A tuberculose é uma doença crônica granulomatosa caracterizada por um déficit de imunidade antígeno específica do hospedeiro, cuja resposta imune é ativamente regulada por citocinas. No Brasil há mais de 50 milhões de habitantes infectados pelo Mycobacterium tuberculosis. O objetivo foi avaliar a linfoproliferação e a produção de citocinas por células mononucleares do sangue periférico (PBMC) estimuladas por quatro diferentes antígenos do M. tuberculosis, um complexo, o antígeno sonicado, e três purificados, ESAT-6, antígeno 85B e antígeno HBHA, eventuais candidatos à vacina anti-tuberculose. Para avaliação da produção de IFN-g e IL-10 foram utilizados dois métodos: Elispot e Elisa à partir de sobrenadante de cultura de PBMC. Para essas avaliações, os pacientes com tuberculose ativa (TB-A) foram comparados a dois subgrupos de indivíduos controles. O primeiro subgrupo foi constituído por indivíduos saudáveis PPD+ e o segundo por indivíduos curados de um episódio de tuberculose (TB-C). Nossos resultados de linfoproliferação e de Elisa revelaram diminuição da resposta linfoproliferativa e da produção de IFN-g dos pacientes em comparação com os indivíduos PPD+, enquanto os indivíduos TB-C apresentaram em geral resultados intermediários. Observou-se também que as respostas à PHA não diferiam significativamente entre os grupos, ressaltando a natureza antígeno específica da hiporreatividade na tuberculose. Adicionalmente, verificamos maior reatividade ao antígeno complexo, sonicado, que aos antígenos purificados, e entre estes, a reatividade foi maior para ESAT-6 e 85B que para HBHA, A resposta ao HBHA pode ter sido eventualmente subestimada por razões técnicas, como utilização de dose sub-ótima ou perda da atividade biológica. Em relação ao Elispot para IFN-g, não pudemos observar diferenças entre os grupos, tanto quando se considerou o número total de spots, como quando se contou apenas spots com diâmetro > 65 mm, apresentando portanto uma sensibilidade aparentemente menor comparado aos outros 2 métodos. A comparação entre os métodos revelou pouca correlação entre seus resultados, que pode ser eventualmente explicado pela diferente contribuição das populações celulares (T CD4+ e T CD8+) para cada uma das provas munológicas. Finalmente, a análise da produção de IL-10 medida por Elisa no sobrenadante de cultura e por spots de IL10, também não revelou diferenças entre os grupos. Convém notar que o Elisa detectou baixas concentrações de IL-10 nos sobrenadantes, porém o Elispot demonstrou número elevado de spots e boa correlação entre as resposta aos antígenos. Em conclusão, nossos resultados sugerem que métodos \'clássicos\', e já estabelecidos, como linfoproliferação e Elisa, persistem válidos para se avaliar a imunidade celular, e que em nossas condições laboratoriais, a técnica de Elispot não representou, até o momento, uma melhora na qualidade da avaliação imunológica. / Tuberculosis is a chronic granulomatous disease characterized by a deficit of the antigen-specific immunity of the host, whose immune response is actively regulated by cytokines. In Brazil there are 50 million people infected with Mycobacterium tuberculosis. The objective of the present work was to evaluate the lymphoproliferative response e the IFN-g response by peripheral blood mononuclear cells (PBMC) indiced with 4 different antigens isolated from Mycobacterium tuberculosis: a complex, crude, the sonicate antigen, and 3 other, purified ones, Esat-6, 85B, and HBHA, the last 3 eventual candidates to the design of a vaccine against tuberculosis. We used 2 methods to evaluate the IFN-g and IL-10 productions, namely Elispot and Elisa of supernatant of PBMC cultures. We studied a group of active tuberculosis patients (TB-A), and compared them with controls individuals comprising 2 groups, one made of healthy PPD+ individuals and the second one of individuals who have been cured from an episode of tuberculosis in the past (TB-C). Our results of lymphoproliferation and Elisa revealed decrease in the lymphoproliferative and IFN-g responses by patients\' PBMC as compared to the PPD+ group, with the TB-C group in general presenting intermediate results. We also observed that the responses to the mitogen PHA were not statisically different among the groups, denoting the antigen-specific nature of the immune deficit in tuberculosis. In addition, we verified that stronger reactivity to the complex antigen than with the purified antigens, and, among the latter, the reactivity was stronger with Esat-6 and 85B as compared to HBHA, Reactivity to HBHA may have been understimated due to technical reasons, such as loss of .the biological activity of the molecule or use of a sub-optimal dose. By using the Elispot for IFN-g we were not able to detect differences among the groups, even when we counted all spots formed or spots with more than > 65 mm in diameter. Thus our Elispot for IFN-g apparently showed lower sensitivity than the other 2 methods. Furthermore, comparisons between the methods revealed low correlation between their results, a finding that may be explained by the differning contribution of different subpopulations (T CD4+ and T CD8+) to each of the results. Finally, analysis of the production of IL-10 as measured by Elisa in the culture supernatants as well as by Elispot revealed no differences among the groups. It is noteworthy that the levels of IL-10 detected by Elisa were low, but the Elispot revealed high number of spots and a good correlation between the antigen responses. In conclusion, we may say that our well standardized \'classical\' methods Elisa and lymphoproliferation persist useful to evaluate cellular immunity responses, and that the Elispot technique, up to now and in our laboratorial conditions, did not represent an improvement in the quality of the immunological evaluation.

