1
|
Jaskulak M, Rostami S, Zorena K, Vandenbulcke F. Transcriptome sequencing of Brassica napus highlights the complex issues with soil supplementation with sewage sludge. CHEMOSPHERE 2022; 298:134321. [PMID: 35306057 DOI: 10.1016/j.chemosphere.2022.134321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
The soil supplementation with sewage sludge (SS) has become a widespread method to improve soil quality, but its long-term possible consequences are still relatively unknown. SS may contain several groups of contaminants to which the biological responses of the organisms are still poorly understood mainly due to the mixture toxicity. In this context, RNA-seq has been used to assess the impact of the exposure to sewage sludge supplemented soil at the whole-transcriptome level in the Brassica napus (B. napus). Although the municipal sewage sludge passed all safety regulations set by the EU commission (86/278/EEC), soil supplementation with SS caused a significant (p < 0.05) increase in the content of lead (by 68.8%, 71.4% in plant shoots and roots, respectively), zinc (by 22.4% and 31.2%), nickel (by 67.0% and 30.2%), and copper (by 33.1% and 39.2%). The de-novo assembled transcriptome of B. napus identified 555 differently expressed genes (DEGs) in a response to sewage sludge supplementation at the false detection rate below 0.001 (FDR <0.001). Among them, 313 genes were up-regulated and 242 genes were down-regulated. The gene ontology analysis (GO) had shown, that significantly enriched GO groups included genes involved in photosynthesis, carbohydrate metabolism and photosystems repair (41 genes), response to oxidative stress (50 genes), response to pathogens (36 genes), response to xenobiotics (15 genes), and heavy metals (41 genes), cell death (8 genes), cell wall structure (15 genes). These results suggest a significant impact of contaminants in sewage sludge on plants transcriptome. The transcriptomic approach facilitated a better understanding of the molecular level of the potential toxicity of sewage sludge in B. napus. RNA-seq allowed for the identification of potential novel early-warning molecular markers of environmental contamination. This work highlights the crucial necessity for rapid legislation change concerning the allowable levels of contaminants in sewage sludge applied on land, to mitigate the possible adverse outcomes in the ecosystem after its use as a fertilizer.
Collapse
Affiliation(s)
- Marta Jaskulak
- University of Lille, IMT Lille Douai, University of Artois, Yncrea Hauts-de-France, ULR4515, LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000, Lille, France; Department of Immunobiology and Environmental Microbiology, Medical University of Gdańsk, Poland; Institute of Environmental Engineering, Czestochowa University of Technology, Czestochowa, Poland.
| | - Saeid Rostami
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Katarzyna Zorena
- Department of Immunobiology and Environmental Microbiology, Medical University of Gdańsk, Poland
| | - Franck Vandenbulcke
- University of Lille, IMT Lille Douai, University of Artois, Yncrea Hauts-de-France, ULR4515, LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000, Lille, France
| |
Collapse
|
2
|
Martin IR, Vigne E, Velt A, Hily JM, Garcia S, Baltenweck R, Komar V, Rustenholz C, Hugueney P, Lemaire O, Schmitt-Keichinger C. Severe Stunting Symptoms upon Nepovirus Infection Are Reminiscent of a Chronic Hypersensitive-like Response in a Perennial Woody Fruit Crop. Viruses 2021; 13:2138. [PMID: 34834945 PMCID: PMC8625034 DOI: 10.3390/v13112138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/02/2022] Open
Abstract
Virus infection of plants can result in various degrees of detrimental impacts and disparate symptom types and severities. Although great strides have been made in our understanding of the virus-host interactions in herbaceous model plants, the mechanisms underlying symptom development are poorly understood in perennial fruit crops. Grapevine fanleaf virus (GFLV) causes variable symptoms in most vineyards worldwide. To better understand GFLV-grapevine interactions in relation to symptom development, field and greenhouse trials were conducted with a grapevine genotype that exhibits distinct symptoms in response to a severe and a mild strain of GFLV. After validation of the infection status of the experimental vines by high-throughput sequencing, the transcriptomic and metabolomic profiles in plants infected with the two viral strains were tested and compared by RNA-Seq and LC-MS, respectively, in the differentiating grapevine genotype. In vines infected with the severe GFLV strain, 1023 genes, among which some are implicated in the regulation of the hypersensitive-type response, were specifically deregulated, and a higher accumulation of resveratrol and phytohormones was observed. Interestingly, some experimental vines restricted the virus to the rootstock and remained symptomless. Our results suggest that GFLV induces a strain- and cultivar-specific defense reaction similar to a hypersensitive reaction. This type of defense leads to a severe stunting phenotype in some grapevines, whereas others are resistant. This work is the first evidence of a hypersensitive-like reaction in grapevine during virus infection.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Corinne Schmitt-Keichinger
- Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, 68000 Colmar, France; (E.V.); (A.V.); (J.-M.H.); (S.G.); (R.B.); (V.K.); (C.R.); (P.H.); (O.L.)
