Navegando por Autor "Assis, Renata de Almeida Barbosa"
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Item Alcaligenes faecalis associated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils.(2017) Felestrino, Érica Barbosa; Assis, Renata de Almeida Barbosa; Lemes, Camila Gracyelle de Carvalho; Cordeiro, Isabella Ferreira; Fonseca, Natasha Peixoto; Villa, Morghana Marina; Vieira, Izadora Tabuso; Kamino, Luciana Hiromi Yoshino; Carmo, Flávio Fonseca do; Moreira, Leandro MarcioThe ferruginous rupestrian grasslands (FRG) in the Iron Quadrangle (IQ) are ecosystems characterized by rocky soils with reduced availability of water and nutrients, but high levels of metals. In order to comprehend the interference of microorganisms on the adaptive process of endemic plant Mimosa calodendrum (Fabaceae), bacteria associated with its roots and rhizosphere were isolated. Fourteen isolates were obtained and subsequently grown in the presence of different concentrations of arsenic (As) species. The isolate Mc250, an Alcaligenes faecalis strain, resisted to 10 mM of As (III) and 800 mM of As (V). In the presence of this strain, atomic spectrometer detected a reduction of 55% for As (III) and 72% for As (V) respectively in 10 mM and 500 mM solution. Scanning electron microscopy of this isolate demonstrated morphological modification and EDX spectroscopy revealed the presence of both As species adsorbed on the membrane, justifying the removal observed in the in vitro assays. To validate this potential removal of As in vivo, tomato plants were used as grown model in the presence and absence of A. faecalis in soil previously contaminated with 5 mM of As (III). After 14 days, plants from contaminated soil had their growth improved when compared to untreated control plants. All these results suggest for the first time that plant-associated bacteria from FRG-IQ present potential for soil rhizoremediation and may benefit the adaptive processes of plants in extreme environments including application in recovering degraded areas.Item Analyses of seven new genomes of Xanthomonas citri pv. aurantifolii strains, causative agents of Citrus Canker B and C, show a reduced repertoire of pathogenicity-related genes.(2019) Fonseca, Natasha Peixoto; Patané, José Salvatore Leister; Varani, Alessandro de Mello; Felestrino, Érica Barbosa; Caneschi, Washington Luiz; Sanchez, Angelica Bianchini; Assis, Renata de Almeida Barbosa; Garcia, Camila Carrião Machado; Belasque Junior, José; Martins Junior, Joaquim; Facincani, Agda PaulaXanthomonas citri pv. aurantifolii pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by Xanthomonas citri pv. citri. The study of the genomes of strains of these related bacterial species has the potential to bring new understanding to the molecular basis of citrus canker as well as their evolutionary history. Up to now only one genome sequence of XauB and only one genome sequence of XauC have been available, both in draft status. Here we present two new genome sequences of XauB (both complete) and five new genome sequences of XauC (two complete). A phylogenomic analysis of these seven genome sequences along with 24 other related Xanthomonas genomes showed that there are two distinct and wellsupported major clades, the XauB and XauC clade and the Xanthomonas citri pv. citri clade. An analysis of 62 Type III Secretion System effector genes showed that there are 42 effectors with variable presence/absence or pseudogene status among the 31 genomes analyzed. A comparative analysis of secretion-system and surfacestructure genes showed that the XauB and XauC genomes lack several key genes in pathogenicity-related subsystems. These subsystems, the Types I and IV Secretion Systems, and the Type IV pilus, therefore emerge as important ones in helping explain the aggressiveness of the A type of citrus canker and the apparent dominance in the field of the corresponding strain over the B and C strains.Item Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil.