Metabolism of D-amino acids is of considerable interest due to their key importance in cellular functions. The enzymes D-serine dehydratase (DSD) and D-cysteine desulfhydrase (DCyD) are involved in the degradation of D-Ser and D-Cys, respectively. We determined the crystal structure of Salmonella typhimurium DSD (StDSD) by multiple anomalous dispersion method of phasing using selenomethione incorporated protein crystals. The structure revealed a fold typical of fold type II PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labeled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other fold type II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggested that Thr166 may be involved in abstraction of proton from the Cα atom of the substrate. Apart from the physiological reaction, StDSD catalyses α, β-elimination of D-Thr, D-Allothr and L-Ser to the corresponding α-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates. Salmonella typhimurium DCyD (StDCyD) is a fold type II PLP-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. We determined the crystal structure of StDCyD using molecular replacement method in two different crystal forms. The better diffracting crystal form obtained in presence of benzamidine illustrated the influence a small molecule in altering protein interfaces and crystal packing. The polypeptide fold of StDCyD consists of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) which resemble other fold type II PLP-dependent enzymes. X-ray crystal structures of StDCyD were also obtained in the presence of substrates, D-Cys and βCDA, and substrate analogs, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS). The structures obtained in the presence of D-Cys and βCDA show the product, pyruvate, bound at a site 4.0-6.0 Å away from the active site. ACC forms an external aldimine complex while D and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Cα proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggested formation of PMP by the hydrolysis of cycloserines. Mutational studies suggested that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Cα proton abstraction from D-Cys. Based on these studies, we proposed a probable mechanism for the degradation of D-Cys by StDCyD. The acid-induced arginine decarboxylase (ADC) is part of an enzymatic system in Salmonella typhimurium that contributes to making this organism acid resistant. ADC is a PLP-dependent enzyme that is active at acidic pH. It consumes a proton in the decarboxylation of arginine to agmatine, and by working in tandem with an arginine-agmatine antiporter, this enzymatic cycle protects the organism by preventing the accumulation of protons inside the cell. We have determined the structure of the acid-induced StADC to 3.1 Å resolution. StADC structure revealed an 800 kDa decamer composed as a pentamer of five homodimers. Each homodimer has an abundance of acidic surface residues, which at neutral pH prevent inactive homodimers from associating into active decamers. Conversely, acidic conditions favor the assembly of active decamers. Therefore, the structure of arginine decarboxylase presents a mechanism by which its activity is modulated by external pH.

The global increasing problem of antibiotic resistance necessarily drives the pursuit and discovery of new antimicrobial agents. Antimicrobial peptides (AMPs) initially seemed like promising new drug candidates. Already members of the innate immune system, it was assumed that they would be bioactive and non-toxic. Their common trait for fundamental, non-specific mode of action also seemed likely to reduce resistance development. In this thesis, we demonstrate the ease with which two species of pathogenic bacteria, the gram-negative Salmonella typhimurium (S. typhimurium), and the gram-positive Staphylococcus aureus (S. aureus), can gain increased tolerance and stable resistance to various AMPs. By serially passaging each bacterial species separately under increasing AMP selection pressure we observed increasing AMP tolerance. Resulting in independent bacterial lineages exposed to four different AMPs (including a two-AMP combination) that exhibited 2 to 16-fold increases in MIC. Substantial cross-resistance between the AMPs was observed. Additionally, the S. aureus mutants were found to be cross-resistant to human beta-defensins 1, 2, 3, and 4. The LPS molecule, with mutations in the waaY, pmrB and phoP genes, was the principal target for S. typhimurium resistance development. The main target for S. aureus remained elusive. Reduced membrane potential was a common change for two of the mutants, but not for the others. All sequenced mutants had one or more mutations in various stress response pathways. Fitness of the resistant mutants was assayed by growth rate analysis and in vitro virulence factor testing (e.g. survival response to bile, superoxide, acidic pH). Furthermore an in vivo survival/virulence test involving a mouse competition experiment (S. typhimurium) and sepsis model (S. aureus) was performed. In the absence of AMPs there was often little or no fitness reduction in the mutants. Our results suggest that AMP resistance mechanisms do not irrevocably weaken either species with regard to virulence characteristics or survival within the host. In light of these findings, we suggest that the progression of therapeutic use of AMPs should proceed with great caution since otherwise we might select for AMP resistant mutants that are more resistant to our innate host defenses and thereby potentially more virulent.