Proteins are essential for the growth, survival and maintenance of the cell. Understanding the functional roles of proteins helps to decipher the working of macromolecular assemblies and cellular machinery of living organisms. A thorough investigation of the link between sequence, structure and function of proteins, helps in building a comprehensive understanding of the complex biological systems. Proteins have been observed to be composed of single and multiple domains. Analysis of proteins encoded in diverse genomes shows the ubiquitous nature of multi-domain proteins. Though the majority of eukaryotic proteins are multi-domain in nature, 3-D structures of only a small proportion of multi-domain proteins are known due to difficulties in crystallizing such proteins. While functions of individual domains are generally extensively studied, the complex interplay of functions of domains is not well understood for most multi-domain proteins. Paucity of structural and functional data, affects our understanding of the evolution of structure and function of multi-domain proteins. The broad objective of this thesis is to achieve an enhanced understanding of structure and function of protein domains by computational analysis of sequence and structural data. Special attention is paid in the first few chapters of this thesis on the multi-domain proteins. Classification of multi-domain proteins by implementation of an alignment-free sequence comparison method has been achieved in Chapters 2 and 3. Studies on organization, interactions and interdependence of domain-domain interactions in multi-domain proteins with respect to sequential separation between domains and N to C-terminal domain order have been described in Chapters 4 and 5. The functional and structural repertoire of organisms can be comprehensively studied and compared using functional and structural domain annotations. Chapter 6, 7 and 8 represent the proteome-wide structure and function comparisons of various pathogenic and non-pathogenic microorganisms. These comparisons help in identifying proteins implicated in virulence of the pathogen and thus predict putative targets for disease treatment and prevention. Chapter 1 forms an introduction to the main subject area of this thesis. Starting with describing protein structure and function, details of the four levels of hierarchical organization of protein structure have been provided, along with the databases that document protein sequences and structures. Classification of protein domains considered as the realm of function, structure and evolution has been described. The usefulness of classification of proteins at the domain level has been highlighted in terms of providing an enhanced understanding of protein structure and function and also their evolutionary relatedness. The details of structure, function and evolution of multi-domain proteins have also been outlined in chapter 1. ! Chapter 2 aims to achieve a biologically meaningful classification scheme for multi-domain protein sequences. The overall function of a multi-domain protein is determined by the functional and structural interplay of its constituent domains. Traditional sequence-based methods utilize only the domain-level information to classify proteins. This does not take into account the contributions of accessory domains and linker regions towards the overall function of a multi-domain protein. An alignment-free protein sequence comparison tool, CLAP (CLAssification of Proteins) previously developed in this laboratory, was assessed and improved when the author joined the group. CLAP was developed especially to handle multi-domain protein sequences without a requirement of defining domain boundaries and sequential order of domains (domain architecture). ! The working principle of CLAP involves comparison of all against all windows of 5-residue sequence patterns between two protein sequences. The sequences compared could be full-length comprising of all the domains in the two proteins. This compilation of comparison is represented as the Local Matching Scores (LMS) between protein sequences (nslab.iisc.ernet.in/clap/). It has been previously shown that the execution time of CLAP is ~7 times faster than other protein sequence comparison methods that employ alignment of sequences. In Chapter 2, CLAP-based classification has been carried out on two test datasets of proteins containing (i) Tyrosine phosphatase domain family and (ii) SH3-domain family. The former dataset comprises both single and multi-domain proteins that sometimes consist of domain repeats of the tyrosine phosphatase domain. The latter dataset consists only of multi-domain proteins with one copy of the SH3-domain. At the domain-level CLAP-based classification scheme resulted in a clustering similar to that obtained from an alignment-based method, ClustalW. CLAP-based clusters obtained for full-length datasets were shown to comprise of proteins with similar functions and domain architectures. Hence, a protein classification scheme is shown to work efficiently that is independent of domain definitions and requires only the full-length amino acid sequences as input.! Chapter 3 explores the limitations of CLAP in large-scale protein sequence comparisons. The potential advantages of full-length protein sequence classification, combined with the availability of the alignment-free sequence comparison tool, CLAP, motivated the conceptualization of full-length sequence classification of the entire protein repertoire. Before undertaking this mammoth task, working of CLAP was tested for a large dataset of 239,461 protein sequences. Chapter 3 discusses the technical details of computation, storage and retrieval of CLAP scores for a large dataset in a feasible timeframe. CLAP scores were examined for protein pairs of same domain architecture and ~22% of these showed 0 CLAP similarity scores. This led to investigation of the sensitivity of CLAP with respect to sequence divergence. Several test datasets of proteins belonging to the same SCOP fold were constructed and CLAP-based classification of these proteins was examined at inter and intra-SCOP family level. CLAP was successful in efficiently clustering evolutionary related proteins (defined as proteins within the same SCOP superfamily) if their sequence identity >35%. At lower sequence identities, CLAP fails to recognize any evolutionary relatedness. Another test dataset consisting of two-domain proteins with domain order swapped was constructed. Domain order swap refers to domain architectures of type AB and BA, consisting of domains A and B. A condition that the sequence identities of homologous domains were greater than 35% was imposed. CLAP could effectively cluster together proteins of the same domain architectures in this case. Thus, the sequence identity threshold of 35% at the domain-level improves the accuracy of CLAP. The analysis also showed that for highly divergent sequences, the expectation of 5-residue pattern match was likely a stringent criterion. Thus, a modification in the 5-residue identical pattern match criterion, by considering even similar residue and gaps within matched patterns may be required to effectuate CLAP-based clustering of remotely related protein sequences. Thus, this study highlights the limitations of CLAP with respect to large-scale analysis and its sensitivity to sequence divergence. ! Chapters 4 and 5 discuss the computational analysis of inter-domain interactions with respect to sequential distance and domain order. Knowledge of domain composition and 3-D structures of individual domains in a multi-domain protein may not be sufficient to predict the tertiary structure of the multi-domain protein. Substantial information about the nature of domain-domain interfaces helps in prediction of the tertiary as well as the quaternary structure of a protein. Therefore, chapter 4 explores the possible relationship between the sequential distance separating two domains in a multi-domain protein and the extent of their interaction. With increasing sequential separation between any two domains, the extent of inter-domain interactions showed a gradual decrease. The trend was more apparent when sequential separation between domains is measured in terms of number of intervening domains. Irrespective of the linker length, extensive interactions were seen more often between contiguous domains than between non-contiguous domains. Contiguous domains show a broader interface area and lower proportion of non-interacting domains (interface area: 0 Å2 to - 4400 Å2, 2.3% non-interacting domains) than non-contiguous domains (interface area: 0 Å2 to - 2000 Å2, 34.7% non-interacting domains). Additionally, as inter-protein interactions are mediated through constituent domains, rules of protein-protein interactions were applied to domain-domain interactions. Tight binding between domains is denoted as putative permanent domain-domain interactions and domains that may dissociate and associate with relatively weak interactions to regulate functional activity are denoted as putative transient domain-domain interactions. An interface area threshold of 600 Å2 was utilized as a binary classifier to distinguish between putative permanent and putative transient domain-domain interactions. Therefore, the state of interaction of a domain pair is defined as either putative permanent or putative transient interaction. Contiguous domains showed a predominance of putative permanent nature of inter-domain interface, whereas non-contiguous domains showed a prevalence of putative transient interfaces. The state of interaction of various SCOP superfamily pairs was studied across different proteins in the dataset. SCOP superfamily pairs mostly showed a conserved state of interaction, i.e. either putative permanent or putative transient in all their occurrences across different proteins. Thus, it is noted that contiguous domains interact extensively more often than non-contiguous domains and specific superfamily pairs tend to interact in a conserved manner. In conclusion, a combination of interface area and other inter-domain properties along with experimental validation will help strengthen the binary classification scheme of putative permanent and transient domain-domain interactions.! Chapter 5 provides structural analysis of domain pairs occurring in different sequential domain orders in mutli-domain proteins. The function and regulation of a multi-domain protein is predominantly determined by the domain-domain interactions. These in turn are influenced by the sequential order of domains in a protein. With domains defined using evolutionary and structural relatedness (SCOP superfamily), their conservation of structure and function was studied across domain order reversal. A domain order reversal indicates different sequential orders of the concerned domains, which may be identified in proteins of same or different domain compositions. Domain order reversals of domains A and B can be indicated in protein pair consisting of the domain architectures xAxBx and xBxAx, where x indicates 0 or more domains. A total of 161 pairs of domain order reversals were identified in 77 pairs of PDB entries. For most of the comparisons between proteins with different domain composition and architecture, large differences in the relative spatial orientation of domains were observed. Although preservation of state of interaction was observed for ~75% of the comparisons, none of the inter-domain interfaces of domains in different order displayed high interface similarity. These domain order reversals in multi-domain proteins are contributed by a limited number of 15 SCOP superfamilies. Majority of the superfamilies undergoing order reversal either function as transporters or regulatory domains and very few are enzymes. A higher proportion of domain order reversals