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Fontes EPB. SERKs and NIKs: Coreceptors or signaling hubs in a complex crosstalk between growth and defense? Curr Opin Plant Biol 2024; 77:102447. [PMID: 37690927 DOI: 10.1016/j.pbi.2023.102447] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) and NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASES (NIKs) belong to superfamily II of leucine-rich repeat receptor-like kinases, which share cytosolic kinase conservation and a similar ectodomain configuration. SERKs have been extensively demonstrated to function as coreceptors of receptor-like kinases, which sense biotic or developmental signals to initiate specific responses. NIKs, on the other hand, have emerged as downstream components in signaling cascades, not functioning as coreceptors but rather serving as hubs that converge information from both biotic and abiotic signals, resulting in a unified response. Like SERKs, NIKs play a crucial role as information spreaders in plant cells, forming hubs of high centrality. However, unlike SERKs, which function as coreceptors and assemble paired receptor-specific responses, NIKs employ a shared signaling circuit to transduce diverse biotic and abiotic signals into the same physiological response. Therefore, this review highlights the concept of signaling hubs that differ from coreceptors in signaling pathways.
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Affiliation(s)
- Elizabeth P B Fontes
- Biochemistry and Molecular Biology Department, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
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Martins LGC, Fontes EPB. Replication Assay of Begomovirus in Arabidopsis Protoplasts. Methods Mol Biol 2024; 2724:111-125. [PMID: 37987902 DOI: 10.1007/978-1-0716-3485-1_9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Protoplasts are isolated plant cells from which the cell walls have been removed by treatment with fungal cellulase and macerozyme enzymes, which degrade the primary components of the cell wall. The protoplasts are totipotent, sensitive, and versatile; thereby, they have been extensively used to study signal transduction pathways, cell-autonomous responses, and replication of plant viruses. This system has several advantages over the use of whole plants for viral replication, including a high percentage of infected cells and uncoupling virus movement from replication assays. Here, we describe a simple and efficient protocol for begomovirus transfection and replication in Arabidopsis protoplasts. The method consists of four steps, (i) protoplast isolation, (ii) PEG-calcium transfection of begomovirus infectious clones, (iii) elimination of input plasmid DNA by DpnI digestion, and (iv) quantification of the viral newly synthesized DNA by qPCR. The protoplasts can be transformed efficiently with begomovirus infectious clones, and virus replication can be monitored by the accumulation of nascent viral DNA in the infected protoplasts.
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Affiliation(s)
- Laura Gonçalves Costa Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Breves SS, Silva FA, Euclydes NC, Saia TFF, Jean-Baptiste J, Andrade Neto ER, Fontes EPB. Begomovirus-Host Interactions: Viral Proteins Orchestrating Intra and Intercellular Transport of Viral DNA While Suppressing Host Defense Mechanisms. Viruses 2023; 15:1593. [PMID: 37515277 PMCID: PMC10384534 DOI: 10.3390/v15071593] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Begomoviruses, which belong to the Geminiviridae family, are intracellular parasites transmitted by whiteflies to dicotyledonous plants thatsignificantly damage agronomically relevant crops. These nucleus-replicating DNA viruses move intracellularly from the nucleus to the cytoplasm and then, like other plant viruses, cause disease by spreading systemically throughout the plant. The transport proteins of begomoviruses play a crucial role in recruiting host components for the movement of viral DNA within and between cells, while exhibiting functions that suppress the host's immune defense. Pioneering studies on species of the Begomovirus genus have identified specific viral transport proteins involved in intracellular transport, cell-to-cell movement, and systemic spread. Recent research has primarily focused on viral movement proteins and their interactions with the cellular host transport machinery, which has significantly expanded understanding on viral infection pathways. This review focuses on three components within this context: (i) the role of viral transport proteins, specifically movement proteins (MPs) and nuclear shuttle proteins (NSPs), (ii) their ability to recruit host factors for intra- and intercellular viral movement, and (iii) the suppression of antiviral immunity, with a particular emphasis on bipartite begomoviral movement proteins.
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Affiliation(s)
- Sâmera S Breves
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Fredy A Silva
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Nívea C Euclydes
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Thainá F F Saia
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - James Jean-Baptiste
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Eugenio R Andrade Neto
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology/Bioagro, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
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Silva JCF, Ferreira MA, Carvalho TFM, Silva FF, de A. Silveira S, Brommonschenkel SH, Fontes EPB. RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors. Int J Mol Sci 2022; 23:ijms232012176. [PMID: 36293031 PMCID: PMC9603095 DOI: 10.3390/ijms232012176] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.
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Affiliation(s)
- Jose Cleydson F. Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa 36570-900, Brazil
| | - Marco Aurélio Ferreira
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Thales F. M. Carvalho
- Institute of Engineering, Science and Technology, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Janaúba 39447-814, Brazil
| | - Fabyano F. Silva
- Departament of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Sabrina de A. Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | | | - Elizabeth P. B. Fontes
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
- Correspondence:
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Silva FDA, Fontes EPB. Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein System for Resistance Against Plant Viruses: Applications and Perspectives. Front Plant Sci 2022; 13:904829. [PMID: 35693174 PMCID: PMC9178237 DOI: 10.3389/fpls.2022.904829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Different genome editing approaches have been used to engineer resistance against plant viruses. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas; CRISPR/Cas) systems to create pinpoint genetic mutations have emerged as a powerful tool for molecular engineering of plant immunity and increasing resistance against plant viruses. This review presents (i) recent advances in engineering resistance against plant viruses by CRISPR/Cas and (ii) an overview of the potential host factors as targets for the CRISPR/Cas system-mediated broad-range resistance and immunity. Applications, challenges, and perspectives in enabling the CRISPR/Cas system for crop protection are also outlined.
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Quadros IPS, Madeira NN, Loriato VAP, Saia TFF, Silva JC, Soares FAF, Carvalho JR, Reis PAB, Fontes EPB, Clarindo WR, Fontes RLF. Cadmium-mediated toxicity in plant cells is associated with the DCD/NRP-mediated cell death response. Plant Cell Environ 2022; 45:556-571. [PMID: 34719793 DOI: 10.1111/pce.14218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/23/2020] [Revised: 09/08/2021] [Accepted: 09/16/2021] [Indexed: 05/13/2023]
Abstract
Cadmium (Cd2+ ) is highly harmful to plant growth. Although Cd2+ induces programmed cell death (PCD) in plant cells, Cd2+ stress in whole plants during later developmental stages and the mechanism underlying Cd2+ -mediated toxicity are poorly understood. Here, we showed that Cd2+ limits plant growth, causes intense redness in leaf vein, leaf yellowing, and chlorosis during the R1 reproductive stage of soybean (Glycine max). These symptoms were associated with Cd2+ -induced PCD, as Cd2+ -stressed soybean leaves displayed decreased number of nuclei, enhanced cell death, DNA damage, and caspase 1 activity compared to unstressed leaves. Accordingly, Cd2+ -induced NRPs, GmNAC81, GmNAC30 and VPE, the DCD/NRP-mediated cell death signalling components, which execute PCD via caspase 1-like VPE activity. Furthermore, overexpression of the positive regulator of this cell death signalling GmNAC81 enhanced sensitivity to Cd2+ stress and intensified the hallmarks of Cd2+ -mediated PCD. GmNAC81 overexpression enhanced Cd2+ -induced H2 O2 production, cell death, DNA damage, and caspase-1-like VPE expression. Conversely, BiP overexpression negatively regulated the NRPs/GmNACs/VPE signalling module, conferred tolerance to Cd2+ stress and reduced Cd2+ -mediated cell death. Collectively, our data indicate that Cd2+ induces PCD in plants via activation of the NRP/GmNAC/VPE regulatory circuit that links developmentally and stress-induced cell death.
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Affiliation(s)
- Iana Pedro Silva Quadros
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Virgílio Adriano Pereira Loriato
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Biochemistry and Molecular Biology Department/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Thaina Fernanda Fillietaz Saia
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jéssica Coutinho Silva
- Cytogenetics and Cytometry Laboratory, Department of General Biology, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Pedro Augusto Braga Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Biochemistry and Molecular Biology Department/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Biochemistry and Molecular Biology Department/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Wellington Ronildo Clarindo
- Cytogenetics and Cytometry Laboratory, Department of General Biology, Universidade Federal de Viçosa, Viçosa, Brazil
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Simoni EB, Oliveira CC, Fraga OT, Reis PAB, Fontes EPB. Cell Death Signaling From Endoplasmic Reticulum Stress: Plant-Specific and Conserved Features. Front Plant Sci 2022; 13:835738. [PMID: 35185996 PMCID: PMC8850647 DOI: 10.3389/fpls.2022.835738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 05/06/2023]
Abstract
The endoplasmic reticulum (ER) stress response is triggered by any condition that disrupts protein folding and promotes the accumulation of unfolded proteins in the lumen of the organelle. In eukaryotic cells, the evolutionarily conserved unfolded protein response is activated to clear unfolded proteins and restore ER homeostasis. The recovery from ER stress is accomplished by decreasing protein translation and loading into the organelle, increasing the ER protein processing capacity and ER-associated protein degradation activity. However, if the ER stress persists and cannot be reversed, the chronically prolonged stress leads to cellular dysfunction that activates cell death signaling as an ultimate attempt to survive. Accumulating evidence implicates ER stress-induced cell death signaling pathways as significant contributors for stress adaptation in plants, making modulators of ER stress pathways potentially attractive targets for stress tolerance engineering. Here, we summarize recent advances in understanding plant-specific molecular mechanisms that elicit cell death signaling from ER stress. We also highlight the conserved features of ER stress-induced cell death signaling in plants shared by eukaryotic cells.
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Teixeira RM, Ferreira MA, Raimundo GAS, Fontes EPB. Geminiviral Triggers and Suppressors of Plant Antiviral Immunity. Microorganisms 2021; 9:microorganisms9040775. [PMID: 33917649 PMCID: PMC8067988 DOI: 10.3390/microorganisms9040775] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Geminiviruses are circular single-stranded DNA plant viruses encapsidated into geminate virion particles, which infect many crops and vegetables and, hence, represent significant agricultural constraints worldwide. To maintain their broad-range host spectrum and establish productive infection, the geminiviruses must circumvent a potent plant antiviral immune system, which consists of a multilayered perception system represented by RNA interference sensors and effectors, pattern recognition receptors (PRR), and resistance (R) proteins. This recognition system leads to the activation of conserved defense responses that protect plants against different co-existing viral and nonviral pathogens in nature. Furthermore, a specific antiviral cell surface receptor signaling is activated at the onset of geminivirus infection to suppress global translation. This review highlighted these layers of virus perception and host defenses and the mechanisms developed by geminiviruses to overcome the plant antiviral immunity mechanisms.
