Academic literature on the topic 'Bacterial transcriptome'
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Journal articles on the topic "Bacterial transcriptome"
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Navarrete-López, Paula, Victoria Asselstine, María Maroto, Marta Lombó, Ángela Cánovas, and Alfonso Gutiérrez-Adán. "RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population." Current Issues in Molecular Biology 46, no. 9 (September 19, 2024): 10430–43. http://dx.doi.org/10.3390/cimb46090620.
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RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.
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Morcillo, Rafael, Juan Vílchez, Song Zhang, Richa Kaushal, Danxia He, Hailing Zi, Renyi Liu, Karsten Niehaus, Avtar Handa, and Huiming Zhang. "Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria." Metabolites 11, no. 6 (June 9, 2021): 369. http://dx.doi.org/10.3390/metabo11060369.
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Water deficit is one of the major constraints to crop production and food security worldwide. Some plant growth-promoting rhizobacteria (PGPR) strains are capable of increasing plant drought resistance. Knowledge about the mechanisms underlying bacteria-induced plant drought resistance is important for PGPR applications in agriculture. In this study, we show the drought stress-mitigating effects on tomato plants by the Bacillus megaterium strain TG1-E1, followed by the profiling of plant transcriptomic responses to TG1-E1 and the profiling of bacterial extracellular metabolites. Comparison between the transcriptomes of drought-stressed plants with and without TG1-E1 inoculation revealed bacteria-induced transcriptome reprograming, with highlights on differentially expressed genes belonging to the functional categories including transcription factors, signal transduction, and cell wall biogenesis and organization. Mass spectrometry-based analysis identified over 40 bacterial extracellular metabolites, including several important regulators or osmoprotectant precursors for increasing plant drought resistance. These results demonstrate the importance of plant transcriptional regulation and bacterial metabolites in PGPR-induced plant drought resistance.
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Nobori, Tatsuya, André C. Velásquez, Jingni Wu, Brian H. Kvitko, James M. Kremer, Yiming Wang, Sheng Yang He, and Kenichi Tsuda. "Transcriptome landscape of a bacterial pathogen under plant immunity." Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): E3055—E3064. http://dx.doi.org/10.1073/pnas.1800529115.
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Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta. We identified specific “immune-responsive” bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.
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Passalacqua, Karla D., Anjana Varadarajan, Brian D. Ondov, David T. Okou, Michael E. Zwick, and Nicholas H. Bergman. "Structure and Complexity of a Bacterial Transcriptome." Journal of Bacteriology 191, no. 10 (March 20, 2009): 3203–11. http://dx.doi.org/10.1128/jb.00122-09.
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ABSTRACT Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. Indeed, these aspects of the prokaryotic transcriptome have been explored on a large scale in only a few instances, and consequently little is known about the absolute composition of the mRNA population within a bacterial cell. Here we report the use of a high-throughput sequencing-based approach in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions and showed that the data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously nonannotated regions with significant transcriptional activity and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance and suggest that there is significant transcriptional heterogeneity within a clonal, synchronized bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.
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Cornforth, Daniel M., Justine L. Dees, Carolyn B. Ibberson, Holly K. Huse, Inger H. Mathiesen, Klaus Kirketerp-Møller, Randy D. Wolcott, Kendra P. Rumbaugh, Thomas Bjarnsholt, and Marvin Whiteley. "Pseudomonas aeruginosa transcriptome during human infection." Proceedings of the National Academy of Sciences 115, no. 22 (May 14, 2018): E5125—E5134. http://dx.doi.org/10.1073/pnas.1717525115.
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Laboratory experiments have uncovered many basic aspects of bacterial physiology and behavior. After the past century of mostly in vitro experiments, we now have detailed knowledge of bacterial behavior in standard laboratory conditions, but only a superficial understanding of bacterial functions and behaviors during human infection. It is well-known that the growth and behavior of bacteria are largely dictated by their environment, but how bacterial physiology differs in laboratory models compared with human infections is not known. To address this question, we compared the transcriptome of Pseudomonas aeruginosa during human infection to that of P. aeruginosa in a variety of laboratory conditions. Several pathways, including the bacterium’s primary quorum sensing system, had significantly lower expression in human infections than in many laboratory conditions. On the other hand, multiple genes known to confer antibiotic resistance had substantially higher expression in human infection than in laboratory conditions, potentially explaining why antibiotic resistance assays in the clinical laboratory frequently underestimate resistance in patients. Using a standard machine learning technique known as support vector machines, we identified a set of genes whose expression reliably distinguished in vitro conditions from human infections. Finally, we used these support vector machines with binary classification to force P. aeruginosa mouse infection transcriptomes to be classified as human or in vitro. Determining what differentiates our current models from clinical infections is important to better understand bacterial infections and will be necessary to create model systems that more accurately capture the biology of infection.
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Beisser, Daniela, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, and Jens Boenigk. "Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes." PeerJ 5 (January 10, 2017): e2832. http://dx.doi.org/10.7717/peerj.2832.
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BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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Chaudhuri, Roy R., Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell, and Andrew J. Grant. "Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome." Microbiology 157, no. 10 (October 1, 2011): 2922–32. http://dx.doi.org/10.1099/mic.0.050278-0.
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C ampylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community.
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González-Torres, Pedro, Leszek P. Pryszcz, Fernando Santos, Manuel Martínez-García, Toni Gabaldón, and Josefa Antón. "Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing." Applied and Environmental Microbiology 81, no. 24 (October 2, 2015): 8445–56. http://dx.doi.org/10.1128/aem.02690-15.
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ABSTRACTComparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacteriumSalinibacter rubergrown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
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Ding, Ting, and Yong Li. "Quorum sensing inhibitory effects of vanillin on the biofilm formation of Pseudomonas fluorescens P07 by transcriptome analysis." SDRP Journal of Food Science & Technology 5, no. 7 (2021): 275–92. http://dx.doi.org/10.25177/jfst.5.7.ra.10686.
