1
|
Peng J, Wang X, Wang H, Li X, Zhang Q, Wang M, Yan J. Advances in understanding grapevine downy mildew: From pathogen infection to disease management. MOLECULAR PLANT PATHOLOGY 2024; 25:e13401. [PMID: 37991155 PMCID: PMC10788597 DOI: 10.1111/mpp.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023]
Abstract
Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.
Collapse
Affiliation(s)
- Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hui Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qi Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Meng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| |
Collapse
|
2
|
Wohor OZ, Rispail N, Ojiewo CO, Rubiales D. Pea Breeding for Resistance to Rhizospheric Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:2664. [PMID: 36235530 PMCID: PMC9572552 DOI: 10.3390/plants11192664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.
Collapse
Affiliation(s)
- Osman Z. Wohor
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale Post TL52, Ghana
| | - Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Chris O. Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue—Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| |
Collapse
|
3
|
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]
|
4
|
Midgley KA, van den Berg N, Swart V. Unraveling Plant Cell Death during Phytophthora Infection. Microorganisms 2022; 10:microorganisms10061139. [PMID: 35744657 PMCID: PMC9229607 DOI: 10.3390/microorganisms10061139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/02/2023] Open
Abstract
Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, of which several hundred organisms are considered among the most devastating plant pathogens—especially members of the genus Phytophthora. Phytophthora spp. have a large repertoire of effectors that aid in eliciting a susceptible response in host plants. What is of increasing interest is the involvement of Phytophthora effectors in regulating programed cell death (PCD)—in particular, the hypersensitive response. There have been numerous functional characterization studies, which demonstrate Phytophthora effectors either inducing or suppressing host cell death, which may play a crucial role in Phytophthora’s ability to regulate their hemi-biotrophic lifestyle. Despite several advances in techniques used to identify and characterize Phytophthora effectors, knowledge is still lacking for some important species, including Phytophthora cinnamomi. This review discusses what the term PCD means and the gap in knowledge between pathogenic and developmental forms of PCD in plants. We also discuss the role cell death plays in the virulence of Phytophthora spp. and the effectors that have so far been identified as playing a role in cell death manipulation. Finally, we touch on the different techniques available to study effector functions, such as cell death induction/suppression.
Collapse
|
5
|
Camborde L, Kiselev A, Pel MJC, Le Ru A, Jauneau A, Pouzet C, Dumas B, Gaulin E. An oomycete effector targets a plant RNA helicase involved in root development and defense. THE NEW PHYTOLOGIST 2022; 233:2232-2248. [PMID: 34913494 DOI: 10.1111/nph.17918] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Oomycete plant pathogens secrete effector proteins to promote disease. The damaging soilborne legume pathogen Aphanomyces euteiches harbors a specific repertoire of Small Secreted Protein effectors (AeSSPs), but their biological functions remain unknown. Here we characterize AeSSP1256. The function of AeSSP1256 is investigated by physiological and molecular characterization of Medicago truncatula roots expressing the effector. A potential protein target of AeSSP1256 is identified by yeast-two hybrid, co-immunoprecipitation, and fluorescent resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) assays, as well as promoter studies and mutant characterization. AeSSP1256 impairs M. truncatula root development and promotes pathogen infection. The effector is localized to the nucleoli rim, triggers nucleoli enlargement and downregulates expression of M. truncatula ribosome-related genes. AeSSP1256 interacts with a functional nucleocytoplasmic plant RNA helicase (MtRH10). AeSSP1256 relocates MtRH10 to the perinucleolar space and hinders its binding to plant RNA. MtRH10 is associated with ribosome-related genes, root development and defense. This work reveals that an oomycete effector targets a plant RNA helicase, possibly to trigger nucleolar stress and thereby promote pathogen infection.
Collapse
Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Andrei Kiselev
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Aurélie Le Ru
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Alain Jauneau
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Cécile Pouzet
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| |
Collapse
|
6
|
Sarkar P, Stefi Raju V, Kuppusamy G, Rahman MA, Elumalai P, Harikrishnan R, Arshad A, Arockiaraj J. Pathogenic fungi affecting fishes through their virulence molecules. AQUACULTURE 2022; 548:737553. [DOI: 10.1016/j.aquaculture.2021.737553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
|
7
|
A Comprehensive Assessment of the Secretome Responsible for Host Adaptation of the Legume Root Pathogen Aphanomyces euteiches. J Fungi (Basel) 2022; 8:jof8010088. [PMID: 35050028 PMCID: PMC8780586 DOI: 10.3390/jof8010088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
The soil-borne oomycete pathogen Aphanomyces euteiches causes devastating root rot diseases in legumes such as pea and alfalfa. The different pathotypes of A. euteiches have been shown to exhibit differential quantitative virulence, but the molecular basis of host adaptation has not yet been clarified. Here, we re-sequenced a pea field reference strain of A. euteiches ATCC201684 with PacBio long-reads and took advantage of the technology to generate the mitochondrial genome. We identified that the secretome of A. euteiches is characterized by a large portfolio of secreted proteases and carbohydrate-active enzymes (CAZymes). We performed Illumina sequencing of four strains of A. euteiches with contrasted specificity to pea or alfalfa and found in different geographical areas. Comparative analysis showed that the core secretome is largely represented by CAZymes and proteases. The specific secretome is mainly composed of a large set of small, secreted proteins (SSP) without any predicted functional domain, suggesting that the legume preference of the pathogen is probably associated with unknown functions. This study forms the basis for further investigations into the mechanisms of interaction of A. euteiches with legumes.
Collapse
|
8
|
Laloum Y, Gangneux C, Gügi B, Lanoue A, Munsch T, Blum A, Gauthier A, Trinsoutrot-Gattin I, Boulogne I, Vicré M, Driouich A, Laval K, Follet-Gueye ML. Faba bean root exudates alter pea root colonization by the oomycete Aphanomyces euteiches at early stages of infection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111032. [PMID: 34620436 DOI: 10.1016/j.plantsci.2021.111032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/14/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Aphanomyces euteiches is an oomycete pathogen that causes the pea root rot. We investigated the potential role of early belowground defense in pea (susceptible plant) and faba bean (tolerant plant) at three days after inoculation. Pea and faba bean were inoculated with A. euteiches zoospores. Root colonization was examined. Root exudates from pea and faba bean were harvested and their impact on A. euteiches development were assessed by using in vitro assays. A. euteiches root colonization and the influence of the oomycete inoculation on specialized metabolites patterns and arabinogalactan protein (AGP) concentration of root exudates were also determined. In faba bean root, A. euteiches colonization was very low as compared with that of pea. Whereas infected pea root exudates have a positive chemotaxis index (CI) on zoospores, faba bean exudate CI was negative suggesting a repellent effect. While furanoacetylenic compounds were only detected in faba bean exudates, AGP concentration was specifically increased in pea.This work showed that early in the course of infection, host susceptibility to A. euteiches is involved via a plant-species specific root exudation opening new perspectives in pea root rot disease management.