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Ferreira DO, Fraga OT, Pimenta MR, Caetano HDN, Machado JPB, Carpinetti PA, Brustolini OJB, Quadros IPS, Reis PAB, Fontes EPB. GmNAC81 Inversely Modulates Leaf Senescence and Drought Tolerance. Front Genet 2020; 11:601876. [PMID: 33329747 PMCID: PMC7732657 DOI: 10.3389/fgene.2020.601876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 01/02/2023] Open
Abstract
Glycine max NAC81 (GmNAC81) is a downstream effector of the DCD/NRP-mediated cell death signaling, which interacts with GmNAC30 to fully induce the caspase 1-like vacuolar processing enzyme (VPE) expression, the executioner of the cell death program. GmNAC81 has been previously shown to positively modulate leaf senescence via the NRP/GmNAC81/VPE signaling module. Here, we examined the transcriptome induced by GmNAC81 overexpression and leaf senescence and showed that GmNAC81 further modulates leaf senescence by regulating an extensive repertoire of functionally characterized senescence-associated genes (SAGs). Because the NRP/GmNAC81/VPE signaling circuit also relays stress-induced cell death signals, we examined the effect of GmNAC81 overexpression in drought responses. Enhanced GmNAC81 expression in the transgenic lines increased sensitivity to water deprivation. Under progressive drought, the GmNAC81-overexpressing lines displayed severe leaf wilting, a larger and faster decline in leaf Ψw, relative water content (RWC), photosynthesis rate, stomatal conductance, and transpiration rate, in addition to higher Ci/Ca and lower Fm/Fv ratios compared to the BR16 control line. Collectively, these results indicate that the photosynthetic activity and apparatus were more affected by drought in the transgenic lines. Consistent with hypersensitivity to drought, chlorophyll loss, and lipid peroxidation were higher in the GmNAC81-overexpressing lines than in BR16 under dehydration. In addition to inducing VPE expression, GmNAC81 overexpression uncovered the regulation of typical drought-responsive genes. In particular, key regulators and effectors of ABA signaling were suppressed by GmNAC81 overexpression. These results suggest that GmNAC81 may negatively control drought tolerance not only via VPE activation but also via suppression of ABA signaling.
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Affiliation(s)
- Dalton O Ferreira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otto T Fraga
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil.,Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maiana R Pimenta
- Núcleo de Graduação de Agronomia, Universidade Federal de Sergipe, Nossa Senhora da Glória, Brazil
| | - Hanna D N Caetano
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil.,Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Paola A Carpinetti
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Iana P S Quadros
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pedro A B Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil.,Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil.,Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
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Gómez JD, Pinheiro VJM, Silva JC, Romero JV, Meriño-Cabrera Y, Coutinho FS, Lourenção AL, Serrão JE, Vital CE, Fontes EPB, Oliveira MGA, Ramos HJO. Leaf metabolic profiles of two soybean genotypes differentially affect the survival and the digestibility of Anticarsia gemmatalis caterpillars. Plant Physiol Biochem 2020; 155:196-212. [PMID: 32771931 DOI: 10.1016/j.plaphy.2020.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/08/2020] [Revised: 06/28/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Insect pests such as Anticarsia gemmatalis cause defoliation and yield losses. Soybean breeding has obtained resistant genotypes, however the mechanism remains unknown. Studies indicated the presence of deterrents compounds in the resistant genotype IAC17, and their leaf metabolite profiles were compared to the susceptible genotype UFV105, which was elicited or not by caterpillar infestation. Cluster analysis indicated a significative distinction between these profiles as well as differences in plant defense pathways. Methylquercetins were constitutively present in the largest concentrations, specifically in the IAC17. Relationship between the resistance and the levels of phytohormones jasmonic acid, abscisic acid and salicylic acid was not observed. However, 1-aminocyclopropane -1carboxylic acid levels indicated that the ethylene may be involved in the constitutive biosynthesis of bioactive compounds. Extracts were added to the diets at three different concentrations to evaluate the effect on caterpillar survival. Lowest survival rates were observed when extracts from the resistant IAC 17 were used, at the lowest concentrations. Survival rates were not higher when IAC 17 infested by caterpillars were used. On the other hand, when extracts from the susceptible were used, the survival reductions were only observed in the highest extract concentrations. These supplementations of the diet reduced the digestive capacity, agreeing with the proteolytic activities, whereas malformations of the intestinal cells were dose dependent. The inhibitory effects persisted in higher dilutions only for the IAC17. Constitutive resistance was also explained by higher levels of protease inhibition. These results can be useful to elucidate the genes and cascades controlling the resistance.
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Affiliation(s)
- Jenny D Gómez
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil; Center for Biomolecules Analysis, NuBioMol, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Valquiria J M Pinheiro
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil
| | - João Carlos Silva
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil
| | - Juan V Romero
- Department of Biology, Universidade Federal de Viçosa UFV, Laboratory of Biometry, Viçosa-MG, Brazil
| | - Yaremis Meriño-Cabrera
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil
| | | | | | - Jose E Serrão
- Department of Biology, Universidade Federal de Viçosa UFV, Laboratory of Biometry, Viçosa-MG, Brazil
| | - Camilo Elber Vital
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil; Center for Biomolecules Analysis, NuBioMol, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil
| | - Maria G A Oliveira
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil
| | - Humberto J O Ramos
- Department of Biochemistry and Molecular Biology, UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil; Center for Biomolecules Analysis, NuBioMol, Universidade Federal de Viçosa, Viçosa-MG, Brazil.
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Liu J, Huang Y, Kong L, Yu X, Feng B, Liu D, Zhao B, Mendes GC, Yuan P, Ge D, Wang WM, Fontes EPB, Li P, Shan L, He P. The malectin-like receptor-like kinase LETUM1 modulates NLR protein SUMM2 activation via MEKK2 scaffolding. Nat Plants 2020; 6:1106-1115. [PMID: 32839517 PMCID: PMC7492416 DOI: 10.1038/s41477-020-0748-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 07/21/2020] [Indexed: 05/04/2023]
Abstract
The innate immune system detects pathogen-derived molecules via specialized immune receptors to prevent infections1-3. Plant immune receptors include cell surface-resident pattern recognition receptors (PRRs, including receptor-like kinases (RLKs)), and intracellular nucleotide-binding domain leucine-rich repeat proteins (NLRs). It remains enigmatic how RLK- and NLR-mediated signalling are connected. Disruption of an immune-activated MEKK1-MKK1/2-MPK4 MAPK cascade activates the NLR SUMM2 via the MAPK kinase kinase MEKK2, leading to autoimmunity4-9. To gain insights into the mechanisms underlying SUMM2 activation, we used an RNA interference-based genetic screen for mekk1 autoimmune suppressors and identified an uncharacterized malectin-like RLK, named LETUM1 (LET1), as a specific regulator of mekk1-mkk1/2-mpk4 autoimmunity via complexing with both SUMM2 and MEKK2. MEKK2 scaffolds LET1 and SUMM2 for protein stability and association, and counter-regulates the F-box protein CPR1-mediated SUMM2 ubiquitination and degradation, thereby regulating SUMM2 accumulation and activation. Our study indicates that malectin-like RLK LET1 senses the perturbance of cellular homoeostasis caused by the deficiency in immune-activated signalling and activates the NLR SUMM2-mediated autoimmunity via MEKK2 scaffolding.
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Affiliation(s)
- Jun Liu
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Yanyan Huang
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, P. R. China
| | - Liang Kong
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Xiao Yu
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA
| | - Baomin Feng
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Derui Liu
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA
| | - Baoyu Zhao
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Giselle C Mendes
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
- National Institute of Science and Technology in Plant-Pest Interactions and Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Peiguo Yuan
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA
| | - Dongdong Ge
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, P. R. China
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions and Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pingwei Li
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Libo Shan
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA
| | - Ping He
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, USA.
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA.
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12
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Loriato VAP, Martins LGC, Euclydes NC, Reis PAB, Duarte CEM, Fontes EPB. Engineering resistance against geminiviruses: A review of suppressed natural defenses and the use of RNAi and the CRISPR/Cas system. Plant Sci 2020; 292:110410. [PMID: 32005374 DOI: 10.1016/j.plantsci.2020.110410] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 08/26/2019] [Revised: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 05/21/2023]
Abstract
The Geminiviridae family is one of the most successful and largest families of plant viruses that infect a large variety of important dicotyledonous and monocotyledonous crops and cause significant yield losses worldwide. This broad spectrum of host range is only possible because geminiviruses have evolved sophisticated strategies to overcome the arsenal of antiviral defenses in such diverse plant species. In addition, geminiviruses evolve rapidly through recombination and pseudo-recombination to naturally create a great diversity of virus species with divergent genome sequences giving the virus an advantage over the host recognition system. Therefore, it is not surprising that efficient molecular strategies to combat geminivirus infection under open field conditions have not been fully addressed. In this review, we present the anti-geminiviral arsenal of plant defenses, the evolved virulence strategies of geminiviruses to overcome these plant defenses and the most recent strategies that have been engineered for transgenic resistance. Although, the in vitro reactivation of suppressed natural defenses as well as the use of RNAi and CRISPR/Cas systems hold the potential for achieving broad-range resistance and/or immunity, potential drawbacks have been associated with each case.
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Affiliation(s)
- Virgílio A P Loriato
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Laura G C Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Nívea C Euclydes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Pedro A B Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Christiane E M Duarte
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
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13
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Martins LGC, Raimundo GAS, Ribeiro NGA, Silva JCF, Euclydes NC, Loriato VAP, Duarte CEM, Fontes EPB. A Begomovirus Nuclear Shuttle Protein-Interacting Immune Hub: Hijacking Host Transport Activities and Suppressing Incompatible Functions. Front Plant Sci 2020; 11:398. [PMID: 32322262 PMCID: PMC7156597 DOI: 10.3389/fpls.2020.00398] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/19/2020] [Indexed: 05/21/2023]
Abstract
Begomoviruses (Geminiviridae family) represent a severe constraint to agriculture worldwide. As ssDNA viruses that replicate in the nuclei of infected cells, the nascent viral DNA has to move to the cytoplasm and then to the adjacent cell to cause disease. The begomovirus nuclear shuttle protein (NSP) assists the intracellular transport of viral DNA from the nucleus to the cytoplasm and cooperates with the movement protein (MP) for the cell-to-cell translocation of viral DNA to uninfected cells. As a facilitator of intra- and intercellular transport of viral DNA, NSP is predicted to associate with host proteins from the nuclear export machinery, the intracytoplasmic active transport system, and the cell-to-cell transport complex. Furthermore, NSP functions as a virulence factor that suppresses antiviral immunity against begomoviruses. In this review, we focus on the protein-protein network that converges on NSP with a high degree of centrality and forms an immune hub against begomoviruses. We also describe the compatible host functions hijacked by NSP to promote the nucleocytoplasmic and intracytoplasmic movement of viral DNA. Finally, we discuss the NSP virulence function as a suppressor of the recently described NSP-interacting kinase 1 (NIK1)-mediated antiviral immunity. Understanding the NSP-host protein-protein interaction (PPI) network will probably pave the way for strategies to generate more durable resistance against begomoviruses.
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14
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Freitas EO, Melo BP, Lourenço-Tessutti IT, Arraes FBM, Amorim RM, Lisei-de-Sá ME, Costa JA, Leite AGB, Faheem M, Ferreira MA, Morgante CV, Fontes EPB, Grossi-de-Sa MF. Identification and characterization of the GmRD26 soybean promoter in response to abiotic stresses: potential tool for biotechnological application. BMC Biotechnol 2019; 19:79. [PMID: 31747926 PMCID: PMC6865010 DOI: 10.1186/s12896-019-0561-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/13/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Drought is one of the most harmful abiotic stresses for plants, leading to reduced productivity of several economically important crops and, consequently, considerable losses in the agricultural sector. When plants are exposed to stressful conditions, such as drought and high salinity, they modulate the expression of genes that lead to developmental, biochemical, and physiological changes, which help to overcome the deleterious effects of adverse circumstances. Thus, the search for new specific gene promoter sequences has proved to be a powerful biotechnological strategy to control the expression of key genes involved in water deprivation or multiple stress responses. RESULTS This study aimed to identify and characterize the GmRD26 promoter (pGmRD26), which is involved in the regulation of plant responses to drought stress. The expression profile of the GmRD26 gene was investigated by qRT-PCR under normal and stress conditions in Williams 82, BR16 and Embrapa48 soybean-cultivars. Our data confirm that GmRD26 is induced under water deficit with different induction folds between analyzed cultivars, which display different genetic background and physiological behaviour under drought. The characterization of the GmRD26 promoter was performed under simulated stress conditions with abscisic acid (ABA), polyethylene glycol (PEG) and drought (air dry) on A. thaliana plants containing the complete construct of pGmRD26::GUS (2.054 bp) and two promoter modules, pGmRD26A::GUS (909 pb) and pGmRD26B::GUS (435 bp), controlling the expression of the β-glucuronidase (uidA) gene. Analysis of GUS activity has demonstrated that pGmRD26 and pGmRD26A induce strong reporter gene expression, as the pAtRD29 positive control promoter under ABA and PEG treatment. CONCLUSIONS The full-length promoter pGmRD26 and the pGmRD26A module provides an improved uidA transcription capacity when compared with the other promoter module, especially in response to polyethylene glycol and drought treatments. These data indicate that pGmRD26A may become a promising biotechnological asset with potential use in the development of modified drought-tolerant plants or other plants designed for stress responses.