(2018) Felestrino, Érica Barbosa; Vieira, Izadora Tabuso; Caneschi, Washington Luiz; Cordeiro, Isabella Ferreira; Assis, Renata de Almeida Barbosa; Lemes, Camila Gracyelle de Carvalho; Fonseca, Natasha Peixoto; Sanchez, Angelica Bianchini; Caicedo Cepeda, Juan Carlos; Ferro, Jesus Aparecido; Garcia, Camila Carrião Machado; Carmo, Flávio Fonseca do; Kamino, Luciana Hiromi Yoshino; Moreira, Leandro MarcioMicroorganisms associated with plants have a great biotechnological potential, but investigations of these microorganisms associated with native plants in peculiar environments has been incipient. The objective of this study was to analyze the plant growth-promoting bacteria potential of cultivable bacteria associated with rare plants from the ferruginous rocky fields of the Brazilian Iron Quadrangle. The roots and rhizospheres of nine endemic plants species and samples of a root found in a lateritiric duricrust (canga) cave were collected, the culturable bacteria isolated and prospected for distinct biotechnological and ecological potentials. Out of the 148 isolates obtained, 8 (5.4%) showed potential to promote plant growth, whereas 4 (2.7%) isolates acted as biocontrol agents against Xanthomonas citri pathotype A (Xac306), reducing the cancrotic lesions by more than 60% when co-inoculated with this phytopathogen in Citrus sinensis plants. Moreover, other 4 (2.7%) isolates were classified as potential bioremediation agents, being able to withstand high concentrations of arsenite (5 mM As3+) and arsenate (800 mM As5+), by removing up to 35% and 15% of this metalloid in solution, respectively. These same four isolates had a positive influence on the growth of both the roots and the aerial parts when inoculated with tomato seeds in the soil contaminated with arsenic. This is the first time that an investigation highlights the potentialities of bacteria associated with rare plants of ferruginous rocky fields as a reservoir of microbiota of biotechnological and ecological interest, highlighting the importance of conservation of this area that is undergoing intense anthropic activityItem Brazilian ironstone plant communities as reservoirs of culturable bacteria with diverse biotechnological potential.(2018) Caneschi, Washington Luiz; Felestrino, Érica Barbosa; Fonseca, Natasha Peixoto; Villa, Morghana Marina; Lemes, Camila Gracyelle de Carvalho; Cordeiro, Isabella Ferreira; Assis, Renata de Almeida Barbosa; Sanchez, Angelica Bianchini; Vieira, Izadora Tabuso; Kamino, Luciana Hiromi Yoshino; Carmo, Flávio Fonseca do; Garcia, Camila Carrião Machado; Moreira, Leandro MarcioExtensive mineral extractivism in the Brazilian Iron Quadrangle (IQ) region has destroyed large areas of land, decimating plant species, and their associated microbiota. Very little is known about the microbiota of the region; hence, cultivable bacteria associated with plants of its soils were investigated for their biotechnological potential. Samples were collected from nine plant species and six soils, and 65 cultivable bacterial isolates were obtained. These represent predominantly gram-positive bacilli (70%) capable of producing amylases (55%), proteases (63%), cellulases (47%), indole acetic acid (IAA) (46%), siderophores (26%), and to solubilize phosphate (9%). In addition, 65% of these were resistant to ampicillin, 100% were sensitive to tetracycline, and 97% were tolerant to high arsenic concentrations. Three isolates were studied further: the isolate FOB3 (Rosenbergiella sp.) produced high concentrations of IAA in vitro in the absence of tryptophan – shown by the significant improvement in plant germination and growth rate where the isolate was present. For isolates C25 (Acinetobacter sp.) and FG3 (Serratia sp.), plasmids were purified and inserted into Escherichia coli cells where they modified the physiological profile of the transformed strains. The E. coli::pFG3B strain showed the highest capacity for biofilm production, as well as an increase in the replication rate, arsenic tolerance and catalase activity. Moreover, this strain increased DNA integrity in the presence of arsenic, compared to the wild-type strain. These results help to explain the importance of bacteria in maintaining plant survival in ferruginous, rocky soils, acting as plant growth promoters, and to highlight the biotechnological potential