51
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Receptor kinases in plant responses to herbivory. Curr Opin Biotechnol 2021; 70:143-150. [PMID: 34023544 DOI: 10.1016/j.copbio.2021.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 01/21/2023]
Abstract
Plants have the ability to detect and respond to biotic stresses. They contain pattern recognition receptors (PRRs) that specifically recognize conserved molecules from their enemies and activate immune responses. In this review, I discuss recent efforts to discover PRRs for herbivory-associated cues that originate from oral secretions, eggs, damaged plant cells or secondary endogenous signals. Although several potential PRRs have been identified and shown to confer resistance to insects, proof of direct binding to a ligand is scarce and there are still many uncharacterized ligand-receptor pairs. However, several studies suggest that, like for microbial pathogens, plants use similar PRR complexes to detect herbivory.
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52
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Pereira Mendes M, Hickman R, Van Verk MC, Nieuwendijk NM, Reinstädler A, Panstruga R, Pieterse CMJ, Van Wees SCM. A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance. PLANTA 2021; 253:102. [PMID: 33856567 PMCID: PMC8049917 DOI: 10.1007/s00425-021-03606-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/24/2021] [Indexed: 06/01/2023]
Abstract
Overexpression of pathogen-induced cysteine-rich transmembrane proteins (PCMs) in Arabidopsis thaliana enhances resistance against biotrophic pathogens and stimulates hypocotyl growth, suggesting a potential role for PCMs in connecting both biological processes. Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Using RNA-seq time series data of Arabidopsis thaliana leaves treated with SA, we identified a largely uncharacterized SA-responsive gene family of eight members that are all activated in response to various pathogens or their immune elicitors and encode small proteins with cysteine-rich transmembrane domains. Based on their nucleotide similarity and chromosomal position, the designated Pathogen-induced Cysteine-rich transMembrane protein (PCM) genes were subdivided into three subgroups consisting of PCM1-3 (subgroup I), PCM4-6 (subgroup II), and PCM7-8 (subgroup III). Of the PCM genes, only PCM4 (also known as PCC1) has previously been implicated in plant immunity. Transient expression assays in Nicotiana benthamiana indicated that most PCM proteins localize to the plasma membrane. Ectopic overexpression of the PCMs in Arabidopsis thaliana resulted in all eight cases in enhanced resistance against the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Additionally, overexpression of PCM subgroup I genes conferred enhanced resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. The PCM-overexpression lines were found to be also affected in the expression of genes related to light signaling and development, and accordingly, PCM-overexpressing seedlings displayed elongated hypocotyl growth. These results point to a function of PCMs in both disease resistance and photomorphogenesis, connecting both biological processes, possibly via effects on membrane structure or activity of interacting proteins at the plasma membrane.
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Affiliation(s)
- Marciel Pereira Mendes
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
| | - Richard Hickman
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
- Bioinformatics, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
| | - Nicole M Nieuwendijk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
| | - Anja Reinstädler
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands.
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53
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Ogawa D, Suzuki Y, Yokoo T, Katoh E, Teruya M, Muramatsu M, Ma JF, Yoshida Y, Isaji S, Ogo Y, Miyao M, Kim JM, Kojima M, Takebayashi Y, Sakakibara H, Takeda S, Okada K, Mori N, Seki M, Habu Y. Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice. Sci Rep 2021; 11:6280. [PMID: 33737547 PMCID: PMC7973560 DOI: 10.1038/s41598-021-85355-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/18/2021] [Indexed: 01/18/2023] Open
Abstract
Conferring drought resistant traits to crops is one of the major aims of current breeding programs in response to global climate changes. We previously showed that exogenous application of acetic acid to roots of various plants could induce increased survivability under subsequent drought stress conditions, but details of the metabolism of exogenously applied acetic acid, and the nature of signals induced by its application, have not been unveiled. In this study, we show that rice rapidly induces jasmonate signaling upon application of acetic acid, resulting in physiological changes similar to those seen under drought. The major metabolite of the exogenously applied acetic acid in xylem sap was determined as glutamine-a common and abundant component of xylem sap-indicating that acetic acid is not the direct agent inducing the observed physiological responses in shoots. Expression of drought-responsive genes in shoot under subsequent drought conditions was attenuated by acetic acid treatment. These data suggest that acetic acid activates root-to-shoot jasmonate signals that partially overlap with those induced by drought, thereby conferring an acclimated state on shoots prior to subsequent drought.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan.,Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8517, Japan
| | - Yuya Suzuki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan
| | - Takayuki Yokoo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan
| | - Etsuko Katoh
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, 305-8517, Japan
| | - Miyu Teruya
- Biotechnology Research Center, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Masayuki Muramatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Yuri Yoshida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan
| | - Shunsaku Isaji
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuko Ogo
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8517, Japan
| | - Mitsue Miyao
- Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Mikiko Kojima
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yumiko Takebayashi
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Hitoshi Sakakibara
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Shin Takeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan.,Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Naoki Mori
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.,Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Yoshiki Habu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan.
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54
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Zarattini M, Farjad M, Launay A, Cannella D, Soulié MC, Bernacchia G, Fagard M. Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1020-1033. [PMID: 33188434 PMCID: PMC7904152 DOI: 10.1093/jxb/eraa531] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/10/2020] [Indexed: 05/03/2023]
Abstract
Current environmental and climate changes are having a pronounced influence on the outcome of plant-pathogen interactions, further highlighting the fact that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization together with primary and specialized metabolism are affected by environmental constraints, and these combine to make an individual plant either a more or less suitable host for a given pathogen. In addition, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, and in water and mineral nutrient availability affect the expression of plant defense genes. The expression of virulence genes, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. In this review, we summarize our current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We also perform a metadata analysis of four different combinations of abiotic and biotic stresses, which identifies 197 common modulated genes with strong enrichment in Gene Ontology terms related to defense . We also describe the multistress-specific responses of selected defense-related genes.
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Affiliation(s)
- Marco Zarattini
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- PhotoBioCatalysis Unit – Crop Production and Biostimulation Lab (CPBL), Interfaculty School of Bioengineers, Université Libre de Bruxelles (ULB), CP150, Avenue F.D. Roosevelt 50, Brussels, Belgium
| | - Mahsa Farjad
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Alban Launay
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - David Cannella
- PhotoBioCatalysis Unit – Crop Production and Biostimulation Lab (CPBL), Interfaculty School of Bioengineers, Université Libre de Bruxelles (ULB), CP150, Avenue F.D. Roosevelt 50, Brussels, Belgium
| | - Marie-Christine Soulié
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Sorbonne Universités, UPMC Univ. Paris 06, UFR 927, 4 place Jussieu, Paris, France
| | - Giovanni Bernacchia
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara, Italy
| | - Mathilde Fagard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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55
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Rasul F, Gupta S, Olas JJ, Gechev T, Sujeeth N, Mueller-Roeber B. Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis. Int J Mol Sci 2021; 22:1469. [PMID: 33540571 PMCID: PMC7867171 DOI: 10.3390/ijms22031469] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Drought represents a major threat to plants in natural ecosystems and agricultural settings. The biostimulant Super Fifty (SF), produced from the brown alga Ascophyllum nodosum, enables ecologically friendly stress mitigation. We investigated the physiological and whole-genome transcriptome responses of Arabidopsis thaliana to drought stress after a treatment with SF. SF strongly decreased drought-induced damage. Accumulation of reactive oxygen species (ROS), which typically stifle plant growth during drought, was reduced in SF-primed plants. Relative water content remained high in SF-treated plants, whilst ion leakage, a measure of cell damage, was reduced compared to controls. Plant growth requires a functional shoot apical meristem (SAM). Expression of a stress-responsive negative growth regulator, RESPONSIVE TO DESICCATION 26 (RD26), was repressed by SF treatment at the SAM, consistent with the model that SF priming maintains the function of the SAM during drought stress. Accordingly, expression of the cell cycle marker gene HISTONE H4 (HIS4) was maintained at the SAMs of SF-primed plants, revealing active cell cycle progression after SF priming during drought. In accordance with this, CYCP2;1, which promotes meristem cell division, was repressed by drought but enhanced by SF. SF also positively affected stomatal behavior to support the tolerance to drought stress. Collectively, our data show that SF priming mitigates multiple cellular processes that otherwise impair plant growth under drought stress, thereby providing a knowledge basis for future research on crops.
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Affiliation(s)
- Fiaz Rasul
- Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany; (F.R.); (S.G.); (J.J.O.)
- BioAtlantis Ltd., Clash Industrial Estate, V92 RWV5 Tralee, Ireland
| | - Saurabh Gupta
- Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany; (F.R.); (S.G.); (J.J.O.)
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Justyna Jadwiga Olas
- Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany; (F.R.); (S.G.); (J.J.O.)
| | - Tsanko Gechev
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria;
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria
| | | | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany; (F.R.); (S.G.); (J.J.O.)
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria;
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56
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O’Rourke JA, Graham MA. Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean. Int J Mol Sci 2021; 22:1252. [PMID: 33513952 PMCID: PMC7866191 DOI: 10.3390/ijms22031252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.
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Affiliation(s)
- Jamie A. O’Rourke
- Corn Insects and Crop Genetics Research Unit, USDA—Agricultural Research Service, Ames, IA 50010, USA;
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57
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Martín G, Márquez Y, Mantica F, Duque P, Irimia M. Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Genome Biol 2021; 22:35. [PMID: 33446251 PMCID: PMC7807721 DOI: 10.1186/s13059-020-02258-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. RESULTS We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. CONCLUSIONS Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.
