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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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O’Rourke JA, Graham MA. Coupling VIGS with Short- and Long-Term Stress Exposure to Understand the Fiskeby III Iron Deficiency Stress Response. Int J Mol Sci 2022; 24:ijms24010647. [PMID: 36614091 PMCID: PMC9820625 DOI: 10.3390/ijms24010647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Yield loss due to abiotic stress is an increasing problem in agriculture. Soybean is a major crop for the upper Midwestern United States and calcareous soils exacerbate iron deficiency for growers, resulting in substantial yield losses. Fiskeby III is a soybean variety uniquely resistant to a variety of abiotic stresses, including iron deficiency. Previous studies identified a MATE transporter (Glyma.05G001700) associated with iron stress tolerance in Fiskeby III. To understand the function of this gene in the Fiskeby III response to iron deficiency, we coupled its silencing using virus-induced gene silencing with RNAseq analyses at two timepoints. Analyses of these data confirm a role for the MATE transporter in Fiskeby III iron stress responses. Further, they reveal that Fiskeby III induces transcriptional reprogramming within 24 h of iron deficiency stress, confirming that like other soybean varieties, Fiskeby III is able to quickly respond to stress. However, Fiskeby III utilizes novel genes and pathways in its iron deficiency response. Identifying and characterizing these genes and pathways in Fiskeby III provides novel targets for improving abiotic stress tolerance in elite soybean lines.
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3
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Wang S, Wang S, Li M, Su Y, Sun Z, Ma H. Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches' broom disease. BMC PLANT BIOLOGY 2022; 22:291. [PMID: 35701735 PMCID: PMC9199210 DOI: 10.1186/s12870-022-03672-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 05/27/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Nerium indicum Mill. is an ornamental plant that is found in parks, riversides, lakesides, and scenic areas in China and other parts of the world. Our recent survey indicated the prevalence of witches' broom disease (WBD) in Guangdong, China. To find out the possible defense strategies against WBD, we performed a MiSeq based ITS sequencing to identify the possible casual organism, then did a de novo transcriptome sequencing and metabolome profiling in the phloem and stem tip of N. indicum plants suffering from WBD compared to healthy ones. RESULTS The survey showed that Wengyuen county and Zengcheng district had the highest disease incidence rates. The most prevalent microbial species in the diseased tissues was Cophinforma mamane. The transcriptome sequencing resulted in the identification of 191,224 unigenes of which 142,396 could be annotated. There were 19,031 and 13,284 differentially expressed genes (DEGs) between diseased phloem (NOWP) and healthy phloem (NOHP), and diseased stem (NOWS) and healthy stem (NOHS), respectively. The DEGs were enriched in MAPK-signaling (plant), plant-pathogen interaction, plant-hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, linoleic acid and α-linoleic acid metabolism pathways. Particularly, we found that N. indicum plants activated the phytohormone signaling, MAPK-signaling cascade, defense related proteins, and the biosynthesis of phenylpropanoids and flavonoids as defense responses to the pathogenic infection. The metabolome profiling identified 586 metabolites of which 386 and 324 metabolites were differentially accumulated in NOHP vs NOWP and NOHS and NOWS, respectively. The differential accumulation of metabolites related to phytohormone signaling, linoleic acid metabolism, phenylpropanoid and flavonoid biosynthesis, nicotinate and nicotinamide metabolism, and citrate cycle was observed, indicating the role of these pathways in defense responses against the pathogenic infection. CONCLUSION Our results showed that Guangdong province has a high incidence of WBD in most of the surveyed areas. C. mamane is suspected to be the causing pathogen of WBD in N. indicum. N. indicum initiated the MAPK-signaling cascade and phytohormone signaling, leading to the activation of pathogen-associated molecular patterns and hypersensitive response. Furthermore, N. indicum accumulated high concentrations of phenolic acids, coumarins and lignans, and flavonoids under WBD. These results provide scientific tools for the formulation of control strategies of WBD in N. indicum.
