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Verma A, Lin M, Smith D, Walker JC, Hewezi T, Davis EL, Hussey RS, Baum TJ, Mitchum MG. A novel sugar beet cyst nematode effector 2D01 targets the Arabidopsis HAESA receptor-like kinase. Mol Plant Pathol 2022; 23:1765-1782. [PMID: 36069343 PMCID: PMC9644282 DOI: 10.1111/mpp.13263] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Plant-parasitic cyst nematodes use a stylet to deliver effector proteins produced in oesophageal gland cells into root cells to cause disease in plants. These effectors are deployed to modulate plant defence responses and developmental programmes for the formation of a specialized feeding site called a syncytium. The Hg2D01 effector gene, coding for a novel 185-amino-acid secreted protein, was previously shown to be up-regulated in the dorsal gland of parasitic juveniles of the soybean cyst nematode Heterodera glycines, but its function has remained unknown. Genome analyses revealed that Hg2D01 belongs to a highly diversified effector gene family in the genomes of H. glycines and the sugar beet cyst nematode Heterodera schachtii. For functional studies using the model Arabidopsis thaliana-H. schachtii pathosystem, we cloned the orthologous Hs2D01 sequence from H. schachtii. We demonstrate that Hs2D01 is a cytoplasmic effector that interacts with the intracellular kinase domain of HAESA (HAE), a cell surface-associated leucine-rich repeat (LRR) receptor-like kinase (RLK) involved in signalling the activation of cell wall-remodelling enzymes important for cell separation during abscission and lateral root emergence. Furthermore, we show that AtHAE is expressed in the syncytium and, therefore, could serve as a viable host target for Hs2D01. Infective juveniles effectively penetrated the roots of HAE and HAESA-LIKE2 (HSL2) double mutant plants; however, fewer nematodes developed on the roots, consistent with a role for this receptor family in nematode infection. Taken together, our results suggest that the Hs2D01-AtHAE interaction may play an important role in sugar beet cyst nematode parasitism.
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Affiliation(s)
- Anju Verma
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Marriam Lin
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
- Boyle Frederickson Intellectual Property LawMilwaukeeWisconsinUSA
| | - Dante Smith
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
- Conagra Brands, Inc., Corporate Microbiology, Research and DevelopmentOmahaNebraskaUSA
| | - John C. Walker
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Eric L. Davis
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Richard S. Hussey
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa G. Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
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2
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Bennett M, Piya S, Baum TJ, Hewezi T. miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism. Plant Physiol 2022; 189:2432-2453. [PMID: 35579365 PMCID: PMC9342967 DOI: 10.1093/plphys/kiac228] [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] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 05/20/2023]
Abstract
Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis-H. schachtii interactions.
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Affiliation(s)
- Morgan Bennett
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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3
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Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, Shao J, Koutsovoulos GD, Zasada I, Matsumoto T, Danchin EGJ, Baum TJ, Eves-van den Akker S, Nemchinov LG. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathog 2021; 17:e1010036. [PMID: 34748609 PMCID: PMC8601627 DOI: 10.1371/journal.ppat.1010036] [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: 06/17/2021] [Revised: 11/18/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Roxana Y. Myers
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Clement Pellegrin
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Wram
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Cedar Hesse
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Thomas R. Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Jonathan Shao
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | | | - Inga Zasada
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Tracie Matsumoto
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Etienne G. J. Danchin
- INRAE, Université Côte d’Azur, CNRS, Institute Sophia Agrobiotech, Sophia Antipolis, France
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | | | - Lev G. Nemchinov
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
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Maier TR, Masonbrink RE, Vijayapalani P, Gardner M, Howland AD, Mitchum MG, Baum TJ. Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines. Mol Plant Microbe Interact 2021; 34:1084-1087. [PMID: 33900122 DOI: 10.1094/mpmi-03-21-0051-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The soybean cyst nematode Heterodera glycines is the most economically devastating pathogen of soybean in the United States and threatens to become even more damaging through the selection of virulent nematode populations in the field that can overcome natural resistance mechanisms in soybean cultivars. This pathogen, therefore, demands intense transcriptomic/genomic research inquiries into the biology of its parasitic mechanisms. H. glycines delivers effector proteins that are produced in specialized gland cells into the soybean root to enable infection. The study of effector proteins, thus, is particularly promising when exploring novel management options against this pathogen. Here, we announce the availability of a gland cell-specific RNA-seq resource. These data represent an expression snapshot of gland cell activity during early soybean infection of a virulent and an avirulent H. glycines population, providing a unique and highly valuable resource for scientists examining effector biology and nematode virulence.[Formula: see text] Copyright © 2021 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)
- Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Rick E Masonbrink
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, U.S.A
| | | | - Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Amanda D Howland
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, U.S.A
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
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Kranse O, Beasley H, Adams S, Pires-daSilva A, Bell C, Lilley CJ, Urwin PE, Bird D, Miska E, Smant G, Gheysen G, Jones J, Viney M, Abad P, Maier TR, Baum TJ, Siddique S, Williamson V, Akay A, Eves-van den Akker S. Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3 (Bethesda) 2021; 11:6135037. [PMID: 33585878 PMCID: PMC8022973 DOI: 10.1093/g3journal/jkaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022]
Abstract
Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterize the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimize various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.
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Affiliation(s)
- Olaf Kranse
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Helen Beasley
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Christopher Bell
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Catherine J Lilley
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter E Urwin
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David Bird
- Entomology and Plant Pathology, NC State University, Raleigh, NC 27695-7613, USA
| | - Eric Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Godelieve Gheysen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - John Jones
- Cell & Molecular Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, UK.,School of Biology, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Valerie Williamson
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Alper Akay
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Wang J, Dhroso A, Liu X, Baum TJ, Hussey RS, Davis EL, Wang X, Korkin D, Mitchum MG. Phytonematode peptide effectors exploit a host post-translational trafficking mechanism to the ER using a novel translocation signal. New Phytol 2021; 229:563-574. [PMID: 32569394 DOI: 10.1111/nph.16765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/14/2020] [Accepted: 06/02/2020] [Indexed: 05/26/2023]
Abstract
Cyst nematodes induce a multicellular feeding site within roots called a syncytium. It remains unknown how root cells are primed for incorporation into the developing syncytium. Furthermore, it is unclear how CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptide effectors secreted into the cytoplasm of the initial feeding cell could have an effect on plant cells so distant from where the nematode is feeding as the syncytium expands. Here we describe a novel translocation signal within nematode CLE effectors that is recognized by plant cell secretory machinery to redirect these peptides from the cytoplasm to the apoplast of plant cells. We show that the translocation signal is functionally conserved across CLE effectors identified in nematode species spanning three genera and multiple plant species, operative across plant cell types, and can traffic other unrelated small peptides from the cytoplasm to the apoplast of host cells via a previously unknown post-translational mechanism of endoplasmic reticulum (ER) translocation. Our results uncover a mechanism of effector trafficking that is unprecedented in any plant pathogen to date, andthey illustrate how phytonematodes can deliver effector proteins into host cells and then hijack plant cellular processes for their export back out of the cell to function as external signaling molecules to distant cells.
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Affiliation(s)
- Jianying Wang
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Xunliang Liu
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Richard S Hussey
- Department of Plant Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiaohong Wang
- Robert W. Holley Center for Agriculture and Health, US Department of Agriculture, Agricultural Research Service and School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
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7
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Vieira P, Shao J, Vijayapalani P, Maier TR, Pellegrin C, Eves-van den Akker S, Baum TJ, Nemchinov LG. A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans. BMC Genomics 2020; 21:738. [PMID: 33096989 PMCID: PMC7585316 DOI: 10.1186/s12864-020-07146-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecular mechanisms employed by this nematode to promote virulence remain largely unknown. RESULTS Here we generated a new and comprehensive esophageal glands-specific transcriptome library for P. penetrans. In-depth analysis of this transcriptome enabled a robust identification of a catalogue of 30 new candidate effector genes, which were experimentally validated in the esophageal glands by in situ hybridization. We further validated the expression of a multifaceted network of candidate effectors during the interaction with different plants. To advance our understanding of the "effectorome" of P. penetrans, we adopted a phylogenetic approach and compared the expanded effector repertoire of P. penetrans to the genome/transcriptome of other nematode species with similar or contrasting parasitism strategies. Our data allowed us to infer plausible evolutionary histories that shaped the effector repertoire of P. penetrans, as well as other close and distant plant-parasitic nematodes. Two remarkable trends were apparent: 1) large scale effector birth in the Pratylenchidae in general and P. penetrans in particular, and 2) large scale effector death in sedentary (endo) plant-parasitic nematodes. CONCLUSIONS Our study doubles the number of validated Pratylenchus penetrans effectors reported in the literature. The dramatic effector gene gain in P. penetrans could be related to the remarkable ability of this nematode to parasitize a large number of plants. Our data provide valuable insights into nematode parasitism and contribute towards basic understating of the adaptation of P. penetrans and other root lesion nematodes to specific host plants.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA.
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Jonathan Shao
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA
| | | | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Clement Pellegrin
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Lev G Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA
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8
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Picart-Picolo A, Grob S, Picault N, Franek M, Llauro C, Halter T, Maier TR, Jobet E, Descombin J, Zhang P, Paramasivan V, Baum TJ, Navarro L, Dvořáčková M, Mirouze M, Pontvianne F. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome Res 2020; 30:1583-1592. [PMID: 33033057 PMCID: PMC7605254 DOI: 10.1101/gr.261586.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 01/23/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.
