Academic literature on the topic 'Bacterial proteome'
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Journal articles on the topic "Bacterial proteome"
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Tjalsma, Harold, Haike Antelmann, Jan D. H. Jongbloed, Peter G. Braun, Elise Darmon, Ronald Dorenbos, Jean-Yves F. Dubois, et al. "Proteomics of Protein Secretion by Bacillus subtilis: Separating the “Secrets” of the Secretome." Microbiology and Molecular Biology Reviews 68, no. 2 (June 2004): 207–33. http://dx.doi.org/10.1128/mmbr.68.2.207-233.2004.
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SUMMARY Secretory proteins perform a variety of important“ remote-control” functions for bacterial survival in the environment. The availability of complete genome sequences has allowed us to make predictions about the composition of bacterial machinery for protein secretion as well as the extracellular complement of bacterial proteomes. Recently, the power of proteomics was successfully employed to evaluate genome-based models of these so-called secretomes. Progress in this field is well illustrated by the proteomic analysis of protein secretion by the gram-positive bacterium Bacillus subtilis, for which ∼90 extracellular proteins were identified. Analysis of these proteins disclosed various“ secrets of the secretome,” such as the residence of cytoplasmic and predicted cell envelope proteins in the extracellular proteome. This showed that genome-based predictions reflect only∼ 50% of the actual composition of the extracellular proteome of B. subtilis. Importantly, proteomics allowed the first verification of the impact of individual secretion machinery components on the total flow of proteins from the cytoplasm to the extracellular environment. In conclusion, proteomics has yielded a variety of novel leads for the analysis of protein traffic in B. subtilis and other gram-positive bacteria. Ultimately, such leads will serve to increase our understanding of virulence factor biogenesis in gram-positive pathogens, which is likely to be of high medical relevance.
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Truong, Thuyen, Li Mei Pang, Suhasini Rajan, Sarah Sze Wah Wong, Yi Man Eva Fung, Lakshman Samaranayake, and Chaminda Jayampath Seneviratne. "The Proteome of Community Living Candida albicans Is Differentially Modulated by the Morphologic and Structural Features of the Bacterial Cohabitants." Microorganisms 8, no. 10 (October 7, 2020): 1541. http://dx.doi.org/10.3390/microorganisms8101541.
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Candida albicans is a commensal polymorphic and opportunistic fungus, which usually resides as a small community in the oral cavities of a majority of humans. The latter eco-system presents this yeast varied opportunities for mutualistic interactions with other cohabitant oral bacteria, that synergizes its persistence and pathogenicity. Collectively, these communities live within complex plaque biofilms which may adversely affect the oral health and increase the proclivity for oral candidiasis. The proteome of such oral biofilms with myriad interkingdom interactions are largely underexplored. Herein, we employed limma differential expression analysis, and cluster analysis to explore the proteomic interactions of C. albicans biofilms with nine different common oral bacterial species, Aggregatibacter actinomycetemcomitans, Actinomyces naeslundii, Fusobacterium nucleatum, Enterococcus faecalis, Porphyromonas gingivalis, Streptococcus mutants, Streptococcus sanguinis, Streptococcus mitis, and Streptococcus sobrinus. Interestingly, upon exposure of C. albicans biofilms to the foregoing heat-killed bacteria, the proteomes of the fungus associated with cellular respiration, translation, oxidoreductase activity, and ligase activity were significantly altered. Subsequent differential expression and cluster analysis revealed the subtle, yet significant alterations in the C. albicans proteome, particularly on exposure to bacteria with dissimilar cell morphologies, and Gram staining characteristics.
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Meng, Wenshu, Chenyang Zhao, and Youhe Gao. "Comparison of urine proteome among rat models by intraperitoneal injection with single bacteria and co-injection with two bacteria." PLOS ONE 16, no. 12 (December 31, 2021): e0261488. http://dx.doi.org/10.1371/journal.pone.0261488.
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Purpose To explore and compare urine proteome changes among rat models by intraperitoneal injection with single bacteria and co-injection with two bacteria. Method Escherichia coli and Staphylococcus aureus are two common human pathogens. Three rat models were established: (i) the intraperitoneal co-injection of E. coli and S. aureus model (ES model), (ii) intraperitoneal injection of E. coli model (E model), and (iii) intraperitoneal injection of S. aureus model (S model). Urinary proteomes on days 0, 1 and 2 of the three models were analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results A total of 111, 34 and 94 differential proteins were identified in the ES model, E model and S model, respectively. Among them, some differential proteins were reported to be associated with bacterial infection. Approximately 47% differential proteins in the E model overlapped with ES model, and 37% differential proteins in the S model overlapped with ES model. Compared with the E model and S model, a total of 71 unique differential proteins were identified in the ES model. Conclusion Our results indicated that (1) the urine proteome could distinguish different bacterial intraperitoneal injections models and (2) the effects of co-injection with two bacteria on the urine proteome were not simple superposition of single injection.
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Wang, Liang, Jianye Yang, Yaping Xu, Xue Piao, and Jichang Lv. "Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter." Current Genomics 20, no. 2 (May 22, 2019): 115–23. http://dx.doi.org/10.2174/1389202920666190320134438.
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Background: Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physiology and lifestyle. Objective: This study aims to understand how domains are distributed and duplicated in bacterial proteomes, in order to better understand bacterial physiology and lifestyles. Methods: In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference proteomes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In addition, the properties of no-domain proteins were investigated in terms of physicochemical properties. Results: The increasing number of non-redundant domains for a bacterial proteome follows the trend of an asymptotic function. The domain duplication rate is positively correlated with proteome size and increases more rapidly. The high percentage of single-domain proteins is more associated with small proteome size. For each proteome, unique domains were also obtained. Moreover, no-domain proteins show differences with the other three groups for several physicochemical properties analysed in this study. Conclusion: The study confirmed that a low domain duplication rate and a high percentage of singledomain proteins are more likely to be associated with bacterial host-dependent or restricted nicheadapted lifestyle. In addition, the unique lifestyle and physiology were revealed based on the analysis of species-specific domains and core domain interactions or co-occurrences.
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Fels, Ursula, Patrick Willems, Margaux De Meyer, Kris Gevaert, and Petra Van Damme. "Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective." PLOS Pathogens 19, no. 8 (August 3, 2023): e1011183. http://dx.doi.org/10.1371/journal.ppat.1011183.
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By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over the time course of infection was obtained. Data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows, especially in identifying the downregulated bacterial proteome response during infection progression by permitting quantification of low abundant bacterial proteins at early times of infection when bacterial infection load is low. S. Typhimurium invasion and replication specific proteomic signatures in epithelial cells revealed interdependent host/pathogen specific responses besides pointing to putative novel infection markers and signalling responses, including regulated host proteins associated with Salmonella-modified membranes.
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Jungblut, Peter R. "Proteome analysis of bacterial pathogens." Microbes and Infection 3, no. 10 (August 2001): 831–40. http://dx.doi.org/10.1016/s1286-4579(01)01441-1.
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Pappa, Eftychia, Heleni Vastardis, Manousos Makridakis, Jerome Zoidakis, Konstantinos Vougas, George Stamatakis, Martina Samiotaki, and Christos Rahiotis. "Analysis of Human and Microbial Salivary Proteomes in Children Offers Insights on the Molecular Pathogenesis of Molar-Incisor Hypomineralization." Biomedicines 10, no. 9 (August 24, 2022): 2061. http://dx.doi.org/10.3390/biomedicines10092061.
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Molar incisor hypomineralization is a complex developmental enamel defect that affects the permanent dentition of children with significant functional and aesthetic implications. Saliva is an ideal diagnostic tool and ensures patients’ compliance by diminishing the discomfort especially in pediatric population. Lately, salivary proteome analysis has progressively evolved in various biomedical disciplines. As changes in saliva composition are associated with oral diseases, it is reasonable to assume that the saliva proteome of MIH-affected children might be altered compared to healthy children. This study analyzed the human and microbial salivary proteome in children with MIH in order to identify salivary markers indicative of the pathology. The conducted proteomic analysis generated a comprehensive dataset comprising a total of 1515 high confidence identifications and revealed a clear discrimination between the two groups. Statistical comparison identified 142 differentially expressed proteins, while the pathway analysis indicated deregulation of inflammation, immune response mechanisms, and defense response to bacteria in MIH patients. Bacterial proteome analysis showed a lower diversity for the microbial species, which highlights the dysbiotic environment established in the MIH pathology.
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Marin, Lina Maria, Yizhi Xiao, Jaime Aparecido Cury, and Walter Luiz Siqueira. "Modulation of Streptococcus mutans Adherence to Hydroxyapatite by Engineered Salivary Peptides." Microorganisms 10, no. 2 (January 20, 2022): 223. http://dx.doi.org/10.3390/microorganisms10020223.
