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Wang Y, Brown LH, Adams TM, Cheung YW, Li J, Young V, Todd DT, Armstrong MR, Neugebauer K, Kaur A, Harrower B, Oome S, Wang X, Bayer M, Hein I. SMRT-AgRenSeq-d in potato ( Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5. Hortic Res 2023; 10:uhad211. [PMID: 38023472 PMCID: PMC10681002 DOI: 10.1093/hr/uhad211] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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Affiliation(s)
- Yuhan Wang
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Lynn H Brown
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas M Adams
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuk Woon Cheung
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Jie Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Vanessa Young
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Drummond T Todd
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles R Armstrong
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Konrad Neugebauer
- Biomathematics and Statistics Scotland, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Crop Research Centre, Teagasc, Oak Park, Carlow R93 XE12, Ireland
| | - Brian Harrower
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Stan Oome
- HZPC Research B.V. HZPC, Edisonweg 5, 8501 XG Joure, Netherlands
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Micha Bayer
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
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2
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Hoopes G, Meng X, Hamilton JP, Achakkagari SR, de Alves Freitas Guesdes F, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bornowski N, Bourke P, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, De Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursum RA, Vales MI, Vining K, Visser RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Strömvik MV, Tai HH, Usadel B, Buell CR, Finkers R. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant 2022; 15:520-536. [PMID: 35026436 DOI: 10.1016/j.molp.2022.01.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 06/19/2021] [Revised: 10/19/2021] [Accepted: 01/07/2022] [Indexed: 05/11/2023]
Abstract
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.
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Affiliation(s)
- Genevieve Hoopes
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Sai Reddy Achakkagari
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | | | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany
| | - Joseph J Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Danny Esselink
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natalie R Kaiser
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Bayer Crop Science, Woodland, CA 95695, USA
| | - Linda Kodde
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Brian Lavrijssen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natascha van Lieshout
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Rachel Shereda
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Heather K Tuttle
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Joshua C Wood
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Peter Bourke
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - David Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Herman J van Eck
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Dave Ellis
- International Potato Center, 1895 Avenida La Molina, Lima, Peru
| | | | - Kyle M Gardner
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Walter S De Jong
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1901, USA
| | - Joseph C Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Richard G Novy
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Stan Oome
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - Vidyasagar Sathuvalli
- Department of Crop and Soil Science, Oregon State University, Hermiston, OR 97838, USA
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall Orono, ME 04469, USA
| | - Remco A Ursum
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA
| | - Kelly Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jack Vossen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA
| | - Noelle L Anglin
- International Potato Center, 1895 Avenida La Molina, Lima, Peru; USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Christian W B Bachem
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura M Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - Martina V Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany; Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, 40225 Düsseldorf, Germany
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA.
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands.
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Willemsen I, Oome S, Verhulst C, Pettersson A, Verduin K, Kluytmans J. Trends in extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae and ESBL genes in a Dutch teaching hospital, measured in 5 yearly point prevalence surveys (2010-2014). Antimicrob Resist Infect Control 2015. [PMCID: PMC4475155 DOI: 10.1186/2047-2994-4-s1-p123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJG, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics 2015; 16:741. [PMID: 26438312 PMCID: PMC4594904 DOI: 10.1186/s12864-015-1904-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. RESULTS Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. CONCLUSIONS The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. .,Present address: Department of Plant Pathology, North Carolina State University Raleigh, Raleigh, NC, 27695, USA.
| | | | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl von Linne´ Weg 10, Cologne, 50829, Germany.
| | - Howard Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Christine Sambles
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - D Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 78371, Olomouc, Czech Republic.