were observed in domains separated by 0 or 1 domains than those separated by more than 1 domain. A thorough analysis of various structural features of domains undergoing order reversal indicates that only one order of domains is strongly preferred over all possible orders. This may be due to either evolutionary selection of one of the orders and its conservation throughout generations, or the fact that domain order reversals rarely conserve the interface between the domains. Further studies (Chapters 6 to 8) utilize the available computational techniques for structural and functional annotation of proteins encoded in a few bacterial genomes. Based on these annotations, proteome-wide structure and function comparisons were performed between two sets of pathogenic and non-pathogenic bacteria. The first study compares the pathogenic Mycobacterium tuberculosis to the closely related organism Mycobacterium smegmatis which is non-pathogenic. The second study primarily identified biologically feasible host-pathogen interactions between the human host and the pathogen Leptospira interrogans and also compared leptospiral-host interactions of the pathogenic Leptospira interrogans and of the saprophytic Leptospira biflexa with the human host. Chapter 6 describes the function and structure annotation of proteins encoded in the genome of M. smegmatis MC2-155. M. smegmatis is a widely used model organism for understanding the pathophysiology of M. tuberculosis, the primary causative agent of tuberculosis in humans. M. smegmatis and M. tuberculosis species of the mycobacterial genus share several features like a similar cell-wall architecture, the ability to oxidise carbon monoxide aerobically and share a huge number of homologues. These features render M. smegmatis particularly useful in identifying critical cellular pathways of M. tuberculosis to inhibit its growth in the human host. In spite of the similarities between M. smegmatis and M. tuberculosis, there are stark differences between the two due to their diverse niche and lifestyle. While there are innumerable studies reporting the structure, function and interaction properties of M. tuberculosis proteins, there is a lack of high quality annotation of M. smegmatis proteins. This makes the understanding of the biology of M. smegmatis extremely important for investigating its competence as a good model organism for M. tuberculosis. With the implementation of available sequence and structural profile-based search procedures, functional and structural characterization could be achieved for ~92% of the M. smegmatis proteome. Structural and functional domain definitions were obtained for a total of 5695 of 6717 proteins in M. smegmatis. Residue coverage >70% was achieved for 4567 proteins, which constitute ~68% of the proteome. Domain unassigned regions more than 30 residues were assessed for their potential to be associated to a domain. For 1022 proteins with no recognizable domains, putative structural and functional information was inferred for 328 proteins by the use of distance relationship detection and fold recognition methods. Although 916 sequences of 1022 proteins with no recognizable domains were found to be specific to M. smegmatis species, 98 of these are specific to its MC2-155 strain. Of the 1828 M. smegmatis proteins classified as conserved hypothetical proteins, 1038 proteins were successfully characterized. A total of 33 Domains of Unknown Function (DUFs) occurring in M. smegmatis could be associated to structural domains. A high representation of the tetR and GntR family of transcription regulators was noted in the functional repertoire of M. smegmatis proteome. As M. smegmatis is a soil-dwelling bacterium, transcriptional regulators are crucial for helping it to adapt and survive the environmental stress. Similarly, the ABC transporter and MFS domain families are highly represented in the M. smegmatis proteome. These are important in enabling the bacteria to uptake carbohydrate from diverse environmental sources. A lower number of virulent proteins were identified in M. smegmatis, which justifies its non-pathogenicity. Thus, a detailed functional and structural annotation of the M. smegmatis proteome was achieved in Chapter 6. Chapter 7 delineates the similarities and difference in the structure and function of proteins encoded in the genomes of the pathogenic M. tuberculosis and the non-pathogenic M. smegmatis. The protocol employed in Chapter 6 to achieve the proteome-wide structure and function annotation of M. smegmatis was also applied to M. tuberculosis proteome in Chapter 7. The number of proteins encoded by the genome of M. smegmatis strain MC2-155 (6717 proteins) is comparatively higher than that in M. tuberculosis strain H37Rv (4018 proteins). A total of 2720 high confidence orthologues sharing ≥30% sequence identity were identified in M. tuberculosis with respect to M. smegmatis. Based on the orthologue information, specific functional clusters, essential proteins, metabolic pathways, transporters and toxin-antitoxin systems of M. tuberculosis were inspected for conservation in M. smegmatis. Among the several categories analysed, 53 metabolic pathways, 44 membrane transporter proteins belonging to secondary transporters and ATP-dependent transporter classes, 73 toxin-antitoxin systems, 23 M. tuberculosis-specific targets, 10 broad-spectrum targets and 34 targets implicated in persistence of M. tuberculosis could not detect any orthologues in M. smegmatis. Several of the MFS superfamily transporters act as drug efflux pumps and are hence associated with drug resistance in M. tuberculosis. The relative abundances of MFS and ABC superfamily transporters are higher in M. smegmatis than in M. tuberculosis. As these transporters are involved in carbohydrate uptake, their higher representation in M. smegmatis than in M. tuberculosis highlights the lack of proficiency of M. tuberculosis to assimilate diverse carbon sources. In the case of porins, MspA-like and OmpA-like porins are selectively present in either M. smegmatis or M. tuberculosis. These differences help to elucidate protein clusters for which M. smegmatis may not be the best model organism to study M. tuberculosis proteins.! At the domain-level, ATP-binding domain of ABC transporters, tetracycline transcriptional regulator (tetR) domain family, major facilitator superfamily (MFS) domain family, AMP-binding domain family and enoyl-CoA hydrolase domain family are highly represented in both M. smegmatis and M. tuberculosis proteomes. These domains play an essential role in the carbohydrate uptake systems and drug-efflux pumps among other diverse functions in mycobacteria. There are several differentially represented domain families in M. tuberculosis and M. smegmatis. For example, the pentapeptide-repeat domain, PE, PPE and PIN domains although abundantly present in M. tuberculosis, are very rare in M. smegmatis. Therefore, such uniquely or differentially represented functional and structural domains in M. tuberculosis as compared to M. smegmatis may be linked to pathogenicity or adaptation of M. tuberculosis in the host. Hence, major differences between M. tuberculosis and M. smegmatis were identified, not only in terms of domain populations but also in terms of domain combinations. Thus, Chapter 7 highlights the similarities and differences between M. smegmatis and M. tuberculosis proteomes in terms of structure and function. These differences provide an understanding of selective utilization of M. smegmatis as a model organism to study M. tuberculosis. ! In Chapter 8, computational tools have been employed to predict biologically feasible host-pathogen interactions between the human host and the pathogenic, Leptospira interrogans. Sensitive profile-based search procedures were used to specifically identify practical drug targets in the genome of Leptospira interrogans, the causative agent of the globally widespread zoonotic disease, Leptospirosis. Traditionally, the genus Leptospira is classified into two species complex- the pathogenic L. interrogans and the non-pathogenic saprophyte L. biflexa. The pathogen gains entry into the human host through direct or indirect contact with fluids of infected animals. Several ambiguities exist in the understanding of L. interrogans pathogenesis. An integration of multiple computational approaches guided by experimentally derived protein-protein interactions, was utilized for recognition of host-pathogen protein-protein interactions. The initial step involved the identification of similarities of host and L. interrogans proteins with crystal structures of experimentally known transient protein-protein complexes. Further, conservation of interfacial nature was used to obtain high confidence predictions for putative host-pathogen protein-protein interactions. These predictions were subjected to further selection based on subcellular localization of proteins of the human host and L. interrogans, and tissue-specific expression profiles of the host proteins. A total of 49 protein-protein interactions mediated by 24 L. interrogans proteins and 17 host proteins were identified and these may be subjected to further experimental investigations to assess their in vivo relevance. The functional relevance of similarities and differences between the pathogenic and non-pathogenic leptospires in terms of interactions with the host has also been explored. For this, protein-protein interactions across human host and the non-pathogenic saprophyte L. biflexa were also predicted. Nearly 39 leptospiral-host interactions were recognized to be similar across both the pathogen and saprophyte in the context of processes that influence the host. The overlapping leptospiral-host interactions of L. interrogans and L. biflexa proteins with the human host proteins are primarily associated with establishment of its entry into the human host. These include adhesion of the leptospiral proteins to host cells, survival in host environment such as iron acquisition and binding to components of extracellular matrix and plasma. The disjoint sets of leptospiral-host interactions are species-specific interactions, more importantly indicative of the establishment of infection by L. interrogans in the human host and immune clearance of L. biflexa by the human host. With respect to L. interrogans, these specific interactions include interference with blood coagulation cascade and dissemination to target organs by means of disruption of cell junction assembly. On the other hand, species-specific interactions of L. biflexa proteins include those with components of host immune system. ! In spite of the limited availability of experimental evidence, these help in identifying functionally relevant interactions between host and pathogen by integrating multiple lines of evidence. Thus, inferences from computational prediction of host-pathogen interactions act as guidelines for experimental studies investigating the in vivo relevance of these predicted protein-protein interactions. This will further help in developing effective measures for treatment and disease prevention. In summary, Chapters 2 and 3 describe the implementation, advantages and limitations of the alignment-free full-length sequence comparison method, CLAP. Chapter 4 and 5 are dedicated to understand the domain-domain interactions in multi-domain protein sequences and structures. In Chapters 6, 7 and 8 the computational analyses of the mycobacterial species and leptospiral species helped in an enhanced understanding of the functional repertoire of these bacteria. These studies were undertaken by utilizing the biological sequence data available in public databases and implementation of powerful homology-detection techniques. The supplemental data associated with the chapters is provided in a compact disc attached with this thesis.!

