Navegando por Autor "Brustolini, Otávio J. B."

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Geminivirus data warehouse: a database enriched with machine learning approaches
(BioMed Central Bioinformatics, 2017-05-05) Silva, Jose Cleydson F.; Carvalho, Thales F. M.; Basso, Marcos F.; Deguchi, Michihito; Pereira, Welison A.; Vidigal, Pedro M. P.; Brustolini, Otávio J. B.; Silva, Fabyano F.; Dal-Bianco, Maximiller; Fontes, Renildes L. F.; Santos, Anésia A.; Zerbini, Francisco Murilo; Cerqueira, Fabio R.; Fontes, Elizabeth P. B.; R. Sobrinho, Roberto
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. 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. 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.
Genomic sequence of the yeast Kluyveromyces marxianus CCT 7735 (UFV-3), a highly lactose-fermenting yeast isolated from the Brazilian dairy industry
(Genome Announcements, 2014-11-06) Silveira, Wendel B.; Diniz, Raphael H. S.; Cerdán, M. Esperanza; González-Siso, María I.; Souza, Robson de A; Vidigal, Pedro M. P.; Brustolini, Otávio J. B.; Prata, Emille R. B. de Almeida; Medeiros, Alexsandra C.; Paiva, Lílian C.; Nascimento, Moysés; Ferreira, Éder G.; Santos, Valdilene C. dos; Bragança, Caio R. S.; Fernandes, Tatiana A. R.; Colombo, Lívia T.; Passos, Flávia M. L.
Here, we present the draft genome sequence of Kluyveromyces marxianus CCT 7735 (UFV-3), including the eight chromosomes and the mitochondrial genomic sequences.
The molecular chaperone binding protein BiP prevents leaf dehydration-induced cellular homeostasis disruption
(Plos One, 2014-01-29) Carvalho, Humberto H.; Brustolini, Otávio J. B.; Pimenta, Maiana R.; Mendes, Giselle C.; Gouveia, Bianca C.; Silva, Priscila A.; Silva, José Cleydson F.; Mota, Clenilso S.; Soares-Ramos, Juliana R. L.; Fontes, Elizabeth P. B.
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.
NIK1-mediated translation suppression functions as a plant antiviral immunity mechanism
(Nature, 2015-04-30) Zorzatto, Cristiane; Machado, João Paulo B.; Lopes, Kênia V. G.; Nascimento, Kelly J. T.; Pereira, Welison A.; Brustolini, Otávio J. B.; Reis, Pedro A. B.; Calil, Iara P.; Deguchi, Michihito; Sachetto-Martins, Gilberto; Gouveia, Bianca C.; Loriato, Virgílio A. P.; Silva, Marcos A. C.; Silva, Fabyano F.; Santos, Anésia A.; Chory, Joanne; Fontes, Elizabeth P. B.
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^ 1–3 . 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^ 1 . 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^ 2,3 . Unlike most eukaryotic organisms, plants are not known to activate mechanisms of host global translation suppression to fight viruses^ 1,2 . 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)^ 4–6 , 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.
Revisiting the soybean GmNAC superfamily
(Frontiers in Plant Science, 2018-12) Melo, Bruno P.; Fraga, Otto T.; Silva, José Cleydson F.; Ferreira, Dalton O.; Brustolini, Otávio J. B.; Carpinetti, Paola A.; Machado, Joao Paulo B.; Reis, Pedro A. B.; Fontes, Elizabeth P. B.
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 H 2 O 2 . 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.
A WW domain-containing protein forms immune nuclear bodies against begomoviruses
(Molecular Plant, 2018-12-03) Calil, Iara P.; Quadros, Iana P. S.; Araújo, Thais C.; Duarte, Christiane E. M.; Gouveia-Mageste, Bianca C.; Silva, José Cleydson F.; Brustolini, Otávio J. B.; Teixeira, Ruan M.; Oliveira, Cauê N.; Milagres, Rafael W. M. M.; Martins, Gilberto S.; Reis, Pedro A. B.; Machado, Joao Paulo B.; Fontes, Elizabeth P. B.; Chory, Joanne
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.