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Affiliation(s)
- Shengjie Wang
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Shengkun Wang
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Ming Li
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yuhang Su
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhan Sun
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Haibin Ma
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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Li X, Li S, Liu Y, He Q, Liu W, Lin C, Miao W. HbLFG1, a Rubber Tree ( Hevea brasiliensis) Lifeguard Protein, Can Facilitate Powdery Mildew Infection by Suppressing Plant Immunity. PHYTOPATHOLOGY 2021; 111:1648-1659. [PMID: 34047620 DOI: 10.1094/phyto-08-20-0362-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Powdery mildew causes substantial losses in crop and economic plant yields worldwide. Although powdery mildew infection of rubber trees (Hevea brasiliensis), caused by the biotrophic fungus Erysiphe quercicola, severely threatens natural rubber production, little is known about the mechanism by which E. quercicola adapts to H. brasiliensis to invade the host plant. In barley and Arabidopsis thaliana, lifeguard (LFG) proteins, which have topological similarity to BAX INHIBITOR-1, are involved in host plant susceptibility to powdery mildew infection. In this study, we characterized an H. brasiliensis LFG protein (HbLFG1) with a focus on its function in regulating defense against powdery mildew. HbLFG1 gene expression was found to be upregulated during E. quercicola infection. HbLFG1 showed conserved functions in cell death inhibition and membrane localization. Expression of HbLFG1 in Nicotiana benthamiana leaves and A. thaliana Col-0 was demonstrated to significantly suppress callose deposition induced by conserved pathogen-associated molecular patterns chitin and flg22. Furthermore, we found that overexpression of HbLFG1 in H. brasiliensis mesophyll protoplasts significantly suppressed the chitin-induced burst of reactive oxygen species. Although A. thaliana Col-0 and E. quercicola displayed an incompatible interaction, Col-0 transformants overexpressing HbLFG1 were shown to be susceptible to E. quercicola. Collectively, the findings of this study provide evidence that HbLFG1 acts as a negative regulator of plant immunity that facilitates E. quercicola infection in H. brasiliensis.
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Affiliation(s)
- Xiao Li
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Sipeng Li
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Yuhan Liu
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Qiguang He
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Wenbo Liu
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Chunhua Lin
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Weiguo Miao
- College of Plant Protection, Hainan University, Haikou 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
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McCollum C, Engelhardt S, Weiss L, Hückelhoven R. ROP INTERACTIVE PARTNER b Interacts with RACB and Supports Fungal Penetration into Barley Epidermal Cells. PLANT PHYSIOLOGY 2020; 184:823-836. [PMID: 32665335 PMCID: PMC7536699 DOI: 10.1104/pp.20.00742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Rho of Plants (ROP) G-proteins are key components of cell polarization processes in plant development. The barley (Hordeum vulgare) ROP protein RACB is a susceptibility factor in the interaction of barley with the barley powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh). RACB also drives polar cell development, and this function might be coopted during the formation of fungal haustoria in barley epidermal cells. To understand RACB signaling during the interaction of barley with Bgh, we searched for potential downstream interactors of RACB. Here, we show that ROP INTERACTIVE PARTNER b (RIPb; synonym: INTERACTOR OF CONSTITUTIVE ACTIVE ROP b) directly interacts with RACB in yeast and in planta. Overexpression of RIPb supports the susceptibility of barley to Bgh RIPb further interacts with itself at microtubules. However, the interaction with activated RACB largely takes place at the plasma membrane. Both RIPb and RACB are recruited to the site of fungal attack around the neck of developing haustoria, suggesting locally enhanced ROP activity. We further assigned different functions to different domains of the RIPb protein. The N-terminal coiled-coil CC1 domain is required for microtubule localization, while the C-terminal coiled-coil CC2 domain is sufficient to interact with RACB and to fulfill a function in susceptibility at the plasma membrane. Hence, RIPb appears to be localized at microtubules and is then recruited by activated RACB for a function at the plasma membrane during formation of the haustorial complex.