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Affiliation(s)
- Elinea O Freitas
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Federal University of Brasília, Brasília, DF, Brazil
| | - Bruno P Melo
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Federal University of Viçosa, Viçosa, MG, Brazil
| | | | - Fabrício B M Arraes
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Regina M Amorim
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Maria E Lisei-de-Sá
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Agricultural Research Company of Minas Gerais State, Uberaba, MG, Brazil
| | - Julia A Costa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Catholic University of Brasilia - Post-Graduation Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Ana G B Leite
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Federal University of Brasília, Brasília, DF, Brazil
| | - Muhammad Faheem
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | | | - Carolina V Morgante
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Embrapa Semi-Arid, Petrolina, PE, Brazil
| | | | - Maria F Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil.
- Catholic University of Brasilia - Post-Graduation Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil.
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15
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Li B, Ferreira MA, Huang M, Camargos LF, Yu X, Teixeira RM, Carpinetti PA, Mendes GC, Gouveia-Mageste BC, Liu C, Pontes CSL, Brustolini OJB, Martins LGC, Melo BP, Duarte CEM, Shan L, He P, Fontes EPB. The receptor-like kinase NIK1 targets FLS2/BAK1 immune complex and inversely modulates antiviral and antibacterial immunity. Nat Commun 2019; 10:4996. [PMID: 31676803 PMCID: PMC6825196 DOI: 10.1038/s41467-019-12847-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/04/2019] [Indexed: 01/23/2023] Open
Abstract
Plants deploy various immune receptors to recognize pathogens and defend themselves. Crosstalk may happen among receptor-mediated signal transduction pathways in the same host during simultaneous infection of different pathogens. However, the related function of the receptor-like kinases (RLKs) in thwarting different pathogens remains elusive. Here, we report that NIK1, which positively regulates plant antiviral immunity, acts as an important negative regulator of antibacterial immunity. nik1 plants exhibit dwarfed morphology, enhanced disease resistance to bacteria and increased PAMP-triggered immunity (PTI) responses, which are restored by NIK1 reintroduction. Additionally, NIK1 negatively regulates the formation of the FLS2/BAK1 complex. The interaction between NIK1 and FLS2/BAK1 is enhanced upon flg22 perception, revealing a novel PTI regulatory mechanism by an RLK. Furthermore, flg22 perception induces NIK1 and RPL10A phosphorylation in vivo, activating antiviral signalling. The NIK1-mediated inverse modulation of antiviral and antibacterial immunity may allow bacteria and viruses to activate host immune responses against each other. Plants deploy numerous receptor-like kinases (RLKs) to respond to pathogens. Here the authors show that NIK1, an RLK that positively regulates antiviral immunity, negatively regulates the response to bacteria by modulating FLS2/BAK1 complex formation, suggesting crosstalk between bacterial and viral immunity.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Marco Aurélio Ferreira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Luiz Fernando Camargos
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil.,Federal Institute of Education from Goias, Science and Technology, Urutaí, GO, 75790-000, Brazil
| | - Xiao Yu
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Ruan M Teixeira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Paola A Carpinetti
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Giselle C Mendes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia Catarinense, Rio do Sul, SC, 89163-356, Brazil
| | - Bianca C Gouveia-Mageste
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil
| | - Chenglong Liu
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Claudia S L Pontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil
| | - Otávio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Laboratório Nacional de Computação Cientifica (LNCC), Petrópolis, RJ, Brazil
| | - Laura G C Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Bruno P Melo
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Christiane E M Duarte
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil
| | - Libo Shan
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Ping He
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Viçosa, MG, 36570.900, Brazil. .,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570.900, Brazil.
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16
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Teixeira RM, Ferreira MA, Raimundo GAS, Loriato VAP, Reis PAB, Fontes EPB. Virus perception at the cell surface: revisiting the roles of receptor-like kinases as viral pattern recognition receptors. Mol Plant Pathol 2019; 20:1196-1202. [PMID: 31094066 PMCID: PMC6715618 DOI: 10.1111/mpp.12816] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 05/04/2023]
Abstract
Activation of antiviral innate immune responses depends on the recognition of viral components or viral effectors by host receptors. This virus recognition system can activate two layers of host defence, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). While ETI has long been recognized as an efficient plant defence against viruses, the concept of antiviral PTI has only recently been integrated into virus-host interaction models, such as the RNA silencing-based defences that are triggered by viral dsRNA PAMPs produced during infection. Emerging evidence in the literature has included the classical PTI in the antiviral innate immune arsenal of plant cells. Therefore, our understanding of PAMPs has expanded to include not only classical PAMPS, such as bacterial flagellin or fungal chitin, but also virus-derived nucleic acids that may also activate PAMP recognition receptors like the well-documented phenomenon observed for mammalian viruses. In this review, we discuss the notion that plant viruses can activate classical PTI, leading to both unique antiviral responses and conserved antipathogen responses. We also present evidence that virus-derived nucleic acid PAMPs may elicit the NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASE 1 (NIK1)-mediated antiviral signalling pathway that transduces an antiviral signal to suppress global host translation.
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Affiliation(s)
- Ruan M. Teixeira
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Departament of Biochemistry and Molecular BiologyUniversidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
| | - Marco Aurélio Ferreira
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Departament of Biochemistry and Molecular BiologyUniversidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
| | - Gabriel A. S. Raimundo
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Agronomy Institute, Universidade Federal de ViçosaCampus FlorestalFlorestalMinas Gerais35690‐000Brazil
| | - Virgílio A. P. Loriato
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Departament of Biochemistry and Molecular BiologyUniversidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
| | - Pedro A. B. Reis
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Departament of Biochemistry and Molecular BiologyUniversidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
| | - Elizabeth P. B. Fontes
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Universidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
- Departament of Biochemistry and Molecular BiologyUniversidade Federal de ViçosaViçosaMinas Gerais36570‐000Brazil
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17
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Silva JCF, Teixeira RM, Silva FF, Brommonschenkel SH, Fontes EPB. Machine learning approaches and their current application in plant molecular biology: A systematic review. Plant Sci 2019; 284:37-47. [PMID: 31084877 DOI: 10.1016/j.plantsci.2019.03.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 12/18/2018] [Revised: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 05/19/2023]
Abstract
Machine learning (ML) is a field of artificial intelligence that has rapidly emerged in molecular biology, thus allowing the exploitation of Big Data concepts in plant genomics. In this context, the main challenges are given in terms of how to analyze massive datasets and extract new knowledge in all levels of cellular systems research. In summary, ML techniques allow complex interactions to be inferred in several biological systems. Despite its potential, ML has been underused due to complex computational algorithms and definition terms. Therefore, a systematic review to disentangle ML approaches is relevant for plant scientists and has been considered in this study. We presented the main steps for ML development (from data selection to evaluation of classification/prediction models) with a respective discussion approaching functional genomics mainly in terms of pathogen effector genes in plant immunity. Additionally, we also considered how to access public source databases under an ML framework towards advancing plant molecular biology and introduced novel powerful tools, such as deep learning.
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Affiliation(s)
- Jose Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Centro, Viçosa, MG, 36570-000, Brazil; Department of Biochemistry and Molecular Biology/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Ruan M Teixeira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Centro, Viçosa, MG, 36570-000, Brazil; Department of Biochemistry and Molecular Biology/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabyano F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Sergio H Brommonschenkel
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Centro, Viçosa, MG, 36570-000, Brazil; Plant Pathology Department /Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Centro, Viçosa, MG, 36570-000, Brazil; Department of Biochemistry and Molecular Biology/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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18
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Calil IP, Quadros IPS, Araújo TC, Duarte CEM, Gouveia-Mageste BC, Silva JCF, Brustolini OJB, Teixeira RM, Oliveira CN, Milagres RWMM, Martins GS, Chory J, Reis PAB, Machado JPB, Fontes EPB. A WW Domain-Containing Protein Forms Immune Nuclear Bodies against Begomoviruses. Mol Plant 2018; 11:1449-1465. [PMID: 30296599 DOI: 10.1016/j.molp.2018.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/27/2018] [Accepted: 09/28/2018] [Indexed: 05/23/2023]
Abstract
The bipartite begomoviruses (Geminiviridae family), which are DNA viruses that replicate in the nucleus of infected cells, encode the nuclear shuttle protein (NSP) to facilitate the translocation of viral DNA from the nucleus to the cytoplasm via nuclear pores. This intracellular trafficking of NSP-DNA complexes is accessorized by the NSP-interacting guanosine triphosphatase (NIG) at the cytosolic side. Here, we report the nuclear redistribution of NIG by AtWWP1, a WW domain-containing protein that forms immune nuclear bodies (NBs) against begomoviruses. We demonstrated that AtWWP1 relocates NIG from the cytoplasm to the nucleus where it is confined to AtWWP1-NBs, suggesting that the NIG-AtWWP1 interaction may interfere with the NIG pro-viral function associated with its cytosolic localization. Consistent with this assumption, loss of AtWWP1 function cuased plants more susceptible to begomovirus infection, whereas overexpression of AtWWP1 enhanced plant resistance to begomovirus. Furthermore, we found that a mutant version of AtWWP1 defective for NB formation was no longer capable of interacting with and relocating NIG to the nucleus and lost its immune function against begomovirus. The antiviral function of AtWWP1-NBs, however, could be antagonized by viral infection that induced either the disruption or a decrease in the number of AtWWP1-NBs. Collectively, these results led us to propose that AtWWP1 organizes nuclear structures into nuclear foci, which provide intrinsic immunity against begomovirus infection.
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Affiliation(s)
- Iara P Calil
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Iana P S Quadros
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Thais C Araújo
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Christiane E M Duarte
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Bianca C Gouveia-Mageste
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Otávio J B Brustolini
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Ruan M Teixeira
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Cauê N Oliveira
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Rafael W M M Milagres
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Gilberto S Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; Departament of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joanne Chory
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - Pedro A B Reis
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Joao Paulo B Machado
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; Agronomy Institute, Universidade Federal de Viçosa, Campus Florestal, Florestal, Minas Gerais 35690-000, Brazil.
| | - Elizabeth P B Fontes
- Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil; National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil.