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Since the modification of the proteinaceous components of the Acquired Enamel Pellicle (AEP) could influence the adhesion of Streptococcus mutans, the most cariogenic bacteria, to dental surfaces, we assessed if engineered salivary peptides would affect the adherence and modulate the bacterial proteome upon adherence. Single-component AEPs were formed onto hydroxyapatite (HAp) discs by incubating them with statherin, histatin-3, DR9, DR9-DR9, DR9-RR14, RR14, and parotid saliva. Then, the discs were inoculated with S. mutans UA159 and the bacteria were allowed to adhere for 2 h, 4 h, and 8 h (n = 12/treatment/time point). The number of bacteria adhered to the HAp discs was determined at each time point and analyzed by two-way ANOVA and Bonferroni tests. Cell-wall proteins were extracted from adhered, planktonic, and inoculum (baseline) bacteria and proteome profiles were obtained after a bottom-up proteomics approach. The number of adhered bacteria significantly increased over time, being the mean values obtained at 8 h, from highest to lowest, as follows: DR9-RR14 > statherin > RR14 = DR9-DR9 > DR9 = histatin3 > saliva (p < 0.05). Treatments modulated the bacterial proteome upon adherence. The findings suggested a potential use of our engineered peptide DR9-DR9 to control S. mutans biofilm development by reducing bacterial colonization.
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Jabbour, Rabih E., Samir V. Deshpande, Mary Margaret Wade, Michael F. Stanford, Charles H. Wick, Alan W. Zulich, Evan W. Skowronski, and A. Peter Snyder. "Double-Blind Characterization of Non-Genome-Sequenced Bacteria by Mass Spectrometry-Based Proteomics." Applied and Environmental Microbiology 76, no. 11 (April 2, 2010): 3637–44. http://dx.doi.org/10.1128/aem.00055-10.
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ABSTRACT Due to the possibility of a biothreat attack on civilian or military installations, a need exists for technologies that can detect and accurately identify pathogens in a near-real-time approach. One technology potentially capable of meeting these needs is a high-throughput mass spectrometry (MS)-based proteomic approach. This approach utilizes the knowledge of amino acid sequences of peptides derived from the proteolysis of proteins as a basis for reliable bacterial identification. To evaluate this approach, the tryptic digest peptides generated from double-blind biological samples containing either a single bacterium or a mixture of bacteria were analyzed using liquid chromatography-tandem mass spectrometry. Bioinformatic tools that provide bacterial classification were used to evaluate the proteomic approach. Results showed that bacteria in all of the double-blind samples were accurately identified with no false-positive assignment. The MS proteomic approach showed strain-level discrimination for the various bacteria employed. The approach also characterized double-blind bacterial samples to the respective genus, species, and strain levels when the experimental organism was not in the database due to its genome not having been sequenced. One experimental sample did not have its genome sequenced, and the peptide experimental record was added to the virtual bacterial proteome database. A replicate analysis identified the sample to the peptide experimental record stored in the database. The MS proteomic approach proved capable of identifying and classifying organisms within a microbial mixture.
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Rohmer, Laurence, Tina Guina, Jinzhi Chen, Byron Gallis, Greg K. Taylor, Scott A. Shaffer, Samuel I. Miller, Mitchell J. Brittnacher, and David R. Goodlett. "Determination and Comparison of theFrancisella tularensissubsp.novicidaU112 Proteome to Other Bacterial Proteomes." Journal of Proteome Research 7, no. 5 (May 2, 2008): 2016–24. http://dx.doi.org/10.1021/pr700760z.
Full textDissertations / Theses on the topic "Bacterial proteome"
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Encheva, Vesela. "Proteome analysis of bacterial pathogens." Thesis, University of East London, 2005. http://roar.uel.ac.uk/1301/.
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The explosive progress over the past decade in the fields of genomics, bioinformatics and mass spectrometry has resulted in an increased capability to investigate and compare the global protein expression of cells, tissues and organisms. The main focus of this study was on characterising the protein expression profiles of different serovars of Salmonella enterica and different serotypeso f Streptococcusp neumoniae in an attempt to identify protein factors associatedw ith host specificity and virulence. A novel approach for typing of bacterial isolates using SELDI TOF MS was developed. A thorough investigation on the effect of different factors on the quality of the SELDI profile was carried out, and the potential of several software programmes to perform cluster analysis of the SELDI data was assessedB. oth cytosolic and membrane-associatepdr oteins were separatedb y 2D GE, and detailed referencem aps of the proteins expressedu nder standardisedc. onditions were created.I n the caseo f Salmonella, it containedm ore than 300 proteins. The comparativea nalysisa t the subspeciesle vel revealedt hat, in many cases,t he variation in the expression patterns was greater between strains with the same serospecificity than betweens erotypes/serovarss, uggestingt hat the serological properties of bacteria do not correlate with differential protein synthesis. However, in the case of Salmonella, where the serovars have different host specificity, the high resolution 2D gel maps revealed several serovar-specific proteins, including enzymes involved in the catabolismo f various substrates,o r in the processo f cell detoxification. Changesi n the expression patterns of the serovars in different growth conditions, such as pH or oxygen availability, were mostly universal amongst the serovars, although a few serovar-specific proteins were also present. The findings revealed parts of the proteome that alter their expression when the microorganism are subjected to unfavourable conditions such as while colonising the host, amongst other parts that remain stable. Overall, the results demonstrated the importance of analysing many different isolates when performing protein expression studies in highly variable microbial populations.
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Lalanne, Jean-Benoît. "Multiscale dissection of bacterial proteome optimization." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/130217.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 315-348).
The quantitative composition of proteomes results from biophysical and biochemical selective pressures acting under system-level resource allocation constraints. The nature and strength of these evolutionary driving forces remain obscure. Through the development of analytical tools and precision measurement platforms spanning biological scales, we found evidence of optimization in bacterial gene expression programs. We compared protein synthesis rates across distant lineages and found tight conservation of in-pathway enzyme expression stoichiometry, suggesting generic selective pressures on expression setpoints. Beyond conservation, we used high-resolution transcriptomics to identify numerous examples of stoichiometry preserving cis-elements compensation in pathway operons. Genome-wide mapping of transcription termination sites also led to the discovery of a phylogenetically widespread mode of bacterial gene expression, 'runaway transcription', whereby RNA polymerases are functionally uncoupled from pioneering ribosomes on mRNAs. To delineate biophysical rationales underlying these pressures, we formulated a parsimonious ribosome allocation model capturing the trade-off between reaction flux and protein production cost. The model correctly predicts the expression hierarchy of key translation factors. We then directly measured the quantitative relationship between expression and fitness for specific translation factors in the Gram-positive species Bacillus subtilis. These precision measurements confirmed that endogenous expression maximizes growth rate. Idiosyncratic transcriptional changes in regulons were however observed away from endogenous expression. The resulting physiological burdens sharpened the fitness landscapes. Spurious system-level responses to targeted expression perturbations, called 'regulatory entrenchment', thus exacerbate the requirement for precisely set expression stoichiometry.
by Jean-Benoît Lalanne.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Physics
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Casas, López Mª Vanessa. "Proteome characterization of Brachyspira strains. Identification of bacterial antigens." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/454775.
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El género Brachyspira incluye varias especies patogénicas que afectan a cerdos, perros, pájaros y humanos. En cerdos, Brachyspira (anteriormente Serpulina y Treponema) hyodysenteriae y Brachyspira pilosicoli son patógenos intestinales bien conocidos. Estas especies son espiroquetas gram-negativas, flageladas y anaeróbicas, las cuales viven en el intestino grueso y que tienen una asociación estrecha con la mucosa del colon. Brachyspira hyodysenteriae es el agente causante de la disentería porcina, mientras que Brachyspira pilosicoli está relacionada con la espiroquetosis intestinal, una colitis más leve, no hemorrágica.
La disentería porcina es una enfermedad con un impacto importante en la producción porcina debido a los costes vinculados a la mortalidad, morbididad, la producción ineficiente y la medicación de los animales.
Aunque la enfermedad puede afectar animales de todas las edades, afecta raramente a lechones menores de tres semanas, produciéndose más frecuentemente durante los periodos de crecimiento y finalización, lo cual agrava las pérdidas económicas.
Las estrategias para tratar estas enfermedades se basan principalmente en el uso de antibióticos como Tiamulin, Valnemulin, Tylosin, Tylvalosin o Lincomycin. Desafortunadamente, cepas resistentes a antibióticos han sido detectadas para ambas especies en diferentes países alrededor del mundo. A pesar de que hace mucho tiempo que se conoce el hecho de que los cerdos que se recuperan de una infección desarrollan Resistencia contra Brachyspira hyodysenteriae, no hay una vacuna disponible todavía.
Los genomas de estas especies están disponibles desde los años 2009-2010, pero la información a nivel proteómico todavía es escasa. En este trabajo se presenta la caracterización de los proteomas de estos patógenos. Se proporciona evidencia experimental del perfil de expresión proteica en estas especies, incluyendo PTMs y SAS, y se ha llevado a cabo en el contexto de la búsqueda de potenciales candidatos para elaborar una vacuna.