of these bacteria. IMPORTANCE The Iron Quadrangle region is responsible for ∼60% of all Brazilian iron production and, at the same time, is responsible for housing a wide diversity of landscapes, and consequently, a series of endemic plant species and dozens of rare species – all of which have been poorly studied. Studies exploring the microbiota associated with these plant species are limited and in the face of the continuous pressure of extractive action, some species along with their microbiota are being decimated. To understand the potential of this microbiota, we discovered that cultivable bacterial isolates obtained from plants in the ferruginous rocky soil of the Iron Quadrangle region have diverse biotechnological potential, revealing a genetic ancestry still unknown.Item A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence.(2021) Assis, Renata de Almeida Barbosa; Varani, Alessandro de Mello; Sagawa, Cintia Helena Duarte; Patané, José Salvatore Leister; Setubal, João Carlos; Uceda-Campos, Guillermo; Silva, Aline Maria da; Zaini, Paulo Adriano; Almeida Junior, Nalvo Franco de; Moreira, Leandro Marcio; Dandekar, Abhaya M.Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic reper- toire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons.Item Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant.(2020) Felestrino, Érica Barbosa; Sanchez, Angelica Bianchini; Caneschi, Washington Luiz; Lemes, Camila Gracyelle de Carvalho; Assis, Renata de Almeida Barbosa; Cordeiro, Isabella Ferreira; Fonseca, Natasha Peixoto; Villa, Morghana Marina; Vieira, Izadora Tabuso; Kamino, Luciana Hiromi Yoshino; Carmo, Flávio Fonseca do; Silva, Aline Maria da; Thomas, Andrew Maltez; Patané, José Salvatore Leister; Ferreira, Fernanda Carla; Freitas, Leandro Grassi de; Varani, Alessandro de Mello; Ferro, Jesus Aparecido; Silva, Robson Soares; Almeida Junior, Nalvo Franco de; Garcia, Camila Carrião Machado; Setubal, João Carlos; Moreira, Leandro MarcioHere we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.Item Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR.(2019) Fonseca, Natasha Peixoto; Felestrino, Érica Barbosa; Caneschi, Washington Luiz; Sanchez, Angelica Bianchini; Cordeiro, Isabella Ferreira; Lemes, Camila Gracyelle de Carvalho; Assis, Renata de Almeida Barbosa; Carvalho, Flávia Maria de Souza; Ferro, Jesus Aparecido; Varani, Alessandro de Mello; Belasque Junior, José; Setubal, João Carlos; Telles, Guilherme Pimentel; Aguena, Deiviston da Silva; Almeida Junior, Nalvo Franco de; Moreira, Leandro MarcioBackground. In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results. Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions. We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism.Item Gene tags assessment by comparative genomics (GTACG) : a user-friendly framework for bacterial comparative genomics.(2019) Santiago, Caio Rafael do Nascimento; Assis, Renata de Almeida Barbosa; Moreira, Leandro Marcio; Digiampietri, Luciano AntonioGenomics research has produced an exponential amount of data. However, the genetic knowledge pertaining to certain phenotypic characteristics is lacking. Also, a considerable part of these genomes have coding sequences (CDSs) with unknown functions, posing additional challenges to researchers. Phylogenetically close microorganisms share much of their CDSs, and certain phenotypes unique to a set of microorganisms may be the result of the genes found exclusively in those microorganisms. This study presents the GTACG framework, an easy-to-use tool for identifying in the subgroups of bacterial genomes whose microorganisms have common phenotypic characteristics, to find data that differentiates them from other associated genomes in a simple and fast way. The GTACG analysis is based on the formation of homologous CDS clusters from local alignments. The frontend is easy to use, and the installation packages have been developed to enable userslacking knowledge of programming languages or bioinformatics analyze high-throughput data using the tool. The validation of the GTACG framework has been carried out based on a case report involving a set of 161 genomes from the Xanthomonadaceae