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Affiliation(s)
- Christopher McCollum
- Phytopathology, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Stefan Engelhardt
- Phytopathology, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Lukas Weiss
- Phytopathology, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Ralph Hückelhoven
- Phytopathology, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
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Kutschera A, Dawid C, Gisch N, Schmid C, Raasch L, Gerster T, Schäffer M, Smakowska-Luzan E, Belkhadir Y, Vlot AC, Chandler CE, Schellenberger R, Schwudke D, Ernst RK, Dorey S, Hückelhoven R, Hofmann T, Ranf S. Bacterial medium-chain 3-hydroxy fatty acid metabolites trigger immunity in
Arabidopsis
plants. Science 2019; 364:178-181. [DOI: 10.1126/science.aau1279] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 01/02/2019] [Accepted: 03/12/2019] [Indexed: 04/09/2023]
Abstract
A fatty acid triggers immune responses
Plants and animals respond to the microbial communities around them, whether in antagonistic or mutualistic ways. Some of these interactions are mediated by lipopolysaccharide—a large, complex, and irregular molecule on the surface of most Gram-negative bacteria. Studying the small mustard plant
Arabidopsis
, Kutschera
et al.
identified a 3-hydroxydecanoyl chain as the structural element sensed by the plant's lectin receptor kinase. Indeed, synthetic 3-hydroxydecanoic acid alone was sufficient to produce a response. A small microbial metabolite may thus suffice to trigger immune responses.
Science
, this issue p.
178
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Affiliation(s)
- Alexander Kutschera
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Christian Schmid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Lars Raasch
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Tim Gerster
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Milena Schäffer
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Elwira Smakowska-Luzan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Youssef Belkhadir
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - A. Corina Vlot
- Helmholtz Zentrum Muenchen, Department of Environmental Science, Institute of Biochemical Plant Pathology, 85764 Neuherberg, Germany
| | - Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Romain Schellenberger
- RIBP-EA 4707, SFR Condorcet-FR CNRS 3417, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Stéphan Dorey
- RIBP-EA 4707, SFR Condorcet-FR CNRS 3417, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Stefanie Ranf
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
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Gamboa-Tuz SD, Pereira-Santana A, Zhao T, Schranz ME, Castano E, Rodriguez-Zapata LC. New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants. Mol Phylogenet Evol 2018; 126:266-278. [PMID: 29702215 DOI: 10.1016/j.ympev.2018.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research.
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Affiliation(s)
- Samuel D Gamboa-Tuz
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205 Yucatan, Mexico
| | | | - Tao Zhao
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Enrique Castano
- Biochemistry and Molecular Biology Unit, Centro de Investigacion Cientifica de Yucatan, 97205 Yucatan, Mexico
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Ospanova AK, Kaliyeva AB, Anuarova LE, Bazargaliyeva AA, Yernazarova GI, Ramazanova AA, Sekenov IE. Mildew of oleaster ( Elaeagnus oxycarpa Schlecht.) registered in large industrial cities (Pavlodar, Aksu, Ekibastuz) of the Pavlodar region. Saudi J Biol Sci 2018; 25:446-451. [PMID: 29686509 PMCID: PMC5910644 DOI: 10.1016/j.sjbs.2016.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 08/16/2016] [Accepted: 09/04/2016] [Indexed: 11/11/2022] Open
Abstract
Purpose: Vegetation plays a very important role in industrial regions in terms of not only air purification, but also oxygen enrichment, air humidity, and city aesthetics. The paper presents the authors’ study of oleaster mildew during 2012–2013 in the cities of Pavlodar, Ekibastuz, and Aksu. Method: The species composition of mildew, patterns of its growth and reproduction, seasonal dynamics, and the level of trees infection according to a six-score scale were determined. Result: Three cultivars of mildew from three genera were registered. The species composition of mildew of oleaster is studied for the first time in large industrial cities of the Pavlodar region. The comparative analysis of the systematic structure of phytopathogenic fungi was followed by the study of the micro flora of green planting in megalopolises. The seasonal dynamics of growth, development, and reproduction was determined. The impact of pests on host-plants was studied. Conclusion: Timely diagnosis and localization of disease outbreak increases the likelihood of successful treatment and saving of plants.