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Pseudomonas fluorescens is an important psychrotrophic food-spoilage bacterium. Quorum sensing (QS) enables bacteria to control various physiological processes. Hence, targeting bacterial QS would be a novel method to improve food quality. In this study, P. fluorescens P07 was treated with vanillin, which showed strong QS inhibitory activity, and its resultant effects on swarming motility, biofilm formation, and extracellular polymeric substance (EPS) secretion were measured. The mechanisms underlying the inhibitory effects were then explored by transcriptomic analysis. The results showed that vanillin had inhibitory effects on swarming motility, biofilm formation, N-acyl-L-homoserine Lactone (AHLs) and EPS secretion of P. fluorescens P07. The result of transcriptionomic tests indicated that the decrease in bacterial biofilm formation was probably due to the influence of vanillin on mobility, adhesion, chemotaxis, EPS secretion, and QS system of the bacteria. Keywords: Pseudomonas fluorescens, quorum sensing, biofilm formation, transcriptome analysis, swarming motility
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Horlock, Anthony D., Rachel L. Piersanti, Rosabel Ramirez-Hernandez, Fahong Yu, Zhengxin Ma, KwangCheol C. Jeong, Martin J. D. Clift, et al. "Uterine infection alters the transcriptome of the bovine reproductive tract three months later." Reproduction 160, no. 1 (July 2020): 93–107. http://dx.doi.org/10.1530/rep-19-0564.
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Infection of the postpartum uterus with pathogenic bacteria is associated with infertility months later in dairy cattle. However, it is unclear whether these bacterial infections lead to long-term changes in the reproductive tract that might help explain this infertility. Here we tested the hypothesis that infusion of pathogenic bacteria into the uterus leads to changes in the transcriptome of the reproductive tract 3 months later. We used virgin Holstein heifers to avoid potential confounding effects of periparturient problems, lactation, and negative energy balance. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes (n = 4) and compared with control animals (n = 6). Three months after infusion, caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from ovarian follicles >8 mm diameter were profiled by RNA sequencing. Bacterial infusion altered the transcriptome of all the tissues when compared with control. Most differentially expressed genes were tissue specific, with 109 differentially expressed genes unique to caruncular endometrium, 57 in intercaruncular endometrium, 65 in isthmus, 298 in ampulla, and 83 in granulosa cells. Surprisingly, despite infusing bacteria into the uterus, granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there were changes in the transcriptome of the endometrium, oviduct and even granulosa cells, 3 months after intrauterine infusion of pathogenic bacteria. These findings imply that long-term changes throughout the reproductive tract could contribute to infertility after bacterial infections of the uterus.
Dissertations / Theses on the topic "Bacterial transcriptome"
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McQuillan, Jonathan. "Bacterial-nanoparticle interactions." Thesis, University of Exeter, 2010. http://hdl.handle.net/10036/3101.
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Bionanotechnology is an intersection between biology and nanotechnology, a field in which novel applications for very small materials are being realised at an alarming rate. Nanoparticles have 3 dimensions that can be measured in nanometers, their small size conferring upon them different properties from individual atoms or the bulk material. The interactions between these unique materials and microorganisms are often toxic, thus have been exploited for antimicrobial applications. However, there is a considerable paucity of data for the underlying molecular mechanisms. This study has been carried out to investigate the interactions that occur between nanoparticles and bacteria with the objective of identifying these toxicological mechanisms and novel nanoparticle effects, using the model Gram negative organism Escherichia coli K12. This study has identified metal nanoparticles that are a superior vehicle for the delivery of toxic metal ions to E. coli. The nanoparticles associate with the bacterial surface, but do not cross the cell wall. They then dissolve, releasing a concentration of metal ions that accumulate at the bacterial-nanoparticle interface, enhancing the antibacterial efficacy compared to the concentration of metal ions in the bulk solution phase. Measurement of the whole transcriptome response to silver nanoparticles in comparison to the silver ion indicates that the different modes of ion delivery may induce a differential stress response. Moreover, this data identifies molecular mechanisms that are involved in the toxicity of this metal that is now becoming increasingly prevalent in society. The dissolution based toxic effects of zinc oxide nanoparticles are augmented by an interaction with ultra-violet light, offering an alternative mode for nanoparticle toxicity.
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Muñoz, Bodnar Alejandra. "Function of TALE1Xam in cassava bacterial blight : a transcriptomic approach." Thesis, Montpellier 2, 2013. http://www.theses.fr/2013MON20009.