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Affiliation(s)
- Ariadna Picart-Picolo
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Stefan Grob
- Institute of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Nathalie Picault
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Christel Llauro
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Thierry Halter
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Edouard Jobet
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Julie Descombin
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Panpan Zhang
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | | | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Lionel Navarro
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Marie Mirouze
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | - Frédéric Pontvianne
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
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9
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Pogorelko G, Wang J, Juvale PS, Mitchum MG, Baum TJ. Screening soybean cyst nematode effectors for their ability to suppress plant immunity. Mol Plant Pathol 2020; 21:1240-1247. [PMID: 32672422 PMCID: PMC7411561 DOI: 10.1111/mpp.12972] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 06/05/2020] [Indexed: 05/19/2023]
Abstract
The soybean cyst nematode (SCN), Heterodera glycines, is one of the most destructive pathogens of soybeans. SCN is an obligate and sedentary parasite that transforms host plant root cells into an elaborate permanent feeding site, a syncytium. Formation and maintenance of a viable syncytium is an absolute requirement for nematode growth and reproduction. In turn, sensing pathogen attack, plants activate defence responses and may trigger programmed cell death at the sites of infection. For successful parasitism, H. glycines must suppress these host defence responses to establish and maintain viable syncytia. Similar to other pathogens, H. glycines engages in these molecular interactions with its host via effector proteins. The goal of this study was to conduct a comprehensive screen to identify H. glycines effectors that interfere with plant immune responses. We used Nicotiana benthamiana plants infected by Pseudomonas syringae and Pseudomonas fluorescens strains. Using these pathosystems, we screened 51 H. glycines effectors to identify candidates that could inhibit effector-triggered immunity (ETI) and/or pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). We identified three effectors as ETI suppressors and seven effectors as PTI suppressors. We also assessed expression modulation of plant immune marker genes as a function of these suppressors.
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Affiliation(s)
- Gennady Pogorelko
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Jianying Wang
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
| | - Parijat S. Juvale
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGAUSA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
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Wang J, Yeckel G, Kandoth PK, Wasala L, Hussey RS, Davis EL, Baum TJ, Mitchum MG. Targeted suppression of soybean BAG6-induced cell death in yeast by soybean cyst nematode effectors. Mol Plant Pathol 2020; 21:1227-1239. [PMID: 32686295 PMCID: PMC7411569 DOI: 10.1111/mpp.12970] [Citation(s) in RCA: 4] [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: 03/06/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 05/29/2023]
Abstract
While numerous effectors that suppress plant immunity have been identified from bacteria, fungi, and oomycete pathogens, relatively little is known for nematode effectors. Several dozen effectors have been reported from the soybean cyst nematode (SCN). Previous studies suggest that a hypersensitive response-like programmed cell death is triggered at nematode feeding sites in soybean during an incompatible interaction. However, virulent SCN populations overcome this incompatibility using unknown mechanisms. A soybean BAG6 (Bcl-2 associated anthanogene 6) gene previously reported by us to be highly up-regulated in degenerating feeding sites induced by SCN in a resistant soybean line was attenuated in response to a virulent SCN population. We show that GmBAG6-1 induces cell death in yeast like its Arabidopsis homolog AtBAG6 and also in soybean. This led us to hypothesize that virulent SCN may target GmBAG6-1 as part of their strategy to overcome soybean defence responses during infection. Thus, we used a yeast viability assay to screen SCN effector candidates for their ability to specifically suppress GmBAG6-1-induced cell death. We identified several effectors that strongly suppressed cell death mediated by GmBAG6-1. Two effectors identified as suppressors showed direct interaction with GmBAG6-1 in yeast, suggesting that one mechanism of cell death suppression may occur through an interaction with this host protein.
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Affiliation(s)
- Jianying Wang
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
| | - Greg Yeckel
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Present address:
Corteva AgriscienceJohnstonIAUSA
| | - Pramod K. Kandoth
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Present address:
National Agri‐food Biotechnology InstituteMohaliIndia
| | - Lakmini Wasala
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Present address:
Department of Veterinary PathobiologyUniversity of MissouriColumbiaMOUSA
| | | | - Eric L. Davis
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGAUSA
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11
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Piya S, Liu J, Burch-Smith T, Baum TJ, Hewezi T. A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism. J Exp Bot 2020; 71:1402-1417. [PMID: 31701146 PMCID: PMC7031083 DOI: 10.1093/jxb/erz502] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 07/15/2019] [Accepted: 11/05/2019] [Indexed: 05/21/2023]
Abstract
Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Jinyi Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Present address: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Correspondence:
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12
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Pogorelko GV, Juvale PS, Rutter WB, Hütten M, Maier TR, Hewezi T, Paulus J, van der Hoorn RA, Grundler FM, Siddique S, Lionetti V, Zabotina OA, Baum TJ. Re-targeting of a plant defense protease by a cyst nematode effector. Plant J 2019; 98:1000-1014. [PMID: 30801789 DOI: 10.1111/tpj.14295] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/08/2019] [Accepted: 02/15/2019] [Indexed: 05/29/2023]
Abstract
Plants mount defense responses during pathogen attacks, and robust host defense suppression by pathogen effector proteins is essential for infection success. 4E02 is an effector of the sugar beet cyst nematode Heterodera schachtii. Arabidopsis thaliana lines expressing the effector-coding sequence showed altered expression levels of defense response genes, as well as higher susceptibility to both the biotroph H. schachtii and the necrotroph Botrytis cinerea, indicating a potential suppression of defenses by 4E02. Yeast two-hybrid analyses showed that 4E02 targets A. thaliana vacuolar papain-like cysteine protease (PLCP) 'Responsive to Dehydration 21A' (RD21A), which has been shown to function in the plant defense response. Activity-based protein profiling analyses documented that the in planta presence of 4E02 does not impede enzymatic activity of RD21A. Instead, 4E02 mediates a re-localization of this protease from the vacuole to the nucleus and cytoplasm, which is likely to prevent the protease from performing its defense function and at the same time, brings it in contact with novel substrates. Yeast two-hybrid analyses showed that RD21A interacts with multiple host proteins including enzymes involved in defense responses as well as carbohydrate metabolism. In support of a role in carbohydrate metabolism of RD21A after its effector-mediated re-localization, we observed cell wall compositional changes in 4E02 expressing A. thaliana lines. Collectively, our study shows that 4E02 removes RD21A from its defense-inducing pathway and repurposes this enzyme by targeting the active protease to different cell compartments.
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Affiliation(s)
- Gennady V Pogorelko
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - William B Rutter
- USDA-ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Marion Hütten
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Judith Paulus
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Florian Mw Grundler
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Vincenzo Lionetti
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185, Rome, Italy
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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Noon JB, Hewezi T, Baum TJ. Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections. J Exp Bot 2019; 70:1653-1668. [PMID: 30715445 PMCID: PMC6411377 DOI: 10.1093/jxb/erz022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 05/20/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, penetrates soybean roots and migrates to the vascular cylinder where it forms a feeding site called the syncytium. MiRNA396 (miR396) targets growth-regulating factor (GRF) genes, and the miR396-GRF1/3 module is a master regulator of syncytium development in model cyst nematode H. schachtii infection of Arabidopsis. Here, we investigated whether this regulatory system operates similarly in soybean roots and is likewise important for H. glycines infection. We found that a network involving nine MIR396 and 23 GRF genes is important for normal development of soybean roots and that GRF function is specified in the root apical meristem by miR396. All MIR396 genes are down-regulated in the syncytium during its formation phase while, specifically, 11 different GRF genes are up-regulated. The switch to the syncytium maintenance phase coincides with up-regulation of MIR396 and down-regulation of the 11 GRF genes specifically via post-transcriptional regulation by miR396. Furthermore, interference with the miR396-GRF6/8-13/15-17/19 regulatory network, through either overexpression or knockdown experiments, does not affect the number of H. glycines juveniles that enter the vascular cylinder to initiate syncytia, but specifically inhibits efficient H. glycines development to adult females. Therefore, homeostasis in the miR396-GRF6/8-13/15-17/19 regulatory network is essential for productive H. glycines infections.
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Affiliation(s)
- Jason B Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
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14
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Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG, Mimee B, den Akker SEV, Hudson M, Severin AJ, Baum TJ. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 2019; 20:119. [PMID: 30732586 PMCID: PMC6367775 DOI: 10.1186/s12864-019-5485-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. RESULTS Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons. CONCLUSIONS This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
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Affiliation(s)
- Rick Masonbrink
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Tom R. Maier
- Department of Plant Pathology, Iowa State University, Ames, IA USA
| | - Usha Muppirala
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Arun S. Seetharam
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Etienne Lord
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nathan T. Johnson
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA USA
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Matthew Hudson
- Department of Crop Sciences University of Illinois, Urbana, IL USA
| | | | - Thomas J. Baum
- Department of Plant Pathology, Iowa State University, Ames, IA USA
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Barnes SN, Masonbrink RE, Maier TR, Seetharam A, Sindhu AS, Severin AJ, Baum TJ. Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1. Sci Rep 2019; 9:1356. [PMID: 30718603 PMCID: PMC6362198 DOI: 10.1038/s41598-018-37857-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 07/06/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Spliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5'-ends of transcripts during RNA-seq library preparation, known as 5'-bias. Existing datasets and novel methodology were used to identify both conserved SLs and unique hypervariable SLs within Heterodera glycines, the soybean cyst nematode. In H. glycines, twenty-one distinct SL sequences were found on 2,532 unique H. glycines transcripts. The SL sequences identified on the H. glycines transcripts demonstrated a high level of promiscuity, meaning that some transcripts produced as many as nine different individual SL-transcript combinations. Most uniquely, transcriptome analysis revealed that H. glycines is the first nematode to demonstrate a higher SL trans-splicing rate using a species-specific SL over well-conserved Caenorhabditis elegans SL-like sequences.