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Guo K, Wang W, Fan W, Wang Z, Zhu M, Tang X, Wu W, Yang X, Shao X, Sun Y, Zhang W, Li X. Arabidopsis GAAP1 and GAAP3 Modulate the Unfolded Protein Response and the Onset of Cell Death in Response to ER Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:348. [PMID: 29616060 PMCID: PMC5864889 DOI: 10.3389/fpls.2018.00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/01/2018] [Indexed: 05/03/2023]
Abstract
The function of human Golgi antiapoptotic proteins (GAAPs) resembles that of BAX inhibitor-1, with apoptosis inhibition triggered by intrinsic and extrinsic stimuli. However, little is known about the function of GAAP-related proteins in plants. Here, we studied Arabidopsis GAAP1 and GAAP3 and found that they were localized on the cellular membrane, including the endoplasmic reticulum (ER) membrane. The function of GAAP1/GAAP3 in ER-stress response was tested, and results showed that single or double mutation in GAAP1 and GAAP3 reduced plant survival and enhanced cell death under ER stress. The expression of both genes was induced by various abiotic stress signals. Quantitative real-time polymerase chain reaction analysis showed that GAAP1/GAAP3 level affected the expression pattern of the unfolded-protein response (UPR) signaling pathway genes upon prolonged ER stress. The mutation in both GAAP1 and GAAP3 genes promoted and enhanced UPR signaling when confronted with mild ER stress. Moreover, GAAP1/GAAP3 inhibited cell death caused by ER stress and promoted plant-growth recovery by turning down inositol-requiring enzyme 1 (IRE1) signaling after ER stress had been relieved. Co-immunoprecipitation (Co-Ip) and BiFC assays showed that GAAP1/GAAP3 interacted with IRE1. These data suggested that GAAP1/GAAP3 played dual roles in the negative regulation of IRE1 activity and anti-programmed cell death.
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Abstract
Fungi are among the dominant causal agents of plant diseases. To colonize plants and cause disease, pathogenic fungi use diverse strategies. Some fungi kill their hosts and feed on dead material (necrotrophs), while others colonize the living tissue (biotrophs). For successful invasion of plant organs, pathogenic development is tightly regulated and specialized infection structures are formed. To further colonize hosts and establish disease, fungal pathogens deploy a plethora of virulence factors. Depending on the infection strategy, virulence factors perform different functions. While basically all pathogens interfere with primary plant defense, necrotrophs secrete toxins to kill plant tissue. In contrast, biotrophs utilize effector molecules to suppress plant cell death and manipulate plant metabolism in favor of the pathogen. This article provides an overview of plant pathogenic fungal species and the strategies they use to cause disease.
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11
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Martínez-Cruz J, Romero D, de Vicente A, Pérez-García A. Transformation of the cucurbit powdery mildew pathogen Podosphaera xanthii by Agrobacterium tumefaciens. THE NEW PHYTOLOGIST 2017; 213:1961-1973. [PMID: 27864969 DOI: 10.1111/nph.14297] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
The obligate biotrophic fungal pathogen Podosphaera xanthii is the main causal agent of powdery mildew in cucurbit crops all over the world. A major limitation of molecular studies of powdery mildew fungi (Erysiphales) is their genetic intractability. In this work, we describe a robust method based on the promiscuous transformation ability of Agrobacterium tumefaciens for reliable transformation of P. xanthii. The A. tumefaciens-mediated transformation (ATMT) system yielded transformants of P. xanthii with diverse transferred DNA (T-DNA) constructs. Analysis of the resultant transformants showed the random integration of T-DNA into the P. xanthii genome. The integrations were maintained in successive generations in the presence of selection pressure. Transformation was found to be transient, because in the absence of selection agent, the introduced genetic markers were lost due to excision of T-DNA from the genome. The ATMT system represents a potent tool for genetic manipulation of P. xanthii and will likely be useful for studying other biotrophic fungi. We hope that this method will contribute to the development of detailed molecular studies of the intimate interaction established between powdery mildew fungi and their host plants.