| |
Collapse
|
3
|
Paudel DB, Sanfaçon H. Exploring the Diversity of Mechanisms Associated With Plant Tolerance to Virus Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:1575. [PMID: 30450108 PMCID: PMC6224807 DOI: 10.3389/fpls.2018.01575] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/09/2018] [Indexed: 05/17/2023]
Abstract
Tolerance is defined as an interaction in which viruses accumulate to some degree without causing significant loss of vigor or fitness to their hosts. Tolerance can be described as a stable equilibrium between the virus and its host, an interaction in which each partner not only accommodate trade-offs for survival but also receive some benefits (e.g., protection of the plant against super-infection by virulent viruses; virus invasion of meristem tissues allowing vertical transmission). This equilibrium, which would be associated with little selective pressure for the emergence of severe viral strains, is common in wild ecosystems and has important implications for the management of viral diseases in the field. Plant viruses are obligatory intracellular parasites that divert the host cellular machinery to complete their infection cycle. Highjacking/modification of plant factors can affect plant vigor and fitness. In addition, the toxic effects of viral proteins and the deployment of plant defense responses contribute to the induction of symptoms ranging in severity from tissue discoloration to malformation or tissue necrosis. The impact of viral infection is also influenced by the virulence of the specific virus strain (or strains for mixed infections), the host genotype and environmental conditions. Although plant resistance mechanisms that restrict virus accumulation or movement have received much attention, molecular mechanisms associated with tolerance are less well-understood. We review the experimental evidence that supports the concept that tolerance can be achieved by reaching the proper balance between plant defense responses and virus counter-defenses. We also discuss plant translation repression mechanisms, plant protein degradation or modification pathways and viral self-attenuation strategies that regulate the accumulation or activity of viral proteins to mitigate their impact on the host. Finally, we discuss current progress and future opportunities toward the application of various tolerance mechanisms in the field.
Collapse
Affiliation(s)
- Dinesh Babu Paudel
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| |
Collapse
|
4
|
Sun F, Fang P, Li J, Du L, Lan Y, Zhou T, Fan Y, Shen W, Zhou Y. RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis. Virol J 2016; 13:202. [PMID: 27912765 PMCID: PMC5134058 DOI: 10.1186/s12985-016-0663-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/29/2016] [Indexed: 11/24/2022] Open
Abstract
Background Virus infection induces and suppresses host gene expression on a global level. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and infects rice and Arabidopsis plants. Microarray-based and next generation sequencing-based transcriptomic approaches have been used to study rice-RSV interactions. However, our knowledge of the response of Arabidopsis plants to RSV infection is limited, and it requires further investigation to determine the similarities (or differences) in virus-host interactions between monocot and dicot hosts infected with RSV. Methods We characterized transcriptome changes in Arabidopsis thaliana infected with rice stripe virus (RSV) with RNA-seq based digital gene expression (DGE) analysis. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 14 and 21 days post-infection (dpi) during different stages of symptom development. Results We identified 624 differentially expressed genes (DEGs) in Arabidopsis influenced by RSV at 14 dpi and 21 dpi, among which at 14 dpi, 255 transcripts were induced, and 38 were repressed; at 21 dpi, 146 were induced, and 237 were repressed. Functional annotation indicated that these DEGs were related to multiple biological functions, including defense response, secondary metabolism, protein amino acid phosphorylation and response to abiotic stress. Conclusions Importantly, the transcription of genes related to host defense systems was activated by RSV infection at an early stage of symptom development (14 dpi), whereas over the infection period (21 dpi), the host defense response systems were suppressed. A total of 52 genes were continuously differentially expressed between the two time points, indicating that the majority of DEGs were transient and unique to a particular time point during symptom development. The DEGs, particularly the defense response genes, identified in this study are candidates suitable for further functional analysis during the RSV-Arabidopsis interaction. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0663-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Feng Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Peng Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.,College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Yongjian Fan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China
| | - Wenbiao Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
| |
Collapse
|
5
|
Fuchs M, Schmitt-Keichinger C, Sanfaçon H. A Renaissance in Nepovirus Research Provides New Insights Into Their Molecular Interface With Hosts and Vectors. Adv Virus Res 2016; 97:61-105. [PMID: 28057260 DOI: 10.1016/bs.aivir.2016.08.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nepoviruses supplied seminal landmarks to the historical trail of plant virology. Among the first agriculturally relevant viruses recognized in the late 1920s and among the first plant viruses officially classified in the early 1970s, nepoviruses also comprise the first species for which a soil-borne ectoparasitic nematode vector was identified. Early research on nepoviruses shed light on the genome structure and expression, biological properties of the two genomic RNAs, and mode of transmission. In recent years, research on nepoviruses enjoyed an extraordinary renaissance. This resurgence provided new insights into the molecular interface between viruses and their plant hosts, and between viruses and dagger nematode vectors to advance our understanding of some of the major steps of the infectious cycle. Here we examine these recent findings, highlight ongoing work, and offer some perspectives for future research.
Collapse
Affiliation(s)
- M Fuchs
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, United States.
| | - C Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - H Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| |
Collapse
|
6
|
Zhao F, Lim S, Igori D, Yoo RH, Kwon SY, Moon JS. Development of tobacco ringspot virus-based vectors for foreign gene expression and virus-induced gene silencing in a variety of plants. Virology 2016; 492:166-78. [PMID: 26950504 DOI: 10.1016/j.virol.2016.02.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/23/2016] [Accepted: 02/27/2016] [Indexed: 10/22/2022]
Abstract
We report here the development of tobacco ringspot virus (TRSV)-based vectors for the transient expression of foreign genes and for the analysis of endogenous gene function in plants using virus-induced gene silencing. The jellyfish green fluorescent protein (GFP) gene was inserted between the TRSV movement protein (MP) and coat protein (CP) regions, resulting in high in-frame expression of the RNA2-encoded viral polyprotein. GFP was released from the polyprotein via an N-terminal homologous MP-CP cleavage site and a C-terminal foot-and-mouth disease virus (FMDV) 2 A catalytic peptide in Nicotiana benthamiana. The VIGS target gene was introduced in the sense and antisense orientations into a SnaBI site, which was created by mutating the sequence following the CP stop codon. VIGS of phytoene desaturase (PDS) in N. benthamiana, Arabidopsis ecotype Col-0, cucurbits and legumes led to obvious photo-bleaching phenotypes. A significant reduction in PDS mRNA levels in silenced plants was confirmed by semi-quantitative RT-PCR.
Collapse
Affiliation(s)
- Fumei Zhao
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Seungmo Lim
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Davaajargal Igori
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Ran Hee Yoo
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Suk-Yoon Kwon
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea.
| | - Jae Sun Moon
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Republic of Korea; Molecular Biofarming Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea.
| |
Collapse
|
7
|
Roux F, Bergelson J. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology. Curr Top Dev Biol 2016; 119:111-56. [PMID: 27282025 DOI: 10.1016/bs.ctdb.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity.