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Affiliation(s)
- Stacey N Barnes
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Thomas R Maier
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA
| | - Arun Seetharam
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | | | - Andrew J Severin
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Baum
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA.
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Masonbrink R, Maier TR, Seetharam AS, Juvale PS, Baber L, Baum TJ, Severin AJ. SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines). Database (Oxford) 2019; 2019:baz111. [PMID: 31680133 PMCID: PMC6853641 DOI: 10.1093/database/baz111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/29/2019] [Revised: 07/22/2019] [Accepted: 08/09/2019] [Indexed: 11/25/2022]
Abstract
Soybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.
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Affiliation(s)
- Rick Masonbrink
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Levi Baber
- Research IT, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
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17
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Vijayapalani P, Hewezi T, Pontvianne F, Baum TJ. An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host rRNA Genes by Altering Histone Acetylation. Plant Cell 2018; 30:2795-2812. [PMID: 30333146 PMCID: PMC6305986 DOI: 10.1105/tpc.18.00570] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/25/2018] [Accepted: 10/14/2018] [Indexed: 05/04/2023]
Abstract
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications. We determined that plants expressing the 32E03 coding sequence exhibited increased acetylation of histone H3 along the rDNA chromatin. At low 32E03 expression levels, these chromatin changes triggered the derepression of a subset of rRNA genes, which were conducive to H. schachtii parasitism. By contrast, high levels of 32E03 caused profound bidirectional transcription along the rDNA, which triggered rDNA-specific small RNA production leading to RNA-directed DNA methylation and silencing of rDNA, which inhibited nematode development. Our data show that the 32E03 effector alters plant rRNA gene expression by modulating rDNA chromatin in a dose-dependent manner. Thus, the 32E03 effector epigenetically regulates plant gene expression to promote cyst nematode parasitism.
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Affiliation(s)
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996
| | - Frederic Pontvianne
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, F-66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, F-66860, Perpignan, France
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Address correspondence to
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Barnes SN, Wram CL, Mitchum MG, Baum TJ. The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein. Mol Plant Pathol 2018; 19:2263-2276. [PMID: 29719112 PMCID: PMC6637993 DOI: 10.1111/mpp.12697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/15/2018] [Revised: 04/23/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
Cyst nematodes are plant pathogens that infect a wide range of economically important crops. One parasitic mechanism employed by cyst nematodes is the production and in planta delivery of effector proteins to modify plant cells and suppress defences to favour parasitism. This study focuses on GLAND4, an effector of Heterodera glycines and H. schachtii, the soybean and sugar beet cyst nematodes, respectively. We show that GLAND4 is recognized by the plant cellular machinery and is transported to the plant nucleus, an organelle for which little is known about plant nematode effector functions. We show that GLAND4 has DNA-binding ability and represses reporter gene expression in a plant transcriptional assay. One DNA fragment that binds to GLAND4 is localized in an Arabidopsis chromosomal region associated with the promoters of two lipid transfer protein genes (LTP). These LTPs have known defence functions and are down-regulated in the nematode feeding site. When expressed in Arabidopsis, the presence of GLAND4 causes the down-regulation of the two LTP genes in question, which is also associated with increased susceptibility to the plant-pathogenic bacterium Pseudomonas syringae. Furthermore, overexpression of one of the LTP genes reduces plant susceptibility to H. schachtii and P. syringae, confirming that LTP repression probably suppresses plant defences. This study makes GLAND4 one of a small subset of characterized plant nematode nuclear effectors and identifies GLAND4 as the first DNA-binding, plant-parasitic nematode effector.
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Affiliation(s)
- Stacey N. Barnes
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
| | - Catherine L. Wram
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
- Present address:
Department of Botany and Plant PathologyOregon State UniversityCorvallisOR 97330USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA
| | - Thomas J. Baum
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
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Verma A, Lee C, Morriss S, Odu F, Kenning C, Rizzo N, Spollen WG, Lin M, McRae AG, Givan SA, Hewezi T, Hussey R, Davis EL, Baum TJ, Mitchum MG. The novel cyst nematode effector protein 30D08 targets host nuclear functions to alter gene expression in feeding sites. New Phytol 2018; 219:697-713. [PMID: 29726613 DOI: 10.1111/nph.15179] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 09/13/2017] [Accepted: 03/15/2018] [Indexed: 05/29/2023]
Abstract
Cyst nematodes deliver effector proteins into host cells to manipulate cellular processes and establish a metabolically hyperactive feeding site. The novel 30D08 effector protein is produced in the dorsal gland of parasitic juveniles, but its function has remained unknown. We demonstrate that expression of 30D08 contributes to nematode parasitism, the protein is packaged into secretory granules and it is targeted to the plant nucleus where it interacts with SMU2 (homolog of suppressor of mec-8 and unc-52 2), an auxiliary spliceosomal protein. We show that SMU2 is expressed in feeding sites and an smu2 mutant is less susceptible to nematode infection. In Arabidopsis expressing 30D08 under the SMU2 promoter, several genes were found to be alternatively spliced and the most abundant functional classes represented among differentially expressed genes were involved in RNA processing, transcription and binding, as well as in development, and hormone and secondary metabolism, representing key cellular processes known to be important for feeding site formation. In conclusion, we demonstrated that the 30D08 effector is secreted from the nematode and targeted to the plant nucleus where its interaction with a host auxiliary spliceosomal protein may alter the pre-mRNA splicing and expression of a subset of genes important for feeding site formation.
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Affiliation(s)
- Anju Verma
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Chris Lee
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Stephanie Morriss
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Fiona Odu
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Charlotte Kenning
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | | | - William G Spollen
- Informatics Research Core Facility, University of Missouri, Columbia, MO, 65211, USA
| | - Marriam Lin
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Amanda G McRae
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Scott A Givan
- Informatics Research Core Facility, University of Missouri, Columbia, MO, 65211, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard Hussey
- Department of Plant Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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20
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Vieira P, Maier TR, Eves‐van den Akker S, Howe DK, Zasada I, Baum TJ, Eisenback JD, Kamo K. Identification of candidate effector genes of Pratylenchus penetrans. Mol Plant Pathol 2018; 19:1887-1907. [PMID: 29424950 PMCID: PMC6638058 DOI: 10.1111/mpp.12666] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 05/02/2023]
Abstract
Pratylenchus penetrans is one of the most important species of root lesion nematodes (RLNs) because of its detrimental and economic impact in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbours a significant number of secreted proteins that play key roles during parasitism. Here, we combined spatially and temporally resolved next-generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the oesophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen.
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Affiliation(s)
- Paulo Vieira
- Department of Plant Pathology, Physiology, and Weed ScienceVirginia TechBlacksburgVA 24061USA
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of AgricultureBeltsvilleMD 20705‐2350USA
| | - Thomas R. Maier
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | - Sebastian Eves‐van den Akker
- Department of Biological ChemistryJohn Innes Centre, Norwich Research ParkNorwich NR4 7UHUK
- School of Life SciencesUniversity of DundeeDundee DD1 5EHUK
| | - Dana K. Howe
- Department of Integrative BiologyOregon State UniversityCorvallisOR 97331USA
| | - Inga Zasada
- Horticultural Crops Research LaboratoryU.S. Department of AgricultureCorvallisOR 97330USA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | - Jonathan D. Eisenback
- Department of Plant Pathology, Physiology, and Weed ScienceVirginia TechBlacksburgVA 24061USA
| | - Kathryn Kamo
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of AgricultureBeltsvilleMD 20705‐2350USA
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21
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Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Sci Rep 2018; 8:2505. [PMID: 29410430 PMCID: PMC5802810 DOI: 10.1038/s41598-018-20536-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 11/04/2017] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
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Affiliation(s)
- Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Nathan Johnson
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, USA
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA.
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA.
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22
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Affiliation(s)
- Parijat S. Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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23
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Qi M, Grayczyk JP, Seitz JM, Lee Y, Link TI, Choi D, Pedley KF, Voegele RT, Baum TJ, Whitham SA. Suppression or Activation of Immune Responses by Predicted Secreted Proteins of the Soybean Rust Pathogen Phakopsora pachyrhizi. Mol Plant Microbe Interact 2018; 31:163-174. [PMID: 29144203 DOI: 10.1094/mpmi-07-17-0173-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Rust fungi, such as the soybean rust pathogen Phakopsora pachyrhizi, are major threats to crop production. They form specialized haustoria that are hyphal structures intimately associated with host-plant cell membranes. These haustoria have roles in acquiring nutrients and secreting effector proteins that manipulate host immune systems. Functional characterization of effector proteins of rust fungi is important for understanding mechanisms that underlie their virulence and pathogenicity. Hundreds of candidate effector proteins have been predicted for rust pathogens, but it is not clear how to prioritize these effector candidates for further characterization. There is a need for high-throughput approaches for screening effector candidates to obtain experimental evidence for effector-like functions, such as the manipulation of host immune systems. We have focused on identifying effector candidates with immune-related functions in the soybean rust fungus P. pachyrhizi. To facilitate the screening of many P. pachyrhizi effector candidates (named PpECs), we used heterologous expression systems, including the bacterial type III secretion system, Agrobacterium infiltration, a plant virus, and a yeast strain, to establish an experimental pipeline for identifying PpECs with immune-related functions and establishing their subcellular localizations. Several PpECs were identified that could suppress or activate immune responses in nonhost Nicotiana benthamiana, N. tabacum, Arabidopsis, tomato, or pepper plants.