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Xanthomonas axonopodis pv. manihotis (Xam) est une bactérie à gram négatif causant le Cassava Bacterial Blight (CBB) sur Manihot esculenta Crantz. Le manioc représente une des sources les plus importantes de carbohydrates pour près d'un milliard de personnes sur terre et une source importante d'énergie du fait de sa forte concentration en amidon. Le CBB constitue une limitation importante à la production massive de manioc et nos connaissances sur cette maladie sont encore insuffisantes. La pathogénie de nombreuses phytobactéries dépend de l'injection d'effecteurs de type III via un système de sécrétion de type III dans la cellule eucaryote hôte Parmi tous les effecteurs référencés aujourd'hui, les effecteurs de type TAL pour Transcription Activator-Like sont particulièrement intéressant. Une fois injectés dans la cellule végétale, les effecteurs TAL sont importés au noyau et y modulent l'expression de gènes cibles au bénéfice de la bactérie. Chez Xam, TALE1Xam est le seul gène de cette famille qui a été étudié au niveau fonctionnel. Cette étude a pour objectif majeur d'identifier les gènes de manioc dont l'expression est modifiée en présence de TALE1Xam. Le transcriptome de plantes de manioc inoculées avec XamΔTALE1Xam vs. XamΔTALE1Xam (TALE1Xam) a été analysé par RNAseq. Les données obtenues confrontées à la recherche bioinformatique de promoteurs de gènes potentiellement directement activés par TALE1Xam ont permis d'établir une liste de gènes ciblés par TALE1Xam candidats. Un candidat majeur ressort de cette analyse comme étant particulièrement intéressant, il s'agit d'un gène codant un facteur de transcription de type B3 régulant l'activité de protéines de type "Heat Shock". L'analyse fonctionnelle de ce candidat permettra de valider sa fonction en tant que gène de sensibilité du manioc à XamXanthomonas axonopodis pv. manihotis (Xam) is a gram negative bacteria causing the Cassava Bacterial Blight (CBB) in Manihot esculenta Crantz . Cassava represents one of the most important sources of carbohydrates for around one billion people around the world as well as a source of energy due to its high starch levels content. The CBB disease represents an important limitation for cassava massive production and little is known about this pathosystem. Bacterial pathogenicity often relies on the injection in eucaryotic host cells of effector proteins via a type III secretion system (TTSS). Between all the type III effectors described up to now, Transcription Activator-Like Type III effectors (TALE) appear as particularly interesting. Once injected into the plant cell, TAL effectors go into the nucleus cell and modulate the expression of target host genes to the benefit of the invading bacteria by interacting directly with plant DNA. In Xam, only one gene belonging to this family has been functionally studied so far. It consists on TALE1xam. This work aim to identify cassava genes whose expression will be modified upon the presence of TALE1xam. By means of cassava plants challenged with Xam Δ TALE1xam vs. Xam + TALE1xam together with the TAL effectors code, statistical analyses between RNAseq experiments and a microarray containing 5700 cassava genes, we seek out direct TALE1xam target genes. Hence, through transcriptomic, functional qRT validation and specific artificial TALEs design we proposed that TALE1xam is potentially interacting with a Heat Shock Transcription Factor B3. Moreover we argue that this gene is responsible of the susceptibility during Xam infection. Furthermore this work represents the first complete transcriptomic approach done in the cassava/Xam interaction and open enormous possibilities to understand and study CBB
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Galletti, Maria Fernanda Bandeira de Melo. "Efeitos da temperatura e da alimentação sanguínea sobre o perfil de expressão gênica de Rickettsia rickettsii durante a infecção do carrapato-vetor Amblyomma aureolatum." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/42/42135/tde-03062014-082614/.
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Rickettsia rickettsii é o agente etiológico da febre maculosa das Montanhas Rochosas, a mais letal dentre as riquetsioses que acometem o homem. A principal espécie de carrapato-vetor de R. rickettsii na área metropolitana da cidade de São Paulo é Amblyomma aureolatum. Quando um carrapato em jejum no solo encontra um hospedeiro vertebrado e inicia a alimentação sanguínea, R. rickettsii é exposta a uma elevação da temperatura e aos componentes da refeição sanguínea. Ambos os estímulos foram previamente associados à reativação da virulência da bactéria em carrapatos, porém, os fatores responsáveis por essa conversão do fenótipo avirulento em virulento não foram completamente elucidados até o momento. Dessa forma, o presente trabalho teve como objetivo determinar os efeitos desses dois estímulos ambientais sobre o perfil de expressão gênica dessa bactéria durante a infecção de A. aureolatum. Inicialmente, estabelecemos um sistema de propagação de riquétsias para obter material genético suficiente para a padronização dos procedimentos de preparação de amostras para os experimentos de microarranjos. Para tal, estabelecemos, pela primeira vez, a infecção de uma cepa patogênica brasileira de R. rickettsii em células embrionárias do carrapato Rhipicephalus (Boophilus) microplus (BME26). Através da utilização de microarranjos de oligonucleotídeos customizados, analisamos os efeitos da elevação da temperatura em 10°C e da alimentação sanguínea sobre o perfil transcricional da bactéria infectando o conjunto de órgãos de fêmeas de A. aureolatum. Esse é o primeiro estudo da expressão gênica global de uma bactéria do gênero Rickettsia infectando um carrapato-vetor natural. Apesar de ambos os estímulos terem promovido um aumento da carga bacteriana, a alimentação sanguínea teve um efeito maior, também modulando cinco vezes mais genes que a elevação da temperatura. Dentre os genes induzidos, alguns codificam fatores de virulência, tais como componentes do sistema de secreção do tipo IV (T4SS), sugerindo que esse importante sistema de secreção bacteriano seja utilizado para secretar efetores durante a ingestão de sangue pelo carrapato. Através de análises in silico de domínios conservados das proteínas hipotéticas, identificamos outros componentes do T4SS de R. rickettsii ainda não descritos na literatura. A alimentação sanguínea também induziu a expressão de genes codificadores de enzimas antioxidantes, o que pode corresponder a uma tentativa de R. rickettsii de se proteger contra os efeitos deletérios de radicais livres produzidos pelos carrapatos alimentados. Por fim, analisamos a transcrição de uma seleção de genes de R. rickettsii em glândulas salivares e intestinos de carrapatos machos e fêmeas através de RT-qPCR microfluídica. Os resultados mostraram que a elevação da temperatura e a alimentação modulam um conjunto específico de genes em cada tecido analisado, tendo sido possível definirem-se assinaturas transcricionais tecido-específicas. Os genes diferencialmente expressos identificados neste estudo devem ser caracterizados funcionalmente, podendo ser considerados como futuros alvos para o desenvolvimento de vacinas.Rickettsia rickettsii is the causative agent of Rocky Mountain Spotted Fever, which is the most lethal spotted fever rickettsiosis that affects humans. The main tick species that transmits R. rickettsii in the metropolitan area of São Paulos city is Amblyomma aureolatum. When an infected and starving tick begins blood feeding from a vertebrate host, R. rickettsii is exposed to a temperature elevation and to components in the blood meal. These two environmental stimuli have been previously associated with the reactivation of rickettsial virulence in ticks, but the factors responsible for this phenotype conversion have not been completely elucidated. The main aim of the present work was to determine the effects of these two environmental stimuli on the R. rickettsii transcriptional profile during A. aureolatum infection. We initially established an effective system for rickettsia propagation to generate a substantial quantity of genetic material for microarray standardization. For that, for the first time, we established an in vitro infection of the virulent Brazilian R. rickettsii strain in the BME26 tick embryonic cell line from Rhipicephalus (Boophilus) microplus. Using customized oligonucleotide microarrays, we analyzed the effects of a 10°C temperature elevation and a blood meal on the transcriptional profile of R. rickettsii infecting whole organs of Amblyomma aureolatum female ticks. This is the first bacterial transcriptome study of the Rickettsia genus when infecting a natural tick vector. Although both stimuli significantly increased the bacterial load, blood feeding had a greater effect, also modulating five-fold more genes than the temperature upshift. Among the genes induced by blood-feeding, some encode virulence factors, such as Type IV Secretion System (T4SS) components, suggesting that this important bacterial transport system is used to secrete effectors during the acquisition of the blood meal by the tick. Using an in silico conserved domain analysis of hypothetical proteins, we identified additional T4SS components of R. rickettsii that were never previously described. Blood-feeding also up-regulated the expression of antioxidant enzymes, which might correspond to an attempt by R. rickettsii to protect itself against the deleterious effects of free radicals produced by fed ticks. Finally, we studied the transcriptional profile of selected genes of R. rickettsii on the salivary glands and midguts of male and female ticks by microfluidic RT-qPCR. Results showed that temperature upshift and blood feeding modulate specific sets of genes in each tissue, allowing for the establishment of a tissue-specific transcriptional signature. The modulated genes identified in this study require further functional analysis and may have potential as future targets for vaccine development.