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Affiliation(s)
- Guiomar Martín
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.
| | - Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain. .,Universitat Pompeu Fabra, Dr. Aiguader, 88, Barcelona, 08003, Spain. .,ICREA, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
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58
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Aerts N, Pereira Mendes M, Van Wees SCM. Multiple levels of crosstalk in hormone networks regulating plant defense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:489-504. [PMID: 33617121 PMCID: PMC7898868 DOI: 10.1111/tpj.15124] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 05/03/2023]
Abstract
Plant hormones are essential for regulating the interactions between plants and their complex biotic and abiotic environments. Each hormone initiates a specific molecular pathway and these different hormone pathways are integrated in a complex network of synergistic, antagonistic and additive interactions. This inter-pathway communication is called hormone crosstalk. By influencing the immune network topology, hormone crosstalk is essential for tailoring plant responses to diverse microbes and insects in diverse environmental and internal contexts. Crosstalk provides robustness to the immune system but also drives specificity of induced defense responses against the plethora of biotic interactors. Recent advances in dry-lab and wet-lab techniques have greatly enhanced our understanding of the broad-scale effects of hormone crosstalk on immune network functioning and have revealed underlying principles of crosstalk mechanisms. Molecular studies have demonstrated that hormone crosstalk is modulated at multiple levels of regulation, such as by affecting protein stability, gene transcription and hormone homeostasis. These new insights into hormone crosstalk regulation of plant defense are reviewed here, with a focus on crosstalk acting on the jasmonic acid pathway in Arabidopsis thaliana, highlighting the transcription factors MYC2 and ORA59 as major targets for modulation by other hormones.
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Affiliation(s)
- Niels Aerts
- Plant‐Microbe InteractionsDepartment of BiologyScience4LifeUtrecht UniversityP.O. Box 800.56Utrecht3408 TBThe Netherlands
| | - Marciel Pereira Mendes
- Plant‐Microbe InteractionsDepartment of BiologyScience4LifeUtrecht UniversityP.O. Box 800.56Utrecht3408 TBThe Netherlands
| | - Saskia C. M. Van Wees
- Plant‐Microbe InteractionsDepartment of BiologyScience4LifeUtrecht UniversityP.O. Box 800.56Utrecht3408 TBThe Netherlands
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59
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Güngör E, Brouwer P, Dijkhuizen LW, Shaffar DC, Nierop KG, de Vos RC, Sastre Toraño J, van der Meer IM, Schluepmann H. Azolla ferns testify: seed plants and ferns share a common ancestor for leucoanthocyanidin reductase enzymes. THE NEW PHYTOLOGIST 2021; 229:1118-1132. [PMID: 32858769 PMCID: PMC7820995 DOI: 10.1111/nph.16896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/12/2020] [Indexed: 05/02/2023]
Abstract
Questions about in vivo substrates for proanthocyanidin (PA) biosynthesis and condensation have not been resolved and wide gaps in the understanding of transport and biogenesis in 'tannosomes' persist. Here we examined the evolution of PA biosynthesis in ferns not previously reported, asking what PAs are synthesised and how. Chemical and gene-expression analyses were combined to characterise PA biosynthesis, leveraging genome annotation from the floating fern Azolla filiculoides. In vitro assay and phylogenomics of PIP-dehydrogenases served to infer the evolution of leucoanthocyanidin reductase (LAR). Sporophyte-synthesised (epi)catechin polymers, averaging only seven subunits, accumulated to 5.3% in A. filiculoides, and 8% in A. pinnata biomass dry weight. Consistently, a LAR active in vitro was highly expressed in A. filiculoides. LAR, and paralogous fern WLAR-enzymes with differing substrate binding sites, represent an evolutionary innovation of the common ancestor of fern and seed plants. The specific ecological niche of Azolla ferns, a floating plant-microbe mat massively fixing CO2 and N2 , shaped their metabolism in which PA biosynthesis predominates and employs novel fern LAR enzymes. Characterisation of in vivo substrates of these LAR, will help to shed light on the recently assigned and surprising dual catalysis of LAR from seed plants.
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Affiliation(s)
- Erbil Güngör
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Paul Brouwer
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- Earth SciencesUtrecht UniversityPrincetonlaan 8Utrecht3584 CBthe Netherlands
| | - Laura W. Dijkhuizen
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Dally Chaerul Shaffar
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Klaas G.J. Nierop
- Earth SciencesUtrecht UniversityPrincetonlaan 8Utrecht3584 CBthe Netherlands
| | - Ric C.H. de Vos
- BioscienceWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Javier Sastre Toraño
- Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrecht3508 TBthe Netherlands
| | - Ingrid M. van der Meer
- BioscienceWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Henriette Schluepmann
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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60
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Yang L, Wang Z, Hua J. A Meta-Analysis Reveals Opposite Effects of Biotic and Abiotic Stresses on Transcript Levels of Arabidopsis Intracellular Immune Receptor Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:625729. [PMID: 33747005 PMCID: PMC7969532 DOI: 10.3389/fpls.2021.625729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/01/2021] [Indexed: 05/06/2023]
Abstract
Plant intracellular immune receptor NLR (nucleotide-binding leucine-rich repeat) proteins sense the presence of pathogens and trigger strong and robust immune responses. NLR genes are known to be tightly controlled at the protein level, but little is known about their dynamics at the transcript level. In this study, we presented a meta-analysis of transcript dynamics of all 207 NLR genes in the Col-0 accession of Arabidopsis thaliana under various biotic and abiotic stresses based on 88 publicly available RNA sequencing datasets from 27 independent studies. We find that about two thirds of the NLR genes are generally induced by pathogens, immune elicitors, or salicylic acid (SA), suggesting that transcriptional induction of NLR genes might be an important mechanism in plant immunity regulation. By contrast, NLR genes induced by biotic stresses are often repressed by abscisic acid, high temperature and drought, suggesting that transcriptional regulation of NLR genes might be important for interaction between abiotic and biotic stress responses. In addition, pathogen-induced expression of some NLR genes are dependent on SA induction. Interestingly, a small group of NLR genes are repressed under certain biotic stress treatments, suggesting an unconventional function of this group of NLRs. This meta-analysis thus reveals the transcript dynamics of NLR genes under biotic and abiotic stress conditions and suggests a contribution of NLR transcript regulation to plant immunity as well as interactions between abiotic and biotic stress responses.
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61
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Reboledo G, Agorio A, Vignale L, Batista-García RA, Ponce De León I. Botrytis cinerea Transcriptome during the Infection Process of the Bryophyte Physcomitrium patens and Angiosperms. J Fungi (Basel) 2020; 7:11. [PMID: 33379257 PMCID: PMC7824268 DOI: 10.3390/jof7010011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Botrytis cinerea is a necrotrophic pathogen that causes grey mold in many plant species, including crops and model plants of angiosperms. B. cinerea also infects and colonizes the bryophyte Physcomitrium patens (previously Physcomitrella patens), which perceives the pathogen and activates defense mechanisms. However, these defenses are not sufficient to stop fungal invasion, leading finally to plant decay. To gain more insights into B. cinerea infection and virulence strategies displayed during moss colonization, we performed genome wide transcriptional profiling of B. cinerea during different infection stages. We show that, in total, 1015 B. cinerea genes were differentially expressed in moss tissues. Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that infection of P. patens tissues by B. cinerea depends on reactive oxygen species generation and detoxification, transporter activities, plant cell wall degradation and modification, toxin production and probable plant defense evasion by effector proteins. Moreover, a comparison with available RNAseq data during angiosperm infection, including Arabidopsis thaliana, Solanum lycopersicum and Lactuca sativa, suggests that B. cinerea has virulence and infection functions used in all hosts, while others are more specific to P. patens or angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Lucía Vignale
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico;
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
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Gruden K, Lidoy J, Petek M, Podpečan V, Flors V, Papadopoulou KK, Pappas ML, Martinez-Medina A, Bejarano E, Biere A, Pozo MJ. Ménage à Trois: Unraveling the Mechanisms Regulating Plant-Microbe-Arthropod Interactions. TRENDS IN PLANT SCIENCE 2020; 25:1215-1226. [PMID: 32828689 DOI: 10.1016/j.tplants.2020.07.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Plant-microbe-arthropod (PMA) three-way interactions have important implications for plant health. However, our poor understanding of the underlying regulatory mechanisms hampers their biotechnological applications. To this end, we searched for potential common patterns in plant responses regarding taxonomic groups or lifestyles. We found that most signaling modules regulating two-way interactions also operate in three-way interactions. Furthermore, the relative contribution of signaling modules to the final plant response cannot be directly inferred from two-way interactions. Moreover, our analyses show that three-way interactions often result in the activation of additional pathways, as well as in changes in the speed or intensity of defense activation. Thus, detailed, basic knowledge of plant-microbe-arthropod regulation will be essential for the design of environmentally friendly crop management strategies.