A contaminação cruzada por Salmonella spp. durante o processo de abate de suínos contribui para o aumento da prevalência de carcaças positivas no pré-resfriamento. Um dos fatores que pode contribuir para a contaminação cruzada é a execução de cortes e palpação de carcaças durante o processo de inspeção. O presente estudo teve como objetivo estimar, por meio de ensaios laboratoriais, a transferência de Salmonella Typhimurium DT 177 entre faca e carne suína, para subsidiar análises futuras aplicadas ao processo de abate. Foram conduzidas observações independentes e aleatórias da transferência de uma cepa de S. Typhimurium resistente a Ampicilina (AmpR), entre faca e carne suína, as quais formaram quatro coleções de dados: Coleção de dados A: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada uma vez (n=20); Coleção de dados B: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada cinco vezes no mesmo lugar (n=20); Coleção de dados C: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de um corte (n=20); Coleção de dados D: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de cinco cortes no mesmo lugar (n=20). As bactérias transferidas foram quantificadas na lâmina da faca e na superfície da carne, a porcentagem de transferência foi calculada em todas as coleções de dados. As porcentagens de transferência entre as coleções de dados foram comparadas por meio de teste t para amostras independentes usando o programa R Core Team. As percentagens médias de transferência na coleção de dados A e B foram de 6,26% (4,7% – 7,7%) e 8,32% (6,4% - 10,2%). Nas coleções de dados C e D, as percentagens médias de transferência foram, respectivamente, 0,42% (0,3% - 0,5%) e 0,3% (0,2% - 0,4%). Não houve diferença significativa entre as percentagens de transferência após um e cinco cortes consecutivos. A partir disso, conclui-se que há transferência de S. Typhimurium da faca para a carne suína, bem como da carne suína para a faca. A porcentagem de transferência da carne suína contaminada para a faca é baixa, ao passo que a faca contaminada transfere alta percentagem do total de células de S. Typhimurium que carreia, durante a realização dos cortes. / Cross-contamination by Salmonella spp. during the pig slaughtering process contributes to increase the prevalence of positive carcasses in pre-chilling. One of the factors that may contribute to cross-contamination is the implementation of cuts and palpation of carcasses during the inspection process. The present study aimed to estimate, through laboratory tests, the transfer of Salmonella Typhimurium between knife and swine meat, to support future analyzes applied to the slaughter process. Independent and random observations of the transfer of a strain of S. Typhimurium Ampicillin-resistant (AmpR) between knife and swine meat were conducted, which formed four collections of data: Data collection A: Transfer of S. Typhimurium AmpR from contaminated knife to one portion of swine meat cut once (n = 20); Data collection B: Transfer of S. Typhimurium AmpR from contaminated knife to swine meat portion cut five times in the same place (n=20); Data collection C: Transfer of S. Typhimurium AmpR from portion of contaminated meat swine to knife after a cut (n=20); Data collection D: Transfer of S. Typhimurium AmpR from swine meat portion contaminated to knife after five cuts in the same place (n=20). The transfer percentages between the data collection were compared by t-test for independent samples using the R Core Team software. The mean transfer percentages in the data collection A and B were 6,26% (4,7% - 7,7%) and 8,32% (6,4% - 10,2%). In the C and D data collections, mean transfer rates were, respectively, 0.42% (0.3% - 0.5%) and 0.3% (0.2% - 0.4%). There was not significant difference between transfer rates after one and five consecutive cuts. From this, it is concluded that there is transfer of S. Typhimurium from the knife to the swine meat as well as from the swine meat to the knife. The percentage of transfer of contaminated pork to the knife is low, while the contaminated knife transfers at high percentage of the total number of S. Typhimurium cells it carries during cuts.

The ƒÑ-toxin of Clostridium perfringens is a toxin involved in numerous diseases of humans and agriculturally important animals. One of these diseases is necrotic enteritis (NE), a sporadic enteric disease which affects avian species world-wide. This study involved the inactivation of alpha-toxin (ƒÑ-toxin) for use as a potential vaccine candidate to combat NE in chickens, and other diseases caused by C. perfringens type A. During the course of this research a number of ƒÑ-toxin recombinant proteins were developed through molecular inactivation of the ƒÑ-toxin gene, plc. Proteins plc316 and plc204 were developed by the deletion of the first three and seven ƒÑ-helices of the N-terminal domain respectively. These deletions resulted in proteins which were unstable in solution, constantly aggregated into insoluble masses and elicited lower overall antibody responses when administered to mice. A third protein, plcInv3 was developed from the deletion of part of the catalytic domain of the ƒÑ-toxin. PlcInv3 was highly soluble and upon immunisation of mice elicited a significant antibody response which was also capable of protecting mice against a live challenge of C. perfringens. The fourth and final protein developed was plc104. The smallest of the recombinant ƒÑ-toxin proteins, it consisted entirely of the C-terminal domain of ƒÑ-toxin. Its small size did not affect its ability to induce a strong antibody response when administered to mice, the antibodies of which were also protective during a challenge with C. perfringens. STM1, an attenuated strain of S. Typhimurium was used in the development of a vectored vaccine for the expression and oral delivery of plcInv3 and plc104 within the mouse host. The proteins were expressed within STM1 from expression plasmids containing the in vivo inducible promoters PhtrA and PpagC. A measurable humoral immune response against ƒÑ-toxin was absent following three oral vaccinations with the vectored vaccines, although, cytokine profiling of splenocytes from vaccinated mice revealed an increase in the number of interleukin-4 (IL-4)secreting cells and the lack of interferon-gamma (IFN-ƒ×) secreting cells. This indicated the stimulation of a T-helper type 2 (TH2) immune response which also lead to partial protection against a live C. perfringens challenge. This study demonstrates the feasibility of using STM1 as a carrier for the in vivo expression of the C. perfringens ƒÑ-toxin recombinant proteins plcInv3 and plc104. It is the first study to express C. perfringens antigens within an attenuated strain of S. Typhimurium, STM1.The partial protection of mice immunised with these vaccines indicates there is potential for this vectored vaccine system to be used in the protection of diseases caused by the ƒÑ-toxin of C. perfringens.