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Findeiß, Sven. "Expanding the repertoire of bacterial (non-)coding RNAs." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-67816.
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The detection of non-protein-coding RNA (ncRNA) genes in bacteria and their diverse regulatory mode of action moved the experimental and bio-computational analysis of ncRNAs into the focus of attention. Regulatory ncRNA transcripts are not translated to proteins but function directly on the RNA level. These typically small RNAs have been found to be involved in diverse processes such as (post-)transcriptional regulation and modification, translation, protein translocation, protein degradation and sequestration.
Bacterial ncRNAs either arise from independent primary transcripts or their mature sequence is generated via processing from a precursor. Besides these autonomous transcripts, RNA regulators (e.g. riboswitches and RNA thermometers) also form chimera with protein-coding sequences. These structured regulatory elements are encoded within the messenger RNA and directly regulate the expression of their “host” gene.
The quality and completeness of genome annotation is essential for all subsequent analyses. In contrast to protein-coding genes ncRNAs lack clear statistical signals on the sequence level. Thus, sophisticated tools have been developed to automatically identify ncRNA genes. Unfortunately, these tools are not part of generic genome annotation pipelines and therefore computational searches for known ncRNA genes are the starting point of each study. Moreover, prokaryotic genome annotation lacks essential features of protein-coding genes. Many known ncRNAs regulate translation via base-pairing to the 5’ UTR (untranslated region) of mRNA transcripts. Eukaryotic 5’ UTRs have been routinely annotated by sequencing of ESTs (expressed sequence tags) for more than a decade. Only recently, experimental setups have been developed to systematically identify these elements on a genome-wide scale in prokaryotes.
The first part of this thesis, describes three experimental surveys of exploratory field studies to analyze transcript organization in pathogenic bacteria. To identify ncRNAs in Pseudomonas aeruginosa we used a combination of an experimental RNomics approach and ncRNA prediction. Besides already known ncRNAs we identified and validated the expression of six novel RNA genes.
Global detection of transcripts by next generation RNA sequencing techniques unraveled an unexpectedly complex transcript organization in many bacteria. These ultra high-throughput methods give us the appealing opportunity to analyze the complete RNA output of any species at once. The development of the differential RNA sequencing (dRNA-seq) approach enabled us to analyze the primary transcriptome of Helicobacter pylori and Xanthomonas campestris. For the first time we generated a comprehensive and precise transcription start site (TSS) map for both species and provide a general framework for the analysis of dRNA-seq data. Focusing on computer-aided analysis we developed new tools to annotate TSS, detect small protein-coding genes and to infer homology of newly detected transcripts. We discovered hundreds of TSS in intergenic regions, upstream of protein-coding genes, within operons and antisense to annotated genes. Analysis of 5’ UTRs (spanning from the TSS to the start codon of the adjacent protein-coding gene) revealed an unexpected size diversity ranging from zero to several hundred nucleotides. We identified and validated the expression of about 60 and about 20 ncRNA candidates in Helicobacter and Xanthomonas, respectively. Among these ncRNA candidates we found several small protein-coding genes that have previously evaded annotation in both species. We showed that the combination of dRNA-seq and computational analysis is a powerful method to examine prokaryotic transcriptomes.
Experimental setups are time consuming and often combined with huge costs. Another limitation of experimental approaches is that genes which are expressed in specific developmental stages or stress conditions are likely to be missed. Bioinformatic tools build an alternative to overcome such restraints. General approaches usually depend on comparative genomic data and evolutionary signatures are used to analyze the (non-)coding potential of multiple sequence alignments. In the second part of my thesis we present our major update of the widely used ncRNA gene finder RNAz and introduce RNAcode, an efficient tool to asses local protein-coding potential of genomic regions.
RNAz has been successfully used to identify structured RNA elements in all domains of life. However, our own experience and the user feedback not only demonstrated the applicability of the RNAz approach, but also helped us to identify limitations of the current implementation. Using a much larger training set and a new classification model we significantly improved the prediction accuracy of RNAz.
During transcriptome analysis we repeatedly identified small protein-coding genes that have not been annotated so far. Only a few of those genes are known to date and standard proteincoding gene finding tools suffer from the lack of training data. To avoid an excess of false positive predictions, gene finding software is usually run with an arbitrary cutoff of 40-50 amino acids and therefore misses the small sized protein-coding genes. We have implemented RNAcode which is optimized for emerging applications not covered by standard protein-coding gene annotation software. In addition to complementing classical protein gene annotation, a major field of application of RNAcode is the functional classification of transcribed regions. RNA sequencing analyses are likely to falsely report transcript fragments (e.g. mRNA degradation products) as non-coding. Hence, an evaluation of the protein-coding potential of these fragments is an essential task. RNAcode reports local regions of high coding potential instead of complete protein-coding genes. A training on known protein-coding sequences is not necessary and RNAcode can therefore be applied to any species. We showed this with our analysis of the Escherichia coli genome where the current annotation could be accurately reproduced. We furthermore identified novel small protein-coding genes with RNAcode in this extensively studied genome. Using transcriptome and proteome data we found compelling evidence that several of the identified candidates are bona fide proteins.
