1
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Lan HJ, Ran J, Wang WX, Zhang L, Wu NN, Zhao YT, Huang MJ, Ni M, Liu F, Cheng N, Nakata PA, Pan J, Whitham SA, Baker BJ, Liu JZ. Clathrin Light Chains negatively regulate plant immunity by hijacking the autophagy pathway. Plant Commun 2024:100937. [PMID: 38693694 DOI: 10.1016/j.xplc.2024.100937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/02/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
The crosstalk between clathrin-mediated endocytosis (CME) and autophagy pathway has been reported in mammals. However, the interconnection of CME with autophagy has not been established in plants. In this report, we showed that Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopied the Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants both in auto-immunity and nutrient sensitivity. Accordingly, the autophagy pathway was significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, we demonstrated with multiple assays that CLC2 directly interacted with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP were subjected to autophagic degradation and the degradation of GFP-ATG8h was significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneously knocking out ATG8h and ATG8i by the CRISPR/CAS9 resulted in an enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results uncovered a link between the function of CLCs and the autophagy pathway in Arabidopsis.
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Affiliation(s)
- Hu-Jiao Lan
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Jie Ran
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Wen-Xu Wang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Ni-Ni Wu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Ting Zhao
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Min-Jun Huang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Min Ni
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Feng Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
| | - Ninghui Cheng
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
| | - Paul A Nakata
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
| | - Jianwei Pan
- College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Barbara J Baker
- Department of Plant and Microbial Biology, University of California, and Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Berkeley, Berkeley, CA 94720, USA
| | - Jian-Zhong Liu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China; Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.
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2
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Holan KL, White CH, Whitham SA. Application of a U-Net Neural Network to the Puccinia sorghi-Maize Pathosystem. Phytopathology 2024:PHYTO09230313KC. [PMID: 38281155 DOI: 10.1094/phyto-09-23-0313-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Computer vision approaches to analyze plant disease data can be both faster and more reliable than traditional, manual methods. However, the requirement of manually annotating training data for the majority of machine learning applications can present a challenge for pipeline development. Here, we describe a machine learning approach to quantify Puccinia sorghi incidence on maize leaves utilizing U-Net convolutional neural network models. We analyzed several U-Net models with increasing amounts of training image data, either randomly chosen from a large data pool or randomly chosen from a subset of disease time course data. As the training dataset size increases, the models perform better, but the rate of performance decreases. Additionally, the use of a diverse training dataset can improve model performance and reduce the amount of annotated training data required for satisfactory performance. Models with as few as 48 whole-leaf training images are able to replicate the ground truth results within our testing dataset. The final model utilizing our entire training dataset performs similarly to our ground truth data, with an intersection over union value of 0.5002 and an F1 score of 0.6669. This work illustrates the capacity of U-Nets to accurately answer real-world plant pathology questions related to quantification and estimation of plant disease symptoms. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Katerina L Holan
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50014
| | - Charles H White
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO 80523
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50014
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3
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Bish MD, Ramachandran SR, Wright A, Lincoln LM, Whitham SA, Graham MA, Pedley KF. The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi. Mol Plant Microbe Interact 2024. [PMID: 38569009 DOI: 10.1094/mpmi-01-24-0007-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max (L.) Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371 kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance.
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Affiliation(s)
- Mandy D Bish
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, Maryland, United States;
| | - Sowmya R Ramachandran
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, Maryland, United States;
| | - Amy Wright
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, Maryland, United States;
| | - Lori M Lincoln
- USDA Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, United States;
| | - Steven A Whitham
- Iowa State Univ, Dept. of Plant Pathology & Microbiology, 4203 Advanced Teaching & Research Bldg, 2213 Pammel Dr, Ames, Iowa, United States, 50011-1101;
| | - Michelle A Graham
- USDA Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Iowa State University, Ames, Iowa, United States, 50010;
| | - Kerry F Pedley
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research Unit, 1301 Ditto Avenue, Ft. Detrick, Maryland, United States, 21702-5023;
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4
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Qi M, Yu H, Bredow M, Chicowski AS, Fields LD, Whitham SA. Insights into Phakopsora pachyrhizi Effector-Effector Interactions. Mol Plant Microbe Interact 2024; 37:227-231. [PMID: 37831963 DOI: 10.1094/mpmi-08-23-0120-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, wherein some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRPs), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, 100193, Beijing, China
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Letícia Dias Fields
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Steven A Whitham
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
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5
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Normantovich M, Amitzur A, Offri S, Pashkovsky E, Shnaider Y, Nizan S, Yogev O, Jacob A, Taylor CG, Desbiez C, Whitham SA, Bar-Ziv A, Perl-Treves R. The melon Fom-1-Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein. Plant Direct 2024; 8:e565. [PMID: 38389929 PMCID: PMC10883720 DOI: 10.1002/pld3.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
The head-to-head oriented pair of melon resistance genes, Fom-1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR-NBS-LRR proteins, and Prv has a C-terminal extra domain with a second NBS homologous sequence. In other systems, paired R-proteins were shown to operate by "labor division," with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near-isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi-directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.
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Affiliation(s)
- Michael Normantovich
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Sharon Offri
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ekaterina Pashkovsky
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Yula Shnaider
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ohad Yogev
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Avi Jacob
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
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6
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Chicowski AS, Bredow M, Utiyama AS, Marcelino‐Guimarães FC, Whitham SA. Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. Plant Biotechnol J 2024; 22:296-315. [PMID: 37883664 PMCID: PMC10826999 DOI: 10.1111/pbi.14206] [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] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/19/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023]
Abstract
Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.
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Affiliation(s)
- Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Alice Satiko Utiyama
- Brazilian Agricultural Research Corporation – National Soybean Research Center (Embrapa Soja)LondrinaParanáBrazil
- Department of AgronomyFederal University of ViçosaViçosaMinas GeraisBrazil
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
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7
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Singh N, Khan RR, Xu W, Whitham SA, Dong L. Plant Virus Sensor for the Rapid Detection of Bean Pod Mottle Virus Using Virus-Specific Nanocavities. ACS Sens 2023; 8:3902-3913. [PMID: 37738225 DOI: 10.1021/acssensors.3c01478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
This study presents a miniaturized sensor for rapid, selective, and sensitive detection of bean pod mottle virus (BPMV) in soybean plants. The sensor employs molecularly imprinted polymer technology to generate BPMV-specific nanocavities in porous polypyrrole. Leveraging the porous structure, high surface reactivity, and electron transfer properties of polypyrrole, the sensor achieves a sensitivity of 143 μA ng-1 mL cm-2, a concentration range of 0.01-100,000 ng/mL, a detection time of less than 2 min, and a detection limit of 41 pg/mL. These capabilities outperform those of conventional methods, such as enzyme-linked immunosorbent assays and reverse transcription polymerase chain reactions. The sensor possesses the ability to distinguish BPMV-infected soybean plants from noninfected ones while rapidly quantifying virus levels. Moreover, it can reveal the spatial distribution of virus concentration across distinct leaves, a capability not previously attained by cost-effective sensors for such detailed viral data within a plant. The BPMV-specific nanocavities can also be easily restored and reactivated for multiple uses through a simple wash with acetic acid. While MIP-based sensors for plant virus detection have been relatively understudied, our findings demonstrate their potential as portable, on-site diagnostic tools that avoid complex and time-consuming sample preparation procedures. This advancement addresses a critical need in plant virology, enhancing the detection and management of plant viral diseases.
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Affiliation(s)
- Nawab Singh
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
- Microelectronics Research Center, Iowa State University, Ames, Iowa 50011, United States
| | - Raufur Rahman Khan
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
- Microelectronics Research Center, Iowa State University, Ames, Iowa 50011, United States
| | - Weihui Xu
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa 50011, United States
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa 50011, United States
| | - Liang Dong
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
- Microelectronics Research Center, Iowa State University, Ames, Iowa 50011, United States
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8
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Beernink BM, Whitham SA. Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. Mol Plant Pathol 2023; 24:811-822. [PMID: 37036421 PMCID: PMC10257046 DOI: 10.1111/mpp.13330] [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] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 06/11/2023]
Abstract
Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize-microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize-microbe interactions and more broadly in the context of the monocot functional genomics toolbox.
