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To determine the impact of stress response on enumeration, cell association status and the viability of Escherichia coli DH5, Staphylococcus aureus ATCC 13565 and Listeria monocytogenes CDC 7762 were evaluated using fluorescence microscopy and were compared with the outcomes of traditional plate count and optical density measurements. Fluorescence microscopy revealed that organic acid stress (acetic and lactic, pH 2.7-3.3) induced cell clumping with little loss of viability in Escherichia coli DH5. Significantly lower values for cell enumeration were found for plate counts and OD600 measurement, likely due to cell clumping in response to organic acid stress. Gram-negative bacteria Escherichia coli DH5 showed higher levels of clumping and subsequent resistance against organic acid stress. Increased cell surface hydrophobicity was found in cells that exhibited more evident clumping. However, inorganic acid stress (hydrochloric and sulfuric, pH 3.0-3.3) induced only very low level of clumping in stationary-phase Escherichia coli DH5 and almost no clumping in other cultures. Osmotic stress, heat and cold shock were not found to induce cell clumping. It has been determined that traditional enumeration methods have significantly underestimated the number of viable bacterial cells when organic acid stress is involved. Plate counts and OD600 measurement therefore need to be reassessed as tools for accurate evaluation of pathogens in food industry. / Food Science and Technology

Thesis advisor: Kenneth Williams / Due to overuse and misuse of antibiotics, the global threat of antibiotic resistance is a growing crisis. Three critical issues surrounding antibiotic resistance are the lack of rapid testing, treatment failure, and evolution of resistance. However, with new technology facilitating data collection and powerful statistical learning advances, our understanding of the bacterial stress response to antibiotics is rapidly expanding. With a recent influx of omics data, it has become possible to develop powerful computational methods that make the best use of growing systems-level datasets. In this work, I present several such approaches that address the three challenges around resistance. While this body of work was motivated by the antibiotic resistance crisis, the approaches presented here favor generalization, that is, applicability beyond just one context. First, I present ShinyOmics, a web-based application that allow visualization, sharing, exploration and comparison of systems-level data. An overview of transcriptomics data in the bacterial pathogen Streptococcus pneumoniae led to the hypothesis that stress-susceptible strains have more chaotic gene expression patterns than stress-resistant ones. This hypothesis was supported by data from multiple strains, species, antibiotics and non-antibiotic stress factors, leading to the development of a transcriptomic entropy based, general predictor for bacterial fitness. I show the potential utility of this predictor in predicting antibiotic susceptibility phenotype, and drug minimum inhibitory concentrations, which can be applied to bacterial isolates from patients in the near future. Predictors for antibiotic susceptibility are of great value when there is large phenotypic variability across isolates from the same species. Phenotypic variability is accompanied by genomic diversity harbored within a species. I address the genomic diversity by developing BFClust, a software package that for the first time enables pan-genome analysis with confidence scores. Using pan-genome level information, I then develop predictors of essential genes unique to certain strains and predictors for genes that acquire adaptive mutations under prolonged stress exposure. Genes that are essential offer attractive drug targets, and those that are essential only in certain strains would make great targets for very narrow-spectrum antibiotics, potentially leading the way to personalized therapies in infectious disease. Finally, the prediction of adaptive outcome can lead to predictions of future cross-resistance or collateral sensitivities. Overall, this body of work exemplifies how computational methods can complement the increasingly rapid data generation in the lab, and pave the way to the development of more effective antibiotic stewardship practices. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Linhagens mutantes foram obtidas para os fatores sigma <font face=\"symbol\">sE (RpoE) e <font face=\"symbol\">sN (RpoN) da bactéria Xylella fastidiosa. O mutante rpoE mostrou-se sensível a etanol e a choque térmico. Análises de microarranjo de DNA, de RT-PCR quantitativo e mapeamento de sítios de início de transcrição permitiram definir o regulon <font face=\"symbol\">sE em resposta ao choque térmico. Verificou-se co-transcrição entre os genes que codificam para <font face=\"symbol\">sE, seu anti-sigma e uma protease, e <font face=\"symbol\">sE não se mostrou auto-regulado, mas regulou o gene do anti-sigma. Análises similares às acima indicaram que o gene pilA, codificando a pilina da fímbria tipo IV, é positivamente regulado por <font face=\"symbol\">sN, enquanto o operon codificando proteínas da fímbria tipo I é regulado negativamente, explicando a maior formação de biofilme e auto-agregação no mutante rpoN. O perfil temporal de expressão da linhagem selvagem J1a12 em carência de nitrogênio foi determinado, além de genes induzidos por carência de nitrogênio via <font face=\"symbol\">sN. Assim, <font face=\"symbol\">sN regula genes de fímbrias e de resposta à carência de nitrogênio em Xylella fastidiosa. / Mutant strains were obtained for the sigma factors <font face=\"symbol\">sE (RpoE) and <font face=\"symbol\">sN (RpoN) in Xylella fastidiosa. The rpoE mutant showed to be sensitive to ethanol and heat shock. Microarray and quantitative RT-PCR analyses and determination of transcription start sites permitted to define the <font face=\"symbol\">sE regulon under heat shock. Co-transcription of the genes encoding <font face=\"symbol\">sE , its anti-sigma factor and a protease was observed, and <font face=\"symbol\">sE did not present auto-regulation, but it regulated the gene encoding the anti-sigma. Similar analyses indicated that the pilA gene, encoding the pilin of the type IV fimbriae, is positively regulated by <font face=\"symbol\">sN, while the operon encoding proteins of the type I fimbriae is negatively regulated, what explains the increased biofilm formation and auto-aggregation in the rpoN strain. Temporal expression profile of wild type strain J1a12 under nitrogen starvation was determined, as well as genes induced by nitrogen starvation via <font face=\"symbol\">sN. Thus, <font face=\"symbol\">sN regulates genes encoding fimbriae and genes for nitrogen starvation response in Xylella fastidiosa.