Esta caracterización se ha llevado a cabo a través del estudio del proteoma total, el proteoma expuesto y el inmunoproteoma de cepas comerciales y aislados de estas especies.
- El proteoma total fue estudiado a través de una aproximación proteómica shotgun, usando una serie de herramientas informáticas dirigidas a optimizar la cantidad de información sobre la secuencia obtenida de los datos espectrométricos. En una primera etapa, los espectros fueron analizados con una combinación de seis motores de búsquedas diferentes usando la aplicación PeptideShaker. Aquellos espectros que no se identificaron en esta primera etapa fueron analizados con una combinación de novo y búsqueda en base de datos con motor de búsqueda usando la aplicación PEAKS. Las secuencias que no se identificaron después de esta etapa se buscaron en BLAST frente a base de datos de Brachyspira total y de mamíferos. En resumen, más de 1500 proteínas fueron identificadas para cada especie. La cobertura del proteoma estimada fue 67-70%. Además, se ha descrito el perfil de PTM, siendo la metilación la modificación más frecuente. A través del enriquecimiento especifico se identificaron 79 y 91 sitios de fosforilación, y 3221 y 5579 sitios de acetilación para B. hyodysenteriae y B. pilosicoli, respectivamente.
- El proteoma expuesto fue estudiado usando sobrenadantes celulares y muestras obtenidas después de un tratamiento enzimático controlado de las células intactas. Entre las proteínas más abundantes identificadas en el proteoma expuesto hay proteínas relacionadas con movimiento/chemotaxis, proteínas ribosomales, enolase, NADH oxidasa, y Heat Shock Proteins.
- El inmunoproteoma fue caracterizado por immunoblot de las proteínas de bacteria con suero de cerdos experimentalmente infectados. Se identificaron once proteínas inmunoreactivas para B. hyodysenteriae y 8 para B. pilosicoli. Dos de estas proteínas, enolase y PEPCK fueron identificadas como inmunoreactivas en las dos especies.The genus Brachyspira includes several pathogenic species affecting pigs, dogs, birds and human. In pigs, Brachyspira (formerly Serpulina and Treponema) hyodysenteriae and Brachyspira pilosicoli are well known intestinal pathogens. These species are flagellated, anaerobic, gram negative spirochetes which inhabit the large intestine and have an intimate association with the colonic mucosa. Brachyspira hyodysenteriae is the causative agent of Swine dysentery, while Brachyspira pilosicoli is associated with Intestinal spirochetosis, a milder, non–haemorrhagic colitis. Swine dysentery is a disease with an important impact on pig production due to the costs associated with mortality, morbidity, inefficient production and medication of the animals. Although the disease can affect animals of all ages, it is rarely detected in piglets younger than three weeks old; occurring more frequently during growing/finishing periods, which aggravates the economic losses. Strategies to treat these diseases rely mainly in the use of antibiotics such as Tiamulin, Valnemulin, Tylosin, Tylvalosin or Lincomycin. Unfortunately, antibiotic resistant strains have been detected for both species in many countries around the world. Despite it is long been known that pigs generate resistance against B. hyodysenteriae after recovering from infection, no vaccine is available yet. The genomes of these species are available since 2009-2010 but proteome information is still scarce. In this work, a large-scale characterization of the proteomes of these pathogens is presented. The work provides experimental evidence of the protein expression profile in these pathogens, including PTMs and SAS and is carried out in the context of the search for potential vaccine candidates. This characterization has been performed through the study of the total proteome, the exposed proteome and the immunoproteome of commercial and environmental strains of these species. - The total proteome was studied through a shotgun proteomics strategy, using a range sofware tools directed to optimize the amount of sequence information extractable from the spectrometric data. In a first stage, spectra were analysed with a combination of six different search engines using the PeptideShaker application. Unmatched spectra were analysed by a combination of de novo and database search engines using the PEAKS application. Unmatched sequence tags after this stage were further BLASTed against Brachyspira and mammals databases. Overall, more than 1500 proteins were identified for each species. The estimated proteome coverage was 67-70%. In addition their PTM profile was described, being methylation the more frequent modification. Specific enrichment allowed identification of 79 and 91 phosphorylation sites and 3221 and 5579 acetylation sites for B. hyodysenteriae and B. pilosicoli, respectively. - The exposed proteome was studied using cell culture supernatants and samples obtained after a controlled enzymatic treatment of intact cells. Among the most abundant exposed proteins are proteins related to movement/chemotaxis, ribosomal proteins, enolase, NADH oxidase and Heat Shock Proteins. - The immunoproteome was characterized immunoblotting the bacterial proteins with sera from challenged pigs. Eleven immunoreactive proteins for B. hyodysenteriae and 8 for B. pilosicoli were identified. Two of these proteins, enolase and PEPCK, were found immunoreactive in the two species.
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Wilson, Kimberly M. Wilson. "Characterizing the Impact of Select Bacterial Isolates on Perinatal Pioneer Microbial Colonization and GIT Development." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1531832465230743.
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Naujoks, Jan. "Type I and II IFNs modify the proteome of bacterial vacuoles to restrict infections via IRG1." Doctoral thesis, Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, 2015. http://dx.doi.org/10.18452/17367.
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Die hier vorgestellte Studie untersucht systematisch die angeborene Immunabwehr gegen L. pneumophila auf Ebene des gesamten Wirtsorganismus, sowie auf molekularer Ebene in Alveolar- und Knochenmarksmakrophagen. Mittels in vivo Transkriptomanalysen werden Typ I und II Interferone (IFN) als Hauptregulatoren der frühen pulmonalen Genexpression in der L. pneumophila-Infektion identifiziert. Infektionsexperimente in Wildtyp- und IFN-Rezeptor-defizienten Tieren offenbaren, dass Typ I und II IFNe maßgeblich die antibakterielle Abwehr gegen L. pneumophila vermitteln. Für die Bekämpfung der Infektion in der Lunge werden CD11c+ Zellen als wichtigste Empfänger der IFN-Signale identifiziert. Des Weiteren wird durch Behandlung von CD11c+ Alveolarmakrophagen mit IFNen ex vivo das intrazelluläre bakterielle Wachstum inhibiert. Mittels subzellulärer quantitativer Massenspektrometrie wird gezeigt, dass die Proteinkomposition der Legionellen-enthaltenden Vakuole substanziell durch beide IFNe modifiziert wird. In einer vergleichenden Netzwerkanalyse werden diese Proteomdaten mit eigenen und öffentlich zugänglichen Transkriptomdaten verglichen. Hierdurch können klar abgegrenzte Untergruppen von einerseits transkriptionell durch IFN-regulierten Proteinen sowie andererseits ausschließlich räumlich IFN-regulierten Proteinen unterschieden werden. Unter den durch IFN an der Vakuole angereicherten Proteinen wird Immunoresponsive gene 1 (IRG1) als zentraler Effektor identifiziert, welcher das Wachstum von L. pneumophila durch die Produktion des antibakteriellen Metaboliten Itaconsäure inhibiert. Zusammenfassend stellt diese Studie eine umfassende Ressource von IFN-vermittelten Effekten auf die Genexpression sowie auf das Proteom der bakteriellen Vakuole dar und deckt einen zellautonomen Abwehrmechanismus gegen L. pneumophila auf, welcher durch die IRG1-abhängige Produktion von Itaconsäure vermittelt wird.The study presented here systemically examines the innate immune response against L. pneumophila on whole organism level as well as on a molecular level within macrophages, L. pneumophilas’ host cell. In vivo transcriptome analyses identify type I and II interferons (IFNs) as master regulators of the early pulmonary gene expression during L. pneumophila infection. Infection experiments in wild-type mice and mice lacking type I and/or II IFN signaling reveal a severe defect of antibacterial defense when IFN signaling is absent. CD11c+ cells were found to be the main targets of IFNs to restrict infection in the lung, and IFNs inhibited bacterial growth in CD11c+ alveolar macrophages ex vivo. Subcellular quantitative mass spectrometry shows that both IFNs substantially modify the protein composition of Legionella-containing vacuoles. Comparative network analysis, combining these proteome data with transcriptome data as well as public database data reveals distinct subsets of transcriptionally regulated IFN-stimulated genes (ISGs) on the one hand, but interestingly also exclusively spatially IFN-regulated vacuolar proteins. Among IFN-regulated vacuolar proteins, Immunoresponsive gene 1 (IRG1) was identified as a central effector that restricts growth of L. pneumophila through production of the antibacterial metabolite itaconic acid in macrophages. Collectively, this study provides a comprehensive resource of IFN-mediated effects on gene expression and the bacterial vacuolar proteome, and uncovers a cell-autonomous defense pathway against L. pneumophila, which is mediated by IFNs, IRG1 and itaconic acid.