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Affiliation(s)
- Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Javier Lidoy
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Vid Podpečan
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Victor Flors
- Metabolic Integration and Cell Signaling Laboratory, Department of Ciencias Agrarias y del Medio Natural, Universitat Jaume I; Unidad Asociada al Consejo Superior de Investigaciones Científicas (EEZ-CSIC)-Universitat Jaume I, Castellón, Spain
| | - Kalliopi K Papadopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, Larissa, Greece
| | - Maria L Pappas
- Department of Agricultural Development, Faculty of Agricultural Sciences and Forestry, Democritus University of Thrace, Orestiada, Greece
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interaction, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Eduardo Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Department Biología Celular, Genética y Fisiología, Universidad de Málaga, Málaga, Spain
| | - Arjen Biere
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
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Chen Y, Jiang Y, Chen Y, Feng W, Liu G, Yu C, Lian B, Zhong F, Zhang J. Uncovering candidate genes responsive to salt stress in Salix matsudana (Koidz) by transcriptomic analysis. PLoS One 2020; 15:e0236129. [PMID: 32760076 PMCID: PMC7410171 DOI: 10.1371/journal.pone.0236129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Salix matsudana, a member of Salicaceae, is an important ornamental tree in China. Because of its capability to tolerate high salt conditions, S. matsudana also plays an important ecological role when grown along Chinese coastal beaches, where the salinity content is high. Here, we aimed to elucidate the mechanism of higher salt tolerance in S. matsudana variety ‘9901’ by identifying the associated genes through RNA sequencing and comparing differential gene expression between the S. matsudana salt-tolerant and salt-sensitive samples treated with 150 mM NaCl. Transcriptomic comparison of the roots of the two samples revealed 2174 and 3159 genes responsive to salt stress in salt-sensitive and salt-tolerant sample, respectively. Real-time polymerase chain reaction analysis of 9 of the responsive genes revealed a strong, positive correlation with RNA sequencing data. The genes were enriched in several pathways, including carbon metabolism pathway, plant-pathogen interaction pathway, and plant hormone signal transduction pathway. Differentially expressed genes (DEGs) encoding transcription factors associated with abiotic stress responses and salt stress response network were identified; their expression levels differed between the two samples in response to salt stress. Hub genes were also revealed by weighted gene co-expression network (WGCNA) analysis. For functional analysis of the DEG encoding sedoheptulose-1,7-bisphosphatase (SBPase), the gene was overexpressed in transgenic Arabidopsis, resulting in increased photosynthetic rates, sucrose and starch accumulation, and enhanced salt tolerance. Further functional characterization of other hub DEGs will reveal the molecular mechanism of salt tolerance in S. matsudana and allow the application of S. matsudana in coastal afforestation.
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Affiliation(s)
- Yanhong Chen
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Yuna Jiang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Yu Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wenxiang Feng
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Guoyuan Liu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Chunmei Yu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Bolin Lian
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Fei Zhong
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Jian Zhang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
- * E-mail:
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Cohen SP, Leach JE. High temperature-induced plant disease susceptibility: more than the sum of its parts. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:235-241. [PMID: 32321671 DOI: 10.1016/j.pbi.2020.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Higher temperatures associated with climate change often increase the severity of plant diseases. An understanding of how plants respond to pathogens during high temperature stress is required for crop improvement, but the molecular mechanisms underlying this response are largely unknown. Mechanistic research has primarily focused on plant responses during either single stresses or heat-induced loss of single gene resistance. Transcriptome analyses of plant responses to a single stress compared to combined-stresses reveal significant differences showing that single-stress response studies are inadequate for determining the mechanisms of high temperature-induced disease susceptibility. To combat plant disease in light of climate change, future research will require comprehensive study designs and analyses.
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Affiliation(s)
- Stephen P Cohen
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523-1177, United States; Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, United States
| | - Jan E Leach
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523-1177, United States.
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Lian S, Zhou Y, Liu Z, Gong A, Cheng L. The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences. BMC PLANT BIOLOGY 2020; 20:277. [PMID: 32546126 PMCID: PMC7298774 DOI: 10.1186/s12870-020-02460-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences and expression differences have arisen due to selective pressures throughout evolution. A comprehensive investigation of the expression patterns of paralogous gene pairs in response to various stresses and a study of correlations between the expression levels and sequence divergences of the paralogs are needed. RESULTS In this study, we analyzed the expression patterns of paralogous genes under different types of stress and investigated the correlations between the expression levels and sequence divergences of the paralogs. We analyzed the differential expression patterns of the paralogs under four different types of stress (drought, cold, infection, and herbivory) and classified them into three main types according to their expression patterns. We then further analyzed the differential expression patterns under various degrees of stress and constructed corresponding co-expression networks of differentially expressed paralogs and transcription factors. Finally, we investigated the correlations between the expression levels and sequence divergences of the paralogs and identified positive correlations between expression level and sequence divergence. With regard to sequence divergence, we identified correlations between selective pressures and phylogenetic relationships. CONCLUSIONS These results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relationships between expression levels and sequences divergences.
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Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Andong Gong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Lin Cheng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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66
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Zhang K, Cui H, Li M, Xu Y, Cao S, Long R, Kang J, Wang K, Hu Q, Sun Y. Comparative time-course transcriptome analysis in contrasting Carex rigescens genotypes in response to high environmental salinity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 194:110435. [PMID: 32169728 DOI: 10.1016/j.ecoenv.2020.110435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/11/2020] [Accepted: 03/03/2020] [Indexed: 05/20/2023]
Abstract
Soil salinization is one of most crucial environmental problems around the world and negatively affects plant growth and production. Carex rigescens is a turfgrass with favorable stress tolerance and great application prospect in salinity soil remediation and utilization; however, the molecular mechanisms behind its salt stress response are unknown. We performed a time-course transcriptome analysis between salt tolerant 'Huanghua' (HH) and salt sensitive 'Beijing' (BJ) genotypes. Physiological changes within 24 h were observed, with the HH genotype exhibiting increased salt tolerance compared to BJ. 5764 and 10752 differentially expressed genes were approved by transcriptome in BJ and HH genotype, respectively, and dynamic analysis showed a discrepant profile between two genotypes. In the BJ genotype, genes related to carbohydrate metabolism and stress response were more active and ABA signal transduction pathway might play a more important role in salt stress tolerance than in HH genotype. In the HH genotype, unique increases in the regulatory network of transcription factors, hormone signal transduction, and oxidation-reduction processes were observed. Moreover, trehalose and pectin biosynthesis and chitin catabolic related genes were specifically involved in the HH genotype, which may have contributed to salt tolerance. Moreover, some candidate genes like mannan endo-1,4-beta-mannosidase and EG45-like domain-containing protein are highlighted for future research about salt stress resistance in C. rigescens and other plant species. Our study revealed unique salt adaptation and resistance characteristics of two C. rigescens genotypes and these findings could help to enrich the currently available knowledge and clarify the detailed salt stress regulatory mechanisms in C. rigescens and other plants.
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Affiliation(s)
- Kun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Huiting Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Mingna Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
| | - Yi Xu
- Texas AgriLife Research and Extension Center, Texas A&M University, Dallas, 75252, USA.
| | - Shihao Cao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Qiannan Hu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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Tuang ZK, Wu Z, Jin Y, Wang Y, Oo PPZ, Zuo G, Shi H, Yang W. Pst DC3000 infection alleviates subsequent freezing and heat injury to host plants via a salicylic acid-dependent pathway in Arabidopsis. PLANT, CELL & ENVIRONMENT 2020; 43:801-817. [PMID: 31851376 DOI: 10.1111/pce.13705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/17/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Abiotic stresses greatly affect the immunity of plants. However, it is unknown whether pathogen infection affects abiotic stress tolerance of host plants. Here, the effect of defense response on cold and heat tolerance of host plants was investigated in Pst DC3000-infected Arabidopsis plants, and it was found that the pathogen-induced defense response could alleviate the injury caused by subsequent cold and heat stress (38°C). Transcriptomic sequencing plus RT-qPCR analyses showed that some abiotic stress genes are up-regulated in transcription by pathogen infection, including cold signaling components ICE1, CBF1, and CBF3, and some heat signaling components HSFs and HSPs. Moreover, the pathogen-induced alleviation of cold and heat injury was lost in NahG transgenic line (SA-deficient), sid2-2 and npr1-1 mutant plants, and pathogen-induced expression of cold and heat tolerance-related genes such as CBFs and HSPs, respectively, was lost or compromised in these plants, indicating that salicylic acid signaling pathway is required for the alleviation of cold and heat injury by pathogen infection. In short, our current work showed that in fighting against pathogens, host plants also enhance their cold and heat tolerance via a salicylic acid-dependent pathway.
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Affiliation(s)
- Za Khai Tuang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhenjiang Wu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ye Jin
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yizhong Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Phyo Phyo Zin Oo
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guoxin Zuo
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Huazhong Shi
- School of Life Sciences, Central China Normal University, Wuhan, China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, China
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Kang WH, Sim YM, Koo N, Nam JY, Lee J, Kim N, Jang H, Kim YM, Yeom SI. Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L. Sci Data 2020; 7:17. [PMID: 31932587 PMCID: PMC6957515 DOI: 10.1038/s41597-020-0352-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/17/2019] [Indexed: 01/17/2023] Open
Abstract
Peppers (Capsicum annuum L.), belonging to the Solanaceae family, are one of the most economically important crops globally. Like other crops, peppers are threatened by diverse environmental conditions due to different pathogens and abiotic stresses. High-quality reference genomes with massive datasets of transcriptomes from various conditions can provide clues to preferred agronomic traits for breeding. However, few global gene expression profiling datasets have been published to examine the environmental stress-resistant mechanisms in peppers. In this study, we report the RNA-seq analyses of peppers treated with heat, cold, salinity, and osmotic stress at six different time points. RNA-seq libraries from 78 RNA samples containing three biological replicates per time point for each of the abiotic stresses and a mock control were constructed. A total of 204.68 Gb of transcriptome data were verified by differentially expressed genes and gene ontology enrichment analysis. Analyses of the transcriptome data in this study will provide useful information for basic studies of various stimuli to facilitate the development of stress-resistant pepper cultivars.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jae-Young Nam
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Junesung Lee
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Nayoung Kim
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hakgi Jang
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea.