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Affiliation(s)
- Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Department of BiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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9
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Bredow M, Natukunda MI, Beernink BM, Chicowski AS, Salas‐Fernandez MG, Whitham SA. Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor. Mol Plant Pathol 2023; 24:71-79. [PMID: 36088637 PMCID: PMC9742499 DOI: 10.1111/mpp.13270] [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] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 05/08/2023]
Abstract
Sorghum is vulnerable to many biotic and abiotic stresses, which cause considerable yield losses globally. Efforts to genetically characterize beneficial sorghum traits, including disease resistance, plant architecture, and tolerance to abiotic stresses, are ongoing. One challenge faced by sorghum researchers is its recalcitrance to transformation, which has slowed gene validation efforts and utilization for cultivar development. Here, we characterize the use of a foxtail mosaic virus (FoMV) vector for virus-induced gene silencing (VIGS) by targeting two previously tested marker genes: phytoene desaturase (PDS) and ubiquitin (Ub). We additionally demonstrate VIGS of a subgroup of receptor-like cytoplasmic kinases (RLCKs) and report the role of these genes as positive regulators of early defence signalling. Silencing of subgroup 8 RLCKs also resulted in higher susceptibility to the bacterial pathogens Pseudomonas syringae pv. syringae (B728a) and Xanthomonas vasicola pv. holcicola, demonstrating the role of these genes in host defence against bacterial pathogens. Together, this work highlights the utility of FoMV-induced gene silencing in the characterization of genes mediating defence responses in sorghum. Moreover, FoMV was able to systemically infect six diverse sorghum genotypes with high efficiency at optimal temperatures for sorghum growth and therefore could be extrapolated to study additional traits of economic importance.
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Affiliation(s)
- Melissa Bredow
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Martha Ibore Natukunda
- Department of AgronomyIowa State UniversityAmesIowaUSA
- Present address:
Department of BiologyAugustana UniversitySioux FallsSouth DakotaUSA.
| | - Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Present address:
Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada.
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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10
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Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics 2022; 23:767. [DOI: 10.1186/s12864-022-09001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.
Results
Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.
Conclusions
Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.
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11
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Elmore MG, Groves CL, Hajimorad MR, Stewart TP, Gaskill MA, Wise KA, Sikora E, Kleczewski NM, Smith DL, Mueller DS, Whitham SA. Detection and discovery of plant viruses in soybean by metagenomic sequencing. Virol J 2022; 19:149. [PMID: 36100874 PMCID: PMC9472442 DOI: 10.1186/s12985-022-01872-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available. METHODS In this study, soybean fields were scouted for virus-like disease symptoms during the 2016-2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes. RESULTS Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common. CONCLUSIONS Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.
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Affiliation(s)
- Manjula G Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 2213 Pammel Drive, Ames, IA, 50011-1101, USA.
| | - Carol L Groves
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - M R Hajimorad
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tracey P Stewart
- Roy J. Carver High Resolution Microscopy Facility, Iowa State University, Ames, IA, 50011, USA
| | - Mikaela A Gaskill
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 2213 Pammel Drive, Ames, IA, 50011-1101, USA
| | - Kiersten A Wise
- Department of Plant Pathology, University of Kentucky, Princeton, KY, 43445, USA
| | - Edward Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | | | - Damon L Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daren S Mueller
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 2213 Pammel Drive, Ames, IA, 50011-1101, USA
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 2213 Pammel Drive, Ames, IA, 50011-1101, USA.
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12
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Yu H, Ruan H, Xia X, Chicowski AS, Whitham SA, Li Z, Wang G, Liu W. Maize FERONIA-like receptor genes are involved in the response of multiple disease resistance in maize. Mol Plant Pathol 2022; 23:1331-1345. [PMID: 35596601 PMCID: PMC9366073 DOI: 10.1111/mpp.13232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/10/2022] [Accepted: 04/30/2022] [Indexed: 05/04/2023]
Abstract
Receptor-like kinases (RLKs) are key modulators of diverse cellular processes such as development and sensing the extracellular environment. FERONIA, a member of the CrRLK1L subfamily, acts as a pleiotropic regulator of plant immune responses, but little is known about how maize FERONIA-like receptors (FLRs) function in responding to the major foliar diseases of maize such as northern corn leaf blight (NLB), northern corn leaf spot (NLS), anthracnose stalk rot (ASR), and southern corn leaf blight (SLB). Here, we identified three ZmFLR homologous proteins that showed cell membrane localization. Transient expression in Nicotiana benthamiana proved that ZmFLRs were capable of inducing cell death. To investigate the role of ZmFLRs in maize, we used virus-induced gene silencing to knock down expression of ZmFLR1/2 and ZmFLR3 resulting in reduced reactive oxygen species production induced by flg22 and chitin. The resistance of maize to NLB, NLS, ASR, and SLB was also reduced in the ZmFLRs knockdown maize plants. These results indicate that ZmFLRs are positively involved in broad-spectrum disease resistance in maize.
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Affiliation(s)
- Haiyue Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of AgricultureAgriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Hongchun Ruan
- Institute of Plant ProtectionFujian Academy of Agricultural SciencesFuzhouChina
| | - Xinyao Xia
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | | | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of AgricultureAgriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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13
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Bueno TV, Fontes PP, Abe VY, Utiyama AS, Senra RL, Oliveira LS, Brombini Dos Santos A, Ferreira EGC, Darben LM, de Oliveira AB, Abdelnoor RV, Whitham SA, Fietto LG, Marcelino-Guimarães FC. A Phakopsora pachyrhizi Effector Suppresses PAMP-Triggered Immunity and Interacts with a Soybean Glucan Endo-1,3-β-Glucosidase to Promote Virulence. Mol Plant Microbe Interact 2022; 35:779-790. [PMID: 35617509 DOI: 10.1094/mpmi-12-21-0301-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Asian soybean rust, caused by the fungus Phakopsora pachyrhizi, is one of the most important diseases affecting soybean production in tropical areas. During infection, P. pachyrhizi secretes proteins from haustoria that are transferred into plant cells to promote virulence. To date, only one candidate P. pachyrhizi effector protein has been characterized in detail to understand the mechanism by which it suppresses plant defenses to enhance infection. Here, we aimed to extend understanding of the pathogenic mechanisms of P. pachyrhizi based on the discovery of host proteins that interact with the effector candidate Phapa-7431740. We demonstrated that Phapa-7431740 suppresses pathogen-associated molecular pattern-triggered immunity (PTI) and that it interacts with a soybean glucan endo-1,3-β-glucosidase (GmβGLU), a pathogenesis-related (PR) protein belonging to the PR-2 family. Structural and phylogenetic characterization of the PR-2 protein family predicted in the soybean genome and comparison to PR-2 family members in Arabidopsis thaliana and cotton, demonstrated that GmβGLU is a type IV β-1,3-glucanase. Transcriptional profiling during an infection time course showed that the GmβGLU mRNA is highly induced during the initial hours after infection, coinciding with peak of expression of Phapa-7431740. The effector was able to interfere with the activity of GmβGLU in vitro, with a dose-dependent inhibition. Our results suggest that Phapa-7431740 may suppress PTI by interfering with glucan endo-1,3-β-glucosidase activity. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Thays V Bueno
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Patrícia P Fontes
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Valeria Y Abe
- Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil
| | - Alice Satiko Utiyama
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Renato L Senra
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Liliane S Oliveira
- Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil
- Department of Computer Science, Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Paraná 86300-000, Brazil
| | | | | | | | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Luciano G Fietto
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
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14
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Beernink BM, Lappe RR, Bredow M, Whitham SA. Impacts of RNA Mobility Signals on Virus Induced Somatic and Germline Gene Editing. Front Genome Ed 2022; 4:925088. [PMID: 35755451 PMCID: PMC9219249 DOI: 10.3389/fgeed.2022.925088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.
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15
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Chung SH, Bigham M, Lappe RR, Chan B, Nagalakshmi U, Whitham SA, Dinesh‐Kumar SP, Jander G. A sugarcane mosaic virus vector for rapid in planta screening of proteins that inhibit the growth of insect herbivores. Plant Biotechnol J 2021; 19:1713-1724. [PMID: 33763921 PMCID: PMC8428830 DOI: 10.1111/pbi.13585] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production worldwide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although additional transgenes have confirmed insecticidal activity, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of both endogenous maize genes and heterologous genes from other organisms for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defence signalling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) scorpion and spider toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with a subset of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors are a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.
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Affiliation(s)
| | | | - Ryan R. Lappe
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Barry Chan
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Savithramma P. Dinesh‐Kumar
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Georg Jander
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
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16
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O’Conner S, Zheng W, Qi M, Kandel Y, Fuller R, Whitham SA, Li L. GmNF-YC4-2 Increases Protein, Exhibits Broad Disease Resistance and Expedites Maturity in Soybean. Int J Mol Sci 2021; 22:3586. [PMID: 33808355 PMCID: PMC8036377 DOI: 10.3390/ijms22073586] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/30/2022] Open
Abstract
The NF-Y gene family is a highly conserved set of transcription factors. The functional transcription factor complex is made up of a trimer between NF-YA, NF-YB, and NF-YC proteins. While mammals typically have one gene for each subunit, plants often have multigene families for each subunit which contributes to a wide variety of combinations and functions. Soybean plants with an overexpression of a particular NF-YC isoform GmNF-YC4-2 (Glyma.04g196200) in soybean cultivar Williams 82, had a lower amount of starch in its leaves, a higher amount of protein in its seeds, and increased broad disease resistance for bacterial, viral, and fungal infections in the field, similar to the effects of overexpression of its isoform GmNF-YC4-1 (Glyma.06g169600). Interestingly, GmNF-YC4-2-OE (overexpression) plants also filled pods and senesced earlier, a novel trait not found in GmNF-YC4-1-OE plants. No yield difference was observed in GmNF-YC4-2-OE compared with the wild-type control. Sequence alignment of GmNF-YC4-2, GmNF-YC4-1 and AtNF-YC1 indicated that faster maturation may be a result of minor sequence differences in the terminal ends of the protein compared to the closely related isoforms.