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Affiliation(s)
- Mingsheng Qi
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - James P Grayczyk
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - Janina M Seitz
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Youngsill Lee
- 3 Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea; and
| | - Tobias I Link
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Doil Choi
- 3 Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea; and
| | - Kerry F Pedley
- 4 Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Ft. Detrick, MD 21702, U.S.A
| | - Ralf T Voegele
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Thomas J Baum
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - Steven A Whitham
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
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24
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Piya S, Kihm C, Rice JH, Baum TJ, Hewezi T. Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism. Plant Physiol 2017; 174:1897-1912. [PMID: 28512179 PMCID: PMC5490899 DOI: 10.1104/pp.17.00273] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/13/2017] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) recently have been established as key regulators of transcriptome reprogramming that define cell function and identity. Nevertheless, the molecular functions of the greatest number of miRNA genes remain to be determined. Here, we report cooperative regulatory functions of miR858 and its MYB83 transcription factor target gene in transcriptome reprogramming during Heterodera cyst nematode parasitism of Arabidopsis (Arabidopsis thaliana). Gene expression analyses and promoter-GUS fusion assays documented a role of miR858 in posttranscriptional regulation of MYB83 in the Heterodera schachtii-induced feeding sites, the syncytia. Constitutive overexpression of miR858 interfered with H. schachtii parasitism of Arabidopsis, leading to reduced susceptibility, while reduced miR858 abundance enhanced plant susceptibility. Similarly, MYB83 expression increases were conducive to nematode infection because overexpression of a noncleavable coding sequence of MYB83 significantly increased plant susceptibility, whereas a myb83 mutation rendered the plants less susceptible. In addition, RNA-seq analysis revealed that genes involved in hormone signaling pathways, defense response, glucosinolate biosynthesis, cell wall modification, sugar transport, and transcriptional control are the key etiological factors by which MYB83 facilitates nematode parasitism of Arabidopsis. Furthermore, we discovered that miR858-mediated silencing of MYB83 is tightly regulated through a feedback loop that might contribute to fine-tuning the expression of more than a thousand of MYB83-regulated genes in the H. schachtii-induced syncytium. Together, our results suggest a role of the miR858-MYB83 regulatory system in finely balancing gene expression patterns during H. schachtii parasitism of Arabidopsis to ensure optimal cellular function.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Christina Kihm
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
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25
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Hewezi T, Piya S, Qi M, Balasubramaniam M, Rice JH, Baum TJ. Arabidopsis miR827 mediates post-transcriptional gene silencing of its ubiquitin E3 ligase target gene in the syncytium of the cyst nematode Heterodera schachtii to enhance susceptibility. Plant J 2016; 88:179-192. [PMID: 27304416 DOI: 10.1111/tpj.13238] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 03/04/2016] [Accepted: 06/08/2016] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a major class of small non-coding RNAs with emerging functions in biotic and abiotic interactions. Here, we report on a new functional role of Arabidopsis miR827 and its NITROGEN LIMITATION ADAPTATION (NLA) target gene in mediating plant susceptibility to the beet cyst nematode Heterodera schachtii. Cyst nematodes are sedentary endoparasites that induce the formation of multinucleated feeding structures termed syncytia in the roots of host plants. Using promoter:GUS fusion assays we established that miR827 was activated in the initial feeding cells and this activation was maintained in the syncytium during all sedentary stages of nematode development. Meanwhile, the NLA target gene, which encodes an ubiquitin E3 ligase enzyme, was post-transcriptionally silenced in the syncytium to permanently suppress its activity during all nematode parasitic stages. Overexpression of miR827 in Arabidopsis resulted in hyper-susceptibility to H. schachtii. In contrast, inactivation of miR827 activity through target mimicry or by overexpression a miR827-resistant cDNA of NLA produced the opposite phenotype of reduced plant susceptibility to H. schachtii. Gene expression analysis of several pathogenesis-related genes together with Agrobacterium-mediated transient expression in Nicotiana benthamiana provided strong evidence that miR827-mediated downregulation of NLA to suppress basal defense pathways. In addition, using yeast two-hybrid screens we identified several candidates of NLA-interacting proteins that are involved in a wide range of biological processes and molecular functions, including three pathogenesis-related proteins. Taken together, we conclude that nematode-activated miR827 in the syncytium is necessary to suppress immune responses in order to establish infection and cause disease.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | | | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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26
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Noon JB, Qi M, Sill DN, Muppirala U, Eves-van den Akker S, Maier TR, Dobbs D, Mitchum MG, Hewezi T, Baum TJ. A Plasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity. New Phytol 2016; 212:444-60. [PMID: 27265684 DOI: 10.1111/nph.14047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 03/16/2016] [Accepted: 05/04/2016] [Indexed: 05/19/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, delivers effector proteins into soybean roots to initiate and maintain an obligate parasitic relationship. HgGLAND18 encodes a candidate H. glycines effector and is expressed throughout the infection process. We used a combination of molecular, genetic, bioinformatic and phylogenetic analyses to determine the role of HgGLAND18 during H. glycines infection. HgGLAND18 is necessary for pathogenicity in compatible interactions with soybean. The encoded effector strongly suppresses both basal and hypersensitive cell death innate immune responses, and immunosuppression requires the presence and coordination between multiple protein domains. The N-terminal domain in HgGLAND18 contains unique sequence similarity to domains of an immunosuppressive effector of Plasmodium spp., the malaria parasites. The Plasmodium effector domains functionally complement the loss of the N-terminal domain from HgGLAND18. In-depth sequence searches and phylogenetic analyses demonstrate convergent evolution between effectors from divergent parasites of plants and animals as the cause of sequence and functional similarity.
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Affiliation(s)
- Jason B Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Danielle N Sill
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Usha Muppirala
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | | | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Drena Dobbs
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
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27
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Qi M, Link TI, Müller M, Hirschburger D, Pudake RN, Pedley KF, Braun E, Voegele RT, Baum TJ, Whitham SA. A Small Cysteine-Rich Protein from the Asian Soybean Rust Fungus, Phakopsora pachyrhizi, Suppresses Plant Immunity. PLoS Pathog 2016; 12:e1005827. [PMID: 27676173 PMCID: PMC5038961 DOI: 10.1371/journal.ppat.1005827] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 07/19/2015] [Accepted: 07/26/2016] [Indexed: 11/25/2022] Open
Abstract
The Asian soybean rust fungus, Phakopsora pachyrhizi, is an obligate biotrophic pathogen causing severe soybean disease epidemics. Molecular mechanisms by which P. pachyrhizi and other rust fungi interact with their host plants are poorly understood. The genomes of all rust fungi encode many small, secreted cysteine-rich proteins (SSCRP). While these proteins are thought to function within the host, their roles are completely unknown. Here, we present the characterization of P. pachyrhizi effector candidate 23 (PpEC23), a SSCRP that we show to suppress plant immunity. Furthermore, we show that PpEC23 interacts with soybean transcription factor GmSPL12l and that soybean plants in which GmSPL12l is silenced have constitutively active immunity, thereby identifying GmSPL12l as a negative regulator of soybean defenses. Collectively, our data present evidence for a virulence function of a rust SSCRP and suggest that PpEC23 is able to suppress soybean immune responses and physically interact with soybean transcription factor GmSPL12l, a negative immune regulator.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Tobias I. Link
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Manuel Müller
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | | | - Ramesh N. Pudake
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida, India
| | - Kerry F. Pedley
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture–Agricultural Research Service, Ft. Detrick, Maryland, United States of America
| | - Edward Braun
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Ralf T. Voegele
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
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28
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Pogorelko G, Juvale PS, Rutter WB, Hewezi T, Hussey R, Davis EL, Mitchum MG, Baum TJ. A cyst nematode effector binds to diverse plant proteins, increases nematode susceptibility and affects root morphology. Mol Plant Pathol 2016; 17:832-44. [PMID: 26575318 PMCID: PMC6638508 DOI: 10.1111/mpp.12330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 07/30/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 05/20/2023]
Abstract
Cyst nematodes are plant-parasitic roundworms that are of significance in many cropping systems around the world. Cyst nematode infection is facilitated by effector proteins secreted from the nematode into the plant host. The cDNAs of the 25A01-like effector family are novel sequences that were isolated from the oesophageal gland cells of the soybean cyst nematode (Heterodera glycines). To aid functional characterization, we identified an orthologous member of this protein family (Hs25A01) from the closely related sugar beet cyst nematode H. schachtii, which infects Arabidopsis. Constitutive expression of the Hs25A01 CDS in Arabidopsis plants caused a small increase in root length, accompanied by up to a 22% increase in susceptibility to H. schachtii. A plant-expressed RNA interference (RNAi) construct targeting Hs25A01 transcripts in invading nematodes significantly reduced host susceptibility to H. schachtii. These data document that Hs25A01 has physiological functions in planta and a role in cyst nematode parasitism. In vivo and in vitro binding assays confirmed the specific interactions of Hs25A01 with an Arabidopsis F-box-containing protein, a chalcone synthase and the translation initiation factor eIF-2 β subunit (eIF-2bs), making these proteins probable candidates for involvement in the observed changes in plant growth and parasitism. A role of eIF-2bs in the mediation of Hs25A01 virulence function is further supported by the observation that two independent eIF-2bs Arabidopsis knock-out lines were significantly more susceptible to H. schachtii.