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Zhang N, Zhou S, Yang D, Fan Z. Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis. FRONTIERS IN PLANT SCIENCE 2020; 11:908. [PMID: 32670328 PMCID: PMC7333171 DOI: 10.3389/fpls.2020.00908] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/03/2020] [Indexed: 05/22/2023]
Abstract
Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.
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Sham A, Al-Ashram H, Whitley K, Iratni R, El-Tarabily KA, AbuQamar SF. Metatranscriptomic Analysis of Multiple Environmental Stresses Identifies RAP2.4 Gene Associated with Arabidopsis Immunity to Botrytis cinerea. Sci Rep 2019; 9:17010. [PMID: 31740741 PMCID: PMC6861241 DOI: 10.1038/s41598-019-53694-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/24/2019] [Indexed: 01/18/2023] Open
Abstract
In this study, we aimed to identify common genetic components during stress response responsible for crosstalk among stresses, and to determine the role of differentially expressed genes in Arabidopsis-Botrytis cinerea interaction. Of 1,554 B. cinerea up-regulated genes, 24%, 1.4% and 14% were induced by biotic, abiotic and hormonal treatments, respectively. About 18%, 2.5% and 22% of B. cinerea down-regulated genes were also repressed by the same stress groups. Our transcriptomic analysis indicates that plant responses to all tested stresses can be mediated by commonly regulated genes; and protein-protein interaction network confirms the cross-interaction between proteins regulated by these genes. Upon challenges to individual or multiple stress(es), accumulation of signaling molecules (e.g. hormones) plays a major role in the activation of downstream defense responses. In silico gene analyses enabled us to assess the involvement of RAP2.4 (related to AP2.4) in plant immunity. Arabidopsis RAP2.4 was repressed by B. cinerea, and its mutants enhanced resistance to the same pathogen. To the best of our knowledge, this is the first report demonstrating the role of RAP2.4 in plant defense against B. cinerea. This research can provide a basis for breeding programs to increase tolerance and improve yield performance in crops.
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Affiliation(s)
- Arjun Sham
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | | | - Kenna Whitley
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | - Rabah Iratni
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | - Khaled A El-Tarabily
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE. .,School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE.
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Derbyshire M, Mbengue M, Barascud M, Navaud O, Raffaele S. Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance. MOLECULAR PLANT PATHOLOGY 2019; 20:1279-1297. [PMID: 31361080 PMCID: PMC6715603 DOI: 10.1111/mpp.12841] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris. We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat-rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down-regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome-wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild-type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.
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Affiliation(s)
- Mark Derbyshire
- Centre for Crop and Disease ManagementCurtin UniversityPerthWestern AustraliaAustralia
| | - Malick Mbengue
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Marielle Barascud
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Olivier Navaud
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
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Jia H, Zhang J, Li J, Sun P, Zhang Y, Xin X, Lu M, Hu J. Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance. BMC PLANT BIOLOGY 2019; 19:356. [PMID: 31416414 PMCID: PMC6694639 DOI: 10.1186/s12870-019-1900-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Drought is a major environmental constraint to plant growth, development and productivity. Compared with most willows that are generally susceptible to drought, the desert willow Salix psammophila has extraordinary adaptation to drought stress. However, its molecular basis of drought tolerance is still largely unknown. RESULTS During polyethylene glycol 6000 (PEG 6000)-simulated drought stress, we found that the osmotic adjustment substances were accumulated and the antioxidant enzyme activities were enhanced in S. psammophila roots. A total of 8172 differentially expressed genes were identified in roots of S. psammophila through RNA-Sequencing. Based on K-means clustering, their expression patterns were classified into nine clusters, which were enriched in several stress-related processes including transcriptional regulation, response to various stresses, cell death, etc. Moreover, 672 transcription factors from 45 gene families were differentially expressed under drought stress. Furthermore, a weighted gene co-expression network was constructed, and eight genes were identified as hub genes. We demonstrated the function of two hub genes, magnesium-dependent phosphatase 1 (SpMDP1) and SpWRKY33, through overexpression in Arabidopsis thaliana. Overexpression of the two hub genes enhanced the drought tolerance in transgenic plants, suggesting that the identification of candidate drought tolerance genes in this study was highly efficient and credible. CONCLUSIONS Our study analyzed the physiological and molecular responses to drought stress in S. psammophila, and these results contribute to dissect the mechanism of drought tolerance of S. psammophila and facilitate identification of critical genes involved in drought tolerance for willow breeding.
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Affiliation(s)
- Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jianbo Li
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300 China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Xuebing Xin
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300 China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
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73
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Oberländer J, Lortzing V, Hilker M, Kunze R. The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist. BMC PLANT BIOLOGY 2019; 19:338. [PMID: 31375063 PMCID: PMC6679549 DOI: 10.1186/s12870-019-1943-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND In native environments plants frequently experience simultaneous or sequential unfavourable abiotic and biotic stresses. The plant's response to combined stresses is usually not the sum of the individual responses. Here we investigated the impact of cold on plant defense against subsequent herbivory by a generalist and specialist insect. RESULTS We determined transcriptional responses of Arabidopsis thaliana to low temperature stress (4 °C) and subsequent larval feeding damage by the lepidopteran herbivores Mamestra brassicae (generalist), Pieris brassicae (specialist) or artificial wounding. Furthermore, we compared the performance of larvae feeding upon cold-experienced or untreated plants. Prior experience of cold strongly affected the plant's transcriptional anti-herbivore and wounding response. Feeding by P. brassicae, M. brassicae and artificial wounding induced transcriptional changes of 1975, 1695, and 2239 genes, respectively. Of these, 125, 360, and 681 genes were differentially regulated when cold preceded the tissue damage. Overall, prior experience of cold mostly reduced the transcriptional response of genes to damage. The percentage of damage-responsive genes, which showed attenuated transcriptional regulation when cold preceded the tissue damage, was highest in M. brassicae damaged plants (98%), intermediate in artificially damaged plants (89%), and lowest in P. brassicae damaged plants (69%). Consistently, the generalist M. brassicae performed better on cold-treated than on untreated plants, whereas the performance of the specialist P. brassicae did not differ. CONCLUSIONS The transcriptional defense response of Arabidopsis leaves to feeding by herbivorous insects and artificial wounding is attenuated by a prior exposure of the plant to cold. This attenuation correlates with improved performance of the generalist herbivore M. brassicae, but not the specialist P. brassicae, a herbivore of the same feeding guild.
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Affiliation(s)
- Jana Oberländer
- Freie Universität Berlin, Institute of Biology - Applied Genetics, Dahlem Centre of Plant Sciences, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
- Present address: University of Bern, Molecular Plant Physiology, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Vivien Lortzing
- Freie Universität Berlin, Institute of Biology - Applied Zoology / Animal Ecology, Dahlem Centre of Plant Sciences, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Monika Hilker
- Freie Universität Berlin, Institute of Biology - Applied Zoology / Animal Ecology, Dahlem Centre of Plant Sciences, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Reinhard Kunze
- Freie Universität Berlin, Institute of Biology - Applied Genetics, Dahlem Centre of Plant Sciences, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
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74
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Nobori T, Tsuda K. The plant immune system in heterogeneous environments. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:58-66. [PMID: 30978554 DOI: 10.1016/j.pbi.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
The plant immune system inhibits pathogen growth and contributes to shaping a healthy microbial community in the plant body. Plants must appropriately respond to both microbial signals and abiotic factors that are diverse in time and space, and thus, proper integration of these inputs at local and systemic levels is of crucial importance for optimal plant responses and fitness in nature. Here, we review our current knowledge of three properties of the plant immune system, resilience, tunability, and balance, which enable plants to deal with complex cocktails of environmental factors. We also discuss future challenges on the path towards a comprehensive understanding of the interactions between plant immunity and pathogenic, non-pathogenic, and beneficial microbes.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, Cologne 50829, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, Cologne 50829, Germany.
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75
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Cruz-Valderrama JE, Gómez-Maqueo X, Salazar-Iribe A, Zúñiga-Sánchez E, Hernández-Barrera A, Quezada-Rodríguez E, Gamboa-deBuen A. Overview of the Role of Cell Wall DUF642 Proteins in Plant Development. Int J Mol Sci 2019; 20:E3333. [PMID: 31284602 PMCID: PMC6651502 DOI: 10.3390/ijms20133333] [Citation(s) in RCA: 14] [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: 05/30/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
The DUF642 protein family is found exclusively in spermatophytes and is represented by 10 genes in Arabidopsis and in most of the 24 plant species analyzed to date. Even though the primary structure of DUF642 proteins is highly conserved in different spermatophyte species, studies of their expression patterns in Arabidopsis have shown that the spatial-temporal expression pattern for each gene is specific and consistent with the phenotypes of the mutant plants studied so far. Additionally, the regulation of DUF642 gene expression by hormones and environmental stimuli was specific for each gene, showing both up- and down-regulation depending of the analyzed tissue and the intensity or duration of the stimuli. These expression patterns suggest that the DUF642 genes are involved throughout the development and growth of plants. In general, changes in the expression patterns of DUF642 genes can be related to changes in pectin methyl esterase activity and/or to changes in the degree of methyl-esterified homogalacturonans during plant development in different cell types. Thus, the regulation of pectin methyl esterases mediated by DUF642 genes could contribute to the regulation of the cell wall properties during plant growth.