Collapse
Affiliation(s)
- F Roux
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| | - J Bergelson
- University of Chicago, Chicago, IL, United States
| |
Collapse
|
8
|
Kim SH, Qi D, Ashfield T, Helm M, Innes RW. Using decoys to expand the recognition specificity of a plant disease resistance protein. Science 2016; 351:684-7. [PMID: 26912853 DOI: 10.1126/science.aad3436] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Maintaining high crop yields in an environmentally sustainable manner requires the development of disease-resistant crop varieties. We describe a method to engineer disease resistance in plants by means of an endogenous disease resistance gene from Arabidopsis thaliana named RPS5, which encodes a nucleotide-binding leucine-rich repeat (NLR) protein. RPS5 is normally activated when a second host protein, PBS1, is cleaved by the pathogen-secreted protease AvrPphB. We show that the AvrPphB cleavage site within PBS1 can be substituted with cleavage sites for other pathogen proteases, which then enables RPS5 to be activated by these proteases, thereby conferring resistance to new pathogens. This "decoy" approach may be applicable to other NLR proteins and should enable engineering of resistance in plants to diseases for which we currently lack robust genetic resistance.
Collapse
Affiliation(s)
- Sang Hee Kim
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Dong Qi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Tom Ashfield
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew Helm
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| |
Collapse
|
9
|
Chang HX, Brown PJ, Lipka AE, Domier LL, Hartman GL. Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of Tobacco ringspot virus in soybean plant introductions. BMC Genomics 2016; 17:153. [PMID: 26924079 PMCID: PMC4770782 DOI: 10.1186/s12864-016-2487-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/17/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genome-wide association study (GWAS) is a useful tool for detecting and characterizing traits of interest including those associated with disease resistance in soybean. The availability of 50,000 single nucleotide polymorphism (SNP) markers (SoySNP50K iSelect BeadChip; www.soybase.org ) on 19,652 soybean and wild soybean plant introductions (PIs) in the USDA Soybean Germplasm Collection allows for fast and robust identification of loci associated with a desired phenotype. By using a genome-wide marker set to predict phenotypic values, genomic prediction for phenotype-unknown but genotype-determined PIs has become possible. The goal of this study was to describe the genetic architecture associated with sensitivity to Tobacco ringspot virus (TRSV) infection in the USDA Soybean Germplasm Collection. RESULTS TRSV-induced disease sensitivities of the 697 soybean PIs were rated on a one to five scale with plants rated as one exhibiting mild symptoms and plants rated as five displaying terminal bud necrosis (i.e., bud blight). The GWAS identified a single locus on soybean chromosome 2 strongly associated with TRSV sensitivity. Cross-validation showed a correlation of 0.55 (P < 0.01) to TRSV sensitivity without including the most significant SNP marker from the GWAS as a covariate, which was a better estimation compared to the mean separation by using significant SNPs. The genomic estimated breeding values for the remaining 18,955 unscreened soybean PIs in the USDA Soybean Germplasm Collection were obtained using the GAPIT R package. To evaluate the prediction accuracy, an additional 55 soybean accessions were evaluated for sensitivity to TRSV, which resulted in a correlation of 0.67 (P < 0.01) between actual and predicted severities. CONCLUSION A single locus responsible for TRSV sensitivity in soybean was identified on chromosome 2. Two leucine-rich repeat receptor-like kinase genes were located near the locus and may control sensitivity of soybean to TRSV infection. Furthermore, a comprehensive genomic prediction for TRSV sensitivity for all accessions in the USDA Soybean Germplasm Collection was completed.
Collapse
Affiliation(s)
- Hao-Xun Chang
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
- USDA-Agricultural Research Service, Urbana, IL, 61801, USA.
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
- USDA-Agricultural Research Service, Urbana, IL, 61801, USA.