Collapse
Affiliation(s)
- Yohana Laloum
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France; Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France
| | - Christophe Gangneux
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France
| | - Bruno Gügi
- Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France
| | - Arnaud Lanoue
- Université de Tours, EA 2106 «Biomolécules et Biotechnologies Végétales», UFR des Sciences Pharmaceutiques, 31 Av. Monge, F37200, Tours, France
| | - Thibaut Munsch
- Université de Tours, EA 2106 «Biomolécules et Biotechnologies Végétales», UFR des Sciences Pharmaceutiques, 31 Av. Monge, F37200, Tours, France
| | - Adrien Blum
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France
| | - Adrien Gauthier
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France
| | - Isabelle Trinsoutrot-Gattin
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France
| | - Isabelle Boulogne
- Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France
| | - Maïté Vicré
- Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France
| | - Azeddine Driouich
- Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France
| | - Karine Laval
- AGHYLE research unit, UP 2018.C101, UniLaSalle Rouen 3 rue du tronquet CS 40118, 76134, Mont Saint Aignan, France
| | - Marie-Laure Follet-Gueye
- Normandie Univ, UNIROUEN, Glyco-MEV, EA4358, SFR NORVEGE FED 4277, I2C Carnot, IRIB, 76000, Rouen, France.
| |
Collapse
|
9
|
Ca 2+-regulated mitochondrial carriers of ATP-Mg 2+/Pi: Evolutionary insights in protozoans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119038. [PMID: 33839167 DOI: 10.1016/j.bbamcr.2021.119038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/23/2022]
Abstract
In addition to its uptake across the Ca2+ uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca2+-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg2+/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca2+ signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg2+/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.
Collapse
|
10
|
Gao RF, Wang JY, Liu KW, Yoshida K, Hsiao YY, Shi YX, Tsai KC, Chen YY, Mitsuda N, Liang CK, Wang ZW, Wang Y, Zhang DY, Huang L, Zhao X, Zhong WY, Cheng YH, Jiang ZD, Li MH, Sun WH, Yu X, Hu W, Zhou Z, Zhou XF, Yeh CM, Katoh K, Tsai WC, Liu ZJ, Martin F, Zhang GM. Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops. Heliyon 2021; 7:e06317. [PMID: 33665461 PMCID: PMC7907477 DOI: 10.1016/j.heliyon.2021.e06317] [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: 10/18/2020] [Revised: 12/14/2020] [Accepted: 02/16/2021] [Indexed: 01/19/2023] Open
Abstract
The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies.
Collapse
Affiliation(s)
- Rui-Fang Gao
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China.,Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ke-Wei Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China.,Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Center for Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute (TBSI), Shenzhen 518055, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Xiang Shi
- Shanghai Major Bio-pharm Technology Co., Ltd., Shanghai 201203, China
| | | | - You-Yi Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Chieh-Kai Liang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Ying Wang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China.,Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China
| | - Di-Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Laiqiang Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China.,Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | | | - Ying-Hui Cheng
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
| | - Zi-De Jiang
- College of Agriculture, South China Agricultural University, Guangzhou 510640, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenqi Hu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Xiao-Fan Zhou
- College of Agriculture, South China Agricultural University, Guangzhou 510640, China
| | - Chuan-Ming Yeh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.,Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.,Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, 250100, Jinan, China
| | - Francis Martin
- Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA Grand Est-Nancy, Université de Lorraine, 54280 Champenoux, France
| | - Gui-Ming Zhang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China.,Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China
| |
Collapse
|
11
|
Stam R, Motion GB, Martinez-Heredia V, Boevink PC, Huitema E. A Conserved Oomycete CRN Effector Targets Tomato TCP14-2 to Enhance Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:309-318. [PMID: 33258418 DOI: 10.1094/mpmi-06-20-0172-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora spp. secrete vast arrays of effector molecules during infection to aid in host colonization. The crinkling and necrosis (CRN) protein family forms an extensive repertoire of candidate effectors that accumulate in the host nucleus to perturb processes required for immunity. Here, we show that CRN12_997 from Phytophthora capsici binds a TCP transcription factor, SlTCP14-2, to inhibit its immunity-associated activity against Phytophthora spp. Coimmunoprecipitation and bimolecular fluorescence complementation studies confirm a specific CRN12_997-SlTCP14-2 interaction in vivo. Coexpression of CRN12_997 specifically counteracts the TCP14-enhanced immunity phenotype, suggesting that CRN mediated perturbation of SlTCP14-2 function. We show that SlTCP14-2 associates with nuclear chromatin and that CRN12_997 diminishes SlTCP14-2 DNA binding. Collectively, our data support a model in which SlTCP14-2 associates with chromatin to enhance immunity. The interaction between CRN12_997 and SlTCP14-2 reduces DNA binding of the immune regulator. We propose that the modulation of SlTCP14-2 chromatin affinity, caused by CRN12-997, enhances susceptibility to P. capsici.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Graham B Motion
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Victor Martinez-Heredia
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Edgar Huitema
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| |
Collapse
|
12
|
Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
Collapse
Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| |
Collapse
|
13
|
Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biol 2019; 8:rsob.170184. [PMID: 29321239 PMCID: PMC5795050 DOI: 10.1098/rsob.170184] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
Collapse
Affiliation(s)
- Guy Leonard
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Aurélie Labarre
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Adam Monier
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Darren Soanes
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jeremy G Wideman
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Finlay Maguire
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sam Stevens
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Divya Sain
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Xavier Grau-Bové
- Institute of Evolutionary Biology, CSIC-UPF, Barcelona, Catalonia, Spain
| | | | - Jason E Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Konrad Paszkiewicz
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Neil Hall
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Thomas A Richards
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| |
Collapse
|
14
|
Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
Collapse
Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
| |
Collapse
|
15
|
Quillévéré-Hamard A, Le Roy G, Moussart A, Baranger A, Andrivon D, Pilet-Nayel ML, Le May C. Genetic and Pathogenicity Diversity of Aphanomyces euteiches Populations From Pea-Growing Regions in France. FRONTIERS IN PLANT SCIENCE 2018; 9:1673. [PMID: 30510559 PMCID: PMC6252352 DOI: 10.3389/fpls.2018.01673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
Aphanomyces euteiches is an oomycete pathogen with a broad host-range on legumes that causes devastating root rot disease in many pea-growing countries and especially in France. Genetic resistance is a promising way to manage the disease since consistent QTL controlling partial resistance have been identified in near isogenic lines of pea. However, there are still no resistant pea varieties cultivated in France. This study aimed to evaluate the phenotypic and genetic diversity of A. euteiches populations from the major pea-growing regions in France. A collection of 205 isolates, from soil samples collected in infested pea fields located in five French regions, was established and genotyped using 20 SSR markers. Thirteen multilocus genotypes were found among the 205 isolates which displayed a low genotypic richness (ranged from 0 to 0.333). Two main clusters of isolates were identified using PCoA and STRUCTURE, including a predominant group comprising 88% of isolates and another group representing 12% of isolates mainly from the Bourgogne region. A subset of 34 isolates, representative of the fields sampled, was phenotyped for aggressiveness on a set of resistant and susceptible varieties of four legume hosts (pea, faba bean, vetch, alfalfa). Significant differences in disease severity were found among isolates and three groups of aggressiveness comprising 16, 17, and 2 isolates, respectively, were identified using HCA analysis. A higher diversity in pathogen aggressiveness was observed among isolates from Bourgogne, which included different legumes in its crop history. Little relationship was observed between genetic clusters and pathogenicity in the subset of 34 isolates, as expected using neutral markers. This study provides useful knowledge on the current state of low to moderate diversity among A. euteiches populations before resistant pea varieties are grown in France. New insights and hypotheses about the major factors shaping the diversity and evolution of A. euteiches are also discussed.
Collapse
Affiliation(s)
- Anne Quillévéré-Hamard
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
| | - Gwenola Le Roy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
| | - Anne Moussart
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
- Terres Inovia, Thiverval Grignon, France
| | - Alain Baranger
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
| | - Didier Andrivon
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie-Laure Pilet-Nayel
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
| | - Christophe Le May
- UMT PISOM INRA/Terres Inovia, Le Rheu, France
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, Rennes, France
| |
Collapse
|
16
|
Voß S, Betz R, Heidt S, Corradi N, Requena N. RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development. Front Microbiol 2018; 9:2068. [PMID: 30233541 PMCID: PMC6131194 DOI: 10.3389/fmicb.2018.02068] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/13/2018] [Indexed: 01/10/2023] Open
Abstract
Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant–microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.