Base teórica: A introdução de agentes biológicos, especialmente os bloqueadores do fator de necrose tumoral (anti-TNF), para o tratamento de doenças reumáticas aumentou o risco de desenvolver tuberculose (TB). O rastreio para infecção tuberculosa latente (ILTB) é fortemente recomendado antes de iniciar a terapia com agentes anti-TNF. Os objetivos deste estudo foram identificar a prevalência de ILTB e TB entre pacientes com doenças reumáticas em uso dos medicamentos anti-TNF. Métodos: Estudo transversal. Foram revisados os registros médicos eletrónicos de todos os doentes adultos (≥ 18 anos) em uso da terapia anti-TNF. Todos os pacientes foram submetidos ao teste tuberculínico (TT) antes de iniciar o tratamento com os medicamentos anti-TNF. Resultados: No total, 176 pacientes foram incluídos no estudo. A idade média de todos os pacientes foi de 51,9 ± 12,4 anos, 34,7% eram do sexo masculino e 90,9% eram brancos. As doenças subjacentes mais comuns foram: Artite Reumatóide (AR) em 89 pacientes (50,6%), Espondilite Anquilosante (EA) em 49 (27,8%) e Artrite Psoriática (AP) em 31 (17,6%). A prevalência de TT positivo foi de 29,5%. O contato domiciliar com TB foi significativamente associado com TT positivo (p = 0,020). Os pacientes com AR apresentaram reações TT menores do que os pacientes com EA (p = 0,022). Houve seis casos de TB (3,4%) diagnosticados durante a terapia anti-TNF. Conclusões: Demonstrou-se alta prevalência de TT positivo (29,5%) em pacientes com doenças reumáticas em uma região com alta prevalência de TB. Nossos dados corroboram a recomendação do Colégio Americano de Reumatologia (ACR) de que os pacientes que vivem em configurações de alta incidência de TB devem ser testados anualmente para ILTB. / Background: The introduction of biological agents, especially the blockers of tumor necrosis factor (anti-TNF), for the treatment of rheumatic diseases increased the risk of developing tuberculosis (TB). Screening for latent TB infection (LTBI|) is strongly recommended before starting therapy with anti-TNF agents. The objectives of this study were to identify the prevalence of LTBI and TB among patients with rheumatic diseases on anti-TNF drugs. Methods: Cross-sectional study. The electronic medical records of all adult patients (≥ 18 years old) undergoing anti-TNF treatment were reviewed. Every patient underwent TST test before starting anti-TNF treatment. Results: In total, 176 patients were included in the study. The mean age of all patients was 51.9 ± 12.4 years, 34.7% were males, and 90.9% were white. The most common underlying diseases were: RA in 89 patients (50.6%), AS in 49 (27.8%), and PA in 31 (17.6%). The prevalence of positive TST was 29.5%. Household contact with TB was significantly associated with a positive TST (p=0.020). RA patients had lower TST reactions than AS patients (p=0.022). There were six cases of TB (3.4%) diagnosed during anti-TNF therapy. Conclusions: We demonstrated a high prevalence of positive TST (29.5%) among patients with rheumatic diseases in a region with high TB prevalence. Our data corroborates the ACR’s recommendation that patients who live in high TB incidence settings should be tested annually for LTBI.

A tuberculose continua sendo um grave problema de saúde pública mundial. O principal agente etiológico da doença é o Mycobacterium tuberculosis, infectando entre outras células, os macrófagos. A infecção pode manter-se latente por vários anos sem causar sintomas clínicos aparentes. Para esta pesquisa, foi proposto o estudo de indução de marcadores de resposta inflamatória em células THP-1 diferenciadas em macrófagos utilizando isolados micobacterianos sensíveis, uni ou multidrogas resistentes transfectados com o plasmídeo pFPCAGFP carreando o gene da proteína verde fluorescente, como marcador de infecção celular. Objetivou também avaliar a relação entre isolados clínicos de M.tuberculosis sensíveis ou com resistência a uma ou multidrogas e sua relação à virulência. Para isso, culturas da linhagem monocítica humana (THP-1) foram mantidas para posterior infecção por isolados clínicos, genotipicamente identificados pertencentes à nossa micobacterioteca. A expressão do RNAm foi quantificada e avaliada por RTPCR e posteriormente, PCR em tempo real foi realizado. Após infecção das células THP-1 diferenciadas em macrófagos, observou-se que houve um aumento na expressão das citocinas pró-inflamatórias (IL-1β, IL-6 e TNF-α) e TLRs (TLR2 e TLR4) em relação ao controle da infecção. As análises estatísticas permitiram a correlação na expressão destas citocinas e TLRs, e através desses resultados, foi possível constatar que TLR2 regula a expressão das citocinas pró-inflamatórias (IL-1β, IL-6 e TNF-α) e que os Isolados clínicos com maior resistência, sinalizam melhor a expressão das citocinas próinflamatórias e TLRs, ao passo que isolados clínicos sensíveis, possuem uma fraca sinalização. / Tuberculosis is the major causative of death and morbidity and still is a serious problem to the health in the world. Mycobacterium tuberculosis is the major causative agent of tuberculosis disease, infecting cells like macrophages. The infection can keep dormant for several years without any clinical symptoms. For this research, the study was proposed for induction of markers of inflammatory response in cells differentiated THP-1 in macrophages by clinical isolates from sensitive or multidrug resistant mycobacteria caring pFPCAGFP plasmid that contains green fluorescent protein gene, a marker of infection cell. Also objective assesses the relationship between clinical isolates of sensitive or with resistance to one or four drugs M.tuberculosis and its relationship to virulence. For this, cultures of monocitic lineage human (THP-1) were kept for subsequent infection by clinical isolates, genotypically identified belonging to our mycobacterioteca. The expression of mRNA was quantified and evaluated by RT-PCR and subsequently, real-time PCR was performed. After infection of the THP-1 differentiated cells in macrophages, it was observed that there was an increase expression of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and TLRs (TLR2 and TLR4) compared to infection control. Statistical analyses allowed expression correlation of these cytokines and TLRs, and through those results, it was possible to see that TLR2 regulates pro-inflammatory cytokines (IL-1β , IL-6 and TNF-α) expression and those clinical isolates with four resistance have better signal of pro-inflammatory cytokines and TLRs expression, while sensitive clinical isolates, has a weak signal.