X-ray crystallography is a powerful method for determining the three-dimensional structures of biological macromolecules at atomic resolution. Crystallography can reliably provide the answer to many structure related questions, from global folds to atomic details of bonding. Crystallographic techniques find wide applications in understanding macromolecular assembly, enzyme mechanism, mode of activation of enzymes, substrate-specificity, ligand-binding properties, domain movement etc. The knowledge of accurate molecular structures is also a prerequisite for rational drug design and for structure based functional studies to aid the development of effective therapeutic agents. The current thesis can be broadly divided into two major parts. The first four chapters deal with assembly studies that have been carried out on Sesbania mosaic virus and the next two chapters describe the structure and function of a stationary phase survival protein, SurE from Salmonella typhimurium. In both studies X-ray crystallographic techniques have been used extensively for the structural studies. Viruses are obligate parasites with a proteinaceous capsid enclosing the genetic material. For genetic economy, several copies of capsid proteins self assemble to form complex virus capsids. Due to their intricate symmetric structures, viruses are considered as minute marvels of molecular architecture and study of virus structures serve as a paradigm for solutions to problems concerning macromolecular assembly and function in general. Crystallography provides a means of visualizing intact virus particles as well as their isolated constituent proteins and enzymes at near-atomic resolution, and is thus an extraordinarily powerful tool for understanding the function of these biological systems. Protein-protein interactions, protein-nucleic acid interactions, metal-ion mediated interactions, interactions between capsid proteins and auxillary or scaffolding proteins and particle maturation or post processing of capsid protein subunits are various elements that play a role in capsid assembly. Many structural and sequential motifs have been proposed as important conformational switches of capsid assembly. A functional analysis of these motifs by way of mutations in the capsid protein and structural studies of these mutants can provide further insight into capsid assembly pathways. Interaction between capsid protein subunits can determine the size and robustness of the capsid. Analysis of protein-protein interactions can help in understanding the principles of self-assembly. Arresting capsid assembly by disrupting intersubunit interactions and trapping the assembly intermediates will be helpful to delineate the changes that happen in capsid protein during the course of assembly and understand assembly pathways. Sesbania mosaic virus (SeMV) is a plant virus with a positive sense single-stranded RNA genome and belongs to the Sobemovirus genus. The protein and nucleic acids of SeMV can be separated and reassembled in vitro. Also, expression of the coat protein (CP) gene of SeMV in E. coli leads to the formation of virus like particles (VLPs). Therefore, SeMV is an excellent model system to study the assembly pathways that lead to the formation of complex virus shells. Earlier structural and functional studies on the native virus and the recombinant capsid protein and its various mutants have revealed the following: SeMV is a T=3 virus with chemically identical A-, B- and C-subunits occupying quasi equivalent positions in the icosahedral asymmetric unit of the virus particle. The A-type subunits form pentamers at the five-fold, and the B- and C- type subunits form hexamers at the icosahedral three-fold axes. The amino terminus of the polypeptide is ordered from residue 72 in the A- and B- subunits whereas it is ordered from residue 44 in the C-subunit. The disordered segment in all the subunits has an arginine rich motif (N-ARM). The segment ordered only in C-subunits has a -annulus structure that promotes intersubunit interactions at the quasi six-fold and a -segment (A). The virus is stabilized by protein-protein, protein–RNA and Ca2+ mediated protein-protein interactions. Virus like particles (VLPs) formed by the expression of full length CP encapsidate 23 S E. coli rRNA and CP mRNA. Expression of a deletion mutant lacking the N-terminal 65 residues (rCP∆N65) which results in the removal of the N-ARM, the -annulus and the A leads to the formation of stable T=1 particles. The -annulus, which was earlier believed to be an important molecular switch controlling the assembly of T=3 VLPs was found to be dispensable. The N-ARM, though important for RNA encapsidation, was not essential for capsid assembly . Depletion of Ca2+ ions led to slight swelling of virus particles and significantly reduced stability. Extensive studies on the VLPs suggested that the assembly is most likely initiated by the dimers of the capsid protein. Following a brief account of the historical highlights in the field of structural virology, a review of current literature on the available crystal structures of viruses and various assembly studies on viruses that have been carried out with emphasis on role of nucleic acid mediated interactions, protein-protein interactions and role of specific residues and ion-mediated interactions in assembly are presented in Chapter I of the thesis. A separate section in this chapter deals with the disassembly experiments that have led to the formation of smaller oligomers of spherical viruses. This chapter also gives an account of the earlier work that has been carried out on SeMV, which is the model system of study for the present thesis. Chapter II describes in detail the structural studies on the β-annulus deletion mutant of SeMV. A unique feature of several T = 3 icosahedral viruses is the presence of a structure called the β-annulus formed by extensive hydrogen bonding between protein subunits related by icosahedral three-fold axis of symmetry. This unique structure has been suggested as a molecular switch that determines the T = 3 capsid assembly. In order to examine the importance of the β-annulus, a deletion mutant of Sesbania mosaic virus coat protein in which residues 48–59 involved in the formation of the β-annulus were deleted retaining the rest of the residues in the amino terminal segment (rCP (Δ48–59)) was constructed. When expressed in Escherichia coli, the mutant protein assembled into virus like particles of size close to that of the wild type virus particles. The purified capsids were crystallized and their three dimensional structure was determined at 3.6Å resolution by X-ray crystallography. The mutant capsid structure closely resembled that of the native virus particles. However, surprisingly, the structure revealed that the assembly of the particles has proceeded without the formation of the β-annulus. Therefore, the β-annulus is not essential for T = 3 capsid assembly as speculated earlier and may be formed as a consequence of the particle assembly. This is the first structural demonstration that the virus particle morphology with and without the β-annulus could be closely similar. Chapter III begins with a detailed description of the interfacial residue mutations that have been carried out in SeMV with the aim of disrupting assembly and trapping an assembly intermediate. These mutations were performed in rCP as well as rCP∆N65 gene. Among these, a single point mutation of a Trp 170 to a charged residue (either Glu or Lys) arrested virus assembly and resulted in stable dimers of the capsid protein. The chapter also gives an account of the biophysical characterization of these mutants. rCP∆N65 dimer mutants showed a characteristic 230 nm peak in CD spectral studies which may be due to the interactions of a stretch of aromatic residues in the capsid protein. The isolated dimers were more susceptible to trypsin cleavage compared to the assembled capsids due to the exposed basic amino terminus. Thermal melting studies showed that the isolated dimer mutants were much less stable when compared to the assembled capsids, probably due to the loss of intersubunit interactions and Ca2+ mediated interactions. The structure of one of the isolated dimer mutant- rCP∆N65W170K was solved to a resolution of 2.65Å. Chapter IV describes the crystal structure analysis of the rCP∆N65W170K mutant dimer and compares its structure with the dimers of native virus, T=3 and T=1 VLPs. A number of structural changes occur especially in the loop and interfacial regions during the course of assembly. The dimer in solution was “more relaxed” than the dimer that initiates assembly. Ca2+ ion is not bound and consequently the C-terminal residues are disordered. The FG loop, which interacts with RNA, was found to be flexible and adopts a different conformation in the unassembled dimer. The present thesis also deals with the structural and functional studies of a phosphatase, SurE, the stationary phase survival protein from Salmonella typhimurium. Chapter V provides a general introduction on Salmonella, which is a mesophilic food borne pathogen, its general features, classification and stress responses. This chapter also gives an account of stationary phase in bacteria and stress responses. A brief description about phosphatases and their classification is also presented in this chapter. Following this, a review of the current literature on the structural, biochemical and functional role of stress related proteins and phylogenetic and enzymatic studies of various homologues of SurE are described in detail. Chapter VI deals with the detailed crystal structure analysis of SurE, the first stationary phase survival protein from a mesophilic organism. SurE, of Salmonella typhimurium forms part of a stress survival operon regulated by the stationary phase RNA polymerase alternative sigma factor. SurE is known to improve bacterial viability during stress conditions. It functions as a phosphatase specific to nucleoside monophosphates. Here we report the X-ray crystal structure of SurE from Salmonella typhimurium (St SurE). The protein crystallized in two forms- orthorhombic F222 and monoclinic C2. The two structures were determined to resolutions of 1.7Å and 2.7Å, respectively. The protein exists as a domain swapped dimer. The residue Asp 230 is involved in several interactions that are probably crucial for domain swapping. A divalent metal ion is found at the active site of the enzyme, which is consistent with the divalent metal-ion dependent activity of the enzyme. Interactions of the conserved DD motif present at the N-terminus with the phosphate and the Mg2+ present in the active site suggest that these residues play an important role in enzyme activity. The divalent metal ion specificity and the kinetic constants of SurE were determined using the generic phosphatase substrate- para- Nitro Phenyl Phosphate. The enzyme was inactive in the absence of divalent cations and was most active in the presence of Mg2+. Thermal denaturation studies showed that St SurE is much less stable compared to its homologues and an attempt was made to understand the molecular basis of the lower thermal stability based on solvation free energy. The thesis concludes with a brief summary of the entire work that have been presented and future prospects. The various crystallographic, biochemical and biophysical techniques employed in the investigations are described under the section experimental techniques in Appendix I and the NCS matrices used in the structure solution of the β-annulus deletion mutant are listed in Appendix II.

