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Hernández-Soto I, González-García Y, Juárez-Maldonado A, Hernández-Fuentes AD. Impact of Argemone mexicana L. on tomato plants infected with Phytophthora infestans. PeerJ 2024; 12:e16666. [PMID: 38188144 PMCID: PMC10771083 DOI: 10.7717/peerj.16666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Background Fungal diseases can cause significant losses in the tomato crop. Phytophthora infestans causes the late blight disease, which considerably affects tomato production worldwide. Weed-based plant extracts are a promising ecological alternative for disease control. Methods In this study, we analyzed the plant extract of Argemone mexicana L. using chromatography-mass spectrometry analysis (GC-MS). We evaluated its impact on the severity of P. infestans, as well as its effect on the components of the antioxidant defense system in tomato plants. Results The extract from A. mexicana contains twelve compounds most have antifungal and biostimulant properties. The findings of the study indicate that applying the A. mexicana extract can reduce the severity of P. infestans, increase tomato fruit yield, enhance the levels of photosynthetic pigments, ascorbic acid, phenols, and flavonoids, as well as decrease the biosynthesis of H2O2, malondialdehyde (MDA), and superoxide anion in the leaves of plants infected with this pathogen. These results suggest that using the extract from A. mexicana could be a viable solution to control the disease caused by P. infestans in tomato crop.
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Affiliation(s)
- Iridiam Hernández-Soto
- Universidad Autónoma del Estado de Hidalgo, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo, Hidalgo, Mexico
| | - Yolanda González-García
- Centro de Investigación Regional Noreste, Campo Experimental Todos Santos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Emiliano Zapata, La Paz, B.C.S, Mexico
| | - Antonio Juárez-Maldonado
- Universidad Autónoma Agraria Antonio Narro, Departamento de Botánica, Saltillo, Coahuila, Mexico
| | - Alma Delia Hernández-Fuentes
- Universidad Autónoma del Estado de Hidalgo, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo, Hidalgo, Mexico
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2
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Agho CA, Kaurilind E, Tähtjärv T, Runno-Paurson E, Niinemets Ü. Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses. Genomics 2023; 115:110678. [PMID: 37406973 PMCID: PMC10548088 DOI: 10.1016/j.ygeno.2023.110678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.
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Affiliation(s)
- C A Agho
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia.
| | - E Kaurilind
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - T Tähtjärv
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, 48309 Jõgeva, Estonia
| | - E Runno-Paurson
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - Ü Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Estonian Academy of Sciences, Kohtu 6, Tallinn 10130, Estonia
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3
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Wang Z, Su C, Hu W, Su Q, Luan Y. The effectors of Phytophthora infestans impact host immunity upon regulation of antagonistic hormonal activities. PLANTA 2023; 258:59. [PMID: 37530861 DOI: 10.1007/s00425-023-04215-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
MAIN CONCLUSION Phytophthora infestans effectors manipulate the antagonism of host hormones to interfere with the immune response of plants at different infection stages. Phytophthora infestans (P. infestans) poses a serious threat to global crop production, and its effectors play an indispensable role in its pathogenicity. However, the function of these effectors during the switch from biotrophy to necrotrophy of P. infestans remains unclear. Further research on the effectors that manipulate the antagonistic response of host hormones is also lacking. In this study, a coexpression analysis and infection assays were performed to identify distinct gene expression changes in both P. infestans and tomato. During the switch from biotrophy to necrotrophy, P. infestans secretes three types of effectors to interfere with host salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) levels. The three aforementioned effectors also regulate the host gene expression including NPR1, TGA2.1, PDF1.2, NDR1, ERF3, NCED6, GAI4, which are involved in hormone crosstalk. The changes in plant hormones are mediated by the three types of effectors, which may accelerate infection and drive completion of the P. infestans lifecycle. Our findings provide new insight into plant‒pathogen interactions that may contribute to the prevention growth of hemibiotrophic pathogens.
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Affiliation(s)
- Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Wenyun Hu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qiao Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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4
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Breeze E, Vale V, McLellan H, Pecrix Y, Godiard L, Grant M, Frigerio L. A tell tail sign: a conserved C-terminal tail-anchor domain targets a subset of pathogen effectors to the plant endoplasmic reticulum. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3188-3202. [PMID: 36860200 DOI: 10.1093/jxb/erad075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is the entry point to the secretory pathway and, as such, is critical for adaptive responses to biotic stress, when the demand for de novo synthesis of immunity-related proteins and signalling components increases significantly. Successful phytopathogens have evolved an arsenal of small effector proteins which collectively reconfigure multiple host components and signalling pathways to promote virulence; a small, but important, subset of which are targeted to the endomembrane system including the ER. We identified and validated a conserved C-terminal tail-anchor motif in a set of pathogen effectors known to localize to the ER from the oomycetes Hyaloperonospora arabidopsidis and Plasmopara halstedii (downy mildew of Arabidopsis and sunflower, respectively) and used this protein topology to develop a bioinformatic pipeline to identify putative ER-localized effectors within the effectorome of the related oomycete, Phytophthora infestans, the causal agent of potato late blight. Many of the identified P. infestans tail-anchor effectors converged on ER-localized NAC transcription factors, indicating that this family is a critical host target for multiple pathogens.
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Affiliation(s)
- Emily Breeze
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Victoria Vale
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Hazel McLellan
- Division of Plant Science, University of Dundee (at JHI), Invergowrie, Dundee DD2 5DA, UK
| | - Yann Pecrix
- CIRAD, UMR PVBMT, Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR C53), Ligne Paradis, 97410 St Pierre, La Réunion, France
| | - Laurence Godiard
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Castanet-Tolosan, France
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lorenzo Frigerio
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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5
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Gu B, Gao W, Liu Z, Shao G, Peng Q, Mu Y, Wang Q, Zhao H, Miao J, Liu X. A single region of the Phytophthora infestans avirulence effector Avr3b functions in both cell death induction and plant immunity suppression. MOLECULAR PLANT PATHOLOGY 2023; 24:317-330. [PMID: 36696541 PMCID: PMC10013827 DOI: 10.1111/mpp.13298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
As a destructive plant pathogen, Phytophthora infestans secretes diverse host-entering RxLR effectors to facilitate infection. One critical RxLR effector, PiAvr3b, not only induces effector-triggered immunity (ETI), which is associated with the potato resistance protein StR3b, but also suppresses pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). To date, the molecular basis underlying such dual activities remains unknown. Based on phylogenetic analysis of global P. infestans isolates, we found two PiAvr3b isoforms that differ by three amino acids. Despite this sequence variation, the two isoforms retain the same properties in activating the StR3b-mediated hypersensitive response (HR) and inhibiting necrosis induced by three PAMPs (PiNpp, PiINF1, and PsXeg1) and an RxLR effector (Pi10232). Using a combined mutagenesis approach, we found that the dual activities of PiAvr3b were tightly linked and determined by 88 amino acids at the C-terminus. We further determined that either the W60 or the E134 residue of PiAvr3b was essential for triggering StR3b-associated HR and inhibiting PiNpp- and Pi10232-associated necrosis, while the S99 residue partially contributed to PTI suppression. Additionally, nuclear localization of PiAvr3b was required to stimulate HR and suppress PTI, but not to inhibit Pi10232-associated cell death. Our study revealed that PiAvr3b suppresses the plant immune response at different subcellular locations and provides an example in which a single amino acid of an RxLR effector links ETI induction and cell death suppression.
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Affiliation(s)
- Biao Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Wenxin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Zeqi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Guangda Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qin Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yinyu Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Hua Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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Duan H, Moresco P, Champouret N. Characterization of host-effector transcription dynamics during pathogen infection in engineered late blight resistant potato. Transgenic Res 2023; 32:95-107. [PMID: 36870023 DOI: 10.1007/s11248-023-00340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023]
Abstract
Phytophthora infestans, the etiologic agent of late blight, is a threat to potato production in areas with high humidity during the growing season. The oomycete pathogen is hemi-biotrophic, it establishes infection on living plant cells and then spreads, kills, and feeds off the necrotized plant tissue material. The interaction between host and pathogen is complex with dynamic pathogen RXLR effectors and potato NB-LRR resistance proteins actively competing for dominance and survival. Late blight protection was brought to several cultivars of potato through insertion of the wild potato (Solanum venturii) NB-LRR resistance gene Rpi-vnt1.1. We have established that the late blight protection trait, mediated by Rpi-vnt1.1, is effective despite low expression of RNA. The RNA expression dynamics of Rpi-vnt1.1 and the cognate pathogen RXLR effector, Avr-vnt1, were evaluated following spray inoculation with up to five different contemporary late blight isolates from North America and South America. Following inoculations, RXLR effector transcript profiles provided insight into interaction compatibility in relation to markers of the late blight hemi-biotrophic lifecycle.
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Affiliation(s)
- Hui Duan
- Simplot Plant Sciences, J. R. Simplot Company, Boise, ID, 83706, USA.
- Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center (BARC)-West, USDA-ARS, U.S. National Arboretum, Beltsville, MD, 20705, USA.
| | - Paul Moresco
- Simplot Plant Sciences, J. R. Simplot Company, Boise, ID, 83706, USA
- , Chicago, IL, 60610, USA
| | - Nicolas Champouret
- Simplot Plant Sciences, J. R. Simplot Company, Boise, ID, 83706, USA
- , Naperville, IL, 60540, USA
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7
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Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. FRONTIERS IN PLANT SCIENCE 2022; 13:980587. [PMID: 36479518 PMCID: PMC9721114 DOI: 10.3389/fpls.2022.980587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
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Affiliation(s)
| | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- LaMME, Université d'Evry Val d'Essonne, INRAE, Evry, France
| | | | | | | | | | - Ingo Hein
- Division Plant Sciences at the JHI, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute (JHI), Dundee, United Kingdom
| | - Kurt Lamour
- INRAE, GAFL, Montfavet, France
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
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Ma X, Duan G, Chen H, Tang P, Su S, Wei Z, Yang J. Characterization of infected process and primary mechanism in rice Acuce defense against rice blast fungus, Magnaporthe oryzae. PLANT MOLECULAR BIOLOGY 2022; 110:219-234. [PMID: 35759052 DOI: 10.1007/s11103-022-01296-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Identification of infection process and defense response during M. oryzae infecting Acuce. Magnaporthe oryzae is a destructive rice pathogen. Recent studies have focused on the initial infectious stage, with a few studies conducted to elucidate the characteristics of the late infectious stages. This study aims to decipher the characteristics at different stages (biotrophic, biotrophy-necrotrophy switch (BNS), and necrotrophic) between the interaction of two M. oryzae-rice combinations and investigate the resistance mechanisms of rice to M. oryzae using cytological and molecular methods. The biotrophic phase of M. oryzae-LTH compatible interaction was found to be longer than that of M. oryzae-Acuce incompatible interaction. We also found that jasmonic acid (JA) signaling plays an important role in defense by regulating antimicrobial compound accumulation in infected Acuce via a synergistic interaction of JA-salicylic acid (SA) and JA-ethylene (ET). In infected LTH, JA-ET/JA-SA showed antagonistic interaction. Ibuprofen (IBU) is a JA inhibitor. Despite the above findings, we found that exogenous JA-Ile and IBU significantly alleviated blast symptoms in infected LTH at 36 hpi (biotrophic) and 72 hpi (BNS), indicating these two-time points may be critical for managing blast disease in the compatible interaction. Conversely, IBU significantly increased blast symptoms on the infected Acuce at 36 hpi, confirming that the JA signal plays a central role in the defense response in infected Acuce. According to transcriptional analysis, the number of genes enriched in the plant hormone signal pathway was significantly higher than in other pathways. Our findings suggested that JA-mediated defense mechanism is essential in regulating Acuce resistance, particularly during the biotrophic and BNS phases.
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Affiliation(s)
- Xiaoqing Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Guihua Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shunyu Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhaoxia Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.
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9
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The molecular dialog between oomycete effectors and their plant and animal hosts. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Fick A, Swart V, van den Berg N. The Ups and Downs of Plant NLR Expression During Pathogen Infection. FRONTIERS IN PLANT SCIENCE 2022; 13:921148. [PMID: 35720583 PMCID: PMC9201817 DOI: 10.3389/fpls.2022.921148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Plant Nucleotide binding-Leucine rich repeat (NLR) proteins play a significant role in pathogen detection and the activation of effector-triggered immunity. NLR regulation has mainly been studied at a protein level, with large knowledge gaps remaining regarding the transcriptional control of NLR genes. The mis-regulation of NLR gene expression may lead to the inability of plants to recognize pathogen infection, lower levels of immune response activation, and ultimately plant susceptibility. This highlights the importance of understanding all aspects of NLR regulation. Three main mechanisms have been shown to control NLR expression: epigenetic modifications, cis elements which bind transcription factors, and post-transcriptional modifications. In this review, we aim to provide an overview of these mechanisms known to control NLR expression, and those which contribute toward successful immune responses. Furthermore, we discuss how pathogens can interfere with NLR expression to increase pathogen virulence. Understanding how these molecular mechanisms control NLR expression would contribute significantly toward building a complete picture of how plant immune responses are activated during pathogen infection-knowledge which can be applied during crop breeding programs aimed to increase resistance toward numerous plant pathogens.
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Affiliation(s)
- Alicia Fick
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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11
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Late Blight Resistance Conferred by Rpi-Smira2/R8 in Potato Genotypes In Vitro Depends on the Genetic Background. PLANTS 2022; 11:plants11101319. [PMID: 35631743 PMCID: PMC9145795 DOI: 10.3390/plants11101319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/28/2022]
Abstract
Potato production worldwide is threatened by late blight, caused by the oomycete Phytophthora infestans (Mont.) de Bary. Highly resistant potato cultivars were developed in breeding programs, using resistance gene pyramiding methods. In Sárpo Mira potatoes, five resistance genes (R3a, R3b, R4, Rpi-Smira1, and Rpi-Smira2/R8) are reported, with the latter gene assumed to be the major contributor. To study the level of late blight resistance conferred by the Rpi-Smira2/R8 gene, potato genotypes with only the Rpi-Smira2/R8 gene were selected from progeny population in which susceptible cultivars were crossed with Sárpo Mira. Ten R8 potato genotypes were obtained using stepwise marker-assisted selection, and agroinfiltration of the avirulence effector gene Avr4. Nine of these R8 genotypes were infected with both Slovenian P. infestans isolates and aggressive foreign isolates. All the progeny R8 genotypes are resistant to the Slovenian P. infestans isolate 02_07, and several show milder late blight symptoms than the corresponding susceptible parent after inoculation with other isolates. When inoculated with foreign P. infestans isolates, the genotype C571 shows intermediate resistance, similar to that of Sárpo Mira. These results suggest that Rpi-Smira2/R8 contributes to late blight resistance, although this resistance is not guaranteed solely by the presence of the R8 in the genome.
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Adhikari TB, Aryal R, Redpath LE, Van den Broeck L, Ashrafi H, Philbrick AN, Jacobs RL, Sozzani R, Louws FJ. RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry. Front Genet 2022; 12:805771. [PMID: 35360413 PMCID: PMC8960243 DOI: 10.3389/fgene.2021.805771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/29/2021] [Indexed: 12/02/2022] Open
Abstract
Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.
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Affiliation(s)
- Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Tika B. Adhikari, ; Frank J. Louws,
| | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Lauren E. Redpath
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Ashley N. Philbrick
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Raymond L. Jacobs
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Tika B. Adhikari, ; Frank J. Louws,
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13
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Chickpea Roots Undergoing Colonisation by Phytophthora medicaginis Exhibit Opposing Jasmonic Acid and Salicylic Acid Accumulation and Signalling Profiles to Leaf Hemibiotrophic Models. Microorganisms 2022; 10:microorganisms10020343. [PMID: 35208798 PMCID: PMC8874544 DOI: 10.3390/microorganisms10020343] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Hemibiotrophic pathogens cause significant losses within agriculture, threatening the sustainability of food systems globally. These microbes colonise plant tissues in three phases: a biotrophic phase followed by a biotrophic-to-necrotrophic switch phase and ending with necrotrophy. Each of these phases is characterized by both common and discrete host transcriptional responses. Plant hormones play an important role in these phases, with foliar models showing that salicylic acid accumulates during the biotrophic phase and jasmonic acid/ethylene responses occur during the necrotrophic phase. The appropriateness of this model to plant roots has been challenged in recent years. The need to understand root responses to hemibiotrophic pathogens of agronomic importance necessitates further research. In this study, using the root hemibiotroph Phytophthora medicaginis, we define the duration of each phase of pathogenesis in Cicer arietinum (chickpea) roots. Using transcriptional profiling, we demonstrate that susceptible chickpea roots display some similarities in response to disease progression as previously documented in leaf plant–pathogen hemibiotrophic interactions. However, our transcriptomic results also show that chickpea roots do not conform to the phytohormone responses typically found in leaf colonisation by hemibiotrophs. We found that quantified levels of salicylic acid concentrations in root tissues decreased significantly during biotrophy while jasmonic acid concentrations were significantly induced. This study demonstrated that a wider spectrum of plant species should be investigated in the future to understand the physiological changes in plants during colonisation by soil-borne hemibiotrophic pathogens before we can better manage these economically important microbes.
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14
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Lu J, Liu T, Zhang X, Li J, Wang X, Liang X, Xu G, Jing M, Li Z, Hein I, Dou D, Zhang Y, Wang X. Comparison of the Distinct, Host-Specific Response of Three Solanaceae Hosts Induced by Phytophthora infestans. Int J Mol Sci 2021; 22:ijms222011000. [PMID: 34681661 PMCID: PMC8537708 DOI: 10.3390/ijms222011000] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
Three Solanaceae hosts (TSHs), S. tuberosum, N. benthamiana and S. lycopersicum, represent the three major phylogenetic clades of Solanaceae plants infected by Phytophthora infestans, which causes late blight, one of the most devastating diseases seriously affecting crop production. However, details regarding how different Solanaceae hosts respond to P. infestans are lacking. Here, we conducted RNA-seq to analyze the transcriptomic data from the TSHs at 12 and 24 h post P. infestans inoculation to capture early expression effects. Macroscopic and microscopic observations showed faster infection processes in S. tuberosum than in N. benthamiana and S. lycopersicum under the same conditions. Analysis of the number of genes and their level of expression indicated that distinct response models were adopted by the TSHs in response to P. infestans. The host-specific infection process led to overlapping but distinct in GO terms and KEGG pathways enriched for differentially expressed genes; many were tightly linked to the immune response in the TSHs. S. tuberosum showed the fastest response and strongest accumulation of reactive oxygen species compared with N. benthamiana and S. lycopersicum, which also had similarities and differences in hormone regulation. Collectively, our study provides an important reference for a better understanding of late blight response mechanisms of different Solanaceae host interactions.