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Affiliation(s)
- Jesús Martínez-Cruz
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
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Kissen R, Øverby A, Winge P, Bones AM. Allyl-isothiocyanate treatment induces a complex transcriptional reprogramming including heat stress, oxidative stress and plant defence responses in Arabidopsis thaliana. BMC Genomics 2016; 17:740. [PMID: 27639974 PMCID: PMC5027104 DOI: 10.1186/s12864-016-3039-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/24/2016] [Indexed: 01/30/2023] Open
Abstract
Background Isothiocyanates (ITCs) are degradation products of the plant secondary metabolites glucosinolates (GSLs) and are known to affect human health as well as plant herbivores and pathogens. To investigate the processes engaged in plants upon exposure to isothiocyanate we performed a genome scale transcriptional profiling of Arabidopsis thaliana at different time points in response to an exogenous treatment with allyl-isothiocyanate. Results The treatment triggered a substantial response with the expression of 431 genes affected (P < 0.05 and log2 ≥ 1 or ≤ -1) already after 30 min and that of 3915 genes affected after 9 h of exposure, most of the affected genes being upregulated. These are involved in a considerable number of different biological processes, some of which are described in detail: glucosinolate metabolism, sulphate uptake and assimilation, heat stress response, oxidative stress response, elicitor perception, plant defence and cell death mechanisms. Conclusion Exposure of Arabidopsis thaliana to vapours of allyl-isothiocyanate triggered a rapid and substantial transcriptional response affecting numerous biological processes. These include multiple stress stimuli such as heat stress response and oxidative stress response, cell death and sulphur secondary defence metabolism. Hence, effects of isothiocyanates on plants previously reported in the literature were found to be regulated at the gene expression level. This opens some avenues for further investigations to decipher the molecular mechanisms underlying the effects of isothiocyanates on plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3039-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ralph Kissen
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Anders Øverby
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.,Present address: Center for Clinical Pharmacy and Clinical Sciences, School of Pharmaceutical Sciences, Kitasato University, Minato-ku, Tokyo, Japan
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
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Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK. Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress. PLoS One 2016; 11:e0152294. [PMID: 27032112 PMCID: PMC4816275 DOI: 10.1371/journal.pone.0152294] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/12/2016] [Indexed: 12/29/2022] Open
Abstract
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.
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Affiliation(s)
- Gyoungju Nah
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
| | - Moonsub Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - Do-Soon Kim
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
| | - A. Lane Rayburn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - Thomas Voigt
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - D. K. Lee
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
- * E-mail:
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Inada N, Higaki T, Hasezawa S. Nuclear Function of Subclass I Actin-Depolymerizing Factor Contributes to Susceptibility in Arabidopsis to an Adapted Powdery Mildew Fungus. PLANT PHYSIOLOGY 2016; 170:1420-34. [PMID: 26747284 PMCID: PMC4775110 DOI: 10.1104/pp.15.01265] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/05/2016] [Indexed: 05/19/2023]
Abstract
Actin-depolymerizing factors (ADFs) are conserved proteins that function in regulating the structure and dynamics of actin microfilaments in eukaryotes. In this study, we present evidence that Arabidopsis (Arabidopsis thaliana) subclass I ADFs, particularly ADF4, functions as a susceptibility factor for an adapted powdery mildew fungus. The null mutant of ADF4 significantly increased resistance against the adapted powdery mildew fungus Golovinomyces orontii. The degree of resistance was further enhanced in transgenic plants in which the expression of all subclass I ADFs (i.e. ADF1-ADF4) was suppressed. Microscopic observations revealed that the enhanced resistance of adf4 and ADF1-4 knockdown plants (ADF1-4Ri) was associated with the accumulation of hydrogen peroxide and cell death specific to G. orontii-infected cells. The increased resistance and accumulation of hydrogen peroxide in ADF1-4Ri were suppressed by the introduction of mutations in the salicylic acid- and jasmonic acid-signaling pathways but not by a mutation in the ethylene-signaling pathway. Quantification by microscopic images detected an increase in the level of actin microfilament bundling in ADF1-4Ri but not in adf4 at early G. orontii infection time points. Interestingly, complementation analysis revealed that nuclear localization of ADF4 was crucial for susceptibility to G. orontii. Based on its G. orontii-infected-cell-specific phenotype, we suggest that subclass I ADFs are susceptibility factors that function in a direct interaction between the host plant and the powdery mildew fungus.
