Legionella pneumophila and other opportunistic pathogens of drinking water pose important problems at the interface of biology, environmental engineering, public health, and governance. In this thesis, I explore the molecular mechanisms permitting survival of L. pneumophila in built water systems is the nature of its physiology under different conditions and different life-phases. In the first chapter, I discuss how various physiological states of L. pneumophila affect the propensity for survival and virulence in relation to drinking water environments. This literature review should provide a perspective important for designing controlled laboratory experiments rooted in a robust understanding of how phenotype dictates experimental results. In the second chapter, I describe sequence and phylogenetic analyses performed to investigate the presence of a type 1 secretion system and virulence factor throughout the Legionella genus. While this system was previously believed to be conserved to L. pneumophila, our analysis indicates that this system is well-distributed throughout the Legionella genus, blurring the lines between "pathogenic" and "non-pathogenic" species. In the third chapter, I report the secretome of endemic Flint, Michigan L. pneumophila in corrosive water, simulating the environmental impact of the Flint Water Crisis on local L. pneumophila populations. Our results from this study have expanded the secretome of L. pneumophila, provided insight on mechanisms it may employ to resist stress in water, and created several novel lines of inquiry at the merging frontier of biochemistry and environmental engineering. / Master of Science in Life Sciences

Mass spectrometry has been recognized as a prominent analytical technique for peptide and protein identification and quantitation. With the advent of soft ionization methods, such as electrospray ionization and matrix assisted laser desorption/ionization, mass spectrometry has opened a new era for protein and proteome analysis. Due to its high-throughput and high-resolution character, along with the development of powerful data analysis software tools, mass spectrometry has become the most popular method for quantitative proteomics. Stable isotope labeling and label-free quantitation methods are widely used in quantitative mass spectrometry experiments. Proteins with stable expression level and key roles in basic cellular functions such as actin, tubulin and glyceraldehyde-3-phosphate dehydrogenase, are frequently utilized as internal controls in biological experiments. However, recent studies have shown that the expression level of such commonly used housekeeping proteins is dependent on cell type, cell cycle or disease status, and that it can change as a result of a biochemical stimulation. Such phenomena can, therefore, substantially compromise the use of these proteins for data validation. In this work, we propose a novel set of proteins for quantitative mass spectrometry that can be used either for data normalization or validation purposes. The protein set was generated from cell cycle experiments performed with MCF-7, an estrogen receptor positive breast cancer cell line, and MCF-10A, a non-tumorigenic immortalized breast cell line. The protein set was selected from a list of 3700 proteins identified in the different cellular sub-fractions and cell cycle stages of MCF-7/MCF-10A cells, based on the stability of spectral count data (CV<30 %) generated with an LTQ ion trap mass spectrometer. A total of 34 proteins qualified as endogenous standards for the nuclear, and 75 for the cytoplasmic cell fractions, respectively. The validation of these proteins was performed with a complementary, Her2+, SKBR-3 cell line. Based on the outcome of these experiments, it is anticipated that the proposed protein set will find applicability for data normalization/validation in a broader range of mechanistic biological studies that involve the use of cell lines. / Master of Science

<p dir="ltr">Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here we described two methods for the LC-MS/MS-based characterization of protein phosphatases and kinases. The first is an <i>in-vitro</i> method designed to probe the inherent substrate specificity of kinase or phosphatases. This method utilizes an enzyme reaction with synthetic peptides, serving served as substrate proxies, coupled with LC-MS/MS for rapid, accurate high-throughput quantification of the specificity constant (<i>k</i>_<em>cat</em><i>/K</i>_<em>M</em>) for each substrate in the reaction and amino acid preference in the enzyme active site, providing insight into their cellular roles. The second couple’s auxin-inducible degradation system (AID) with phosphoproteomics for protein functional characterization. AID is a surrogate for specific chemical inhibition, which minimizes non-specific effects associated with long-term target perturbation. Using this system, we demonstrate-PP2A in complex with its B-subunit Rox Three Suppressor 1 (PP2A^Rts1) contributes to the phosphoregulation of a conserved fungal-specific membrane protein complex called the eisosome. By maintaining eisosomes in their hypophosphorylated state, PP2A^Rts1 aids fungal cells in preserving metabolic homeostasis. This work demonstrates the power of mass spectrometry as a critical tool for protein functional characterization.</p>