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Affiliation(s)
- Jie Lu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China;
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
- Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China; (X.W.); (Z.L.)
| | - Tingli Liu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
| | - Jie Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
| | - Xun Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China; (X.W.); (Z.L.)
| | - Xiangxiu Liang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
| | - Guangyuan Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
| | - Maofeng Jing
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhugang Li
- Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China; (X.W.); (Z.L.)
| | - Ingo Hein
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Daolong Dou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Yanju Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China;
- Correspondence: (Y.Z.); (X.W.)
| | - Xiaodan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (X.L.); (G.X.); (D.D.)
- Correspondence: (Y.Z.); (X.W.)
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15
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Joubert M, Backer R, Engelbrecht J, van den Berg N. Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado. PLoS One 2021; 16:e0254645. [PMID: 34260624 PMCID: PMC8279351 DOI: 10.1371/journal.pone.0254645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Phytophthora cinnamomi is a plant pathogenic oomycete that causes Phytophthora root rot of avocado (PRR). Currently, there is a limited understanding of the molecular interactions underlying this disease. Other Phytophthora species employ an arsenal of effector proteins to manipulate host physiology, of which the RxLR effectors contribute to virulence by interfering with host immune responses. The aim of this study was to identify candidate RxLR effectors in P. cinnamomi that play a role in establishing PRR, and to infer possible functions for these effectors. We identified 61 candidate RxLR genes which were expressed during infection of a susceptible avocado rootstock. Several of these genes were present in multiple copies in the P. cinnamomi genome, suggesting that they may contribute to pathogen fitness. Phylogenetic analysis of the manually predicted RxLR protein sequences revealed 12 P. cinnamomi RxLRs that were related to characterised effectors in other Phytophthora spp., providing clues to their functions in planta. Expression profiles of nine more RxLRs point to possible virulence roles in avocado-highlighting a way forward for studies of this interaction. This study represents the first investigation of the expression of P. cinnamomi RxLR genes during the course of avocado infection, and puts forward a pipeline to pinpoint effector genes with potential as virulence determinants, providing a foundation for the future functional characterization of RxLRs that contribute to P. cinnamomi virulence in avocado.
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Affiliation(s)
- Melissa Joubert
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Robert Backer
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Juanita Engelbrecht
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Noëlani van den Berg
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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16
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Gómez-Pérez D, Kemen E. Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes. Pathogens 2021; 10:807. [PMID: 34202069 PMCID: PMC8308905 DOI: 10.3390/pathogens10070807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022] Open
Abstract
As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.
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Affiliation(s)
| | - Eric Kemen
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany;
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17
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Mazumdar P, Singh P, Kethiravan D, Ramathani I, Ramakrishnan N. Late blight in tomato: insights into the pathogenesis of the aggressive pathogen Phytophthora infestans and future research priorities. PLANTA 2021; 253:119. [PMID: 33963935 DOI: 10.1007/s00425-021-03636-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
This review provides insights into the molecular interactions between Phytophthora infestans and tomato and highlights research gaps that need further attention. Late blight in tomato is caused by the oomycota hemibiotroph Phytophthora infestans, and this disease represents a global threat to tomato farming. The pathogen is cumbersome to control because of its fast-evolving nature, ability to overcome host resistance and inefficient natural resistance obtained from the available tomato germplasm. To achieve successful control over this pathogen, the molecular pathogenicity of P. infestans and key points of vulnerability in the host plant immune system must be understood. This review primarily focuses on efforts to better understand the molecular interaction between host pathogens from both perspectives, as well as the resistance genes, metabolomic changes, quantitative trait loci with potential for improvement in disease resistance and host genome manipulation via transgenic approaches, and it further identifies research gaps and provides suggestions for future research priorities.
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Affiliation(s)
- Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Pooja Singh
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Dharane Kethiravan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Idd Ramathani
- National Crops Resources Research Institute, Gayaza Road Namulonge, 7084, Kampala, Uganda
| | - N Ramakrishnan
- ECSE, School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
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18
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de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
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19
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Hu Z, Ma Q, Foyer CH, Lei C, Choi HW, Zheng C, Li J, Zuo J, Mao Z, Mei Y, Yu J, Klessig DF, Shi K. High CO 2 - and pathogen-driven expression of the carbonic anhydrase βCA3 confers basal immunity in tomato. THE NEW PHYTOLOGIST 2021; 229:2827-2843. [PMID: 33206385 DOI: 10.1111/nph.17087] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/01/2020] [Indexed: 05/12/2023]
Abstract
Atmospheric CO2 concentrations exert a strong influence on the susceptibility of plants to pathogens. However, the mechanisms involved in the CO2 -dependent regulation of pathogen resistance are largely unknown. Here we show that the expression of tomato (Solanum lycopersicum) β-CARBONIC ANHYDRASE 3 (βCA3) is induced by the virulent pathogen Pseudomonas syringae pv. tomato DC3000. The role of βCA3 in the high CO2 -mediated response in tomato and two other Solanaceae crops is distinct from that in Arabidopsis thaliana. Using βCA3 knock-out and over-expression plants, we demonstrate that βCA3 plays a positive role in the activation of basal immunity, particularly under high CO2 . βCA3 is transcriptionally activated by the transcription factor NAC43 and is also post-translationally regulated by the receptor-like kinase GRACE1. The βCA3 pathway of basal immunity is independent on stomatal- and salicylic-acid-dependent regulation. Global transcriptome analysis and cell wall metabolite measurement implicate cell wall metabolism/integrity in βCA3-mediated basal immunity under both CO2 conditions. These data not only highlight the importance of βCA3 in plant basal immunity under high CO2 in a well-studied susceptible crop-pathogen system, but they also point to new targets for disease management strategies in a changing climate.
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Affiliation(s)
- Zhangjian Hu
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qiaomei Ma
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Cui Lei
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hyong Woo Choi
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
- Department of Plant Medicals, Andong National University, Andong, 36729, Republic of Korea
| | - Chenfei Zheng
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jianxin Li
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jinhua Zuo
- National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Zhuo Mao
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yuyang Mei
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Daniel F Klessig
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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20
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Peptide-Based Identification of Phytophthora Isolates and Phytophthora Detection in Planta. Int J Mol Sci 2020; 21:ijms21249463. [PMID: 33322721 PMCID: PMC7763169 DOI: 10.3390/ijms21249463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Phytophthora is arguably one of the most damaging genera of plant pathogens. This pathogen is well suited to transmission via the international plant trade, and globalization has been promoting its spread since the 19th century. Early detection is essential for reducing its economic and ecological impact. Here, a shotgun proteomics approach was utilized for Phytophthora analysis. The collection of 37 Phytophthora isolates representing 12 different species was screened for species-specific peptide patterns. Next, Phytophthora proteins were detected in planta, employing model plants Solanum tuberosum and Hordeum vulgare. Although the evolutionarily conserved sequences represented more than 10% of the host proteome and limited the pathogen detection, the comparison between qPCR and protein data highlighted more than 300 protein markers, which correlated positively with the amount of P. infestans DNA. Finally, the analysis of P. palmivora response in barley revealed significant alterations in plant metabolism. These changes included enzymes of cell wall metabolism, ROS production, and proteins involved in trafficking. The observed root-specific attenuation in stress-response mechanisms, including the biosynthesis of jasmonates, ethylene and polyamines, and an accumulation of serotonin, provided the first insight into molecular mechanisms behind this particular biotic interaction.
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21
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Integrated Proteomic and Metabolomic Profiling of Phytophthora cinnamomi Attack on Sweet Chestnut ( Castanea sativa) Reveals Distinct Molecular Reprogramming Proximal to the Infection Site and Away from It. Int J Mol Sci 2020; 21:ijms21228525. [PMID: 33198329 PMCID: PMC7697766 DOI: 10.3390/ijms21228525] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire of studied Phytophthora-woody plant interactions and identify molecular mechanisms that can facilitate discovery of novel ways to control its spread and damaging effects, we focused on the interaction between P. cinnamomi and sweet chestnut (Castanea sativa), an economically important tree for the wood processing industry. By using a combination of proteomics, metabolomics, and targeted hormonal analysis, we mapped the effects of P. cinnamomi attack on stem tissues immediately bordering the infection site and away from it. P. cinnamomi led to a massive reprogramming of the chestnut proteome and accumulation of the stress-related hormones salicylic acid (SA) and jasmonic acid (JA), indicating that stem inoculation can be used as an easily accessible model system to identify novel molecular players in P. cinnamomi pathogenicity.