O objetivo desse trabalho foi construir o fago recombinante D29::gfp e testar a sua utilização como um agente revelador da viabilidade bacilar na determinação da concentração inibitória mínima (GIM) aos principais fármacos administrados no tratamento da tuberculose. O fago recombinante contém o promotor hsp70 e o gene da proteína verde fluorescente (gfp) e foi construído através da restrição pela Spe I em uma região intergênica próxima a extremidade coesiva direita no genoma do fago D29. O promotor hsp70 e gfp clonados no pYL GFP foram amplificados pela PCR utilizando iniciadores com sítios para Spe I. O DNA do fago D29 digerido pela Spe I foi ligado com o fragmento hsp 70- gfp empregando a T 4 DNA ligase e os produtos da reação de ligação foram transformados de acordo com o protocolo de encapsulamento. A infecção do M.smegmatis com esse fago recombinante induziu a expressão da proteína verde fluorescente (GFP). Para avaliar o uso do fago recombinante em teste de sensibilidade aos fármacos anti-tuberculose, 100 isolados clínicos foram testados quanto ao perfil de sensibilidade a isoniazida (H), rifampicina (R), estreptomicina (S) e etambutol (E), utilizando o método das proporções em Lowenstein-Jensen (L-J), técnica em microplaca com a resazurina (REMA) e técnica em microplaca com D29::gfp. Os resultados do REMA demonstraram que 30 isolados clínicos foram sensíveis à H e 58 (66 %) isolados clínicos foram resistentes, dentre os quais a CIM foi 1 µg/mL ou maior para 41 (71 %). A CIM da R para 49 (56%) dos isolados clínicos resistentes foi de 0,5 µg/mL para 17 (35%). A CIM da S para 33 (37%) dos isolados clínicos resistentes foi de 2 µg/mL para 13 (40%) e CIM do E para 34 (39%) dos isolados clínicos resistentes foi de 16 µg/mL ou maior para 19 (56%). A caracterização molecular pela PCR IS6110 identificou 88 isolados clínicos como M.tuberculosis e pelo PRA hsp65, sete isolados clínicos foram M.kansasii, quatro foram M.abscessus e um M.szulgai. Após empregar o fago recombinante como um agente indicador da viabilidade bacilar para testar a atividade dos fármacos anti-tuberculose conclui-se que a expressão da proteína verde fluorescente foi inespecífica e não reprodutiva, não justificando o seu uso para determinar a CIM para os principais fármacos administrados no tratamento da tuberculose. / The objective of this work was to construct the recombinant phage D29::gfp and to use this phage as an indicator agent of cell viability in a minimal inhibitory concentration (MIC) assay for the mains drugs used for tuberculosis treatment. The recombinant phage contains the mycobacteria-specific hsp70 promoter controlling the green fluorescent protein gene (gfp) and was constructed by Spe I restriction in the intergenic region next to the right cohesive termini of the D29 phage genome. An hsp 70 promoter and gfp previously cloned in p YL GFP was amplified by PCR using primers with Spe I sites. The Spe I-restricted D29 phage DNA was ligated with the hsp 70-gfp fragment using T4 DNA ligase and ligated product was transformed using the packing protocol. Infection of M.smegmatis with this recombinant phage indicated the expression of green f1uorescent protein (GFP). To use the recombinant phage for assaying the activity of anti-TB drugs, 100 clinical isolates was tested for susceptibility to isoniazid (H), rifampicin (R), streptomycin (S), and ethambutol (E) using both the proportion method on Lowenstein-Jensen (L-J) medium, resazurin microtiter assay plate (REMA), as well as a microplate assay using D29::gfp. The REMA plate method showed that 30 clinical isolates were susceptible to H and 58 (66%) clinical isolates were resistant, where the MICs were 1 µg/mL or higher for 41 (71%). The R MICs for 49 (56%) resistant clinical isolates were 0,5 µg/mL for 17 (35%). The S MICs for 33 (37%) resistant clinical isolates were 2 µg/mL for 13 (40%) and E MICs for 34 (39%) resistant clinical isolates were 16 µg/mL or higher for 19 (56%). Molecular characterization by PCR IS6110 showed that 88 clinical isolates were M.tuberculosis and by PRA hsp65 were seven clinical isolates were M.kansasii and four was M.abscessus, and one M.zulgai. After using the recombinant phage as an indicator agent of cell viability for assaying the activitity of anti-TB drugs we can conclude that the expression of green fluorescent protein was non-specific and not reproducible, rendering it not useful for the determination of the MIC of the principal drugs used for the treatment of tb.

La tuberculose (TB), provoquée par Mycobacterium tuberculosis, est une des trois maladies prioritaires dans le monde. Les TB multi-résistantes (MDR) et ultra-résistantes (XDR-TB) représentent des obstacles majeurs pour la lutte antituberculeuse. Dans les pays à MDR-TB élevée, comme le Vietnam, la détection insuffisante de la résistance aux antibiotiques est un des facteurs principaux qui favorisent la transmission des souches résistantes. De plus, dans ces pays, encore très peu de choses sont connues sur la résistance à la pyrazinamide et aux antibiotiques de seconde ligne et sur les déterminants génétiques liés à ces résistances. Dans ce contexte, ce travail vise donc à acquérir des connaissances sur la résistance aux antibiotiques au Vietnam et à étudier comment M. tuberculosis évolue de l’état sensible à l’état ultra-résistant.260 isolats cliniques collectés au Vietnam entre 2005 et 2009 ont été inclus. Diverses techniques et analyses ont été utilisées: tests de sensibilité aux médicaments (développement d'un test à temps réduit), spoligotypage et MIRU-VNTR (24 loci) et séquençage de gènes. Les données ont été analysées par des analyses statistiques et phylogénétiques. Ce travail s’est d’abord focalisé sur la caractérisation d’isolats hautement résistants et sur la résistance à la pyrazinamide. Une forte proportion d'isolats quadruple résistants aux antibiotiques de première ligne a été identifiée comme pré-XDR et XDR et en majorité appartenant à la famille Beijing. L'analyse moléculaire a également révélé une forte proportion d'isolats, en particulier MDR, quadruple résistants et de la famille Beijing, portant des mutations associées à la résistance à la pyrazinamide.L'analyse génétique et phylogénétique globale a ensuite montré une grande diversité de profils de mutations dans chaque famille et chaque cluster MIRU-VNTR. Ces données suggèrent que M. tuberculosis peut suivre des chemins évolutifs variés pour devenir ultra-résistant. La prédominance de mutations et de combinaisons de mutations associées à un haut niveau de résistance et à un faible coût en termes de fitness suggère un effet cumulatif des mutations et un rôle de l’épistasie dans l'acquisition de la résistance multiple. De plus, une fréquence élevée de mutations compensatoires associées à la résistance à la rifampicine a été détectée chez les isolats très résistants. Ces processus semblent donc influencer fortement l'évolution de la résistance dans notre échantillon. Il est à noter que les mutations liées à des niveaux de résistance élevée et à de faibles coûts en termes de fitness, ainsi que les mutations compensatoires étaient plus particulièrement associées à la famille Beijing.En conclusion, ce travail fournit des connaissances uniques sur la résistance aux antibiotiques chez M. tuberculosis au Vietnam. En particulier, ces données prédisent une évolution de la résistance vers une situation de plus en plus préoccupante. Premièrement, la famille Beijing, en cours d’invasion au Vietnam, apparaît associée à de hauts niveaux de résistance, de faible coût en termes de fitness et aux mutations compensatoires. Deuxièmement, le risque élevé de résistance à la pyrazinamide remet en question son efficacité et son utilisation dans les traitements contre la MDR et la XDR-TB. Troisièmement, les données suggèrent une évolution de M. tuberculosis vers un potentiel de résistance plus élevé par effet cumulatif des mutations associés à la résistance et l’existence de phénomènes d’épistasie. Comme les échantillons étudiés dans ce travail ont été collectés, l’étape suivante est de valider nos hypothèses sur des données actualisées.Enfin, ce travail avec les données déjà publiées a permis d’établir, pour la première fois, un inventaire des mutations associées à la résistance aux antibiotiques chez M. tuberculosis au Vietnam. Cette base de données sera utilisée pour le développement d'une puce à ADN pour la détection rapide de la résistance aux antibiotiques au Vietnam. / Tuberculosis (TB) is one of the deadliest infectious diseases worldwide, mainly caused by Mycobacterium tuberculosis. Multidrug resistant (MDR) and extensively drug resistant (XDR) TB are currently main challenges for TB control. In high MDR-TB burden countries like Vietnam, one of the main factors of drug resistant strain spread is the