family, in which 19 families of orthologous proteins were found in 90% of the plant-associated genomes, allowing the identification of the proteins potentially associated with adaptation and virulence in plant tissue. The results show the potential use of GTACG in the search for new targets for molecular studies, and GTACG can be used as a research tool by biologists who lack advanced knowledge in the use of computational tools for bacterial comparative genomics.Item Genome-wide profiling and phylogenetic analysis of the SWEET sugar transporter gene family in walnut and their lack of responsiveness to Xanthomonas arboricola pv. juglandis infection.(2020) Jiang, Shijiao; Balan, Bipin; Assis, Renata de Almeida Barbosa; Sagawa, Cintia Helena Duarte; Wan, Xueqin; Han, Shan; Wang, Le; Zhang, Lanlan; Zaini, Paulo Adriano; Walawage, Sriema Lalani; Jacobson, Aaron; Lee, Steven H.; Moreira, Leandro Marcio; Leslie, Charles A.; Dandekar, Abhaya M.Following photosynthesis, sucrose is translocated to sink organs, where it provides the primary source of carbon and energy to sustain plant growth and development. Sugar transporters from the SWEET (sugar will eventually be exported transporter) family are rate-limiting factors that mediate sucrose transport across concentration gradients, sustain yields, and participate in reproductive development, plant senescence, stress responses, as well as support plant–pathogen interaction, the focus of this study. We identified 25 SWEET genes in the walnut genome and distinguished each by its individual gene structure and pattern of expression in different walnut tissues. Their chromosomal locations, cis-acting motifs within their 50 regulatory elements, and phylogenetic relationship patterns provided the first comprehensive analysis of the SWEET gene family of sugar transporters in walnut. This family is divided into four clades, the analysis of which suggests duplication and expansion of the SWEET gene family in Juglans regia. In addition, tissue-specific gene expression signatures suggest diverse possible functions for JrSWEET genes. Although these are commonly used by pathogens to harness sugar products from their plant hosts, little was known about their role during Xanthomonas arboricola pv. juglandis (Xaj) infection. We monitored the expression profiles of the JrSWEET genes in different tissues of “Chandler” walnuts when challenged with pathogen Xaj417 and concluded that SWEET-mediated sugar translocation from the host is not a trigger for walnut blight disease development. This may be directly related to the absence of type III secretion system-dependent transcription activator-like effectors (TALEs) in Xaj417, which suggests different strategies are employed by this pathogen to promote susceptibility to this major aboveground disease of walnuts.Item Genomics and walnut hull proteomics of Xanthomonas arboricola pv. juglandis 417 for the development of new disease control.(2021) Assis, Renata de Almeida Barbosa; Moreira, Leandro Marcio; Dandekar, Abhaya M.; Moreira, Leandro Marcio; Ferro, Jesus Aparecido; Souza, Robson Francisco de; Cruz, Izinara Rosse da; Borges, William de CastroXanthomonas arboricola pv. juglandis 417 (Xaj417) is the causal agent of walnut bacterial blight, the most significant above-ground disease of walnuts (Juglans regia L.). Walnut producers have registered losses of up to 40% in local production annually. Disease management uses copper-based pesticides which induce pathogen resistance despite being harmful for the environment. Our aim was to evaluate the genome content of the pathogen, dissect the host-pathogen response to define determinants that regulate the host susceptibility and assess the mutation effect of a conserved secreted protein among plant-associated Xanthomonadaceae. Our study focused on Xaj417 to understand the proteo-genomics attributes to colonize its host. We investigated the genome sequence and proteome of this plant pathogen by performing a comparative analysis with other sequenced Xaj and inoculating walnut fruits with Xaj417. The comparison of 32 Xaj genomes revealed that the adaptive evolution generated by intensive spray