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Affiliation(s)
- Noriko Inada
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Takumi Higaki
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Seiichiro Hasezawa
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
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Reiner T, Hoefle C, Huesmann C, Ménesi D, Fehér A, Hückelhoven R. The Arabidopsis ROP-activated receptor-like cytoplasmic kinase RLCK VI_A3 is involved in control of basal resistance to powdery mildew and trichome branching. PLANT CELL REPORTS 2015; 34:457-468. [PMID: 25487440 DOI: 10.1007/s00299-014-1725-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 06/04/2023]
Abstract
The Arabidopsis receptor-like cytoplasmic kinase AtRLCK VI_A3 is activated by AtROPs and is involved in trichome branching and pathogen interaction. Receptor-like cytoplasmic kinases (RLCKs) belong to the large superfamily of receptor-like kinases, which are involved in a variety of cellular processes like plant growth, development and immune responses. Recent studies suggest that RLCKs of the VI_A subfamily are possible downstream effectors of the small monomeric G proteins of the plant-specific Rho family, called 'Rho of plants' (RAC/ROPs). Here, we describe Arabidopsis thaliana AtRLCK VI_A3 as a molecular interactor of AtROPs. In Arabidopsis epidermal cells, transient co-expression of plasma membrane located constitutively activated (CA) AtROP4 or CA AtROP6 resulting in the recruitment of green fluorescent protein-tagged AtRLCK VI_A3 to the cell periphery. Intrinsic kinase activity of AtRLCK VI_A3 was enhanced in the presence of CA AtROP6 in vitro and further suggested a functional interaction between the proteins. In the interaction of the biotrophic powdery mildew fungus Erysiphe cruciferarum (E. cruciferarum) and its host plant Arabidopsis, Atrlck VI_A3 mutant lines supported enhanced fungal reproduction. Furthermore Atrlck VI_A3 mutant lines showed slightly reduced size and an increase in trichome branch number compared to wild-type plants. In summary, our data suggest a role of the AtROP-regulated AtRLCK VI_A3 in basal resistance to E. cruciferarum as well as in plant growth and cellular differentiation during trichome morphogenesis. Results are discussed in the context of literature suggesting a function of RAC/ROPs in both resistance and susceptibility to pathogen infection.
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Affiliation(s)
- Tina Reiner
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann Straße 2, 85350, Freising-Weihenstephan, Germany
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Mariotti M, Smith TF, Sudmant PH, Goldberger G. Pseudogenization of testis-specific Lfg5 predates human/Neanderthal divergence. J Hum Genet 2014; 59:288-91. [PMID: 24599118 DOI: 10.1038/jhg.2014.6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/30/2013] [Accepted: 01/06/2014] [Indexed: 01/06/2023]
Abstract
Recent reviews discussed the critical roles of apoptosis in human spermatogenesis and infertility. These reviews highlight the FasL-induced caspase cascade in apoptosis lending importance to our discovery of the pseudogene status of the Lfg5 gene in modern humans, Neanderthal and the Denisovan. This gene is a member of the ancient and highly conserved apoptosis Lifeguard family. This pseudogenization is the result of a premature stop codon at the 3'-end of exon 8 not found in any other ortholog. With the current exception of the domesticated bovine and buffalo, Lfg5's expression in mammals is testis-specific. A full analysis of this gene, its phylogenetic context and its recent hominin changes suggest its inactivation was likely under selection in human evolution.
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Affiliation(s)
| | - Temple F Smith
- Department of BioMedical Engineering, Boston University, Boston, MA, USA
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gabriel Goldberger
- Department of Psychiatry, Beth Israel Deaconess Medical Center, BSHC, Boston, MA, USA
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Abstract
To confer resistance against pathogens and pests in plants, typically dominant resistance genes are deployed. However, because resistance is based on recognition of a single pathogen-derived molecular pattern, these narrow-spectrum genes are usually readily overcome. Disease arises from a compatible interaction between plant and pathogen. Hence, altering a plant gene that critically facilitates compatibility could provide a more broad-spectrum and durable type of resistance. Here, such susceptibility (S) genes are reviewed with a focus on the mechanisms underlying loss of compatibility. We distinguish three groups of S genes acting during different stages of infection: early pathogen establishment, modulation of host defenses, and pathogen sustenance. The many examples reviewed here show that S genes have the potential to be used in resistance breeding. However, because S genes have a function other than being a compatibility factor for the pathogen, the side effects caused by their mutation demands a one-by-one assessment of their usefulness for application.
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Ellinger D, Voigt CA. The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration. FRONTIERS IN PLANT SCIENCE 2014; 5:270. [PMID: 24995012 PMCID: PMC4061529 DOI: 10.3389/fpls.2014.00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 05/08/2023]
Abstract
Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant-pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant-pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.
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Affiliation(s)
| | - Christian A. Voigt
- *Correspondence: Christian A. Voigt, Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany e-mail:
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