Collapse
Affiliation(s)
- Stefanie Voß
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ruben Betz
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sven Heidt
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Nicolas Corradi
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - Natalia Requena
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| |
Collapse
|
17
|
Gaulin E, Pel MJC, Camborde L, San-Clemente H, Courbier S, Dupouy MA, Lengellé J, Veyssiere M, Le Ru A, Grandjean F, Cordaux R, Moumen B, Gilbert C, Cano LM, Aury JM, Guy J, Wincker P, Bouchez O, Klopp C, Dumas B. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biol 2018; 16:43. [PMID: 29669603 PMCID: PMC5907361 DOI: 10.1186/s12915-018-0508-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms. Results By carrying out genomic analyses of the plant pathogen A. euteiches and the crustacean pathogen A. astaci, we show that host specialization is correlated with specialized secretomes that are adapted to the deconstruction of the plant cell wall in A. euteiches and protein degradation in A. astaci. The A. euteiches genome is characterized by a large repertoire of small secreted protein (SSP)-encoding genes that are highly induced during plant infection, and are not detected in other oomycetes. Functional analysis revealed an SSP from A. euteiches containing a predicted nuclear-localization signal which shuttles to the plant nucleus and increases plant susceptibility to infection. Conclusion Collectively, our results show that Aphanomyces host adaptation is associated with evolution of specialized secretomes and identify SSPs as a new class of putative oomycete effectors. Electronic supplementary material The online version of this article (10.1186/s12915-018-0508-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France.
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Hélène San-Clemente
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Sarah Courbier
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France.,Present Address: Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Marie-Alexane Dupouy
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Juliette Lengellé
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Marine Veyssiere
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Aurélie Le Ru
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, 31326, Castanet-Tolosan, France
| | - Frédéric Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS Université Paris-Sud UMR 9191, IRD 247, Gif sur Yvette, France
| | - Liliana M Cano
- University of Florida, UF/IFAS, Indian River Research and Education Center IRREC, 2199 South Rock Road, Fort Pierce, FL, 34945, USA
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, F-92057, Evry, France
| | - Julie Guy
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, F-92057, Evry, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, CNRS UMR 8030, Université d'Evry, Evry, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, UR875, Plateforme Bioinformatique Genotoul, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| |
Collapse
|
18
|
Thalineau E, Fournier C, Gravot A, Wendehenne D, Jeandroz S, Truong H. Nitrogen modulation of Medicago truncatula resistance to Aphanomyces euteiches depends on plant genotype. MOLECULAR PLANT PATHOLOGY 2018; 19:664-676. [PMID: 28296004 PMCID: PMC6638142 DOI: 10.1111/mpp.12550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/02/2017] [Accepted: 03/08/2017] [Indexed: 05/25/2023]
Abstract
Nitrogen (N) availability can impact plant resistance to pathogens by the regulation of plant immunity. To better understand the links between N nutrition and plant defence, we analysed the impact of N availability on Medicago truncatula resistance to the root pathogen Aphanomyces euteiches. This oomycete is considered to be the most limiting factor for legume production. Ten plant genotypes were tested in vitro for their resistance to A. euteiches in either complete or nitrate-deficient medium. N deficiency led to enhanced or reduced susceptibility depending on the plant genotype. Focusing on four genotypes displaying contrasting responses, we determined the impact of N deficiency on plant growth and shoot N concentration, and performed expression analyses on N- and defence-related genes, as well as the quantification of soluble phenolics and different amino acids in roots. Our analyses suggest that N modulation of plant resistance is not linked to plant response to N deprivation or to mechanisms previously identified to be involved in plant resistance. Furthermore, our studies highlight a role of glutamine in mediating the susceptibility to A. euteiches in M. truncatula.
Collapse
Affiliation(s)
- Elise Thalineau
- Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche‐ComtéDijonFrance
| | - Carine Fournier
- Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche‐ComtéDijonFrance
| | | | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche‐ComtéDijonFrance
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche‐ComtéDijonFrance
| | - Hoai‐Nam Truong
- Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche‐ComtéDijonFrance
| |
Collapse
|
19
|
Abstract
The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.
Collapse
Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| |
Collapse
|
20
|
Evolution of the Sterol Biosynthetic Pathway of Pythium insidiosum and Related Oomycetes Contributes to Antifungal Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02352-16. [PMID: 28115356 DOI: 10.1128/aac.02352-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Pythiosis is a life-threatening infectious disease caused by the oomycete Pythium insidiosum Direct exposure to Py. insidiosum zoospores can initiate infections of the eye, limb, gastrointestinal tract, or skin/subcutaneous tissue. Treatments for pythiosis have mostly relied on surgery. Antifungal drugs are generally ineffective against Py. insidiosum However, one patient with an invasive Py. insidiosum infection recovered completely following treatment with terbinafine and itraconazole. Additionally, the drug target sterol biosynthetic enzymes have been identified in the oomycete Aphanomyces euteiches It remains an open question whether Py. insidiosum is susceptible to the antifungal drugs and harbors any of the known drug target enzymes. Here, we determined the in vitro susceptibilities of terbinafine and itraconazole against 30 isolates of Py. insidiosum We also analyzed endogenous sterols and searched for genes encoding the sterol biosynthetic enzymes in the genomes of Py. insidiosum and related oomycetes. The susceptibility assay showed that the growth of each of the Py. insidiosum isolates was inhibited by the antifungal agents, but only at difficult-to-achieve concentrations, which explains the clinical resistance of the drugs in the treatment of pythiosis patients. Genome searches of Py. insidiosum and related oomycetes demonstrated that these organisms contained an incomplete set of sterol biosynthetic enzymes. Gas chromatographic mass spectrometry did not detect any sterol end products in Py. insidiosum In conclusion, Py. insidiosum possesses an incomplete sterol biosynthetic pathway. Resistance to antifungal drugs targeting enzymes in the ergosterol biosynthetic pathway in Py. insidiosum was due to modifications or losses of some of the genes encoding the drug target enzymes.
Collapse
|
21
|
Amaro TMMM, Thilliez GJA, Motion GB, Huitema E. A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited. FRONTIERS IN PLANT SCIENCE 2017; 8:99. [PMID: 28217133 PMCID: PMC5289972 DOI: 10.3389/fpls.2017.00099] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/17/2017] [Indexed: 05/20/2023]
Abstract
Plant associated microbes rely on secreted virulence factors (effectors) to modulate host immunity and ensure progressive infection. Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across several kingdoms. CRN proteins were first identified in plant pathogenic oomycetes where they were found to be modular factors that are secreted and translocated inside host cells by means of a conserved N-terminal domain. Subsequent localization and functional studies have led to the view that CRN C-termini execute their presumed effector function in the host nucleus, targeting processes required for immunity. These findings have led to great interest in this large protein family and driven the identification of additional CRN-like proteins in other organisms. The identification of CRN proteins and subsequent functional studies have markedly increased the number of candidate CRN protein sequences, expanded the range of phenotypes tentatively associated with function and revealed some of their molecular functions toward virulence. The increased number of characterized CRNs also has presented a set of challenges that may impede significant progress in the future. Here, we summarize our current understanding of the CRNs and re-assess some basic assumptions regarding this protein family. We will discuss the latest findings on CRN biology and highlight exciting new hypotheses that have emanated from the field. Finally, we will discuss new approaches to study CRN functions that would lead to a better understanding of CRN effector biology as well as the processes that lead to host susceptibility and immunity.