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Affiliation(s)
- Seth O’Conner
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; (S.O.); (R.F.)
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA; (M.Q.); (Y.K.); (S.A.W.)
| | - Yuba Kandel
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA; (M.Q.); (Y.K.); (S.A.W.)
| | - Robert Fuller
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; (S.O.); (R.F.)
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA; (M.Q.); (Y.K.); (S.A.W.)
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; (S.O.); (R.F.)
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17
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Beernink BM, Holan KL, Lappe RR, Whitham SA. Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones. J Vis Exp 2021. [PMID: 33720142 DOI: 10.3791/62277] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Agrobacterium-based inoculation approaches are widely used for introducing viral vectors into plant tissues. This study details a protocol for the injection of maize seedlings near meristematic tissue with Agrobacterium carrying a viral vector. Recombinant foxtail mosaic virus (FoMV) clones engineered for gene silencing and gene expression were used to optimize this method, and its use was expanded to include a recombinant sugarcane mosaic virus (SCMV) engineered for gene expression. Gene fragments or coding sequences of interest are inserted into a modified, infectious viral genome that has been cloned into the binary T-DNA plasmid vector pCAMBIA1380. The resulting plasmid constructs are transformed into Agrobacterium tumefaciens strain GV3101. Maize seedlings as young as 4 days old can be injected near the coleoptilar node with bacteria resuspended in MgSO4 solution. During infection with Agrobacterium, the T-DNA carrying the viral genome is transferred to maize cells, allowing for the transcription of the viral RNA genome. As the recombinant virus replicates and systemically spreads throughout the plant, viral symptoms and phenotypic changes resulting from the silencing of the target genes lesion mimic 22 (les22) or phytoene desaturase (pds) can be observed on the leaves, or expression of green fluorescent protein (GFP) can be detected upon illumination with UV light or fluorescence microscopy. To detect the virus and assess the integrity of the insert simultaneously, RNA is extracted from the leaves of the injected plant and RT-PCR is conducted using primers flanking the multiple cloning site (MCS) carrying the inserted sequence. This protocol has been used effectively in several maize genotypes and can readily be expanded to other viral vectors, thereby offering an accessible tool for viral vector introduction in maize.
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Affiliation(s)
- Bliss M Beernink
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Katerina L Holan
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Ryan R Lappe
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University;
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18
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McCaghey M, Shao D, Kurcezewski J, Lindstrom A, Ranjan A, Whitham SA, Conley SP, Williams B, Smith DL, Kabbage M. Host-Induced Gene Silencing of a Sclerotinia sclerotiorum oxaloacetate acetylhydrolase Using Bean Pod Mottle Virus as a Vehicle Reduces Disease on Soybean. Front Plant Sci 2021; 12:677631. [PMID: 34354721 PMCID: PMC8329588 DOI: 10.3389/fpls.2021.677631] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/26/2021] [Indexed: 05/05/2023]
Abstract
A lack of complete resistance in the current germplasm complicates the management of Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum in soybean. In this study, we used bean pod mottle virus (BPMV) as a vehicle to down-regulate expression of a key enzyme in the production of an important virulence factor in S. sclerotiorum, oxalic acid (OA). Specifically, we targeted a gene encoding oxaloacetate acetylhydrolase (Ssoah1), because Ssoah1 deletion mutants are OA deficient and non-pathogenic on soybean. We first established that S. sclerotiorum can uptake environmental RNAs by monitoring the translocation of Cy3-labeled double-stranded and small interfering RNA (ds/siRNAs) into fungal hyphae using fluorescent confocal microscopy. This translocation led to a significant decrease in Ssoah1 transcript levels in vitro. Inoculation of soybean plants with BPMV vectors targeting Ssoah1 (pBPMV-OA) also led to decreased expression of Ssoah1. Importantly, pBPMV-OA inoculated plants showed enhanced resistance to S. sclerotiorum compared to empty-vector control plants. Our combined results provide evidence supporting the use of HIGS and exogenous applications of ds/siRNAs targeting virulence factors such as OA as viable strategies for the control of SSR in soybean and as discovery tools that can be used to identify previously unknown virulence factors.
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Affiliation(s)
- Megan McCaghey
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Dandan Shao
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jake Kurcezewski
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Ally Lindstrom
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Ashish Ranjan
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Shawn P. Conley
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Damon L. Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
- Damon L. Smith
| | - Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Mehdi Kabbage
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19
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Zheng N, Li T, Dittman JD, Su J, Li R, Gassmann W, Peng D, Whitham SA, Liu S, Yang B. CRISPR/Cas9-Based Gene Editing Using Egg Cell-Specific Promoters in Arabidopsis and Soybean. Front Plant Sci 2020; 11:800. [PMID: 32612620 PMCID: PMC7309964 DOI: 10.3389/fpls.2020.00800] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 05/19/2020] [Indexed: 05/20/2023]
Abstract
CRISPR/Cas9-based systems are efficient genome editing tools in a variety of plant species including soybean. Most of the gene edits in soybean plants are somatic and non-transmissible when Cas9 is expressed under control of constitutive promoters. Tremendous effort, therefore, must be spent to identify the inheritable edits occurring at lower frequencies in plants of successive generations. Here, we report the development and validation of genome editing systems in soybean and Arabidopsis based on Cas9 driven under four different egg-cell specific promoters. A soybean ubiquitin gene promoter driving expression of green fluorescent protein (GFP) is incorporated in the CRISPR/Cas9 constructs for visually selecting transgenic plants and transgene-evicted edited lines. In Arabidopsis, the four systems all produced a collection of mutations in the T2 generation at frequencies ranging from 8.3 to 42.9%, with egg cell-specific promoter AtEC1.2e1.1p being the highest. In soybean, function of the gRNAs and Cas9 expressed under control of the CaMV double 35S promoter (2x35S) in soybean hairy roots was tested prior to making stable transgenic plants. The 2x35S:Cas9 constructs yielded a high somatic mutation frequency in soybean hairy roots. In stable transgenic soybean T1 plants, AtEC1.2e1.1p:Cas9 yielded a mutation rate of 26.8%, while Cas9 expression driven by the other three egg cell-specific promoters did not produce any detected mutations. Furthermore, the mutations were inheritable in the T2 generation. Our study provides CRISPR gene-editing platforms to generate inheritable mutants of Arabidopsis and soybean without the complication of somatic mutagenesis, which can be used to characterize genes of interest in Arabidopsis and soybean.