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McWilliams, Tracy. "Proteome comparison of helicobacter pylori isolates associated with four disease groups." Thesis, Curtin University, 2006. http://hdl.handle.net/20.500.11937/1114.
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The Gram-negative bacterium Helicobacter pylori is found in human gastric mucosa. H. pylori, one of the most common chronic bacterial infections of humans, is present in almost half of the world population. It is associated with chronic gastritis, non-ulcer dyspepsia, gastric and duodenal ulcers, and malignant neoplasms. The aim of this study was to detect microbial candidate protein markers whose presence might be correlated with the development of four different clinical consequences of H. pylori infection, gastric ulceration [GU], duodenal ulceration [DU], non-ulcer dyspepsia [NUD] and gastritis [GI]. Eleven H. pylori isolates associated with these outcomes were analysed. The total complement of protein from these H. pylori isolates were resolved by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and compared using PDQUEST pattern analysis software. Relationships between the isolates associated with specific disease outcomes were determined by cluster analysis.Fifty six disease specific proteins were then characterised by tryptic peptide-mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Up to 1165 protein species were resolved from each H. pylori strain. Proteome analysis revealed that only 470 (40%) of the proteins detected were common to all eleven isolates. Twenty six of the 56 disease specific proteins that were selected for identification consisted of spots whose expression is altered in response to stress conditions or those that can affect H. pylori cell division and the cell membrane. The remaining 30 proteins had no known function. This study has provided further confirmation of the extensive variation that the bacterium H. pylori exhibits at the proteome level. Most significantly this study has found, through the application of cluster analysis and protein matching, that isolates do form disease groups. Comparative proteome analysis is a useful method for highlighting the extensive strain variation that H. pylori exhibits and to determine if any disease specific proteins exist.
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Cogo, Karina 1980. "Avaliação in vitro dos efeitos da nicotina e cotinina sobre a expressão de proteinas e capacidade de adesão e invasão de Porphyromonas gingivalis." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/288971.
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Orientadores: Francisco Carlos Groppo, Reginaldo Bruno GonçalvesTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
Made available in DSpace on 2018-08-12T19:00:41Z (GMT). No. of bitstreams: 1 Cogo_Karina_D.pdf: 3355648 bytes, checksum: d8afd799c6d162cda6cbb9bad9d225a5 (MD5) Previous issue date: 2009
Resumo: O uso do cigarro tem sido associado com a progressão da periodontite bem como com a redução da resposta à terapia aplicada a essa doença. Porphyromonas gingivalis é um importante colonizador do biofilme subgengival além de ser um dos principais patógenos envolvidos no estabelecimento e progressão da doença periodontal. No entanto, os possíveis efeitos dos principais derivados do cigarro sobre P. gingivalis ainda não foram totalmente investigados. Dessa forma, os objetivos deste estudo foram avaliar os efeitos da nicotina e cotinina sobre a expressão de proteínas e sobre a capacidade de adesão e invasão celular de P. gingivalis. A fim de avaliar a expressão de proteínas, culturas de P. gingivalis W83 foram expostas à nicotina e cotinina nas concentrações de 6 e 600µg/mL, as proteínas foram extraídas, separadas por eletroforese bidimensional em gel de poliacrilamida (12.5% SDS-PAGE) e identificadas por LC-MS/MS. Os géis e suas corridas eletroforéticas foram feitas em triplicatas e a detecção de proteínas nos mesmos foi feita através de coloração com corante Coomassie. Proteínas diferentemente expressas foram digeridas com tripsina e as amostras de peptídeos sequenciadas utilizando um sistema Q-TOF API LC-MS/MS. A busca MS/MS foi realizada utilizando os bancos de dados MSDB e NCBI através do programa Mascot. Para examinar a capacidade de adesão e invasão de P. gingivalis, monocamadas de células KB e culturas de P. gingivalis ATCC 33277 foram expostas às concentrações de 0.1, 10 e 100 µg/mL de nicotina e cotinina. As células epiteliais foram incubadas por 24 h enquanto P. gingivalis foi exposta a essas substâncias até atingir a fase logarítmica. Após o período de incubação, P. gingivalis foi submetida aos ensaios de adesão e invasão às células KB. O número de bactérias associadas às células foi obtido através de contagem de unidades formadoras de colônia. Os resultados obtidos da análise expressão de proteínas mostraram que a adição de nicotina e cotinina promoveram alterações no proteoma de P. gingivalis. Entre os ± 430 spots de proteínas reproduzíveis detectados em cada gel, 20 proteínas foram menos expressas e 42 foram mais expressas em pelo menos um dos tratamentos (p<0.05; ANOVA - Tukey). Entre as proteínas identificadas, muitas estavam envolvidas em processos como produção de energia celular, síntese de proteínas, estresse oxidativo, virulência, transporte, etc. Em relação aos resultados obtidos nos ensaios de adesão e invasão, foi evidenciado que, quando as células epiteliais foram inoculadas com nicotina e cotinina, nenhuma diferença significativa na colonização de P. gingivalis foi encontrada. Quando P. gingivalis foi exposta à maior concentração de cotinina, sua capacidade de adesão e invasão às células epiteliais aumentou de forma expressiva (p<0.05; ANOVA - Tukey). No entanto, a nicotina e as outras concentrações de cotinina testadas não alteraram a capacidade de colonização. Esses achados indicam que a nicotina e a cotinina podem afetar a expressão de proteínas de P. gingivalis. Ainda, a cotinina pode alterar positivamente a eficiência de adesão e invasão de P. gingivalis.
Abstract: Cigarette smoking is associated with the development of periodontitis and the decreased response to periodontal therapy. P. gingivalis is an important colonizer of the subgingival biofilm and is one of the major pathogens involved in the initiation and progression of periodontal disease. However, the possible effects of major cigarette's derivatives on P. gingivalis were not fully investigated. Thus, the purpose of the present study was to evaluate the effects of nicotine and cotinine on the protein expression and cellular adhesion and invasion abilities of P. gingivalis. To evaluate protein expression, P. gingivalis W83 cultures were exposed to nicotine and cotinine 6 and 600µg/mL concentrations, the proteins were extracted, separated by two-dimensional polyacrylamide gel electrophoresis (12.5% PAGE) and identified with LC-MS/MS. The gels were run in triplicates and detection of proteins was obtained by staining the gels with Coomassie blue. Proteins differentially expressed were digested with trypsin, and the peptide samples sequenced using a Q-TOF API LC-MS/MS system. The MS/MS was searched against the MSDB and NCBI databank using Mascot program. In order to assess P. gingivalis adhesion and invasion abilities, KB cells monolayers and P. gingivalis ATCC 33277 cultures were exposed to 0.1, 10 and 100 µg/mL nicotine and cotinine concentrations. The epithelial cells were incubated for 24 h while P. gingivalis was exposed to these substances until early logarithmic phase. After incubation period, P. gingivalis were submitted to assays to evaluate adhesion to and invasion of KB cells. The number of bacteria associated with these cells was assessed by counting the colony-forming unities. The results from protein expression analyses showed that addition of nicotine and cotinine promoted alterations in proteome profile of P. gingivalis. Among ± 430 protein spots reproducibly detected on each gel, 20 protein spots were downregulated, and 42 were upregulated at least in one treatment (p<0.05; ANOVA - Tukey test). The identified proteins are involved in several processes, i.e. energy production, protein synthesis, oxidative stress, virulence, transport and binding activities. Data obtained from adhesion and invasion assays evidenced that epithelial cells inoculated with nicotine and cotinine did not show any significant differences in P. gingivalis colonization. When P. gingivalis was exposed to the higher concentration of cotinine, adherence and invasion of this bacterium to the epithelial cells markedly increased (p<0.05; ANOVA - Tukey test). However, nicotine and the other concentrations of cotinine did not alter the colonization ability. These findings indicate that nicotine and cotinine may affect P. gingivalis protein expression. In addition, cotinine may alter positively P. gingivalis adhesion and invasion efficiencies.
Doutorado
Farmacologia, Anestesiologia e Terapeutica
Doutor em Odontologia
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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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Naujoks, Jan Verfasser], Bastian [Akademischer Betreuer] Opitz, Thomas F. [Akademischer Betreuer] [Meyer, and Bernd [Akademischer Betreuer] Lepenies. "Type I and II IFNs modify the proteome of bacterial vacuoles to restrict infections via IRG1 / Jan Naujoks. Gutachter: Bastian Opitz ; Thomas F. Meyer ; Bernd Lepenies." Berlin : Lebenswissenschaftliche Fakultät, 2015. http://d-nb.info/1079901205/34.
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Naujoks, Jan [Verfasser], Bastian Akademischer Betreuer] Opitz, Thomas F. [Akademischer Betreuer] [Meyer, and Bernd [Akademischer Betreuer] Lepenies. "Type I and II IFNs modify the proteome of bacterial vacuoles to restrict infections via IRG1 / Jan Naujoks. Gutachter: Bastian Opitz ; Thomas F. Meyer ; Bernd Lepenies." Berlin : Lebenswissenschaftliche Fakultät, 2015. http://d-nb.info/1079901205/34.
