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Sperschneider J, Yildirir G, Rizzi YS, Malar C M, Mayrand Nicol A, Sorwar E, Villeneuve-Laroche M, Chen ECH, Iwasaki W, Brauer EK, Bosnich W, Gutjahr C, Corradi N. Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host-plant interactions. Nat Microbiol 2024; 9:1393. [PMID: 37989883 DOI: 10.1038/s41564-023-01562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Yanina S Rizzi
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Eric C H Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Elizabeth K Brauer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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Sperschneider J, Yildirir G, Rizzi YS, Malar C M, Mayrand Nicol A, Sorwar E, Villeneuve-Laroche M, Chen ECH, Iwasaki W, Brauer EK, Bosnich W, Gutjahr C, Corradi N. Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host-plant interactions. Nat Microbiol 2023; 8:2142-2153. [PMID: 37884816 DOI: 10.1038/s41564-023-01495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts that can carry thousands of nuclei deriving from two parental strains in a large syncytium. These co-existing genomes can also vary in abundance with changing environmental conditions. Here we assemble the nuclear genomes of all four publicly available AMF heterokaryons using PacBio high-fidelity and Hi-C sequencing. We find that the two co-existing genomes of these strains are phylogenetically related but differ in structure, content and epigenetics. We confirm that AMF heterokaryon genomes vary in relative abundance across conditions and show this can lead to nucleus-specific differences in expression during interactions with plants. Population analyses also reveal signatures of genetic exchange indicative of past events of sexual reproduction in these strains. This work uncovers the origin and contribution of two nuclear genomes in AMF heterokaryons and opens avenues for the improvement and environmental application of these strains.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Yanina S Rizzi
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Eric C H Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Elizabeth K Brauer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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Brauer EK, Ahsan N, Popescu GV, Thelen JJ, Popescu SC. Back From the Dead: The Atypical Kinase Activity of a Pseudokinase Regulator of Cation Fluxes During Inducible Immunity. Front Plant Sci 2022; 13:931324. [PMID: 36035673 PMCID: PMC9403797 DOI: 10.3389/fpls.2022.931324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Pseudokinases are thought to lack phosphotransfer activity due to altered canonical catalytic residues within their kinase domain. However, a subset of pseudokinases maintain activity through atypical phosphotransfer mechanisms. The Arabidopsis ILK1 is a pseudokinase from the Raf-like MAP3K family and is the only known plant pseudokinase with confirmed protein kinase activity. ILK1 activity promotes disease resistance and molecular pattern-induced root growth inhibition through its stabilization of the HAK5 potassium transporter with the calmodulin-like protein CML9. ILK1 also has a kinase-independent function in salt stress suggesting that it interacts with additional proteins. We determined that members of the ILK subfamily are the sole pseudokinases within the Raf-like MAP3K family and identified 179 novel putative ILK1 protein interactors. We also identified 70 novel peptide targets for ILK1, the majority of which were phosphorylated in the presence of Mn2+ instead of Mg2+ in line with modifications in ILK1's DFG cofactor binding domain. Overall, the ILK1-targeted or interacting proteins included diverse protein types including transporters (HAK5, STP1), protein kinases (MEKK1, MEKK3), and a cytokinin receptor (AHK2). The expression of 31 genes encoding putative ILK1-interacting or phosphorylated proteins, including AHK2, were altered in the root and shoot in response to molecular patterns suggesting a role for these genes in immunity. We describe a potential role for ILK1 interactors in the context of cation-dependent immune signaling, highlighting the importance of K+ in MAMP responses. This work further supports the notion that ILK1 is an atypical kinase with an unusual cofactor dependence that may interact with multiple proteins in the cell.