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Affiliation(s)
- Na Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Ting Li
- The Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jaime D. Dittman
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Jianbin Su
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Riqing Li
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Walter Gassmann
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
- *Correspondence: Steven A. Whitham,
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Shiming Liu,
| | - Bing Yang
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Bing Yang,
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20
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Mei Y, Beernink BM, Ellison EE, Konečná E, Neelakandan AK, Voytas DF, Whitham SA. Protein expression and gene editing in monocots using foxtail mosaic virus vectors. Plant Direct 2019; 3:e00181. [PMID: 31768497 PMCID: PMC6874699 DOI: 10.1002/pld3.181] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/08/2019] [Accepted: 10/24/2019] [Indexed: 05/03/2023]
Abstract
Plant viruses can be engineered to carry sequences that direct silencing of target host genes, expression of heterologous proteins, or editing of host genes. A set of foxtail mosaic virus (FoMV) vectors was developed that can be used for transient gene expression and single guide RNA delivery for Cas9-mediated gene editing in maize, Setaria viridis, and Nicotiana benthamiana. This was accomplished by duplicating the FoMV capsid protein subgenomic promoter, abolishing the unnecessary open reading frame 5A, and inserting a cloning site containing unique restriction endonuclease cleavage sites immediately after the duplicated promoter. The modified FoMV vectors transiently expressed green fluorescent protein (GFP) and bialaphos resistance (BAR) protein in leaves of systemically infected maize seedlings. GFP was detected in epidermal and mesophyll cells by epifluorescence microscopy, and expression was confirmed by Western blot analyses. Plants infected with FoMV carrying the bar gene were temporarily protected from a glufosinate herbicide, and expression was confirmed using a rapid antibody-based BAR strip test. Expression of these proteins was stabilized by nucleotide substitutions in the sequence of the duplicated promoter region. Single guide RNAs expressed from the duplicated promoter mediated edits in the N. benthamiana Phytoene desaturase gene, the S. viridis Carbonic anhydrase 2 gene, and the maize HKT1 gene encoding a potassium transporter. The efficiency of editing was enhanced in the presence of synergistic viruses and a viral silencing suppressor. This work expands the utility of FoMV for virus-induced gene silencing (VIGS), virus-mediated overexpression (VOX), and virus-enabled gene editing (VEdGE) in monocots.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Bliss M. Beernink
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Evan E. Ellison
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Eva Konečná
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | | | - Daniel F. Voytas
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
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21
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Mei Y, Liu G, Zhang C, Hill JH, Whitham SA. A sugarcane mosaic virus vector for gene expression in maize. Plant Direct 2019; 3:e00158. [PMID: 31410390 PMCID: PMC6686331 DOI: 10.1002/pld3.158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/18/2019] [Indexed: 05/09/2023]
Abstract
Zea mays L. ssp. mays (maize) is an important crop plant as well as model system for genetics and plant biology. The ability to select among different virus-based platforms for transient gene silencing or protein expression experiments is expected to facilitate studies of gene function in maize and complement experiments with stable transgenes. Here, we describe the development of a sugarcane mosaic virus (SCMV) vector for the purpose of protein expression in maize. An infectious SCMV cDNA clone was constructed, and heterologous genetic elements were placed between the protein 1 (P1) and helper component-proteinase (HC-Pro) cistrons in the SCMV genome. Recombinant SCMV clones engineered to express green fluorescent protein (GFP), β-glucuronidase (GUS), or bialaphos resistance (BAR) protein were introduced into sweet corn (Golden × Bantam) plants. Documentation of developmental time courses spanning maize growth from seedling to tasseling showed that the SCMV genome tolerates insertion of foreign sequences of at least 1,809 nucleotides at the P1/HC-Pro junction. Analysis of insert stability showed that the integrity of GFP and BAR coding sequences was maintained longer than that of the much larger GUS coding sequence. The SCMV isolate from which the expression vector is derived is able to infect several important maize inbred lines, suggesting that this SCMV vector has potential to be a valuable tool for gene functional analysis in a broad range of experimentally important maize genotypes.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Chunquan Zhang
- Department of AgricultureAlcorn State UniversityLormanMississippi
| | - John H. Hill
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
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22
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Helm M, Qi M, Sarkar S, Yu H, Whitham SA, Innes RW. Engineering a Decoy Substrate in Soybean to Enable Recognition of the Soybean Mosaic Virus NIa Protease. Mol Plant Microbe Interact 2019; 32:760-769. [PMID: 30676230 DOI: 10.1094/mpmi-12-18-0324-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Arabidopsis, recognition of the AvrPphB effector protease from Pseudomonas syringae is mediated by the disease resistance (R) protein RPS5, which is activated by AvrPphB-induced cleavage of the Arabidopsis protein kinase PBS1. The recognition specificity of RPS5 can be altered by substituting the AvrPphB cleavage site within PBS1 with cleavage sequences for other proteases, including proteases from viruses. AvrPphB also activates defense responses in soybean (Glycine max), suggesting that soybean may contain an R protein analogous to RPS5. It was unknown, however, whether this response is mediated by cleavage of a soybean PBS1-like protein. Here, we show that soybean contains three PBS1 orthologs and that their products are cleaved by AvrPphB. Further, transient expression of soybean PBS1 derivatives containing a five-alanine insertion at their AvrPphB cleavage sites activated cell death in soybean protoplasts, demonstrating that soybean likely contains an AvrPphB-specific resistance protein that is activated by a conformational change in soybean PBS1 proteins. Significantly, we show that a soybean PBS1 decoy protein modified to contain a cleavage site for the soybean mosaic virus (SMV) NIa protease triggers cell death in soybean protoplasts when cleaved by this protease, indicating that the PBS1 decoy approach will work in soybean, using endogenous PBS1 genes. Lastly, we show that activation of the AvrPphB-dependent cell death response effectively inhibits systemic spread of SMV in soybean. These data also indicate that decoy engineering may be feasible in other crop plant species that recognize AvrPphB protease activity.
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Affiliation(s)
- Matthew Helm
- 1 Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
| | - Mingsheng Qi
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Shayan Sarkar
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Steven A Whitham
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Roger W Innes
- 1 Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
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23
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Chang HX, Tan R, Hartman GL, Wen Z, Sang H, Domier LL, Whitham SA, Wang D, Chilvers MI. Characterization of Soybean STAY-GREEN Genes in Susceptibility to Foliar Chlorosis of Sudden Death Syndrome. Plant Physiol 2019; 180:711-717. [PMID: 30952683 PMCID: PMC6548243 DOI: 10.1104/pp.19.00046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/27/2019] [Indexed: 05/10/2023]
Abstract
Genetic mappings for soybean sudden death syndrome foliar chlorosis suggested that STAY-GREEN genes with loss-of-susceptibility mechanism may have different breeding merits for disease resistance.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Ruijuan Tan
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
- U.S. Department of Agriculture-Agricultural Research Service, Urbana, Illinois 61801
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Hyunkyu Sang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
- U.S. Department of Agriculture-Agricultural Research Service, Urbana, Illinois 61801
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
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24
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Qi M, Zheng W, Zhao X, Hohenstein JD, Kandel Y, O'Conner S, Wang Y, Du C, Nettleton D, MacIntosh GC, Tylka GL, Wurtele ES, Whitham SA, Li L. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnol J 2019; 17:252-263. [PMID: 29878511 PMCID: PMC6330549 DOI: 10.1111/pbi.12961] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 03/22/2018] [Accepted: 06/04/2018] [Indexed: 05/19/2023]
Abstract
Enhancing the nutritional quality and disease resistance of crops without sacrificing productivity is a key issue for developing varieties that are valuable to farmers and for simultaneously improving food security and sustainability. Expression of the Arabidopsis thaliana species-specific AtQQS (Qua-Quine Starch) orphan gene or its interactor, NF-YC4 (Nuclear Factor Y, subunit C4), has been shown to increase levels of leaf/seed protein without affecting the growth and yield of agronomic species. Here, we demonstrate that overexpression of AtQQS and NF-YC4 in Arabidopsis and soybean enhances resistance/reduces susceptibility to viruses, bacteria, fungi, aphids and soybean cyst nematodes. A series of Arabidopsis mutants in starch metabolism were used to explore the relationships between QQS expression, carbon and nitrogen partitioning, and defense. The enhanced basal defenses mediated by QQS were independent of changes in protein/carbohydrate composition of the plants. We demonstrate that either AtQQS or NF-YC4 overexpression in Arabidopsis and in soybean reduces susceptibility of these plants to pathogens/pests. Transgenic soybean lines overexpressing NF-YC4 produce seeds with increased protein while maintaining healthy growth. Pull-down studies reveal that QQS interacts with human NF-YC, as well as with Arabidopsis NF-YC4, and indicate two QQS binding sites near the NF-YC-histone-binding domain. A new model for QQS interaction with NF-YC is speculated. Our findings illustrate the potential of QQS and NF-YC4 to increase protein and improve defensive traits in crops, overcoming the normal growth-defense trade-offs.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological StatisticsIowa State UniversityAmesIAUSA
| | - Jessica D. Hohenstein
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Yuba Kandel
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Seth O'Conner
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
| | - Yifan Wang
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Chuanlong Du
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Dan Nettleton
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Gregory L. Tylka
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Ling Li
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
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25
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Qi M, Mei Y, Grayczyk JP, Darben LM, Rieker MEG, Seitz JM, Voegele RT, Whitham SA, Link TI. Candidate Effectors From Uromyces appendiculatus, the Causal Agent of Rust on Common Bean, Can Be Discriminated Based on Suppression of Immune Responses. Front Plant Sci 2019; 10:1182. [PMID: 31636645 PMCID: PMC6787271 DOI: 10.3389/fpls.2019.01182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/29/2019] [Indexed: 05/07/2023]
Abstract
Rust fungi are devastating pathogens for several important crop plants. The biotrophic lifestyle of rust fungi requires that they influence their host plants to create a favorable environment for growth and reproduction. Rust fungi secrete a variety of effector proteins that manipulate host target proteins to alter plant metabolism and suppress defense responses. Because of the obligate biotrophic lifestyle of rust fungi, direct evidence for effector function is difficult to obtain, and so suites of experiments utilizing expression in heterologous systems are necessary. Here, we present results from a yeast cell death suppression assay and assays for suppression of PAMP-triggered immunity (PTI) and effector triggered immunity (ETI) based on delivery of effectors through the bacterial type III secretion system. In addition, subcellular localization was tested using transient expression of GFP fusion proteins in Nicotiana benthamiana through Agrobacterium infiltration. We tested 31 representative effector candidates from the devastating common bean rust pathogen Uromyces appendiculatus. These effector candidates were selected based on features of their gene families, most important lineage specificity. We show that several of our effector candidates suppress plant defense. Some of them also belong to families of effector candidates that are present in multiple rust species where their homologs probably also have effector functions. In our analysis of candidate effector mRNA expression, some of those effector candidates that gave positive results in the other assays were not up-regulated during plant infection, indicating that either these proteins have functions at multiple life stages or that strong up-regulation of RNA level in planta may not be as important a criterion for identifying effectors as previously thought. Overall, our pipeline for selecting effector candidates based on sequence features followed by screening assays using heterologous expression systems was successful in discriminating effector candidates. This work lays the foundation for functional characterization of U. appendiculatus effectors, the identification of effector targets, and identification of novel sources for resistance in common bean.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - James P. Grayczyk
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | | | | | - Janina M. Seitz
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Ralf T. Voegele
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Tobias I. Link
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
- *Correspondence: Tobias Link,
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26
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Pedley KF, Pandey AK, Ruck A, Lincoln LM, Whitham SA, Graham MA. Rpp1 Encodes a ULP1-NBS-LRR Protein That Controls Immunity to Phakopsora pachyrhizi in Soybean. Mol Plant Microbe Interact 2019; 32:120-133. [PMID: 30303765 DOI: 10.1094/mpmi-07-18-0198-fi] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phakopsora pachyrhizi is the causal agent of Asian soybean rust. Susceptible soybean plants infected by virulent isolates of P. pachyrhizi are characterized by tan-colored lesions and erumpent uredinia on the leaf surface. Germplasm screening and genetic analyses have led to the identification of seven loci, Rpp1 to Rpp7, that provide varying degrees of resistance to P. pachyrhizi (Rpp). Two genes, Rpp1 and Rpp1b, map to the same region on soybean chromosome 18. Rpp1 is unique among the Rpp genes in that it confers an immune response (IR) to avirulent P. pachyrhizi isolates. The IR is characterized by a lack of visible symptoms, whereas resistance provided by Rpp1b to Rpp7 results in red-brown foliar lesions. Rpp1 maps to a region spanning approximately 150 kb on chromosome 18 between markers Sct_187 and Sat_064 in L85-2378 (Rpp1), an isoline developed from Williams 82 and PI 200492 (Rpp1). To identify Rpp1, we constructed a bacterial artificial chromosome library from soybean accession PI 200492. Sequencing of the Rpp1 locus identified three homologous nucleotide binding site-leucine rich repeat (NBS-LRR) candidate resistance genes between Sct_187 and Sat_064. Each candidate gene is also predicted to encode an N-terminal ubiquitin-like protease 1 (ULP1) domain. Cosilencing of the Rpp1 candidates abrogated the immune response in the Rpp1 resistant soybean accession PI 200492, indicating that Rpp1 is a ULP1-NBS-LRR protein and plays a key role in the IR.