application to control bacterial diseases possibly led to selection of resistant bacteria and emergence of pathogenic strains (Chapter I). The results revealed that bacterial virulence and copper resistance emerged by the acquisition of specific sets of pathogenesis-related genes commonly transferred among the members of the Xanthomonas genus on mobile genetic elements. This was evidenced for the reference strain Xaj417, a copper-resistant Californian isolate, that acquired a new copper resistance cassette by HGT associated with a new transposon family in Xanthomonas (TnXaj417). The expansion of mobile genetic elements in the most virulent strains influence the repertoire of virulence effectors and adaptation strategies shaping the evolution of pathogenic strains. On Chapter II, we dissected this pathosystem using tandem mass tag quantitative proteomics. This is the first proteome study of this pathosystem examining the molecular responses during the disease development by comparing the proteomes of infected fruit hulls to healthy tissue. Xaj proteins detected in infected tissues demonstrated its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Finally, on Chapter III the secreted monofunctional chorismate mutase mutant (XajCM) was created in Xaj417 and showed increased virulence in walnut nuts. The bacterial morphology was characterized and IX changes in the protein profile of the mutant in planta were tested. The proteomic results suggested intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Overall, this study offers new insights into the emergence of virulence, adaptation, and tolerance to disease management strategies used in orchard ecosystems. It also provides knowledge into molecular mechanisms highlighting potential molecular tools for early detection and disease control strategies.Item Identificação de proteínas exclusivas de fitopatógenos da família Xanthomonadaceae : uso de genômica comparativa para identificação de novos alvos de combate.(2016) Assis, Renata de Almeida Barbosa; Moreira, Leandro Marcio; Guttman, David S.; Moreira, Leandro Marcio; Garcia, Camila Carrião Machado; Laia, Marcelo Luiz deA família Xanthomonadaceae compreende espécies diferentes de proteobactérias não patogênicas e patogênicas que infectam diferentes hospedeiros, incluindo humanos e plantas. Nesse estudo, foi realizado uma análise comparativa usando o genoma completo de 69 cepas bacterianas pertencentes à família Xanthomonadaceae com foco na identificação de famílias de proteínas exclusivas de fitopatógenos que poderiam justificar o estilo de vida e a capacidade desses microrganismos infectarem hospedeiros compatíveis. Foram identificadas sete famílias de proteínas fitopatógeno-específicas, todas supostamente secretadas pelo sistema secretório tipo II: PheA (CMs), LipA/LesA, VirK, e quatro famílias de proteínas envolvidas na degradação de N-glicanos, NixE, NixF, NixL e FucA1. Análises filogenéticas e in silico dessas famílias de proteínas revelaram que todas elas possuem ortólogos em outras bactérias simbióticas ou patogênicas de plantas e estão envolvidas na modulação e evasão do sistema imune. Uma vez que esse estudo inclui microrganismos estreitamente relacionados, com estilos de vida diferenciados e evidencia proteínas diretamente relacionadas com adaptação dentro dos tecidos vegetais, abordagens inovadoras podem ser implementadas visando não somente a utilização destas proteínas como alvos biotecnológicos para o controle da doença, mas também contribuindo para a nossa compreensão da coevolução de bactérias associadas a plantas.Item Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.(2017) Assis, Renata de Almeida Barbosa; Polloni, Lorraine Cristina; Patané, José Salvatore Leister; Thakur, Shalabh; Felestrino, Érica Barbosa; Diaz Caballero, Julio; Digiampietri, Luciano Antonio; Goulart Filho, Luiz Ricardo; Almeida Junior, Nalvo Franco de; Nascimento, Rafael; Dandekar, Abhaya M.; Zaini, Paulo Adriano; Setubal, João Carlos; Guttman, David S.; Moreira, Leandro MarcioThe Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria.Item Proteome analysis of walnut bacterial blight disease.