In summary, this thesis clearly demonstrates that bioinformatic methods are mandatory to analyze the huge amount of transcriptome data and to identify novel (non-)coding RNA genes. With the major update of RNAz and the implementation of RNAcode we contributed to complete the repertoire of gene finding software which will help to unearth hidden treasures of the RNA World.
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Ramos, Cruz Ana Raquel. "Characterization of the surface of segmented filamentous bacteria from the unicellular to filamentous stage." Electronic Thesis or Diss., Université Paris Cité, 2024. http://www.theses.fr/2024UNIP5192.
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Bellac, Caroline. "Pathomechanisms of bacterial meningitis based on transcriptome analysis : role of kynurenine 3-hydroxylase and galectin-3/-9 in brain injury /." [S.l.] : [s.n.], 2007. http://www.zb.unibe.ch/download/eldiss/07bellac_c.pdf.
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Gupta, Shishir Kumar [Verfasser], Thomas [Gutachter] Dandekar, and Roy [Gutachter] Gross. "Re-annotation of Camponotus floridanus Genome and Characterization of Innate Immunity Transcriptome Responses to Bacterial Infections / Shishir Kumar Gupta ; Gutachter: Thomas Dandekar, Roy Gross." Würzburg : Universität Würzburg, 2017. http://d-nb.info/1171132700/34.
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Kupper, Maria [Verfasser], Roy [Gutachter] Gross, and Heike [Gutachter] Feldhaar. "The immune transcriptome and proteome of the ant Camponotus floridanus and vertical transmission of its bacterial endosymbiont Blochmannia floridanus / Maria Kupper ; Gutachter: Roy Gross, Heike Feldhaar." Würzburg : Universität Würzburg, 2017. http://d-nb.info/1123505934/34.
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Rey, Camille. "Cytosolic bacterial subversions of mucosal immunity : a study of microfold (M) cell and enterocyte infections by S. flexneri and L. monocytogenes." Thesis, Sorbonne Paris Cité, 2018. https://theses.md.univ-paris-diderot.fr/Rey_camille_1_va_20180321.pdf.
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Les pathogènes bactériens cytosoliques S. flexneri et L. monocytogenes échappent à l'immunité extracellulaire de la muqueuse en induisant leur entrée et leur mode de vie intracellulaire dans l'épithélium intestinal. Dans leur cellule hôte, ils peuvent rapidement s’échapper de leur vacuole d'internalisation, envahir le cytosol et éviter l’élimination par la dégradation cellulaire en se propageant directement de cellule à cellule.Afin d’initier l’invasion intestinale, ces deux pathogènes ciblent les cellules M préleveusesd'antigènes qui recouvrent les sites d'induction immunitaire. Toutefois le mode de vie de ces pathogènes dans les cellules M, le mécanisme de propagation de l'infection à partir de ce pointd’entrée vers les entérocytes voisins ainsi que le mécanisme d'évasion de l'induction de l'immunité adaptative sont très peu caractérisés. Dans cette étude, nous présentons un nouveau modèle physiologique d'infection apicale par S. flexneri de cellules M humaines in vitro, qui récapitule les étapes précoces de l'invasion de l’épithelium intestinal par le pathogène. Nous montrons qu'une population de S. flexneri est rapidement transcytosée, en 15 minutes, à travers les cellules M. Nous amenons une nouvelle approche microscopie en temps réel de l'infection des cellules M, qui révèle qu'une deuxième sous-population de bactéries induit son entrée plus tardivement dans les cellules M, accompagnée de projections membranaires apicales, suivie par une rupture vacuolaire et l’initiation de la réplication cytosoliique des bactéries dans les cellules M. Nous découvrons que S.flexneri a également la capacité de se propager des cellules M aux cellules voisines par la motilité liéeà l'actine, qui constitue la voie principale de propagation basolatérale de l'infection. En étendant notre étude à L. monocytogenes, nous observons qu’à la différence de S. flexneri, cette bactérie détourne le processus de transcytose à travers les cellules M en utilisant le facteur de virulence ActA. Cependant, nous notons que L. monocytogenes se propage dans l'épithélium exclusivement par la motilité liée à l'actine, de façon similaire à S. flexneri. Nous proposons que la subversion de la voie de transcytose au travers des cellules M et l'évitement des tissus immunitaires sous-jacents sont des caractéristiques partagées par les pathogènes cytosoliques, leur permettant d'échapper à l'induction de l'immunité adaptative.Par ailleurs, nous présentons une approche de tri basée sur la fluorescence d’entérocytes individuels aux stades successifs de l'infection par S. flexneri, combinée avec une analyse transcriptomique parPCR quantitative en multiplex. Cette méthode révèle la production de réponses distinctes chez les entérocytes hôtes en fonction de la localisation subcellulaire du pathogène. Nous observons la production d'une réponse bystander forte, impliquant de multiples voies de signalisation corrélées chez les enterocytes non infectés. De plus nous détectons la production de profils de réponses distincts chez l’hôte en fonction de la localisation vacuolaire ou cytosolique de la bactérie chez les entérocytes infectés. Nous montrons que le facteur de virulence OspF contribue à atténuer les réponses des entérocytes infectés et à perturber des voies de signalisation autrement corrélées chez l’hôte.En conclusion, nos études exposent de nouvelles stratégies de subversion immunitaire liées aux modes de vie intracellulaires de bactéries entériques cytosoliques, soulignant l'importance des cellules M dans la propagation bactérienne initiale et le détournement de l'immunité adaptative, ainsi que l'organisation et la perturbation des réponses immunitaires innées chez les entérocytes au cours de l’infectionCytosolic bacterial pathogens S. flexneri and L. monocytogenes subvert extracellular mucosal immunity by inducing their uptake and intracellular lifestyle in the intestinal epithelium. Within the host, they are able to rapidly escape their internalization vacuole, invade the cytosol and escape cellular degradation by spreading from cell-to-cell. Antigen sampling M cells overlying immune induction sites are targeted by these pathogens to initiate intestinal invasion. However, the intracellular lifestyle of these pathogens within M cells, the mechanism of spread of the infection toneigh boring enterocytes from this entry point and the mechanism of S. flexneri evasion of adaptive immunity is poorly characterized. We present a novel physiologic model of apical S. flexneri infection of human