insufficient capacity of drug resistance detection. Besides, still little is known in these countries about the resistance to second line and pyrazinamide drugs (key drugs in the MDR-TB treatment) and the genetic determinants linked to these resistances. In this context, this work aimed to acquire knowledge on drug resistance in Vietnam and to understand how M. tuberculosis evolved from sensitive to highly drug resistance form by molecular analysis.260 clinical isolates collected in Vietnam between 2005 and 2009 were included. Various techniques and analyses were used: drug susceptibility testing (development of a test with a reduced turn-around time), spoligotyping and 24-MIRU-VNTR typing and gene sequencing. The data were analyzed by statistical and phylogenetic analyses.First, this work was focused on highly drug resistant M. tuberculosis clinical isolates and pyrazinamide resistance. A high proportion of quadruple first-line drug resistant isolates (resistant to isoniazid, rifampicin, streptomycin and ethambutol) have been characterized as pre-XDR and XDR isolates, belonging especially to Beijing family. The molecular analysis revealed also high proportion of drug resistant isolates carrying highly confident pyrazinamide resistance-associated mutations, particularly in MDR and quadruple resistant isolates and in Beijing family.Second, the genetic and phylogenetic analyses showed high diversity of mutation patterns within each family and each MIRU-VNTR cluster suggesting various evolutionary trajectories towards first and second-line drug resistance. The predominance of specific mutations and combinations of mutations associated with high level of resistance and low fitness cost suggests a cumulative effect of mutations and a role for epistasis in multiple-drug resistance acquisition. In addition, high frequency of fitness-compensatory mutations associated with rifampicin resistant mutations was detected in highly drug resistant isolates. These processes may drive the evolution of drug resistance in this sample and lead to a successful spread of highly drug resistant strains. It is worth noting that Beijing family was specifically linked to high-level drug resistance and low fitness cost mutations and to compensatory mutations.In conclusion, this work provides knowledge on the resistance to the first and second-line anti-TB drugs in clinical M. tuberculosis samples collected in Vietnam between 2005 and 2009. These data predict an evolution towards a more problematic situation in terms of drug resistance. First, because the Beijing family, which is currently invading Vietnam, is associated with highly drug resistance, mutations linked to high-level drug resistance and low fitness cost and compensatory mutations. Second, the high risk of pyrazinamide resistance in our sample challenges the efficacy and the use of this drug in MDR-TB treatment. Third, our data suggest an evolution of M. tuberculosis towards a higher potential of drug resistance because of a probable cumulative effect of drug resistant mutations and epistatic interactions. Since the samples under study were collected between 2005-2009, the next step is to test our hypotheses on a recent sampling. Finally, this study together with published data allowed making, for the first time, an inventory of the drug resistance associated mutations in M. tuberculosis isolates from Vietnam.

Tee PhD thesis presents the study of the response of Mycobacterium tuberculosis, the causative agent of tuberculosis, upon prolonged exposure to lethal concentrations of the first line anti-tuberculosis drug, rifampicin. The study shows that prolonged exposure to lethal concentration of rifampicin causes cell death initially by several log orders of cells, followed by a persistence phase, from where rifampicin resisters emerge carrying mutation in the RRDR locus of the rpoB gene. This phenomenon was found to occur even when the drug concentration is well above MBC levels. Luria-Delbruck experiment, in a modified format, showed that the resisters emerged as fresh mutants, and not due to the growth of pre-existing natural resisters to rifampicin. The per sister cells, which showed high levels of hydroxyl radical generation, were found to have thickened outer layer, unlike the mid-log phase cells, which restricts the permeability of a fluorescent-conjugate of rifampicin, 5-FAM-rifampicin, 10-fold less in per sister cells, as compared to mid-log phase cells. The thickened outer layer has high negative surface charge and is hydrophilic in nature. It is proposed that the hydrophilic-natured thickened outer layer might have restricted the permeability of lethal concentrations of hydrophobic-natured rifampicin. This, in turn, might have ensured the presence of sub-lethal concentration rifampicin inside the per sisters, which in turn might have generated the hydroxyl radical that caused mutagenesis to generate rifampicin resisters. The Chapter 1 is the Introduction to the thesis presented in 4 parts – Part 1.1, 1.2, 1.3 and 1.4, introducing briefly the history of antibiotics, antibiotic resistance, antibiotic persistence and a brief history of tuberculosis respectively. It is concluded with a rationale behind the present study. The Chapter 2 presents the entire Materials and Methods used in the experiments described in the thesis. The Chapter 3 presents the data on the response of M. tuberculosis to rifampicin upon extended exposure. Rifampicin exposure of susceptible M. tuberculosis H37Ra cells showed a decrease in their CFU/ml followed by a persistence phase wherein the CFU/ml remained constant. However, prolonged exposure of rifampicin even at higher concentrations showed regrowth in the culture, which was found to be due to the emergence of rifampicin-resistant bacteria. Screening of rifampicin-resistant mutants showed point mutations in the rifampicin resistance determining region (RRDR) of the rpoB gene in all the mutants. In parallel, using trans formants of M. tuberculosis expressing unstable GFP under the respective native ribosomal RNA promoter, the metabolic status of the per sister cells was determined. When actively growing highly fluorescing cells were exposed to lethal concentration of rifampicin, their metabolism diminished, as illustrated by the decrease in their fluorescence during persistence phase, followed by the emergence of a sub-population of bacteria which were again metabolically active. In order to verify whether the rifampicin resisters are freshly formed mutants or have come from the naturally existing resisters, Luria-Delbruck fluctuation test was performed in a modified manner. The number of rifampicin resisters that emerged from the persistent phase was found to vary amongst different cultures from different days and different times of exposure, showing fluctuation. However, the addition of theorem before persistence phase almost abolished the generation of the rifampicin-resistant bacilli, indicating the role of hydroxyl radical in the emergence of rifampicin resisters. The generation of hydroxyl radical in mycobacteria exposed to rifampicin was confirmed using electron para-magnetic resonance spectrometry (EPR), with the spin trap agent, 5,5- Dimethyl-1-pyrroline N-oxide (DMPO) specific for hydroxyl radical. An increase in the formation DMPO-OH adduct in the persistence phase cells was observed, in comparison to mid-log phase cells. Exposure to theorem significantly diminished the adduct formation. The persistence phase cells also showed significantly high levels of signal specific to the hydroxyl-specific fluorescent dye, hydroxyphenyl fluorescein (HPF), as compared to the mid-log phase cells. In addition we have determined the oxidative stress in the bacilli upon rifampicin exposure using a redox biosensor (Mrx1-roGFP) which also showed high oxidative stress in the persistent phase. These observations confirmed the presence of high levels of oxidative stress and hydroxyl radical in the rifampicin persistent cells, in comparison with mid-log phase cells. Whole genome sequencing of the four independently isolated rifampicin resistant M. tuberculosis showed genome wide mutations having less common mutations with respect to the wild type genome, indicative of the occurrence of random mutagenesis. In addition mutation frequencies were comparable between the samples with respect to the wild type sample. About 69% of the mutations were A-C or T-G, followed by A-T or T-A, which is known to be due to oxidative stress in the cells. Variations in the colony morphology were also observed on the persistent phase cells, indicating the occurrence of mutagenesis in the bacterial genome during rifampicin treatment. The Chapter 4 is on the morphological and ultrastructural studies on rifampicin-exposed M. tuberculosis cells. Transmission