The genus Mycobacterium comprises some of the most devastating pathogens that infect humans. Mycobacterium tuberculosis causes tuberculosis in humans leading to high morbidity and mortality. The disease is especially prevalent in the under-developed and developing countries of the tropics. Diseases like AIDS and cancer compromise the immune system of an individual leaving him/her susceptible to secondary infections, particularly of tuberculosis. Thus, tuberculosis is making reappearance even in the well-developed countries of the west. The emergence of multi drug resistant strains of tuberculosis makes this deadly disease difficult to cure. A vaccine against tuberculosis is therefore the need of the hour. Mycobacterium smegmatis is a non-pathogenic member of the same family. It has a relatively fast multiplication time when compared to M. tuberculosis and shares the same unique features of the family that make pathogenic members extremely resistant to chemicals and drugs. Proteins of M. smegmatis and M. tuberculosis share high sequence identities, making M. smegmatis the microorganism of choice to study its more deadly counterpart from the same family. A striking feature of all mycobacterial genomes is the abundance of genes coding for enzymes involved in fatty acid and lipid metabolism; more than 250 in Mycobacterium tuberculosis compared to only 50 in Escherichia coli. The mycobacterial genome codes for over a hundred enzymes involved in fatty acid degradation. Apart from providing energy, lipids and fatty acids also form an integral part of the cell wall and cell membrane of Mycobacteria. The abundance and importance of lipid metabolizing enzymes in Mycobacteria make them attractive targets for drug discovery. It is therefore of interest to biochemically and structurally characterize these enzymes. Thiolases are a group of enzymes that are involved in lipid metabolism. In the last step of the β-oxidation pathway, degradative thiolases catalyze the shortening of fatty acid chains by degrading 3-keto acyl CoA to acetyl CoA and a shortened acyl CoA molecule. Thiolases are a subfamily of the thiolase superfamily. This superfamily also includes the Ketoacyl-(Acyl-carrier-protein)-Synthase (KAS) enzymes, polyketide synthases and chalcone synthases. Most members of this superfamily are dimers and while only a few have been found to be tetramers. The tetramers are loosely held dimers of tight dimers. Examination of the Mycobacterium smegmatis genome revealed the presence of several putative thiolase genes. These genes have been annotated as thiolases on the basis of sequence analysis. However, none of them has been biochemically or structurally characterized. The sequence identity between some of these proteins and the other well-characterized thiolases is rather low. The work described in this thesis attempts to characterize two such enzymes from M. smegmatis structurally and functionally. Chapter 1 begins with a brief introduction to the genus Mycobacteria and the role of fatty acid metabolism in mycobacterial virulence. This is followed by a review of the current literature on the enzymes of the thiolase superfamily and their role in fatty acid metabolism. The chapter concludes with a brief summary on the aims and objectives of the work. Chapter 2 describes all the common experimental procedures and computational methods used during the course of these investigations, as most of them are applicable to all the structure determinations and analyses presented in later chapters. The experimental procedures described include overexpression, purification, site directed mutagenesis, isolation of plasmids, crystallization of proteins and X-ray diffraction data collection. Computational methods include structure determination protocols along with details of various programs used during data processing, structure determination, refinement, model building, structure validation and analysis. Chapter 3 describes the cloning, expression, purification, crystallization and structure determination of a thiolase-like protein (TLP1) from M. smegmatis. All enzymes of the thiolase superfamily that have been structurally characterized so far share four features: 1) conservation of the core α/β/α/β/α-layered structure of the thiolase domain, 2) conservation of the extensive dimerization interface, 3) the location of the active site pocket and conservation of key active site residues and 4) the use of a nucleophilic cysteine residue in catalysis. The crystal structure of MsTLP1 revealed some interesting differences when compared to classical thiolases. Of the four characteristic features of thiolases, MsTLP1 has the conserved thiolase fold. The location of its putative active site is similar to that in classical thiolases. However, the dimerization is not a conserved feature in MsTLP1, which appears to be a monomer in solution as well as in the crystal structure. The ligand binding groove of MsTLP1, identified by structural superposition with Z. ramigera thiolase, is larger than that of Z. ramigera. The absence of the catalytic cysteine suggested that though the protein has the strictly conserved thiolase fold, it might perform an entirely different function. A unique extra C-terminal domain of unknown function present only in MsTLP1 has been described towards the end of the chapter. A thorough sequence and structural analysis suggested that MsTLP1 might belong to a new subfamily in the thiolase superfamily. Chapter 4 describes the attempts made towards the biochemical characterization of MsTLP1. Thiolase assays carried out for the synthetic and degradative reactions revealed