in vitro M cells which recapitulates the early steps of epithelial invasion. We show that a subset of S. flexneri is rapidly transcytosed, within 15 minutes, through M cells. We establish a newtime-lapse imaging approach of M cell infections, which reveals that another subset of bacteriainduces apical ruffling upon entry, vacuolar rupture and replicates within the M cells at later timepoints. Remarkably, these bacteria are able to spread from M cells to neighboring cells by actinbased-motility, which we show constitutes the main route of basolateral spreading of the infection.As we extend our study to L. monocytogenes, we observe that unlike S. flexneri, the bacterium diverts M cell transcytosis via the virulence factor ActA. However, we discover that L. monocytogenes spreads within the epithelium exclusively by actin-based motility, similar to S. flexneri. We propose that subversion of M cell transcytosis and avoidance of underlying immune tissues are features shared by cytosolic pathogens, allowing their escape from induction of adaptive immunity.In addition, we submit a pipeline of fluorescence-based single cell sorting of enterocytes atsuccessive stages of infection combined with transcriptional analysis by multiplex qPCR. This methodreveals the production of distinct responses in host enterocytes according to subcellular pathogen localizations. We observe the production of a strong bystander response involving multiplecorrelated host pathways in non-infected enterocytes. Moreover, we detect the output of distinct host response patterns according to vacuolar or cytosolic bacterial localizations in infectedenterocytes. We further show that the virulence effector OspF contributes to dampen infected host responses and disrupt otherwise correlated host signaling pathways. To conclude, our studies expose new immune subversion strategies linked to the intracellular life styles of cytosolic enteric bacteria, highlighting the importance of M cells in initial bacterial dissemination and diversion of adaptive immunity, and the organization and disruption of innate immune responses provoked in enterocytes during infection
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Tufail, Muhammad Aammar. "Use of plant growth promoting endophytic bacteria to alleviate the effects of individual and combined abiotic stresses on plants as an innovative approach to discover new delivery strategies for bacterial bio-stimulants." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/305571.
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Bacterial endophytes are the organisms that live inside the plant for a full or a part of their life cycle. Endophytic bacteria have captured the interest of agriculture industry due to their plant beneficial properties, such as synthesis of phytohormones, solubilization of soil nutrients, and alleviation of biotic and abiotic stresses. Several studies have reported that stress tolerant endophytic bacteria can work with a similar performance as non-stressed conditions when inoculated to the plants under stressed conditions. Combination of abiotic stresses such as salinity, drought and low nitrogen stress can have additive or agonistic effects on bacterial and plant growth, and their interactions. However, very few studies have reported the impact of combined stress on endophytic bacterial assisted plant growth promotion. Therefore, understanding the underlying mechanisms of endophytic bacterial assisted plant’s tolerance abiotic stresses may provide the means of better exploiting the beneficial abilities of endophytic bacteria in agricultural production. Thus, the aim of this thesis was to study the stress tolerance mechanisms, beneficial characteristics, and plant growth promotion characteristics of endophytic bacteria under individual and combined abiotic stresses. Transcriptome analysis of endophytic bacteria revealed that tolerance mechanisms to deal with one kind of stress is different than concurrent stresses. Salinity and drought stress largely modulated the genes involved in flagellar assembly and membrane transport, showing reduced motility under stress conditions to preserve the energy. Additionally, bacterial endophyte that can fix nitrogen was studied with maize plant growth promotion under drought and low nitrogen stress conditions. The results suggested that diazotrophic bacterial endophyte can promote plant growth under moderate individual and combined stress conditions. Plant growth promoting endophytic bacteria can be utilized as an efficient tool to increase crop production under individual and concurrent abiotic stresses.
Book chapters on the topic "Bacterial transcriptome"
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Ying, Bei-Wen, and Tetsuya Yomo. "Comparative Analyses of Bacterial Transcriptome Reorganisation in Response to Temperature Increase." In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 757–65. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781119004813.ch73.
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Akama, Takeshi, Kazuaki Nakamura, Akito Tanoue, and Koichi Suzuki. "Design of Tiling Arrays and Their Application to Bacterial Transcriptome Analysis." In Methods in Molecular Biology, 23–34. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-607-8_2.
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Chan, Kok-Gan. "Transcriptome Analysis of Bacterial Response to Heat Shock Using Next-Generation Sequencing." In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 754–56. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781119004813.ch72.
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Al Kadi, Mohamad, and Daisuke Okuzaki. "Unfolding the Bacterial Transcriptome Landscape Using Oxford Nanopore Technology Direct RNA Sequencing." In Methods in Molecular Biology, 269–79. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2996-3_19.
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Snyder, Lori A. S. "Transcriptomes." In Bacterial Genetics and Genomics, 105–19. 2nd ed. Boca Raton: Garland Science, 2024. http://dx.doi.org/10.1201/9781003380436-9.
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Rice, Scott A., and Bert C. Lampson. "Bacterial Reverse Transcriptase and msDNA." In Molecular Evolution of Viruses — Past and Present, 23–32. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-1407-3_3.
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Fields, Matthew W. "Transcriptome Analysis of Metal-Reducing Bacteria." In Microbial Metal and Metalloid Metabolism, edited by Dwayne A. Elias, 211—P1. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817190.ch12.