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Affiliation(s)
- Gennady Pogorelko
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66505, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard Hussey
- Department of Plant Pathology, The University of Georgia, Athens, GA, 30602, USA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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29
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Noon JB, Baum TJ. Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. BMC Evol Biol 2016; 16:74. [PMID: 27068610 PMCID: PMC4828791 DOI: 10.1186/s12862-016-0651-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/05/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. RESULTS Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches. CONCLUSIONS GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.
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Affiliation(s)
- Jason B. Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
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Noon JB, Hewezi T, Maier TR, Simmons C, Wei JZ, Wu G, Llaca V, Deschamps S, Davis EL, Mitchum MG, Hussey RS, Baum TJ. Eighteen New Candidate Effectors of the Phytonematode Heterodera glycines Produced Specifically in the Secretory Esophageal Gland Cells During Parasitism. Phytopathology 2015; 105:1362-72. [PMID: 25871857 DOI: 10.1094/phyto-02-15-0049-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, is the number one pathogen of soybean (Glycine max). This nematode infects soybean roots and forms an elaborate feeding site in the vascular cylinder. H. glycines produces an arsenal of effector proteins in the secretory esophageal gland cells. More than 60 H. glycines candidate effectors were identified in previous gland-cell-mining projects. However, it is likely that additional candidate effectors remained unidentified. With the goal of identifying remaining H. glycines candidate effectors, we constructed and sequenced a large gland cell cDNA library resulting in 11,814 expressed sequence tags. After bioinformatic filtering for candidate effectors using a number of criteria, in situ hybridizations were performed in H. glycines whole-mount specimens to identify candidate effectors whose mRNA exclusively accumulated in the esophageal gland cells, which is a hallmark of many nematode effectors. This approach resulted in the identification of 18 new H. glycines esophageal gland-cell-specific candidate effectors. Of these candidate effectors, 11 sequences were pioneers without similarities to known proteins while 7 sequences had similarities to functionally annotated proteins in databases. These putative homologies provided the bases for the development of hypotheses about potential functions in the parasitism process.
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Affiliation(s)
- Jason B Noon
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Tarek Hewezi
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas R Maier
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Carl Simmons
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Jun-Zhi Wei
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Gusui Wu
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Victor Llaca
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Stéphane Deschamps
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Eric L Davis
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Melissa G Mitchum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Richard S Hussey
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas J Baum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
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Wubben MJ, Gavilano L, Baum TJ, Davis EL. Sequence and Spatiotemporal Expression Analysis of CLE-Motif Containing Genes from the Reniform Nematode (Rotylenchulus reniformis Linford & Oliveira). J Nematol 2015; 47:159-165. [PMID: 26170479 PMCID: PMC4492292] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 06/04/2023] Open
Abstract
The reniform nematode, Rotylenchulus reniformis, is a sedentary semi-endoparasitic species with a host range that encompasses more than 77 plant families. Nematode effector proteins containing plant-ligand motifs similar to CLAVATA3/ESR (CLE) peptides have been identified in the Heterodera, Globodera, and Meloidogyne genera of sedentary endoparasites. Here, we describe the isolation, sequence analysis, and spatiotemporal expression of three R. reniformis genes encoding putative CLE motifs named Rr-cle-1, Rr-cle-2, and Rr-cle-3. The Rr-cle cDNAs showed >98% identity with each other and the predicted peptides were identical with the exception of a short stretch of residues at the carboxy(C)-terminus of the variable domain (VD). Each RrCLE peptide possessed an amino-terminal signal peptide for secretion and a single C-terminal CLE motif that was most similar to Heterodera CLE motifs. Aligning the Rr-cle cDNAs with their corresponding genomic sequences showed three exons with an intron separating the signal peptide from the VD and a second intron separating the VD from the CLE motif. An alignment of the RrCLE1 peptide with Heterodera glycines and Heterodera schachtii CLE proteins revealed a high level of homology within the VD region associated with regulating in planta trafficking of the processed CLE peptide. Quantitative RT-PCR (qRT-PCR) showed similar expression profiles for each Rr-cle transcript across the R. reniformis life-cycle with the greatest transcript abundance being in sedentary parasitic female nematodes. In situ hybridization showed specific Rr-cle expression within the dorsal esophageal gland cell of sedentary parasitic females.
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Affiliation(s)
- Martin J Wubben
- USDA-ARS, Crop Science Research Lab, Genetics and Precision Agriculture Research Unit, Mississippi State, MS. ; Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS
| | - Lily Gavilano
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC
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Hewezi T, Juvale PS, Piya S, Maier TR, Rambani A, Rice JH, Mitchum MG, Davis EL, Hussey RS, Baum TJ. The cyst nematode effector protein 10A07 targets and recruits host posttranslational machinery to mediate its nuclear trafficking and to promote parasitism in Arabidopsis. Plant Cell 2015; 27:891-907. [PMID: 25715285 PMCID: PMC4558665 DOI: 10.1105/tpc.114.135327] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/29/2015] [Accepted: 02/10/2015] [Indexed: 05/18/2023]
Abstract
Plant-parasitic cyst nematodes synthesize and secrete effector proteins that are essential for parasitism. One such protein is the 10A07 effector from the sugar beet cyst nematode, Heterodera schachtii, which is exclusively expressed in the nematode dorsal gland cell during all nematode parasitic stages. Overexpression of H. schachtii 10A07 in Arabidopsis thaliana produced a hypersusceptible phenotype in response to H. schachtii infection along with developmental changes reminiscent of auxin effects. The 10A07 protein physically associates with a plant kinase and the IAA16 transcription factor in the cytoplasm and nucleus, respectively. The interacting plant kinase (IPK) phosphorylates 10A07 at Ser-144 and Ser-231 and mediates its trafficking from the cytoplasm to the nucleus. Translocation to the nucleus is phosphorylation dependent since substitution of Ser-144 and Ser-231 by alanine resulted in exclusive cytoplasmic accumulation of 10A07. IPK and IAA16 are highly upregulated in the nematode-induced syncytium (feeding cells), and deliberate manipulations of their expression significantly alter plant susceptibility to H. schachtii in an additive fashion. An inactive variant of IPK functioned antagonistically to the wild-type IPK and caused a dominant-negative phenotype of reduced plant susceptibility. Thus, exploitation of host processes to the advantage of the parasites is one mechanism by which cyst nematodes promote parasitism of host plants.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Parijat S Juvale
- Department of Plant Pathology, Iowa State University, Ames, Iowa 50011
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Tom R Maier
- Department of Plant Pathology, Iowa State University, Ames, Iowa 50011
| | - Aditi Rambani
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Eric L Davis
- North Carolina State University, Raleigh, North Carolina 27695
| | - Richard S Hussey
- Department of Plant Pathology, University of Georgia, Athens, Georgia 30602
| | - Thomas J Baum
- Department of Plant Pathology, Iowa State University, Ames, Iowa 50011
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Rutter WB, Hewezi T, Abubucker S, Maier TR, Huang G, Mitreva M, Hussey RS, Baum TJ. Mining novel effector proteins from the esophageal gland cells of Meloidogyne incognita. Mol Plant Microbe Interact 2014; 27:965-74. [PMID: 24875667 PMCID: PMC4249689 DOI: 10.1094/mpmi-03-14-0076-r] [Citation(s) in RCA: 21] [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] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Meloidogyne incognita is one of the most economically damaging plant pathogens in agriculture and horticulture. Identifying and characterizing the effector proteins which M. incognita secretes into its host plants during infection is an important step toward finding new ways to manage this pest. In this study, we have identified the cDNAs for 18 putative effectors (i.e., proteins that have the potential to facilitate M. incognita parasitism of host plants). These putative effectors are secretory proteins that do not contain transmembrane domains and whose genes are specifically expressed in the secretory gland cells of the nematode, indicating that they are likely secreted from the nematode through its stylet. We have determined that, in the plant cells, these putative effectors are likely to localize to the cytoplasm. Furthermore, the transcripts of many of these novel effectors are specifically upregulated during different stages of the nematode's life cycle, indicating that they function at specific stages during M. incognita parasitism. The predicted proteins showed little to no homology to known proteins from free-living nematode species, suggesting that they evolved recently to support the parasitic lifestyle. On the other hand, several of the effectors are part of gene families within the M. incognita genome as well as that of M. hapla, which points to an important role that these putative effectors are playing in both parasites. With the discovery of these putative effectors, we have increased our knowledge of the effector repertoire utilized by root-knot nematodes to infect, feed on, and reproduce on their host plants. Future studies investigating the roles that these proteins play in planta will help mitigate the effects of this damaging pest.