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Melo BP, Fraga OT, Silva JCF, Ferreira DO, Brustolini OJB, Carpinetti PA, Machado JPB, Reis PAB, Fontes EPB. Revisiting the Soybean GmNAC Superfamily. Front Plant Sci 2018; 9:1864. [PMID: 30619426 PMCID: PMC6305603 DOI: 10.3389/fpls.2018.01864] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 05/07/2023]
Abstract
The NAC (NAM, ATAF, and CUC) genes encode transcription factors involved with the control of plant morph-physiology and stress responses. The release of the last soybean (Glycine max) genome assembly (Wm82.a2.v1) raised the possibility that new NAC genes would be present in the soybean genome. Here, we interrogated the last version of the soybean genome against a conserved NAC domain structure. Our analysis identified 32 putative novel NAC genes, updating the superfamily to 180 gene members. We also organized the genes in 15 phylogenetic subfamilies, which showed a perfect correlation among sequence conservation, expression profile, and function of orthologous Arabidopsis thaliana genes and NAC soybean genes. To validate our in silico analyses, we monitored the stress-mediated gene expression profiles of eight new NAC-genes by qRT-PCR and monitored the GmNAC senescence-associated genes by RNA-seq. Among ER stress, osmotic stress and salicylic acid treatment, all the novel tested GmNAC genes responded to at least one type of stress, displaying a complex expression profile under different kinetics and extension of the response. Furthermore, we showed that 40% of the GmNACs were differentially regulated by natural leaf senescence, including eight (8) newly identified GmNACs. The developmental and stress-responsive expression profiles of the novel NAC genes fitted perfectly with their phylogenetic subfamily. Finally, we examined two uncharacterized senescence-associated proteins, GmNAC065 and GmNAC085, and a novel, previously unidentified, NAC protein, GmNAC177, and showed that they are nuclear localized, and except for GmNAC065, they display transactivation activity in yeast. Consistent with a role in leaf senescence, transient expression of GmNAC065 and GmNAC085 induces the appearance of hallmarks of leaf senescence, including chlorophyll loss, leaf yellowing, lipid peroxidation and accumulation of H2O2. GmNAC177 was clustered to an uncharacterized subfamily but in close proximity to the TIP subfamily. Accordingly, it was rapidly induced by ER stress and by salicylic acid under late kinetic response and promoted cell death in planta. Collectively, our data further substantiated the notion that the GmNAC genes display functional and expression profiles consistent with their phylogenetic relatedness and established a complete framework of the soybean NAC superfamily as a foundation for future analyses.
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Affiliation(s)
- Bruno P. Melo
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otto T. Fraga
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José Cleydson F. Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Dalton O. Ferreira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otávio J. B. Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Paola A. Carpinetti
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Pedro A. B. Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P. B. Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
- *Correspondence: Elizabeth P. B. Fontes
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20
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Silva JCF, Carvalho TFM, Fontes EPB, Cerqueira FR. Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae. BMC Bioinformatics 2017; 18:431. [PMID: 28964254 PMCID: PMC5622471 DOI: 10.1186/s12859-017-1839-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/20/2017] [Indexed: 11/14/2022] Open
Abstract
Background Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns. Results This study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively. Conclusions Therefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp. Electronic supplementary material The online version of this article (10.1186/s12859-017-1839-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Cleydson F Silva
- Department of Informatics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Thales F M Carvalho
- Department of Informatics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil. .,Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
| | - Fabio R Cerqueira
- Department of Informatics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil. .,Department of Production Engineering, Universidade Federal Fluminense, Rua Domingos Silvério, s/n, Bairro Quitandinha, Petrópolis, Rio de Janeiro, 25650-050, Brazil.
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21
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Silva JCF, Carvalho TFM, Basso MF, Deguchi M, Pereira WA, Sobrinho RR, Vidigal PMP, Brustolini OJB, Silva FF, Dal-Bianco M, Fontes RLF, Santos AA, Zerbini FM, Cerqueira FR, Fontes EPB. Geminivirus data warehouse: a database enriched with machine learning approaches. BMC Bioinformatics 2017; 18:240. [PMID: 28476106 PMCID: PMC5420152 DOI: 10.1186/s12859-017-1646-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/25/2017] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. RESULTS Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. CONCLUSIONS The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.
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Affiliation(s)
- Jose Cleydson F Silva
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Marcos F Basso
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Michihito Deguchi
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Welison A Pereira
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Roberto R Sobrinho
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pedro M P Vidigal
- Núcleo de Biomoléculas, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Anésia A Santos
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Francisco Murilo Zerbini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabio R Cerqueira
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Engenharia de Produção, Universidade Federal Fluminense, Petrópolis, Rio de Janeiro, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil. .,Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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Abstract
BACKGROUND Among the environmental limitations that affect plant growth, viruses cause major crop losses worldwide and represent serious threats to food security. Significant advances in the field of plant-virus interactions have led to an expansion of potential strategies for genetically engineered resistance in crops during recent years. Nevertheless, the evolution of viral virulence represents a constant challenge in agriculture that has led to a continuing interest in the molecular mechanisms of plant-virus interactions that affect disease or resistance. SCOPE AND CONCLUSION This review summarizes the molecular mechanisms of the antiviral immune system in plants and the latest breakthroughs reported in plant defence against viruses. Particular attention is given to the immune receptors and transduction pathways in antiviral innate immunity. Plants counteract viral infection with a sophisticated innate immune system that resembles the non-viral pathogenic system, which is broadly divided into pathogen-associated molecular pattern (PAMP)-triggered immunity and effector-triggered immunity. An additional recently uncovered virus-specific defence mechanism relies on host translation suppression mediated by a transmembrane immune receptor. In all cases, the recognition of the virus by the plant during infection is central for the activation of these innate defences, and, conversely, the detection of host plants enables the virus to activate virulence strategies. Plants also circumvent viral infection through RNA interference mechanisms by utilizing small RNAs, which are often suppressed by co-evolving virus suppressors. Additionally, plants defend themselves against viruses through hormone-mediated defences and activation of the ubiquitin-26S proteasome system (UPS), which alternatively impairs and facilitates viral infection. Therefore, plant defence and virulence strategies co-evolve and co-exist; hence, disease development is largely dependent on the extent and rate at which these opposing signals emerge in host and non-host interactions. A deeper understanding of plant antiviral immunity may facilitate innovative biotechnological, genetic and breeding approaches for crop protection and improvement.
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Affiliation(s)
- Iara P. Calil
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
| | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
- For correspondence. E-mail
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23
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Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
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Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
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Gouveia BC, Calil IP, Machado JPB, Santos AA, Fontes EPB. Immune Receptors and Co-receptors in Antiviral Innate Immunity in Plants. Front Microbiol 2017; 7:2139. [PMID: 28105028 PMCID: PMC5214455 DOI: 10.3389/fmicb.2016.02139] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023] Open
Abstract
Plants respond to pathogens using an innate immune system that is broadly divided into PTI (pathogen-associated molecular pattern- or PAMP-triggered immunity) and ETI (effector-triggered immunity). PTI is activated upon perception of PAMPs, conserved motifs derived from pathogens, by surface membrane-anchored pattern recognition receptors (PRRs). To overcome this first line of defense, pathogens release into plant cells effectors that inhibit PTI and activate effector-triggered susceptibility (ETS). Counteracting this virulence strategy, plant cells synthesize intracellular resistance (R) proteins, which specifically recognize pathogen effectors or avirulence (Avr) factors and activate ETI. These coevolving pathogen virulence strategies and plant resistance mechanisms illustrate evolutionary arms race between pathogen and host, which is integrated into the zigzag model of plant innate immunity. Although antiviral immune concepts have been initially excluded from the zigzag model, recent studies have provided several lines of evidence substantiating the notion that plants deploy the innate immune system to fight viruses in a manner similar to that used for non-viral pathogens. First, most R proteins against viruses so far characterized share structural similarity with antibacterial and antifungal R gene products and elicit typical ETI-based immune responses. Second, virus-derived PAMPs may activate PTI-like responses through immune co-receptors of plant PTI. Finally, and even more compelling, a viral Avr factor that triggers ETI in resistant genotypes has recently been shown to act as a suppressor of PTI, integrating plant viruses into the co-evolutionary model of host-pathogen interactions, the zigzag model. In this review, we summarize these important progresses, focusing on the potential significance of antiviral immune receptors and co-receptors in plant antiviral innate immunity. In light of the innate immune system, we also discuss a newly uncovered layer of antiviral defense that is specific to plant DNA viruses and relies on transmembrane receptor-mediated translational suppression for defense.
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Affiliation(s)
- Bianca C. Gouveia
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de ViçosaViçosa, Brazil
| | - Iara P. Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de ViçosaViçosa, Brazil
| | - João Paulo B. Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de ViçosaViçosa, Brazil
| | - Anésia A. Santos
- Department of General Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de ViçosaViçosa, Brazil
| | - Elizabeth P. B. Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de ViçosaViçosa, Brazil
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25
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Abstract
Receptor-like kinases (RLKs) play key roles during development and in responses to the environment. In plant immunity, some members of RLKs function as pattern recognition receptors (PRRs), which, upon recognition of pathogen-associated molecular patterns (PAMP), are recruited into active complexes to induce pathogen-triggered immunity (PTI). In this chapter, we describe the bioinformatics tools and procedures for the identification and phylogenetic classification of RLKs from different plant species as a framework for understanding RLK function in signal transduction and immunity.
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Affiliation(s)
- Otávio J B Brustolini
- Department of Biochemistry and Molecular Biology, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
| | - José Cleydson F Silva
- Department of Biochemistry and Molecular Biology, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
- Department of Informatics, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
| | - Tetsu Sakamoto
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
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26
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Reis PAB, Carpinetti PA, Freitas PP, Santos EG, Camargos LF, Oliveira IH, Silva JCF, Carvalho HH, Dal-Bianco M, Soares-Ramos JR, Fontes EPB. Functional and regulatory conservation of the soybean ER stress-induced DCD/NRP-mediated cell death signaling in plants. BMC Plant Biol 2016; 16:156. [PMID: 27405371 PMCID: PMC4943007 DOI: 10.1186/s12870-016-0843-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/01/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The developmental and cell death domain (DCD)-containing asparagine-rich proteins (NRPs) were first identified in soybean (Glycine max) as transducers of a cell death signal derived from prolonged endoplasmic reticulum (ER) stress, osmotic stress, drought or developmentally-programmed leaf senescence via the GmNAC81/GmNAC30/GmVPE signaling module. In spite of the relevance of the DCD/NRP-mediated signaling as a versatile adaptive response to multiple stresses, mechanistic knowledge of the pathway is lacking and the extent to which this pathway may operate in the plant kingdom has not been investigated. RESULTS Here, we demonstrated that the DCD/NRP-mediated signaling also propagates a stress-induced cell death signal in other plant species with features of a programmed cell death (PCD) response. In silico analysis revealed that several plant genomes harbor conserved sequences of the pathway components, which share functional analogy with their soybean counterparts. We showed that GmNRPs, GmNAC81and VPE orthologs from Arabidopsis, designated as AtNRP-1, AtNRP-2, ANAC036 and gVPE, respectively, induced cell death when transiently expressed in N. benthamiana leaves. In addition, loss of AtNRP1 and AtNRP2 function attenuated ER stress-induced cell death in Arabidopsis, which was in marked contrast with the enhanced cell death phenotype displayed by overexpressing lines as compared to Col-0. Furthermore, atnrp-1 knockout mutants displayed enhanced sensitivity to PEG-induced osmotic stress, a phenotype that could be complemented with ectopic expression of either GmNRP-A or GmNRP-B. In addition, AtNRPs, ANAC036 and gVPE were induced by osmotic and ER stress to an extent that was modulated by the ER-resident molecular chaperone binding protein (BiP) similarly as in soybean. Finally, as putative downstream components of the NRP-mediated cell death signaling, the stress induction of AtNRP2, ANAC036 and gVPE was dependent on the AtNRP1 function. BiP overexpression also conferred tolerance to water stress in Arabidopsis, most likely due to modulation of the drought-induced NRP-mediated cell death response. CONCLUSION Our results indicated that the NRP-mediated cell death signaling operates in the plant kingdom with conserved regulatory mechanisms and hence may be target for engineering stress tolerance and adaptation in crops.
