pv. phaseolicola PAI revealed the greatest divergence of the sequences surrounding virPphA to be in P. syringae pv. tomato.
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Affiliation(s)
- Robert W Jackson
- Centre for Research in Plant Science, Faculty of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
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Affiliation(s)
- J Boch
- Institut für Genetik, Martin-Luther-Universität, Halle, Deutschland.
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Boch J, Joardar V, Gao L, Robertson TL, Lim M, Kunkel BN. Identification of Pseudomonas syringae pv. tomato genes induced during infection of Arabidopsis thaliana. Mol Microbiol 2002; 44:73-88. [PMID: 11967070 DOI: 10.1046/j.1365-2958.2002.02877.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phytopathogenic bacteria possess a large number of genes that allow them to grow and cause disease on plants. Many of these genes should be induced when the bacteria come in contact with plant tissue. We used a modified in vivo expression technology (IVET) approach to identify genes from the plant pathogen Pseudomonas syringae pv. tomato that are induced upon infection of Arabidopsis thaliana and isolated over 500 in planta-expressed (ipx) promoter fusions. Sequence analysis of 79 fusions revealed several known and potential virulence genes, including hrp/hrc, avr and coronatine biosynthetic genes. In addition, we identified metabolic genes presumably important for adaptation to growth in plant tissue, as well as several genes with unknown function that may encode novel virulence factors. Many ipx fusions, including several corresponding to novel genes, are dependent on HrpL, an alternative RNA polymerase sigma factor that regulates the expression of virulence genes. Expression analysis indicated that several ipx fusions are strongly induced upon inoculation into plant tissue. Disruption of one ipx gene, conserved effector locus (CEL) orf1, encoding a putative lytic murein transglycosylase, resulted in decreased virulence of P. syringae. Our results demonstrate that this screen can be used successfully to isolate genes that are induced in planta, including many novel genes potentially involved in pathogenesis.
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Affiliation(s)
- Jens Boch
- Department of Biology, Campus Box 1137, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
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