Full textBooks on the topic "Bacterial proteome"
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Leather, Robert Victor. Peptide synthesis mediated by a bacterial high alkaline protease. Birmingham: University of Birmingham, 1991.
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Bridge, Paul, David Smith, and Erko Stackebrandt, eds. Trends in the systematics of bacteria and fungi. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0000.
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Abstract There are fundamental differences between the current levels of genomic and proteomic knowledge for bacteria and fungi. With multiple growth forms and over 100,000 known species, the fungi probably present a more complex situation, but genomic studies are hindered by the lack of reliable reference data for many species. As activities such as environmental sampling, and genomic and proteomic profiling, become more important in extending our understanding of ecosystems, there is an increasing imperative for researchers in microbial systematics to develop the methods and concepts required to interpret the information being generated. This volume presents a collection of chapters that provide some insights into how current methods and resources are being used in microbial systematics, together with some thoughts and suggestions about how both methodologies and concepts may develop in the future.
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Kalbhenn, Eva Maria. Bacterial Adaptive Response to Osmotic Stress. Proteome Alterations. GRIN Verlag GmbH, 2017.
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Wilson, Van G. Sumoylation: Molecular Biology and Biochemistry (Horizonbioscience). Taylor & Francis, 2004.
Find full textBook chapters on the topic "Bacterial proteome"
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Raschdorf, Oliver, Dirk Schüler, and René Uebe. "Preparation of Bacterial Magnetosomes for Proteome Analysis." In Methods in Molecular Biology, 45–57. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8695-8_5.
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Cash, Phillip. "Analyzing Bacterial Pathogenesis at Level of Proteome." In Methods of Biochemical Analysis, 209–35. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2005. http://dx.doi.org/10.1002/0471973165.ch13.
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Nyström, Thomas. "Oxidation of Bacterial Proteome in Response to Starvation." In Methods of Biochemical Analysis, 89–95. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2005. http://dx.doi.org/10.1002/0471973165.ch7.
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Slonczewski, Joan L., and Darcy Blankenhorn. "Acid and Base Regulation in the Proteome of Escherichia Coli." In Novartis Foundation Symposium 221 - Bacterial Responses to pH, 75–92. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470515631.ch6.
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Leontiadou, Fotini, Christina Matragkou, Filippos Kottakis, Dimitrios L. Kalpaxis, Ioannis S. Vizirianakis, Sofia Kouidou, Asterios S. Tsiftsoglou, and Theodora Choli-Papadopoulou. "Genetic Engineering of Bacterial and Eukaryotic Ribosomal Proteins for Investigation on Elongation Arrest of Nascent Polypeptides and Cell Differentiation." In Methods in Proteome and Protein Analysis, 251–59. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-662-08722-0_16.
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Cassin, Erin K., and Boo Tseng. "The Matrix Proteome: Protein Actors in the Extracellular Bacterial Biofilm." In Springer Series on Biofilms, 91–130. Cham: Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-70476-5_3.
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Zhou, Jianwei, Lu Zhang, Huixia Chuan, Angela Sloan, Raymond Tsang, and Keding Cheng. "Mass Spectrometry to Study the Bacterial Proteome from a Single Colony." In Methods in Molecular Biology, 113–21. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9199-0_10.
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Brychta, Martin, and Ivona Pávková. "Proteome Analysis of Bacterial Protein Expression after Ingestion of Microbes by Macrophages." In BSL3 and BSL4 Agents, 223–31. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527638192.ch19.
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Norais, Nathalie, Ignazio Garaguso, Germano Ferrari, and Guido Grandi. "In Vitro Transcription and Translation Coupled to Two-Dimensional Electrophoresis for Bacterial Proteome Analysis." In In Vitro Transcription and Translation Protocols, 183–209. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-388-2_10.
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Kan, Jinjun, Thomas E. Hanson, and Feng Chen. "Synchronicity Between Population Structure and Proteome Profiles: A Metaproteomic Analysis of Chesapeake Bay Bacterial Communities." In Handbook of Molecular Microbial Ecology I, 637–44. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010518.ch68.
Full textConference papers on the topic "Bacterial proteome"
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Arias-Rojas, Tatiana, Silvia Mau-Incháustegui, J. J. Saavedra-Arias, and Stefany Solano-González. "Computational Proteomic Profiling of Putative Magnetotactic Bacterial Proteins." In 2024 IEEE 6th International Conference on BioInspired Processing (BIP), 1–6. IEEE, 2024. https://doi.org/10.1109/bip63158.2024.10885381.
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Constantinescu, Rodica Roxana, Mariana Ferdes, Madalina Ignat, Ciprian Chelaru, Ana-Maria Ciobanu, and Denis-Andrei Drusan. "Isolation and Characterization of Bacterial Protease Enzyme of Leather Waste." In The 9th International Conference on Advanced Materials and Systems. INCDTP - Leather and Footwear Research Institute (ICPI), Bucharest, Romania, 2022. http://dx.doi.org/10.24264/icams-2022.ii.6.
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The objectives of this study were to isolate and characterize bacteria which produced protease enzyme from tannery solid waste. A solid leather waste sample was used for bacterial isolation, taken from different waste warehouses (solid waste in unhairing phase). Several bacterial strains were isolated from the cultures in Petri dishes, after the growth of the colonies. These strains were characterized in terms of the production of proteolytic enzymes, by a method of screening on the media with casein, which allows the determination of proteolytic indices of microorganisms, the colony diameter, diameter of clear zone, proteolytic index, and enzymatic activities characterization on difference of pH and temperature.
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Toplaghaltsyan, Anna, Zhaneta Karapetyan, Susanna Keleshyan, G. Avetisova, L. Melkonyan, G. Tsarukyan, and V. Ghochikyan. "Enzymatic activity of nitrogen-fixing soil bacteria." In 5th International Scientific Conference on Microbial Biotechnology. Institute of Microbiology and Biotechnology, Republic of Moldova, 2022. http://dx.doi.org/10.52757/imb22.37.
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Soil is a medium for more than 100 enzymes. During soil deterioration the change of enzymes occurs much sooner than of other parameters in the soil so they are considered the best indicators of soil health. These enzymes play a vital role in supporting soil ecology and health by direct agents of the biological catabolism of soil organic and mineral components. Еnzymatic activities in the soil are mainly of microbial origin. In a number of potential bacterial enzymes that play an important role in maintaining soil health, some of the important ones are protease, lipase, cellulase, amylase and urease [1]. The aim of this work was the study of enzymatic activity in nitrogen-fixing bacteria, such as protease, lipase, cellulose, amylase and urease. The bacteria used in the experiments were Agrobacterium sp. strain M-1 (MN717167) and Agrobacterium sp. strain Y-2 (MN721294), previously isolated by us from saline soils of the villages Mrgashat and Yeghegnut of Armenia, respectively [2]. Proteolytic activity of nitrogen-fixing strains was determined using Skim Milk Agar, lipolytic activity - by Burk's Agar with 2% Tween 80, cellulolytic activity - by Cellulose Congo Red Agar. Bacterial suspension (107-108 CFU/ml) was added into punch holes in the agar and plates were incubated at 30 °C during 3-7 days. Enzymatic activity was detected by clear zones around holes. In case of amylolytic activity Starch Agar was used. A fresh colony of bacteria was streaked on the surface of the agar by double streak and was incubated for 3-5 days at 30 °C. Then the surface of the agar was flooded with Gram’s iodine solution. A clear zone surrounding the bacterial growth confirmed the hydrolysis of starch. Urease activity was investigated by using Urea broth. The cultures were inoculated separately into test tubes and incubated at 30 °C for 4 days. The appearance of a deep pink color indicated a positive result. The results of the experiments presented in Table 1 show the presence of a fairly wide range of enzymes in cultures Agrobacterium sp. strain M-1 and Agrobacterium sp. strain Y-2. Table 1. Enzymatic activity of nitrogen-fixing bacteria Nitrogen-fixing bacteria Enzymatic activity Protease Lipase Cellulase Amylase Urease Agrobacterium sp. strain M-1 - + + + + Agrobacterium sp. strain Y-2 + + + + + Therefore, it can be assumed that the use of Agrobacterium sp. strain M-1 and Agrobacterium sp. strain Y-2 with a variety of enzymatic activities can provide the soil with the enzymes necessary for the normal course of global carbon and nutrient cycles.
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Broeseker, T. A., M. D. P. Boyle, and R. Lottenberg. "PATHOGENIC BACTERIA HAVE HIGH AFFINITY RECEPTORS SPECIFIC FOR PLASMIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644391.
