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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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2
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Martho KF, Brustolini OJB, Vasconcelos AT, Vallim MA, Pascon RC. The Glycerol Phosphatase Gpp2: A Link to Osmotic Stress, Sulfur Assimilation and Virulence in Cryptococcus neoformans. Front Microbiol 2019; 10:2728. [PMID: 31849880 PMCID: PMC6901960 DOI: 10.3389/fmicb.2019.02728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/13/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Cryptococcus neoformans is an opportunist fungal pathogen that causes meningoencephalitis in immunocompromised patients. During infection, this basidiomycete yeast has to adapt to several adverse conditions, especially nutrient availability. The interruption on various amino acid biosynthetic pathways and on amino acid uptake causes reduced viability, inability to cope with various stresses, failure in virulence factors expression and avirulence in animal model of infection. The sulfur amino acid biosynthesis and uptake is an important feature for pathogen survival in vivo and in vitro. Our previous work demonstrates that C. neoformans Cys3 BZip transcription factor controls the gene expression in several steps of the sulfur assimilation and sulfur amino acid biosynthesis. Also, we have shown that Gpp2 phosphatase modulates Cys3 activity. In Saccharomyces cerevisiae Gpp2 is induced in response to hyper osmotic or oxidative stress and during diauxic shift. In this work, we will show that, in C. neoformans, Gpp2 is required to respond to stresses, mainly osmotic stress; also its transcription is induced during exposure to NaCl. Global transcriptional profile of gpp2Δ by RNAseq shows that CYS3 and other genes in the sulfur assimilation pathway are up regulated, which is consistent with our previous report, in which Gpp2 acts by avoiding Cys3 accumulation and nuclear localization. In addition, several transporters genes, especially amino acid permeases and oxidative stress genes are induced in the gpp2Δ strain; on the contrary, genes involved in glucose and tricarboxylic acid metabolism are down regulated. gpp2Δ strain fails to express virulence factors, as melanin, phospholipase, urease and has virulence attenuation in Galleria mellonella. Our data suggest that Gpp2 is an important factor for general pathogen adaptation to various stresses and also to the host, and perhaps it could be an interesting target for therapeutic use.
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Affiliation(s)
- Kevin Felipe Martho
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Otávio J B Brustolini
- Laboratório Nacional de Computação Científica - LNCC, Labinfo - Laboratório de Bioinformática, Petrópolis, Brazil
| | - Ana Tereza Vasconcelos
- Laboratório Nacional de Computação Científica - LNCC, Labinfo - Laboratório de Bioinformática, Petrópolis, Brazil
| | - Marcelo A Vallim
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata C Pascon
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
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3
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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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4
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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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5
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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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6
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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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7
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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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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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9
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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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