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Affiliation(s)
- Kerry F Pedley
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Ajay K Pandey
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Amy Ruck
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
| | - Steven A Whitham
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
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27
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Bao Y, Zarecor S, Shah D, Tuel T, Campbell DA, Chapman AVE, Imberti D, Kiekhaefer D, Imberti H, Lübberstedt T, Yin Y, Nettleton D, Lawrence-Dill CJ, Whitham SA, Tang L, Howell SH. Assessing plant performance in the Enviratron. Plant Methods 2019; 15:117. [PMID: 31660060 PMCID: PMC6806530 DOI: 10.1186/s13007-019-0504-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/15/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Enviratron at Iowa State University is a facility for testing under controlled conditions the effects of the environment on plant growth and development. Crop plants (including maize) can be grown to maturity in the Enviratron, and the performance of plants under different environmental conditions can be monitored 24 h per day, 7 days per week throughout the growth cycle. RESULTS The Enviratron is an array of custom-designed plant growth chambers that simulate different environmental conditions coupled with precise sensor-based phenotypic measurements carried out by a robotic rover. The rover has workflow instructions to periodically visit plants growing in the different chambers where it measures various growth and physiological parameters. The rover consists of an unmanned ground vehicle, an industrial robotic arm and an array of sensors including RGB, visible and near infrared (VNIR) hyperspectral, thermal, and time-of-flight (ToF) cameras, laser profilometer and pulse-amplitude modulated (PAM) fluorometer. The sensors are autonomously positioned for detecting leaves in the plant canopy, collecting various physiological measurements based on computer vision algorithms and planning motion via "eye-in-hand" movement control of the robotic arm. In particular, the automated leaf probing function that allows the precise placement of sensor probes on leaf surfaces presents a unique advantage of the Enviratron system over other types of plant phenotyping systems. CONCLUSIONS The Enviratron offers a new level of control over plant growth parameters and optimizes positioning and timing of sensor-based phenotypic measurements. Plant phenotypes in the Enviratron are measured in situ-in that the rover takes sensors to the plants rather than moving plants to the sensors.
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Affiliation(s)
- Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
- Present Address: Department of Biosystems Engineering, Auburn University, 213 Corley Building, 350 Mell St, Auburn, AL 36830 USA
| | - Scott Zarecor
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
| | - Dylan Shah
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
- Present Address: The Faboratory, Yale University, 9 Hillhouse Ave, ML 118, New Haven, CT 06511 USA
| | - Taylor Tuel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
| | - Darwin A. Campbell
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
| | - Antony V. E. Chapman
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
| | | | | | | | | | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA USA
| | - Carolyn J. Lawrence-Dill
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
- Department of Agronomy, Iowa State University, Ames, IA USA
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
| | - Stephen H. Howell
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
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28
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Xu HY, Zhang C, Li ZC, Wang ZR, Jiang XX, Shi YF, Tian SN, Braun E, Mei Y, Qiu WL, Li S, Wang B, Xu J, Navarre D, Ren D, Cheng N, Nakata PA, Graham MA, Whitham SA, Liu JZ. The MAPK Kinase Kinase GmMEKK1 Regulates Cell Death and Defense Responses. Plant Physiol 2018; 178:907-922. [PMID: 30158117 PMCID: PMC6181047 DOI: 10.1104/pp.18.00903] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/18/2018] [Indexed: 05/13/2023]
Abstract
MAPK signaling pathways play critical roles in plant immunity. Here, we silenced multiple genes encoding MAPKs using virus-induced gene silencing mediated by Bean pod mottle virus to identify MAPK genes involved in soybean (Glycine max) immunity. Surprisingly, a strong hypersensitive response (HR) cell death was observed when soybean MAPK KINASE KINASE1 (GmMEKK1), a homolog of Arabidopsis (Arabidopsis thaliana) MEKK1, was silenced. The HR was accompanied by the overaccumulation of defense signaling molecules, salicylic acid (SA) and hydrogen peroxide. Genes involved in primary metabolism, translation/transcription, photosynthesis, and growth/development were down-regulated in GmMEKK1-silenced plants, while the expression of defense-related genes was activated. Accordingly, GmMEKK1-silenced plants were more resistant to downy mildew (Peronospora manshurica) and Soybean mosaic virus compared with control plants. Silencing GmMEKK1 reduced the activation of GmMPK6 but enhanced the activation of GmMPK3 in response to flg22 peptide. Unlike Arabidopsis MPK4, GmMPK4 was not activated by either flg22 or SA. Interestingly, transient overexpression of GmMEKK1 in Nicotiana benthamiana also induced HR. Our results indicate that GmMEKK1 plays both positive and negative roles in immunity and appears to differentially activate downstream MPKs by promoting GmMPK6 activation but suppressing GmMPK3 activation in response to flg22. The involvement of GmMPK4 kinase activity in cell death and in flg22- or SA-triggered defense responses in soybean requires further investigation.
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Affiliation(s)
- Hui-Yang Xu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Chi Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhen-Chao Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhi-Rong Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xu-Xu Jiang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Fei Shi
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Sheng-Nan Tian
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Edward Braun
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Wen-Li Qiu
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Sen Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Juan Xu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Duroy Navarre
- U.S. Department of Agriculture-Agricultural Research Service, Prosser, Washington 99350
| | - Dongtao Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ninghui Cheng
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
| | - Paul A Nakata
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
| | - Michelle A Graham
- U.S. Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Jian-Zhong Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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29
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Abstract
Virus-induced gene silencing (VIGS) is a powerful technology for rapidly and transiently knocking down the expression of plant genes to study their functions. A VIGS vector for maize derived from Foxtail mosaic virus (FoMV), a positive-sense single-stranded RNA virus, was recently developed. A cloning site created near the 3' end of the FoMV genome enables insertion of 200-400 nucleotide fragments of maize genes targeted for silencing. The recombinant FoMV clones are inoculated into leaves of maize seedlings by biolistic particle delivery, and silencing is typically observed within 2 weeks after inoculation. This chapter provides a protocol for constructing FoMV VIGS clones and inoculating them into maize seedlings.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey, Ames, IA, 50011, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey, Ames, IA, 50011, USA.