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Otmar Spring
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Reinhard Zipper
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - David J Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Integrative Fungal Research (IPF), Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
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Albert I, Böhm H, Albert M, Feiler CE, Imkampe J, Wallmeroth N, Brancato C, Raaymakers TM, Oome S, Zhang H, Krol E, Grefen C, Gust AA, Chai J, Hedrich R, Van den Ackerveken G, Nürnberger T. An RLP23-SOBIR1-BAK1 complex mediates NLP-triggered immunity. Nat Plants 2015; 1:15140. [PMID: 27251392 DOI: 10.1038/nplants.2015.140] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
Plants and animals employ innate immune systems to cope with microbial infection. Pattern-triggered immunity relies on the recognition of microbe-derived patterns by pattern recognition receptors (PRRs). Necrosis and ethylene-inducing peptide 1-like proteins (NLPs) constitute plant immunogenic patterns that are unique, as these proteins are produced by multiple prokaryotic (bacterial) and eukaryotic (fungal, oomycete) species. Here we show that the leucine-rich repeat receptor protein (LRR-RP) RLP23 binds in vivo to a conserved 20-amino-acid fragment found in most NLPs (nlp20), thereby mediating immune activation in Arabidopsis thaliana. RLP23 forms a constitutive, ligand-independent complex with the LRR receptor kinase (LRR-RK) SOBIR1 (Suppressor of Brassinosteroid insensitive 1 (BRI1)-associated kinase (BAK1)-interacting receptor kinase 1), and recruits a second LRR-RK, BAK1, into a tripartite complex upon ligand binding. Stable, ectopic expression of RLP23 in potato (Solanum tuberosum) confers nlp20 pattern recognition and enhanced immunity to destructive oomycete and fungal plant pathogens, such as Phytophthora infestans and Sclerotinia sclerotiorum. PRRs that recognize widespread microbial patterns might be particularly suited for engineering immunity in crop plants.
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Affiliation(s)
- Isabell Albert
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Hannah Böhm
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Markus Albert
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Christina E Feiler
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Julia Imkampe
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Niklas Wallmeroth
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Caterina Brancato
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Tom M Raaymakers
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Heqiao Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elzbieta Krol
- Department of Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, Würzburg D-97082, Germany
| | - Christopher Grefen
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Andrea A Gust
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
| | - Jijie Chai
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rainer Hedrich
- Department of Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, Würzburg D-97082, Germany
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen D-72076, Germany
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Böhm H, Albert I, Oome S, Raaymakers TM, Van den Ackerveken G, Nürnberger T. A conserved peptide pattern from a widespread microbial virulence factor triggers pattern-induced immunity in Arabidopsis. PLoS Pathog 2014; 10:e1004491. [PMID: 25375108 PMCID: PMC4223075 DOI: 10.1371/journal.ppat.1004491] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [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: 06/01/2014] [Accepted: 09/27/2014] [Indexed: 11/18/2022] Open
Abstract
Microbe- or host damage-derived patterns mediate activation of pattern-triggered immunity (PTI) in plants. Microbial virulence factor (effector)-triggered immunity (ETI) constitutes a second layer of plant protection against microbial attack. Various necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) produced by bacterial, oomycete and fungal microbes are phytotoxic virulence factors that exert immunogenic activities through phytotoxin-induced host cell damage. We here show that multiple cytotoxic NLPs also carry a pattern of 20 amino acid residues (nlp20) that triggers immunity-associated plant defenses and immunity to microbial infection in Arabidopsis thaliana and related plant species with similar characteristics as the prototype pattern, bacterial flagellin. Characteristic differences in flagellin and nlp20 plant responses exist however, as nlp20s fail to trigger extracellular alkalinization in Arabidopsis cell suspensions and seedling growth inhibition. Immunogenic nlp20 peptide motifs are frequently found in bacterial, oomycete and fungal NLPs. Such an unusually broad taxonomic distribution within three phylogenetic kingdoms is unprecedented among microbe-derived triggers of immune responses in either metazoans or plants. Our findings suggest that cytotoxic NLPs carrying immunogenic nlp20 motifs trigger PTI in two ways as typical patterns and by inflicting host cell damage. We further propose that conserved structures within a microbial virulence factor might have driven the emergence of a plant pattern recognition system mediating PTI. As this is reminiscent of the evolution of immune receptors mediating ETI, our findings support the idea that there is a continuum between PTI and ETI.