I formally joined Prof. M. R. N. Murthy’s laboratory at the Molecular Biophysics Unit, Indian institute of Science, on 1st August 2001. During that time, the interest in the laboratory was mainly focused on structural studies on a number of capsid mutants of two plant viruses, sesbania mosaic virus and physalis mottle virus, to gain an insight into the virus structure and its assembly. Besides these two projects, there were a few other collaborative projects running in the lab at that time such as NIa protease from pepper vein banding virus and diaminopropionate ammonia lyase from Escherichia coli with Prof. H. S. Savithri, triosephosphate isomerase from Plasmodium falciparum with Prof. P. Balaram and Prof. H. Balaram and a DNA binding protein (TP2) with Prof. M. R. S. Rao. During my first semester, along with my course work, I was assigned to make an attempt to purify and crystallize recombinant NIa protease and TP2 protein. I started with NIa protease which could be purified using one step Ni-NTA affinity column chromatography. Although the expression and protein yield were reasonably good, protein precipitated with in a couple of hours after purification. Attempts were made to prevent the precipitation of the purified enzyme and towards this end we were successful to some extent. However, during crystallization trials most of the crystallization drops precipitated completely even at low protein oncentration. TP2 protein was purified using three-step chromatographic techniques by one of the project assistant in Prof. M. R. S. Rao’s laboratory. Because of low expression level and three step purification protocol, protein yield was not good enough for complete crystallization screening. Hits obtained from our initial screening could not be confirmed because of low protein yield as well as batch to batch variation. My attempts to crystallize these two proteins remained unsuccessful but in due course I had learnt a great deal about the tips and tricks of expression, purification and mainly crystallization. To overcome the problems faced with these two proteins, we decided to make some changes in the gene construct and try different expression systems. By this time (beginning of 2002), I had finished my first semester and a major part of the course work, so we decided to start a new project focusing on some of the unknown enzymes from a metabolic pathway. Dr. Parthasarathy, who had finished his Ph. D. from the lab, helped me in literature work and in finding targets for structural studies. Finally, we decided to target enzymes involved in the propionate etabolism. The pathways for propionate metabolism in Escherichia coli as well as Salmonella typhimurium were just established and there were no structural information available for most of the enzymes involved in these pathways. Since, propionate metabolic pathways were well described in the case of Salmonella typhimurium, we decided to use this as the model organism. We first started with the enzymes present in the propionate catabolic pathway “2-methylcitrate pathway”, which converts propionate into pyruvate and succinate. 2-methylcitrate pathway resembles the well-studied glyoxylate and TCA cycle. Most of the enzymes involved in 2-methylcitrate pathway were not characterized biochemically as well as structurally. First, we cloned all the four enzymes PrpB, PrpC, PrpD and PrpE present in the prpBCDE operon along with PrpR, a transcription factor, with the help of Dr. P.S. Satheshkumar from Prof. H. S. Savithri’s laboratory. Since these five proteins were cloned with either N- or C-terminal hexa-histidine tag, they could be purified easily using one-step Ni-NTA affinity column chromatography. PrpB, PrpC and PrpD had good expression levels but with PrpE and PrpR, more than 50% of the expressed protein went into insoluble fraction, probably due to the presence of membrane spanning domains in these two enzymes. Around this time, crystallization report for the PrpD from Salmonella was published by Ivan Rayment’s group, so after that we focused only on the remaining four proteins leaving out PrpD. Our initial attempts to crystallize these proteins became successful in case of PrpB, 2-methylisocitrate lyase. We collected a complete diffraction data to a resolution of 2.5 Å which was later on extended to a resolution of 2.1 Å using another crystal. Repeated crystallization trials with PrpC also gave small protein crystals but they were not easy to reproduce and size and diffraction quality always remained a problem. Using one good crystal obtained for PrpC, data to a resolution of 3.5 Å could be collected. Unfortunately, during data collection due to failure of the cryo-system, a complete dataset could not be collected. Further attempts to crystallize this protein made by Nandashree, one of my colleagues in the lab at that time, was also without much success. Attempts to purify and crystallize PrpE and PrpR were made by me as well as one of my colleagues, Anupama. In this case, besides crystallization, low expression and precipitation of the protein after purification were major problems. Our attempt to phase the PrpB data using the closest search model (phosphoenolpyruvate mutase) by molecular replacement technique was unsuccessful,probably because of low sequence identity between them (24%). Further attempts were made to obtain heavy atom derivatives of PrpB crystal. We could obtain a mercury derivative using PCMBS. However, an electron density map based on this single derivative was not nterpretable. Around this time, the structure of 2-methylisocitrate lyase (PrpB) from E. coli was published by Grimm et. al. The structure of Salmonella PrpB could easily be determined using the E. coli PrpB enzyme as the starting model. We also solved the structure of PrpB in complex with pyruvate and Mg2+. Our attempts to crystallize PrpB with other ligands were not successful. Using the structures of PrpB and its complex with pyruvate and Mg2+, we carried out comparative studies with the well-studied structural and functional homologue, isocitrate lyase. These studies provided the plausible rationale for different substrate specificities of these two enzymes. Due to unavailability of PrpB substrate commercially and the extensive biochemical and mutational studies carried out by two different groups made us turn our attention to other enzymes in this metabolic pathway. Since our repeated attempts to obtain good diffraction quality crystals of PrpC, PrpE and PrpR continued to be unsuccessful, we decided to target other enzymes involved in propionate metabolism. We looked into the literature for the metabolic pathways by which propionate is synthesized in the Salmonella typhimurium and finally decided to target enzymes present in the metabolic pathway which converts L-threonine to propionate. Formation of propionate from L-threonine is the most direct route in many organisms. During February 2003, we initiated these studies with the last enzyme of this pathway, propionate kinase (TdcD), and within a couple of months we could obtain a well-diffracting crystal in complex with ADP and with a non-hydrolysable ATP analog, AMPPNP. TdcD