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30
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Ranjan A, Jayaraman D, Grau C, Hill JH, Whitham SA, Ané J, Smith DL, Kabbage M. The pathogenic development of Sclerotinia sclerotiorum in soybean requires specific host NADPH oxidases. Mol Plant Pathol 2018; 19:700-714. [PMID: 28378935 PMCID: PMC6638103 DOI: 10.1111/mpp.12555] [Citation(s) in RCA: 12] [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: 10/19/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 05/15/2023]
Abstract
The plant membrane-localized NADPH oxidases, also known as respiratory burst oxidase homologues (RBOHs), play crucial roles in various cellular activities, including plant disease responses, and are a major source of reactive oxygen species (ROS). Sclerotinia sclerotiorum is a cosmopolitan fungal pathogen that causes Sclerotinia stem rot (SSR) in soybean. Via a key virulence factor, oxalic acid, it induces programmed cell death (PCD) in the host plant, a process that is reliant on ROS generation. In this study, using protein sequence similarity searches, we identified 17 soybean RBOHs (GmRBOHs) and studied their contribution to SSR disease development, drought tolerance and nodulation. We clustered the soybean RBOH genes into six groups of orthologues based on phylogenetic analysis with their Arabidopsis counterparts. Transcript analysis of all 17 GmRBOHs revealed that, of the six identified groups, group VI (GmRBOH-VI) was specifically and drastically induced following S. sclerotiorum challenge. Virus-induced gene silencing (VIGS) of GmRBOH-VI using Bean pod mottle virus (BPMV) resulted in enhanced resistance to S. sclerotiorum and markedly reduced ROS levels during disease development. Coincidently, GmRBOH-VI-silenced plants were also found to be drought tolerant, but showed a reduced capacity to form nodules. Our results indicate that the pathogenic development of S. sclerotiorum in soybean requires the active participation of specific host RBOHs, to induce ROS and cell death, thus leading to the establishment of disease.
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Affiliation(s)
- Ashish Ranjan
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | | | - Craig Grau
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - John H. Hill
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Jean‐Michel Ané
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of AgronomyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Damon L. Smith
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Mehdi Kabbage
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
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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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32
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Burkhow SJ, Stephens NM, Mei Y, Dueñas ME, Freppon DJ, Ding G, Smith SC, Lee YJ, Nikolau BJ, Whitham SA, Smith EA. Characterizing virus-induced gene silencing at the cellular level with in situ multimodal imaging. Plant Methods 2018; 14:37. [PMID: 29849743 PMCID: PMC5968576 DOI: 10.1186/s13007-018-0306-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/12/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Reverse genetic strategies, such as virus-induced gene silencing, are powerful techniques to study gene function. Currently, there are few tools to study the spatial dependence of the consequences of gene silencing at the cellular level. RESULTS We report the use of multimodal Raman and mass spectrometry imaging to study the cellular-level biochemical changes that occur from silencing the phytoene desaturase (pds) gene using a Foxtail mosaic virus (FoMV) vector in maize leaves. The multimodal imaging method allows the localized carotenoid distribution to be measured and reveals differences lost in the spatial average when analyzing a carotenoid extraction of the whole leaf. The nature of the Raman and mass spectrometry signals are complementary: silencing pds reduces the downstream carotenoid Raman signal and increases the phytoene mass spectrometry signal. CONCLUSIONS Both Raman and mass spectrometry imaging show that the biochemical changes from FoMV-pds silencing occur with a mosaic spatial pattern at the cellular level, and the Raman images show carotenoid expression was reduced at discrete locations but not eliminated. The data indicate the multimodal imaging method has great utility to study the biochemical changes that result from gene silencing at the cellular spatial level of expression in many plant tissues including the stem and leaf. Our demonstrated method is the first to spatially characterize the biochemical changes as a result of VIGS at the cellular level using commonly available instrumentation.
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Affiliation(s)
- Sadie J. Burkhow
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
| | - Nicole M. Stephens
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Maria Emilia Dueñas
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
| | - Daniel J. Freppon
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
| | - Geng Ding
- Department of Biochemistry Biophysics, and Molecular Biology, Center for Metabolic Biology, Iowa State University, Ames, IA 50011 USA
| | - Shea C. Smith
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA 50011 USA
| | - Young-Jin Lee
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
| | - Basil J. Nikolau
- Department of Biochemistry Biophysics, and Molecular Biology, Center for Metabolic Biology, Iowa State University, Ames, IA 50011 USA
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Emily A. Smith
- The Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3111 USA
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111 USA
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33
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Abstract
Virus-induced gene silencing (VIGS) is a powerful technology for rapidly and transiently knocking down the expression of plant genes to study their functions. A VIGS vector for maize derived from Foxtail mosaic virus (FoMV), a positive-sense single-stranded RNA virus, was recently developed. A cloning site created near the 3' end of the FoMV genome enables insertion of 200-400 nucleotide fragments of maize genes targeted for silencing. The recombinant FoMV clones are inoculated into leaves of maize seedlings by biolistic particle delivery, and silencing is typically observed within 2 weeks after inoculation. This chapter provides a protocol for constructing FoMV VIGS clones and inoculating them into maize seedlings.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey, Ames, IA, 50011, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey, Ames, IA, 50011, USA.
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34
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Liu JZ, Duan J, Ni M, Liu Z, Qiu WL, Whitham SA, Qian WJ. S-Nitrosylation inhibits the kinase activity of tomato phosphoinositide-dependent kinase 1 (PDK1). J Biol Chem 2017; 292:19743-19751. [PMID: 28972151 DOI: 10.1074/jbc.m117.803882] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/13/2017] [Indexed: 01/01/2023] Open
Abstract
It is well known that the reactive oxygen species NO can trigger cell death in plants and other organisms, but the underlying molecular mechanisms are not well understood. Here we provide evidence that NO may trigger cell death in tomato (Solanum lycopersicum) by inhibiting the activity of phosphoinositide-dependent kinase 1 (SlPDK1), a conserved negative regulator of cell death in yeasts, mammals, and plants, via S-nitrosylation. Biotin-switch assays indicated that SlPDK1 is a target of S-nitrosylation. Moreover, the kinase activity of SlPDK1 was inhibited by S-nitrosoglutathione in a concentration-dependent manner, indicating that SlPDK1 activity is abrogated by S-nitrosylation. The S-nitrosoglutathione-induced inhibition was reversible in the presence of a reducing agent but additively enhanced by hydrogen peroxide (H2O2). Our LC-MS/MS analyses further indicated that SlPDK1 is primarily S-nitrosylated on a cysteine residue at position 128 (Cys128), and substitution of Cys128 with serine completely abolished SlPDK1 kinase activity, suggesting that S-nitrosylation of Cys128 is responsible for SlPDK1 inhibition. In summary, our results establish a potential link between NO-triggered cell death and inhibition of the kinase activity of tomato PDK1.
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Affiliation(s)
- Jian-Zhong Liu
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China,
| | - Jicheng Duan
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and
| | - Min Ni
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China
| | - Zhen Liu
- From the College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China
| | - Wen-Li Qiu
- the Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Steven A Whitham
- the Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and
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35
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Lu H, Tang L, Whitham SA, Mei Y. A Robotic Platform for Corn Seedling Morphological Traits Characterization. Sensors (Basel) 2017; 17:s17092082. [PMID: 28895892 PMCID: PMC5621065 DOI: 10.3390/s17092082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/03/2017] [Accepted: 09/06/2017] [Indexed: 12/03/2022]
Abstract
Crop breeding plays an important role in modern agriculture, improving plant performance, and increasing yield. Identifying the genes that are responsible for beneficial traits greatly facilitates plant breeding efforts for increasing crop production. However, associating genes and their functions with agronomic traits requires researchers to observe, measure, record, and analyze phenotypes of large numbers of plants, a repetitive and error-prone job if performed manually. An automated seedling phenotyping system aimed at replacing manual measurement, reducing sampling time, and increasing the allowable work time is thus highly valuable. Toward this goal, we developed an automated corn seedling phenotyping platform based on a time-of-flight of light (ToF) camera and an industrial robot arm. A ToF camera is mounted on the end effector of the robot arm. The arm positions the ToF camera at different viewpoints for acquiring 3D point cloud data. A camera-to-arm transformation matrix was calculated using a hand-eye calibration procedure and applied to transfer different viewpoints into an arm-based coordinate frame. Point cloud data filters were developed to remove the noise in the background and in the merged seedling point clouds. A 3D-to-2D projection and an x-axis pixel density distribution method were used to segment the stem and leaves. Finally, separated leaves were fitted with 3D curves for morphological traits characterization. This platform was tested on a sample of 60 corn plants at their early growth stages with between two to five leaves. The error ratios of the stem height and leave length measurements are 13.7% and 13.1%, respectively, demonstrating the feasibility of this robotic system for automated corn seedling phenotyping.
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Affiliation(s)
- Hang Lu
- Department of Agricultural and Biosystems Engineering, Iowa State University, 2346 Elings Hall, Ames, IA 50011, USA.
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, 2346 Elings Hall, Ames, IA 50011, USA.