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Affiliation(s)
- Elizabeth K. Brauer
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States
| | - Nagib Ahsan
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - George V. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Jay J. Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sorina C. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
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Manes N, Brauer EK, Hepworth S, Subramaniam R. MAMP and DAMP signaling contributes resistance to Fusarium graminearum in Arabidopsis. J Exp Bot 2021; 72:6628-6639. [PMID: 34405877 DOI: 10.1093/jxb/erab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Plants perceive externally produced microbe-associated molecular patterns (MAMPs) and endogenously produced danger-associated molecular patterns (DAMPs) to activate inducible immunity. While several inducible immune responses have been observed during Fusarium graminearum infection, the identity of the signaling pathways involved is only partly known. We screened 227 receptor kinase and innate immune response genes in Arabidopsis to identify nine genes with a role in F. graminearum resistance. Resistance-promoting genes included the chitin receptors LYK5 and CERK1, and the reactive oxygen species (ROS)-producing NADPH oxidase RbohF, which were required for full inducible immune responses during infection. Two of the genes identified in our screen, APEX and the PAMP-induced peptide 1 (PIP1) DAMP receptor RLK7, repressed F. graminearum resistance. Both RbohF and RLK7 were required for full chitin-induced immune responses and PIP1 precursor expression was induced by chitin and F. graminearum infection. Together, this indicates that F. graminearum resistance is mediated by MAMP and DAMP signaling pathways and that chitin-induced signaling is enhanced by PIP1 perception and ROS production.
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Affiliation(s)
- Nimrat Manes
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Shelley Hepworth
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
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Abstract
Fungal pathogens survive harsh environments and overcome physical, temporal, and chemical barriers to colonize their hosts and reproduce. Fusarium graminearum was one of the first fungal plant pathogens for which transcriptomic tools were developed, making analysis of gene expression a cornerstone approach in studying its biology. The analysis of gene expression in diverse in vitro conditions and during infection of different cereal crops has revealed subsets of both unique and shared transcriptionally regulated genes. Together with genetic studies, these approaches have enhanced our understanding of the development and infection cycle of this economically important pathogen. Here, we will outline recent advances in transcriptional profiling during sporogenesis, spore germination, vegetative growth, and host infection. Several transcriptional regulators have been identified as essential components in these responses and the role of select transcription factors will be highlighted. Finally, we describe some of the gaps in our understanding of F. graminearum biology and how expression analysis could help to address these gaps.
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Affiliation(s)
- Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
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Brauer EK, Balcerzak M, Rocheleau H, Leung W, Schernthaner J, Subramaniam R, Ouellet T. Genome Editing of a Deoxynivalenol-Induced Transcription Factor Confers Resistance to Fusarium graminearum in Wheat. Mol Plant Microbe Interact 2020; 33:553-560. [PMID: 31790345 DOI: 10.1094/mpmi-11-19-0332-r] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Deoxynivalenol (DON) is a mycotoxin virulence factor that promotes growth of the Fusarium graminearum fungus in wheat floral tissues. To further our understanding of the effects of DON exposure on plant cell function, we characterized DON-induced transcriptional changes in wheat spikelets. Four hundred wheat genes were differentially expressed during infection with wild-type F. graminearum as compared with a Δtri5 mutant strain that is unable to produce DON. Most of these genes were more induced by the DON-producing strain and included genes involved in secondary metabolism, signaling, transport, and stress responses. DON induction was confirmed for a subset of the genes, including TaNFXL1, by treating tissues with DON directly. Previous work indicates that the NFXL1 ortholog represses trichothecene-induced defense responses and bacterial resistance in Arabidopsis, but the role of the NFXL family has not been studied in wheat. We observed greater DON-induced TaNFXL1 gene expression in a susceptible wheat genotype relative to the F. graminearum-resistant genotype Wuhan 1. Functional testing using both virus-induced gene silencing and CRISPR-mediated genome editing indicated that TaNFXL1 represses F. graminearum resistance. Together, this suggests that targeting the TaNFXL1 gene may help to develop disease resistance in cultivated wheat.
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Affiliation(s)
- Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Winnie Leung
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. Correction to: An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. Plant Methods 2019; 15:163. [PMID: 31892936 PMCID: PMC6936137 DOI: 10.1186/s13007-019-0539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
[This corrects the article DOI: 10.1186/s13007-019-0500-2.].