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22
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Rangel LI, Spanner RE, Ebert MK, Pethybridge SJ, Stukenbrock EH, de Jonge R, Secor GA, Bolton MD. Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. MOLECULAR PLANT PATHOLOGY 2020; 21:1020-1041. [PMID: 32681599 PMCID: PMC7368123 DOI: 10.1111/mpp.12962] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 05/07/2023]
Abstract
Cercospora leaf spot, caused by the fungal pathogen Cercospora beticola, is the most destructive foliar disease of sugar beet worldwide. This review discusses C. beticola genetics, genomics, and biology and summarizes our current understanding of the molecular interactions that occur between C. beticola and its sugar beet host. We highlight the known virulence arsenal of C. beticola as well as its ability to overcome currently used disease management strategies. Finally, we discuss future prospects for the study and management of C. beticola infections in the context of newly employed molecular tools to uncover additional information regarding the biology of this pathogen. TAXONOMY Cercospora beticola Sacc.; Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Capnodiales, Family Mycosphaerellaceae, Genus Cercospora. HOST RANGE Well-known pathogen of sugar beet (Beta vulgaris subsp. vulgaris) and most species of the Beta genus. Reported as pathogenic on other members of the Chenopodiaceae (e.g., lamb's quarters, spinach) as well as members of the Acanthaceae (e.g., bear's breeches), Apiaceae (e.g., Apium), Asteraceae (e.g., chrysanthemum, lettuce, safflower), Brassicaceae (e.g., wild mustard), Malvaceae (e.g., Malva), Plumbaginaceae (e.g., Limonium), and Polygonaceae (e.g., broad-leaved dock) families. DISEASE SYMPTOMS Leaves infected with C. beticola exhibit circular lesions that are coloured tan to grey in the centre and are often delimited by tan-brown to reddish-purple rings. As disease progresses, spots can coalesce to form larger necrotic areas, causing severely infected leaves to wither and die. At the centre of these spots are black spore-bearing structures (pseudostromata). Older leaves often show symptoms first and younger leaves become infected as the disease progresses. MANAGEMENT Application of a mixture of fungicides with different modes of action is currently performed although elevated resistance has been documented in most employed fungicide classes. Breeding for high-yielding cultivars with improved host resistance is an ongoing effort and prudent cultural practices, such as crop rotation, weed host management, and cultivation to reduce infested residue levels, are widely used to manage disease. USEFUL WEBSITE: https://www.ncbi.nlm.nih.gov/genome/11237?genome_assembly_id=352037.
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Affiliation(s)
- Lorena I. Rangel
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
| | - Rebecca E. Spanner
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Malaika K. Ebert
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMIUSA
| | - Sarah J. Pethybridge
- Plant Pathology & Plant‐Microbe Biology SectionSchool of Integrative Plant ScienceCornell AgriTech at The New York State Agricultural Experiment StationCornell UniversityGenevaNYUSA
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Christian‐Albrechts University of KielKielGermany
| | - Ronnie de Jonge
- Department of Plant‐Microbe InteractionsUtrecht UniversityUtrechtNetherlands
| | - Gary A. Secor
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Melvin D. Bolton
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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23
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Potato Late Blight Detection at the Leaf and Canopy Levels Based in the Red and Red-Edge Spectral Regions. REMOTE SENSING 2020. [DOI: 10.3390/rs12081292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Potato late blight, caused by Phytophthora infestans, is a major disease worldwide that has a significant economic impact on potato crops, and remote sensing might help to detect the disease in early stages. This study aims to determine changes induced by potato late blight in two parameters of the red and red-edge spectral regions: the red-well point (RWP) and the red-edge point (REP) as a function of the number of days post-inoculation (DPI) at the leaf and canopy levels. The RWP or REP variations were modelled using linear or exponential regression models as a function of the DPI. A Support Vector Machine (SVM) algorithm was used to classify healthy and infected leaves or plants using either the RWP or REP wavelength as well as the reflectances at 668, 705, 717 and 740 nm. Higher variations in the RWP and REP wavelengths were observed for the infected leaves compared to healthy leaves. The linear and exponential models resulted in higher adjusted R2 for the infected case than for the healthy case. The SVM classifier applied to the reflectance of the red and red-edge bands of the Micasense® Dual-X camera was able to sort healthy and infected cases with both the leaf and canopy measurements, reaching an overall classification accuracy of 89.33% at 3 DPI when symptoms were visible for the first time with the leaf measurements and of 89.06% at 5 DPI, i.e., two days after the symptoms became apparent, with the canopy measurements. The study shows that RWP and REP at leaf and canopy levels allow detecting potato late blight, but these parameters are less efficient to sort healthy and infected leaves or plants than the reflectance at 668, 705, 717 and 740 nm. Future research should consider larger samples, other cultivars and the test of unmanned aerial vehicle (UAV) imagery for field-based detection.
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Zhang Q, Li W, Yang J, Xu J, Meng Y, Shan W. Two Phytophthora parasitica cysteine protease genes, PpCys44 and PpCys45, trigger cell death in various Nicotiana spp. and act as virulence factors. MOLECULAR PLANT PATHOLOGY 2020; 21:541-554. [PMID: 32077241 PMCID: PMC7060141 DOI: 10.1111/mpp.12915] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 05/19/2023]
Abstract
Proteases secreted by pathogens have been shown to be important virulence factors modifying plant immunity, and cysteine proteases have been demonstrated to participate in different pathosystems. However, the virulence functions of the cysteine proteases secreted by Phytophthora parasitica are poorly understood. Using a publicly available genome database, we identified 80 cysteine proteases in P. parasitica, 21 of which were shown to be secreted. Most of the secreted cysteine proteases are conserved among different P. parasitica strains and are induced during infection. The secreted cysteine protease proteins PpCys44/45 (proteases with identical protein sequences) and PpCys69 triggered cell death on the leaves of different Nicotiana spp. A truncated mutant of PpCys44/45 lacking a signal peptide failed to trigger cell death, suggesting that PpCys44/45 functions in the apoplastic space. Analysis of three catalytic site mutants showed that the enzyme activity of PpCys44/45 is required for its ability to trigger cell death. A virus-induced gene silencing assay showed that PpCys44/45 does not induce cell death on NPK1 (Nicotiana Protein Kinase 1)-silenced Nicotiana benthamiana plants, indicating that the cell death phenotype triggered by PpCys44/45 is dependent on NPK1. PpCys44- and PpCys45-deficient double mutants showed decreased virulence, suggesting that PpCys44 and PpCys45 positively promote pathogen virulence during infection. PpCys44 and PpCys45 are important virulence factors of P. parasitica and trigger NPK1-dependent cell death in various Nicotiana spp.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Weiwei Li
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jiapeng Yang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Junjie Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
- College of AgronomyNorthwest A&F UniversityYanglingChina
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25
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Plant Cells under Attack: Unconventional Endomembrane Trafficking during Plant Defense. PLANTS 2020; 9:plants9030389. [PMID: 32245198 PMCID: PMC7154882 DOI: 10.3390/plants9030389] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022]
Abstract
Since plants lack specialized immune cells, each cell has to defend itself independently against a plethora of different pathogens. Therefore, successful plant defense strongly relies on precise and efficient regulation of intracellular processes in every single cell. Smooth trafficking within the plant endomembrane is a prerequisite for a diverse set of immune responses. Pathogen recognition, signaling into the nucleus, cell wall enforcement, secretion of antimicrobial proteins and compounds, as well as generation of reactive oxygen species, all heavily depend on vesicle transport. In contrast, pathogens have developed a variety of different means to manipulate vesicle trafficking to prevent detection or to inhibit specific plant responses. Intriguingly, the plant endomembrane system exhibits remarkable plasticity upon pathogen attack. Unconventional trafficking pathways such as the formation of endoplasmic reticulum (ER) bodies or fusion of the vacuole with the plasma membrane are initiated and enforced as the counteraction. Here, we review the recent findings on unconventional and defense-induced trafficking pathways as the plant´s measures in response to pathogen attack. In addition, we describe the endomembrane system manipulations by different pathogens, with a focus on tethering and fusion events during vesicle trafficking.
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26
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Deep RNA-seq analysis reveals key responding aspects of wild banana relative resistance to Fusarium oxysporum f. sp. cubense tropical race 4. Funct Integr Genomics 2020; 20:551-562. [PMID: 32064548 DOI: 10.1007/s10142-020-00734-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/26/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
Tropical race 4 of Fusarium oxysporum f. sp. cubense (FocTR4) is seriously threatening the banana industry worldwide. Resistant genotypes are present in wild relatives of banana, but little is known about the genetic and molecular mechanisms driving resistance responses. In this work, through in-depth expression analysis, we compared the responses of the resistant wild relative Musa acuminata ssp. burmanicoides (WTB) with the susceptible banana cultivar "Brizilian" (CAV, as it belongs to the Cavendish subgroup) to FocTR4 infection. Our findings showed that 1196 defense-related genes in the resistant WTB were differentially expressed genes (DEGs); only 358 defense-related DEGs were detected in CAV. DEGs related to pattern recognition receptors (PRRs) and disease resistance (R genes) were found in both genotypes, indicating the onset of both basal and specific defenses to FocTR4. Genes associated with cell wall modification exhibited a more remarkable upregulation in WTB than in CAV and might be involved in resistance during penetration steps. Our data also suggested that the high resistance of WTB is quantitatively driven with larger numbers and higher expression levels of defense-related DEGs. Fine-tuning studies to understand the resistance responses of WTB at early stages should be conducted to better support banana breeding programs. Further investigations are also required to validate the role of key genes screened in this study.