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Affiliation(s)
- Pedro A. B. Reis
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Paola A. Carpinetti
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Paula P.J. Freitas
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Eulálio G.D. Santos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Luiz F. Camargos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Igor H.T. Oliveira
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - José Cleydson F. Silva
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Humberto H. Carvalho
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Maximiller Dal-Bianco
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Juliana R.L. Soares-Ramos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Elizabeth P. B. Fontes
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
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Machado JPB, Brustolini OJB, Mendes GC, Santos AA, Fontes EPB. NIK1, a host factor specialized in antiviral defense or a novel general regulator of plant immunity? Bioessays 2015; 37:1236-42. [PMID: 26335701 DOI: 10.1002/bies.201500066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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] [Indexed: 12/16/2023]
Abstract
NIK1 is a receptor-like kinase involved in plant antiviral immunity. Although NIK1 is structurally similar to the plant immune factor BAK1, which is a key regulator in plant immunity to bacterial pathogens, the NIK1-mediated defenses do not resemble BAK1 signaling cascades. The underlying mechanism for NIK1 antiviral immunity has recently been uncovered. NIK1 activation mediates the translocation of RPL10 to the nucleus, where it interacts with LIMYB to fully down-regulate translational machinery genes, resulting in translation inhibition of host and viral mRNAs and enhanced tolerance to begomovirus. Therefore, the NIK1 antiviral immunity response culminates in global translation suppression, which represents a new paradigm for plant antiviral defenses. Interestingly, transcriptomic analyses in nik1 mutant suggest that NIK1 may suppress antibacterial immune responses, indicating a possible opposite effect of NIK1 in bacterial and viral infections.
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Affiliation(s)
- Joao P B Machado
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otavio J B Brustolini
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Giselle C Mendes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Anésia A Santos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P B Fontes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
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Silva PA, Silva JCF, Caetano HDN, Machado JPB, Mendes GC, Reis PAB, Brustolini OJB, Dal-Bianco M, Fontes EPB. Comprehensive analysis of the endoplasmic reticulum stress response in the soybean genome: conserved and plant-specific features. BMC Genomics 2015; 16:783. [PMID: 26466891 PMCID: PMC4606518 DOI: 10.1186/s12864-015-1952-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/23/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the relevance of the eukaryotic endoplasmic reticulum (ER)-stress response as an integrator of multiple stress signals into an adaptive response, knowledge about these ER-mediated cytoprotective pathways in soybean (Glycine max) is lacking. Here, we searched for genes involved in the highly conserved unfolded protein response (UPR) and ER stress-induced plant-specific cell death signaling pathways in the soybean genome. METHODS Previously characterized Arabidopsis UPR genes were used as prototypes for the identification of the soybean orthologs and the in silico assembly of the UPR in soybean, using eggNOG v4.0 software. Functional studies were also conducted by analyzing the transcriptional activity of soybean UPR transducers. RESULTS As a result of this search, we have provided a complete profile of soybean UPR genes with significant predicted protein similarities to A. thaliana UPR-associated proteins. Both arms of the plant UPR were further examined functionally, and evidence is presented that the soybean counterparts are true orthologs of previously characterized UPR transducers in Arabidopsis. The bZIP17/bZI28 orthologs (GmbZIP37 and GmbZIP38) and ZIP60 ortholog (GmbZIP68) from soybean have similar structural organizations as their Arabidopsis counterparts, were induced by ER stress and activated an ERSE- and UPRE-containing BiP promoter. Furthermore, the transcript of the putative substrate of GmIREs, GmbZIP68, harbors a canonical site for IRE1 endonuclease activity and was efficiently spliced under ER stress conditions. In a reverse approach, we also examined the Arabidopsis genome for components of a previously characterized ER stress-induced cell death signaling response in soybean. With the exception of GmERD15, which apparently does not possess an Arabidopsis ortholog, the Arabidopsis genome harbors conserved GmNRP, GmNAC81, GmNAC30 and GmVPE sequences that share significant structural and sequence similarities with their soybean counterparts. These results suggest that the NRP/GmNAC81 + GmNAC30/VPE regulatory circuit may transduce cell death signals in plant species other than soybean. CONCLUSIONS Our in silico analyses, along with current and previous functional data, permitted generation of a comprehensive overview of the ER stress response in soybean as a framework for functional prediction of ER stress signaling components and their possible connections with multiple stress responses.
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Affiliation(s)
- Priscila Alves Silva
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Hanna D N Caetano
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Joao Paulo B Machado
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Giselle C Mendes
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Pedro A B Reis
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Otavio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
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Zorzatto C, Machado JPB, Lopes KVG, Nascimento KJT, Pereira WA, Brustolini OJB, Reis PAB, Calil IP, Deguchi M, Sachetto-Martins G, Gouveia BC, Loriato VAP, Silva MAC, Silva FF, Santos AA, Chory J, Fontes EPB. NIK1-mediated translation suppression functions as a plant antiviral immunity mechanism. Nature 2015; 520:679-82. [PMID: 25707794 DOI: 10.1038/nature14171] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 12/19/2014] [Indexed: 12/17/2022]
Abstract
Plants and plant pathogens are subject to continuous co-evolutionary pressure for dominance, and the outcomes of these interactions can substantially impact agriculture and food security. In virus-plant interactions, one of the major mechanisms for plant antiviral immunity relies on RNA silencing, which is often suppressed by co-evolving virus suppressors, thus enhancing viral pathogenicity in susceptible hosts. In addition, plants use the nucleotide-binding and leucine-rich repeat (NB-LRR) domain-containing resistance proteins, which recognize viral effectors to activate effector-triggered immunity in a defence mechanism similar to that employed in non-viral infections. Unlike most eukaryotic organisms, plants are not known to activate mechanisms of host global translation suppression to fight viruses. Here we demonstrate in Arabidopsis that the constitutive activation of NIK1, a leucine-rich repeat receptor-like kinase (LRR-RLK) identified as a virulence target of the begomovirus nuclear shuttle protein (NSP), leads to global translation suppression and translocation of the downstream component RPL10 to the nucleus, where it interacts with a newly identified MYB-like protein, L10-INTERACTING MYB DOMAIN-CONTAINING PROTEIN (LIMYB), to downregulate translational machinery genes fully. LIMYB overexpression represses ribosomal protein genes at the transcriptional level, resulting in protein synthesis inhibition, decreased viral messenger RNA association with polysome fractions and enhanced tolerance to begomovirus. By contrast, the loss of LIMYB function releases the repression of translation-related genes and increases susceptibility to virus infection. Therefore, LIMYB links immune receptor LRR-RLK activation to global translation suppression as an antiviral immunity strategy in plants.
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Affiliation(s)
- Cristiane Zorzatto
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - João Paulo B Machado
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Kênia V G Lopes
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Kelly J T Nascimento
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Welison A Pereira
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Otávio J B Brustolini
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Pedro A B Reis
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Iara P Calil
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Michihito Deguchi
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Gilberto Sachetto-Martins
- 1] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] Departamento de Genética, Universidade Federal do Rio de Janeiro, 21944.970 Rio de Janeiro, Brazil
| | - Bianca C Gouveia
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Virgílio A P Loriato
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Marcos A C Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Anésia A Santos
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
| | - Joanne Chory
- 1] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Elizabeth P B Fontes
- 1] Departamento de Bioquímica e Biologia Molecular, National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil [2] National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, 36570.000 Viçosa, Minas Gerais, Brazil
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Carvalho HH, Brustolini OJB, Pimenta MR, Mendes GC, Gouveia BC, Silva PA, Silva JCF, Mota CS, Soares-Ramos JRL, Fontes EPB. The molecular chaperone binding protein BiP prevents leaf dehydration-induced cellular homeostasis disruption. PLoS One 2014; 9:e86661. [PMID: 24489761 PMCID: PMC3906070 DOI: 10.1371/journal.pone.0086661] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
BiP overexpression improves leaf water relations during droughts and delays drought-induced leaf senescence. However, whether BiP controls cellular homeostasis under drought conditions or simply delays dehydration-induced leaf senescence as the primary cause for water stress tolerance remains to be determined. To address this issue, we examined the drought-induced transcriptomes of BiP-overexpressing lines and wild-type (WT) lines under similar leaf water potential (ψw) values. In the WT leaves, a ψw reduction of -1.0 resulted in 1339 up-regulated and 2710 down-regulated genes; in the BiP-overexpressing line 35S::BiP-4, only 334 and 420 genes were induced and repressed, respectively, at a similar leaf ψw = -1.0 MPa. This level of leaf dehydration was low enough to induce a repertory of typical drought-responsive genes in WT leaves but not in 35S::BiP-4 dehydrated leaves. The responders included hormone-related genes, functional and regulatory genes involved in drought protection and senescence-associated genes. The number of differentially expressed genes in the 35S::BiP-4 line approached the wild type number at a leaf ψw = -1.6 MPa. However, N-rich protein (NRP)- mediated cell death signaling genes and unfolded protein response (UPR) genes were induced to a much lower extent in the 35S::BiP-4 line than in the WT even at ψw = -1.6 MPa. The heatmaps for UPR, ERAD (ER-associated degradation protein system), drought-responsive and cell death-associated genes revealed that the leaf transcriptome of 35S::BiP-4 at ψw = -1.0 MPa clustered together with the transcriptome of well-watered leaves and they diverged considerably from the drought-induced transcriptome of the WT (ψw = -1.0, -1.7 and -2.0 MPa) and 35S::BiP-4 leaves at ψw = -1.6 MPa. Taken together, our data revealed that BiP-overexpressing lines requires a much higher level of stress (ψw = -1.6 MPa) to respond to drought than that of WT (ψw = -1.0). Therefore, BiP overexpression maintains cellular homeostasis under water stress conditions and thus ameliorates endogenous osmotic stress.
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Affiliation(s)
- Humberto H. Carvalho
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J. B. Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Maiana R. Pimenta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Giselle C. Mendes
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Bianca C. Gouveia
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Priscila A. Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | - Clenilso S. Mota
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana R. L. Soares-Ramos
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Elizabeth P. B. Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Mendes GC, Reis PAB, Calil IP, Carvalho HH, Aragão FJL, Fontes EPB. GmNAC30 and GmNAC81 integrate the endoplasmic reticulum stress- and osmotic stress-induced cell death responses through a vacuolar processing enzyme. Proc Natl Acad Sci U S A 2013; 110:19627-32. [PMID: 24145438 PMCID: PMC3845183 DOI: 10.1073/pnas.1311729110] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [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] [Indexed: 11/18/2022] Open
Abstract
Prolonged endoplasmic reticulum and osmotic stress synergistically activate the stress-induced N-rich protein-mediated signaling that transduces a cell death signal by inducing GmNAC81 (GmNAC6) in soybean. To identify novel regulators of the stress-induced programmed cell death (PCD) response, we screened a two-hybrid library for partners of GmNAC81. We discovered another member of the NAC (NAM-ATAF1,2-CUC2) family, GmNAC30, which binds to GmNAC81 in the nucleus of plant cells to coordinately regulate common target promoters that harbor the core cis-regulatory element TGTG[TGC]. We found that GmNAC81 and GmNAC30 can function either as transcriptional repressors or activators and cooperate to enhance the transcriptional regulation of common target promoters, suggesting that heterodimerization may be required for the full regulation of gene expression. Accordingly, GmNAC81 and GmNAC30 display overlapping expression profiles in response to multiple environmental and developmental stimuli. Consistent with a role in PCD, GmNAC81 and GmNAC30 bind in vivo to and transactivate hydrolytic enzyme promoters in soybean protoplasts. A GmNAC81/GmNAC30 binding site is located in the promoter of the caspase-1-like vacuolar processing enzyme (VPE) gene, which is involved in PCD in plants. We demonstrated that the expression of GmNAC81 and GmNAC30 fully transactivates the VPE gene in soybean protoplasts and that this transactivation was associated with an increase in caspase-1-like activity. Collectively, our results indicate that the stress-induced GmNAC30 cooperates with GmNAC81 to activate PCD through the induction of the cell death executioner VPE.