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Affiliation(s)
| | - Ximena Gómez-Maqueo
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | - Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | - Esther Zúñiga-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | | | - Elsa Quezada-Rodríguez
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
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76
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Weng X, Lovell JT, Schwartz SL, Cheng C, Haque T, Zhang L, Razzaque S, Juenger TE. Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass. PLANT, CELL & ENVIRONMENT 2019; 42:2165-2182. [PMID: 30847928 DOI: 10.1111/pce.13546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost-effective 3'-Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C4 perennial grass, Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine-scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis-regulatory elements and biological processes under short- and long-day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod-dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well-known GI-interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.
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Affiliation(s)
- Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806
| | - Scott L Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Changde Cheng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Taslima Haque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
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Fernández I, Cosme M, Stringlis IA, Yu K, de Jonge R, van Wees SM, Pozo MJ, Pieterse CMJ, van der Heijden MGA. Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism. THE NEW PHYTOLOGIST 2019; 223:867-881. [PMID: 30883790 DOI: 10.1111/nph.15798] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the nonhost Arabidopsis thaliana, and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the nonhost-AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA-seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus-mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and nonhost interactions.
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Affiliation(s)
- Iván Fernández
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Marco Cosme
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - SaskiaC M van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), Granada, 18008, Spain
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
- Plant-Soil-Interactions, Agroscope, Zürich, 8046, Switzerland
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78
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Wolinska KW, Berens ML. Optimal Defense Theory 2.0: tissue-specific stress defense prioritization as an extra layer of complexity. Commun Integr Biol 2019; 12:91-95. [PMID: 31308873 PMCID: PMC6615527 DOI: 10.1080/19420889.2019.1625661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/21/2022] Open
Abstract
In nature, plants need to be able to quickly adapt to changing environments during their lifetime in order to maintain fitness. Different defense responses are not only costly, but often also antagonistic to one another. Hence, when faced with multiple stresses simultaneously, plants likely have to prioritize their defense responses. This type of crosstalk between different stress response pathways is suggested to balance the high costs of triggering and maintaining stress responses with the limited amount of resources available to a plant. This assumption is in accordance with the optimal defense theory (ODT), which states that living organisms put more resources into protection of the most valuable tissues, but does not explain how plants survive combined stress conditions in nature. In this review, we describe recent evidence that expands on the framework of the ODT by suggesting that under combined stress plants spatially separate contrasting stress responses, rather than protecting the most valuable tissues to simultaneously protect themselves from contrasting stressors. We discuss the implications of these findings for understanding plant responses to combined stresses and suggest potentially fruitful avenues for further research.
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Affiliation(s)
- Katarzyna Wiktoria Wolinska
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Leonhard Berens
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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79
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Osthoff A, Donà Dalle Rose P, Baldauf JA, Piepho HP, Hochholdinger F. Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress. BMC Genomics 2019; 20:325. [PMID: 31035922 PMCID: PMC6489292 DOI: 10.1186/s12864-019-5634-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Background Water deficit and soil salinity substantially influence plant growth and productivity. When occurring individually, plants often exhibit reduced growth resulting in yield losses. The simultaneous occurrence of these stresses enhances their negative effects. Unraveling the molecular mechanisms of combined abiotic stress responses is essential to secure crop productivity under unfavorable environmental conditions. Results This study examines the effects of water deficit, salinity and a combination of both on growth and transcriptome plasticity of barley seminal roots by RNA-Seq. Exposure to water deficit and combined stress for more than 4 days significantly reduced total seminal root length. Transcriptome sequencing demonstrated that 60 to 80% of stress type-specific gene expression responses observed 6 h after treatment were also present after 24 h of stress application. However, after 24 h of stress application, hundreds of additional genes were stress-regulated compared to the short 6 h treatment. Combined salt and water deficit stress application results in a unique transcriptomic response that cannot be predicted from individual stress responses. Enrichment analyses of gene ontology terms revealed stress type-specific adjustments of gene expression. Further, global reprogramming mediated by transcription factors and consistent over-representation of basic helix-loop-helix (bHLH) transcription factors, heat shock factors (HSF) and ethylene response factors (ERF) was observed. Conclusion This study reveals the complex transcriptomic responses regulating the perception and signaling of multiple abiotic stresses in barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5634-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alina Osthoff
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Petra Donà Dalle Rose
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599, Stuttgart, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany.
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80
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de Vries S, de Vries J, Rose LE. The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant⁻Microbe Interactions. Genes (Basel) 2019; 10:genes10040310. [PMID: 31010062 PMCID: PMC6523410 DOI: 10.3390/genes10040310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plants are exposed to diverse abiotic and biotic stimuli. These require fast and specific integrated responses. Such responses are coordinated at the protein and transcript levels and are incorporated into larger regulatory networks. Here, we focus on the evolution of transcriptional regulatory networks involved in plant–pathogen interactions. We discuss the evolution of regulatory networks and their role in fine-tuning plant defense responses. Based on the observation that many of the cornerstones of immune signaling in angiosperms are also present in streptophyte algae, it is likely that some regulatory components also predate the origin of land plants. The degree of functional conservation of many of these ancient components has not been elucidated. However, ongoing functional analyses in bryophytes show that some components are conserved. Hence, some of these regulatory components and how they are wired may also trace back to the last common ancestor of land plants or earlier. Of course, an understanding of the similarities and differences during the evolution of plant defense networks cannot ignore the lineage-specific coevolution between plants and their pathogens. In this review, we specifically focus on the small RNA regulatory networks involved in fine-tuning of the strength and timing of defense responses and highlight examples of pathogen exploitation of the host RNA silencing system. These examples illustrate well how pathogens frequently target gene regulation and thereby alter immune responses on a larger scale. That this is effective is demonstrated by the diversity of pathogens from distinct kingdoms capable of manipulating the same gene regulatory networks, such as the RNA silencing machinery.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, 38106 Braunschweig, Germany.
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
- CEPLAS-Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany.
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81
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Coolen S, Van Pelt JA, Van Wees SCM, Pieterse CMJ. Mining the natural genetic variation in Arabidopsis thaliana for adaptation to sequential abiotic and biotic stresses. PLANTA 2019; 249:1087-1105. [PMID: 30547240 DOI: 10.1007/s00425-018-3065-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/05/2018] [Indexed: 05/24/2023]
Abstract
In this genome-wide association study, we obtained novel insights into the genetic basis of the effect of herbivory or drought stress on the level of resistance against the fungus Botrytis cinerea. In nature, plants function in complex environments where they encounter different biotic and abiotic stresses individually, sequentially or simultaneously. The adaptive response to a single stress does not always reflect how plants respond to such a stress in combination with other stresses. To identify genetic factors that contribute to the plant's ability to swiftly adapt to different stresses, we investigated the response of Arabidopsis thaliana to infection by the necrotrophic fungus B. cinerea when preceded by Pieris rapae herbivory or drought stress. Using 346 natural A. thaliana accessions, we found natural genetic variation in the level of resistance against single B. cinerea infection. When preceded by herbivory or drought stress, the level of B. cinerea resistance was differentially influenced in the 346 accessions. To study the genetic factors contributing to the differential adaptation of A. thaliana to B. cinerea infection under multi-stress conditions, we performed a genome-wide association study supported by quantitative trait loci mapping and fine mapping with full genome sequences of 164 accessions. This yielded several genes previously associated with defense to B. cinerea and additional candidate genes with putative roles in the plant's adaptive response to a combination of herbivory, drought and B. cinerea infection.
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Affiliation(s)
- Silvia Coolen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 80056, 3508 TB, Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 80056, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 80056, 3508 TB, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 80056, 3508 TB, Utrecht, The Netherlands.
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Rubio B, Cosson P, Caballero M, Revers F, Bergelson J, Roux F, Schurdi-Levraud V. Genome-wide association study reveals new loci involved in Arabidopsis thaliana and Turnip mosaic virus (TuMV) interactions in the field. THE NEW PHYTOLOGIST 2019; 221:2026-2038. [PMID: 30282123 DOI: 10.1111/nph.15507] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/18/2018] [Indexed: 05/12/2023]
Abstract
The genetic architecture of plant response to viruses has often been studied in model nonnatural pathosystems under controlled conditions. There is an urgent need to elucidate the genetic architecture of the response to viruses in a natural setting. A field experiment was performed in each of two years. In total, 317 Arabidopsis thaliana accessions were inoculated with its natural Turnip mosaic virus (TuMV). The accessions were phenotyped for viral accumulation, frequency of infected plants, stem length and symptoms. Genome-wide association mapping was performed. Arabidopsis thaliana exhibits extensive natural variation in its response to TuMV in the field. The underlying genetic architecture reveals a more quantitative picture than in controlled conditions. Ten genomic regions were consistently identified across the two years. RTM3 (Restricted TEV Movement 3) is a major candidate for the response to TuMV in the field. New candidate genes include Dead box helicase 1, a Tim Barrel domain protein and the eukaryotic translation initiation factor eIF3b. To our knowledge, this study is the first to report the genetic architecture of quantitative response of A. thaliana to a naturally occurring virus in a field environment, thereby highlighting relevant candidate genes involved in plant virus interactions in nature.