Collapse
Affiliation(s)
- Tiago M. M. M. Amaro
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Gaëtan J. A. Thilliez
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
- Cell and Molecular Sciences, The James Hutton InstituteInvergowrie, UK
| | - Graham B. Motion
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Edgar Huitema
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| |
Collapse
|
22
|
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.
Collapse
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:
| |
Collapse
|
23
|
Raaymakers TM, Van den Ackerveken G. Extracellular Recognition of Oomycetes during Biotrophic Infection of Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:906. [PMID: 27446136 PMCID: PMC4915311 DOI: 10.3389/fpls.2016.00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/08/2016] [Indexed: 05/23/2023]
Abstract
Extracellular recognition of pathogens by plants constitutes an important early detection system in plant immunity. Microbe-derived molecules, also named patterns, can be recognized by pattern recognition receptors (PRRs) on the host cell membrane that trigger plant immune responses. Most knowledge on extracellular pathogen detection by plants comes from research on bacterial and fungal pathogens. For oomycetes, that comprise some of the most destructive plant pathogens, mechanisms of extracellular pattern recognition have only emerged recently. These include newly recognized patterns, e.g., cellulose-binding elicitor lectin, necrosis and ethylene-inducing peptide 1-like proteins (NLPs), and glycoside hydrolase 12, as well as their receptors, e.g., the putative elicitin PRR elicitin response and the NLP PRR receptor-like protein 23. Immunity can also be triggered by the release of endogenous host-derived patterns, as a result of oomycete enzymes or damage. In this review we will describe the types of patterns, both pathogen-derived exogenous and plant-derived endogenous ones, and what is known about their extracellular detection during (hemi-)biotrophic oomycete infection of plants.
Collapse
|
24
|
Ramirez-Garcés D, Camborde L, Pel MJC, Jauneau A, Martinez Y, Néant I, Leclerc C, Moreau M, Dumas B, Gaulin E. CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNA-binding proteins which trigger host DNA damage response. THE NEW PHYTOLOGIST 2016; 210:602-17. [PMID: 26700936 DOI: 10.1111/nph.13774] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/21/2015] [Indexed: 05/20/2023]
Abstract
To successfully colonize their host, pathogens produce effectors that can interfere with host cellular processes. Here we investigated the function of CRN13 candidate effectors produced by plant pathogenic oomycetes and detected in the genome of the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis (BdCRN13). When expressed in Nicotiana, AeCRN13, from the legume root pathogen Aphanomyces euteiches, increases the susceptibility of the leaves to the oomycete Phytophthora capsici. When transiently expressed in amphibians or plant cells, AeCRN13 and BdCRN13 localize to the cell nuclei, triggering aberrant cell development and eventually causing cell death. Using Förster resonance energy transfer experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR). Mutating key amino acid residues in a predicted HNH-like endonuclease motif abolished the interaction of AeCRN13 with DNA, the induction of DDR and the enhancement of Nicotiana susceptibility to P. capsici. Finally, H2AX phosphorylation, a marker of DNA damage, and enhanced expression of genes involved in the DDR were observed in A. euteiches-infected Medicago truncatula roots. These results show that CRN13 from plant and animal eukaryotic pathogens promotes host susceptibility by targeting nuclear DNA and inducing DDR.
Collapse
Affiliation(s)
- Diana Ramirez-Garcés
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Yves Martinez
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Isabelle Néant
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Catherine Leclerc
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Marc Moreau
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| |
Collapse
|
25
|
Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, Amirebrahimi M, Hesse CN, Spatafora JW, Henrissat B, Hainaut M, Grigoriev IV, Hibbett DS. The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol 2015; 120:26-42. [PMID: 26693682 DOI: 10.1016/j.funbio.2015.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Xylona heveae has only been isolated as an endophyte of rubber trees. In an effort to understand the genetic basis of endophytism, we compared the genome contents of X. heveae and 36 other Ascomycota with diverse lifestyles and nutritional modes. We focused on genes that are known to be important in the host-fungus interaction interface and that presumably have a role in determining the lifestyle of a fungus. We used phylogenomic data to infer the higher-level phylogenetic position of the Xylonomycetes, and mined ITS sequences to explore its taxonomic and ecological diversity. The X. heveae genome contains a low number of enzymes needed for plant cell wall degradation, suggesting that Xylona is a highly adapted specialist and likely dependent on its host for survival. The reduced repertoire of carbohydrate active enzymes could reflect an adaptation to intercellulary growth and to the avoidance of the host's immune system, suggesting that Xylona has a strictly endophytic lifestyle. Phylogenomic data resolved the position of Xylonomycetes as sister to Lecanoromycetes and Eurotiomycetes and placed the beetle-endosymbiont Symbiotaphrina as a member of this class. ITS data revealed that Trinosporium is also part of the Xylonomycetes, extending the taxonomic and ecological diversity of this group.
Collapse
Affiliation(s)
- Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester, MA 01610, USA.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Junyan Lin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Cedar N Hesse
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, USA; Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Joseph W Spatafora
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, USA
| | - Bernard Henrissat
- Aix-Marseille Université, CNRS, UMR 7257, Marseille, France; Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille cedex 9, France; King Abdulaziz University, Department of Biological Sciences, Jeddah 21589, Saudi Arabia
| | | | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - David S Hibbett
- Clark University, Biology Department, 950 Main Street, Worcester, MA 01610, USA
| |
Collapse
|
26
|
Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJG, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics 2015; 16:741. [PMID: 26438312 PMCID: PMC4594904 DOI: 10.1186/s12864-015-1904-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. RESULTS Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. CONCLUSIONS The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
Collapse
Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. .,Present address: Department of Plant Pathology, North Carolina State University Raleigh, Raleigh, NC, 27695, USA.
| | | | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl von Linne´ Weg 10, Cologne, 50829, Germany.
| | - Howard Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Christine Sambles
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - D Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 78371, Olomouc, Czech Republic.
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Otmar Spring
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Reinhard Zipper
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - David J Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Integrative Fungal Research (IPF), Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
| |
Collapse
|
27
|
Hosseini S, Elfstrand M, Heyman F, Funck Jensen D, Karlsson M. Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi. BMC Genomics 2015; 16:627. [PMID: 26293353 PMCID: PMC4546216 DOI: 10.1186/s12864-015-1829-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 08/07/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Root rot caused by Aphanomyces euteiches is one of the most destructive pea diseases while a distantly related species P. pisi has been recently described as the agent of pea and faba bean root rot. These two oomycete pathogens with different pathogenicity factor repertories have both evolved specific mechanisms to infect pea. However, little is known about the genes and mechanisms of defence against these pathogens in pea. In the present study, the transcriptomic response of pea to these two pathogens was investigated at two time points during early phase of infection using a Medicago truncatula microarray. RESULTS Of the 37,976 genes analysed, 574 and 817 were differentially expressed in response to A. euteiches at 6 hpi and 20 hpi, respectively, while 544 and 611 genes were differentially regulated against P. pisi at 6 hpi and 20 hpi, respectively. Differentially expressed genes associated with plant immunity responses were involved in cell wall reinforcement, hormonal signalling and phenylpropanoid metabolism. Activation of cell wall modification, regulation of jasmonic acid biosynthesis and induction of ethylene signalling pathway were among the common transcriptional responses to both of these oomycetes. However, induction of chalcone synthesis and the auxin pathway were specific transcriptional changes against A. euteiches. CONCLUSIONS Our results demonstrate a global view of differentially expressed pea genes during compatible interactions with P. pisi and A. euteiches at an early phase of infection. The results suggest that distinct signalling pathways are triggered in pea by these two pathogens that lead to common and specific immune mechanisms in response to these two oomycetes. The generated knowledge may eventually be used in breeding pea varieties with resistance against root rot disease.