As mutações pontuais nos dois domínios de CspC proporcionam fenótipos mais severos que a falta de cspC. Nenhuma CSP de C. crescentus é capaz de complementar o fenótipo de sensibilidade ao frio de E. coli BX04. Entretanto, os domínios de choque frio de CspC de C. crescentus individualmente são capazes de complementar este fenótipo. Uma análise transcricional global mostrou que a ausência de cspC afeta a transcrição de 11 genes na fase exponencial e 60 genes na fase estacionária. A meia vida dos genes sciP, aceA e CC0682 se mostrou menor no mutante cspC, sugerindo que é possível que CspC desempenhe uma regulação pós-transcricional. / Point mutations in the CspC CSDs caused a more severe phenotype than that of the null strain. None of the C. crescentus CSPs complemented the cold sensitivity of E. coli BX04 mutant. However, the individual CSDs of C. crescentus CspC complemented this phenotype. A microarray global transcriptional profiling showed the absence of cspC affected the transcription of 11 genes at exponential phase and 60 genes at stationary phase. mRNA decay experiments showed that the sciP, aceA e CC0682 mRNAs were less stable in the cspC mutant, indicating that its effect could be at least partially due to posttranscriptional regulation.

O choque frio em bactérias causa a indução de proteínas de choque frio de baixo peso molecular (CSPs), que desestabilizam estruturas secundárias do mRNA, permitindo sua tradução. Caulobacter crescentus possui quatro genes codificando CSPs: cspA e cspB são induzidos sob choque frio, e cspC e cspD, na fase estacionária. Neste trabalho, foi determinada uma nova seqüência para o gene cspC, revelando que a proteína CspC possui dois domínios CSD, como CspD. O mutante nulo para cspC apresentou sensibilidade em baixa temperatura e menor viabilidade em fase estacionária, com alterações na morfologia. A região regulatória foi mapeada por fusões de transcrição, e uma região ativadora da expressão foi identificada, mostrando uma regulação transcricional. Algumas condições nutricionais que disparam a indução do gene foram determinadas, indicando que sua expressão é influenciada pela ausência de glicose no meio, mas não pela ausência de nitrogênio. Este perfil de indução não depende da região ativadora, que, por sua vez, é necessária para os máximos níveis de expressão. / The cold shock response in bacteria involves the expression of cold shock proteins (CSPs), which destabilize secondary structures on mRNAs, allowing their translation. Caulobacter crescentus possesses four genes encoding CSPs: cspA and cspB are induced upon cold shock, while cspC and cspD are induced at stationary phase. In this work, a new sequence for the coding region of the cspC gene was determined, revealing that CspC contains two cold shock domains, like CspD. A null cspC mutant was sensitive to low temperature, presented reduced viability at stationary phase, and altered morphology. The regulatory region of cspC was mapped by transcriptional fusions, identifying a region responsible for activation of cspC expression, suggesting a transcriptional regulation. Some nutritional conditions triggering cspC induction were determined, indicating that its expression is influenced by glucose starvation, but not by nitrogen starvation. This expression profile was not dependent on the activation region, which, in turn, was required for maximum levels of expression.