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Zhang, Wei, Edward G. Dudley, and Joseph T. Wade. "Genomic and Transcriptomic Analyses of Foodborne Bacterial Pathogens." In Genomics of Foodborne Bacterial Pathogens, 311–41. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-7686-4_10.
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Kuipers, Oscar P., Anne de Jong, Richard J. S. Baerends, Sacha A. F. T. van Hijum, Aldert L. Zomer, Harma A. Karsens, Chris D. den Hengst, Naomi E. Kramer, Girbe Buist, and Jan Kok. "Transcriptome analysis and related databases of Lactococcus lactis." In Lactic Acid Bacteria: Genetics, Metabolism and Applications, 113–22. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-017-2029-8_7.
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Dermastia, Marina, Michael Kube, and Martina Šeruga-Musić. "Transcriptomic and Proteomic Studies of Phytoplasma-Infected Plants." In Phytoplasmas: Plant Pathogenic Bacteria - III, 35–55. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-9632-8_3.
Full textConference papers on the topic "Bacterial transcriptome"
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Konnova, T. A., A. S. Balkin, T. T. Ismailov, T. C. Ermekkaliev, S. A. Dmitrieva, N. E. Gogolev, and Yu V. Gogolev. "Transcriptome responses of ABA-degrading bacteria Novosphingobium sp.P6W." In IX Congress of society physiologists of plants of Russia "Plant physiology is the basis for creating plants of the future". Kazan University Press, 2019. http://dx.doi.org/10.26907/978-5-00130-204-9-2019-225.
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Sagawa, Cintia. "Identification of HLB Susceptibility Genes in a Citrus Population Generated Using Multiplexed CRISPR/Cas9 Gene Editing." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-6.
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Citrus greening or Huanglongbing (HLB) disease is caused by the bacteria Candidatus Liberibacter spp. which is a major threat to the citrus industry worldwide. This has led to the generation of a large number of genomic databases characterizing HLB at the molecular level. Based on the genomic information of 71 published transcriptomic and proteomic datasets we selected 1,200 potential susceptibility genes associated with HLB in citrus. By using CRISPR/Cas9 technology combined with a multiplex approach, we generated 300 constructs targeting a combination of four of those genes in each construct. We currently have a population of over 3,000 transformed lines of Carrizo, a commercial rootstock hybrid (Citrus sinensis 'Washington' sweet orange X Poncirus trifoliata) and population of Valencia sweet orange lines with a diversified combination of mutations. To aid in genotyping, our group is performing a whole genome sequencing of the hybrid Carrizo. Biallelic/homozygous mutants were confirmed by Sanger sequencing of target sites and alignment with respective genomes. Confirmed mutants are currently being tested for bacterial resistance. Identification and stacking of susceptibility gene mutations will be valuable in developing tolerance to HLB and these mutations can subsequently be introduced into other economically significant citrus cultivars and evaluated in the field.
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Darie, A., D. M. Schumann, L. Grize, K. Jahn, M. J. Herrmann, W. Strobel, H. Hirsch, M. Tamm, and D. Stolz. "Host transcriptomic signature for viral and bacterial infection at exacerbation of COPD–The longitudinal PAX-I study." In ERS International Congress 2022 abstracts. European Respiratory Society, 2022. http://dx.doi.org/10.1183/13993003.congress-2022.2600.
Full textReports on the topic "Bacterial transcriptome"
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Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
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PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.
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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697123.bard.
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Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In plants, one set of this defense system is characterized by large families of TIR–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) resistance genes. The direct interaction between plant proteins harboring the TIR domain with proteins that transmit and facilitate a signaling pathway has yet to be shown. The Arabidopsis genome encodes TIR-domain containing genes that lack NBS and LRR whose functions are unknown. Here we investigated the functional role of such protein, TLW1 (TIR LECTIN WOUNDRESPONSIVE1). The TLW1 gene encodes a protein with two domains: a TIR domain linked to a lectin-containing domain. Our specific aim in this proposal was to examine the ramifications of the TL1-glycan interaction by; A) The functional characterization of TL1 activity in the context of plant wound response and B) Examine the hypothesis that wounding induced specific polysaccharides and examine them as candidates for TL-1 interactive glycan compounds. The Weizmann group showed TLW1 transcripts are rapidly induced by wounding in a JA-independent pathway and T-DNA-tagged tlw1 mutants that lack TLW1 transcripts, fail to initiate the full systemic wound response. Transcriptome methodology analysis was set up and transcriptome analyses indicates a two-fold reduced level of JA-responsive but not JA-independent transcripts. The TIR domain of TLW1 was found to interact directly with the KAT2/PED1 gene product responsible for the final b-oxidation steps in peroxisomal-basedJA biosynthesis. To identify potential binding target(s) of TL1 in plant wound response, the CCRC group first expressed recombinant TL1 in bacterial cells and optimized conditions for the protein expression. TL1 was most highly expressed in ArcticExpress cell line. Different types of extraction buffers and extraction methods were used to prepare plant extracts for TL1 binding assay. Optimized condition for glycan labeling was determined, and 2-aminobenzamide was used to label plant extracts. Sensitivity of MALDI and LC-MS using standard glycans. THAP (2,4,6- Trihydroxyacetophenone) showed minimal background peaks at positive mode of MALDI, however, it was insensitive with a minimum detection level of 100 ng. Using LC-MS, sensitivity was highly increased enough to detect 30 pmol concentration. However, patterns of total glycans displayed no significant difference between different extraction conditions when samples were separated with Dionex ICS-2000 ion chromatography system. Transgenic plants over-expressing lectin domains were generated to obtain active lectin domain in plant cells. Insertion of the overexpression construct into the plant genome was confirmed by antibiotic selection and genomic DNA PCR. However, RT-PCR analysis was not able to detect increased level of the transcripts. Binding ability of azelaic acid to recombinant TL1. Azelaic acid was detected in GST-TL1 elution fraction, however, DHB matrix has the same mass in background signals, which needs to be further tested on other matrices. The major findings showed the importance of TLW1 in regulating wound response. The findings demonstrate completely novel and unexpected TIR domain interactions and reveal a control nexus and mechanism that contributes to the propagation of wound responses in Arabidopsis. The implications are to our understanding of the function of TIR domains and to the notion that early molecular events occur systemically within minutes of a plant sustaining a wound. A WEB site (http://genome.weizmann.ac.il/hormonometer/) was set up that enables scientists to interact with a collated plant hormone database.