Collapse
Affiliation(s)
- Sara Hosseini
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Fredrik Heyman
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| |
Collapse
|
28
|
Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins. PLoS One 2015; 10:e0135240. [PMID: 26252511 PMCID: PMC4529148 DOI: 10.1371/journal.pone.0135240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022] Open
Abstract
RxLR effectors represent one of the largest and most diverse effector families in oomycete plant pathogens. These effectors have attracted enormous attention since they can be delivered inside the plant cell and manipulates host immunity. With the exceptions of a signal peptide and the following RxLR-dEER and C-terminal W/Y/L motifs identified from the sequences themselves, nearly no functional domains have been found. Recently, protein structures of several RxLRs were revealed to comprise alpha-helical bundle repeats. However, approximately half of all RxLRs lack obvious W/Y/L motifs, which are associated with helical structures. In this study, secondary structure prediction of the putative RxLR proteins was performed. We found that the C-terminus of the majority of these RxLR proteins, irrespective of the presence of W/Y/L motifs, contains abundant short alpha-helices. Since a large-scale experimental determination of protein structures has been difficult to date, results of the current study extend our understanding on the oomycete RxLR effectors in protein secondary structures from individual members to the entire family. Moreover, we identified less alpha-helix-rich proteins from secretomes of several oomycete and fungal organisms in which RxLRs have not been identified, providing additional evidence that these organisms are unlikely to harbor RxLR-like proteins. Therefore, these results provide additional information that will aid further studies on the evolution and functional mechanisms of RxLR effectors.
Collapse
|
29
|
Lerksuthirat T, Lohnoo T, Inkomlue R, Rujirawat T, Yingyong W, Khositnithikul R, Phaonakrop N, Roytrakul S, Sullivan TD, Krajaejun T. The elicitin-like glycoprotein, ELI025, is secreted by the pathogenic oomycete Pythium insidiosum and evades host antibody responses. PLoS One 2015; 10:e0118547. [PMID: 25793767 PMCID: PMC4368664 DOI: 10.1371/journal.pone.0118547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/20/2015] [Indexed: 12/31/2022] Open
Abstract
Pythium insidiosum is a unique oomycete that can infect humans and animals. Patients with a P. insidiosum infection (pythiosis) have high rates of morbidity and mortality. The pathogen resists conventional antifungal drugs. Information on the biology and pathogenesis of P. insidiosum is limited. Many pathogens secrete proteins, known as effectors, which can affect the host response and promote the infection process. Elicitins are secretory proteins and are found only in the oomycetes, primarily in Phytophthora and Pythium species. In plant-pathogenic oomycetes, elicitins function as pathogen-associated molecular pattern molecules, sterol carriers, and plant defense stimulators. Recently, we reported a number of elicitin-encoding genes from the P. insidiosum transcriptome. The function of elicitins during human infections is unknown. One of the P. insidiosum elicitin-encoding genes, ELI025, is highly expressed and up-regulated at body temperature. This study aims to characterize the biochemical, immunological, and genetic properties of the elicitin protein, ELI025. A 12.4-kDa recombinant ELI025 protein (rELI025) was expressed in Escherichia coli. Rabbit anti-rELI025 antibodies reacted strongly with the native ELI025 in P. insidiosum’s culture medium. The detected ELI025 had two isoforms: glycosylated and non-glycosylated. ELI025 was not immunoreactive with sera from pythiosis patients. The region near the transcriptional start site of ELI025 contained conserved oomycete core promoter elements. In conclusion, ELI025 is a small, abundant, secreted glycoprotein that evades host antibody responses. ELI025 is a promising candidate for development of diagnostic and therapeutic targets for pythiosis.
Collapse
Affiliation(s)
- Tassanee Lerksuthirat
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tassanee Lohnoo
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ruchuros Inkomlue
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wanta Yingyong
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rommanee Khositnithikul
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Narumon Phaonakrop
- Proteomics Research Laboratory, Genome Institute, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thomas D. Sullivan
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
| |
Collapse
|
30
|
Gascuel Q, Martinez Y, Boniface MC, Vear F, Pichon M, Godiard L. The sunflower downy mildew pathogen Plasmopara halstedii. MOLECULAR PLANT PATHOLOGY 2015; 16:109-22. [PMID: 25476405 PMCID: PMC6638465 DOI: 10.1111/mpp.12164] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED Downy mildew of sunflower is caused by Plasmopara halstedii (Farlow) Berlese & de Toni. Plasmopara halstedii is an obligate biotrophic oomycete pathogen that attacks annual Helianthus species and cultivated sunflower, Helianthus annuus. Depending on the sunflower developmental stage at which infection occurs, the characteristic symptoms range from young seedling death, plant dwarfing, leaf bleaching and sporulation to the production of infertile flowers. Downy mildew attacks can have a great economic impact on sunflower crops, and several Pl resistance genes are present in cultivars to protect them against the disease. Nevertheless, some of these resistances have been overcome by the occurrence of novel isolates of the pathogen showing increased virulence. A better characterization of P. halstedii infection and dissemination mechanisms, and the identification of the molecular basis of the interaction with sunflower, is a prerequisite to efficiently fight this pathogen. This review summarizes what is currently known about P. halstedii, provides new insights into its infection cycle on resistant and susceptible sunflower lines using scanning electron and light microscopy imaging, and sheds light on the pathogenicity factors of P. halstedii obtained from recent molecular data. TAXONOMY Kingdom Stramenopila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Plasmopara; Species Plasmopara halstedii. DISEASE SYMPTOMS Sunflower seedling damping off, dwarfing of the plant, bleaching of leaves, starting from veins, and visible white sporulation, initially on the lower side of cotyledons and leaves. Plasmopara halstedii infection may severely impact sunflower seed yield. INFECTION PROCESS In spring, germination of overwintered sexual oospores leads to sunflower root infection. Intercellular hyphae are responsible for systemic plant colonization and the induction of disease symptoms. Under humid and fresh conditions, dissemination structures are produced by the pathogen on all plant organs to release asexual zoosporangia. These zoosporangia play an important role in pathogen dissemination, as they release motile zoospores that are responsible for leaf infections on neighbouring plants. DISEASE CONTROL Disease control is obtained by both chemical seed treatment (mefenoxam) and the deployment of dominant major resistance genes, denoted Pl. However, the pathogen has developed fungicide resistance and has overcome some plant resistance genes. Research for more sustainable strategies based on the identification of the molecular basis of the interaction are in progress. USEFUL WEBSITES http://www.heliagene.org/HP, http://lipm-helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start, https://www.heliagene.org/PlasmoparaSpecies (soon available).
Collapse
Affiliation(s)
- Quentin Gascuel
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | | | | | | | | | | |
Collapse
|
31
|
Krajaejun T, Lerksuthirat T, Garg G, Lowhnoo T, Yingyong W, Khositnithikul R, Tangphatsornruang S, Suriyaphol P, Ranganathan S, Sullivan TD. Transcriptome analysis reveals pathogenicity and evolutionary history of the pathogenic oomycete Pythium insidiosum. Fungal Biol 2014; 118:640-53. [DOI: 10.1016/j.funbio.2014.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 12/03/2013] [Accepted: 01/24/2014] [Indexed: 12/14/2022]
|
32
|
Adhikari BN, Hamilton JP, Zerillo MM, Tisserat N, Lévesque CA, Buell CR. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS One 2013; 8:e75072. [PMID: 24124466 PMCID: PMC3790786 DOI: 10.1371/journal.pone.0075072] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.
Collapse
Affiliation(s)
- Bishwo N. Adhikari
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - John P. Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Marcelo M. Zerillo
- Department of Bioagricultural Sciences and Pest Management Colorado State University, Fort Collins, Colorado, United States of America
| | - Ned Tisserat
- Department of Bioagricultural Sciences and Pest Management Colorado State University, Fort Collins, Colorado, United States of America
| | - C. André Lévesque
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|
33
|
Aphanomyces euteiches cell wall fractions containing novel glucan-chitosaccharides induce defense genes and nuclear calcium oscillations in the plant host Medicago truncatula. PLoS One 2013; 8:e75039. [PMID: 24086432 PMCID: PMC3781040 DOI: 10.1371/journal.pone.0075039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/08/2013] [Indexed: 01/15/2023] Open
Abstract
N-acetylglucosamine-based saccharides (chitosaccharides) are components of microbial cell walls and act as molecular signals during host-microbe interactions. In the legume plant Medicago truncatula, the perception of lipochitooligosaccharide signals produced by symbiotic rhizobia and arbuscular mycorrhizal fungi involves the Nod Factor Perception (NFP) lysin motif receptor-like protein and leads to the activation of the so-called common symbiotic pathway. In rice and Arabidopsis, lysin motif receptors are involved in the perception of chitooligosaccharides released by pathogenic fungi, resulting in the activation of plant immunity. Here we report the structural characterization of atypical chitosaccharides from the oomycete pathogen Aphanomyces euteiches, and their biological activity on the host Medicago truncatula. Using a combination of biochemical and biophysical approaches, we show that these chitosaccharides are linked to β-1,6-glucans, and contain a β-(1,3;1,4)-glucan backbone whose β-1,3-linked glucose units are substituted on their C-6 carbon by either glucose or N-acetylglucosamine residues. This is the first description of this type of structural motif in eukaryotic cell walls. Glucan-chitosaccharide fractions of A. euteiches induced the expression of defense marker genes in Medicago truncatula seedlings independently from the presence of a functional Nod Factor Perception protein. Furthermore, one of the glucan-chitosaccharide fractions elicited calcium oscillations in the nucleus of root cells. In contrast to the asymmetric oscillatory calcium spiking induced by symbiotic lipochitooligosaccharides, this response depends neither on the Nod Factor Perception protein nor on the common symbiotic pathway. These findings open new perspectives in oomycete cell wall biology and elicitor recognition and signaling in legumes.
Collapse
|
34
|
Pais M, Win J, Yoshida K, Etherington GJ, Cano LM, Raffaele S, Banfield MJ, Jones A, Kamoun S, Saunders DGO. From pathogen genomes to host plant processes: the power of plant parasitic oomycetes. Genome Biol 2013; 14:211. [PMID: 23809564 PMCID: PMC3706818 DOI: 10.1186/gb-2013-14-6-211] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences.
Collapse
|
35
|
Jiang RHY, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJG, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JHM, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P. Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet 2013; 9:e1003272. [PMID: 23785293 PMCID: PMC3681718 DOI: 10.1371/journal.pgen.1003272] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/10/2012] [Indexed: 01/31/2023] Open
Abstract
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica. Fish are an increasingly important source of animal protein globally, with aquaculture production rising dramatically over the past decade. Saprolegnia is a fungal-like oomycete and one of the most destructive fish pathogens, causing millions of dollars in losses to the aquaculture industry annually. Saprolegnia has also been linked to a worldwide decline in wild fish and amphibian populations. Here we describe the genome sequence of the first animal pathogenic oomycete and compare the genome content with the available plant pathogenic oomycetes. We found that Saprolegnia lacks the large effector families that are hallmarks of plant pathogenic oomycetes, showing evolutionary adaptation to the host. Moreover, Saprolegnia harbors pathogenesis-related genes that were derived by lateral gene transfer from the host and other animal pathogens. The retrotransposon LINE family also appears to be acquired from animal lineages. By transcriptome analysis we show a high rate of allelic variation, which reveals rapidly evolving genes and potentially adaptive evolutionary mechanisms coupled to selective pressures exerted by the animal host. The genome and transcriptome data, as well as subsequent biochemical analyses, provided us with insight in the disease process of Saprolegnia at a molecular and cellular level, providing us with targets for sustainable control of Saprolegnia.
Collapse
Affiliation(s)
- Rays H Y Jiang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
|
37
|
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME JOURNAL 2013; 7:1678-95. [PMID: 23575371 PMCID: PMC3749498 DOI: 10.1038/ismej.2013.59] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/28/2013] [Accepted: 03/06/2013] [Indexed: 11/17/2022]
Abstract
Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.
Collapse
Affiliation(s)
- Pascal Hingamp
- CNRS, Aix-Marseille Université, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Stam R, Jupe J, Howden AJM, Morris JA, Boevink PC, Hedley PE, Huitema E. Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity. PLoS One 2013; 8:e59517. [PMID: 23536880 PMCID: PMC3607596 DOI: 10.1371/journal.pone.0059517] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/15/2013] [Indexed: 11/19/2022] Open
Abstract
Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN) gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemi-biotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions.
Collapse
Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee, Invergowrie, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Julietta Jupe
- Division of Plant Sciences, University of Dundee, Invergowrie, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Andrew J. M. Howden
- Division of Plant Sciences, University of Dundee, Invergowrie, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Jenny A. Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Petra C. Boevink
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Pete E. Hedley
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Edgar Huitema
- Division of Plant Sciences, University of Dundee, Invergowrie, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| |
Collapse
|
39
|
Stam R, Howden AJM, Delgado-Cerezo M, M. M. Amaro TM, Motion GB, Pham J, Huitema E. Characterization of cell death inducing Phytophthora capsici CRN effectors suggests diverse activities in the host nucleus. FRONTIERS IN PLANT SCIENCE 2013; 4:387. [PMID: 24155749 PMCID: PMC3803116 DOI: 10.3389/fpls.2013.00387] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/11/2013] [Indexed: 05/20/2023]
Abstract
Plant-Microbe interactions are complex associations that feature recognition of Pathogen Associated Molecular Patterns by the plant immune system and dampening of subsequent responses by pathogen encoded secreted effectors. With large effector repertoires now identified in a range of sequenced microbial genomes, much attention centers on understanding their roles in immunity or disease. These studies not only allow identification of pathogen virulence factors and strategies, they also provide an important molecular toolset suited for studying immunity in plants. The Phytophthora intracellular effector repertoire encodes a large class of proteins that translocate into host cells and exclusively target the host nucleus. Recent functional studies have implicated the CRN protein family as an important class of diverse effectors that target distinct subnuclear compartments and modify host cell signaling. Here, we characterized three necrosis inducing CRNs and show that there are differences in the levels of cell death. We show that only expression of CRN20_624 has an additive effect on PAMP induced cell death but not AVR3a induced ETI. Given their distinctive phenotypes, we assessed localization of each CRN with a set of nuclear markers and found clear differences in CRN subnuclear distribution patterns. These assays also revealed that expression of CRN83_152 leads to a distinct change in nuclear chromatin organization, suggesting a distinct series of events that leads to cell death upon over-expression. Taken together, our results suggest diverse functions carried by CRN C-termini, which can be exploited to identify novel processes that take place in the host nucleus and are required for immunity or susceptibility.
Collapse
Affiliation(s)
- Remco Stam
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Andrew J. M. Howden
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Magdalena Delgado-Cerezo
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Tiago M. M. M. Amaro
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Graham B. Motion
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Jasmine Pham
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
| | - Edgar Huitema
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, UK
- Dundee Effector Consortium, The James Hutton Institute, Dundee, UK
- *Correspondence: Edgar Huitema, Division of Plant Science, College of Life Sciences, University of Dundee at JHI, Errol Road, Invergowrie, Dundee DD2 5DA, UK e-mail:
| |
Collapse
|
40
|
Wawra S, Belmonte R, Löbach L, Saraiva M, Willems A, van West P. Secretion, delivery and function of oomycete effector proteins. Curr Opin Microbiol 2012. [DOI: 10.1016/j.mib.2012.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
41
|
Larroque M, Barriot R, Bottin A, Barre A, Rougé P, Dumas B, Gaulin E. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses. BMC Genomics 2012; 13:605. [PMID: 23140525 PMCID: PMC3532174 DOI: 10.1186/1471-2164-13-605] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/25/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Oomycetes are fungal-like microorganisms evolutionary distinct from true fungi, belonging to the Stramenopile lineage and comprising major plant pathogens. Both oomycetes and fungi express proteins able to interact with cellulose, a major component of plant and oomycete cell walls, through the presence of carbohydrate-binding module belonging to the family 1 (CBM1). Fungal CBM1-containing proteins were implicated in cellulose degradation whereas in oomycetes, the Cellulose Binding Elicitor Lectin (CBEL), a well-characterized CBM1-protein from Phytophthora parasitica, was implicated in cell wall integrity, adhesion to cellulosic substrates and induction of plant immunity. RESULTS To extend our knowledge on CBM1-containing proteins in oomycetes, we have conducted a comprehensive analysis on 60 fungi and 7 oomycetes genomes leading to the identification of 518 CBM1-containing proteins. In plant-interacting microorganisms, the larger number of CBM1-protein coding genes is expressed by necrotroph and hemibiotrophic pathogens, whereas a strong reduction of these genes is observed in symbionts and biotrophs. In fungi, more than 70% of CBM1-containing proteins correspond to enzymatic proteins in which CBM1 is associated with a catalytic unit involved in cellulose degradation. In oomycetes more than 90% of proteins are similar to CBEL in which CBM1 is associated with a non-catalytic PAN/Apple domain, known to interact with specific carbohydrates or proteins. Distinct Stramenopile genomes like diatoms and brown algae are devoid of CBM1 coding genes. A CBM1-PAN/Apple association 3D structural modeling was built allowing the identification of amino acid residues interacting with cellulose and suggesting the putative interaction of the PAN/Apple domain with another type of glucan. By Surface Plasmon Resonance experiments, we showed that CBEL binds to glycoproteins through galactose or N-acetyl-galactosamine motifs. CONCLUSIONS This study provides insight into the evolution and biological roles of CBM1-containing proteins from oomycetes. We show that while CBM1s from fungi and oomycetes are similar, they team up with different protein domains, either in proteins implicated in the degradation of plant cell wall components in the case of fungi or in proteins involved in adhesion to polysaccharidic substrates in the case of oomycetes. This work highlighted the unique role and evolution of CBM1 proteins in oomycete among the Stramenopile lineage.
Collapse
Affiliation(s)
- Mathieu Larroque
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Roland Barriot
- Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaire, Toulouse F-31000, France
- Centre National de la Recherche Scientifique; LMGM, Toulouse F-31000, France
| | - Arnaud Bottin
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Annick Barre
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
- Present address: Université de Toulouse, UPS, Laboratoire PHARMA-DEV IRD UMR 152, 35 Chemin des Maraîchers, Toulouse 31400, France
| | - Pierre Rougé
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
- Present address: Université de Toulouse, UPS, Laboratoire PHARMA-DEV IRD UMR 152, 35 Chemin des Maraîchers, Toulouse 31400, France
| | - Bernard Dumas
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Elodie Gaulin
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| |
Collapse
|
42
|
Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution. EUKARYOTIC CELL 2012; 11:1304-12. [PMID: 22923046 DOI: 10.1128/ec.00155-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.
Collapse
|
43
|
Adhikari BN, Savory EA, Vaillancourt B, Childs KL, Hamilton JP, Day B, Buell CR. Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis. PLoS One 2012; 7:e34954. [PMID: 22545095 PMCID: PMC3335828 DOI: 10.1371/journal.pone.0034954] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/08/2012] [Indexed: 11/29/2022] Open
Abstract
The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.
Collapse
Affiliation(s)
- Bishwo N. Adhikari
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Elizabeth A. Savory
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - John P. Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Brad Day
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|
44
|
Beakes GW, Glockling SL, Sekimoto S. The evolutionary phylogeny of the oomycete "fungi". PROTOPLASMA 2012; 249:3-19. [PMID: 21424613 DOI: 10.1007/s00709-011-0269-2] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 02/28/2011] [Indexed: 05/09/2023]
Abstract
Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate "superkingdom" clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum "Pseudofungi", which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main "saprolegnian" and "peronosporalean" lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host-pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic "saprolegnian line" is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.
Collapse
Affiliation(s)
- Gordon W Beakes
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | | | | |
Collapse
|
45
|
Abstract
Many destructive diseases of plants and animals are caused by oomycetes, a group of eukaryotic pathogens important to agricultural, ornamental, and natural ecosystems. Understanding the mechanisms underlying oomycete virulence and the genomic processes by which those mechanisms rapidly evolve is essential to developing effective long-term control measures for oomycete diseases. Several common mechanisms underlying oomycete virulence, including protein toxins and cell-entering effectors, have emerged from comparing oomycetes with different genome characteristics, parasitic lifestyles, and host ranges. Oomycete genomes display a strongly bipartite organization in which conserved housekeeping genes are concentrated in syntenic gene-rich blocks, whereas virulence genes are dispersed into highly dynamic, repeat-rich regions. There is also evidence that key virulence genes have been acquired by horizontal transfer from other eukaryotic and prokaryotic species.
Collapse
Affiliation(s)
- Rays H Y Jiang
- The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.
| | | |
Collapse
|
46
|
Rivas S, Genin S. A plethora of virulence strategies hidden behind nuclear targeting of microbial effectors. FRONTIERS IN PLANT SCIENCE 2011; 2:104. [PMID: 22639625 PMCID: PMC3355726 DOI: 10.3389/fpls.2011.00104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 12/09/2011] [Indexed: 05/24/2023]
Abstract
Plant immune responses depend on the ability to couple rapid recognition of the invading microbe to an efficient response. During evolution, plant pathogens have acquired the ability to deliver effector molecules inside host cells in order to manipulate cellular and molecular processes and establish pathogenicity. Following translocation into plant cells, microbial effectors may be addressed to different subcellular compartments. Intriguingly, a significant number of effector proteins from different pathogenic microorganisms, including viruses, oomycetes, fungi, nematodes, and bacteria, is targeted to the nucleus of host cells. In agreement with this observation, increasing evidence highlights the crucial role played by nuclear dynamics, and nucleocytoplasmic protein trafficking during a great variety of analyzed plant-pathogen interactions. Once in the nucleus, effector proteins are able to manipulate host transcription or directly subvert essential host components to promote virulence. Along these lines, it has been suggested that some effectors may affect histone packing and, thereby, chromatin configuration. In addition, microbial effectors may either directly activate transcription or target host transcription factors to alter their regular molecular functions. Alternatively, nuclear translocation of effectors may affect subcellular localization of their cognate resistance proteins in a process that is essential for resistance protein-mediated plant immunity. Here, we review recent progress in our field on the identification of microbial effectors that are targeted to the nucleus of host plant cells. In addition, we discuss different virulence strategies deployed by microbes, which have been uncovered through examination of the mechanisms that guide nuclear localization of effector proteins.
Collapse
Affiliation(s)
- Susana Rivas
- Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-MicroorganismesUMR 441, Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-MicroorganismesUMR 2594, Castanet-Tolosan, France
| | - Stéphane Genin
- Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-MicroorganismesUMR 441, Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-MicroorganismesUMR 2594, Castanet-Tolosan, France
| |
Collapse
|
47
|
Links MG, Holub E, Jiang RHY, Sharpe AG, Hegedus D, Beynon E, Sillito D, Clarke WE, Uzuhashi S, Borhan MH. De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes. BMC Genomics 2011; 12:503. [PMID: 21995639 PMCID: PMC3206522 DOI: 10.1186/1471-2164-12-503] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/13/2011] [Indexed: 11/28/2022] Open
Abstract
Background Albugo candida is a biotrophic oomycete that parasitizes various species of Brassicaceae, causing a disease (white blister rust) with remarkable convergence in behaviour to unrelated rusts of basidiomycete fungi. Results A recent genome analysis of the oomycete Hyaloperonospora arabidopsidis suggests that a reduction in the number of genes encoding secreted pathogenicity proteins, enzymes for assimilation of inorganic nitrogen and sulphur represent a genomic signature for the evolution of obligate biotrophy. Here, we report a draft reference genome of a major crop pathogen Albugo candida (another obligate biotrophic oomycete) with an estimated genome of 45.3 Mb. This is very similar to the genome size of a necrotrophic oomycete Pythium ultimum (43 Mb) but less than half that of H. arabidopsidis (99 Mb). Sequencing of A. candida transcripts from infected host tissue and zoosporangia combined with genome-wide annotation revealed 15,824 predicted genes. Most of the predicted genes lack significant similarity with sequences from other oomycetes. Most intriguingly, A. candida appears to have a much smaller repertoire of pathogenicity-related proteins than H. arabidopsidis including genes that encode RXLR effector proteins, CRINKLER-like genes, and elicitins. Necrosis and Ethylene inducing Peptides were not detected in the genome of A. candida. Putative orthologs of tat-C, a component of the twin arginine translocase system, were identified from multiple oomycete genera along with proteins containing putative tat-secretion signal peptides. Conclusion Albugo candida has a comparatively small genome amongst oomycetes, retains motility of sporangial inoculum, and harbours a much smaller repertoire of candidate effectors than was recently reported for H. arabidopsidis. This minimal gene repertoire could indicate a lack of expansion, rather than a reduction, in the number of genes that signify the evolution of biotrophy in oomycetes.
Collapse
Affiliation(s)
- Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2 Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Horner NR, Grenville-Briggs LJ, van West P. The oomycete Pythium oligandrum expresses putative effectors during mycoparasitism of Phytophthora infestans and is amenable to transformation. Fungal Biol 2011; 116:24-41. [PMID: 22208599 DOI: 10.1016/j.funbio.2011.09.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 01/22/2023]
Abstract
The oomycete Pythium oligandrum is a mycoparasitic biocontrol agent that is able to antagonise several plant pathogens, and can promote plant growth. In order to test the potential usefulness of P. oligandrum as a biocontrol agent against late blight disease caused by the oomycete Phytophthora infestans, we investigated the interaction between P. oligandrum and Ph. infestans using the green fluorescent protein (GFP) as a reporter gene. A CaCl(2) and polyethylene-glycol-based DNA transformation protocol was developed for P. oligandrum and transformants constitutively expressing GFP were produced. Up to 56 % of P. oligandrum transformants showed both antibiotic resistance and fluorescence. Mycoparasitic interactions, including coiling of P. oligandrum hyphae around Ph. infestans hyphae, were observed with fluorescent microscopy. To gain further insights into the nature of P. oligandrum mycoparasitism, we sequenced 2376 clones from cDNA libraries of P. oligandrum mycelium grown in vitro, or on heat-killed Ph. infestans mycelium as the sole nutrient source. 1219 consensus sequences were obtained including transcripts encoding glucanases, proteases, protease inhibitors, putative effectors and elicitors, which may play a role in mycoparasitism. This represents the first published expressed sequence tag (EST) resource for P. oligandrum and provides a platform for further molecular studies and comparative analysis in the Pythiales.
Collapse
Affiliation(s)
- Neil R Horner
- Aberdeen Oomycete Laboratory, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
| | | | | |
Collapse
|
49
|
Grenville-Briggs L, Gachon CMM, Strittmatter M, Sterck L, Küpper FC, van West P. A molecular insight into algal-oomycete warfare: cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii. PLoS One 2011; 6:e24500. [PMID: 21935414 PMCID: PMC3174193 DOI: 10.1371/journal.pone.0024500] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 08/11/2011] [Indexed: 02/01/2023] Open
Abstract
Brown algae are the predominant primary producers in coastal habitats, and like land plants are subject to disease and parasitism. Eurychasma dicksonii is an abundant, and probably cosmopolitan, obligate biotrophic oomycete pathogen of marine brown algae. Oomycetes (or water moulds) are pathogenic or saprophytic non-photosynthetic Stramenopiles, mostly known for causing devastating agricultural and aquacultural diseases. Whilst molecular knowledge is restricted to crop pathogens, pathogenic oomycetes actually infect hosts from most eukaryotic lineages. Molecular evidence indicates that Eu. dicksonii belongs to the most early-branching oomycete clade known so far. Therefore Eu. dicksonii is of considerable interest due to its presumed environmental impact and phylogenetic position. Here we report the first large scale functional molecular data acquired on the most basal oomycete to date. 9873 unigenes, totalling over 3.5 Mb of sequence data, were produced from Sanger-sequenced and pyrosequenced EST libraries of infected Ectocarpus siliculosus. 6787 unigenes (70%) were of algal origin, and 3086 (30%) oomycete origin. 57% of Eu. dicksonii sequences had no similarity to published sequence data, indicating that this dataset is largely unique. We were unable to positively identify sequences belonging to the RXLR and CRN groups of oomycete effectors identified in higher oomycetes, however we uncovered other unique pathogenicity factors. These included putative algal cell wall degrading enzymes, cell surface proteins, and cyclophilin-like proteins. A first look at the host response to infection has also revealed movement of the host nucleus to the site of infection as well as expression of genes responsible for strengthening the cell wall, and secretion of proteins such as protease inhibitors. We also found evidence of transcriptional reprogramming of E. siliculosus transposable elements and of a viral gene inserted in the host genome.
Collapse
|
50
|
Abstract
Fungal and oomycete pathogens cause many destructive diseases of plants and important diseases of humans and other animals. Fungal and oomycete plant pathogens secrete numerous effector proteins that can enter inside host cells to condition susceptibility. Until recently it has been unknown if these effectors enter via pathogen-encoded translocons or via pathogen-independent mechanisms. Here we review recent evidence that many fungal and oomycete effectors enter via receptor-mediated endocytosis, and can do so in the absence of the pathogen. Surprisingly, a large number of these effectors utilize cell surface phosphatidyinositol-3-phosphate (PI-3-P) as a receptor, a molecule previously known only inside cells. Binding of effectors to PI-3-P appears to be mediated by the cell entry motif RXLR in oomycetes, and by diverse RXLR-like variants in fungi. PI-3-P appears to be present on the surface of animal cells also, suggesting that it may mediate entry of effectors of fungal and oomycete animal pathogens, for example, RXLR effectors found in the oomycete fish pathogen, Saprolegnia parasitica. Reagents that can block PI-3-P-mediated entry have been identified, suggesting new therapeutic strategies.
Collapse
Affiliation(s)
- Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061-0477, USA
| | | |
Collapse
|