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Affiliation(s)
- Giselle C. Mendes
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Instituto Nacional de Ciência e Tecnologia em interacoes planta-praga, Universidade Federal de Viçosa, 36570-000 Viçosa MG, Brazil; and
| | - Pedro A. B. Reis
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Instituto Nacional de Ciência e Tecnologia em interacoes planta-praga, Universidade Federal de Viçosa, 36570-000 Viçosa MG, Brazil; and
| | - Iara P. Calil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Instituto Nacional de Ciência e Tecnologia em interacoes planta-praga, Universidade Federal de Viçosa, 36570-000 Viçosa MG, Brazil; and
| | - Humberto H. Carvalho
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Instituto Nacional de Ciência e Tecnologia em interacoes planta-praga, Universidade Federal de Viçosa, 36570-000 Viçosa MG, Brazil; and
| | | | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular/Bioagro, Instituto Nacional de Ciência e Tecnologia em interacoes planta-praga, Universidade Federal de Viçosa, 36570-000 Viçosa MG, Brazil; and
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Coco D, Calil IP, Brustolini OJB, Santos AA, Inoue-Nagata AK, Fontes EPB. Soybean chlorotic spot virus, a novel begomovirus infecting soybean in Brazil. Arch Virol 2013; 158:457-62. [PMID: 23053525 DOI: 10.1007/s00705-012-1499-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 06/20/2012] [Accepted: 08/25/2012] [Indexed: 11/27/2022]
Abstract
A novel soybean-infecting begomovirus from Brazil was identified in Jaíba, in the state of Minas Gerais, and molecularly characterized. By using rolling-circle amplification-based cloning of viral DNAs, three DNA-A variants and a cognate DNA-B were isolated from infected samples. The DNA variants share more than 98 % sequence identity but have less than 89 % identity to other reported begomovirus, the limit for demarcation of new species. In a phylogenetic analysis, both DNA-A and DNA-B clustered with other Brazilian begomoviruses. Infectious cloned DNA-A and DNA-B components induced distinct symptoms in Solanaceae and Fabaceae species by biolistic inoculation. In soybean, the virus induced mild symptoms, i.e., chlorotic spots on the leaves, from which the name soybean chlorotic spot virus (SoCSV) was proposed. The most severe symptoms were displayed by common beans, which exhibited leaf distortion, blistering, interveinal chlorosis, mosaic and golden mosaic. The possibility that SoCSV may become a threat to bean production in Brazil is discussed.
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Affiliation(s)
- Daniela Coco
- Departamento de Bioquimica e Biologia Molecular, Universidade Federal de Vicosa, Vicosa, Brazil
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Alves MS, Reis PAB, Dadalto SP, Faria JAQA, Fontes EPB, Fietto LG. A novel transcription factor, ERD15 (Early Responsive to Dehydration 15), connects endoplasmic reticulum stress with an osmotic stress-induced cell death signal. J Biol Chem 2011; 286:20020-30. [PMID: 21482825 PMCID: PMC3103375 DOI: 10.1074/jbc.m111.233494] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/07/2011] [Indexed: 11/06/2022] Open
Abstract
As in all other eukaryotic organisms, endoplasmic reticulum (ER) stress triggers the evolutionarily conserved unfolded protein response in soybean, but it also communicates with other adaptive signaling responses, such as osmotic stress-induced and ER stress-induced programmed cell death. These two signaling pathways converge at the level of gene transcription to activate an integrated cascade that is mediated by N-rich proteins (NRPs). Here, we describe a novel transcription factor, GmERD15 (Glycine max Early Responsive to Dehydration 15), which is induced by ER stress and osmotic stress to activate the expression of NRP genes. GmERD15 was isolated because of its capacity to stably associate with the NRP-B promoter in yeast. It specifically binds to a 187-bp fragment of the NRP-B promoter in vitro and activates the transcription of a reporter gene in yeast. Furthermore, GmERD15 was found in both the cytoplasm and the nucleus, and a ChIP assay revealed that it binds to the NRP-B promoter in vivo. Expression of GmERD15 in soybean protoplasts activated the NRP-B promoter and induced expression of the NRP-B gene. Collectively, these results support the interpretation that GmERD15 functions as an upstream component of stress-induced NRP-B-mediated signaling to connect stress in the ER to an osmotic stress-induced cell death signal.
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Affiliation(s)
- Murilo S. Alves
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | - Pedro A. B. Reis
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | | | | | - Elizabeth P. B. Fontes
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
| | - Luciano G. Fietto
- From the Departamento de Bioquímica e Biologia Molecular, BIOAGRO and
- National Institute of Science and Technology in Plant-Pest Interactions,Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
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Abstract
The NSP-interacting kinase, NIK, belongs to the five leucine-rich repeats-containing receptor-like serine/threonine kinase subfamily that includes members involved in plant development and defence. NIK was first identified by its capacity to interact with the geminivirus nuclear shuttle protein (NSP) and has been strongly associated with plant defence against geminivirus. Recent studies corroborate its function in transducing a defence signal against virus infection and describe components of the NIK-mediated antiviral signalling pathway. This mini-review describes the role of NIK as a transducer of a novel layer of plant innate defence, presents new data on NIK function, and discusses its possible involvement in plant development.
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Affiliation(s)
- Anésia A Santos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
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Pinheiro GL, Marques CS, Costa MDBL, Reis PAB, Alves MS, Carvalho CM, Fietto LG, Fontes EPB. Complete inventory of soybean NAC transcription factors: sequence conservation and expression analysis uncover their distinct roles in stress response. Gene 2009; 444:10-23. [PMID: 19497355 DOI: 10.1016/j.gene.2009.05.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [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: 04/01/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
We performed an inventory of soybean NAC transcription factors, in which 101 NAC domain-containing proteins were annotated into 15 different subgroups, showing a clear relationship between structure and function. The six previously described GmNAC proteins (GmNAC1 to GmNAC6) were located in the nucleus and a transactivation assay in yeast confirmed that GmNAC2, GmNAC3, GmNAC4 and GmNAC5 function as transactivators. We also analyzed the expression of the six NAC genes in response to a variety of stress conditions. GmNAC2, GmNAC3 and GmNAC4 were strongly induced by osmotic stress. GmNAC3 and GmNAC4 were also induced by ABA, JA and salinity but differed in their response to cold. Consistent with an involvement in cell death programs, the transient expression of GmNAC1, GmNAC5 and GmNAC6 in tobacco leaves resulted in cell death and enhanced expression of senescence markers. Our results indicate that the described soybean NACs are functionally non-redundant transcription factors involved in response to abiotic stresses and in cell death events in soybean.
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Affiliation(s)
- Guilherme L Pinheiro
- Departamento de Bioquímica e Biologia Molecular, Laboratório de Biologia Molecular de Plantas, BIOAGRO, Universidade Federal de Viçosa, 36570.000, Viçosa, Minas Gerais, Brazil
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36
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Santos AA, Carvalho CM, Florentino LH, Ramos HJO, Fontes EPB. Conserved threonine residues within the A-loop of the receptor NIK differentially regulate the kinase function required for antiviral signaling. PLoS One 2009; 4:e5781. [PMID: 19492062 PMCID: PMC2686266 DOI: 10.1371/journal.pone.0005781] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 05/12/2009] [Indexed: 11/18/2022] Open
Abstract
NSP-interacting kinase (NIK1) is a receptor-like kinase identified as a virulence target of the begomovirus nuclear shuttle protein (NSP). We found that NIK1 undergoes a stepwise pattern of phosphorylation within its activation-loop domain (A-loop) with distinct roles for different threonine residues. Mutations at Thr-474 or Thr-468 impaired autophosphorylation and were defective for kinase activation. In contrast, a mutation at Thr-469 did not impact autophosphorylation and increased substrate phosphorylation, suggesting an inhibitory role for Thr-469 in kinase function. To dissect the functional significance of these results, we used NSP-expressing virus infection as a mechanism to interfere with wild type and mutant NIK1 action in plants. The NIK1 knockout mutant shows enhanced susceptibility to virus infections, a phenotype that could be complemented with ectopic expression of a 35S-NIK1 or 35S-T469A NIK1 transgenes. However, ectopic expression of an inactive kinase or the 35S-T474A NIK1 mutant did not reverse the enhanced susceptibility phenotype of knockout lines, demonstrating that Thr-474 autophosphorylation was needed to transduce a defense response to geminiviruses. Furthermore, mutations at Thr-474 and Thr-469 residues antagonistically affected NIK-mediated nuclear relocation of the downstream effector rpL10. These results establish that NIK1 functions as an authentic defense receptor as it requires activation to elicit a defense response. Our data also suggest a model whereby phosphorylation-dependent activation of a plant receptor-like kinase enables the A-loop to control differentially auto- and substrate phosphorylation.
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Affiliation(s)
- Anésia A. Santos
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Claudine M. Carvalho
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lilian H. Florentino
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Humberto J. O. Ramos
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Valente MAS, Faria JAQA, Soares-Ramos JRL, Reis PAB, Pinheiro GL, Piovesan ND, Morais AT, Menezes CC, Cano MAO, Fietto LG, Loureiro ME, Aragão FJL, Fontes EPB. The ER luminal binding protein (BiP) mediates an increase in drought tolerance in soybean and delays drought-induced leaf senescence in soybean and tobacco. J Exp Bot 2008; 60:533-46. [PMID: 19052255 PMCID: PMC2651463 DOI: 10.1093/jxb/ern296] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [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: 09/17/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 05/17/2023]
Abstract
The ER-resident molecular chaperone BiP (binding protein) was overexpressed in soybean. When plants growing in soil were exposed to drought (by reducing or completely withholding watering) the wild-type lines showed a large decrease in leaf water potential and leaf wilting, but the leaves in the transgenic lines did not wilt and exhibited only a small decrease in water potential. During exposure to drought the stomata of the transgenic lines did not close as much as in the wild type, and the rates of photosynthesis and transpiration became less inhibited than in the wild type. These parameters of drought resistance in the BiP overexpressing lines were not associated with a higher level of the osmolytes proline, sucrose, and glucose. It was also not associated with the typical drought-induced increase in root dry weight. Rather, at the end of the drought period, the BiP overexpressing lines had a lower level of the osmolytes and root weight than the wild type. The mRNA abundance of several typical drought-induced genes [NAC2, a seed maturation protein (SMP), a glutathione-S-transferase (GST), antiquitin, and protein disulphide isomerase 3 (PDI-3)] increased in the drought-stressed wild-type plants. Compared with the wild type, the increase in mRNA abundance of these genes was less (in some genes much less) in the BiP overexpressing lines that were exposed to drought. The effect of drought on leaf senescence was investigated in soybean and tobacco. It had previously been reported that tobacco BiP overexpression or repression reduced or accentuated the effects of drought. BiP overexpressing tobacco and soybean showed delayed leaf senescence during drought. BiP antisense tobacco plants, conversely, showed advanced leaf senescence. It is concluded that BiP overexpression confers resistance to drought, through an as yet unknown mechanism that is related to ER functioning. The delay in leaf senescence by BiP overexpression might relate to the absence of the response to drought.