- National Soybean Research Center, University of Illinois, 1101 W. Peabody Dr., Urbana, IL, 61801, USA.
| |
Collapse
|
10
|
Zhao F, Hwang US, Lim S, Yoo RH, Igori D, Lee SH, Lim HS, Moon JS. Complete genome sequence and construction of infectious full-length cDNA clones of tobacco ringspot Nepovirus, a viral pathogen causing bud blight in soybean. Virus Genes 2015; 51:163-6. [PMID: 26159876 DOI: 10.1007/s11262-015-1221-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
Abstract
Tobacco ringspot virus (TRSV, genus Nepovirus), causes severe diseases in soybean and tobacco plants. TRSV-induced bud blight disease significantly reduced both the yield and quality of soybeans. The function of the encoded viral gene product involved in TRSV infection was unclear due to the limitation of reverse genetics studies on the viral genome. Here, we represent the successful construction of infectious full-length cDNA clones of TRSV genome (RNA1 and RNA2). The cDNAs of TRSV RNA1 and RNA2 were cloned into the binary vector pPZP211 immediately downstream of a double cauliflower mosaic virus 35S promoter and upstream of the nopaline synthase terminator. Seven days after agrobacterium-mediated co-inoculation of these two constructs, Nicotiana benthamiana plants developed a systemic infection with necrotic ringspot symptoms and weak stunting of the leaves, similar to that induced by natural TRSV. The systemic infection was confirmed by transmission electron microscopy and Western blot analysis. Simultaneously, soybean, tomato, and Arabidopsis ecotype Estland were mechanically inoculated with sap prepared from TRSV-agroinfiltrated N. benthamiana leaves, showing typical symptoms of bud blight, necrotic spots, and lethal systemic necrosis, respectively. The system developed herein will be an appealing way to determine TRSV viral gene functions and study host-TRSV interactions.
Collapse
Affiliation(s)
- Fumei Zhao
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 305-350, South Korea
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Hashimoto M, Komatsu K, Iwai R, Keima T, Maejima K, Shiraishi T, Ishikawa K, Yoshida T, Kitazawa Y, Okano Y, Yamaji Y, Namba S. Cell Death Triggered by a Putative Amphipathic Helix of Radish mosaic virus Helicase Protein Is Tightly Correlated With Host Membrane Modification. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:675-88. [PMID: 25650831 DOI: 10.1094/mpmi-01-15-0004-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Systemic necrosis is one of the most severe symptoms caused by plant RNA viruses. Recently, systemic necrosis has been suggested to have similar features to a defense response referred to as the hypersensitive response (HR), a form of programmed cell death. In virus-infected plant cells, host intracellular membrane structures are changed dramatically for more efficient viral replication. However, little is known about whether this replication-associated membrane modification is the cause of the symptoms. In this study, we identified an amino-terminal amphipathic helix of the helicase encoded by Radish mosaic virus (RaMV) (genus Comovirus) as an elicitor of cell death in RaMV-infected plants. Cell death caused by the amphipathic helix had features similar to HR, such as SGT1-dependence. Mutational analyses and inhibitor assays using cerulenin demonstrated that the amphipathic helix-induced cell death was tightly correlated with dramatic alterations in endoplasmic reticulum (ER) membrane structures. Furthermore, the cell death-inducing activity of the amphipathic helix was conserved in Cowpea mosaic virus (genus Comovirus) and Tobacco ringspot virus (genus Nepovirus), both of which are classified in the family Secoviridae. Together, these results indicate that ER membrane modification associated with viral intracellular replication may be recognized to prime defense responses against plant viruses.
Collapse
Affiliation(s)
- Masayoshi Hashimoto
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ken Komatsu
- 2 Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Ryo Iwai
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Keima
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kensaku Maejima
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Shiraishi
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuya Ishikawa
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuya Yoshida
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yugo Kitazawa
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukari Okano
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigetou Namba
- 1 Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
12
|
Peele HM, Guan N, Fogelqvist J, Dixelius C. Loss and retention of resistance genes in five species of the Brassicaceae family. BMC PLANT BIOLOGY 2014; 14:298. [PMID: 25365911 PMCID: PMC4232680 DOI: 10.1186/s12870-014-0298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/20/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants have evolved disease resistance (R) genes encoding for nucleotide-binding site (NB) and leucine-rich repeat (LRR) proteins with N-terminals represented by either Toll/Interleukin-1 receptor (TIR) or coiled-coil (CC) domains. Here, a genome-wide study of presence and diversification of CC-NB-LRR and TIR-NB-LRR encoding genes, and shorter domain combinations in 19 Arabidopsis thaliana accessions and Arabidopsis lyrata, Capsella rubella, Brassica rapa and Eutrema salsugineum are presented. RESULTS Out of 528 R genes analyzed, 12 CC-NB-LRR and 17 TIR-NB-LRR genes were conserved among the 19 A. thaliana genotypes, while only two CC-NB-LRRs, including ZAR1, and three TIR-NB-LRRs were conserved when comparing the five species. The RESISTANCE TO LEPTOSPHAERIA MACULANS 1 (RLM1) locus confers resistance to the Brassica pathogen L. maculans the causal agent of blackleg disease and has undergone conservation and diversification events particularly in B. rapa. On the contrary, the RLM3 locus important in the immune response towards Botrytis cinerea and Alternaria spp. has recently evolved in the Arabidopsis genus. CONCLUSION Our genome-wide analysis of the R gene repertoire revealed a large sequence variation in the 23 cruciferous genomes. The data provides further insights into evolutionary processes impacting this important gene family.