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Affiliation(s)
- Bernadette Rubio
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Patrick Cosson
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Mélodie Caballero
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Frédéric Revers
- INRA, UMR 1202 BIOGECO, Université de Bordeaux, 69 Route d'Arcachon, 33612, Cestas Cedex, France
| | - Joy Bergelson
- Ecology & Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Fabrice Roux
- LIPM, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Valérie Schurdi-Levraud
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
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Zhang X, Zhang Y, Wang YH, Shen SK. Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses. Front Genet 2018; 9:505. [PMID: 30455715 PMCID: PMC6231050 DOI: 10.3389/fgene.2018.00505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 10/08/2018] [Indexed: 12/26/2022] Open
Abstract
Cinnamomum chago, an endangered species endemic to Yunnan province, possesses large economic and phylogenetic values in Lauraceae. However, the genomic information of this species remains relatively unexplored. In this study, we used RNAseq technology to characterize and annotate the C. chago transcriptome and identify candidate genes involved in special metabolic pathways and gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP). A total of 129,097 unigenes, with a mean length of 667 bp and an N50 length of 1,062 bp, were assembled. Among these genes, 56,887 (44.07%) unigenes were successfully annotated using at least one database. Furthermore, 47 and 46 candidate genes were identified in terpenoid biosynthesis and fatty acid biosynthesis, respectively. A total of 22 candidate genes participated in at least one abiotic stress response of C. chago. Additionally, a total of 25,654 SSRs and 640 SNPs were also identified. Based on these potential loci, 55 novel expressed sequence tag (EST)-SSR primers were successfully developed. This work provides comprehensive transcriptomic data that can be used to establish a valuable information platform for gene prediction, signaling pathway investigation, and molecular marker development for C. chago and other related species. Such a platform can facilitate further studies on germplasm conservation and utilization of Lauraceae species.
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Affiliation(s)
| | | | | | - Shi-Kang Shen
- School of Life Sciences, Yunnan University, Kunming, China
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84
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Nitrogen Limitation Alters the Response of Specific Genes to Biotic Stress. Int J Mol Sci 2018; 19:ijms19113364. [PMID: 30373239 PMCID: PMC6275003 DOI: 10.3390/ijms19113364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/21/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022] Open
Abstract
In their natural environment, plants are generally confronted with multiple co-occurring stresses. However, the interaction between stresses is not well known and transcriptomic data in response to combined stresses remain scarce. This study aims at characterizing the interaction between transcriptomic responses to biotic stress and nitrogen (N) limitation. Plants were grown in low or full N, infected or not with Erwinia amylovora (Ea) and plant gene expression was analyzed through microarray and qRT-PCR. Most Ea-responsive genes had the same profile (induced/repressed) in response to Ea in low and full N. In response to stress combination, one third of modulated transcripts responded in a manner that could not be deduced from their response to each individual stress. Many defense-related genes showed a prioritization of their response to biotic stress over their response to N limitation, which was also observed using Pseudomonas syringae as a second pathosystem. Our results indicate an interaction between transcriptomic responses to N and biotic stress. A small fraction of transcripts was prioritized between antagonistic responses, reflecting a preservation of the plant defense program under N limitation. Furthermore, this interaction also led to a complex and specific response in terms of metabolism and cellular homeostasis-associated genes.
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85
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Avila LM, Obeidat W, Earl H, Niu X, Hargreaves W, Lukens L. Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure. BMC Genomics 2018; 19:761. [PMID: 30342485 PMCID: PMC6196024 DOI: 10.1186/s12864-018-5134-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation. Genes that respond differently to temperature changes across genotypes may have limited functional importance. We investigate if these genes share functions, and if their genotype-specific gene expression levels change in magnitude or rank across temperatures. RESULTS We estimate transcript abundances from over 22,000 genes in two unrelated Zea mays inbred lines during and after cold temperature exposure. Genotype and temperature contribute to many genes' abundances. Past cold exposure affects many fewer genes. Genes up-regulated in cold encode many cytokinin glucoside biosynthesis enzymes, transcription factors, signalling molecules, and proteins involved in diverse environmental responses. After cold exposure, protease inhibitors and cuticular wax genes are newly up-regulated, and environmentally responsive genes continue to be up-regulated. Genes down-regulated in response to cold include many photosynthesis, translation, and DNA replication associated genes. After cold exposure, DNA replication and translation genes are still preferentially downregulated. Lignin and suberin biosynthesis are newly down-regulated. DNA replication, reactive oxygen species response, and anthocyanin biosynthesis genes have strong, genotype-specific temperature responses. The ranks of genotypes' transcript abundances often change across temperatures. CONCLUSIONS We report a large, core transcriptome response to cold and the alleviation of cold. In cold, many of the core suite of genes are up or downregulated to control plant growth and photosynthesis and limit cellular damage. In recovery, core responses are in part to prepare for future stress. Functionally related genes are consistently and greatly up-regulated in a single genotype in response to cold or its alleviation, suggesting positive selection has driven genotype-specific temperature responses in maize.
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Affiliation(s)
- Luis M Avila
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Wisam Obeidat
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Hugh Earl
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Xiaomu Niu
- Dupont/Pioneer, 7300 NW 62nd Ave, DuPont Pioneer, Johnston, Iowa, 50131 USA
| | - William Hargreaves
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
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86
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Ximénez-Embún MG, González-Guzmán M, Arbona V, Gómez-Cadenas A, Ortego F, Castañera P. Plant-Mediated Effects of Water Deficit on the Performance of Tetranychus evansi on Tomato Drought-Adapted Accessions. FRONTIERS IN PLANT SCIENCE 2018; 9:1490. [PMID: 30386357 PMCID: PMC6199365 DOI: 10.3389/fpls.2018.01490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/25/2018] [Indexed: 05/25/2023]
Abstract
Climate change is expected to increase drought periods and the performance and dispersal of some invasive species such as Tetranychus evansi, which has been reported to take advantage of the nutritional changes induced by water-shortage on the tomato cultivar Moneymaker (MM). We have examined the implications for mite's biology of four accessions of the drought-adapted tomatoes, "Tomàtiga de Ramellet" (TR), under moderate drought stress. Mite performance was enhanced by drought in two accessions (TR61 and TR154), but not in the other two accessions (TR58 and TR126). We selected one accession of each outcome (i.e., TR154 and TR126) to further analyze plant nutritional parameters. We found that free sugars and most essential amino acids for mites were induced by drought and/or mite infestation on MM and TR154 plants, whereas sugars were not altered and a reduced number of essential amino acids were induced by drought in TR126. Remarkably, mite performance was enhanced by leaf infiltration of free sugars, essential amino acids mixture, and L-proline on well-watered MM and by free sugars on drought-stressed TR126 plants. These results indicate a positive link between the induction of soluble carbohydrates and amino acids used by the plant for osmotic adjustment and mite performance. The effects of drought and/or mite infestation on the defense response of plants was analyzed at three levels: phytohormone accumulation, the transcript levels of marker genes linked to jasmonates (JAs), salicylic acid (SA), and abscisic acid (ABA) pathways, and the activity of defense proteins. The ability of T. evansi to downregulate the accumulation of defense-related phytohormones was noted on MM and the two TR accessions analyzed (TR126 and TR154), though differences in the induction of protein defense genes and activities by drought and/or mite infestation were observed among them. These results emphasize the importance of studying plant biotic and abiotic stress factors in combination and provides an experimental framework for screening drought-tolerant tomato accessions that will be also resistant to herbivore mites.
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Affiliation(s)
- Miguel G. Ximénez-Embún
- Laboratorio de Interacción Planta-Insecto, Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Miguel González-Guzmán
- Laboratorio de Interacción Planta-Insecto, Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Vicent Arbona
- Ecofisiologia i Biotecnologia, Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Aurelio Gómez-Cadenas
- Ecofisiologia i Biotecnologia, Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Félix Ortego
- Laboratorio de Interacción Planta-Insecto, Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Pedro Castañera
- Laboratorio de Interacción Planta-Insecto, Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
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87
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Proietti S, Caarls L, Coolen S, Van Pelt JA, Van Wees SC, Pieterse CM. Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis. PLANT, CELL & ENVIRONMENT 2018; 41:2342-2356. [PMID: 29852537 PMCID: PMC6175328 DOI: 10.1111/pce.13357] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/04/2018] [Accepted: 05/18/2018] [Indexed: 05/22/2023]
Abstract
Jasmonic acid (JA) regulates plant defenses against necrotrophic pathogens and insect herbivores. Salicylic acid (SA) and abscisic acid (ABA) can antagonize JA-regulated defenses, thereby modulating pathogen or insect resistance. We performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis thaliana for the effect of SA and ABA on the JA pathway. We treated 349 Arabidopsis accessions with methyl JA (MeJA), or a combination of MeJA and either SA or ABA, after which expression of the JA-responsive marker gene PLANT DEFENSIN1.2 (PDF1.2) was quantified as a readout for GWA analysis. Both hormones antagonized MeJA-induced PDF1.2 in the majority of the accessions but with a large variation in magnitude. GWA mapping of the SA- and ABA-affected PDF1.2 expression data revealed loci associated with crosstalk. GLYI4 (encoding a glyoxalase) and ARR11 (encoding an Arabidopsis response regulator involved in cytokinin signalling) were confirmed by T-DNA insertion mutant analysis to affect SA-JA crosstalk and resistance against the necrotroph Botrytis cinerea. In addition, At1g16310 (encoding a cation efflux family protein) was confirmed to affect ABA-JA crosstalk and susceptibility to Mamestra brassicae herbivory. Collectively, this GWA study identified novel players in JA hormone crosstalk with potential roles in the regulation of pathogen or insect resistance.