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Binding of the key fibrinolytic enzyme, plasmin, to certain pathogenic group A streptococci was studied. In these experiments the ability of a group A streptococcal strain, 64/14, to bind either 125I-human plasminogen or the same label following activation with urokinase was measured. It was found that this strain bound <10% of the labeled plasminogen but >70% of labeled plasmin. This property distinguishes the plasmin receptor from streptokinase. These bacteria did not express a common serine protease receptor/inhibitor since they failed to bind labeled trypsin or urokinase. Maximal binding of plasmin occurred between pH 6.0 and 8.0 and in the ionic strength range of 50-200 mM salt. The Kd of plasmin binding to bacteria was approximately 10-10 M at pH 7.4 in 150 mM salt. This was determined by a non-linear least squares analysis of equilibrium binding data. Binding was reversibly inhibited by either epsilon aminocaproic acid (I50 of 0.2 mM) or lysine (I50 of 3.0 mM) suggesting the involvement of the high affinity lysine binding site of plasmin in its binding to bacteria. Bacterial bound plasmin retains its enzymatic activity, being capable of cleaving chromogenic substrates and solubilizing a fibrin- clot. The bacterial bound enzyme activity was inhibited by the low molecular weight inhibitors aprotinin and phe-pro-arg chloromethyl ketone but not by alpha-2 plasmin inhibitor. The ability of bacteria to acquire membrane associated proteolytic activity which cannot be physiologically inhibited may contribute to their tissue invasive properties.
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Egbring, R., R. Seitz, M. Wolf, L. Lerch, and T. Menges. "PROTEINASE-INHIBITOR COMPLEXES (PIC) IN SEPTIC AND NON-SEPTIC SHOCK. COAGULATION; LEUKOCYTE AND BACTERIAL PROTEASE INHIBITION BY MEANS OF PLASMA-INHIBITOR REPLACEMENT." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644244.
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In septic or cardiac shock antithrombin III-thrombin (AT III-Thr) and a1antitrypsin-elastase(a1AT-ELP) as well as a2antiplas-min-plasmin (a2AP-Pl) are found to be elevated to different extents. In cardiac shock AT III-Thr is predominantly increased, while in septic disorders a2AT-ELP as indicator of leukocyte stimulation is additionally found to be elevated. Stimuli for leukocyte activation are bacterial endotoxins, immune complexes, factor Xlla and others. The possible action of bacterial proteases during septic infections is only known in animal models. To stop hemorrhagic complications in disseminated intravascular coagulation (DIC) following septic (n=24) or non-septic (n=15) shock, we treated the patients with AT III concentrate and FFP in relatively high amounts containing a2macroglobulin (a2M), a1antitrypsin (a1AT) and others which are not available as concentrates. Subsequent to the procedure PIC's decreased, coagulation factors and inhibitors as well as thrombocyte counts increased. In in vitro models bacterial proteases have been shown to destroy a1AT, activate prothrombin and others. Only a2M may inhibit proteolytic activity of Staph aureus, N. meningitidis, P. aeroginosa and K1. pneumoniae and E. coli as our in vitro studies, using fibrin plates containing a2M, demonstrated. Not only bleeding or microthrombotic complications might be influenced by plasma derivative substitution, but also proteases released from bacteria
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Taguchi, Y., and A. Okamoto. "Principal component analysis for bacterial proteomic analysis." In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2011. http://dx.doi.org/10.1109/bibmw.2011.6112520.
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Domnin, P. A., A. S. Kononikhin, V. A. Parfenov, S. A. Ermolaeva, and Yu D. Khesuani. "A COMPARATIVE STUDY OF THE IMPACT OF MICROGRAVITY AND MAGNETIC LEVITATION ON ESCHERICHIA COLI PROTEOME." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-315.
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Here we investigated whether it is possible to use magnetic levitation as a model of microgravity. The proteome of E. coli grown under spaceflight or combined spaceflight and magnetic force conditions were compared with ground cultivated bacteria grown under standard (control) or magnetic levitation conditions.
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Kusumaningtyas, Eni, and Dwi Endrawati. "Determination of protease-producing bacteria for bioactive peptide production." In THE FIRST INTERNATIONAL CONFERENCE ON NEUROSCIENCE AND LEARNING TECHNOLOGY (ICONSATIN 2021). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0118419.
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Veríssimo, Graciete Soares Libório, Ivanize Barbosa De Souza, and Paula Carvalhal Lage Von Buettner Ristow. "BIOFILME: MECANISMO DE VIRULÊNCIA BACTERIANA." In II Congresso Brasileiro de Saúde On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/1503.
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Introdução: Biofilmes são comunidades microbianas complexas associada à superfícies bióticas ou abióticas, circundada por uma matriz extracelular polimérica autoproduzida pelos microrganismos ali presente. A formação de biofilme protege os microrganismos de condições ambientais desafiadoras, tornando a antibioticoterapia e mecanismos de defesa imunológica do hospedeiro ineficazes contra bactérias associadas ao biofilme. Objetivo: Este estudo buscou analisar o papel do biofilme como mecanismo que contribui para virulência bacteriana. Material e métodos: Consistiu-se em uma revisão de literatura, a partir de uma abordagem qualitativa, na base de dados Pubmed, utilizando como termo de busca booleano ((biofilm[Title/Abstract]) AND (virulence mechanism[Title/Abstract])) AND (bacteria*[Title/Abstract]). Foram encontrados 19 artigos, compreendendo o período de 2003 a 2021. Resultados: Por muito tempo acreditava-se que as bactérias viviam isoladas no ambiente, hoje é notório que o fenótipo de biofilme ocorre de forma ubíqua e é a principal forma de vida bacteriana. A formação de biofilme por patógenos oportunistas em implantes biomédicos, é considerado sério problema de saúde pública. Implantes biomédicos colonizados por essas bactérias, são mais resistentes a antibioticoterapia, tempo de internação e gerar maior custo ao sistema. A formação de biofilmes em hospedeiros pode ocorrer também com microrganismos aderindo diretamente a órgãos. Pacientes com fibrose cística, infectados de forma crônica por Pseudomonas aeruginosa com capacidade de formação de biofilme nos pulmões do hospedeiro, são a principal causa de mortalidade em pacientes com esta doença. O desenvolvimento de biofilmes também é um fator relacionado à infecções alimentares. Listeria monocytogenes pode causar gastroenterite, listeriose, septicemia, encefalite, endocardite, meningite e abortos, principalmente quando associado a formação de biofilme. A formação de biofilmes também pode contribuir para a transmissão de genes de resistência a antibióticos em sistemas de distribuição de água potável. Estudos detectaram um aumento da presença de bactérias resistentes à antibióticos em tubulações industriais com presença de biofilmes. Conclusão: Biofilmes compreendem o principal estilo de vida bacteriano. A melhor compreensão do estabelecimento desse fenótipo como um mecanismo de virulência e a sua relevância biológica são essenciais para criar soluções para problemas causados por biofilmes, bem como para aplicar a biossíntese de biofilmes sem situações benéficas.
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Jordan, Robert E., Mark Nedelman, and Susan H. Tam. "734 The bacterial IdeS protease as a strategy for tumor regression." In SITC 39th Annual Meeting (SITC 2024) Abstracts, A837. BMJ Publishing Group Ltd, 2024. http://dx.doi.org/10.1136/jitc-2024-sitc2024.0734.
Full textReports on the topic "Bacterial proteome"
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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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Manulis, Shulamit, Christine D. Smart, Isaac Barash, Guido Sessa, and Harvey C. Hoch. Molecular Interactions of Clavibacter michiganensis subsp. michiganensis with Tomato. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7697113.bard.