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
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36
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Rajamäki ML, Xi D, Sikorskaite-Gudziuniene S, Valkonen JPT, Whitham SA. Differential Requirement of the Ribosomal Protein S6 and Ribosomal Protein S6 Kinase for Plant-Virus Accumulation and Interaction of S6 Kinase with Potyviral VPg. Mol Plant Microbe Interact 2017; 30:374-384. [PMID: 28437137 DOI: 10.1094/mpmi-06-16-0122-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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
Ribosomal protein S6 (RPS6) is an indispensable plant protein regulated, in part, by ribosomal protein S6 kinase (S6K) which, in turn, is a key regulator of plant responses to stresses and developmental cues. Increased expression of RPS6 was detected in Nicotiana benthamiana during infection by diverse plant viruses. Silencing of the RPS6 and S6K genes in N. benthamiana affected accumulation of Cucumber mosaic virus, Turnip mosaic virus (TuMV), and Potato virus A (PVA) in contrast to Turnip crinkle virus and Tobacco mosaic virus. In addition, the viral genome-linked protein (VPg) of TuMV and PVA interacted with S6K in plant cells, as detected by bimolecular fluorescence complementation assay. The VPg-S6K interaction was detected in cytoplasm, nucleus, and nucleolus, whereas the green fluorescent protein-tagged S6K alone showed cytoplasmic localization only. These results demonstrate that the requirement for RPS6 and S6K differs for diverse plant viruses with different translation initiation strategies and suggest that potyviral VPg-S6K interaction may affect S6K functions in both the cytoplasm and the nucleus.
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Affiliation(s)
- Minna-Liisa Rajamäki
- 1 Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Helsinki, Finland
| | - Dehui Xi
- 2 College of Life Science, Sichuan University, Chengdu, 610064, China; and
| | | | - Jari P T Valkonen
- 1 Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Helsinki, Finland
| | - Steven A Whitham
- 3 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
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37
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de Carvalho MCDCG, Costa Nascimento L, Darben LM, Polizel‐Podanosqui AM, Lopes‐Caitar VS, Qi M, Rocha CS, Carazzolle MF, Kuwahara MK, Pereira GAG, Abdelnoor RV, Whitham SA, Marcelino‐Guimarães FC. Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families. Mol Plant Pathol 2017; 18:363-377. [PMID: 27010366 PMCID: PMC6638266 DOI: 10.1111/mpp.12405] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, can cause losses greater than 80%. Despite its economic importance, there is no soybean cultivar with durable ASR resistance. In addition, the P. pachyrhizi genome is not yet available. However, the availability of other rust genomes, as well as the development of sample enrichment strategies and bioinformatics tools, has improved our knowledge of the ASR secretome and its potential effectors. In this context, we used a combination of laser capture microdissection (LCM), RNAseq and a bioinformatics pipeline to identify a total of 36 350 P. pachyrhizi contigs expressed in planta and a predicted secretome of 851 proteins. Some of the predicted secreted proteins had characteristics of candidate effectors: small size, cysteine rich, do not contain PFAM domains (except those associated with pathogenicity) and strongly expressed in planta. A comparative analysis of the predicted secreted proteins present in Pucciniales species identified new members of soybean rust and new Pucciniales- or P. pachyrhizi-specific families (tribes). Members of some families were strongly up-regulated during early infection, starting with initial infection through haustorium formation. Effector candidates selected from two of these families were able to suppress immunity in transient assays, and were localized in the plant cytoplasm and nuclei. These experiments support our bioinformatics predictions and show that these families contain members that have functions consistent with P. pachyrhizi effectors.
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Affiliation(s)
| | - Leandro Costa Nascimento
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | - Luana M. Darben
- Embrapa sojaPlant BiotechnologyLondrinaParanáCEP 70770‐901Brazil
| | | | - Valéria S. Lopes‐Caitar
- Embrapa sojaPlant BiotechnologyLondrinaParanáCEP 70770‐901Brazil
- Universidade Estadual de LondrinaLondrinaParanáCEP 86057‐970Brazil
| | - Mingsheng Qi
- Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | | | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | | | - Goncalo A. G. Pereira
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | | | - Steven A. Whitham
- Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
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38
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Bak A, Cheung AL, Yang C, Whitham SA, Casteel CL. A viral protease relocalizes in the presence of the vector to promote vector performance. Nat Commun 2017; 8:14493. [PMID: 28205516 PMCID: PMC5316897 DOI: 10.1038/ncomms14493] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 01/18/2016] [Accepted: 12/31/2016] [Indexed: 12/22/2022] Open
Abstract
Vector-borne pathogens influence host characteristics relevant to host-vector contact, increasing pathogen transmission and survival. Previously, we demonstrated that infection with Turnip mosaic virus, a member of one of the largest families of plant-infecting viruses, increases vector attraction and reproduction on infected hosts. These changes were due to a single viral protein, NIa-Pro. Here we show that NIa-Pro responds to the presence of the aphid vector during infection by relocalizing to the vacuole. Remarkably, vacuolar localization is required for NIa-Pro's ability to enhance aphid reproduction on host plants, vacuole localization disappears when aphids are removed, and this phenomenon occurs for another potyvirus, Potato virus Y, suggesting a conserved role for the protein in vector-host interactions. Taken together, these results suggest that potyviruses dynamically respond to the presence of their vectors, promoting insect performance and transmission only when needed.
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Affiliation(s)
- Aurélie Bak
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Andrea L. Cheung
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Chunling Yang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Clare L. Casteel
- Department of Plant Pathology, University of California, Davis, California 95616, USA
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39
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Bak A, Cheung AL, Yang C, Whitham SA, Casteel CL. A viral protease relocalizes in the presence of the vector to promote vector performance. Nat Commun 2017. [PMID: 28205516 DOI: 10.1038/ncomms14493c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Vector-borne pathogens influence host characteristics relevant to host-vector contact, increasing pathogen transmission and survival. Previously, we demonstrated that infection with Turnip mosaic virus, a member of one of the largest families of plant-infecting viruses, increases vector attraction and reproduction on infected hosts. These changes were due to a single viral protein, NIa-Pro. Here we show that NIa-Pro responds to the presence of the aphid vector during infection by relocalizing to the vacuole. Remarkably, vacuolar localization is required for NIa-Pro's ability to enhance aphid reproduction on host plants, vacuole localization disappears when aphids are removed, and this phenomenon occurs for another potyvirus, Potato virus Y, suggesting a conserved role for the protein in vector-host interactions. Taken together, these results suggest that potyviruses dynamically respond to the presence of their vectors, promoting insect performance and transmission only when needed.
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Affiliation(s)
- Aurélie Bak
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Andrea L Cheung
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Chunling Yang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Clare L Casteel
- Department of Plant Pathology, University of California, Davis, California 95616, USA
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40
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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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41
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Martin K, Singh J, Hill JH, Whitham SA, Cannon SB. Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.). BMC Genomics 2016; 17:613. [PMID: 27515794 PMCID: PMC4982238 DOI: 10.1186/s12864-016-2976-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 05/15/2016] [Accepted: 07/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized. RESULTS We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar 'Stringless green refugee') to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns. CONCLUSIONS We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense.
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Affiliation(s)
- Kathleen Martin
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Jugpreet Singh
- ORISE Fellow, USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - John H. Hill
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011 USA
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011 USA
| | - Steven B. Cannon
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Laboratory, Iowa State University, Ames, IA 50011 USA
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Abstract
Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| | - Valéria Lopes-Caitar
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
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Whitham SA, Lincoln LM, Chowda-Reddy RV, Dittman JD, O'Rourke JA, Graham MA. Virus-Induced Gene Silencing and Transient Gene Expression in Soybean (Glycine max) Using Bean Pod Mottle Virus Infectious Clones. ACTA ACUST UNITED AC 2016; 1:263-283. [PMID: 30775861 DOI: 10.1002/cppb.20012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Virus-induced gene silencing (VIGS) is a powerful and rapid approach for determining the functions of plant genes. The basis of VIGS is that a viral genome is engineered so that it can carry fragments of plant genes, typically in the 200 to 300 base pair size range. The recombinant viruses are used to infect experimental plants, and wherever the virus invades, the target gene or genes will be silenced. VIGS is thus transient, and in the span of a few weeks, it is possible to design VIGS constructs and then generate loss-of-function phenotypes through RNA silencing of the target genes. In soybean (Glycine max), the Bean pod mottle virus (BPMV) has been engineered to be valuable tool for silencing genes with diverse functions and also for over-expression of foreign genes. This protocol describes a method for designing BPMV constructs and using them to silence or transiently express genes in soybean. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa.,These authors contributed equally to this work
| | - Lori M Lincoln
- Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Ames, Iowa
| | | | - Jaime D Dittman
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa
| | - Jamie A O'Rourke
- Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Ames, Iowa
| | - Michelle A Graham
- Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Ames, Iowa.,These authors contributed equally to this work
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Mei Y, Zhang C, Kernodle BM, Hill JH, Whitham SA. A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize. Plant Physiol 2016; 171:760-72. [PMID: 27208311 PMCID: PMC4902600 DOI: 10.1104/pp.16.00172] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/25/2016] [Indexed: 05/18/2023]
Abstract
Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (Y.M., B.M.K., J.H.H., S.A.W.);Department of Agriculture, Alcorn State University, Lorman, Mississippi 39096 (C.Z.); andDuPont Pioneer, Johnston, Iowa 50131 (B.M.K.)
| | - Chunquan Zhang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (Y.M., B.M.K., J.H.H., S.A.W.);Department of Agriculture, Alcorn State University, Lorman, Mississippi 39096 (C.Z.); andDuPont Pioneer, Johnston, Iowa 50131 (B.M.K.)
| | - Bliss M Kernodle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (Y.M., B.M.K., J.H.H., S.A.W.);Department of Agriculture, Alcorn State University, Lorman, Mississippi 39096 (C.Z.); andDuPont Pioneer, Johnston, Iowa 50131 (B.M.K.)
| | - John H Hill
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (Y.M., B.M.K., J.H.H., S.A.W.);Department of Agriculture, Alcorn State University, Lorman, Mississippi 39096 (C.Z.); andDuPont Pioneer, Johnston, Iowa 50131 (B.M.K.)