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Sela, Shlomo, and Michael McClelland. Desiccation Tolerance in Salmonella and its Implications. United States Department of Agriculture, May 2013. http://dx.doi.org/10.32747/2013.7594389.bard.
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Salmonella enterica is a worldwide food-borne pathogen, which regularly causes large outbreaks of food poisoning. Recent outbreaks linked to consumption of contaminated foods with low water-activity, have raised interest in understanding the factors that control fitness of this pathogen to dry environment. Consequently, the general objective of this study was to extend our knowledge on desiccation tolerance and long-term persistence of Salmonella. We discovered that dehydrated STm entered into a viable-but-nonculturable state, and that addition of chloramphenicol reduced bacterial survival. This finding implied that adaptation to desiccation stress requires de-novo protein synthesis. We also discovered that dried STm cells develop cross-tolerance to multiple stresses that the pathogen might encounter in the agriculture/food environment, such as high or low temperatures, salt, and various disinfectants. These findings have important implications for food safety because they demonstrate the limitations of chemical and physical treatments currently utilized by the food industry to completely inactivate Salmonella. In order to identify genes involved in desiccation stress tolerance, we employed transcriptomic analysis of dehydrated and wet cells and direct screening of knock-out mutant and transposon libraries. Transcriptomic analysis revealed that dehydration induced expression of ninety genes and down-regulated seven. Ribosomal structural genes represented the most abundant functional group with a relatively higher transcription during dehydration. Other large classes of induced functional groups included genes involved in amino acid metabolism, energy production, ion transport, transcription, and stress response. Initial genetic analysis of a number of up-regulated genes was carried out). It was found that mutations in rpoS, yahO, aceA, nifU, rpoE, ddg,fnr and kdpE significantly compromised desiccation tolerance, supporting their role in desiccation stress response.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.
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The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)
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Sessa, Guido, and Gregory B. Martin. molecular link from PAMP perception to a MAPK cascade associated with tomato disease resistance. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597918.bard.
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The research problem: The detection of pathogen-associated molecular patterns (PAMPs) by plant pattern recognition receptors (PRRs) is a key mechanism by which plants activate an effective immune response against pathogen attack. MAPK cascades are important signaling components downstream of PRRs that transduce the PAMP signal to activate various defense responses. Preliminary experiments suggested that the receptor-like cytoplasmickinase (RLCK) Mai5 plays a positive role in pattern-triggered immunity (PTI) and interacts with the MAPKKK M3Kε. We thus hypothesized that Mai5, as other RLCKs, functions as a component PRR complexes and acts as a molecular link between PAMP perception and activation of MAPK cascades. Original goals: The central goal of this research was to investigate the molecular mechanisms by which Mai5 and M3Kε regulate plant immunity. Specific objectives were to: 1. Determine the spectrum of PAMPs whose perception is transmitted by M3Kε; 2. Identify plant proteins that act downstream of M3Kε to mediate PTI; 3. Investigate how and where Mai5 interacts with M3Kε in the plant cell; 4. Examine the mechanism by which Mai5 contributes to PTI. Changes in research directions: We did not find convincing evidence for the involvement of M3Kε in PTI signaling and substituted objectives 1 and 3 with research activities aimed at the analysis of transcriptomic profiles of tomato plants during the onset of plant immunity, isolation of the novel tomato PRR FLS3, and investigation of the involvement of the RLCKBSKs in PTI. Main achievements during this research program are in the following major areas: 1. Functional characterization of Mai5. The function of Mai5 in PTI signaling was demonstrated by testing the effect of silencing the Mai5 gene by virus-induced gene silencing (VIGS) experiments and in cell death assays. Domains of Mai5 that interact with MAPKKKs and subcellular localization of Mai5 were analyzed in detail. 2. Analysis of transcriptional profiles during the tomato immune responses to Pseudomonas syringae (Pombo et al., 2014). We identified tomato genes whose expression is induced specifically in PTI or in effector-triggered immunity (ETI). Thirty ETI-specific genes were examined by VIGS for their involvement in immunity and the MAPKKK EPK1, was found to be required for ETI. 3. Dissection of MAP kinase cascades downstream of M3Kε (Oh et al., 2013; Teper et al., 2015). We identified genes that encode positive (SGT and EDS1) and negative (WRKY1 and WRKY2) regulators of the ETI-associated cell death mediated by M3Kε. In addition, the MKK2 MAPKK, which acts downstream of M3Kε, was found to interact with the MPK3 MAPK and specific MPK3 amino acids involved interaction were identified and found to be required for induction of cell death. We also identified 5 type III effectors of the bacterial pathogen Xanthomonaseuvesicatoria that inhibited cell death induced by components of ETI-associated MAP kinase cascades. 4. Isolation of the tomato PRR FLS3 (Hind et al., submitted). FLS3, a novel PRR of the LRR-RLK family that specifically recognizes the flagellinepitope flgII-28 was isolated. FLS3 was shown to bind flgII-28, to require kinase activity for function, to act in concert with BAK1, and to enhance disease resistance to Pseudomonas syringae. 5. Functional analysis of RLCKs of the brassinosteroid signaling kinase (BSK) family.Arabidopsis and tomato BSKs were found to interact with PRRs. In addition, certain ArabidospsisBSK mutants were found to be impaired in PAMP-induced resistance to Pseudomonas syringae. Scientific and agricultural significance: Our research activities discovered and characterized new molecular components of signaling pathways mediating recognition of invading pathogens and activation of immune responses against them. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease.