Submitted by Edisangela Bastos (edisangela@ufpa.br) on 2015-07-02T18:26:26Z No. of bitstreams: 2 license_rdf: 22974 bytes, checksum: 99c771d9f0b9c46790009b9874d49253 (MD5) Dissertacao_MaoGarraProposta.pdf: 2975755 bytes, checksum: 5f51278808e0bfb22292f60ae9fb8907 (MD5) / Approved for entry into archive by Ana Rosa Silva (arosa@ufpa.br) on 2015-07-21T16:26:18Z (GMT) No. of bitstreams: 2 license_rdf: 22974 bytes, checksum: 99c771d9f0b9c46790009b9874d49253 (MD5) Dissertacao_MaoGarraProposta.pdf: 2975755 bytes, checksum: 5f51278808e0bfb22292f60ae9fb8907 (MD5) / Made available in DSpace on 2015-07-21T16:26:18Z (GMT). No. of bitstreams: 2 license_rdf: 22974 bytes, checksum: 99c771d9f0b9c46790009b9874d49253 (MD5) Dissertacao_MaoGarraProposta.pdf: 2975755 bytes, checksum: 5f51278808e0bfb22292f60ae9fb8907 (MD5) Previous issue date: 2013 / A hanseníase é uma doença infecciosa crônica, granulomatosa, de curso lento, causada pelo Mycobacterium Leprae. O bacilo acomete principalmente os nervos periféricos, causando lesões na face, mãos e pés, que podem gerar incapacidades físicas severas que contribuem para a instalação de padrões deformantes e incapacidades. A lesão do tipo mão em garra é uma sequela que pode ser observada em pacientes com lesões ao nível dos membros superiores sendo muito incapacitante, dificultando a realização das atividades de vida diária destes indivíduos e consequentemente prejudicando sua qualidade de vida e satisfação pessoal. Estas lesões geram repercussões no contexto de vida do indivíduo contribuindo para a instalação de alterações nos aspectos psicoemocionais, além do estigma próprio da doença. A intervenção terapêutica ocupacional utilizando a tecnologia assistiva de baixo custo para auxílio nas atividades de vida diária de pacientes com mão em garra objetiva a minimização dos déficits funcionais apresentados durante a utilização de adaptações funcionais utilizadas na realização de suas atividades cotidianas como alimentação, higiene pessoal e vestuário. A intervenção realizou-se através da aplicação de um protocolo de avaliação em Terapia Ocupacional conhecido como Medida Canadense de Desempenho Ocupacional (COPM) que mede o grau de desempenho e Satisfação do paciente ao realizar suas atividades de vida diária. O protocolo foi aplicado inicialmente junto aos pacientes coletando dados sobre a realização das suas atividades de vida diária sem a utilização de recursos de tecnologia assistiva. A aplicação do protocolo baseou-se na definição de cinco problemas comuns a todos os participantes, revelando graus muito baixos de desempenho e satisfação obtidos durante a realização das atividades avaliadas. Posteriormente realizou-se o processo de prescrição, confecção e treinamento das adaptações desenvolvidas para cada paciente, somando-se um total de cento e vinte aparelhos (120) desenvolvidos. Aplicou-se novamente o mesmo protocolo com os mesmos pacientes abordando os mesmos problemas após a realização de um período de treinamento das adaptações funcionais desenvolvidas, comparando-se os dados coletados no primeiro e segundo COPM. Comparando-se aos dados iniciais apresentados, os dados coletados na segunda avaliação do COPM apontaram um aumento significativo do grau de desempenho e satisfação dos pacientes além de ganho funcional. Concluí-se com esta pesquisa que a proposta de intervenção terapêutica ocupacional utilizando equipamentos de tecnologia assistiva de baixo custo (adaptações) é viável, possui resultados satisfatórios e favorece um grande alcance social devido à redução de custos dos dispositivos desenvolvidos. / Leprosy is an infectious disease, granulomatous, of slow progress, caused by Mycobacterium Leprae. The bacillus affects mainly peripheral nerves, causing face, hands and feet lesions, which can generate severe physical disabilities which contribute for installation of disabling and deforming patterns. The lesion of claw hand type is a sequel which can be observed in patients with lesions at the level of the upper limbs being very incapacitating, hindering the performance of activities of daily living of these individuals and consequently damaging quality of life and personal satisfaction. These lesions generate repercussions in the individual's context of life contributing to installation of alterations in psychoemotionall aspects, in addition of the stigma inherent to disease. The occupational therapy intervention using low cost assistive technology to assistance of activities of daily living in patients with claw hand objectives minimization of functional deficits presented while using functional adaptations used in performance of their daily activities as food, personal hygiene and clothing. The intervention was performed by applying an assessment protocol in occupational therapy known as the Canadian Occupational Performance Measure (COPM) which measures the degree of performance and satisfaction of the patient to perform activities of daily living. The protocol was applied initially with patients collecting data about performance of activities of daily living without the use of assistive technology resources. The application protocol was based on the definition of five problems common to all participants revealed very low levels of performance and satisfaction obtained during the performance of activities evaluated. Subsequently was performed the process of prescription, preparation and training of adaptations developed for each patient, adding to a total of one hundred twenty appliances (120) developed. Again applied the same protocol with the same patients addressing the same problems after conducting a training period of functional adaptations developed, comparing the data collected in the first and second COPM. Comparing the initial data presented, the data collected in the second evaluation of COPM showed a significantly increased level of patient's performance and satisfaction in addition to functional gain. It was concluded with this research that the proposed occupational therapy intervention using low cost assistive technology equipments (adaptations) is feasible, have satisfactory results and favor a great social reach due to cost reduction of developed devices.

Submitted by Cássio da Cruz Nogueira (cassionogueirakk@gmail.com) on 2017-03-22T12:50:42Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AvaliacaoSorologicaAntigenos.pdf: 2016250 bytes, checksum: 5c55e6862a67c22e0b059a3f35491561 (MD5) / Approved for entry into archive by Edisangela Bastos (edisangela@ufpa.br) on 2017-03-27T12:35:39Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AvaliacaoSorologicaAntigenos.pdf: 2016250 bytes, checksum: 5c55e6862a67c22e0b059a3f35491561 (MD5) / Made available in DSpace on 2017-03-27T12:35:39Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AvaliacaoSorologicaAntigenos.pdf: 2016250 bytes, checksum: 5c55e6862a67c22e0b059a3f35491561 (MD5) Previous issue date: 2014-04-05 / FAPESPA - Fundação Amazônia de Amparo a Estudos e Pesquisas / Apesar dos esforços para sua eliminação como problema de saúde pública, a hanseníase permanece com alta prevalência em alguns países, como o Brasil, sendo o Estado do Pará responsável pelo diagnóstico de aproximadamente 10% dos cerca de 400.000 casos novos do Brasil nos últimos 10 anos. Até o momento, não existe nenhum teste de diagnóstico para detectar a hanseníase nos estágios iniciais, contribuindo assim para a manutenção das altas taxas de incidência da doença. Neste sentido, novos antígenos específicos do M. leprae que possibilitem o desenvolvimento de novos métodos de diagnóstico podem facilitar a detecção precoce de casos novos e contribuir para alcançar as metas de controle da hanseníase. Neste estudo, foi realizada avaliação clínica e dermatoneurológica dos participantes para a detecção de casos novos e foram coletadas amostras de sangue para pesquisa de anticorpos em dois momentos diferentes, T1 e T2, em um intervalo de tempo de 2 anos entre os mesmos. Os anticorpos IgM anti-ND-O-BSA e IgG anti-LID-1 foram detectados por ELISA, além de anti-IgM e anti-IgG associados para a pesquisa de anti-NDO-LID em amostras de plasma, também por ELISA ou sangue total pelo teste rápido OrangeLife® (OL) de 79 pessoas com hanseníase, 131 contatos e 331 estudantes do município de Breves, Estado do Pará. Nossos resultados mostraram alta incidência de hanseníase de 18,6% e 6,1% em contatos e estudantes respectivamente em T1 e de 19,8% e 9,4% em T2 e neste momento, entre contatos, foram positivos 44,3% para anti-ND-O-BSA, 7,86% para o anti-LID-1 e 37,4% para o anti-NDO-LID e para estudantes foram 49,5% para o anti-ND-O-BSA, 5,1% para o anti-LID-1 e 45% para o anti-NDO-LID. A associação entre os antígenos mostrou uma forte correlação para o ND-O-BSA e NDO-LID. A positividade para o OL em casos novos foi de 44,3% para MB, a maioria BT, em estudantes foi 47,4% e em contatos foi de 36,3%, com baixa concordância com ELISA anti-NDO-LID. No seguimento (T2), o percentual de casos novos foi de 35% e o maior percentual foi identificado entre indivíduos positivos para anti-ND-O-BSA. Os dados mostram alta incidência em contatos e estudantes através de busca ativa e seguimento sorológico, e concluímos que o antígeno ND-O-BSA se mostrou mais sensível no ensaio de ELISA para a identificação de casos novos em populações endêmicas. / Despite efforts for its elimination as a public health problem, leprosy remains highly prevalence in some countries, including Brazil, specially in the state of Pará, which accounts for approximately 10% of the 400,000 new cases in Brazil during the last 10 years. To date, there is no diagnostic test to detect leprosy in its early stages, thus contributing to the maintenance of high rates of disease incidence. In this sense, the Discovery of new specific antigens of M. leprae to enable the development of new diagnostic methods may facilitate early detection of disease prior to the onset of disfigurement and nerve damage and contribute to achieving the goals of leprosy control. In this study, dermatological clinical evaluation of the participants was performed to detect new cases and blood samples were collected for antibody screening at two different timpoints, T1 (2011) and T2 (2013), two years apart. IgM anti-ND-O-BSA and IgG anti-LID-1 titers were detected by ELISA, and anti-IgM and anti-IgG were combined for detection of both in plasma samples by ELISA or also the whole blood by OrangeLife® (OL) rapid test in 79 leprosy patients, 131 household contacts and 331 students from the municipality of Breves, Pará State. Samples collected at T1 showed a high number of new cases detected, with 18.6% of household contacts and 6.1% of students diagnosed, while two years later at T2, there were 19.8% of household contacts and 9.4% of students diagnosed. At T2, 44.3% of contacts were positive for anti-ND-O-BSA, 7.8% for anti-LID-1 and 37.4% for anti-NDO-LID. Mong the students 49.5% were positive for anti-ND-O-BSA, 5.1% for anti-LID-1 and 37% for anti-NDO-LID. The association between antigens showed a strong correlation to ND-O-BSA and NDO-LID. Positivity of the OL rapide test was 44.3% for newly diagnosed MB cases (BT majority), in students was 47.4% and 36.3% in household contacts, with poor agreement with ELISA anti-NDO-LID. At follow-up (T2), the percentage of new cases was 35% and the largest number was identified among individuals positive for anti-ND-O-BSA. The data show a high incidence in contacts and students through active search and serologic follow-up, and we concluded that the antigen ND-O-BSA was more sensitive in the ELISA assay for identifying new cases in populations endemic.

Mobile genetic elements are DNA sequences that move around to different positions within one genome or between different genomes. Mobile DNA elements were initially considered as selfish DNA sequences parasitizing the organism’s genome. However, this view has changed with the discovery of several mobile genetic elements which play important evolutionary and functional roles. Such understanding has led to a new connotation for these genetic elements such as drivers or natural molecular tools of genome evolution. Extensive research over the past several years has also led to the identification of several new mobile genetic elements including transposons, segregation distorters, heritable organisms, introns and inteins. Homing endonucleases (HEnases) are a group of rare cutting site-specific doublestranded DNA endonucleases encoded by open reading frames within introns, inteins or free standing genes in all the three forms of life including viruses. These enzymes confer mobility to themselves and their encoding sequences by a gene conversion event termed “homing”. During the homing process, the endonuclease inflicts a double-strand break at or near the homing site of the intein-/intron-less allele, which is subsequently repaired by the host DNA repair machinery resulting in the inheritance of intein/intron. The first homing endonuclease identified was the Saccharomyces cerevisiae mitochondrial genetic marker ‘ω’, which affects the polarity of recombination. This genetic marker, which was later shown to be a mobile group I intron, was present in the mitochondrial 21S rRNA gene and encodes a homing endonuclease. HEnases are distinguished for being able to recognise long DNA sequences (14-40 bp), and display disparate cleavage mechanisms. Unlike restriction endonucleases, these enzymes tolerate sequence polymorphism in their recognition region which provides a mechanism for increasing their genetic diversity. Substantial efforts are underway to explore the possibility of utilizing HEnases as tools for genome mapping, cloning