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Affiliation(s)
- William B. Rutter
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Tarek Hewezi
- University of Tennessee, Department of Plant Sciences, Knoxville, TN 37996-4561
| | - Sahar Abubucker
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Tom R. Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Guozhong Huang
- Department of Plant Pathology, University of Georgia, Athens 30602-7274
| | - Makedonka Mitreva
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Richard S. Hussey
- Department of Plant Pathology, University of Georgia, Athens 30602-7274
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Address correspondence to 351 Bessey Hall, , phone: 515-294-2398, Fax: 515-294-9420
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Rutter WB, Hewezi T, Maier TR, Mitchum MG, Davis EL, Hussey RS, Baum TJ. Members of the Meloidogyne avirulence protein family contain multiple plant ligand-like motifs. Phytopathology 2014; 104:879-85. [PMID: 25014776 DOI: 10.1094/phyto-11-13-0326-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Sedentary plant-parasitic nematodes engage in complex interactions with their host plants by secreting effector proteins. Some effectors of both root-knot nematodes (Meloidogyne spp.) and cyst nematodes (Heterodera and Globodera spp.) mimic plant ligand proteins. Most prominently, cyst nematodes secrete effectors that mimic plant CLAVATA3/ESR-related (CLE) ligand proteins. However, only cyst nematodes have been shown to secrete such effectors and to utilize CLE ligand mimicry in their interactions with host plants. Here, we document the presence of ligand-like motifs in bona fide root-knot nematode effectors that are most similar to CLE peptides from plants and cyst nematodes. We have identified multiple tandem CLE-like motifs conserved within the previously identified Meloidogyne avirulence protein (MAP) family that are secreted from root-knot nematodes and have been shown to function in planta. By searching all 12 MAP family members from multiple Meloidogyne spp., we identified 43 repetitive CLE-like motifs composing 14 unique variants. At least one CLE-like motif was conserved in each MAP family member. Furthermore, we documented the presence of other conserved sequences that resemble the variable domains described in Heterodera and Globodera CLE effectors. These findings document that root-knot nematodes appear to use CLE ligand mimicry and point toward a common host node targeted by two evolutionarily diverse groups of nematodes. As a consequence, it is likely that CLE signaling pathways are important in other phytonematode pathosystems as well.
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Liu J, Rice JH, Chen N, Baum TJ, Hewezi T. Synchronization of developmental processes and defense signaling by growth regulating transcription factors. PLoS One 2014; 9:e98477. [PMID: 24875638 PMCID: PMC4038601 DOI: 10.1371/journal.pone.0098477] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [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: 12/17/2013] [Accepted: 05/02/2014] [Indexed: 02/07/2023] Open
Abstract
Growth regulating factors (GRFs) are a conserved class of transcription factor in seed plants. GRFs are involved in various aspects of tissue differentiation and organ development. The implication of GRFs in biotic stress response has also been recently reported, suggesting a role of these transcription factors in coordinating the interaction between developmental processes and defense dynamics. However, the molecular mechanisms by which GRFs mediate the overlaps between defense signaling and developmental pathways are elusive. Here, we report large scale identification of putative target candidates of Arabidopsis GRF1 and GRF3 by comparing mRNA profiles of the grf1/grf2/grf3 triple mutant and those of the transgenic plants overexpressing miR396-resistant version of GRF1 or GRF3. We identified 1,098 and 600 genes as putative targets of GRF1 and GRF3, respectively. Functional classification of the potential target candidates revealed that GRF1 and GRF3 contribute to the regulation of various biological processes associated with defense response and disease resistance. GRF1 and GRF3 participate specifically in the regulation of defense-related transcription factors, cell-wall modifications, cytokinin biosynthesis and signaling, and secondary metabolites accumulation. GRF1 and GRF3 seem to fine-tune the crosstalk between miRNA signaling networks by regulating the expression of several miRNA target genes. In addition, our data suggest that GRF1 and GRF3 may function as negative regulators of gene expression through their association with other transcription factors. Collectively, our data provide new insights into how GRF1 and GRF3 might coordinate the interactions between defense signaling and plant growth and developmental pathways.
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Affiliation(s)
- Jinyi Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - J. Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Nana Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Link TI, Lang P, Scheffler BE, Duke MV, Graham MA, Cooper B, Tucker ML, van de Mortel M, Voegele RT, Mendgen K, Baum TJ, Whitham SA. The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. Mol Plant Pathol 2014; 15:379-93. [PMID: 24341524 PMCID: PMC6638672 DOI: 10.1111/mpp.12099] [Citation(s) in RCA: 27] [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
Haustoria of biotrophic rust fungi are responsible for the uptake of nutrients from their hosts and for the production of secreted proteins, known as effectors, which modulate the host immune system. The identification of the transcriptome of haustoria and an understanding of the functions of expressed genes therefore hold essential keys for the elucidation of fungus-plant interactions and the development of novel fungal control strategies. Here, we purified haustoria from infected leaves and used 454 sequencing to examine the haustorial transcriptomes of Phakopsora pachyrhizi and Uromyces appendiculatus, the causal agents of soybean rust and common bean rust, respectively. These pathogens cause extensive yield losses in their respective legume crop hosts. A series of analyses were used to annotate expressed sequences, including transposable elements and viruses, to predict secreted proteins from the assembled sequences and to identify families of candidate effectors. This work provides a foundation for the comparative analysis of haustorial gene expression with further insights into physiology and effector evolution.
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Affiliation(s)
- Tobias I Link
- Institut für Phytomedizin, FG Phytopathologie, Universität Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
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Morales AMAP, O Rourke JA, van de Mortel M, Scheider KT, Bancroft TJ, Bor M AZ, Nelson RT, Nettleton D, Baum TJ, Shoemaker RC, Frederick RD, Abdelnoor RV, Pedley KF, Whitham SA, Graham MA. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. Funct Plant Biol 2013; 40:1029-1047. [PMID: 32481171 DOI: 10.1071/fp12296] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/12/2013] [Indexed: 05/24/2023]
Abstract
Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.
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Affiliation(s)
- Aguida M A P Morales
- Universidade Federal de Viçosa, Departamento de Fitotecnia, 36.570-000, Viçosa, MG, Brazil
| | - Jamie A O Rourke
- USDA-Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN 55108, USA
| | - Martijn van de Mortel
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Katherine T Scheider
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | | | - Alu Zio Bor M
- Universidade Federal de Viçosa, Departamento de Fitotecnia, 36.570-000, Viçosa, MG, Brazil
| | - Rex T Nelson
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50014, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Randy C Shoemaker
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
| | - Reid D Frederick
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | - Ricardo V Abdelnoor
- Laboratório de Biotecnologia Vegetal e Bioinformática, Embrapa Soja, Rod. Carlos João Strass, 86001-970, Londrina - PR, Brazil
| | - Kerry F Pedley
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Michelle A Graham
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
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Mitchum MG, Hussey RS, Baum TJ, Wang X, Elling AA, Wubben M, Davis EL. Nematode effector proteins: an emerging paradigm of parasitism. New Phytol 2013; 199:879-894. [PMID: 23691972 DOI: 10.1111/nph.12323] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [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: 02/01/2013] [Accepted: 04/05/2013] [Indexed: 05/18/2023]
Abstract
Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda.
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Affiliation(s)
- Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Richard S Hussey
- Department of Plant Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Xiaohong Wang
- USDA-ARS, Robert W. Holley Center for Agriculture and Health and Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Axel A Elling
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Martin Wubben
- USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit and Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
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Kandoth PK, Heinz R, Yeckel G, Gross NW, Juvale PS, Hill J, Whitham SA, Baum TJ, Mitchum MG. A virus-induced gene silencing method to study soybean cyst nematode parasitism in Glycine max. BMC Res Notes 2013; 6:255. [PMID: 23830484 PMCID: PMC3708766 DOI: 10.1186/1756-0500-6-255] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/03/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Bean pod mottle virus (BPMV) based virus-induced gene silencing (VIGS) vectors have been developed and used in soybean for the functional analysis of genes involved in disease resistance to foliar pathogens. However, BPMV-VIGS protocols for studying genes involved in disease resistance or symbiotic associations with root microbes have not been developed. FINDINGS Here we describe a BPMV-VIGS protocol suitable for reverse genetic studies in soybean roots. We use this method for analyzing soybean genes involved in resistance to soybean cyst nematode (SCN). A detailed SCN screening pipeline is described. CONCLUSIONS The VIGS method described here provides a new tool to identify genes involved in soybean-nematode interactions. This method could be adapted to study genes associated with any root pathogenic or symbiotic associations.