The major goal of this study was to develop an experimental proteomics approach for deciphering protein complexes and protein interaction networks in the budding and fission yeasts. Key steps of the employed analytical routine, including the purification of complexes and mass spectrometric identification of their subunits, were investigated in detail. Archiving, storage and handling of polyacylamide gels, visualization of protein bands and their effect on the efficiency of in-gel digestion and mass spectrometric identification of proteins were quantitatively evaluated. It was further demonstrated that a combination of several mass spectrometric techniques based on MALDI and ES ionization provided complementary data and enabled comprehensive characterization of protein digests. The optimized analytical procedures were employed in deciphering protein complexes and protein interaction networks in the budding and fission yeasts. A combination of Tandem Affinity Purification (TAP) and mass spectrometric identification of gel separated protein subunits is generic and robust strategy that provided accurate and reproducible data. The evaluation of TAP success rate, reproducibility and typical protein background presented in this work is based on TAP tagging and immunoprecepitation of 75 genes in S. cerevisiae and 22 in S. pombe. The molecular composition of characterized protein complexes was compared with protein-protein interactions uncovered by other established methods, such as yeast two hybrid screens or proteome-wide purification of protein complexes. We found that repetitive purification of protein complexes using different subunits as baits is crucially important for confident charting of proteomic environments. Accurate dissection of individual protein complexes and identification of their proteomic hyperlinks enabled to consider proteomic environments in the phylogenetic perspective and paved the way to reliable projection of proteomics data obtained in lower eukaryotic model organisms to higher eukaryotes, including humans.