(2020) Sagawa, Cintia Helena Duarte; Assis, Renata de Almeida Barbosa; Zaini, Paulo Adriano; Wilmarth, Phillip A.; Phinney, Brett S.; Moreira, Leandro Marcio; Dandekar, Abhaya M.The interaction between the plant host, walnut (Juglans regia; Jr), and a deadly pathogen (Xanthomonas arboricola pv. juglandis 417; Xaj) can lead to walnut bacterial blight (WB), which depletes walnut productivity by degrading the nut quality. Here, we dissect this pathosystem using tandem mass tag quantitative proteomics. Walnut hull tissues inoculated with Xaj were compared to mock-inoculated tissues, and 3972 proteins were identified, of which 3296 are from Jr and 676 from Xaj. Proteins with differential abundance include oxidoreductases, proteases, and enzymes involved in energy metabolism and amino acid interconversion pathways. Defense responses and plant hormone biosynthesis were also increased. Xaj proteins detected in infected tissues demonstrate its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Secreted proteases and extracellular secretion apparatus such as type IV pilus for twitching motility and type III secretion effectors indicate putative factors recognized by the host. Taken together, these results suggest intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Our results provide insights into molecular mechanisms and highlight potential molecular tools for early detection and disease control strategies.Item Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection.(2017) Moreira, Leandro Marcio; Silva, Marcia Regina Soares da; Facincani, Agda Paula; Ferreira, Cristiano Barbalho; Ferreira, Rafael Marini; Ferro, Maria Inês Tiraboschi; Gozzo, Fabio Cesar; Felestrino, Érica Barbosa; Assis, Renata de Almeida Barbosa; Garcia, Camila Carrião Machado; Setubal, João Carlos; Ferro, Jesus Aparecido; Oliveira, Julio Cezar Franco deBackground: Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. A proteomic analysis under in planta infectious and non-infectious conditions was conducted in order to increase our knowledge about the adaptive process of Xac during infection. Results: For that, a 2D–based proteomic analysis of Xac at 1, 3 and 5 days after inoculation, in comparison to Xac growth in NB media was carried out and followed by MALDI-TOF-TOF identification of 124 unique differentially abundant proteins. Among them, 79 correspond to up-regulated proteins in at least one of the three stages of infection. Our results indicate an important role of proteins related to biofilm synthesis, lipopolysaccharides biosynthesis, and iron uptake and metabolism as possible modulators of plant innate immunity, and revealed an intricate network of proteins involved in reactive oxygen species adaptation during Plants` Oxidative Burst response. We also identified proteins previously unknown to be involved in Xac-Citrus interaction, including the hypothetical protein XAC3981. A mutant strain for this gene has proved to be non-pathogenic in respect to classical symptoms of citrus canker induced in compatible plants. Conclusions: This is the first time that a protein repertoire is shown to be active and working in an integrated manner during the infection process in a compatible host, pointing to an elaborate mechanism for adaptation of Xac once inside the plant.Item A secreted chorismate mutase from Xanthomonas arboricola pv. juglandis attenuates virulence and walnut blight symptoms.(2021) Assis, Renata de Almeida Barbosa; Sagawa, Cintia Helena Duarte; Zaini, Paulo Adriano; Saxe, Houston J.; Wilmarth, Phillip A.; Phinney, Brett S.; Salemi, Michelle; Moreira, Leandro Marcio; Dandekar, Abhaya M.Walnut blight is a significant above-ground disease of walnuts caused by Xanthomonas arboricola pv. juglandis (Xaj). The secreted form of chorismate mutase (CM), a key enzyme of the shikimate pathway regulating plant immunity, is highly conserved between plant-associated beta and gamma proteobacteria including phytopathogens belonging to the Xanthomonadaceae family. To define its role in walnut blight disease, a dysfunctional mutant of chorismate mutase was created in a copper resistant strain Xaj417 (XajCM). Infections of immature walnut Juglans regia (Jr) fruit with XajCM were