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Affiliation(s)
- Silvia Proietti
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
| | - Lotte Caarls
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
| | - Silvia Coolen
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
| | - Johan A. Van Pelt
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
| | - Saskia C.M. Van Wees
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
| | - Corné M.J. Pieterse
- Plant‐Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtThe Netherlands
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88
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Qi H, Jiang Z, Zhang K, Yang S, He F, Zhang Z. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:283-293. [PMID: 30266409 PMCID: PMC6205082 DOI: 10.1016/j.gpb.2018.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/02/2018] [Accepted: 08/13/2018] [Indexed: 01/01/2023]
Abstract
High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation data. Second, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-scale transcriptome analysis to explore the global landscape of gene expression in the curated data. We found that only a small fraction of genes were differentially expressed under multiple conditions, which might be explained by their tendency of having more network connections and shorter network distances in gene networks. Collectively, we hope that PlaD can serve as an important and comprehensive knowledgebase to the community of plant sciences, providing insightful clues to better understand the molecular mechanisms underlying plant immune responses. PlaD is freely available at http://systbio.cau.edu.cn/plad/index.php or http://zzdlab.com/plad/index.php.
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Affiliation(s)
- Huan Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenhong Jiang
- Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Kang Zhang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Biology Department, Brookhaven National Lab, Upton, NY 11967, USA.
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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89
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Arnaiz A, Talavera-Mateo L, Gonzalez-Melendi P, Martinez M, Diaz I, Santamaria ME. Arabidopsis Kunitz Trypsin Inhibitors in Defense Against Spider Mites. FRONTIERS IN PLANT SCIENCE 2018; 9:986. [PMID: 30042779 PMCID: PMC6048452 DOI: 10.3389/fpls.2018.00986] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/18/2018] [Indexed: 05/06/2023]
Abstract
Tetranychus urticae (two-spotted spider mite) is a striking example of polyphagy among herbivores with an extreme record of pesticide resistance and one of the most significant pests in agriculture. The T. urticae genome contains a large number of cysteine- and serine-proteases indicating their importance in the spider mite physiology. This work is focused on the potential role of the Kunitz trypsin inhibitor (KTI) family on plant defense responses against spider mites. The molecular characterization of two of these genes, AtKTI4 and AtKTI5, combined with feeding bioassays using T-DNA insertion lines for both genes was carried out. Spider mite performance assays showed that independent KTI silencing Arabidopsis lines conferred higher susceptibility to T. urticae than WT plants. Additionally, transient overexpression of these inhibitors in Nicotiana benthamiana demonstrated their ability to inhibit not only serine- but also cysteine-proteases, indicating the bifunctional inhibitory role against both types of enzymes. These inhibitory properties could be involved in the modulation of the proteases that participate in the hydrolysis of dietary proteins in the spider mite gut, as well as in other proteolytic processes.
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Affiliation(s)
- Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Lucia Talavera-Mateo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. E. Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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90
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Lee J, Shim D, Moon S, Kim H, Bae W, Kim K, Kim YH, Rhee SK, Hong CP, Hong SY, Lee YJ, Sung J, Ryu H. Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:553-560. [PMID: 29723826 DOI: 10.1016/j.plaphy.2018.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 05/03/2023]
Abstract
Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (Solanum lycopersicum), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a SlDWARF gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Republic of Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Yang-Hoon Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Chang Pyo Hong
- TheragenEtex Bio Institute, Suwon 16229, Republic of Korea.
| | - Suk-Young Hong
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Ye-Jin Lee
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Jwakyung Sung
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
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91
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Steenbergen M, Abd-El-Haliem A, Bleeker P, Dicke M, Escobar-Bravo R, Cheng G, Haring MA, Kant MR, Kappers I, Klinkhamer PGL, Leiss KA, Legarrea S, Macel M, Mouden S, Pieterse CMJ, Sarde SJ, Schuurink RC, De Vos M, Van Wees SCM, Broekgaarden C. Thrips advisor: exploiting thrips-induced defences to combat pests on crops. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1837-1848. [PMID: 29490080 DOI: 10.1093/jxb/ery060] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding.
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Affiliation(s)
- Merel Steenbergen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, , TB Utrecht, The Netherlands
| | - Ahmed Abd-El-Haliem
- Department of Plant Physiology, University of Amsterdam, Science Park, XH Amsterdam, The Netherlands
| | - Petra Bleeker
- Department of Plant Physiology, University of Amsterdam, Science Park, XH Amsterdam, The Netherlands
- Enza Zaden BV, AA Enkhuizen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
| | - Rocio Escobar-Bravo
- Plant Sciences and Natural Products, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gang Cheng
- Plant Sciences and Natural Products, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Michel A Haring
- Department of Plant Physiology, University of Amsterdam, Science Park, XH Amsterdam, The Netherlands
| | - Merijn R Kant
- Molecular & Chemical Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, GE Amsterdam, The Netherlands
| | - Iris Kappers
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Peter G L Klinkhamer
- Plant Sciences and Natural Products, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Kirsten A Leiss
- Wageningen UR Greenhouse Horticulture, Bleiswijk, The Netherlands
| | - Saioa Legarrea
- Molecular & Chemical Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, GE Amsterdam, The Netherlands
| | - Mirka Macel
- Molecular Interactions Ecology, Radboud University, NL Nijmegen, The Netherlands
| | - Sanae Mouden
- Plant Sciences and Natural Products, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, , TB Utrecht, The Netherlands
| | - Sandeep J Sarde
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
| | - Robert C Schuurink
- Department of Plant Physiology, University of Amsterdam, Science Park, XH Amsterdam, The Netherlands
| | | | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, , TB Utrecht, The Netherlands
| | - Colette Broekgaarden
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, , TB Utrecht, The Netherlands
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92
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Santamaria ME, Diaz I, Martinez M. Dehydration Stress Contributes to the Enhancement of Plant Defense Response and Mite Performance on Barley. FRONTIERS IN PLANT SCIENCE 2018; 9:458. [PMID: 29681917 PMCID: PMC5898276 DOI: 10.3389/fpls.2018.00458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/22/2018] [Indexed: 05/26/2023]
Abstract
Under natural conditions, plants suffer different stresses simultaneously or in a sequential way. At present, the combined effect of biotic and abiotic stressors is one of the most important threats to crop production. Understanding how plants deal with the panoply of potential stresses affecting them is crucial to develop biotechnological tools to protect plants. As well as for drought stress, the economic importance of the spider mite on agriculture is expected to increase due to climate change. Barley is a host of the polyphagous spider mite Tetranychus urticae and drought produces important yield losses. To obtain insights on the combined effect of drought and mite stresses on the defensive response of this cereal, we have analyzed the transcriptomic responses of barley plants subjected to dehydration (water-deficit) treatment, spider mite attack, or to the combined dehydration-spider mite stress. The expression patterns of mite-induced responsive genes included many jasmonic acid responsive genes and were quickly induced. In contrast, genes related to dehydration tolerance were later up-regulated. Besides, a higher up-regulation of mite-induced defenses was showed by the combined dehydration and mite treatment than by the individual mite stress. On the other hand, the performance of the mite in dehydration stressed and well-watered plants was tested. Despite the stronger defensive response in plants that suffer dehydration and mite stresses, the spider mite demonstrates a better performance under dehydration condition than in well-watered plants. These results highlight the complexity of the regulatory events leading to the response to a combination of stresses and emphasize the difficulties to predict their consequences on crop production.
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Affiliation(s)
- M. E. Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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93
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Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, Burmølle M, Herschend J, Bakker PAHM, Pieterse CMJ. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME JOURNAL 2018. [PMID: 29520025 PMCID: PMC5956071 DOI: 10.1038/s41396-018-0093-1] [Citation(s) in RCA: 411] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.
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Affiliation(s)
- Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Gilles Vismans
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Yang Song
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Jiangsu Provincial Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Wilco P Burgman
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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94
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Overmyer K, Vuorinen K, Brosché M. Interaction points in plant stress signaling pathways. PHYSIOLOGIA PLANTARUM 2018; 162:191-204. [PMID: 28857168 DOI: 10.1111/ppl.12639] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 05/29/2023]
Abstract
Plants live in a world where they are challenged by abiotic and biotic stresses. In response to unfavorable conditions or an acute challenge like a pathogen attack, plants use various signaling pathways that regulate expression of defense genes and other mechanisms to provide resistance or stress adaptation. Identification of the regulatory steps in defense signaling has seen much progress in recent years. Many of the identified signaling pathways show interactions with each other, exemplified by the modulation of the jasmonic acid response by salicylic acid. Accordingly, defense regulation is more appropriately thought of as a web of interactions, rather than linear pathways. Here we describe various regulatory components and how they interact to provide an appropriate defense response. One of the common assays to monitor the output of defense signaling, as well as interaction between signaling pathways, is the measurement of altered gene expression. We illustrate that, while this is a suitable assay to monitor defense regulation, it can also inadvertently provide overstated conclusions about interaction among signaling pathways.
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Affiliation(s)
- Kirk Overmyer
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Katariina Vuorinen
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Mikael Brosché
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
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95
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Yuan Y, Lee H, Hu H, Scheben A, Edwards D. Single-Cell Genomic Analysis in Plants. Genes (Basel) 2018; 9:genes9010050. [PMID: 29361790 PMCID: PMC5793201 DOI: 10.3390/genes9010050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 12/26/2022] Open
Abstract
Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.