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Brauer EK, Manes N, Bonner C, Subramaniam R. Two 14-3-3 proteins contribute to nitrogen sensing through the TOR and glutamine synthetase-dependent pathways in Fusarium graminearum. Fungal Genet Biol 2019; 134:103277. [PMID: 31605748 DOI: 10.1016/j.fgb.2019.103277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/25/2022]
Abstract
Fusarium graminearum responds to environmental cues to modulate its growth and metabolism during wheat pathogenesis. Nitrogen limitation activates virulence-associated behaviours in F. graminearum including mycotoxin production and penetrative growth. In other filamentous fungi, nitrogen sensing is mediated by both the Target of Rapamycin (TOR) and the glutamine synthetase (GS)-dependent signaling pathways. While TOR-dependent nitrogen responses have been demonstrated in F. graminearum, the involvement of GS remains unclear. Our study indicates that both the TOR and GS signalling pathways are involved in nitrogen sensing in F. graminearum and contribute to glutamine-induced mycelial growth. However, neither pathway is required for glutamine-induced repression of the mycotoxin deoxynivalenol (DON) indicating that an additional nitrogen sensing pathway must exist. Further, two genes FgBMH1 and FgBMH2 encoding 14-3-3 proteins regulate nitrogen responses with effects on gene expression, DON production and mycelial growth. Unlike yeast, where 14-3-3s function redundantly in regulating nitrogen sensing, the 14-3-3 proteins have differing functions in F. graminearum. While both FgBMH1 and FgBMH2 regulate early glutamine-induced DON repression, only FgBMH2 is involved in regulating reproduction, virulence and glutamine-induced AreA repression. Together, our findings help to clarify the nitrogen sensing pathways in F. graminearum and highlight the involvement of 14-3-3s in the nitrogen response of filamentous fungi.
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Affiliation(s)
- Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Nimrat Manes
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Christopher Bonner
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada.
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. Plant Methods 2019; 15:119. [PMID: 31673276 PMCID: PMC6814032 DOI: 10.1186/s13007-019-0500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgRNA) and the CRISPR/Cas9 system, small editing events such as deletions of few bases can be obtained. However larger deletions are required for some applications. In addition, identification and characterization of edited events can be challenging in plants with complex genomes, such as wheat. RESULTS In this study, we used the CRISPR/Cas9 system and developed a protocol that yielded high number of large deletions employing a pair of co-expressed sgRNA to target the same gene. The protocol was validated by targeting three genes, TaABCC6, TaNFXL1 and TansLTP9.4 in a wheat protoplast assay. Deletions of sequences located between the two sgRNA in each gene were the most frequent editing events observed for two of the three genes. A comparative assessment of editing frequencies between a codon-optimized Cas9 for expression in algae, crCas9, and a plant codon-optimized Cas9, pcoCas9, showed more consistent results with the vector expressing pcoCas9. Editing of TaNFXL1 by co-expression of sgRNA pair was investigated in transgenic wheat plants. Given the ploidy of bread wheat, a rapid, robust and inexpensive genotyping protocol was also adapted for hexaploid genomes and shown to be a useful tool to identify homoeolog-specific editing events in wheat. CONCLUSIONS Co-expressed pairs of sgRNA targeting single genes in conjunction with the CRISPR/Cas9 system produced large deletions in wheat. In addition, a genotyping protocol to identify editing events in homoeologs of TaNFXL1 was successfully adapted.