that the enzyme is inactive in both the directions. However, surface plasmon resonance binding studies revealed that the protein could bind to Coenzyme A, a feature it shares with other enzymes of the thiolase superfamily. Thorough bioinformatics analyses of the structure to determine the residues involved in CoA binding have also been described. The chapter ends with a discussion on the probable function of TLPs in Mycobacteria. Chapter 5 describes the cloning, expression, purification and X-ray structural studies on MsT1-L thiolase. This is the first structural report of a probable T1-thiolase. The protein crystallized in three different space groups, in all of which the enzyme was found to be in a tetrameric form. Analysis of the tetramer structures from the three different crystal forms revealed that MsT1-L exhibits some rotational flexibility about the central tetramerization loop. A qualitative and quantitative analysis of this movement has been described. Structural comparisons revealed that the overall structure of MsT1-L is very similar to that of the well-characterized biosynthetic thiolase form Z. ramigera. However, a detailed analysis of the ordered waters near the active site cavity revealed interesting differences between the two. The probable functional relevance of this observation has been discussed. The crystal structure of MsT1-L complexed with CoA has also been described in detail. Structural comparisons with classical thiolases also revealed significant differences in the organization of the loop domain that harbors most of the residues required for catalysis. These differences cause the active site cavity of MsT1-L to be larger than that of biosynthetic thiolase suggesting that MsT1-L thiolase could probably bind larger substrates. This cavity is large enough to accommodate a medium chain length fatty acyl CoA as substrate. Co-crystallization experiments with hexanoyl CoA revealed a novel binding site for the fatty acyl chain in MsT1-L and this has been described in detail. Contributions made towards the cloning and expression of other thiolases from S. typhimurium and P. falciparum have been described in Chapters 6 and 7. The thesis concludes with a brief discussion on the future prospects of the investigations presented here.

The thesis describes structural and functional studies of two PLP-dependent enzymes, diaminopropionate (DAP) ammonia lyase (DAPAL) and N-acetylornithine aminotransferase (AcOAT). The main objective of this work was to understand the structural features that control and impart specificity for PLP-dependent catalysis. DAPAL is a prokaryotic enzyme that catalyzes the degradation of D and L forms of DAP to pyruvate and ammonia. The first crystal structure of DAPAL was determined from Escherichia coli (EcDAPAL) in holo and apo forms, and in complex with various ligands. The structure with a transient reaction intermediate (aminoacrylate-PLP azomethine) bound at the active site was obtained from crystals soaked with substrate, DL-DAP. Apo and holo structures revealed that the region around the active site undergoes transition from disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. Based on the crystal structures and biochemical studies, as well as studies on active site mutant enzymes, a two base mechanism of catalysis involving Asp120 and Lys77 is suggested. AcOAT is an enzyme of arginine biosynthesis pathway that catalyses the reversible conversion of N-acetylglutamate semialdehyde and glutamate to N-acetyl ornithine and α-ketoglutarate. It belongs to subgroup III of fold type I PLP dependent enzymes. Many clinically important aminotransferases belong to the same subgroup and share many structural similarities. We have carried out extensive comparative analysis of these enzymes to identify the unique features important for substrate specificity. Crystal structures of AcOAT from Salmonella typhimurium were determined in presence of two ligands, canaline and gabaculine, which are known to act as general inhibitors for most of the enzymes of this class. There structures provided important insights into the mode of binding of the substrates. The structures illustrated the switching of conformation of an active site glutamate side chain on binding of the two substrates. In addition to that, structural transitions involving three loop regions near the active site were observed in different ligand bound structures. Kinetics of single turnover fast reactions and multiple turnover steady state reactions indicated that N-AcOAT dimer might follow a mechanism involving sequential half site reactivity for efficient catalysis. The changes observed in loop conformation that resulted in asymmetric forms of the dimer enzyme might form the structural basis for half site reactivity. Single site mutants were designed to understand the significance of these structural transitions and the specific role of active site residues in determining substrate specificity and catalysis. Biochemical characterization of wild type and mutant enzymes by steady state and fast kinetic studies, along with their crystal structures provided detailed insights into subtlety of active site features that manifest substrate specificity and catalytic activity. The thesis also describes the investigations on fold type II enzymes directed towards analyses of polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance. Contributions made towards structural and functional studies of three other PLP-dependent enzymes, serine hydoxymethyltransferase (SHMT), D-serine deaminase (DSD) and D-cysteine desulfhydrase (DCyD) are described in an appendix.