Collapse
Affiliation(s)
- Hanneke M Peele
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Na Guan
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| |
Collapse
|
13
|
Harris CJ, Slootweg EJ, Goverse A, Baulcombe DC. Stepwise artificial evolution of a plant disease resistance gene. Proc Natl Acad Sci U S A 2013; 110:21189-94. [PMID: 24324167 PMCID: PMC3876221 DOI: 10.1073/pnas.1311134110] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genes encoding plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins confer dominant resistance to diverse pathogens. The wild-type potato NB-LRR protein Rx confers resistance against a single strain of potato virus X (PVX), whereas LRR mutants protect against both a second PVX strain and the distantly related poplar mosaic virus (PopMV). In one of the Rx mutants there was a cost to the broad-spectrum resistance because the response to PopMV was transformed from a mild disease on plants carrying wild-type Rx to a trailing necrosis that killed the plant. To explore the use of secondary mutagenesis to eliminate this cost of broad-spectrum resistance, we performed random mutagenesis of the N-terminal domains of this broad-recognition version of Rx and isolated four mutants with a stronger response against the PopMV coat protein due to enhanced activation sensitivity. These mutations are located close to the nucleotide-binding pocket, a highly conserved structure that likely controls the "switch" between active and inactive NB-LRR conformations. Stable transgenic plants expressing one of these versions of Rx are resistant to the strains of PVX and the PopMV that previously caused trailing necrosis. We conclude from this work that artificial evolution of NB-LRR disease resistance genes in crops can be enhanced by modification of both activation and recognition phases, to both accentuate the positive and eliminate the negative aspects of disease resistance.
Collapse
Affiliation(s)
- C. Jake Harris
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; and
| | - Erik J. Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; and
| |
Collapse
|
14
|
Ouibrahim L, Caranta C. Exploitation of natural genetic diversity to study plant-virus interactions: what can we learn from Arabidopsis thaliana? MOLECULAR PLANT PATHOLOGY 2013; 14:844-54. [PMID: 23790151 PMCID: PMC6638744 DOI: 10.1111/mpp.12052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The development and use of cultivars that are genetically resistant to viruses is an efficient strategy to tackle the problems of virus diseases. Over the past two decades, the model plant Arabidopsis thaliana has been documented as a host for a broad range of viral species, providing access to a large panel of resources and tools for the study of viral infection processes and resistance mechanisms. Exploration of its natural genetic diversity has revealed a wide range of genes conferring virus resistance. The molecular characterization of some of these genes has unveiled resistance mechanisms distinct from those described in crops. In these respects, Arabidopsis represents a rich and largely untapped source of new genes and mechanisms involved in virus resistance. Here, we review the current status of our knowledge concerning natural virus resistance in Arabidopsis. We also address the impact of environmental conditions on Arabidopsis-virus interactions and resistance mechanisms, and discuss the potential of applying the knowledge gained from the study of Arabidopsis natural diversity for crop improvement.
Collapse
Affiliation(s)
- Laurence Ouibrahim
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, CEA/CNRS, Aix Marseille Université, Faculté des Sciences de Luminy, 163 Avenue de Luminy, Marseille, France
| | | |
Collapse
|