O choque frio em bactérias causa a indução de proteínas de choque frio de baixo peso molecular (CSPs), que desestabilizam estruturas secundárias do mRNA, permitindo sua tradução. Caulobacter crescentus possui quatro genes codificando CSPs: cspA e cspB são induzidos sob choque frio, e cspC e cspD, na fase estacionária. Neste trabalho, foi determinada uma nova seqüência para o gene cspC, revelando que a proteína CspC possui dois domínios CSD, como CspD. O mutante nulo para cspC apresentou sensibilidade em baixa temperatura e menor viabilidade em fase estacionária, com alterações na morfologia. A região regulatória foi mapeada por fusões de transcrição, e uma região ativadora da expressão foi identificada, mostrando uma regulação transcricional. Algumas condições nutricionais que disparam a indução do gene foram determinadas, indicando que sua expressão é influenciada pela ausência de glicose no meio, mas não pela ausência de nitrogênio. Este perfil de indução não depende da região ativadora, que, por sua vez, é necessária para os máximos níveis de expressão. / The cold shock response in bacteria involves the expression of cold shock proteins (CSPs), which destabilize secondary structures on mRNAs, allowing their translation. Caulobacter crescentus possesses four genes encoding CSPs: cspA and cspB are induced upon cold shock, while cspC and cspD are induced at stationary phase. In this work, a new sequence for the coding region of the cspC gene was determined, revealing that CspC contains two cold shock domains, like CspD. A null cspC mutant was sensitive to low temperature, presented reduced viability at stationary phase, and altered morphology. The regulatory region of cspC was mapped by transcriptional fusions, identifying a region responsible for activation of cspC expression, suggesting a transcriptional regulation. Some nutritional conditions triggering cspC induction were determined, indicating that its expression is influenced by glucose starvation, but not by nitrogen starvation. This expression profile was not dependent on the activation region, which, in turn, was required for maximum levels of expression.

Linhagens mutantes foram obtidas para os fatores sigma <font face=\"symbol\">sE (RpoE) e <font face=\"symbol\">sN (RpoN) da bactéria Xylella fastidiosa. O mutante rpoE mostrou-se sensível a etanol e a choque térmico. Análises de microarranjo de DNA, de RT-PCR quantitativo e mapeamento de sítios de início de transcrição permitiram definir o regulon <font face=\"symbol\">sE em resposta ao choque térmico. Verificou-se co-transcrição entre os genes que codificam para <font face=\"symbol\">sE, seu anti-sigma e uma protease, e <font face=\"symbol\">sE não se mostrou auto-regulado, mas regulou o gene do anti-sigma. Análises similares às acima indicaram que o gene pilA, codificando a pilina da fímbria tipo IV, é positivamente regulado por <font face=\"symbol\">sN, enquanto o operon codificando proteínas da fímbria tipo I é regulado negativamente, explicando a maior formação de biofilme e auto-agregação no mutante rpoN. O perfil temporal de expressão da linhagem selvagem J1a12 em carência de nitrogênio foi determinado, além de genes induzidos por carência de nitrogênio via <font face=\"symbol\">sN. Assim, <font face=\"symbol\">sN regula genes de fímbrias e de resposta à carência de nitrogênio em Xylella fastidiosa. / Mutant strains were obtained for the sigma factors <font face=\"symbol\">sE (RpoE) and <font face=\"symbol\">sN (RpoN) in Xylella fastidiosa. The rpoE mutant showed to be sensitive to ethanol and heat shock. Microarray and quantitative RT-PCR analyses and determination of transcription start sites permitted to define the <font face=\"symbol\">sE regulon under heat shock. Co-transcription of the genes encoding <font face=\"symbol\">sE , its anti-sigma factor and a protease was observed, and <font face=\"symbol\">sE did not present auto-regulation, but it regulated the gene encoding the anti-sigma. Similar analyses indicated that the pilA gene, encoding the pilin of the type IV fimbriae, is positively regulated by <font face=\"symbol\">sN, while the operon encoding proteins of the type I fimbriae is negatively regulated, what explains the increased biofilm formation and auto-aggregation in the rpoN strain. Temporal expression profile of wild type strain J1a12 under nitrogen starvation was determined, as well as genes induced by nitrogen starvation via <font face=\"symbol\">sN. Thus, <font face=\"symbol\">sN regulates genes encoding fimbriae and genes for nitrogen starvation response in Xylella fastidiosa.

Com a construção da linhagem RlhE fusionada a um epitopo, fomos capazes de investigar o acúmulo da proteína após choque frio, em fase estacionária, durante o ciclo celular de Caulobacter crescentus, sob diferentes condições de estresses e, finalmente, após a adição de cloranfenicol, para o estudo a estabilidade protéica. Foi observado um aumento no acúmulo da proteína após choque frio. Além disso, quando em diferentes condições de estresses, RlhE obteve uma leve indução na presença de NaCl e Sacarose; mas permanaceu constante em fase estacionária e durante o ciclo celular. Finalmente, vimos que a estabilidade de RlhE varia de acordo com a temperatura, tendo um aumento da estabilidade a 10°C. As análises de expressão do gene rhlE foram realizadas por ensaios de atividade de betagalactosidase. Demonstramos que a presença da região 5UTR é importante para a indução, e que rlhE possui, pelo menos em parte, uma regulação pós-transcricional. Uma análise transcriptômica global da linhagem selvagem e mutante para rhlE, após o choque frio, foi realizada por RNAseq, o qual nos auxiliou na identificação de genes envolvidos em diversos processos biológicos. Finalmente, a co-imunoprecipitação e identificação dos RNAs por sequenciamento em larga escala revelou que RlhE interage com 51 mRNAs. / Here, we constructed a strain in which the RhIE protein was fusioned to an epitope that allowed the investigation of the protein profile after cold-shock, at stationary phase, during cell cycle of Caulobacter crescentus, under different environmental stresses, and, finally, after chloramphenicol addition to study protein stability. The results showed an increase in protein concentration after cold shock stress. When exposed to different stresses RhlE was slightly induced in the presence of NaCl and Sucrose; but its abundance remained constant at stationary phase and during C. crescentus cell cycle. Lastly, the protein stability varies depending on temperature - increasing at low temperature. Gene expression analysis was performed using beta-galactosidase assays. We showed that the presence of the 5UTR is important for the induction of rhlE, and that RhlE is posttranscriptionally regulated. A global transcriptome analysis was performed using RNAseq after cold shock stress of the wild type strain and null mutant for rhlE, and several genes involved in a wide range of biological process were identified. Finally, High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation revealed interactions of RhlE with 51 mRNAs.

This thesis deals with the characterization of bacterial cells capable of polyhydroxyalkanoates (PHA) accumulation. The dissertation thesis is written in the form of a discussed published publications which are attached to the thesis as appendixes. The work develops a study of the current topic of the protective functions of PHA and clarifies protective mechanisms against selected stressors. Firstly, we focused on the protective effects of PHA granules against UV radiation and osmotic stress, specifically hypotonic conditions. In the case of UV exposition, the cells protected themselves by scattering UV radiation on the intracellular granules protecting especially nucleoid. When exposed to osmotic stress, the amorphous state of PHA granules is very important since it is capable of stabilization of cell membranes under hypertonic stress, afterwards, bacterial cells can maintain their integrity during the subsequent hypotonic challenge. In general, the amorphous state of PHA granules is key to ensure the proper biological functions of PHA whether as storage or protective polymer. Therefore, in the next part of this work, we focused on the core of the stabilization mechanism that protects native PHA granules from crystallization and thus the intracellular polymer maintains in a thermodynamically unfavorable amorphous phase state. Based on experimental work, we applied selected stresses because we proposed a new model of stabilization of the amorphous state of PHA granules in vivo. It consists of two mechanisms, where small volumes of PHA granules reduce the rates of crystallization and at the same time the water present in the granules plays the role of a low molecular plasticizer. Due to the metabolic apparatus of bacterial cells, PHA are simultaneously synthesized and degraded which leads to an increment of intracellular concentration of monomers that also figure in the protective effect of PHA. In this context, we aimed at the description of the mechanism of cryoprotective effects of 3-hydroxybutyrate, the monomer of the most common of PHA, poly(3-hydroxybutyrate). Hence, we constructed an equilibrium and non-equilibrium phase diagram of the 3HB-water system to prove that 3HB is a very effective cryoprotectant. This fundamental understanding of the protective properties of PHA monomers could be also used in the food industry or cryopreservation of biological samples.