electron micrographs of rifampicin per sisters showed significant thickening of the outermost capsular layer (OL), as compared to the mid-log phase cells. This observation was verified by staining the cells with ruthenium red, which specifically stains anionic polysaccharide of the OL. Zeta potential (ZP) measurement of the surface charge of the persistent cells showed high negative ZP, as compared to the mid-log phase cells. The negative ZP value was found to gradually increase during the course of rifampicin treatment and to decrease during the regrowth phase. Hexadecane assay showed larger proportion of per sister cells being retained in the aqueous phase, as compared to the mid-log phase cells. This indicated the higher hydrophilicity of the per sister cells, which was in agreement with the higher surface negative charge of the cells. The permeability of rifampicin per sister cells to 5-FAM-rifampicin (rifampicin conjugated to 5-carboxy fluorescein, which is as hydrophobic as rifampicin) was found to be 10-fold less than that of the mid-log phase cells. However, removal of the thick OL by bead beating (BB) with 4 mm glass beads significantly improved the permeability of per sister cells to 5-FAM-rifampicin. On the contrary, no difference in the 5-FAM-rifampicin uptake was observed in mid-log phase cells, with or without BB. These observations implied that the thick hydrophilic-natured OL with high negative surface charge may be playing a significant role in limiting the permeability of hydrophobic-natured rifampicin entry into the persisted cells. This in turn may ensure the presence of sub-lethal concentration of rifampicin inside the persisted cells that are exposed to lethal concentration of the antibiotic. Exposure of bacteria to sub-lethal concentration of antibiotics has been reported to generate oxidative stress in the bacteria, leading to mutagenesis. A model has been proposed based on these observations in which the persistent mycobacteria are protected from lethal concentrations of the rifampicin by the thick OL which in turn ensures sub-lethal intracellular antibiotic concentration, leading to the generation of hydroxyl radical mediated mutagenesis and thereby emergence of rifampicin resisters. This thesis is concluded with the list of salient findings, publications and references.

Structural investigations on two mycobacterial enzymes were carried out. Tuberculosis still remains a major threat to mankind even though drugs against it have been in use for many decades. The emergence of drug resistant strains of the bacteria calls for the identification of new targets based on which new drugs can be developed to combat the disease. A thorough understanding of the functioning of the target molecules is essential for this approach. We have taken up the structural studies on two such molecules, aspartic proteinases and adenylyl cyclases, of Mycobacterium tuberculosis with a view to obtain insights into their mechanisms of action at the atomic level. The work presented in the thesis includes (i) the identification, cloning, expression, purification and structure determination of a putative aspartic proteinase domain of M. tuberculosis and (ii) the crystal structure of an adenylyl cyclase of M. tuberculosis and its mutant; and also of an adenylyl cyclase from M. avium. Chapter 1 presents an overview of aspartic proteinases and nucleotide cyclases with an emphasis on their structural features. The methods employed during the course of the present work are described in Chapter 2. Work on the putative aspartic proteinase domain identified in M. tuberculosis is presented in Chapter 3. The structure of the aspartic proteinase domain is the first structural report of such domain from any bacteria. A search in the genome of M. tuberculosis showed a weak similarity to the HIV aspartic proteinase sequence. This region corresponds to the C-terminal domain of a PE family protein in M. tuberculosis. The presence of two signature motifs, DTG and DSG, of aspartic proteinases in the full sequence of this domain encouraged us to take up further studies on this domain. Previous reports identifying the protein as a surface antigen and our findings on the occurrence of similar domains in two other PE proteins of M. tuberculosis and also in other pathological strains of Mycobacteria indicated that these domains probably play an important role in infecting the host. The crystal structure of one of the domains showed that it has a pepsin-like fold and the catalytic site architecture of known aspartic proteinases. However, no proteolytic activity was detected. The size of the molecule is intermediate to eukaryotic pepsins and the homodimeric retroviral pepsins. A close examination of the binding site revealed subtle differences when compared to the active enzyme structures. Appropriate mutations of some of the residues in this region to convert it to an active enzyme did not make it active. Once the in vivo function of these putative aspartic proteinase domains is established, their potential to act as drug targets can be probed as the PE proteins are present exclusively in pathogenic Mycobacteria. As part of an ongoing project on adenylyl cyclases of Mycobacteria, we have taken up the structure analysis of the catalytic domains of two adenylyl cyclases; Rv1625c from M. tuberculosis and Ma1120 from M. avium. This work is described in Chapter 4. The wild-type of Rv1625c crystallized as a domain swapped head to head inactive dimer even though it is an active dimer in solution and expected to have a head to tail arrangement as in the previously reported structures of the active forms of the enzyme. Mutation of a phenylalanine residue presumed to occur at the subunit interface of the active dimeric structure of the enzyme to an arginine residue, a conserved residue of guanylyl cyclases, resulted in reduced adenylyl cyclase activity. This mutant crystallized as a monomer though it was expected to be an active dimer. Similarly, Ma1120 also has a monomeric structure in the crystal in spite of showing activity in solution. Though our aim was to capture the active dimers in the crystalline state we did not succeed in this effort in any of the three cases. The catalytic reaction probably takes place very rapidly with the formation of a transient active form of the dimer which cannot be easily crystallized. However, the analysis revealed new structures which are likely to represent the stable states of the enzyme when it is required to stay inactive in certain conditions. We have also established that the N-terminal segments of the enzyme, a loop at the dimeric interface and external factors like pH are involved in determining the oligomeric status of the enzyme thereby regulating its function. Publications 1 Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16; Deivanayaga V. Barathy and K. Suguna; FEBS Open Bio (In Press) 2 New structural forms of mycobacterial adenylyl cyclases (in preparation)

La tuberculose est une maladie contagieuse causée par une infection avec M. tuberculosis. Son incidence globale élevée, des traitements longs et coûteux, l’apparition de souches résistantes aux antibiotiques disponibles et la co-infection avec le VIH en font un problème de santé publique de premier plan. En effet, l’Organisation Mondiale de la Santé estime qu’un tiers de la population mondiale est infectée de façon latente par M. tuberculosis. La mise au point d’un vaccin efficace serait un des moyens de mieux contrôler cette maladie et pour cela une meilleure compréhension de la réponse immunitaire contre M. tuberculosis est indispensable. Il est cependant clair que la réponse Th1 et l’IFN-γ sont essentiels pour la protection contre M. tuberculosis. Cependant, beaucoup d’aspects de cette immunité restent encore indéterminés dont le rôle de la réponse IL-17A. Dans ce travail, nous avons analysé la susceptibilité de souris génétiquement déficientes pour la sous-unité A du récepteur de l’IL-17A à une infection par M. tuberculosis. Nous montrons que la signalisation induite par l’IL-17A est indispensable pour le contrôle à long terme de l’infection et ce malgré une augmentation de la réponse IFN-γ.<p>Dans la deuxième partie du travail, nous avons analysé l’effet de la neutralisation de l’IL-12 sur la susceptibilité de souris préalablement vaccinées avec le Bacille de Calmette et Guérin (BCG) à une infection par M. tuberculosis. La neutralisation de l’IL-12 a été réalisée en utilisant un auto-vaccin anti-IL-12. Les résultats ont confirmé le rôle essentiel de l’IL-12 dans la protection contre une infection primaire avec M. tuberculosis ;ils ont cependant également permis de démontrer que la neutralisation de l’IL-12 n’exerce qu’un effet très modeste sur la protection conférée par le vaccin BCG. Ainsi, la diminution d’IFN-γ induite par la neutralisation de l’IL-12 semble être compensée par une augmentation de la production de TNF-α, d’IL-6 et plus particulièrement de l’IL-17A.