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Clavibacter michiganensis subsp. michiganensis (Cmm), the causal agent of bacterial wilt and canker of tomato, is the most destructive bacterial disease of tomato causing substantial economic losses in Israel, the U.S.A. and worldwide. The molecular strategies that allow Cmm, a Gram-positive bacterium, to develop a successful infection in tomato plants are largely unknown. The goal of the project was to elucidate the molecular interactions between Cmmand tomato. The first objective was to analyze gene expression profiles of susceptible tomato plants infected with pathogenic and endophytic Cmmstrains. Microarray analysis identified 122 genes that were differentially expressed during early stages of infection. Cmm activated typical basal defense responses in the host including induction of defense-related genes, production of scavenging of free oxygen radicals, enhanced protein turnover and hormone synthesis. Proteomic investigation of the Cmm-tomato interaction was performed with Multi-Dimensional Protein Identification Technology (MudPIT) and mass spectroscopy. A wide range of enzymes secreted by Cmm382, including cell-wall degrading enzymes and a large group of serine proteases from different families were identified in the xylem sap of infected tomato. Based on proteomic results, the expression pattern of selected bacterial virulence genes and plant defense genes were examined by qRT-PCR. Expression of the plasmid-borne cellulase (celA), serine protease (pat-1) and serine proteases residing on the chp/tomA pathogenicity island (chpCandppaA), were significantly induced within 96 hr after inoculation. Transcription of chromosomal genes involved in cell wall degradation (i.e., pelA1, celB, xysA and xysB) was also induced in early infection stages. The second objective was to identify by VIGS technology host genes affecting Cmm multiplication and appearance of disease symptoms in plant. VIGS screening showed that out of 160 tomato genes, which could be involved in defense-related signaling, suppression of 14 genes led to increase host susceptibility. Noteworthy are the genes Snakin-2 (inhibitor of Cmm growth) and extensin-like protein (ELP) involved in cell wall fortification. To further test the significance of Snakin -2 and ELP in resistance towards Cmm, transgenic tomato plants over-expressing the two genes were generated. These plants showed partial resistance to Cmm resulting in a significant delay of the wilt symptoms and reduction in size of canker lesion compared to control. Furthermore, colonization of the transgenic plants was significantly lower. The third objective was to assess the involvement of ethylene (ET), jasmonate (JA) and salicylic acid (SA) in Cmm infection. Microarray and proteomic studies showed the induction of enzymes involved in ET and JA biosynthesis. Cmm promoted ET production 8 days after inoculation and SIACO, a key enzyme of ET biosynthesis, was upregulated. Inoculation of the tomato mutants Never ripe (Nr) impaired in ET perception and transgenic plants with reduced ET synthesis significantly delayed wilt symptoms as compared to the wild-type plants. The retarded wilting in Nr plants was shown to be a specific effect of ET insensitivity and was not due to altered expression of defense related genes, reduced bacterial population or decrease in ethylene biosynthesis . In contrast, infection of various tomato mutants impaired in JA biosynthesis (e.g., def1, acx1) and JA insensitive mutant (jai1) yielded unequivocal results. The fourth objective was to determine the role of cell wall degrading enzymes produced by Cmm in xylem colonization and symptoms development. A significance increase (2 to 7 fold) in expression of cellulases (CelA, CelB), pectate lyases (PelA1, PelA2), polygalacturonase and xylanases (XylA, XylB) was detected by qRT-PCR and by proteomic analysis of the xylem sap. However, with the exception of CelA, whose inactivation led to reduced wilt symptoms, inactivation of any of the other cell wall degrading enzymes did not lead to reduced virulence. Results achieved emphasized the complexity involved in Cmm-tomato interactions. Nevertheless they provide the basis for additional research which will unravel the mechanism of Cmm pathogenicity and formulating disease control measures.
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Altindis, E., R. Cozzi, B. Di Palo, F. Necchi, R. P. Mishra, M. R. Fontana, M. Soriani, et al. Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery. Cold Spring Harbor Laboratory, January 2014. http://dx.doi.org/10.1101/002089.
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Splitter, Gary A., Menachem Banai, and Jerome S. Harms. Brucella second messenger coordinates stages of infection. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699864.bard.
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Aim 1: To determine levels of this second messenger in: a) B. melitensiscyclic-dimericguanosinemonophosphate-regulating mutants (BMEI1448, BMEI1453, and BMEI1520), and b) B. melitensis16M (wild type) and mutant infections of macrophages and immune competent mice. (US lab primary) Aim 2: To determine proteomic differences between Brucelladeletion mutants BMEI1453 (high cyclic-dimericguanosinemonophosphate, chronic persistent state) and BMEI1520 (low cyclicdimericguanosinemonophosphate, acute virulent state) compared to wild type B. melitensisto identify the role of this second messenger in establishing the two polar states of brucellosis. (US lab primary with synergistic assistance from the Israel lab Aim 3: Determine the level of Brucellacyclic-dimericguanosinemonophosphate and transcriptional expression from naturally infected placenta. (Israel lab primary with synergistic assistance from the US lab). B. Background Brucellaspecies are Gram-negative, facultative intracellular bacterial pathogens that cause brucellosis, the most prevalent zoonosis worldwide. Brucellosis is characterized by increased abortion, weak offspring, and decreased milk production in animals. Humans are infected with Brucellaby consuming contaminated milk products or via inhalation of aerosolized bacteria from occupational hazards. Chronic human infections can result in complications such as liver damage, orchitis, endocarditis, and arthritis. Brucellaspp. have the ability to infect both professional and non-professional phagocytes. Because of this, Brucellaencounter varied environments both throughout the body and within a cell and must adapt accordingly. To date, few virulence factors have been identified in B. melitensisand even less is known about how these virulence factors are regulated. Subsequently, little is known about how Brucellaadapt to its rapidly changing environments, and how it alternates between acute and chronic virulence. Our studies suggest that decreased concentrations of cyclic dimericguanosinemonophosphate (c-di-GMP) lead to an acute virulent state and increased concentrations of c-di-GMP lead to persistent, chronic state of B. melitensisin a mouse model of infection. We hypothesize that B. melitensisuses c-di-GMP to transition from the chronic state of an infected host to the acute, virulent stage of infection in the placenta where the bacteria prepare to infect a new host. Studies on environmental pathogens such as Vibrio choleraeand Pseudomonas aeruginosasupport a mechanism where changes in c-di-GMP levels cause the bacterium to alternate between virulent and chronic states. Little work exists on understanding the role of c-di-GMP in dangerous intracellular pathogens, like Brucellathat is a frequent pathogen in Israeli domestic animals and U.S. elk and bison. Brucellamust carefully regulate virulence factors during infection of a host to ensure proper expression at appropriate times in response to host cues. Recently, the novel secondary signaling molecule c-di-GMP has been identified as a major component of bacterial regulation and we have identified c-di-GMP as an important signaling factor in B. melitensishost adaptation. C. Major conclusions, solutions, achievements 1. The B. melitensis1453 deletion mutant has increased c-di-GMP, while the 1520 deletion mutant has decreased c-di-GMP. 2. Both mutants grow similarly in in vitro cultures; however, the 1453 mutant has a microcolony phenotype both in vitro and in vivo 3. The 1453 mutant has increased crystal violet staining suggesting biofilm formation. 4. Scanning electron microscopy revealed an abnormal coccus appearance with in increased cell area. 5. Proteomic analysis revealed the 1453 mutant possessed increased production of proteins involved in cell wall processes, cell division, and the Type IV secretion system, and a decrease in proteins involved in amino acid transport/metabolism, carbohydrate metabolism, fatty acid production, and iron acquisition suggesting less preparedness for intracellular survival. 6. RNAseq analysis of bone marrow derived macrophages infected with the mutants revealed the host immune response is greatly reduced with the 1453 mutant infection. These findings support that microlocalization of proteins involved in c-di-GMP homeostasis serve a second messenger to B. melitensisregulating functions of the bacteria during infection of the host.
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Adam, Zach, and Eran Pichersky. Degradation of Abnormal Proteins in Chloroplasts of Higher Plants. United States Department of Agriculture, August 1994. http://dx.doi.org/10.32747/1994.7568768.bard.
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In this study we attempted to get a better understanding of processes involved in the degradation of abnormal proteins i chloroplasts. To achieve this goal, we used a number of complementary approaches. We first characterized the expression of the two subunits of Clp protease. We demonstrated that both of them were expressed in chloroplasts in a constitutive fashion, but the expression of the regulatory subunit ClpC was enhanced by light. We generated a mutant the lumenal protein OEE33 which was targeted to the stroma in in vitro experiments. In the wrong compartment it was found unstable, and characterization of its degradation revealed that it was degraded by a soluble, ATP-dependent serine protease, which are also the characteristics of Clp protease. In search of other homologues of bacterial proteases, we found that chloroplasts contain a homologue of the FtsH protease. It is an ATP-dependent metallo-protease, bound to the stromal side of the thylakoid membrane, whose expression is dependent on light. The gene encodig this protease was cloned and characterized. In attempt to generate Arabidopsis mutant plants impaired in their capability to degrade abnormal chloroplast proteins, we fused the gene for mistargeted OEE33 to the streptomycin-detoxifying gene. This chimeric gene was introduced into Arabodipsis plants, to generate transformed plants. This transformants plants were sensitive to streptomycin due to the rapid turn-over of the chimeric protein. Seeds from these plants were then chemically mutagenised, and seedlings were selected for their capability to grow on streptomycin. The ability of these mutant transformants to grow on streptomycin is presumably due to stabilization of the chimeric protein. These plants will allow us in the future to identify the effected genes, which are likely to be involved in the protein degradation process.
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Sessa, Guido, and Gregory Martin. A functional genomics approach to dissect resistance of tomato to bacterial spot disease. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7695876.bard.