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Hyperspectral Measurements Enable Pre-Symptomatic Detection and Differentiation of Contrasting Physiological Effects of Late Blight and Early Blight in Potato. REMOTE SENSING 2020. [DOI: 10.3390/rs12020286] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In-vivo foliar spectroscopy, also known as contact hyperspectral reflectance, enables rapid and non-destructive characterization of plant physiological status. This can be used to assess pathogen impact on plant condition both prior to and after visual symptoms appear. Challenging this capacity is the fact that dead tissue yields relatively consistent changes in leaf optical properties, negatively impacting our ability to distinguish causal pathogen identity. Here, we used in-situ spectroscopy to detect and differentiate Phytophthora infestans (late blight) and Alternaria solani (early blight) on potato foliage over the course of disease development and explored non-destructive characterization of contrasting disease physiology. Phytophthora infestans, a hemibiotrophic pathogen, undergoes an obligate latent period of two–seven days before disease symptoms appear. In contrast, A. solani, a necrotrophic pathogen, causes symptoms to appear almost immediately when environmental conditions are conducive. We found that respective patterns of spectral change can be related to these differences in underlying disease physiology and their contrasting pathogen lifestyles. Hyperspectral measurements could distinguish both P. infestans-infected and A. solani-infected plants with greater than 80% accuracy two–four days before visible symptoms appeared. Individual disease development stages for each pathogen could be differentiated from respective controls with 89–95% accuracy. Notably, we could distinguish latent P. infestans infection from both latent and symptomatic A. solani infection with greater than 75% accuracy. Spectral features important for late blight detection shifted over the course of infection, whereas spectral features important for early blight detection remained consistent, reflecting their different respective pathogen biologies. Shortwave infrared wavelengths were important for differentiation between healthy and diseased, and between pathogen infections, both pre- and post-symptomatically. This proof-of-concept work supports the use of spectroscopic systems as precision agriculture tools for rapid and early disease detection and differentiation tools, and highlights the importance of careful consideration of underlying pathogen biology and disease physiology for crop disease remote sensing.
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Overexpression of Magnaporthe Oryzae Systemic Defense Trigger 1 (MoSDT1) Confers Improved Rice Blast Resistance in Rice. Int J Mol Sci 2019; 20:ijms20194762. [PMID: 31557947 PMCID: PMC6802482 DOI: 10.3390/ijms20194762] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 12/20/2022] Open
Abstract
The effector proteins secreted by a pathogen not only promote virulence and infection of the pathogen, but also trigger plant defense response. Therefore, these proteins could be used as important genetic resources for transgenic improvement of plant disease resistance. Magnaporthe oryzae systemic defense trigger 1 (MoSDT1) is an effector protein. In this study, we compared the agronomic traits and blast disease resistance between wild type (WT) and MoSDT1 overexpressing lines in rice. Under control conditions, MoSDT1 transgenic lines increased the number of tillers without affecting kernel morphology. In addition, MoSDT1 transgenic lines conferred improved blast resistance, with significant effects on the activation of callose deposition, reactive oxygen species (ROS) accumulation and cell death. On the one hand, overexpression of MoSDT1 could delay biotrophy-necrotrophy switch through regulating the expression of biotrophy-associated secreted protein 4 (BAS4) and Magnaporthe oryzaecell death inducing protein 1 (MoCDIP1), and activate plant defense response by regulating the expression of Bsr-d1, MYBS1, WRKY45, peroxidase (POD), heat shock protein 90 (HSP90), allenoxide synthase 2 (AOS2), phenylalanine ammonia lyase (PAL), pathogenesis-related protein 1a (PR1a) in rice. On the other hand, overexpression of MoSDT1 could increase the accumulation of some defense-related primary metabolites such as two aromatic amino acids (L-tyrosine and L-tryptohan), 1-aminocyclopropane carboxylic acid, which could be converted to ethylene, vanillic acid and L-saccharopine. Taken together, overexpression of MoSDT1 confers improved rice blast resistance in rice, through modulation of callose deposition, ROS accumulation, the expression of defense-related genes, and the accumulation of some primary metabolites.
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Becker MG, Haddadi P, Wan J, Adam L, Walker P, Larkan NJ, Daayf F, Borhan MH, Belmonte MF. Transcriptome Analysis of Rlm2-Mediated Host Immunity in the Brassica napus- Leptosphaeria maculans Pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1001-1012. [PMID: 30938576 DOI: 10.1094/mpmi-01-19-0028-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Our study investigated disease resistance in the Brassica napus-Leptosphaeria maculans pathosystem using a combination of laser microdissection, dual RNA sequencing, and physiological validations of large-scale gene sets. The use of laser microdissection improved pathogen detection and identified putative L. maculans effectors and lytic enzymes operative during host colonization. Within 24 h of inoculation, we detected large shifts in gene activity in resistant cotyledons associated with jasmonic acid and calcium signaling pathways that accelerated the plant defense response. Sequencing data were validated through the direct quantification of endogenous jasmonic acid levels. Additionally, resistance against L. maculans was abolished when the calcium chelator EGTA was applied to the inoculation site, providing physiological evidence of the role of calcium in B. napus immunity against L. maculans. We integrated gene expression data with all available information on cis-regulatory elements and transcription factor binding affinities to better understand the gene regulatory networks underpinning plant resistance to hemibiotrophic pathogens. These in silico analyses point to early cellular reprogramming during host immunity that are coordinated by CAMTA, BZIP, and bHLH transcription factors. Together, we provide compelling genetic and physiological evidence into the programming of plant resistance against fungal pathogens.
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Affiliation(s)
- Michael G Becker
- 1Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Parham Haddadi
- 2Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Joey Wan
- 1Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lorne Adam
- 3Department of Plant Science, University of Manitoba
| | - Philip Walker
- 1Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Fouad Daayf
- 3Department of Plant Science, University of Manitoba
| | - M Hossein Borhan
- 2Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Mark F Belmonte
- 1Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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30
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Liu D, Li K, Hu J, Wang W, Liu X, Gao Z. Biocontrol and Action Mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in Soybean Phytophthora Blight. Int J Mol Sci 2019; 20:E2908. [PMID: 31207889 PMCID: PMC6628291 DOI: 10.3390/ijms20122908] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/17/2019] [Accepted: 05/30/2019] [Indexed: 02/08/2023] Open
Abstract
With the improper application of fungicides, Phytophthora sojae begins to develop resistance to fungicides, and biological control is one of the potential ways to control it. We screened two strains of Bacillus; Bacillus amyloliquefaciens JDF3 and Bacillus subtilis RSS-1, which had an efficient inhibitory effect on P. sojae. They could inhibit mycelial growth, the germination of the cysts, and the swimming of the motile zoospores. To elucidate the response of P. sojae under the stress of B. amyloliquefaciens and B. subtilis, and the molecular mechanism of biological control, comparative transcriptome analysis was applied. Transcriptome analysis revealed that the expression gene of P. sojae showed significant changes, and a total of 1616 differentially expressed genes (DEGs) were detected. They participated in two major types of regulation, namely "specificity" regulation and "common" regulation. They might inhibit the growth of P. sojae mainly by inhibiting the activity of ribosome. A pot experiment indicated that B. amyloliquefaciens and B. subtilis enhanced the resistance of soybean to P. sojae, and their control effects of them were 70.7% and 65.5%, respectively. In addition, B. amyloliquefaciens fermentation broth could induce an active oxygen burst, NO production, callose deposition, and lignification. B. subtilis could also stimulate the systemic to develop the resistance of soybean by lignification, and phytoalexin.
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Affiliation(s)
- Dong Liu
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
- School of life sciences, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
- Department of Horticulture and Landscape, Anqing Vocational and Technical College, 99 North of Tianzhushan Road, Anqing 246003, Anhui, China.
| | - Kunyuan Li
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
| | - Jiulong Hu
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
| | - Weiyan Wang
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
| | - Xiao Liu
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
| | - Zhimou Gao
- College of plant protection, Anhui Agricultural University, 130 West of Changjiang Road, Hefei 230036, Anhui, China.
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31
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Fry WE, Patev SP, Myers KL, Bao K, Fei Z. Phytophthora infestans Sporangia Produced in Culture and on Tomato Leaflet Lesions Show Marked Differences in Indirect Germination Rates, Aggressiveness, and Global Transcription Profiles. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:515-526. [PMID: 30480479 DOI: 10.1094/mpmi-09-18-0255-ta] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sporangia of Phytophthora infestans from pure cultures on agar plates are typically used in lab studies, whereas sporangia from leaflet lesions drive natural infections and epidemics. Multiple assays were performed to determine if sporangia from these two sources are equivalent. Sporangia from plate cultures showed much lower rates of indirect germination and produced much less disease in field and moist-chamber tests. This difference in aggressiveness was observed whether the sporangia had been previously incubated at 4°C (to induce indirect germination) or at 21°C (to prevent indirect germination). Furthermore, lesions caused by sporangia from plates produced much less sporulation. RNA-Seq analysis revealed that thousands of the >17,000 P. infestans genes with a RPKM (reads per kilobase of exon model per million mapped reads) >1 were differentially expressed in sporangia obtained from plate cultures of two independent field isolates compared with sporangia of those isolates from leaflet lesions. Among the significant differentially expressed genes (DEGs), putative RxLR effectors were overrepresented, with almost half of the 355 effectors with RPKM >1 being up- or downregulated. DEGs of both isolates include nine flagellar-associated genes, and all were down-regulated in plate sporangia. Ten elicitin genes were also detected as DEGs in both isolates, and nine (including INF1) were up-regulated in plate sporangia. These results corroborate previous observations that sporangia produced from plates and leaflets sometimes yield different experimental results and suggest hypotheses for potential mechanisms. We caution that use of plate sporangia in assays may not always produce results reflective of natural infections and epidemics.