Salmonella enterica subtype Typhimurium (S. Typhimurium) is one of many non-typhoidal Salmonella enterica strains responsible for over one million cases of salmonellosis in the United States each year. These Salmonella strains are also a leading cause of diarrheal disease in developing countries. Nontyphoidal salmonellosis induces gastrointestinal distress that is characterized histopathologically by an influx of polymorphonuclear leukocytes (PMNs), the non-specific effects of which lead to tissue damage and contribute to diarrhea. Prior studies from our lab have demonstrated that the type III secreted bacterial effector SipA is a key regulator of PMN influx during S. Typhimurium infection and that its activity requires processing by caspase-3. Although we established caspase-3 activity is required for the activation of inflammatory pathways during S. Typhimurium infection, the mechanisms by which caspase-3 is activated remain incompletely understood. Most challenging is the fact that SipA is responsible for activating caspase-3, which begs the question of how SipA can activate an enzyme it requires for its own activity. In the present study, we describe our findings that the eukaryotic tetraspanning membrane protein PERP is required for the S. Typhimuriuminduced influx of PMNs. We further show that S. Typhimurium infection induces PERP accumulation at the apical surface of polarized colonic epithelial cells, and that this accumulation requires SipA. Strikingly, PERP accumulation occurs in the absence of caspase-3 processing of SipA, which is the first time we have shown SipA mediates a cellular event without first requiring caspase-3 processing. Previous work demonstrates that PERP mediates the activation of caspase-3, and we find that PERP is required for Salmonella-induced caspase-3 activation. Our combined data support a model in which SipA triggers caspase-3 activation via its cellular modulation of PERP. Since SipA can set this pathway in motion without being cleaved by caspase-3, we propose that PERP-mediated caspase-3 activation is required for the activation of SipA, and thus is a key step in the inflammatory response to S. Typhimurium infection. Our findings further our understanding of how SipA induces inflammation during S. Typhimurium infection, and also provide additional insight into how type III secreted effectors manipulate host cells.

No description available.

<p>Unsafe food is responsible for causing more than 600 million cases of foodborne illnesses and 420,000 deaths each year. These foodborne illnesses have direct impact on growth and development in children, food and nutrition security, national economies, and sustainable development. Food manufactures, research institutions, governments, and consumers, together, play a pivotal role in establishing and implementing effective food safety systems. <em>Salmonella</em> spp. and <em>Listeria monocytogenes</em> are recognized as major threats to global food safety and security among other 31 known and unknown pathogens associated with foodborne illnesses and deaths. Since these pathogens can be transmitted through contaminated food and water, contaminated environmental surfaces, and subsequently from environment to food via cross-contamination, there is an urgent need for data-driven approaches to identify key points of contamination along the food systems to suggest interventions. While it is important to enhance food safety research in developed economies, developing capacity to enable conditions for food safety research translation and practice in developing economies is crucial for global food safety. In this dissertation, we presented three different research projects as summarized below-</p> <p>In Chapter 2 “Evaluating the efficacy of celery powder in ready-to-eat deli style turkey breast against <em>L. monocytogenes</em> under ideal and temperature abuse conditions”. In this study, we artificially inoculated “clean label” deli style turkey breast formulated with celery powder to evaluate the efficacy of this natural antimicrobial in inhibiting the growth of this pathogen. We stored the inoculated samples at ideal (4 °C) and abuse temperature conditions (7 °C, 10 °C, and 15 °C) for 21 d mimicking the possible temperature abuse along the cold chain, transportation, and at consumer refrigerator. Our findings indicated that although deli meat samples stored at 4 °C and 7 °C did not achieve significant growth of <em>L. monocytogenes;</em> increasing temperatures to 10 °C and 15 °C led to significant increase in the growth rate of this pathogen. This study evaluates the use and effectiveness of celery powder as an antimicrobial used by deli meat processors against <em>L. monocytogenes</em> in deli products. These data underscore the importance of maintaining refrigeration temperatures to complement the efficacy of antimicrobials. </p> <p>Chapter 3 “Investigating sanitary solutions to <em>L. monocytogenes, Salmonella enterica</em> ser. Typhimurium, and <em>Pseudomonas aeruginosa</em> dry surface biofilms”. In this study, we developed <em>in vitro</em> mono- and mix-culture dry surface biofilm (DSB) models of <em>L. monocytogenes, Salmonella enterica</em> ser. Typhimurium, and <em>Pseudomonas aeruginosa</em> leveraging the EPA MLB SOP MB-19 standard protocol using the CDC Biofilm Reactor and evaluated sanitation control strategies currently adopted by low-moisture food (LMF) food processors to determine their ability to inactive DSB, a decidedly difficult reservoir to eliminate. This study targets multiple biological hazards in a research area with very limited publicly available data and is the first of its kind to refine mono- and multi-species <em>in vitro</em> DSB models that mimic LMF facility conditions and combinations of relevant microorganisms for use cases (e.g., EPA adoption). The findings from this study indicated that these foodborne pathogens could form DSBs and serve as a source of pathogen reservoir and cross-contamination. Results from the efficacy testing of sanitizer and microfiber swabbing suggested that current sanitation practices may not be sufficient to remove or inactivate DSBs. This study will define future needs and new strategies to improve confidence in sanitation efficacy with private sector practitioners.</p> <p>Chapter 4 “Enhancing research for development opportunities for Minority Serving Institutions: a case study in food safety”. Most developing economies have limited viable food safety systems due to underdeveloped research capabilities, competing resource demands, and insufficient enabling conditions, which undermines food security. United States Minority Serving Institution (MSIs) researchers and outreach specialists are familiar with and arguably best positioned to address global food safety and security challenges and needs, but MSIs implement limited research for development programs (e.g., U.S. university-led Feed the Future (FTF) Innovation Labs (ILs) funded by the United States Agency for International Development (USAID)) aimed to solve these challenges. Recognizing this opportunity, the Feed the Future Innovation Lab for Food Safety (FSIL) led by Purdue University in partnership with Cornell University, created and implemented an MSI-led research partnerships for global food safety research programs. In this chapter, we put together the process of a three-stage Request for Applications (RFA) process, which included non-competitive and competitive stages to encourage partnership and to refine ideas.  At the end of this process, seven individuals were invited to submit full proposals; two were funded. Intentional research opportunities and partnerships are essential to strengthen MSI competitiveness for research for development programs that develop and scale technologies to address urgent global agriculture, food security, and safety challenges.</p>

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La creciente demanda de alimentos con características lo más parecidas al producto fresco, está impulsando el desarrollo de nuevas tecnologías "no térmicas" de conservación. Dentro de las más prometedoras se encuentran el tratamiento por Pulsos Eléctricos de Alta Intensidad (PEF) y la tecnología de Altas Presiones Hidrostáticas (HHP). Estas tecnologías permiten conservar, en mayor medida que los tratamientos térmicos, la calidad (sabor, aroma, color y vitaminas) de determinados alimentos frescos e inactivar microorganismos y enzimas, incrementando su vida útil en refrigeración y facilitando su comercialización. El objetivo general de la presente tesis doctoral ha sido estudiar la posibilidad de procesar por PEF y HHP solos o combinados con calor de una nueva bebida mezcla de zumo de naranja y leche incluyendo aspectos microbiológicos y de calidad. El plan de trabajo comenzó con la elaboración y caracterización físico-química y sensorial del nuevo producto eligiendo la formulación adecuada para desarrollar los estudios cinéticos y de vida útil. Los parámetros de calidad más importantes en los zumos de fruta son la actividad enzimática y el contenido en aroma (concentración de compuestos volátiles). En el caso del zumo de naranja la pectin metil esterasa (PME) es una de las enzimas de mayor importancia. Se evaluó el efecto del tratamiento por PEF, HHP y calor en la inactivación de PME. Todas las tecnologías estudiadas lograron un nivel de inactivación enzimática del 90%. Se observó la aparición de dos fracciones con diferente resistencia al tratamiento, por ello, el modelo bifásico fue el que mejor describió las curvas de inactivación de PME mediante tratamiento combinado de HHP y calor en el producto. Posteriormente se estudió la variación en el contenido en aroma (concentración de compuestos volátiles) tras el tratamiento de HHP, PEF y calor en el producto siendo la tecnología por PEF la que mejor preservó el aroma original del producto fresco. Una vez establecidos / Sampedro Parra, F. (2008). Impacto del tratamiento por pulsos eléctricos de alta intensidad y altas presiones hidrostáticas sobre la calidad y seguridad microbiológica de un alimento mezcla de zumo de naranja y leche [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/1992

MSc (Microbiology) / Department of Microbiology / See the attached abstract below