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Affiliation(s)
- Hannah Böhm
- Center of Plant Molecular Biology (ZMBP)-Plant Biochemistry, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Isabell Albert
- Center of Plant Molecular Biology (ZMBP)-Plant Biochemistry, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Tom M. Raaymakers
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP)-Plant Biochemistry, Eberhard-Karls-University Tübingen, Tübingen, Germany
- * E-mail:
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7
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Oome S, Van den Ackerveken G. Comparative and functional analysis of the widely occurring family of Nep1-like proteins. Mol Plant Microbe Interact 2014; 27:1081-94. [PMID: 25025781 DOI: 10.1094/mpmi-04-14-0118-r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nep1-like proteins (NLP) are best known for their cytotoxic activity in dicot plants. NLP are taxonomically widespread among microbes with very different lifestyles. To learn more about this enigmatic protein family, we analyzed more than 500 available NLP protein sequences from fungi, oomycetes, and bacteria. Phylogenetic clustering showed that, besides the previously documented two types, an additional, more divergent, third NLP type could be distinguished. By closely examining the three NLP types, we identified a noncytotoxic subgroup of type 1 NLP (designated type 1a), which have substitutions in amino acids making up a cation-binding pocket that is required for cytotoxicity. Type 2 NLP were found to contain a putative calcium-binding motif, which was shown to be required for cytotoxicity. Members of both type 1 and type 2 NLP were found to possess additional cysteine residues that, based on their predicted proximity, make up potential disulfide bridges that could provide additional stability to these secreted proteins. Type 1 and type 2 NLP, although both cytotoxic to plant cells, differ in their ability to induce necrosis when artificially targeted to different cellular compartments in planta, suggesting they have different mechanisms of cytotoxicity.
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Jiang RHY, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJG, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JHM, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P. Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet 2013; 9:e1003272. [PMID: 23785293 PMCID: PMC3681718 DOI: 10.1371/journal.pgen.1003272] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/10/2012] [Indexed: 01/31/2023] Open
Abstract
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica. Fish are an increasingly important source of animal protein globally, with aquaculture production rising dramatically over the past decade. Saprolegnia is a fungal-like oomycete and one of the most destructive fish pathogens, causing millions of dollars in losses to the aquaculture industry annually. Saprolegnia has also been linked to a worldwide decline in wild fish and amphibian populations. Here we describe the genome sequence of the first animal pathogenic oomycete and compare the genome content with the available plant pathogenic oomycetes. We found that Saprolegnia lacks the large effector families that are hallmarks of plant pathogenic oomycetes, showing evolutionary adaptation to the host. Moreover, Saprolegnia harbors pathogenesis-related genes that were derived by lateral gene transfer from the host and other animal pathogens. The retrotransposon LINE family also appears to be acquired from animal lineages. By transcriptome analysis we show a high rate of allelic variation, which reveals rapidly evolving genes and potentially adaptive evolutionary mechanisms coupled to selective pressures exerted by the animal host. The genome and transcriptome data, as well as subsequent biochemical analyses, provided us with insight in the disease process of Saprolegnia at a molecular and cellular level, providing us with targets for sustainable control of Saprolegnia.
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Affiliation(s)
- Rays H Y Jiang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Cabral A, Oome S, Sander N, Küfner I, Nürnberger T, Van den Ackerveken G. Nontoxic Nep1-like proteins of the downy mildew pathogen Hyaloperonospora arabidopsidis: repression of necrosis-inducing activity by a surface-exposed region. Mol Plant Microbe Interact 2012; 25:697-708. [PMID: 22235872 DOI: 10.1094/mpmi-10-11-0269] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The genome of the downy mildew pathogen Hyaloperonospora arabidopsidis encodes necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP). Although NLP are widely distributed in eukaryotic and prokaryotic plant pathogens, it was surprising to find these proteins in the obligate biotrophic oomycete H. arabidopsidis. Therefore, we analyzed the H. arabidopsidis NLP (HaNLP) family and identified 12 HaNLP genes and 15 pseudogenes. Most of the 27 genes form an H. arabidopsidis-specific cluster when compared with other oomycete NLP genes, suggesting this class of effectors has recently expanded in H. arabidopsidis. HaNLP transcripts were mainly detected during early infection stages. Agrobacterium tumefaciens-mediated transient expression and infiltration of recombinant NLP into tobacco and Arabidopsis leaves revealed that all HaNLP tested are noncytotoxic proteins. Even HaNLP3, which is most similar to necrosis-inducing NLP proteins of other oomycetes and which contains all amino acids that are critical for necrosis-inducing activity, did not induce necrosis. Chimeras constructed between HaNLP3 and the necrosis-inducing PsojNIP protein demonstrated that most of the HaNLP3 protein is functionally equivalent to PsojNIP, except for an exposed domain that prevents necrosis induction. The early expression and species-specific expansion of the HaNLP genes is suggestive of an alternative function of noncytolytic NLP proteins during biotrophic infection of plants.
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Affiliation(s)
- Adriana Cabral
- Plant-microbe interactions, Department of Biology, Utrecht University, Padualaan 8, 3508 CH Utrecht, The Netherlands
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