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Brauer EK, Popescu GV, Singh DK, Calviño M, Gupta K, Gupta B, Chakravarthy S, Popescu SC. Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae. PLoS Biol 2018; 16:e2005956. [PMID: 30540739 PMCID: PMC6322785 DOI: 10.1371/journal.pbio.2005956] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 01/07/2019] [Accepted: 11/16/2018] [Indexed: 11/18/2022] Open
Abstract
Plant protein kinases form redundant signaling pathways to perceive microbial pathogens and activate immunity. Bacterial pathogens repress cellular immune responses by secreting effectors, some of which bind and inhibit multiple host kinases. To understand how broadly bacterial effectors may bind protein kinases and the function of these kinase interactors, we first tested kinase–effector (K-E) interactions using the Pseudomonas syringae pv. tomato–tomato pathosystem. We tested interactions between five individual effectors (HopAI1, AvrPto, HopA1, HopM1, and HopAF1) and 279 tomato kinases in tomato cells. Over half of the tested kinases interacted with at least one effector, and 48% of these kinases interacted with more than three effectors, suggesting a role in the defense. Next, we characterized the role of select multi-effector–interacting kinases and revealed their roles in basal resistance, effector-triggered immunity (ETI), or programmed cell death (PCD). The immune function of several of these kinases was only detectable in the presence of effectors, suggesting that these kinases are critical when particular cell functions are perturbed or that their role is typically masked. To visualize the kinase networks underlying the cellular responses, we derived signal-specific networks. A comparison of the networks revealed a limited overlap between ETI and basal immunity networks. In addition, the basal immune network complexity increased when exposed to some of the effectors. The networks were used to successfully predict the role of a new set of kinases in basal immunity. Our work indicates the complexity of the larger kinase-based defense network and demonstrates how virulence- and avirulence-associated bacterial effectors alter sectors of the defense network. Some bacterial pathogens secrete virulence factors called effectors, which influence host tissues during infection. The impact of such bacterial effectors on the transmission of immune signals in plants remains poorly understood. In this study, we developed an integrative network approach to discover interactions between bacterial effectors and a class of host signal-mediating enzymes called protein kinases. We also characterized the functions of the targets of these kinases in order to understand how bacterial effectors might disrupt the flow of information in signaling pathways within plant cells. We show that plants activate larger signaling networks when inoculated with pathogens that produce effectors. We also find that plant signaling networks are specific to individual effectors and that the networks include kinases with both positive and negative effects on plant resistance to pathogens. We propose that the topology of immune signaling networks is determined by the plant’s ability to activate compensatory pathways in response to the effectors’ network-disruptive actions. Conversely, pathogens may increase their virulence both by disrupting host signaling at the membrane-located end of the signaling network and by recruiting cytosolic kinases. This work provides a framework for the study of plant–pathogen communication and could be used to prioritize targets for improving resistance in crops.
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Affiliation(s)
- Elizabeth K. Brauer
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
- The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania
| | - Dharmendra K. Singh
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Mauricio Calviño
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Kamala Gupta
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Bhaskar Gupta
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Suma Chakravarthy
- Department of Plant Pathology, Cornell University, Ithaca, New York, United States of America
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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Bahadoor A, Brauer EK, Bosnich W, Schneiderman D, Johnston A, Aubin Y, Blackwell B, Melanson JE, Harris LJ. Gramillin A and B: Cyclic Lipopeptides Identified as the Nonribosomal Biosynthetic Products of Fusarium graminearum. J Am Chem Soc 2018; 140:16783-16791. [PMID: 30395461 DOI: 10.1021/jacs.8b10017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The virulence and broad host range of Fusarium graminearum is associated with its ability to secrete an arsenal of phytotoxic secondary metabolites, including the regulated mycotoxins belonging to the deoxynivalenol family. The TRI genes responsible for the biosynthesis of deoxynivalenol and related compounds are usually expressed during fungal infection. However, the F. graminearum genome harbors an array of unexplored biosynthetic gene clusters that are also co-induced with the TRI genes, including the nonribosomal peptide synthetase 8 ( NRPS8) gene cluster. Here, we identify two bicyclic lipopeptides, gramillin A (1) and B (2), as the biosynthetic end products of NRPS8. Structural elucidation by high-resolution LC-MS and NMR, including 1H-15N-13C HNCO and HNCA on isotopically enriched compounds, revealed that the gramillins possess a fused bicyclic structure with ring closure of the main peptide macrocycle occurring via an anhydride bond. Through targeted gene disruption, we characterized the GRA1 biosynthetic gene and its transcription factor GRA2 in the NRPS8 gene cluster. Further, we show that the gramillins are produced in planta on maize silks, promoting fungal virulence on maize but have no discernible effect on wheat head infection. Leaf infiltration of the gramillins induces cell death in maize, but not in wheat. Our results show that F. graminearum deploys the gramillins as a virulence agent in maize, but not in wheat, thus displaying host-specific adaptation.