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Affiliation(s)
- William E Fry
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Sean P Patev
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Kevin L Myers
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Kan Bao
- 2 Boyce Thompson Institute, Cornell University
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32
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A Computational Protocol to Analyze Metatranscriptomic Data Capturing Fungal-Host Interactions. Methods Mol Biol 2019; 1848:207-233. [PMID: 30182238 DOI: 10.1007/978-1-4939-8724-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Plant diseases cause significant losses to agricultural production and pose serious threats to food security worldwide. Understanding the mechanism of host-pathogen interaction is essential for the development of novel diagnostic methods and disease management strategies. RNA sequencing (or RNA-Seq) technology enables a global characterization and quantification of all transcripts of organisms from which RNA can be obtained, and it is particularly useful in identifying pathogen virulence factors involved in disease development and host immunity involved in the development of resistance. This chapter describes a computational protocol to manage, analyze and interpret RNA-Seq data. We have included two transcriptome analysis approaches, one reference-guided and the other de novo assembly-based, and discuss pros and cons for each method. We have also presented visualization methods to generate high quality figures as well as data mining strategies for identifying candidate genes/pathways involved in host immunity and pathogen virulence. In summary, this protocol captures the fungal-plant interactions at the transcriptional level and facilitates rapid gene discovery and expression analysis using next-generation sequencing data of mixed host and pathogen transcripts (i.e., metatranscriptomics). All bioinformatic tools used to build this protocol are publically available, and we strove to make them accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-fungal interactions.
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33
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Meijer HJG, Schoina C, Wang S, Bouwmeester K, Hua C, Govers F. Phytophthora infestans small phospholipase D-like proteins elicit plant cell death and promote virulence. MOLECULAR PLANT PATHOLOGY 2019; 20:180-193. [PMID: 30171659 PMCID: PMC6637911 DOI: 10.1111/mpp.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The successful invasion of host tissue by (hemi-)biotrophic plant pathogens is dependent on modifications of the host plasma membrane to facilitate the two-way transfer of proteins and other compounds. Haustorium formation and the establishment of extrahaustorial membranes are probably dependent on a variety of enzymes that modify membranes in a coordinated fashion. Phospholipases, enzymes that hydrolyse phospholipids, have been implicated as virulence factors in several pathogens. The oomycete Phytophthora infestans is a hemibiotrophic pathogen that causes potato late blight. It possesses different classes of phospholipase D (PLD) proteins, including small PLD-like proteins with and without signal peptide (sPLD-likes and PLD-likes, respectively). Here, we studied the role of sPLD-like-1, sPLD-like-12 and PLD-like-1 in the infection process. They are expressed in expanding lesions on potato leaves and during in vitro growth, with the highest transcript levels in germinating cysts. When expressed in planta in the presence of the silencing suppressor P19, all three elicited a local cell death response that was visible at the microscopic level as autofluorescence and strongly boosted in the presence of calcium. Moreover, inoculation of leaves expressing the small PLD-like genes resulted in increased lesion growth and greater numbers of sporangia, but this was abolished when mutated PLD-like genes were expressed with non-functional PLD catalytic motifs. These results show that the three small PLD-likes are catalytically active and suggest that their enzymatic activity is required for the promotion of virulence, possibly by executing membrane modifications to support the growth of P. infestans in the host.
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Affiliation(s)
- Harold J. G. Meijer
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
- Wageningen Plant ResearchWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
| | - Charikleia Schoina
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
| | - Shutong Wang
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
- College of Plant ProtectionAgricultural University of HebeiBaoding071001China
| | - Klaas Bouwmeester
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
| | - Chenlei Hua
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
- Present address:
Center of Plant Molecular Biology (ZMBP)Eberhard‐Karls‐University TübingenTübingenD‐72076Germany
| | - Francine Govers
- Laboratory of PhytopathologyWageningen University and ResearchPO Box 16Wageningen6700AAthe Netherlands
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Quantitative Proteomics of Potato Leaves Infected with Phytophthora infestans Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages. Int J Mol Sci 2019; 20:ijms20010136. [PMID: 30609684 PMCID: PMC6337297 DOI: 10.3390/ijms20010136] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 01/20/2023] Open
Abstract
In order to get a better understanding of protein association during Solanum tuberosum (cv. Sarpo Mira)–Phytophthora infestans incompatible interaction, we investigated the proteome dynamics of cv. Sarpo Mira, after foliar application of zoospore suspension from P. infestans isolate, at three key time-points: zero hours post inoculation (hpi) (Control), 48 hpi (EI), and 120 hpi (LI); divided into early and late disease stages by the tandem mass tagging (TMT) method. A total of 1229 differentially-expressed proteins (DEPs) were identified in cv. Sarpo Mira in a pairwise comparison of the two disease stages, including commonly shared DEPs, specific DEPs in early and late disease stages, respectively. Over 80% of the changes in protein abundance were up-regulated in the early stages of infection, whereas more DEPs (61%) were down-regulated in the later disease stage. Expression patterns, functional category, and enrichment tests highlighted significant coordination and enrichment of cell wall-associated defense response proteins during the early stage of infection. The late stage was characterized by a cellular protein modification process, membrane protein complex formation, and cell death induction. These results, together with phenotypic observations, provide further insight into the molecular mechanism of P. infestans resistance in potatos.
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35
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Yin J, Gu B, Huang G, Tian Y, Quan J, Lindqvist-Kreuze H, Shan W. Conserved RXLR Effector Genes of Phytophthora infestans Expressed at the Early Stage of Potato Infection Are Suppressive to Host Defense. FRONTIERS IN PLANT SCIENCE 2017; 8:2155. [PMID: 29312401 PMCID: PMC5742156 DOI: 10.3389/fpls.2017.02155] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/06/2017] [Indexed: 05/20/2023]
Abstract
Late blight has been the most devastating potato disease worldwide. The causal agent, Phytophthora infestans, is notorious for its capability to rapidly overcome host resistance. Changes in the expression pattern and the encoded protein sequences of effector genes in the pathogen are responsible for the loss of host resistance. Among numerous effector genes, the class of RXLR effector genes is well-known in mediating host genotype-specific resistance. We therefore performed deep sequencing of five genetically diverse P. infestans strains using in planta materials infected with zoospores (12 h post inoculation) and focused on the identification of RXLR effector genes that are conserved in coding sequences, are highly expressed in early stages of plant infection, and have defense suppression activities. In all, 245 RXLR effector genes were expressed in five transcriptomes, with 108 being co-expressed in all five strains, 47 of them comparatively highly expressed. Taking sequence polymorphism into consideration, 18 candidate core RXLR effectors that were conserved in sequence and with higher in planta expression levels were selected for further study. Agrobacterium tumefaciens-mediated transient expression of the selected effector genes in Nicotiana benthamiana and potato demonstrated their potential virulence function, as shown by suppression of PAMP-triggered immunity (PTI) or/and effector-triggered immunity (ETI). The identified collection of core RXLR effectors will be useful in the search for potential durable late blight resistance genes. Analysis of 10 known Avr RXLR genes revealed that the resistance genes R2, Rpi-blb2, Rpi-vnt1, Rpi-Smira1, and Rpi-Smira2 may be effective in potato cultivars. Analysis of 8 SFI (Suppressor of early Flg22-induced Immune response) RXLR effector genes showed that SFI2, SFI3, and SFI4 were highly expressed in all examined strains, suggesting their potentially important function in early stages of pathogen infection.
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Affiliation(s)
- Junliang Yin
- College of Plant Protection, Northwest A&F University, Xianyang, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang, China
| | - Biao Gu
- College of Plant Protection, Northwest A&F University, Xianyang, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang, China
| | - Guiyan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang, China
- College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Yuee Tian
- College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Junli Quan
- College of Plant Protection, Northwest A&F University, Xianyang, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang, China
| | | | - Weixing Shan
- College of Plant Protection, Northwest A&F University, Xianyang, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang, China
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Biotrophy-necrotrophy switch in pathogen evoke differential response in resistant and susceptible sesame involving multiple signaling pathways at different phases. Sci Rep 2017; 7:17251. [PMID: 29222513 PMCID: PMC5722813 DOI: 10.1038/s41598-017-17248-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/23/2017] [Indexed: 12/16/2022] Open
Abstract
Infection stages of charcoal rot fungus Macrophomina phaseolina in sesame revealed for the first time a transition from biotrophy via BNS (biotrophy-to-necrotrophy switch) to necrotrophy as confirmed by transcriptional studies. Microscopy using normal and GFP-expressing pathogen showed typical constricted thick intercellular bitrophic hyphae which gave rise to thin intracellular necrotrophic hyphae during BNS and this stage was delayed in a resistant host. Results also show that as the pathogen switched its strategy of infection, the host tailored its defense strategy to meet the changing situation. Less ROS accumulation, upregulation of ROS signaling genes and higher antioxidant enzyme activities post BNS resulted in resistance. There was greater accumulation of secondary metabolites and upregulation of secondary metabolite-related genes after BNS. A total of twenty genes functioning in different aspects of plant defense that were monitored over a time course during the changing infection phases showed a coordinated response. Experiments using phytohormone priming and phytohormone inhibitors showed that resistance resulted from activation of JA-ET signaling pathway. Most importantly this defense response was more prompt in the resistant than the susceptible host indicating that a resistant host makes different choices from a susceptible host during infection which ultimately influences the severity of the disease.