structure was solved by molecular replacement using acetate kinase as a search model. Propionate kinase, like acetate kinase, contains a fold with the topology βββαβαβα, identical with that of glycerol kinase, hexokinase, heat shock cognate 70 (Hsc70) and actin, the superfamily of phosphotransferases. Examination of the active site pocket in propionate kinase revealed a plausible structural rationale for the greater specificity of the enzyme towards propionate than acetate. One of the datasets of TdcD obtained in the presence of ATP showed extra continuous density beyond the γ-phosphate. Careful examination of this extra electron density finally allowed us to build diadenosine tetraphosphate (Ap4A) into the active site pocket, which fitted the density very well. Since the data was collected at a synchrotron source to a resolution of 1.98 Å, we could identify the ligand in the active site pocket solely on the basis of difference Fourier map. Later on, co-crystallization trials of TdcD with commercially available Ap4A confirmed its binding to the enzyme. These studies suggested the presence of a novel Ap4A synthetic activity in TdcD, which is further being examined by biochemical experiments using mass-spectrometry as well as thin-layer chromatography experiments. By the end of 2004, we shifted our focus to the first enzyme involved in the anaerobic degradation of L-threonine to propionate, a biodegradative threonine deaminase (TdcB). Sagar Chittori, who had joined the lab as an integrated Ph. D student, helped me in cloning this enzyme. My attempt to crystallize this protein became finally successful and datasets in three different crystal forms were collected. Dataset for TdcB in complex with CMP was collected during a synchrotron trip to SPring8, Japan by my colleague P. Gayathri and Prof. Murthy. TdcB structure was solved by molecular replacement using the N-terminal domain of biosynthetic threonine deaminase as a search model. Structure of TdcB in the native form and in complex with CMP helped us to understand several unanswered questions related to ligand mediated oligomerization and enzyme activation observed in this enzyme. The structural studies carried out on these three enzymes have provided structural as well as functional insights into the catalytic process and revealed many unique features of these metabolic enzymes. All these have been possible mainly due to proper guidance and encouragement from Prof. Murthy and Prof. Savithri. Prof. Murthy’s teaching as well as discussions during the course of investigation has helped me in a great deal to learn and understand crystallography. Collaboration with Prof. Savithri kept me close to biochemistry and molecular biology, the background with which I entered the world of structural biology. The freedom to choose the project and carry forward some of my own ideas has given me enough confidence to enjoy doing research in future.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2010.

A contaminação cruzada por Salmonella spp. durante o processo de abate de suínos contribui para o aumento da prevalência de carcaças positivas no pré-resfriamento. Um dos fatores que pode contribuir para a contaminação cruzada é a execução de cortes e palpação de carcaças durante o processo de inspeção. O presente estudo teve como objetivo estimar, por meio de ensaios laboratoriais, a transferência de Salmonella Typhimurium DT 177 entre faca e carne suína, para subsidiar análises futuras aplicadas ao processo de abate. Foram conduzidas observações independentes e aleatórias da transferência de uma cepa de S. Typhimurium resistente a Ampicilina (AmpR), entre faca e carne suína, as quais formaram quatro coleções de dados: Coleção de dados A: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada uma vez (n=20); Coleção de dados B: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada cinco vezes no mesmo lugar (n=20); Coleção de dados C: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de um corte (n=20); Coleção de dados D: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de cinco cortes no mesmo lugar (n=20). As bactérias transferidas foram quantificadas na lâmina da faca e na superfície da carne, a porcentagem de transferência foi calculada em todas as coleções de dados. As porcentagens de transferência entre as coleções de dados foram comparadas por meio de teste t para amostras independentes usando o programa R Core Team. As percentagens médias de transferência na coleção de dados A e B foram de 6,26% (4,7% – 7,7%) e 8,32% (6,4% - 10,2%). Nas coleções de dados C e D, as percentagens médias de transferência foram, respectivamente, 0,42% (0,3% - 0,5%) e 0,3% (0,2% - 0,4%). Não houve diferença significativa entre as percentagens de transferência após um e cinco cortes consecutivos. A partir disso, conclui-se que há transferência de S. Typhimurium da faca para a carne suína, bem como da carne suína para a faca. A porcentagem de transferência da carne suína contaminada para a faca é baixa, ao passo que a faca contaminada transfere alta percentagem do total de células de S. Typhimurium que carreia, durante a realização dos cortes. / Cross-contamination by Salmonella spp. during the pig slaughtering process contributes to increase the prevalence of positive carcasses in pre-chilling. One of the factors that may contribute to cross-contamination is the implementation of cuts and palpation of carcasses during the inspection process. The present study aimed to estimate, through laboratory tests, the transfer of Salmonella Typhimurium between knife and swine meat, to support future analyzes applied to the slaughter process. Independent and random observations of the transfer of a strain of S. Typhimurium Ampicillin-resistant (AmpR) between knife and swine meat were conducted, which formed four collections of data: Data collection A: Transfer of S. Typhimurium AmpR from contaminated knife to one portion of swine meat cut once (n = 20); Data collection B: Transfer of S. Typhimurium AmpR from contaminated knife to swine meat portion cut five times in the same place (n=20); Data collection C: Transfer of S. Typhimurium AmpR from portion of contaminated meat swine to knife after a cut (n=20); Data collection D: Transfer of S. Typhimurium AmpR from swine meat portion contaminated to knife after five cuts in the same place (n=20). The transfer percentages between the data collection were compared by t-test for independent samples using the R Core Team software. The mean transfer percentages in the data collection A and B were 6,26% (4,7% - 7,7%) and 8,32% (6,4% - 10,2%). In the C and D data collections, mean transfer rates were, respectively, 0.42% (0.3% - 0.5%) and 0.3% (0.2% - 0.4%). There was not significant difference between transfer rates after one and five consecutive cuts. From this, it is concluded that there is transfer of S. Typhimurium from the knife to the swine meat as well as from the swine meat to the knife. The percentage of transfer of contaminated pork to the knife is low, while the contaminated knife transfers at high percentage of the total number of S. Typhimurium cells it carries during cuts.