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Affiliation(s)
- Pramod K Kandoth
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Robert Heinz
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Greg Yeckel
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
- Current address: Pioneer Hi-Bred, Johnston IA, 50131, USA
| | - Nathan W Gross
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
- Current address: Beadle Center for Biotechnology, University of Nebraska, Lincoln NE, 68588, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - John Hill
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
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40
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Chronis D, Chen S, Lu S, Hewezi T, Carpenter SCD, Loria R, Baum TJ, Wang X. A ubiquitin carboxyl extension protein secreted from a plant-parasitic nematode Globodera rostochiensis is cleaved in planta to promote plant parasitism. Plant J 2013; 74:185-96. [PMID: 23346875 DOI: 10.1111/tpj.12125] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/08/2013] [Accepted: 01/17/2013] [Indexed: 05/19/2023]
Abstract
Nematode effector proteins originating from esophageal gland cells play central roles in suppressing plant defenses and in formation of the plant feeding cells that are required for growth and development of cyst nematodes. A gene (GrUBCEP12) encoding a unique ubiquitin carboxyl extension protein (UBCEP) that consists of a signal peptide for secretion, a mono-ubiquitin domain, and a 12 amino acid carboxyl extension protein (CEP12) domain was cloned from the potato cyst nematode Globodera rostochiensis. This GrUBCEP12 gene was expressed exclusively within the nematode's dorsal esophageal gland cell, and was up-regulated in the parasitic second-stage juvenile, correlating with the time when feeding cell formation is initiated. We showed that specific GrUBCEP12 knockdown via RNA interference reduced nematode parasitic success, and that over-expression of the secreted Gr(Δ) (SP) UBCEP12 protein in potato resulted in increased nematode susceptibility, providing direct evidence that this secreted effector is involved in plant parasitism. Using transient expression assays in Nicotiana benthamiana, we found that Gr(Δ) (SP) UBCEP12 is processed into free ubiquitin and a CEP12 peptide (GrCEP12) in planta, and that GrCEP12 suppresses resistance gene-mediated cell death. A target search showed that expression of RPN2a, a gene encoding a subunit of the 26S proteasome, was dramatically suppressed in Gr(Δ) (SP) UBCEP12 but not GrCEP12 over-expression plants when compared with control plants. Together, these results suggest that, when delivered into host plant cells, Gr(Δ) (SP) UBCEP12 becomes two functional units, one acting to suppress plant immunity and the other potentially affecting the host 26S proteasome, to promote feeding cell formation.
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Affiliation(s)
- Demosthenis Chronis
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853, USA
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Xue B, Hamamouch N, Li C, Huang G, Hussey RS, Baum TJ, Davis EL. The 8D05 parasitism gene of Meloidogyne incognita is required for successful infection of host roots. Phytopathology 2013; 103:175-81. [PMID: 23294405 DOI: 10.1094/phyto-07-12-0173-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Parasitism genes encode effector proteins that are secreted through the stylet of root-knot nematodes to dramatically modify selected plant cells into giant-cells for feeding. The Mi8D05 parasitism gene previously identified was confirmed to encode a novel protein of 382 amino acids that had only one database homolog identified on contig 2374 within the Meloidogyne hapla genome. Mi8D05 expression peaked in M. incognita parasitic second-stage juveniles within host roots and its encoded protein was limited to the subventral esophageal gland cells that produce proteins secreted from the stylet. Constitutive expression of Mi8D05 in transformed Arabidopsis thaliana plants induced accelerated shoot growth and early flowering but had no visible effects on root growth. Independent lines of transgenic Arabidopsis that expressed a double-stranded RNA complementary to Mi8D05 in host-derived RNA interference (RNAi) tests had up to 90% reduction in infection by M. incognita compared with wild-type control plants, suggesting that Mi8D05 plays a critical role in parasitism by the root-knot nematode. Yeast two-hybrid experiments confirmed the specific interaction of the Mi8D05 protein with plant aquaporin tonoplast intrinsic protein 2 (TIP2) and provided evidence that the Mi8D05 effector may help regulate solute and water transport within giant-cells to promote the parasitic interaction.
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Affiliation(s)
- Bingye Xue
- North Carolina State University, Department of Plant Pathology, Raleigh 27607, USA
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42
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Maier TR, Hewezi T, Peng J, Baum TJ. Isolation of whole esophageal gland cells from plant-parasitic nematodes for transcriptome analyses and effector identification. Mol Plant Microbe Interact 2013; 26:31-35. [PMID: 22876962 DOI: 10.1094/mpmi-05-12-0121-fi] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Esophageal glands of plant-parasitic nematodes are highly specialized cells whose gene expression products include secreted effector proteins, which govern nematode parasitism of host plants. Therefore, elucidating the transcriptomes of esophageal glands with the goal of identifying nematode effectors is a promising avenue to understanding nematode parasitism and its evolutionary origins as well as to devising nematode control strategies. We have developed a method to separate and isolate individual esophageal gland cells from multiple species of plant-parasitic nematodes while preserving RNA quality. We have used such isolated gland cells for transcriptome analysis via high-throughput DNA sequencing. This method relies on the differential histochemical staining of the gland cells after homogenization of phytonematode tissues. Total RNA was extracted from whole gland cells isolated from eight different plant-parasitic nematode species. To validate this approach, the isolated RNA from three plant-parasitic nematode species-Globodera rostochiensis, Pratylenchus penetrans, and Radopholus similis-was amplified, gel purified, and used for 454 sequencing. We obtained 456,801 total reads with an average read length of 409 bp. Sequence analyses revealed the presence of homologs of previously known nematode effectors in these libraries, thus validating our approach. These data provide compelling evidence that this technical advance can be used to relatively easily and expediently discover effector repertoires of plant-parasitic nematodes.
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Affiliation(s)
- Tom R Maier
- Department of Plant Pathology and microbiology, Iowa State University, Ames, IA, USA
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43
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Abstract
A key feature of sedentary plant-parasitic nematodes is the release of effector proteins from their esophageal gland cells through their stylets into host roots. These proteinaceous stylet secretions have been shown to be crucial for successful parasitism by mediating the transition of normal root cells into specialized feeding sites and by negating plant defenses. Recent technical advances of purifying mRNA from esophageal gland cells of plant-parasitic nematodes coupled with emerging sequencing technologies is steadily expanding our knowledge of nematode effector repertoires. Host targets and biological activities of a number of nematode effectors are continuously being reported and, by now, a first picture of the complexity of sedentary nematode parasitism at the molecular level is starting to take shape. In this review, we highlight effector mechanisms that recently have been uncovered by studying the host-pathogen interaction. These mechanisms range from mediating susceptibility of host plants to the actual triggering of defense responses. In particular, we portray and discuss the mechanisms by which nematode effectors modify plant cell walls, negate host defense responses, alter auxin and polyamine signaling, mimic plant molecules, regulate stress signaling, and activate hypersensitive responses. Continuous molecular characterization of newly discovered nematode effectors will be needed to determine how these effectors orchestrate host signaling pathways and biological processes leading to successful parasitism.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant pathology and Microbiology, Iowa State University, Ames, IA, USA
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44
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Liu S, Kandoth PK, Warren SD, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale PS, Hill J, Baum TJ, Cianzio S, Whitham SA, Korkin D, Mitchum MG, Meksem K. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 2012; 492:256-60. [PMID: 23235880 DOI: 10.1038/nature11651] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [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: 06/04/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important crop that provides a sustainable source of protein and oil worldwide. Soybean cyst nematode (Heterodera glycines Ichinohe) is a microscopic roundworm that feeds on the roots of soybean and is a major constraint to soybean production. This nematode causes more than US$1 billion in yield losses annually in the United States alone, making it the most economically important pathogen on soybean. Although planting of resistant cultivars forms the core management strategy for this pathogen, nothing is known about the nature of resistance. Moreover, the increase in virulent populations of this parasite on most known resistance sources necessitates the development of novel approaches for control. Here we report the map-based cloning of a gene at the Rhg4 (for resistance to Heterodera glycines 4) locus, a major quantitative trait locus contributing to resistance to this pathogen. Mutation analysis, gene silencing and transgenic complementation confirm that the gene confers resistance. The gene encodes a serine hydroxymethyltransferase, an enzyme that is ubiquitous in nature and structurally conserved across kingdoms. The enzyme is responsible for interconversion of serine and glycine and is essential for cellular one-carbon metabolism. Alleles of Rhg4 conferring resistance or susceptibility differ by two genetic polymorphisms that alter a key regulatory property of the enzyme. Our discovery reveals an unprecedented plant resistance mechanism against a pathogen. The mechanistic knowledge of the resistance gene can be readily exploited to improve nematode resistance of soybean, an increasingly important global crop.
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Affiliation(s)
- Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901, USA
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Juvale PS, Hewezi T, Zhang C, Kandoth PK, Mitchum MG, Hill JH, Whitham SA, Baum TJ. Temporal and spatial Bean pod mottle virus-induced gene silencing in soybean. Mol Plant Pathol 2012; 13:1140-8. [PMID: 22738403 PMCID: PMC6638800 DOI: 10.1111/j.1364-3703.2012.00808.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Virus-induced gene silencing (VIGS) is a powerful reverse genetics tool in plant science. In this study, we investigated the temporal and spatial silencing patterns achieved by Bean pod mottle virus (BPMV)-based VIGS in soybean using virus constructs targeting green fluorescence protein (GFP). Silencing GFP enabled an in-depth analysis of silencing in soybean tissues over time in a transgenic line constitutively expressing GFP. We discovered evidence for variable GFP silencing based on insert orientation and targeted region in the coding sequence. A 3' sequence in reverse orientation produced the strongest silencing phenotypes. Furthermore, we documented that BPMV VIGS can achieve widespread silencing in a broad range of tissues, including leaves, stems, flowers and roots. Near-complete silencing was attained in leaves and flowers. Although weaker than in shoots, the observed gene silencing in soybean roots will also allow reverse genetics studies in this tissue. When GFP fluorescence was assayed in cross-sections of stems and leaf petioles, near-complete and uniform silencing was observed in all cell types. Silencing was observed from as early as 2 weeks post-virus inoculation in leaves to 7 weeks post-virus inoculation in flowers, suggesting that this system can induce and maintain silencing for significant durations.