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Affiliation(s)
- Adilah Bahadoor
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Elizabeth K Brauer
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Anne Johnston
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Yves Aubin
- Centre for Biologics Evaluation, Biologics, and Genetic Therapies Directorate , Health Canada , Ottawa , Ontario K1A 0K9 , Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Jeremy E Melanson
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Linda J Harris
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
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12
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De Benedictis M, Brunetti C, Brauer EK, Andreucci A, Popescu SC, Commisso M, Guzzo F, Sofo A, Ruffini Castiglione M, Vatamaniuk OK, Sanità di Toppi L. The Arabidopsis thaliana Knockout Mutant for Phytochelatin Synthase1 ( cad1-3) Is Defective in Callose Deposition, Bacterial Pathogen Defense and Auxin Content, But Shows an Increased Stem Lignification. Front Plant Sci 2018; 9:19. [PMID: 29403524 PMCID: PMC5786554 DOI: 10.3389/fpls.2018.00019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/04/2018] [Indexed: 05/15/2023]
Abstract
The enzyme phytochelatin synthase (PCS) has long been studied with regard to its role in metal(loid) detoxification in several organisms, i.e., plants, yeasts, and nematodes. It is in fact widely recognized that PCS detoxifies a number of heavy metals by catalyzing the formation of thiol-rich oligomers, namely phytochelatins, from glutathione and related peptides. However, recent investigations have highlighted other possible roles played by the PCS enzyme in the plant cell, e.g., the control of pathogen-triggered callose deposition. In order to examine novel aspects of Arabidopsis thaliana PCS1 (AtPCS1) functions and to elucidate its possible roles in the secondary metabolism, metabolomic data of A. thaliana wild-type and cad1-3 mutant were compared, the latter lacking AtPCS1. HPLC-ESI-MS analysis showed differences in the relative levels of metabolites from the glucosinolate and phenylpropanoid pathways between cad1-3 and wild-type plants. Specifically, in control (Cd-untreated) plants, higher levels of 4-methoxy-indol-3-ylmethylglucosinolate were found in cad1-3 plants vs. wild-type. Moreover, the cad1-3 mutant showed to be impaired in the deposit of callose after Cd exposure, suggesting that AtPCS1 protects the plant against the toxicity of heavy metals not only by synthesizing PCs, but also by contributing to callose deposition. In line with the contribution of callose in counteracting Cd toxicity, we found that another callose-defective mutant, pen2-1, was more sensitive to high concentrations of Cd than wild-type plants. Moreover, cad1-3 plants were more susceptible than wild-type to the hemibiotrophic bacterial pathogen Pseudomonas syringae. The metabolome also revealed differences in the relative levels of hydroxycinnamic acids and flavonols, with consequences on cell wall properties and auxin content, respectively. First, increased lignification in the cad1-3 stems was found, probably aimed at counteracting the entry of Cd into the inner tissues. Second, in cad1-3 shoots, increased relative levels of kaempferol 3,7 dirhamnoside and quercetin hexoside rhamnoside were detected. These flavonols are endogenous inhibitors of auxin transport in planta; auxin levels in both roots and shoots of the cad1-3 mutant were in fact lower than those of the wild-type. Overall, our data highlight novel aspects of AtPCS1 functions in A. thaliana.