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2017-01-23T10:29:06Z No. of bitstreams: 1 TeseCRS.pdf: 3506039 bytes, checksum: 68f4c5fe1c6ae3672adcedf3450e2f31 (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-01-23T15:48:35Z (GMT) No. of bitstreams: 1 TeseCRS.pdf: 3506039 bytes, checksum: 68f4c5fe1c6ae3672adcedf3450e2f31 (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-01-23T15:48:42Z (GMT) No. of bitstreams: 1 TeseCRS.pdf: 3506039 bytes, checksum: 68f4c5fe1c6ae3672adcedf3450e2f31 (MD5) / Made available in DSpace on 2017-01-23T15:48:50Z (GMT). No. of bitstreams: 1 TeseCRS.pdf: 3506039 bytes, checksum: 68f4c5fe1c6ae3672adcedf3450e2f31 (MD5) Previous issue date: 2015-08-27 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The genus Salmonella spp. has been extensively investigated because these bacteria are important pathogens that frequently cause severe diseases and gastrointestinal infections in humans and animals. Moreover, in recent years, Salmonella has called attention due to the excellent results in the production and in vivo delivery of various substances with potential application in Vaccinology. However, there is still little information available concerning aspects of its metabolism, which hampers both the development of new attenuated strains and the large-scale production of live cells and cellular components. Thus, this work aimed to study the S. typhimurium LT2 metabolism, using traditional and innovative approaches to investigate different carbon sources as well as different bioreactor operation modes and aeration conditions (aerobic and anaerobic). Results obtained in batch and chemostat cultivations indicated that S. typhimurium metabolism differs significantly from E. coli metabolism, closely related bacteria species with regard to the central carbon metabolism. The main difference observed between these bacteria was the high level of acetate production exhibited by S. typhimurium LT2 cells, which, differently from E. coli, occurred even at the lowest dilution rate evaluated. Currently, genome scale metabolic models are important tools for better understanding the phenotypic behavior of many organisms. Therefore the model STM_v1.0 reconstructed for S. typhimurium LT2 was evaluated, comparing experimental data, obtained in chemostat cultivations, with model predictions. Since this model was derived from E. coli model, the simulated results for biomass formation were overestimated and, consequently, predicted acetate fluxes were lower than those obtained experimentally. Therefore, to obtain experimental data useful to improve the model and to reach a better comprehension of S. typhimurium metabolism, the technique of metabolic flux analysis using isotopic labeled substrate was adopted, allowing determination of the fluxes for the main pathways of central carbon metabolism of Salmonella. This analysis revealed different preferred metabolic pathways depending on the specific growth rate. At the lowest dilution rate evaluated, D = 0.24 h-1, glucose was catabolized predominantly by the pentose phosphate and glycolysis pathways, while at the dilution rate of 0.48 h-1, the major pathway of glucose oxidation was Entner-Doudoroff. In addition, a relatively high flux through the citric acid cycle at the higher dilution rate studied was observed. / Bactérias do gênero Salmonella spp. são extensivamente estudadas por serem importantes patógenos, causando frequentemente graves doenças e infecções gastrointestinais em humanos e animais. Além disso, nos últimos anos, estas bactérias vêm ganhando um destaque ainda maior na área da biotecnologia por apresentarem ótimos resultados na produção e veiculação in vivo de diversas substâncias com fins vacinais. No entanto, ainda há poucas informações a respeito de seu metabolismo, dificultando tanto o desenvolvimento de novas linhagens atenuadas, como também a produção em larga escala de células vivas e de componentes celulares. Neste sentido, este trabalho se propôs a estudar o metabolismo de S. typhimurium LT2, utilizando inicialmente abordagens tradicionais para investigar seu comportamento na presença de diferentes fontes de carbono, em diferentes modos de operação de biorreator e de aeração (aeróbias e anaeróbias). Os resultados obtidos em cultivos em batelada e em quimiostatos evidenciaram que o metabolismo da S. typhimurium difere bastante do metabolismo da E. coli, espécies consideradas semelhantes com relação ao metabolismo do carbono central. A principal diferença observada entre essas duas bactérias foi a elevada produção de acetato pelas células de S. typhimurium LT2, mesmo em baixas velocidades de crescimento nas quais este metabólito não é produzido por diversas estirpes de E. coli. Atualmente, modelos metabólicos em escala genômica são ferramentas importantes para que o comportamento do fenótipo de diversos organismos sejam melhor compreendidos. Assim, avaliou-se o modelo STM_v1.0 reconstruído para S. typhimurium LT2, comparando-se dados obtidos experimentalmente, em quimiostatos, e os preditos pelo modelo. No entanto, como este modelo foi baseado no modelo da E. coli, os resultados simulados para produção de biomassa foram superestimados e, consequentemente, os fluxos de acetato foram inferiores aos obtidos experimentalmente. Sendo assim, para se obter dados experimentais úteis para aprimorar o modelo e para uma compreensão maior do metabolismo de S. typhimurium, utilizou-se a técnica de análise dos fluxos metabólicos com substrato isotopicamente marcado, permitindo a determinação dos fluxos das principais vias do metabolismo do carbono central da bactéria em estudo. Essa análise revelou diferenças na utilização das vias metabólicas em função da velocidade específica de crescimento, sendo que na menor taxa de diluição avaliada, D = 0,24 h-1, a glicose foi predominantemente catabolizada pelas vias pentose fosfato e glicólise, enquanto na taxa de diluição de 0,48 h-1, a via principal de oxidação da glicose foi a Entner- Doudoroff. Além disso, também observou-se um fluxo relativamente maior na via do ciclo do ácido cítrico na maior taxa de diluição estudada.