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Affiliation(s)
- Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
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46
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Abstract
The beet cyst nematode, Heterodera schachtii, is a sedentary root parasite that induces the formation of a specialized root feeding structure, the syncytium. We previously have shown that coordinated regulation of miR396 and its target genes GRF1 and GRF3 in the syncytium is required for proper formation. To gain a better understanding of this coordinated regulation, we used quantitative real-time PCR to assess the abundance of primary (pri)-miRNA396a, pri-miRNA396b and mature miRNA396 in transgenic Arabidopsis plants overexpressing either wild-type variants of the GRF1 or GRF3 coding sequences or miR396-resistant variants. We also included a grf1/grf2/grf3 triple mutant in these analyses. We observed significant decreases in the abundance of pri-miRNA396a, pri-miRNA396b and mature miR396 in the transgenic plants overexpressing GRF1 or GRF3, particularly with the miRNA396-resistant variants. In contrast, the primary transcripts and mature miRNA396 abundance were significantly increased in the grf1/grf2/grf3 triple knockout mutant. These results demonstrate that homeostasis between miR396 and the target genes GRF1 and GRF3 is established through reciprocal feedback regulation, in which GRF1/GRF3 and miR396 negatively regulate each other's expression. In addition, we found that constitutive expression of GRF1 or GRF3 decreases the mRNA abundance of other GRFs, even those that are not targeted by miR396, as well as their own endogenous transcripts, which documents further regulatory facets of this equilibrium.
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47
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Hamamouch N, Li C, Hewezi T, Baum TJ, Mitchum MG, Hussey RS, Vodkin LO, Davis EL. The interaction of the novel 30C02 cyst nematode effector protein with a plant β-1,3-endoglucanase may suppress host defence to promote parasitism. J Exp Bot 2012; 63:3683-95. [PMID: 22442414 PMCID: PMC3388836 DOI: 10.1093/jxb/ers058] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 09/12/2011] [Revised: 01/30/2012] [Accepted: 02/06/2012] [Indexed: 05/18/2023]
Abstract
Phytoparasitic nematodes secrete an array of effector proteins to modify selected recipient plant cells into elaborate and essential feeding sites. The biological function of the novel 30C02 effector protein of the soybean cyst nematode, Heterodera glycines, was studied using Arabidopsis thaliana as host and the beet cyst nematode, Heterodera schachtii, which contains a homologue of the 30C02 gene. Expression of Hg30C02 in Arabidopsis did not affect plant growth and development but increased plant susceptibility to infection by H. schachtii. The 30C02 protein interacted with a specific (AT4G16260) host plant β-1,3-endoglucanase in both yeast and plant cells, possibly to interfere with its role as a plant pathogenesis-related protein. Interestingly, the peak expression of 30C02 in the nematode and peak expression of At4g16260 in plant roots coincided at around 3-5 d after root infection by the nematode, after which the relative expression of At4g16260 declined significantly. An Arabidopsis At4g16260 T-DNA mutant showed increased susceptibility to cyst nematode infection, and plants that overexpressed At4g16260 were reduced in nematode susceptibility, suggesting a potential role of host β-1,3-endoglucanase in the defence response against H. schachtii infection. Arabidopsis plants that expressed dsRNA and its processed small interfering RNA complementary to the Hg30C02 sequence were not phenotypically different from non-transformed plants, but they exhibited a strong RNA interference-mediated resistance to infection by H. schachtii. The collective results suggest that, as with other pathogens, active suppression of host defence is a critical component for successful parasitism by nematodes and a vulnerable target to disrupt the parasitic cycle.
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Affiliation(s)
- Noureddine Hamamouch
- Longwood University, Department of Biological & Environmental Sciences, Farmville, VA 23909, USA
| | - Chunying Li
- North Carolina State University, Department of Plant Pathology, Raleigh, NC 27607, USA
| | - Tarek Hewezi
- Iowa State University, Department of Plant Pathology, Ames, IA 50011, USA
| | - Thomas J. Baum
- Iowa State University, Department of Plant Pathology, Ames, IA 50011, USA
| | - Melissa G. Mitchum
- University of Missouri, Division of Plant Sciences, Columbia, MO 65211, USA
| | - Richard S. Hussey
- University of Georgia, Department of Plant Pathology, Athens, GA 30602, USA
| | - Lila O. Vodkin
- University of Illinois, Crop Sciences, Urbana-Champaign, IL 61801, USA
| | - Eric L. Davis
- North Carolina State University, Department of Plant Pathology, Raleigh, NC 27607, USA
- To whom correspondence should be addressed: E-mail.
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48
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Hewezi T, Maier TR, Nettleton D, Baum TJ. The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiol 2012; 159:321-35. [PMID: 22419826 PMCID: PMC3375968 DOI: 10.1104/pp.112.193649] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/13/2012] [Indexed: 05/18/2023]
Abstract
The syncytium is a unique plant root organ whose differentiation is induced by plant-parasitic cyst nematodes to create a source of nourishment. Syncytium formation involves the redifferentiation and fusion of hundreds of root cells. The underlying regulatory networks that control this unique change of plant cell fate are not understood. Here, we report that a strong down-regulation of Arabidopsis (Arabidopsis thaliana) microRNA396 (miR396) in cells giving rise to the syncytium coincides with the initiation of the syncytial induction/formation phase and that specific miR396 up-regulation in the developed syncytium marks the beginning of the maintenance phase, when no new cells are incorporated into the syncytium. In addition, our results show that miR396 in fact has a role in the transition from one phase to the other. Expression modulations of miR396 and its Growth-Regulating Factor (GRF) target genes resulted in reduced syncytium size and arrested nematode development. Furthermore, genome-wide expression profiling revealed that the miR396-GRF regulatory system can alter the expression of 44% of the more than 7,000 genes reported to change expression in the Arabidopsis syncytium. Thus, miR396 represents a key regulator for the reprogramming of root cells. As such, this regulatory unit represents a powerful molecular target for the parasitic animal to modulate plant cells and force them into novel developmental pathways.
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Abstract
Cyst nematodes establish and maintain feeding sites (syncytia) in the roots of host plants by altering expression of host genes. Among these genes are members of the large gene family of class III peroxidases, which have reported functions in a variety of biological processes. In this study, we used Arabidopsis-Heterodera schachtii as a model system to functionally characterize peroxidase 53 (AtPRX53). Promoter assays showed that under non-infected conditions AtPRX53 is expressed mainly in the root, the hypocotyl and the base of the pistil. Under infected conditions, the AtPRX53 promoter showed upregulation at the nematode penetration sites and in their migration paths. Interestingly, strong GUS activity was observed in H. schachtii-induced syncytia during the early stage of infection and remained strong in the syncytia of third-stage juveniles. Also, AtPRX53 showed upregulation in response to wounding and jasmonic acid treatments. Manipulation of AtPRX53 expression through overexpression and knockout mutation affected both plant morphology and nematode susceptibility. While AtPRX53 overexpression lines exhibited short hypocotyls, aberrant flower development and reduced nematode susceptibility to H. schachtii, the atprx53 mutant showed long hypocotyls and a 3-carpel silique phenotype as well as a non significant increase of nematode susceptibility. Taken together these data, therefore, indicate diverse roles of AtPRX53 in the wound response, flower development and syncytium formation.
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Affiliation(s)
- Jing Jin
- Department of Plant Pathology and Microbiology, Iowa State University; Ames, IA USA
- Molecular, Cellular and Developmental Biology Graduate Program; Iowa State University; Ames, IA USA
| | - Tarek Hewezi
- Department of Plant Pathology and Microbiology, Iowa State University; Ames, IA USA
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University; Ames, IA USA
- Molecular, Cellular and Developmental Biology Graduate Program; Iowa State University; Ames, IA USA
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50
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Schneider KT, van de Mortel M, Bancroft TJ, Braun E, Nettleton D, Nelson RT, Frederick RD, Baum TJ, Graham MA, Whitham SA. Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. Plant Physiol 2011; 157:355-71. [PMID: 21791600 PMCID: PMC3165884 DOI: 10.1104/pp.111.181149] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 07/22/2011] [Indexed: 05/18/2023]
Abstract
Inoculation of soybean (Glycine max) plants with Phakopsora pachyrhizi, the causal organism of Asian soybean rust, elicits a biphasic response characterized by a burst of differential gene expression in the first 12 h. A quiescent period occurs from 24 to 48 h after inoculation, in which P. pachyrhizi continues to develop but does not elicit strong host responses, followed by a second phase of intense gene expression. To correlate soybean responses with P. pachyrhizi growth and development, we inoculated the soybean cultivar Ankur (accession PI462312), which carries the Rpp3 resistance gene, with avirulent and virulent isolates of P. pachyrhizi. The avirulent isolate Hawaii 94-1 elicits hypersensitive cell death that limits fungal growth on Ankur and results in an incompatible response, while the virulent isolate Taiwan 80-2 grows extensively, sporulates profusely, and produces a compatible reaction. Inoculated leaves were collected over a 288-h time course for microarray analysis of soybean gene expression and microscopic analysis of P. pachyrhizi growth and development. The first burst in gene expression correlated with appressorium formation and penetration of epidermal cells, while the second burst of gene expression changes followed the onset of haustoria formation in both compatible and incompatible interactions. The proliferation of haustoria coincided with the inhibition of P. pachyrhizi growth in the incompatible interaction or the beginning of accelerated growth in the compatible interaction. The temporal relationships between P. pachyrhizi growth and host responses provide an important context in which to view interacting gene networks that mediate the outcomes of their interactions.
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