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Affiliation(s)
- Maria De Benedictis
- Department of Life Sciences, University of Parma, Parma, Italy
- Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Cecilia Brunetti
- National Research Council of Italy, Istituto Per La Valorizzazione Del Legno E Delle Specie Arboree, Florence, Italy
| | | | | | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Mauro Commisso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Flavia Guzzo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Adriano Sofo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | | | - Olena K. Vatamaniuk
- Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Luigi Sanità di Toppi
- Department of Biology, University of Pisa, Pisa, Italy
- *Correspondence: Luigi Sanità di Toppi,
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13
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Popescu SC, Brauer EK, Dimlioglu G, Popescu GV. Insights into the Structure, Function, and Ion-Mediated Signaling Pathways Transduced by Plant Integrin-Linked Kinases. Front Plant Sci 2017; 8:376. [PMID: 28421082 PMCID: PMC5376563 DOI: 10.3389/fpls.2017.00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/06/2017] [Indexed: 05/04/2023]
Abstract
Kinases facilitate detection of extracellular signals and set in motion cellular responses for plant adaptation and survival. Some of the energy utilized for kinase signal processing is produced through the activity of ion transporters. Additionally, the synergy between cellular ions and signal transduction influences plant response to pathogens, and their growth and development. In plants, the signaling elements that connect cell wall and membrane sensors with ion homeostasis and transport-mediated processes are largely unknown. Current research indicates that plant Integrin-Linked Kinases (ILKs), a subfamily Raf-like MAP2K Kinases, may have evolved to fulfill this role. In this review, we explore new findings on plant ILKs placing a particular focus on the connection between ILKs proteins unique structural features and ILKs functions. The ankyrin repeat motifs and the kinase domains of ILKs in Arabidopsis and land plants lineage, respectively, are analyzed and discussed as potential determinants of ILKs' metal ion cofactor specificity and their enzymatic and interaction activities. Further, ILKs regulation through gene expression, subcellular localization, and ions and ion transporters is reviewed in the context of recent studies. Finally, using evidence from literature and interactomics databanks, we infer ILKs-dependent cellular pathways and highlight their potential in transmitting multiple types of signals originating at the interface between the cell wall and plasma membrane.
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Affiliation(s)
- Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Plant Pathology, and Entomology, Mississippi State University, StarkvilleMS, USA
| | - Elizabeth K. Brauer
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Plant Pathology, and Entomology, Mississippi State University, StarkvilleMS, USA
| | - George V. Popescu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, StarkvilleMS, USA
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14
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Brauer EK, Ahsan N, Dale R, Kato N, Coluccio AE, Piñeros MA, Kochian LV, Thelen JJ, Popescu SC. The Raf-like Kinase ILK1 and the High Affinity K+ Transporter HAK5 Are Required for Innate Immunity and Abiotic Stress Response. Plant Physiol 2016; 171:1470-84. [PMID: 27208244 PMCID: PMC4902592 DOI: 10.1104/pp.16.00035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 05/04/2023]
Abstract
Plant perception of pathogen-associated molecular patterns (PAMPs) and other environmental stresses trigger transient ion fluxes at the plasma membrane. Apart from the role of Ca(2+) uptake in signaling, the regulation and significance of PAMP-induced ion fluxes in immunity remain unknown. We characterized the functions of INTEGRIN-LINKED KINASE1 (ILK1) that encodes a Raf-like MAP2K kinase with functions insufficiently understood in plants. Analysis of ILK1 mutants impaired in the expression or kinase activity revealed that ILK1 contributes to plant defense to bacterial pathogens, osmotic stress sensitivity, and cellular responses and total ion accumulation in the plant upon treatment with a bacterial-derived PAMP, flg22. The calmodulin-like protein CML9, a negative modulator of flg22-triggered immunity, interacted with, and suppressed ILK1 kinase activity. ILK1 interacted with and promoted the accumulation of HAK5, a putative (H(+))/K(+) symporter that mediates a high-affinity uptake during K(+) deficiency. ILK1 or HAK5 expression was required for several flg22 responses including gene induction, growth arrest, and plasma membrane depolarization. Furthermore, flg22 treatment induced a rapid K(+) efflux at both the plant and cellular levels in wild type, while mutants with impaired ILK1 or HAK5 expression exhibited a comparatively increased K(+) loss. Taken together, our results position ILK1 as a link between plant defense pathways and K(+) homeostasis.
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Affiliation(s)
- Elizabeth K Brauer
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Nagib Ahsan
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Renee Dale
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Naohiro Kato
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Alison E Coluccio
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Miguel A Piñeros
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Leon V Kochian
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Jay J Thelen
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
| | - Sorina C Popescu
- The Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 (E.K.B., S.C.P.); Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211 (N.A., J.T.T.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (R.D., N.K.); and Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York 14853 (A.E.C., M.A.P., L.V.K.)
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15
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Abstract
A Report on the Plant Genomes & Biotechnology: From Genes to Networks meeting, held at the Cold Spring Harbor Laboratories, USA, December 4–7, 2013.