JEREISSATI, Camila Barbosa Pinheiro. Análise proteômica de plastídeos do endosperma de sementes em desenvolvimento de pinhão manso (Jatropha curcas L.). 2015. 127 f. Tese (Doutorado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2015. / Submitted by Vitor Campos (vitband@gmail.com) on 2016-09-01T22:55:24Z No. of bitstreams: 1 2015_teses_cbpjereissati.pdf: 1568499 bytes, checksum: 2f41598abfda8cf6bcab51817b1b742a (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2016-09-02T21:06:57Z (GMT) No. of bitstreams: 1 2015_teses_cbpjereissati.pdf: 1568499 bytes, checksum: 2f41598abfda8cf6bcab51817b1b742a (MD5) / Made available in DSpace on 2016-09-02T21:06:57Z (GMT). No. of bitstreams: 1 2015_teses_cbpjereissati.pdf: 1568499 bytes, checksum: 2f41598abfda8cf6bcab51817b1b742a (MD5) Previous issue date: 2015 / Jatropha curcas L. is a plant native to America and belongs to the Euphorbiaceae family. Currently it is gaining economical interest mainly because it is an oilseed crop with potential to produce biodiesel. However, presence of phorbol esters (a class of diterpenes) that are the major toxic constituents of the seeds, limits a better usage of the plant, by making the use of the residue, obtained after the oil extraction from the seeds, unfeasible for animal feed, due to its pro-carcinogenic activity and inflammatory action. Proteomic analysis of the plastids isolated from developing seeds of Jatropha is important because the synthesis of fatty acid as well as phorbol esters, the two most attractive compounds in the study of Jatropha curcas, occur in plastids. Proteomic analysis of this organelle is crucial to better understand and explore not only the biosynthetic pathway of these two compounds but other metabolic pathways , and addtionaly providing foundation for researchs that aimed to develope genotypes with more suitable characteristics for industrial applications. In this study, we performed a proteomic analysis of plastids isolated from the endosperm of developing Jatropha curcas seeds that were in the initial stage of deposition of protein and lipid reserves. Proteins extracted from the plastids were digested with trypsin, and the peptides were applied to an EASY-nano LC system coupled online to an ESI-LTQ-Orbitrap Velos mass spectrometer, and this led to the identification of 1103 proteins representing 804 protein groups, of which 923 were considered as true identifications, and this considerably expands the repertoire of J. curcas proteins identified so far. Of the identified proteins, only five are encoded in the plastid genome, and none of them are involved in photosynthesis, evidentiating the nonphotosynthetic nature of the isolated plastids. Homologues for 824 out of 923 identified proteins were present in three different plastids proteins databases i.e. PPDB, SUBA and PlProt, while homologues for 13 proteins were not found in any of these three databases but were marked as plastidial by at least one of the three prediction programs used (TargetP, ChloroP and PlantMPloc). Functional classification showed that proteins belonging to amino acids metabolism comprise the main functional class, followed by carbohydrate, energy, and lipid metabolisms. The small and large subunits of Rubisco were identified, and their presence in plastids is considered to be an adaptive feature counterbalancing for the loss of one-third of the carbon as CO2 as a result of the conversion of carbohydrate to oil through glycolysis. While several enzymes involved in the biosynthesis of several precursors of diterpenoids were identified, we were unable to identify any terpene synthase/cyclase, which suggests that the plastids isolated from the endosperm of developing seeds do not synthesize phorbol esters. In conclusion, this study provides insights into the major biosynthetic pathways and certain unique features of the plastids from the endosperm of developing seeds at the whole proteome level. / O pinhão manso (Jatropha curcas L.) é uma planta nativa da América, pertencente à família Euphorbiaceae. Atualmente, ela desperta interesse econômico principalmente por se tratar de uma oleaginosa com potencial para a produção de biodiesel. Entretanto, a presença de ésteres de forbol (uma classe de diterpeno), que são os principais constituintes tóxicos das sementes, limita uma melhor utilização dessa planta, por inviabilizar o uso do resíduo de extração do óleo das sementes na alimentação animal, bem como, por apresentar atividade pró-carcinogênica e ação inflamatória. A análise proteômica de plastídeos, isolados de sementes em desenvolvimento de pinhão manso, é uma importante vertente de estudo, pois tanto a síntese de ácidos graxos como dos ésteres de forbol, os dois compostos mais atrativos no estudo de Jatropha curcas, ocorrem nos plastídeos. O estudo proteômico dessa organela torna-se crucial para melhor compreender e explorar não somente as vias biossintéticas desses dois compostos, como de outras vias metabólicas, além de proporcionar um conjunto de dados que pode ser utilizado em pesquisas voltadas para o desenvolvimento de genótipos com características mais adequadas para aplicações industriais. No presente trabalho, realizou-se uma análise proteômica de plastídeos isolados do endosperma de sementes em desenvolvimento do pinhão manso, que estavam nos estágios iniciais de deposição de lipídios e proteínas de reserva (25-30DAA), confirmados por meio de análises histológica e histoquímica. As proteínas extraídas dos plastídeos foram digeridas com tripsina e os peptídeos foram aplicados no sistema de nano-LC EASYII acoplado online ao espectrômetro de massa nano ESI LTQ-Orbitrap velos, o que resultou na identificação 1103 proteínas, representando 804 grupos de proteínas, dos quais 923 foram consideradas identificações verdadeiras. Isso expandiu consideravelmente o repertório de proteínas do pinhão manso até agora identificas. Dentre as proteínas identificadas, apenas 5 são codificadas pelo genoma plastidial, e nenhuma delas está envolvida na fotossíntese, o que evidencia a natureza não fotossintética dos plastídeos isolados. Homólogos de 824, dentre as 923 proteínas identificadas, estavam presentes nos bancos de dados PPDB, SUBA e PlProt, enquanto homólogos para 13 proteínas não foram encontrados em nenhum dos três bancos de dados plastidiais, mas foram detectados como plastidiais por pelo menos um dos três programas de predição de localização subcelular utilizados (TargetP, ChloroP, PlantMPloc). A classificação funcional mostrou que a maioria das proteínas identificadas pertencia ao metabolismo dos aminoácidos, seguido dos metabolismos dos carboidratos, energético e dos lipídios. As subunidades maiores e menores da Rubisco foram identificadas, e sua presença nos plastídeos foi considerada uma característica adaptativa para contrabalancear a perda de um terço do carbono na forma de CO2 como um resultado da conversão de carboidratos em óleo através da glicólise. Apesar de enzimas envolvidas na biossíntese de diversos precursores dos diterpenóides terem sido identificadas, não foi detectado nenhuma terpeno sintase/ciclase, o que sugere que os plastídeos isolados do endosperma de sementes em desenvolvimento não sintetizam ésteres de forbol, apesar de uma grande quantidade desse composto ser encontrada neste tecido. Como conclusão, o presente trabalho proporciona insights sobre as principais vias biossíntéticas, e sobre características peculiares dos plastideos isolados do endosperma de sementes em desenvolvimento.