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Schoina C, Bouwmeester K, Govers F. Infection of a tomato cell culture by Phytophthora infestans; a versatile tool to study Phytophthora-host interactions. PLANT METHODS 2017; 13:88. [PMID: 29090012 PMCID: PMC5657071 DOI: 10.1186/s13007-017-0240-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/17/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND The oomycete Phytophthora infestans causes late blight on potato and tomato. Despite extensive research, the P. infestans-host interaction is still poorly understood. To find new ways to further unravel this interaction we established a new infection system using MsK8 tomato cells. These cells grow in suspension and can be maintained as a stable cell line that is representative for tomato. RESULTS MsK8 cells can host several Phytophthora species pathogenic on tomato. Species not pathogenic on tomato could not infect. Microscopy revealed that 16 h after inoculation up to 36% of the cells were infected. The majority were penetrated by a germ tube emerging from a cyst (i.e. primary infection) while other cells were already showing secondary infections including haustoria. In incompatible interactions, MsK8 cells showed defense responses, namely reactive oxygen species production and cell death leading to a halt in pathogen spread at the single cell level. In compatible interactions, several P. infestans genes, including RXLR effector genes, were expressed and in both, compatible and incompatible interactions tomato genes involved in defense were differentially expressed. CONCLUSIONS Our results show that P. infestans can prosper as a pathogen in MsK8 cells; it not only infects, but also makes haustoria and sporulates, and it receives signals that activate gene expression. Moreover, MsK8 cells have the ability to support pathogen growth but also to defend themselves against infection in a similar way as whole plants. An advantage of MsK8 cells compared to leaves is the more synchronized infection, as all cells have an equal chance of being infected. Moreover, analyses and sampling of infected tissue can be performed in a non-destructive manner from early time points of infection onwards and as such the MsK8 infection system offers a potential platform for large-scale omics studies and activity screenings of inhibitory compounds.
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Affiliation(s)
- Charikleia Schoina
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
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Ah-Fong AMV, Shrivastava J, Judelson HS. Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. BMC Genomics 2017; 18:764. [PMID: 29017458 PMCID: PMC5635513 DOI: 10.1186/s12864-017-4151-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/02/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND How pathogen genomes evolve to support distinct lifestyles is not well-understood. The oomycete Phytophthora infestans, the potato blight agent, is a largely biotrophic pathogen that feeds from living host cells, which become necrotic only late in infection. The related oomycete Pythium ultimum grows saprophytically in soil and as a necrotroph in plants, causing massive tissue destruction. To learn what distinguishes their lifestyles, we compared their gene contents and expression patterns in media and a shared host, potato tuber. RESULTS Genes related to pathogenesis varied in temporal expression pattern, mRNA level, and family size between the species. A family's aggregate expression during infection was not proportional to size due to transcriptional remodeling and pseudogenization. Ph. infestans had more stage-specific genes, while Py. ultimum tended towards more constitutive expression. Ph. infestans expressed more genes encoding secreted cell wall-degrading enzymes, but other categories such as secreted proteases and ABC transporters had higher transcript levels in Py. ultimum. Species-specific genes were identified including new Pythium genes, perforins, which may disrupt plant membranes. Genome-wide ortholog analyses identified substantial diversified expression, which correlated with sequence divergence. Pseudogenization was associated with gene family expansion, especially in gene clusters. CONCLUSION This first large-scale analysis of transcriptional divergence within oomycetes revealed major shifts in genome composition and expression, including subfunctionalization within gene families. Biotrophy and necrotrophy seem determined by species-specific genes and the varied expression of shared pathogenicity factors, which may be useful targets for crop protection.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Jolly Shrivastava
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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Tomada S, Sonego P, Moretto M, Engelen K, Pertot I, Perazzolli M, Puopolo G. Dual RNA-Seq of Lysobacter capsici
AZ78 - Phytophthora infestans
interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses. Environ Microbiol 2017; 19:4113-4125. [DOI: 10.1111/1462-2920.13861] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Selena Tomada
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Agricultural Science and Biotechnology, Department of Agricultural, Food, Environmental and Animal Sciences; University of Udine; Udine Italy
| | - Paolo Sonego
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Marco Moretto
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Kristof Engelen
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Center Agriculture Food Environment; University of Trento; San Michele all'Adige Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
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Vega-Arreguín JC, Shimada-Beltrán H, Sevillano-Serrano J, Moffett P. Non-host Plant Resistance against Phytophthora capsici Is Mediated in Part by Members of the I2 R Gene Family in Nicotiana spp. FRONTIERS IN PLANT SCIENCE 2017; 8:205. [PMID: 28261255 PMCID: PMC5309224 DOI: 10.3389/fpls.2017.00205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/03/2017] [Indexed: 05/29/2023]
Abstract
The identification of host genes associated with resistance to Phytophthora capsici is crucial to developing strategies of control against this oomycete pathogen. Since there are few sources of resistance to P. capsici in crop plants, non-host plants represent a promising source of resistance genes as well as excellent models to study P. capsici - plant interactions. We have previously shown that non-host resistance to P. capsici in Nicotiana spp. is mediated by the recognition of a specific P. capsici effector protein, PcAvr3a1 in a manner that suggests the involvement of a cognate disease resistance (R) genes. Here, we have used virus-induced gene silencing (VIGS) and transgenic tobacco plants expressing dsRNA in Nicotiana spp. to identify candidate R genes that mediate non-host resistance to P. capsici. Silencing of members of the I2 multigene family in the partially resistant plant N. edwardsonii and in the resistant N. tabacum resulted in compromised resistance to P. capsici. VIGS of two other components required for R gene-mediated resistance, EDS1 and SGT1, also enhanced susceptibility to P. capsici in N. edwardsonii, as well as in the susceptible plants N. benthamiana and N. clevelandii. The silencing of I2 family members in N. tabacum also compromised the recognition of PcAvr3a1. These results indicate that in this case, non-host resistance is mediated by the same components normally associated with race-specific resistance.
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Affiliation(s)
- Julio C. Vega-Arreguín
- Boyce Thompson Institute for Plant Research, IthacaNY, USA
- Laboratorio de Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores – León, Universidad Nacional Autónoma de MexicoLeón, Mexico
| | - Harumi Shimada-Beltrán
- Laboratorio de Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores – León, Universidad Nacional Autónoma de MexicoLeón, Mexico
| | - Jacobo Sevillano-Serrano
- Laboratorio de Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores – León, Universidad Nacional Autónoma de MexicoLeón, Mexico
| | - Peter Moffett
- Boyce Thompson Institute for Plant Research, IthacaNY, USA
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, SherbrookeQC, Canada
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Ali SS, Shao J, Lary DJ, Kronmiller BA, Shen D, Strem MD, Amoako-Attah I, Akrofi AY, Begoude BD, ten Hoopen GM, Coulibaly K, Kebe BI, Melnick RL, Guiltinan MJ, Tyler BM, Meinhardt LW, Bailey BA. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biol Evol 2017; 9:2982378. [PMID: 28186564 PMCID: PMC5381587 DOI: 10.1093/gbe/evx021] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta . Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.
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Affiliation(s)
- Shahin S. Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Jonathan Shao
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, China
| | - Mary D. Strem
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - B.A. Didier Begoude
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
| | - G. Martijn ten Hoopen
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
- CIRAD, UPR 106 Bioagresseurs, Montpellier, France
| | | | | | - Rachel L. Melnick
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | - Brett M. Tyler
- Center for Genome Research and Biocomputing, Oregon State University
- Department of Botany and Plant Pathology, Oregon State University
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
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Dahlin P, Srivastava V, Ekengren S, McKee LS, Bulone V. Comparative analysis of sterol acquisition in the oomycetes Saprolegnia parasitica and Phytophthora infestans. PLoS One 2017; 12:e0170873. [PMID: 28152045 PMCID: PMC5289490 DOI: 10.1371/journal.pone.0170873] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/11/2017] [Indexed: 11/19/2022] Open
Abstract
The oomycete class includes pathogens of animals and plants which are responsible for some of the most significant global losses in agriculture and aquaculture. There is a need to replace traditional chemical means of controlling oomycete growth with more targeted approaches, and the inhibition of sterol synthesis is one promising area. To better direct these efforts, we have studied sterol acquisition in two model organisms: the sterol-autotrophic Saprolegnia parasitica, and the sterol-heterotrophic Phytophthora infestans. We first present a comprehensive reconstruction of a likely sterol synthesis pathway for S. parasitica, causative agent of the disease saprolegniasis in fish. This pathway shows multiple potential routes of sterol synthesis, and draws on several avenues of new evidence: bioinformatic mining for genes with sterol-related functions, expression analysis of these genes, and analysis of the sterol profiles in mycelium grown in different media. Additionally, we explore the extent to which P. infestans, which causes the late blight in potato, can modify exogenously provided sterols. We consider whether the two very different approaches to sterol acquisition taken by these pathogens represent any specific survival advantages or potential drug targets.