A contaminação cruzada por Salmonella spp. durante o processo de abate de suínos contribui para o aumento da prevalência de carcaças positivas no pré-resfriamento. Um dos fatores que pode contribuir para a contaminação cruzada é a execução de cortes e palpação de carcaças durante o processo de inspeção. O presente estudo teve como objetivo estimar, por meio de ensaios laboratoriais, a transferência de Salmonella Typhimurium DT 177 entre faca e carne suína, para subsidiar análises futuras aplicadas ao processo de abate. Foram conduzidas observações independentes e aleatórias da transferência de uma cepa de S. Typhimurium resistente a Ampicilina (AmpR), entre faca e carne suína, as quais formaram quatro coleções de dados: Coleção de dados A: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada uma vez (n=20); Coleção de dados B: transferência de S. Typhimurium AmpR de faca contaminada para porção de carne suína cortada cinco vezes no mesmo lugar (n=20); Coleção de dados C: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de um corte (n=20); Coleção de dados D: Transferência de S. Typhimurium AmpR de porção de carne suína contaminada para faca após execução de cinco cortes no mesmo lugar (n=20). As bactérias transferidas foram quantificadas na lâmina da faca e na superfície da carne, a porcentagem de transferência foi calculada em todas as coleções de dados. As porcentagens de transferência entre as coleções de dados foram comparadas por meio de teste t para amostras independentes usando o programa R Core Team. As percentagens médias de transferência na coleção de dados A e B foram de 6,26% (4,7% – 7,7%) e 8,32% (6,4% - 10,2%). Nas coleções de dados C e D, as percentagens médias de transferência foram, respectivamente, 0,42% (0,3% - 0,5%) e 0,3% (0,2% - 0,4%). Não houve diferença significativa entre as percentagens de transferência após um e cinco cortes consecutivos. A partir disso, conclui-se que há transferência de S. Typhimurium da faca para a carne suína, bem como da carne suína para a faca. A porcentagem de transferência da carne suína contaminada para a faca é baixa, ao passo que a faca contaminada transfere alta percentagem do total de células de S. Typhimurium que carreia, durante a realização dos cortes. / Cross-contamination by Salmonella spp. during the pig slaughtering process contributes to increase the prevalence of positive carcasses in pre-chilling. One of the factors that may contribute to cross-contamination is the implementation of cuts and palpation of carcasses during the inspection process. The present study aimed to estimate, through laboratory tests, the transfer of Salmonella Typhimurium between knife and swine meat, to support future analyzes applied to the slaughter process. Independent and random observations of the transfer of a strain of S. Typhimurium Ampicillin-resistant (AmpR) between knife and swine meat were conducted, which formed four collections of data: Data collection A: Transfer of S. Typhimurium AmpR from contaminated knife to one portion of swine meat cut once (n = 20); Data collection B: Transfer of S. Typhimurium AmpR from contaminated knife to swine meat portion cut five times in the same place (n=20); Data collection C: Transfer of S. Typhimurium AmpR from portion of contaminated meat swine to knife after a cut (n=20); Data collection D: Transfer of S. Typhimurium AmpR from swine meat portion contaminated to knife after five cuts in the same place (n=20). The transfer percentages between the data collection were compared by t-test for independent samples using the R Core Team software. The mean transfer percentages in the data collection A and B were 6,26% (4,7% - 7,7%) and 8,32% (6,4% - 10,2%). In the C and D data collections, mean transfer rates were, respectively, 0.42% (0.3% - 0.5%) and 0.3% (0.2% - 0.4%). There was not significant difference between transfer rates after one and five consecutive cuts. From this, it is concluded that there is transfer of S. Typhimurium from the knife to the swine meat as well as from the swine meat to the knife. The percentage of transfer of contaminated pork to the knife is low, while the contaminated knife transfers at high percentage of the total number of S. Typhimurium cells it carries during cuts.