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The research problem. Bacterial spot disease in tomato is of great economic importance worldwide and it is particularly severe in warm and moist areas affecting yield and quality of tomato fruits. Causal agent of spot disease is the Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv), which can be a contaminant on tomato seeds, or survive in plant debris and in association with certain weeds. Despite the economic significance of spot disease, plant protection against Xcvby cultural practices and chemical control have so far proven unsuccessful. In addition, breeding for resistance to bacterial spot in tomato has been undermined by the genetic complexity of the available sources of resistance and by the multiple races of the pathogen. Genetic resistance to specific Xcvraces have been identified in tomato lines that develop a hypersensitive response and additional defense responses upon bacterial challenge. Central goals of this research were: 1. To identify plant genes involved in signaling and defense responses that result in the onset of resistance. 2. To characterize molecular properties and mode of action of bacterial proteins, which function as avirulence or virulence factors during the interaction between Xcvand resistant or susceptible tomato plants, respectively. Our main achievements during this research program are in three major areas: 1. Identification of differentially expressed genes during the resistance response of tomato to Xcvrace T3. A combination of suppression subtractive hybridization and microarray analysis identified a large set of tomato genes that are induced or repressed during the response of resistant plants to avirulent XcvT3 bacteria. These genes were grouped in clusters based on coordinate expression kinetics, and classified into over 20 functional classes. Among them we identified genes that are directly modulated by expression of the type III effector protein AvrXv3 and genes that are induced also during the tomato resistance response to Pseudomonas syringae pv. tomato. 2. Characterization of molecular and biochemical properties of the tomato LeMPK3MAP kinase. A detailed molecular and biochemical analysis was performed for LeMPK3 MAP kinase, which was among the genes induced by XcvT3 in resistant tomato plants. LeMPK3 was induced at the mRNA level by different pathogens, elicitors, and wounding, but not by defense-related plant hormones. Moreover, an induction of LeMPK3 kinase activity was observed in resistant tomato plants upon Xcvinfection. LeMPK3 was biochemically defined as a dual-specificity MAP kinase, and extensively characterized in vitro in terms of kinase activity, sites and mechanism of autophosphorylation, divalent cation preference, Kₘand Vₘₐₓ values for ATP. 3. Characteriztion of molecular properties of the Xcveffector protein AvrRxv. The avirulence gene avrRxvis involved in the genetic interaction that determines tomato resistance to Xcvrace T1. We found that AvrRxv functions inside the plant cell, localizes to the cytoplasm, and is sufficient to confer avirulence to virulent Xcvstrains. In addition, we showed that the AvrRxv cysteine protease catalytic core is essential for host recognition. Finally, insights into cellular processes activated by AvrRxv expression in resistant plants were obtained by microarray analysis of 8,600 tomato genes. Scientific and agricultural significance: The findings of these activities depict a comprehensive and detailed picture of cellular processes taking place during the onset of tomato resistance to Xcv. In this research, a large pool of genes, which may be involved in the control and execution of plant defense responses, was identified and the stage is set for the dissection of signaling pathways specifically triggered by Xcv.
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Chen, Junping, Zach Adam, and Arie Admon. The Role of FtsH11 Protease in Chloroplast Biogenesis and Maintenance at Elevated Temperatures in Model and Crop Plants. United States Department of Agriculture, May 2013. http://dx.doi.org/10.32747/2013.7699845.bard.
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specific objectives of this proposal were to: 1) determine the location, topology, and oligomerization of FtsH11 protease; 2) identify the substrate/s of FtsH11 and the downstream components involved in maintaining thermostability of chloroplasts; 3) identify new elements involved in FtsH11 protease regulatory network related to HT adaptation processes in chloroplast; 4) Study the role of FtsH11 homologs from crop species in HT tolerance. Background to the topic: HT-tolerant varieties that maintain high photosynthetic efficiency at HT, and cope better with daily and seasonal temperature fluctuations are in great need to alleviate the effect of global warming on food production. Photosynthesis is a very complex process requiring accurate coordination of many complex systems and constant adjustments to the changing environments. Proteolytic activities mediated by various proteases in chloroplast are essential part of this process and critical for maintaining normal chloroplast functions under HT. However, little is known about mechanisms that contribute to adaptation of photosynthetic processes to HT. Our study has shown that a chloroplast-targeted Arabidopsis FtsH11 protease plays an essential and specific role in maintaining thermostability of thylakoids and normal photosynthesis at moderate HT. We hypothesized that FtsH11 homologs recently identified in other plant species might have roles similarly to that of AtFtsH1. Thus, dissecting the underlying mechanisms of FtsH11 in the adaptation mechanisms in chloroplasts to HT stress and other elements involved will aid our effort to produce more agricultural products in less favorable environments. Major conclusions, solutions, achievements - Identified the chloroplast inner envelope membrane localization of FtsH11. - Revealed a specific association of FtsH11 with the a and b subunits of CPN60. - Identified the involvement of ARC6, a protein coordinates chloroplast division machineries in plants, in FtsH11 mediated HT adaptation process in chloroplast. -Reveal possible association of a polyribonucleotide nucleotidyltransferase (cpPNPase), coded by At3G03710, with FtsH11 mediated HT adaptation process in chloroplast. - Mapped 4 additional loci in FtsH11 mediated HT adaptation network in chloroplast. - Demonstrated importance of the proteolytic activity of FtsH11 for thermotolerance, in addition to the ATPase activity. - Demonstrated a conserved role of plant FtsH11 proteases in chloroplast biogenesis and in maintaining structural and functional thermostability of chloroplast at elevated temperatures. Implications, both scientific and agricultural:Three different components interacting with FtsH11 were identified during the course of this study. At present, it is not known whether these proteins are directly involved in FtsH11mediated thermotolerance network in chloroplast and/or how these elements are interrelated. Studies aiming to connect the dot among biological functions of these networks are underway in both labs. Nevertheless, in bacteria where it was first studied, FtsH functions in heat shock response by regulating transcription level of σ32, a heat chock factor regulates HSPsexpression. FtsH also involves in control of biosynthesis of membrane components and quality control of membrane proteins etc. In plants, both Arc 6 and CPN60 identified in this study are essential in chloroplast division and developments as mutation of either one impairs chloroplast division in Arabidopsis. The facts that we have found the specific association of both α and β CPN60 with FtsH11 protein biochemically, the suppression/ enhancement of ftsh11 thermosensitive phenotype by arc6 /pnp allele genetically, implicate inter-connection of these networks via FtsH11 mediated network(s) in regulating the dynamic adaptation processes of chloroplast to temperature increases at transcriptional, translational and post-translational levels. The conserved role of FtsH11 proteases in maintaining thermostability of chloroplast at HT demonstrated here provides a foundation for improving crop photosynthetic performance at high temperatures.
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Gafni, Yedidya, Moshe Lapidot, and Vitaly Citovsky. Dual role of the TYLCV protein V2 in suppressing the host plant defense. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7597935.bard.
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TYLCV-Is is a major tomato pathogen, causing extensive crop losses in Israel and the U.S. We have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing. Intriguingly, the counter-defense function of V2 may not be limited to silencing suppression. Our recent data suggest that V2 interacts with the tomato CYP1 protease. CYP1 belongs to the family of papain-like cysteine proteases which participate in programmed cell death (PCD) involved in plant defense against pathogens. Based on these data we proposed a model for dual action of V2 in suppressing the host antiviral defense: V2 targets SGS3 for degradation and V2 inhibits CYP1 activity. To study this we proposed to tackle three specific objectives. I. Characterize the role of V2 in SGS3 proteasomal degradation ubiquitination, II. Study the effects of V2 on CYP1 maturation, enzymatic activity, and accumulation and, III. Analyze the effects of the CYP1-V2 interaction on TYLCV-Is infection. Here we describe results from our study that support our hypothesis: the involvement of the host's innate immune system—in this case, PCD—in plant defense against TYLCV-Is. Also, we use TYLCV-Is to discover the molecular pathway(s) by which this plant virus counters this defense. Towards the end of our study we discovered an interesting involvement of the C2 protein encoded by TYLCV-Is in inducing Hypersensitive Response in N. benthamianaplants which is not the case when the whole viral genome is introduced. This might lead to a better understanding of the multiple processes involved in the way TYLCV is overcoming the defense mechanisms of the host plant cell. In a parallel research supporting the main goal described, we also investigated Agrobacteriumtumefaciens-encoded F-box protein VirF. It has been proposed that VirF targets a host protein for the UPS-mediated degradation, very much the way TYLCV V2 does. In our study, we identified one such interactor, an Arabidopsistrihelix-domain transcription factor VFP3, and further show that its very close homolog VFP5 also interacted with VirF. Interestingly, interactions of VirF with either VFP3 or VFP5 did not activate the host UPS, suggesting that VirF might play other UPS-independent roles in bacterial infection. Another target for VirF is VFP4, a transcription factor that both VirF and its plant functional homolog VBF target to degradation by UPS. Using RNA-seqtranscriptome analysis we showed that VFP4 regulates numerous plant genes involved in disease response, including responses to viral and bacterial infections. Detailed analyses of some of these genes indicated their involvement in plant protection against Agrobacterium infection. Thus, Agrobacterium may facilitate its infection by utilizing the host cell UPS to destabilize transcriptional regulators of the host disease response machinery that limits the infection.