This project is concerned with method development in mass spectrometry (MS)-based proteomics in order to find putative biomarkers for early pregnancy ofdomesticated dogs. It is of importance for dog breeders to know whether the dogsbecome pregnant post-mating. Unlike humans, dogs are not known to possess aspecific hormone that indicates fetal development; therefore other biomarkers mustbe investigated. The approach of choice in this project was to look at proteins throughMS-based proteomics. For this purpose, serum samples from 11 pregnant dogs (case,different breeds) and 7 non-pregnant dogs (control, all beagle dogs) were sampledbefore-hand at the Swedish University of Agricultural Sciences. Each dog wassampled Day 1, Day 8, Day 15, Day 22 and Day 29 after optimal mating. Twodifferent proteomics approaches were conducted: Bottom-up (“Shotgun”) proteomicsand targeted proteomics (“targeted analysis”). In this study, Label-free Quantification(LFQ) was employed, which is a relative quantitative technique. The massspectrometer of choice was the Quadrupole-Orbitrap QExactive plus massspectrometer coupled to a nano-Ultra Performance Liquid Chromatography (UPLC).Method optimization was done with respect to concentration of samples prior to MSanalysis, as well as different LC-gradients. From shotgun screening experiments, itwas possible to identify 252 proteins. Ultimately, 9 proteins were investigated usingtargeted final analysis: CRP, SERPINC1, CP, PROS1, SERPING1, A2M, AGP,SERPINA1 and HP. For targeted final analysis, 21 peptides were considered.Calibration curves were constructed using 8 of the 21 targeted peptides; 1 peptide perprotein, except for HP which had 2 peptides per protein. The SERPINA1 and CPproteins had no appropriate peptides for targeted final analysis and were thusexcluded. It was confirmed that CRP was up-regulated in case dogs compared tocontrol dogs. The other investigatedproteins showed no significant signs of regulation. In order to improve the results; itwould be desirable to include more dogs in the study which would benefit thestatistics of protein regulation. However, the use of isotopic labeled standards andemployment of a Parallel Reaction Monitoring (PRM) method should be prioritizedfor obtaining absolute quantitative data.

DCs are critical to the early events of HIV-1 infection. They are the first cells that HIV-1 encounters at mucosal surfaces and as sentinel antigen-presenting cells of the immune system these should alarm the immune system and activate innate immune defences to recruit effective adaptive immunity and viral clearance. A peculiar characteristic of HIV – in contrast to other ssRNA viruses – is its ability to completely evade host innate recognition pathways. Additionally, it has the unique ability to manipulate the endo-lysosomal system of DCs and promote transmission via trans-infection to CD4+ T cells across virological synapses. However, it is largely unknown how HIV-1 is sensed by the innate immune system. Here, a multipronged experimental approach based on phosphoproteomics, transcriptomics and custom RNAi screen was developed to characterize the early signaling complex induced by HIV-1 in DCs. A novel method of phosphoproteomics to identify the HIV-1 phosphoproteome in DCs showed that 342 proteins were differentially phosphorylated following 10 min of HIV-1 infection compared to time-matched mock-infected DCs. Functional analysis of these phosphoproteins showed enrichments in several cellular pathways, including vesicular trafficking, cytoskeletal rearrangements and the secretory pathway and a relative paucity of signaling molecules involved in inflammatory pathways. Proteomics analysis of HIV-1 virions was undertaken to identify host molecules hijacked by HIV-1 during viral replication and revealed a close interaction between the virus and the endo-lysosomal system. Transcriptomics analysis of HIV-1 infected DCs showed a muted immune response with no detectable differentially regulated genes. The results of the phoshoproteomic screen provided the basis for a custom RNAi screen to identify host proteins that are differentially phosphorylated by the virus and required for efficient trans-infection from DCs to CD4+ lymphocytes. The results of this screen showed that 54 of the 120 host factors tested were required for efficient viral transfer to CD4+ T cells and characterize the compartment that HIV-1 is internalized in on a molecular level. Two host factors identified within the HIV-1 phosphoproteome were chosen for further studies. Studies of BLOC-1 (biogenesis of lysosome-related organelles complex-1) and its subunits identified a role for snapin in HIV-1 trans-infection and HIV-1 and TLR8 sensing. Snapin may act as determinant of sorting of HIV-1 intraluminal vesicles to non-degradative, non-immunogenic compartments by activating mammalian target of rapamycin, mTOR, and inhibiting autophagy. Furthermore, HIV-1 triggered dephosphorylation of the cytosolic tyrosine phosphatase possibly via the interaction of host CD47 incorporated in the virion and the transmembrane glycoprotein SIRPα expressed on DCs. Blocking of this interaction with an inhibitory CD47 antibody resulted in a reduction of HIV-1 replication. Taken together, this multipronged approach reveals the complexity of the interaction of HIV-1 with the host cell machinery and identifies novel mechanism of the immune evasion tactics usurped by HIV-1.

published_or_final_version / abstract / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Clinical Oncology / Doctoral / Doctor of Philosophy