hypervirulent compared with infections with the wildtype Xaj417 strain. The in vitro growth rate, size and cellular morphology were similar between the wild-type and XajCM mutant strains, however the quantification of bacterial cells by dPCR within walnut hull tissues showed a 27% increase in XajCM seven days post-infection. To define the mechanism of hypervirulence, proteome analysis was conducted to compare walnut hull tissues inoculated with the wild type to those inoculated with the XajCM mutant strain. Proteome analysis revealed 3296 Jr proteins (five decreased and ten increased with FDR ≤ 0.05) and 676 Xaj417 proteins (235 increased in XajCM with FDR ≤ 0.05). Interestingly, the most abundant protein in Xaj was a polygalacturonase, while in Jr it was a polygalacturonase inhibitor. These results suggest that this secreted chorismate mutase may be an important virulence suppressor gene that regulates Xaj417 virulence response, allowing for improved bacterial survival in the plant tissues.Item Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments.(2019) Caneschi, Washington Luiz; Sanchez, Angelica Bianchini; Felestrino, Érica Barbosa; Lemes, Camila Gracyelle de Carvalho; Cordeiro, Isabella Ferreira; Fonseca, Natasha Peixoto; Villa, Morghana Marina; Vieira, Izadora Tabuso; Moraes, Lauro Ângelo Gonçalves de; Assis, Renata de Almeida Barbosa; Carmo, Flávio Fonseca do; Kamino, Luciana Hiromi Yoshino; Silva, Robson Soares; Ferro, Jesus Aparecido; Ferro, Maria Inês Tiraboschi; Ferreira, Rafael Marini; Santos, Vera Lúcia; Silva, Ubiana de Cássia Mourão; Almeida Junior, Nalvo Franco de; Varani, Alessandro de Mello; Garcia, Camila Carrião Machado; Setubal, João Carlos; Moreira, Leandro MarcioSerratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.Item TabPath : interactive tables for metabolic pathway analysis.(2017) Moraes, Lauro Ângelo Gonçalves de; Felestrino, Érica Barbosa; Assis, Renata de Almeida Barbosa; Matos, Diogo; Lima, Joubert de Castro; Lima, Leandro de Araújo; Almeida Junior, Nalvo Franco de; Setubal, João Carlos; Garcia, Camila Carrião Machado; Moreira, Leandro MarcioInformation about metabolic pathways in a comparative context is one of the most powerful tool to help the understanding of genome-based differences in phenotypes among organisms. Although several platforms exist that provide a wealth of information on metabolic pathways of diverse organisms, the comparison among organisms using metabolic pathways is still a difficult task. We present TabPath (Tables for Metabolic Pathway), a web-based tool to facilitate comparison of metabolic pathways in genomes based on KEGG. From a selection of pathways and genomes of interest on the menu, TabPath generates user-friendly tables that facilitate analysis of variations in metabolism among the selected organisms.Item Universalizabilidade das razões de decidir : liberdade de imprensa e direito à honra no Superior Tribunal de Justiça.(2021) Guimarães, Esthefânia Guerra; Arantes, Bruno Camilloto; Arantes, Bruno Camilloto; Assis, Renata de Almeida Barbosa; Ferreira, Mateus de MouraEsta pesquisa tem por objetivo averiguar, nos termos propostos por Neil MacCormick, se há aplicação da universalizabilidade das razões de decidir quando o Superior Tribunal de Justiça precisa decidir sobre a responsabilidade civil em litígios que envolvem Liberdade de Imprensa e Direito à Honra, tendo como pano de fundo o ideal político do Estado Democrático de Direito. Foram coletados e produzidos dados sobre a universalidade das razões nos casos concretos julgados pelo Superior Tribunal de Justiça, a fim de testar a hipótese de que não há comprometimento com a universalizabilidade das razões justificatórias. A hipótese foi construída a partir da constatação de que há uma intuição geral que o judiciário brasileiro decide caso a caso, não sendo possível identificar um padrão argumentativo capaz de orientar o cidadão. Assim, constatada ou não a hipótese, espera-se que a produção de dados sobre a universalizabilidade das razões de decidir nos possibilite ter mais clareza sobre a racionalidade argumentativa das decisões judiciais proferidas pelo Superior Tribunal de Justiça nesses casos.