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Affiliation(s)
- Maria Anete S. Valente
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Jerusa A. Q. A. Faria
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Juliana R. L. Soares-Ramos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Pedro A. B. Reis
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Guilherme L. Pinheiro
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Newton D. Piovesan
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Angélica T. Morais
- Embrapa Recursos Genéticos e Biotecnologia, PqEB W5 Norte, 70770-900, Brasília, DF, Brazil
| | - Carlos C. Menezes
- Universidade de Rio Verde, Fazenda Fontes do Saber, 75901-970, Rio Verde, GO, Brazil
| | - Marco A. O. Cano
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Luciano G. Fietto
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
| | - Marcelo E. Loureiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Francisco J. L. Aragão
- Embrapa Recursos Genéticos e Biotecnologia, PqEB W5 Norte, 70770-900, Brasília, DF, Brazil
| | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Avenida PH Rolfs s/n, 36571.000 Viçosa, MG, Brazil
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Carvalho CM, Fontenelle MR, Florentino LH, Santos AA, Zerbini FM, Fontes EPB. A novel nucleocytoplasmic traffic GTPase identified as a functional target of the bipartite geminivirus nuclear shuttle protein. Plant J 2008; 55:869-80. [PMID: 18489709 DOI: 10.1111/j.1365-313x.2008.03556.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
SUMMARY In contrast to the accumulated data on nuclear transport mechanisms of macromolecules, little is known concerning the regulated release of nuclear-exported complexes and their subsequent trans-cytoplasmic movement. The bipartite begomovirus nuclear shuttle protein (NSP) facilitates the nuclear export of viral DNA and cooperates with the movement protein (MP) to transport viral DNA across the plant cell wall. Here, we identified a cellular NSP-interacting GTPase (NIG) with biochemical properties consistent with a nucleocytoplasmic transport role. We show that NIG is a cytosolic GTP-binding protein that accumulates around the nuclear envelope and possesses intrinsic GTPase activity. NIG interacts with NSP in vitro and in vivo (under transient expression), and redirects the viral protein from the nucleus to the cytoplasm. We propose that NIG acts as a positive contributor to geminivirus infection by modulating NSP nucleocytoplasmic shuttling and hence facilitating MP-NSP interaction in the cortical cytoplasm. In support of this, overexpression of NIG in Arabidopsis enhances susceptibility to geminivirus infection. In addition to highlighting the relevance of NIG as a cellular co-factor for NSP function, our findings also have implications for general nucleocytoplasmic trafficking of cellular macromolecules.
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Affiliation(s)
- Claudine M Carvalho
- Departamento de Bioquímica e Biologia Molecular, Vicosa, Minas Gerais, Brazil
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39
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Costa MDL, Reis PAB, Valente MAS, Irsigler AST, Carvalho CM, Loureiro ME, Aragão FJL, Boston RS, Fietto LG, Fontes EPB. A new branch of endoplasmic reticulum stress signaling and the osmotic signal converge on plant-specific asparagine-rich proteins to promote cell death. J Biol Chem 2008; 283:20209-19. [PMID: 18490446 DOI: 10.1074/jbc.m802654200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NRPs (N-rich proteins) were identified as targets of a novel adaptive pathway that integrates endoplasmic reticulum (ER) and osmotic stress signals based on coordinate regulation and synergistic up-regulation by tunicamycin and polyethylene glycol treatments. This integrated pathway diverges from the molecular chaperone-inducing branch of the unfolded protein response (UPR) in several ways. While UPR-specific targets were inversely regulated by ER and osmotic stresses, NRPs required both signals for full activation. Furthermore, BiP (binding protein) overexpression in soybean prevented activation of the UPR by ER stress inducers, but did not affect activation of NRPs. We also found that this integrated pathway transduces a PCD signal generated by ER and osmotic stresses that result in the appearance of markers associated with leaf senescence. Overexpression of NRPs in soybean protoplasts induced caspase-3-like activity and promoted extensive DNA fragmentation. Furthermore, transient expression of NRPs in planta caused leaf yellowing, chlorophyll loss, malondialdehyde production, ethylene evolution, and induction of the senescence marker gene CP1. This phenotype was alleviated by the cytokinin zeatin, a potent senescence inhibitor. Collectively, these results indicate that ER stress induces leaf senescence through activation of plant-specific NRPs via a novel branch of the ER stress response.
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Affiliation(s)
- Maximiller D L Costa
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Abstract
The Geminiviridae family is a large family of plant viruses that has single-stranded DNA genomes and infects a large variety of crop species. In this chapter, we describe a biolistic inoculation protocol that has been successfully used to propagate new species of geminivirus in permissive hosts with total DNA extracted from infected plants. This allows us to directly investigate the biological properties of uncloned and not sap-transmissible geminiviruses.
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Affiliation(s)
- Anésia A Santos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO- Universidade Federal de Viçosa-36571.000, Viçosa, MG, Brazil
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41
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Florentino LH, Santos AA, Zerbini FM, Fontes EPB. Begomoviruses: molecular cloning and identification of replication origin. Methods Mol Biol 2008; 451:145-166. [PMID: 18370254 DOI: 10.1007/978-1-59745-102-4_11] [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] [Indexed: 05/26/2023]
Abstract
The Begomovirus genus is the largest genus of the Geminiviridae family and comprises the whitefly transmitted geminiviruses that infect dicotyledonous plants. They can be either mono or bipartite. In this chapter, we describe the cloning of begomovirus replication modules and the subsequent functional characterization of geminivirus replication origins.
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Affiliation(s)
- Lilian H Florentino
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO-Universidade, Federal de Viçosa-36571.000, Viçosa, MG, Brazil
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42
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Freitas RL, Carvalho CM, Fietto LG, Loureiro ME, Almeida AM, Fontes EPB. Distinct repressing modules on the distal region of the SBP2 promoter contribute to its vascular tissue-specific expression in different vegetative organs. Plant Mol Biol 2007; 65:603-14. [PMID: 17710554 DOI: 10.1007/s11103-007-9225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/08/2007] [Indexed: 05/16/2023]
Abstract
The Glycine max sucrose binding protein (GmSBP2) promoter directs vascular tissue-specific expression of reporter genes in transgenic tobacco. Here we showed that an SBP2-GFP fusion protein under the control of the GmSBP2 promoter accumulates in the vascular tissues of vegetative organs, which is consistent with the proposed involvement of SBP in sucrose transport-dependent physiological processes. Through gain-of-function experiments we confirmed that the tissue-specific determinants of the SBP2 promoter reside in the distal cis-regulatory domain A, CRD-A (position -2000 to -700) that is organized into a modular configuration to suppress promoter activity in tissues other than vascular tissues. The four analyzed CRD-A sub-modules, designates Frag II (-1785/-1508), Frag III (-1507/-1237), Frag IV (-1236/-971) and Frag V (-970/-700), act independently to alter the constitutive pattern of -92pSBP2-mediated GUS expression in different organs. Frag V fused to -92pSBP2-GUS restored the tissue-specific pattern of the full-length promoter in the shoot apex, but not in other organs. Likewise, Frag IV confined GUS expression to the vascular bundle of leaves, whereas Frag II mediated vascular specific expression in roots. Strong stem expression-repressing elements were located at positions -1485 to -1212, as Frag III limited GUS expression to the inner phloem. We have also mapped a procambium silencer to the consensus sequence CAGTTnCaAccACATTcCT which is located in both distal and proximal upstream modules. Fusion of either repressing element-containing module to the constitutive -92pSBP2 promoter suppresses GUS expression in the elongation zone of roots. Together our results demonstrate the unusual aspect of distal sequences negatively controlling tissue-specificity of a plant promoter.
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Affiliation(s)
- Rejane L Freitas
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36571-000 Vicosa, MG, Brazil
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43
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Fontenelle MR, Luz DF, Gomes APS, Florentino LH, Zerbini FM, Fontes EPB. Functional analysis of the naturally recombinant DNA-A of the bipartite begomovirus Tomato chlorotic mottle virus. Virus Res 2007; 126:262-7. [PMID: 17367887 DOI: 10.1016/j.virusres.2007.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 01/10/2007] [Revised: 02/08/2007] [Accepted: 02/09/2007] [Indexed: 11/18/2022]
Abstract
All geminiviruses found in Brazil belong to the Begomovirus genus with a bipartite genome that is split between two genomic components, DNA-A and DNA-B. The DNA-A of the bipartite begomovirus ToCMoV-[MG-Bt] (Tomato chlorotic mottle virus), however, possesses as a peculiar characteristic the capacity to systemically infect Nicotiana benthamiana. Here we further characterize this variant DNA-A and show that it also infects Solanum lycopersicum and other host plants, in the absence of DNA-B. The ToCMoV-[MG-Bt]-DNA-A encodes an additional ORF, designated AC5, but otherwise its genome organization is similar to other DNA-A from Western Hemisphere begomoviruses. We showed that this AC5 putative ORF is not essential for infection, as disruption of its coding capacity caused no effect on ToCMoV-[MG-Bt]-DNA-A-mediated infection process. Likewise, the ToCMoV-[MG-Bt]-DNA-A ac4 mutant was indistinguishable from its wild type counterpart in all hosts tested. In contrast, an av1 (coat protein) mutant was unable to infect systemically N. benthamiana and Chenopodium quinoa in the absence of DNA-B. However, inclusion of DNA-B in the infection assay fully rescued the movement defect of the ToCMoV-[MG-Bt]-DNA-A av1 mutant. These results suggest that at suboptimal conditions for infection the coat protein is required for ToCMoV-[MG-Bt] systemic movement.
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Affiliation(s)
- Mariana R Fontenelle
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
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Rocha CS, Luz DF, Oliveira ML, Baracat-Pereira MC, Medrano FJ, Fontes EPB. Expression of the sucrose binding protein from soybean: renaturation and stability of the recombinant protein. Phytochemistry 2007; 68:802-10. [PMID: 17222874 DOI: 10.1016/j.phytochem.2006.11.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 09/12/2006] [Accepted: 11/29/2006] [Indexed: 05/13/2023]
Abstract
The sucrose binding protein (SBP) belongs to the cupin family of proteins and is structurally related to vicilin-like storage proteins. In this investigation, a SBP isoform (GmSBP2/S64) was expressed in E. coli and large amounts of the protein accumulated in the insoluble fraction as inclusion bodies. The renatured protein was studied by circular dichroism (CD), intrinsic fluorescence, and binding of the hydrophobic probes ANS and Bis-ANS. The estimated content of secondary structure of the renatured protein was consistent with that obtained by theoretical modeling with a large predominance of beta-strand structure (42%) over the alpha-helix (9.9%). The fluorescence emission maximum of 303 nm for SBP2 indicated that the fluorescent tryptophan was completely buried within a highly hydrophobic environment. We also measured the equilibrium dissociation constant (K(d)) of sucrose binding by fluorescence titration using the refolded protein. The low sucrose binding affinity (K(d)=2.79+/-0.22 mM) of the renatured protein was similar to that of the native protein purified from soybean seeds. Collectively, these results indicate that the folded structure of the renatured protein was similar to the native SBP protein. As a member of the bicupin family of proteins, which includes highly stable seed storage proteins, SBP2 was fairly stable at high temperatures. Likewise, it remained folded to a similar extent in the presence or absence of 7.6M urea or 6.7 M GdmHCl. The high stability of the renatured protein may be a reminiscent property of SBP from its evolutionary relatedness to the seed storage proteins.