<p>En conclusion, notre travail indique que la réponse IL-17A est importante pour la protection contre M. tuberculosis que ce soit lors d’une infection primaire ou en cas de réponse mémoire. De plus, nos observations renforcent l’idée de plus en plus communément admise que l’IFN-γ seul n’est pas suffisant pour protéger contre M. tuberculosis/Tuberculosis is a contagious disease caused by infection with M. tuberculosis. Due to its high global incidence, the length and cost of antibiotic treatments, the emergence of antibiotics resistant strains and co-infection with HIV, Tuberculosis remains a major health problem. In addition, World Health Organization estimates that one-third of the world population is latently infected with M. tuberculosis. The development of an efficient vaccine could lead to a better control of this disease, but for that purpose a better understanding of the protective immune response against M. tuberculosis is essential. It is clear that Th1 immunity and IFN-γ play an essential role in protection against M. tuberculosis. However, numerous aspects of this immune response are still poorly understood, such as the role of the IL-17A response. <p>In this work, we have analyzed the susceptibility to M. tuberculosis infection in mice genetically inactivated in the IL-17 receptor.A subunit. We have shown that IL-17A signalling is required for long-term control of M. tuberculosis infection, even if the IFN-γ response is increased. <p>In the second part of this work, we have analyzed the effect of IL-12 in resistance against M. tuberculosis infection and in the protection conferred by the BCG vaccine. For that purpose, IL-12 was neutralized using an anti-IL-12 auto-vaccine. Our results confirm the essential role of IL-12 in the protection against a primary M. tuberculosis infection. Nevertheless, these results also demonstrate that IL-12 neutralization only marginally affect the protection conferred by the BCG vaccine. Indeed, the decreased IFN-γ production induced by IL-12 neutralization in BCG-vaccinated mice seems compensated by increased TNF-α, IL-6 and more specifically IL-17A production.<p>In conclusion, our data indicate that the IL-17A response is important in protection against M. tuberculosis, both in primary infection or in the case of memory responses. Moreover, our results emphasize the emerging idea that a functional IFN-γ response alone is not sufficient to protect against M. tuberculosis.<p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Pantothenate kinase (PanK) is an ubiquitous and essential enzyme that catalyzes the first step in the universal Coenzyme (CoA) biosynthesis pathway. In this step, pantothenate (Vitamin B5) is converted to 4′-phosphopantothenate, which subsequently forms CoA in four enzymatic steps. In bacteria, three types of PanK’s have been identified which exhibit wide variations in their distribution, mechanisms of regulation and affinity for substrates. Type I PanK is a key regulatory enzyme in the CoA biosynthesis pathway and its activity is feedback regulated by CoA and its thioesters. As part of a major programme on mycobacterial proteins in this laboratory, structural studies on type I PanK from Mycobacterium tuberculosis (MtPanK) was initiated and the structure of this enzyme in complex with a CoA derivative has been reported earlier. To further elucidate the structural basis of the enzyme action of MtPanK, several crystal structures of the enzyme in complex with different ligands have been determined in the present study. In conjunction to this, solution studies on the enzyme were also carried out. The structures were solved using the well-established techniques of protein X-ray crystallography. The hanging drop vapour diffusion method was used for crystallization in all cases. The X-ray intensity data were collected using a MAR Research imaging plate system mounted on a Rigaku RU200 and Bruker-AXS Microstar Ultra II rotating anode X-ray generator. The data were processed using the HKL and MOSFLM and SCALA from the CCP4 suite. The structures were solved by the molecular replacement method using the program AMoRe and PHASER. Structure refinements were carried out using the programs CNS and REFMAC. Model building was carried out using COOT and the refined structures were validated using PROCHECK and MOLPROBITY. Secondary structure was assigned using DSSP, structural superpositions were made using ALIGN and buried surface area was calculated using NACCESS. Solution studies on CoA binding and catalytic activity were carried out using Isothermal titration calorimetry (ITC). To start with, the crystal structures of the complexes of MtPanK were determined with (a) citrate, (b) the non-hydrolysable ATP analog AMPPCP and pantothenate (initiation complex), (c) ADP and phosphopantothenate resulting from phosphorylation of pantothenate by ATP in the crystal (end complex), (d) ATP and ADP, each with half occupancy, resulting from a quick soak of crystals in ATP (intermediate complex), (e) CoA, (f) ADP prepared by soaking and co-crystallization, which turned out to have identical structures and (g) ADP and pantothenate. Unlike in the case of the homologous E.coli enzyme (EcPanK), AMPPCP and ADP occupied different, though overlapping, locations in the respective complexes; the same was true of pantothenate in the initiation complex and phosphopantothenate in the end complex. The binding site of MtPanK was found to be substantially preformed while that of EcPanK exhibited considerable plasticity. The difference in the behavior of the E.coli and M.tuberculosis enzymes could be explained in terms of changes in local structure resulting from substitutions. It is unusual for two homologous enzymes to exhibit such striking differences in action and the changes in the locations of ligands exhibited by M.tuberculosis pantothenate kinase are remarkable and novel. The movement of ligands exhibited by MtPanK during enzyme action appeared to indicate that the binding site of the enzyme was less specific for a particular type of ligand than EcPanK. Kinetic measurements of enzyme activity showed that MtPanK had dual substrate specificity for ATP and GTP, unlike the enzyme from E.coli which showed a much higher specificity for ATP. A molecular explanation for the difference in the specificities of the two homologous enzymes was provided by the crystal structures of the complexes of the M. tuberculosis enzyme with (1) GMPPCP and pantothenate (2) GDP and phosphopantothenate (3) GDP (4) GDP and pantothenate (5) AMPPCP and (6) GMPPCP and the structures of the complexes of the two enzymes involving CoA and different adenyl nucleotides. The explanation was substantially based on two critical substitutions in the amino acid sequence and the local conformational change resulting from them. Dual specificity of the type exhibited by this enzyme is rare and so are the striking difference between two homologous enzymes in the geometry of the binding site, locations of ligands and specificity. The crystal structures of MtPanK in binary complexes with nucleoside diphosphate (NDP) and nucleoside triphosphate (NTP) provided insights about the natural location and conformation of nucleotides. In the absence of pantothenate, the NDP and the NTP bound with an extended conformation at the same site. In the presence of pantothenate, as seen in the initiation complexes, the NTP had a closed conformation and an altered location. However, the effect of the nucleotide on the conformation and the location of pantothenate were yet to be elucidated as the natural location of the ligand in MtPanK was not known. This lacuna was sought to be filled through X-ray analysis of the binary complexes of MtPanK with pantothenate and two of its derivatives, namely, pantothenol and N-nonyl pantothenamide (N9-Pan). These structures demonstrated that pantothenate, with a somewhat open conformation occupied a location similar to that occupied by phosphopantothenate in the “end” complexes, which was distinctly different from the location of pantothenate in “closed” conformation in the ternary “initiation” complexes. The conformation and the location of the nucleotide were also different in the initiation and end complexes. An invariant arginine appeared to play a critical role in the movement of ligand that took place during enzyme action. The structure analysis of the binary complexes with the vitamin and its derivatives completed the description of the locations and conformations of nucleoside di and triphosphates and pantothenate in different binary and ternary complexes. These complexes provide snapshots of the course of action of MtPanK.