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Affiliation(s)
- Paul Dahlin
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University (SU), Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Sophia Ekengren
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University (SU), Stockholm, Sweden
| | - Lauren S. McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Australia
- * E-mail:
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de Vries S, von Dahlen JK, Uhlmann C, Schnake A, Kloesges T, Rose LE. Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2. MOLECULAR PLANT PATHOLOGY 2017; 18:110-124. [PMID: 27503598 PMCID: PMC6638260 DOI: 10.1111/mpp.12465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 08/04/2016] [Indexed: 05/04/2023]
Abstract
Phytophthora infestans is a devastating pathogen in agricultural systems. Recently, an RNA silencing suppressor (PSR2, 'Phytophthora suppressor of RNA silencing 2') has been described in P. infestans. PSR2 has been shown to increase the virulence of Phytophthora pathogens on their hosts. This gene is one of the few effectors present in many economically important Phytophthora species. In this study, we investigated: (i) the evolutionary history of PSR2 within and between species of Phytophthora; and (ii) the interaction between sequence variation, gene expression and virulence. In P. infestans, the highest PiPSR2 expression was correlated with decreased symptom expression. The highest gene expression was observed in the biotrophic phase of the pathogen, suggesting that PSR2 is important during early infection. Protein sequence conservation was negatively correlated with host range, suggesting host range as a driver of PSR2 evolution. Within species, we detected elevated amino acid variation, as observed for other effectors; however, the frequency spectrum of the mutations was inconsistent with strong balancing selection. This evolutionary pattern may be related to the conservation of the host target(s) of PSR2 and the absence of known corresponding R genes. In summary, our study indicates that PSR2 is a conserved effector that acts as a master switch to modify plant gene regulation early during infection for the pathogen's benefit. The conservation of PSR2 and its important role in virulence make it a promising target for pathogen management.
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Affiliation(s)
- Sophie de Vries
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Janina K. von Dahlen
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Constanze Uhlmann
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Anika Schnake
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Thorsten Kloesges
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Laura E. Rose
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- Ceplas, Cluster of Excellence in Plant SciencesHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
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Cheng F, Cheng ZH, Meng HW. Transcriptomic insights into the allelopathic effects of the garlic allelochemical diallyl disulfide on tomato roots. Sci Rep 2016; 6:38902. [PMID: 27941943 PMCID: PMC5150855 DOI: 10.1038/srep38902] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/14/2016] [Indexed: 01/01/2023] Open
Abstract
Garlic is an allelopathic crop that can alleviate the obstacles to continuous cropping of vegetable crops. Diallyl disulfide (DADS), one of the most important allelochemicals in garlic, promotes tomato root growth. Therefore, the global transcriptome profiles of DADS-treated tomato roots over time were investigated to reveal the potential growth-promoting mechanisms. We detected 1828, 1296 and 1190 differentially expressed genes (DEGs) in the 4, 24 and 48 h samples, respectively. Most DEGs involved in assimilatory sulfate reduction and glutathione metabolism were up-regulated after short-term (4 h) DADS treatment. In addition, increased activity of defensive enzymes and up-regulation of six peroxidase genes were observed, suggesting that DADS could induce tomato resistance. In plant-pathogen interactions, DEGs related to calcium signaling were primarily inhibited, while those encoding pathogenesis-related proteins were primarily up-regulated. Although plant hormone synthesis and signal transduction were both significantly affected by DADS, the expression trends of the genes in these two pathways were conflicting. This research provides comprehensive information concerning the changes in the tomato root transcriptome affected by DADS and may help direct further studies on DADS-responsive genes to enhance the current understanding of the mechanisms by which DADS alleviates the obstacles to continuous cropping.
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Affiliation(s)
- Fang Cheng
- College of Horticulture, Northwest A&F University, Taicheng Road No. 3,Yangling, Shaanxi 712100 China
| | - Zhi-Hui Cheng
- College of Horticulture, Northwest A&F University, Taicheng Road No. 3,Yangling, Shaanxi 712100 China
| | - Huan-Wen Meng
- College of Horticulture, Northwest A&F University, Taicheng Road No. 3,Yangling, Shaanxi 712100 China
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Abrahamian M, Ah-Fong AMV, Davis C, Andreeva K, Judelson HS. Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis. PLoS Pathog 2016; 12:e1006097. [PMID: 27936244 PMCID: PMC5176271 DOI: 10.1371/journal.ppat.1006097] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/21/2016] [Accepted: 11/28/2016] [Indexed: 11/19/2022] Open
Abstract
To help learn how phytopathogens feed from their hosts, genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated. This identified 453 genes from 19 families. Comparisons with a necrotrophic oomycete, Pythium ultimum var. ultimum, and a hemibiotrophic fungus, Magnaporthe oryzae, revealed diversity in the size of some families although a similar fraction of genes encoded transporters. RNA-seq of infected potato tubers, tomato leaves, and several artificial media revealed that 56 and 207 transporters from P. infestans were significantly up- or down-regulated, respectively, during early infection timepoints of leaves or tubers versus media. About 17 were up-regulated >4-fold in both leaves and tubers compared to media and expressed primarily in the biotrophic stage. The transcription pattern of many genes was host-organ specific. For example, the mRNA level of a nitrate transporter (NRT) was about 100-fold higher during mid-infection in leaves, which are nitrate-rich, than in tubers and three types of artificial media, which are nitrate-poor. The NRT gene is physically linked with genes encoding nitrate reductase (NR) and nitrite reductase (NiR), which mobilize nitrate into ammonium and amino acids. All three genes were coregulated. For example, the three genes were expressed primarily at mid-stage infection timepoints in both potato and tomato leaves, but showed little expression in potato tubers. Transformants down-regulated for all three genes were generated by DNA-directed RNAi, with silencing spreading from the NR target to the flanking NRT and NiR genes. The silenced strains were nonpathogenic on leaves but colonized tubers. We propose that the nitrate assimilation genes play roles both in obtaining nitrogen for amino acid biosynthesis and protecting P. infestans from natural or fertilization-induced nitrate and nitrite toxicity. Little is known of how plant pathogens adapt to different growth conditions and host tissues. To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts, we mined the genome for genes encoding proteins involved in nutrient uptake and measured their expression in leaves, tubers, and three artificial media. We observed dynamic changes between the growth conditions, and identified transporters expressed mainly in the biotrophic stage, leaves, tubers, or artificial media. When we blocked the expression of a nitrate transporter and two other genes involved in assimilating nitrate, we observed that those genes were required for successful colonization of nitrate-rich leaves but not nitrate-poor tissues, and that nitrate had become toxic to the silenced strains. We therefore hypothesize that the nitrate assimilation pathway may help the pathogen use inorganic nitrogen for nutrition and/or detoxify nitrate when its levels may become damaging.
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Affiliation(s)
- Melania Abrahamian
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Carol Davis
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Kalina Andreeva
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
- * E-mail:
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Guo L, Allen KS, Deiulio G, Zhang Y, Madeiras AM, Wick RL, Ma LJ. A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies. FRONTIERS IN PLANT SCIENCE 2016; 7:925. [PMID: 27462318 PMCID: PMC4939292 DOI: 10.3389/fpls.2016.00925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/10/2016] [Indexed: 05/24/2023]
Abstract
Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e., metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host-pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems.
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Affiliation(s)
- Li Guo
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MAUSA
| | - Kelly S. Allen
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MAUSA
| | - Greg Deiulio
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MAUSA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MAUSA
| | - Angela M. Madeiras
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MAUSA
| | - Robert L. Wick
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MAUSA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MAUSA
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Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L. Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. Nucleic Acids Res 2016; 44:3513-33. [PMID: 27060143 PMCID: PMC4857004 DOI: 10.1093/nar/gkw221] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/22/2016] [Indexed: 01/13/2023] Open
Abstract
Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics we identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal 'Header' domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora Remarkably, we also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. We present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Newton D Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Zuluaga AP, Vega-Arreguín JC, Fei Z, Matas AJ, Patev S, Fry WE, Rose JKC. Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans. MOLECULAR PLANT PATHOLOGY 2016; 17:42-54. [PMID: 25808779 PMCID: PMC6638369 DOI: 10.1111/mpp.12260] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The infection of plants by hemibiotrophic pathogens involves a complex and highly regulated transition from an initial biotrophic, asymptomatic stage to a later necrotrophic state, characterized by cell death. Little is known about how this transition is regulated, and there are conflicting views regarding the significance of the plant hormones jasmonic acid (JA) and salicylic acid (SA) in the different phases of infection. To provide a broad view of the hemibiotrophic infection process from the plant perspective, we surveyed the transcriptome of tomato (Solanum lycopersicum) during a compatible interaction with the hemibiotrophic oomycete Phytophthora infestans during three infection stages: biotrophic, the transition from biotrophy to necrotrophy, and the necrotrophic phase. Nearly 10 000 genes corresponding to proteins in approximately 400 biochemical pathways showed differential transcript abundance during the three infection stages, revealing a major reorganization of plant metabolism, including major changes in source-sink relations, as well as secondary metabolites. In addition, more than 100 putative resistance genes and pattern recognition receptor genes were induced, and both JA and SA levels and associated signalling pathways showed dynamic changes during the infection time course. The biotrophic phase was characterized by the induction of many defence systems, which were either insufficient, evaded or suppressed by the pathogen.
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Affiliation(s)
- Andrea P Zuluaga
- Section of Plant Pathology and Plant Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Julio C Vega-Arreguín
- Section of Plant Pathology and Plant Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Laboratory of Agrigenomics, Universidad Nacional Autónoma de México (UNAM), ENES-León, 37684, Guanajuato, Mexico
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Antonio J Matas
- Departamento de Biología Vegetal, Campus de Teatinos, Universidad de Málaga, 29071, Málaga, Spain
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sean Patev
- Section of Plant Pathology and Plant Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - William E Fry
- Section of Plant Pathology and Plant Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jocelyn K C Rose
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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