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Affiliation(s)
- Carolina S Rocha
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa - MG, Brazil
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Andrade EC, Manhani GG, Alfenas PF, Calegario RF, Fontes EPB, Zerbini FM. Tomato yellow spot virus, a tomato-infecting begomovirus from Brazil with a closer relationship to viruses from Sida sp., forms pseudorecombinants with begomoviruses from tomato but not from Sida. J Gen Virol 2006; 87:3687-3696. [PMID: 17098986 DOI: 10.1099/vir.0.82279-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Geminiviruses are characterized by a circular, single-stranded DNA genome and twinned icosahedral particles. Begomoviruses (whitefly-transmitted geminiviruses) are a major constraint to crop production worldwide. In Brazil, tomato-infecting begomoviruses emerged as serious pathogens over the last 10 years, due to the introduction of a new biotype of the insect vector. Tomato yellow spot virus (ToYSV) is a newly described begomovirus originally isolated from tomato, but phylogenetically closer to viruses from Sida sp. A study was performed to determine the viability of pseudorecombinants formed between the DNA components of ToYSV and other weed- and tomato-infecting begomoviruses from Brazil. Despite its closer relationship to weed-infecting viruses, ToYSV was only capable of forming viable pseudorecombinants with tomato viruses. An infectious pseudorecombinant formed between ToYSV DNA-A and tomato crinkle leaf yellows virus (TCrLYV) DNA-B induced severe symptoms in Nicotiana benthamiana. This was attributed, at least in part, to the fact that the origins of replication of both components had identical Rep-binding sequences. However, this was not the case for another infectious pseudorecombinant formed between tomato golden mosaic virus (TGMV) DNA-A and ToYSV DNA-B, which have different Rep-binding sequences. These results reinforce the notion that pseudorecombinant formation cannot be explained solely on the basis of phylogenetic relationships and conserved iteron sequences, and suggest that the TGMV Rep protein may be more versatile in terms of recognizing heterologous DNA components than that of ToYSV.
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Affiliation(s)
- E C Andrade
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - G G Manhani
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - P F Alfenas
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - R F Calegario
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - E P B Fontes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - F M Zerbini
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
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46
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Florentino LH, Santos AA, Fontenelle MR, Pinheiro GL, Zerbini FM, Baracat-Pereira MC, Fontes EPB. A PERK-like receptor kinase interacts with the geminivirus nuclear shuttle protein and potentiates viral infection. J Virol 2006; 80:6648-56. [PMID: 16775352 PMCID: PMC1488943 DOI: 10.1128/jvi.00173-06] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The nuclear shuttle protein (NSP) from bipartite geminiviruses facilitates the intracellular transport of viral DNA from the nucleus to the cytoplasm and acts in concert with the movement protein (MP) to promote the cell-to-cell spread of the viral DNA. A proline-rich extensin-like receptor protein kinase (PERK) was found to interact specifically with NSP of Cabbage leaf curl virus (CaLCuV) and of tomato-infecting geminiviruses through a yeast two-hybrid screening. The PERK-like protein, which we designated NsAK (for NSP-associated kinase), is structurally organized into a proline-rich N-terminal domain, followed by a transmembrane segment and a C-terminal serine/threonine kinase domain. The viral protein interacted stably with defective versions of the NsAK kinase domain, but not with the potentially active enzyme, in an in vitro binding assay. In vitro-translated NsAK enhanced the phosphorylation level of NSP, indicating that NSP functions as a substrate for NsAK. These results demonstrate that NsAK is an authentic serine/threonine kinase and suggest a functional link for NSP-NsAK complex formation. This interpretation was corroborated by in vivo infectivity assays showing that loss of NsAK function reduces the efficiency of CaLCuV infection and attenuates symptom development. Our data implicate NsAK as a positive contributor to geminivirus infection and suggest it may regulate NSP function.
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Affiliation(s)
- Lilian H Florentino
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, MG, Brazil
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Lunz W, Oliveira EC, Neves MTD, Fontes EPB, Dias CMGC, Natali AJ. Anabolic steroid- and exercise-induced cardiac stress protein (HSP72) in the rat. Braz J Med Biol Res 2006; 39:889-93. [PMID: 16862279 DOI: 10.1590/s0100-879x2006000700006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 09/20/2005] [Accepted: 04/26/2006] [Indexed: 11/21/2022] Open
Abstract
The present study investigated the effects of exercise and anabolic-androgenic steroids on cardiac HSP72 expression. Male Wistar rats were divided into experimental groups: nandrolone exercise (NE, N = 6), control exercise (CE, N = 6), nandrolone sedentary (NS, N = 6), and control sedentary (CS, N = 6). Animals in the NE and NS groups received a weekly intramuscular injection (6.5 mg/kg of body weight) of nandrolone decanoate, while those in the CS and CE groups received mineral oil as vehicle. Animals in the NE and CE groups were submitted to a progressive running program on a treadmill, for 8 weeks. Fragments of the left ventricle were collected at sacrifice and the relative immunoblot contents of HSP72 were determined. Heart weight to body weight ratio was higher in exercised than in sedentary animals (P < 0.05, 4.65 +/- 0.38 vs 4.20 +/- 0.47 mg/g, respectively), independently of nandrolone, and in nandrolone-treated than untreated animals (P < 0.05, 4.68 +/- 0.47 vs 4.18 +/- 0.32 mg/g, respectively), independently of exercise. Cardiac HSP72 accumulation was higher in exercised than in sedentary animals (P < 0.05, 677.16 +/- 129.14 vs 246.24 +/- 46.30 relative unit, respectively), independently of nandrolone, but not different between nandrolone-treated and untreated animals (P > 0.05, 560.88 +/- 127.53 vs 362.52 +/- 95.97 relative unit, respectively) independently of exercise. Exercise-induced HSP72 expression was not affected by nandrolone. These levels of HSP72 expression in response to nandrolone administration suggest either a low intracellular stress or a possible less protection to the myocardium.
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Affiliation(s)
- W Lunz
- Departamento de Nutrição e Saúde, Universidade Federal de Viçosa, MG, Brasil
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Rodrigues SM, Andrade MO, Gomes APS, Damatta FM, Baracat-Pereira MC, Fontes EPB. Arabidopsis and tobacco plants ectopically expressing the soybean antiquitin-like ALDH7 gene display enhanced tolerance to drought, salinity, and oxidative stress. J Exp Bot 2006; 57:1909-18. [PMID: 16595581 DOI: 10.1093/jxb/erj132] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Despite extensive studies in eukaryotic aldehyde dehydrogenases, functional information about the ALDH7 antiquitin-like proteins is lacking. A soybean antiquitin homologue gene, designated GmTP55, has been isolated which encodes a dehydrogenase motif-containing 55 kDa protein induced by dehydration and salt stress. GmTP55 is closely related to the stress-induced plant antiquitin-like proteins that belong to the ALDH7 family. Transgenic tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana) plants constitutively expressing GmTP55 have been obtained in order to examine the physiological role of this enzyme under a variety of stress conditions. Ectopic expression of GmTP55 in both Arabidopsis and tobacco conferred tolerance to salinity during germination and to water deficit during plant growth. Under salt stress, the germination efficiency of both transgenic tobacco and Arabidopsis seeds was significantly higher than that of their control counterparts. Likewise, under progressive drought, the transgenic tobacco lines apparently kept the shoot turgidity to a normal level, which contrasted with the leaf wilt phenotype of control plants. The transgenic plants also exhibited an enhanced tolerance to H(2)O(2)- and paraquat-induced oxidative stress. Both GmTP55-expressing Arabidopsis and tobacco seeds germinated efficiently in medium supplemented with H(2)O(2), whereas the germination of control seeds was drastically impaired. Similarly, transgenic tobacco leaf discs treated with paraquat displayed a significant reduction in the necrotic lesions as compared with control leaves. These transgenic lines also exhibited a lower concentration of lipid peroxidation-derived reactive aldehydes under oxidative stress. These results suggest that antiquitin may be involved in adaptive responses mediated by a physiologically relevant detoxification pathway in plants.
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Affiliation(s)
- Simone M Rodrigues
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, MG, Brasil
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Waclawovsky AJ, Freitas RL, Rocha CS, Contim LAS, Fontes EPB. Combinatorial regulation modules on GmSBP2 promoter: a distal cis-regulatory domain confines the SBP2 promoter activity to the vascular tissue in vegetative organs. Biochim Biophys Acta 2006; 1759:89-98. [PMID: 16574256 DOI: 10.1016/j.bbaexp.2006.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Revised: 02/03/2006] [Accepted: 02/06/2006] [Indexed: 11/27/2022]
Abstract
The Glycine max sucrose binding protein (GmSBP2) promoter directs phloem-specific expression of reporter genes in transgenic tobacco. Here, we identified cis-regulatory domains (CRD) that contribute with positive and negative regulation for the tissue-specific pattern of the GmSPB2 promoter. Negative regulatory elements in the distal CRD-A (-2000 to -700) sequences suppressed expression from the GmSBP2 promoter in tissues other than seed tissues and vascular tissues of vegetative organs. Deletion of this region relieved repression resulting in a constitutive promoter highly active in all tissues analyzed. Further deletions from the strong constitutive -700GmSBP2 promoter delimited several intercalating enhancer-like and repressing domains that function in a context-dependent manner. Histochemical examination revealed that the CRD-C (-445 to -367) harbors both negative and positive elements. This region abolished promoter expression in roots and in all tissues of stems except for the inner phloem. In contrast, it restores root meristem expression when fused to the -132pSBP2-GUS construct, which contains root meristem expression-repressing determinants mapped to the 44-bp CRD-G (-136 to -92). Thus, the GmSBP2 promoter is functionally organized into a proximal region with the combinatorial modular configuration of plant promoters and a distal domain, which restricts gene expression to the vascular tissues in vegetative organs.
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Fontes EPB, Santos AA, Luz DF, Waclawovsky AJ, Chory J. The geminivirus nuclear shuttle protein is a virulence factor that suppresses transmembrane receptor kinase activity. Genes Dev 2004; 18:2545-56. [PMID: 15489295 PMCID: PMC529541 DOI: 10.1101/gad.1245904] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Despite the large number of leucine-rich-repeat (LRR) receptor-like-kinases (RLKs) in plants and their conceptual relevance in signaling events, functional information is restricted to a few family members. Here we describe the characterization of new LRR-RLK family members as virulence targets of the geminivirus nuclear shuttle protein (NSP). NSP interacts specifically with three LRR-RLKs, NIK1, NIK2, and NIK3, through an 80-amino acid region that encompasses the kinase active site and A-loop. We demonstrate that these NSP-interacting kinases (NIKs) are membrane-localized proteins with biochemical properties of signaling receptors. They behave as authentic kinase proteins that undergo autophosphorylation and can also phosphorylate exogenous substrates. Autophosphorylation occurs via an intermolecular event and oligomerization precedes the activation of the kinase. Binding of NSP to NIK inhibits its kinase activity in vitro, suggesting that NIK is involved in antiviral defense response. In support of this, infectivity assays showed a positive correlation between infection rate and loss of NIK1 and NIK3 function. Our data are consistent with a model in which NSP acts as a virulence factor to suppress NIK-mediated antiviral responses.
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Affiliation(s)
- Elizabeth P B Fontes
- Departamento de Bioquímica e Biologia Molecular/BIOGRO/UFV, 36571.000, Viçosa, MG, Brazil. bbfontes.ufv.br
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