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Affiliation(s)
- Yuxuan Yuan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - HueyTyng Lee
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
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96
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Stringlis IA, Proietti S, Hickman R, Van Verk MC, Zamioudis C, Pieterse CMJ. Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:166-180. [PMID: 29024173 PMCID: PMC5765484 DOI: 10.1111/tpj.13741] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/28/2017] [Accepted: 09/29/2017] [Indexed: 05/05/2023]
Abstract
Below ground, microbe-associated molecular patterns (MAMPs) of root-associated microbiota can trigger costly defenses at the expense of plant growth. However, beneficial rhizobacteria, such as Pseudomonas simiae WCS417, promote plant growth and induce systemic resistance without being warded off by local root immune responses. To investigate early root responses that facilitate WCS417 to exert its plant-beneficial functions, we performed time series RNA-Seq of Arabidopsis roots in response to live WCS417 and compared it with MAMPs flg22417 (from WCS417), flg22Pa (from pathogenic Pseudomonas aeruginosa) and fungal chitin. The MAMP transcriptional responses differed in timing, but displayed a large overlap in gene identity. MAMP-upregulated genes are enriched for genes with functions in immunity, while downregulated genes are enriched for genes related to growth and development. Although 74% of the transcriptional changes inflicted by live WCS417 overlapped with the flg22417 profile, WCS417 actively suppressed more than half of the MAMP-triggered transcriptional responses, possibly to allow the establishment of a mutually beneficial interaction with the host root. Interestingly, the sector of the flg22417 -repressed transcriptional network that is not affected by WCS417 has a strong auxin signature. Using auxin response mutant tir1afb2afb3, we demonstrate a dual role for auxin signaling in finely balancing growth-promoting and defense-eliciting activities of beneficial microbes in plant roots.
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Affiliation(s)
- Ioannis A. Stringlis
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
| | - Silvia Proietti
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
- Present address:
Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
| | - Richard Hickman
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
| | - Marcel C. Van Verk
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
- Present address:
Keygene N.V.P.O. Box 2166700 AEWageningenthe Netherlands
| | - Christos Zamioudis
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
- Present address:
Rijk Zwaan Breeding B.V.P.O. Box 402678ZG De Lierthe Netherlands
| | - Corné M. J. Pieterse
- Plant‐Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityP.O. Box 800.563508 TBUtrechtthe Netherlands
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97
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Frachon L, Bartoli C, Carrère S, Bouchez O, Chaubet A, Gautier M, Roby D, Roux F. A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale. FRONTIERS IN PLANT SCIENCE 2018; 9:967. [PMID: 30042773 PMCID: PMC6048436 DOI: 10.3389/fpls.2018.00967] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome-environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.
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Affiliation(s)
- Léa Frachon
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Department of Systematic and Evolutionary Botany, University of Zurich, Zürich, Switzerland
| | - Claudia Bartoli
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Olivier Bouchez
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Adeline Chaubet
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut de Recherche pour le Développement, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- *Correspondence: Fabrice Roux,
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98
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de Bobadilla MF, Friman J, Pangesti N, Dicke M, van Loon JJA, Pineda A. Does drought stress modify the effects of plant-growth promoting rhizobacteria on an aboveground chewing herbivore? INSECT SCIENCE 2017; 24:1034-1044. [PMID: 28498521 DOI: 10.1111/1744-7917.12477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/10/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
Soil microbes have important effects on the interactions of plants with their environment, by promoting plant growth, inducing resistance to pests or by conferring tolerance to abiotic stress. However, their effects are variable and the factors responsible for this variation are mainly unknown. Our aim was to assess how drought stress modifies the effect of the nonpathogenic rhizobacterium Pseudomonas simiae WCS417r on plant growth and resistance against the generalist leaf-chewing caterpillar Mamestra brassicae. We studied Arabidopsis thaliana Col-0 plants, as well as mutants altered in the biosynthesis of the phytohormones jasmonic acid (JA) and abscisic acid (ABA). Caterpillars did not prefer rhizobacteria-treated plants, independently of drought stress. Rhizobacteria colonization had a variable effect on caterpillar performance, which ranged from positive in one experiment to neutral in a second one. Drought had a consistent negative effect on herbivore performance; however, it did not modify the effect of rhizobacteria on herbivore performance. The effect of drought on herbivore performance was JA-mediated (confirmed with the use of the dde2-2 mutant), but it was still present in the ABA-deficient mutant aba2-1. Plant biomass was reduced by both drought and herbivory but it was enhanced by rhizobacterial colonization. Pseudomonas simiae WCS417r is able to promote plant growth even when plants are suffering herbivory. Nevertheless, the microbial effect on the herbivore is variable, independently of drought stress. To get the best possible outcome from the rhizobacteria-plant mutualism it is important to understand which other factors may be responsible for its context-dependency.
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Affiliation(s)
| | - Julia Friman
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Nurmi Pangesti
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Joop J A van Loon
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Ana Pineda
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, The Netherlands
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99
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Zhang H, Guiguet A, Dubreuil G, Kisiala A, Andreas P, Emery RJN, Huguet E, Body M, Giron D. Dynamics and origin of cytokinins involved in plant manipulation by a leaf-mining insect. INSECT SCIENCE 2017; 24:1065-1078. [PMID: 28636152 DOI: 10.1111/1744-7917.12500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/03/2017] [Accepted: 06/08/2017] [Indexed: 05/22/2023]
Abstract
Several herbivorous insects and plant-associated microorganisms control the phytohormonal balance, thus enabling them to successfully exploit the plant by inhibiting plant defenses and withdrawing plant resources for their own benefit. The leaf-mining moth Phyllonorycter blancardella modifies the cytokinin (CK) profile of mined leaf-tissues, and the insect symbiotic bacteria Wolbachia is involved in the plant manipulation to the benefit of the insect host. To gain a deeper understanding into the possible origin and dynamics of CKs, we conducted an extensive characterization of CKs in larvae and in infected apple leaves. Our results show the enhanced CK levels in mines, both on green and yellow leaves, allowing insects to control their nutritional supply under fluctuating environmental conditions. The spatial distribution of CKs within the mined leaves shows that hormone manipulation is strictly limited to the mine suggesting the absence of CK translocation from distant leaf areas toward the insect feeding site. Mass spectrometry analyses reveal that major CK types accumulating in mines and larvae are similar to what is observed for most gall-inducers, suggesting that strategies underlying the plant manipulation may be shared between herbivorous insects with distinct life histories. Results further show that CKs are detected in the highest levels in larvae, reinforcing our hypothesis that CKs accumulating in the mines originate from the insect itself. Presence of bacteria-specific methylthio-CKs is consistent with previous results suggesting that insect bacterial symbionts contribute to the observed phenotype. Our study provides key findings toward the understanding of molecular mechanisms underlying this intricate plant-insect-microbe interaction.
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Affiliation(s)
- Hui Zhang
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
| | - Antoine Guiguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
- Département de Biologie, École Normale Supérieure de Lyon, Lyon, France
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
| | - Anna Kisiala
- Department of Biology, Trent University, Peterborough, Canada
| | - Peter Andreas
- Department of Biology, Trent University, Peterborough, Canada
| | - R J Neil Emery
- Department of Biology, Trent University, Peterborough, Canada
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
| | - Mélanie Body
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - David Giron
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
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100
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STAM JELTJEM, CHRÉTIEN LUCILLE, DICKE MARCEL, POELMAN ERIKH. Response of Brassica oleracea to temporal variation in attack by two herbivores affects preference and performance of a third herbivore. ECOLOGICAL ENTOMOLOGY 2017; 42:803-815. [PMID: 29200601 PMCID: PMC5698737 DOI: 10.1111/een.12455] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/13/2017] [Accepted: 06/30/2017] [Indexed: 05/21/2023]
Abstract
1. Plants are frequently under attack by multiple insect herbivores, which may interact indirectly through herbivore-induced changes in the plant's phenotype. The identity, order, and timing of herbivore arrivals may influence the outcome of interactions between two herbivores. How these aspects affect, in turn, subsequently arriving herbivores that feed on double herbivore-induced plants has not been widely investigated. 2. This study tested whether the order and timing of arrival of two inducing herbivores from different feeding guilds affected the preference and performance of a subsequently arriving third herbivore, caterpillars of Mamestra brassicae L. (Lepidoptera: Noctuidae). Aphids [Brevicoryne brassicae L. (Hemiptera: Aphididae)] and caterpillars [Plutella xylostella L. (Lepidoptera: Yponomeutidae)] were introduced onto wild Brassica oleracea L. (Brassicaceae) plants in different sequences and with different arrival times. The effects of these plant treatments on M. brassicae caterpillars were assessed in pairwise preference tests and no-choice performance tests. 3. The caterpillars of M. brassicae preferred to feed from undamaged plants rather than double herbivore-induced plants. Compared with undamaged plants, they preferred plant material on which aphids had arrived first followed by caterpillars, whereas they avoided plant material with the reverse order of herbivore arrival. Performance of the caterpillars increased with increasing arrival time between herbivore infestations in double herbivore-induced plants. Although M. brassicae grew faster on plants induced by aphids than on those induced by caterpillars alone, its performance was not affected by the order of previous herbivore arrival. 4. These results imply that the timing of colonisation by multiple herbivores determines the outcome of plant-mediated herbivore-herbivore interactions.
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Affiliation(s)
- JELTJE M. STAM
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
| | - LUCILLE CHRÉTIEN
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
- Biology Department, Master Biosciences, École Normale Supérieure de LyonUniversité Claude Bernard Lyon 1Lyon Cedex 07France
| | - MARCEL DICKE
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
| | - ERIK H. POELMAN
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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