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (Y.M., B.M.K., J.H.H., S.A.W.);Department of Agriculture, Alcorn State University, Lorman, Mississippi 39096 (C.Z.); andDuPont Pioneer, Johnston, Iowa 50131 (B.M.K.)
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Carr JP, Whitham SA. Focus on Noncoding RNA Regulation of Plant-Microbe Interactions. Mol Plant Microbe Interact 2016; 29:155. [PMID: 26881987 DOI: 10.1094/mpmi-01-16-0009-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Investigations in recent years have uncovered important roles for RNA molecules that do not encode proteins (‘noncoding RNAs’) but which, nevertheless, exert powerful effects on gene expression at both transcriptional and posttranscriptional levels. Our late colleague Biao Ding, who died unexpectedly on June 25, 2015, proposed a Focus Issue on the roles in plant-microbe interactions of noncoding RNAs, whether of plant or microbial origin and including small interfering (si)RNAs, microRNAs, phased siRNAs, and long noncoding RNAs, as well as viroids and satellite RNAs. The Editorial Board of MPMI has decided to dedicate this Focus Issue to the memory of Professor Biao Ding, a valued and deeply missed colleague and friend.
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Casteel CL, De Alwis M, Bak A, Dong H, Whitham SA, Jander G. Disruption of Ethylene Responses by Turnip mosaic virus Mediates Suppression of Plant Defense against the Green Peach Aphid Vector. Plant Physiol 2015; 169:209-18. [PMID: 26091820 PMCID: PMC4577379 DOI: 10.1104/pp.15.00332] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/17/2015] [Indexed: 05/19/2023]
Abstract
Plants employ diverse responses mediated by phytohormones to defend themselves against pathogens and herbivores. Adapted pathogens and herbivores often manipulate these responses to their benefit. Previously, we demonstrated that Turnip mosaic virus (TuMV) infection suppresses callose deposition, an important plant defense induced in response to feeding by its aphid vector, the green peach aphid (Myzus persicae), and increases aphid fecundity compared with uninfected control plants. Further, we determined that production of a single TuMV protein, Nuclear Inclusion a-Protease (NIa-Pro) domain, was responsible for changes in host plant physiology and increased green peach aphid reproduction. To characterize the underlying molecular mechanisms of this phenomenon, we examined the role of three phytohormone signaling pathways, jasmonic acid, salicylic acid, and ethylene (ET), in TuMV-infected Arabidopsis (Arabidopsis thaliana), with or without aphid herbivory. Experiments with Arabidopsis mutants ethylene insensitive2 and ethylene response1, and chemical inhibitors of ET synthesis and perception (aminoethoxyvinyl-glycine and 1-methylcyclopropene, respectively), show that the ET signaling pathway is required for TuMV-mediated suppression of Arabidopsis resistance to the green peach aphid. Additionally, transgenic expression of NIa-Pro in Arabidopsis alters ET responses and suppresses aphid-induced callose formation in an ET-dependent manner. Thus, disruption of ET responses in plants is an additional function of NIa-Pro, a highly conserved potyvirus protein. Virus-induced changes in ET responses may mediate vector-plant interactions more broadly and thus represent a conserved mechanism for increasing transmission by insect vectors across generations.
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Affiliation(s)
- Clare L Casteel
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
| | - Manori De Alwis
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
| | - Aurélie Bak
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
| | - Haili Dong
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
| | - Steven A Whitham
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
| | - Georg Jander
- Department of Plant Pathology, University of California, Davis, California 95616 (C.L.C., A.B.); Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (M.D.A., G.J.); andDepartment of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (H.D., S.A.W.)
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Liu JZ, Graham MA, Pedley KF, Whitham SA. Gaining insight into soybean defense responses using functional genomics approaches. Brief Funct Genomics 2015; 14:283-90. [PMID: 25832523 DOI: 10.1093/bfgp/elv009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Soybean pathogens significantly impact yield, resulting in over $4 billion dollars in lost revenue annually in the United States. Despite the deployment of improved soybean cultivars, pathogens continue to evolve to evade plant defense responses. Thus, there is an urgent need to identify and characterize gene networks controlling defense responses to harmful pathogens. In this review, we focus on major advances that have been made in identifying the genes and gene networks regulating defense responses with an emphasis on soybean-pathogen interactions that have been amenable to gene function analyses using gene silencing technologies. Further we describe new research striving to identify genes involved in durable broad-spectrum resistance. Finally, we consider future prospects for functional genomic studies in soybean and demonstrate that understanding soybean disease and stress tolerance will be expedited at an unprecedented pace.
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Moran Lauter AN, Peiffer GA, Yin T, Whitham SA, Cook D, Shoemaker RC, Graham MA. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. BMC Genomics 2014; 15:702. [PMID: 25149281 PMCID: PMC4161901 DOI: 10.1186/1471-2164-15-702] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [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: 05/14/2014] [Accepted: 08/12/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causing a reduction in photosynthesis and interveinal yellowing of leaves. Soybeans (Glycine max (L.) Merr.) grown in high pH soils often suffer from IDC, resulting in substantial yield losses. Iron efficient soybean cultivars maintain photosynthesis and have higher yields under IDC-promoting conditions than inefficient cultivars. RESULTS To capture signaling between roots and leaves and identify genes acting early in the iron efficient cultivar Clark, we conducted a RNA-Seq study at one and six hours after replacing iron sufficient hydroponic media (100 μM iron(III) nitrate nonahydrate) with iron deficient media (50 μM iron(III) nitrate nonahydrate). At one hour of iron stress, few genes were differentially expressed in leaves but many were already changing expression in roots. By six hours, more genes were differentially expressed in the leaves, and a massive shift was observed in the direction of gene expression in both roots and leaves. Further, there was little overlap in differentially expressed genes identified in each tissue and time point. CONCLUSIONS Genes involved in hormone signaling, regulation of DNA replication and iron uptake utilization are key aspects of the early iron-efficiency response. We observed dynamic gene expression differences between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. In roots, genes involved iron uptake and development of Casparian strips were induced one hour after iron stress. In leaves, genes involved in DNA replication and sugar signaling responded to iron deficiency. The differentially expressed genes (DEGs) and signaling components identified here represent new targets for soybean improvement.
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Affiliation(s)
- Adrienne N Moran Lauter
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
| | - Gregory A Peiffer
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
| | - Tengfei Yin
- />Department of Statistics, Iowa State University, Ames, Iowa 50011 USA
| | - Steven A Whitham
- />Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 USA
| | - Dianne Cook
- />Department of Statistics, Iowa State University, Ames, Iowa 50011 USA
| | - Randy C Shoemaker
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, Iowa 50011 USA
| | - Michelle A Graham
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, Iowa 50011 USA
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Liu JZ, Braun E, Qiu WL, Shi YF, Marcelino-Guimarães FC, Navarre D, Hill JH, Whitham SA. Positive and negative roles for soybean MPK6 in regulating defense responses. Mol Plant Microbe Interact 2014; 27:824-34. [PMID: 24762222 DOI: 10.1094/mpmi-11-13-0350-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It has been well established that MPK6 is a positive regulator of defense responses in model plants such as Arabidopsis and tobacco. However, the functional importance of soybean MPK6 in disease resistance has not been investigated. Here, we showed that silencing of GmMPK6 in soybean using virus-induced gene silencing mediated by Bean pod mottle virus (BPMV) caused stunted growth and spontaneous cell death on the leaves, a typical phenotype of activated defense responses. Consistent with this phenotype, expression of pathogenesis-related (PR) genes and the conjugated form of salicylic acid were significantly increased in GmMPK6-silenced plants. As expected, GmMPK6-silenced plants were more resistant to downy mildew and Soybean mosaic virus compared with vector control plants, indicating a negative role of GmMPK6 in disease resistance. Interestingly, overexpression of GmMPK6, either transiently in Nicotiana benthamiana or stably in Arabidopsis, resulted in hypersensitive response (HR)-like cell death. The HR-like cell death was accompanied by increased PR gene expression, suggesting that GmMPK6, like its counterpart in other plant species, also plays a positive role in cell death induction and defense response. Using bimolecular fluorescence complementation analysis, we determined that GmMKK4 might function upstream of GmMPK6 and GmMKK4 could interact with GmMPK6 independent of its phosphorylation status. Taken together, our results indicate that GmMPK6 functions as both repressor and activator in defense responses of soybean.
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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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