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16
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Singh DK, Calviño M, Brauer EK, Fernandez-Pozo N, Strickler S, Yalamanchili R, Suzuki H, Aoki K, Shibata D, Stratmann JW, Popescu GV, Mueller LA, Popescu SC. The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species. Mol Plant Microbe Interact 2014; 27:7-17. [PMID: 24047240 DOI: 10.1094/mpmi-08-13-0218-ta] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein kinase-driven phosphorylation constitutes the core of cellular signaling. Kinase components of signal transduction pathways are often targeted for inactivation by pathogens. The study of kinases and immune signal transduction in the model crop tomato (Solanum lycopersicum) would benefit from the availability of community-wide resources for large scale and systems-level experimentation. Here, we defined the tomato kinome and performed a comprehensive comparative analysis of the tomato kinome and 15 other plant species. We constructed a tomato kinase library (TOKN 1.0) of over 300 full-length open reading frames (ORF) cloned into a recombination-based vector. We developed a high-throughput pipeline to isolate and transform tomato protoplasts. A subset of the TOKN 1.0 library kinases were expressed in planta, were purified, and were used to generate a functional tomato protein microarray. All resources created were utilized to test known and novel associations between tomato kinases and Pseudomonas syringae DC3000 effectors in a large-scale format. Bsk7 was identified as a component of the plant immune response and a candidate effector target. These resources will enable comprehensive investigations of signaling pathways and host-pathogen interactions in tomato and other Solanaceae spp.
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17
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Abstract
Comprehensive analysis of protein kinases and cellular signaling pathways requires the identification of kinase substrates and interaction partners using large-scale amenable approaches. Here, we describe our methods for producing plant protein microarrays (PMAs) and discuss various parameters critical to the quality of PMAs. Next, we describe methods for detecting protein-protein interactions and kinase activity including auto-phosphorylation and substrate phosphorylation. We have provided a short video demonstrating how to conduct an interaction assay and how to properly handle a protein microarray. Finally, a set of analytical methods are presented as a bioinformatics pipeline for the acquisition of PMA data and for selecting PMA candidates using statistical testing. The experimental and analytical protocols described here outline the steps to produce and utilize PMAs to analyze signaling networks.
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Affiliation(s)
- Elizabeth K Brauer
- The Boyce Thompson Institute for Plant Research, 533 Tower Road, Office 121, Ithaca, NY, 14850, USA
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18
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Brauer EK, Rochon A, Bi YM, Bozzo GG, Rothstein SJ, Shelp BJ. Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase1. Physiol Plant 2011; 141:361-72. [PMID: 21214879 DOI: 10.1111/j.1399-3054.2011.01443.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cytosolic glutamine synthetase (GS1) is responsible for the primary assimilation of ammonia, and a role in nitrogen (N) remobilization is implicated from its vascular localization and enhanced expression during senescence. This paper tested the hypothesis that overexpression (OX) of GS1 in rice improves utilization N use efficiency (UtE = spikelet yield/shoot N content). Three GS1 OX lines were identified using activity assays and quantitative polymerase chain reaction. Physiological analysis of the OX lines, as well as azygous and wild-type (Wt) controls, was conducted with mature plants after growth under varying nitrate conditions (non-limiting N, limiting N, transfer from non-limiting N to limiting N at panicle emergence) and growth environments (growth chamber vs greenhouse). Overall, OX lines did not differ from azygous controls in vegetative yield or shoot N content. In two of the three growth trials (i.e. the growth chamber trials) harvest index, N harvest index (spikelet N content/shoot N content) and UtE were generally enhanced in the OX lines relative to their azygous controls. These characteristics were highly correlated with percent spikelets filled and spikelet number. Thus, N partitioning in rice during grain filling could be altered by GS1 OX, resulting in improved UtE. Unfortunately, GS OX did not result in more efficient use of N under limiting N than under non-limiting N, and is therefore unlikely to result in the use of less N under field conditions. Transformation effects significantly hindered the productivity of the OX lines, but backcrossing to the Wt should overcome this.
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Affiliation(s)
- Elizabeth K Brauer
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
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