of megabase DNA fragments and gene targeting. HEnases are divided into five sub-families on the basis of their conserved sequence and structural motifs: LAGLIDADG, GIY-YIG, H-N-H, His-Cys box and PD-(D/E)-XK families. Among these, LAGLIDADG family is the largest, most prevalent and well-studied class of HEnases. Homing enzymes that contain a single copy of LAGLIDADG motif per polypeptide chain, such as ICreI, I-MsoI and I-CeuI function as homodimers and recognize and cleave palindromic and pseudo-palindromic DNA sequences. On the other hand, HEnases that harbour two copies of LAGLIDADG motifs including I-AniI, PI-SceI and I-SceI act as monomers and recognize and cleave their DNA target sites with considerable asymmetry. Eubacterial RecA proteins are important for a number of cellular processes such as homologous recombination, DNA repair, restoration of stalled replication forks and SOS response. RecA protein and the process of homologous recombination, which is the main mechanism of genetic exchange, are evolutionarily conserved among a range of organisms. However, few mycobacterial species such as Mycobacterium tuberculosis and Mycobacterium leprae were found to be an exception as they harboured in-frame insertion of an intein-coding sequence in their recA genes. In these organisms, RecA is synthesized as a large precursor, which undergoes protein splicing resulting in the formation of an intein and functionally active RecA protein. The milieu in which RecA precursor undergoes splicing differs substantially between M. tuberculosis and M. leprae. M. leprae RecA precursor (79 kDa) undergoes splicing only in mycobacterial species, whereas M. tuberculosis RecA precursor (85 kDa) is spliced efficiently in Escherichia coli as well. Intriguingly, M. tuberculosis and M. leprae RecA inteins differ greatly in their size, primary sequence and location within the recA gene, thereby suggesting two independent origins during evolution. The occurrence of inteins in the obligate mycobacterial pathogens M. tuberculosis, M. leprae and M. microti, initially suggested that RecA inteins might play a role in pathogenesis or virulence, however this was found to be not the case due to the subsequent identification of these intervening sequences in several non pathogenic mycobacterial strains. Sequence comparison of RecA inteins suggested that they belong to the LAGLIDADG class of homing endonucleases. Accordingly, we have shown earlier that M. tuberculosis RecA intein (PI-MtuI), is a novel LAGLIDADG homing endonuclease, which displays dual target specificity in the presence of alternative cofactors in an ATP-dependent manner. The genome of M. leprae, a gram positive bacillus reveals that in contrast to the genomes of other mycobacterial species, it has undergone extensive deletions and decay and thereby represents an extreme case of reductive evolution. In such a scenario of massive gene decay and function loss in the leprosy bacillus, and dissimilarities in size and primary structures among mycobacterial RecA inteins, it was of interest to examine whether M. leprae recA intervening sequence can encode a catalytically active homing endonuclease. To this end, the intervening sequence corresponding to M. leprae recA intein was PCR amplified, cloned, overexpressed and purified to homogeneity using IMPACT protocol. The identity of the purified RecA intein was ascertained by sequencing 9 amino acid residues at the N-terminal end and Western blot analysis using anti-PI-MleI antibodies. Purified enzyme was found to be devoid of any contaminating exonuclease. Protein crosslinking experiments using glutaraldehyde suggested that PI-MleI exists in solution as a monomer, consistent with double-motif LAGLIDADG enzymes. To test whether the purified PI-MleI can bind to the DNA and display any DNA-binding specificity, we carried out electrophoretic mobility shift assays with both single-stranded and double-stranded cognate DNA. The enzyme displayed robust binding to cognate doublestranded DNA, compared to the cognate single-stranded DNA. DNA binding was further found to be sequence independent though the presence of the cognate sequence was required for maximal binding. The stability and specificity of PI-MleI-cognate DNA complexes were further examined by salt titration and competition experiments, which indicated high stability and specificity. After establishing the stable binding of recombinant PI-MleI to the cognate duplex DNA, we next investigated its endonuclease activity on the cognate plasmid pMLR containing the intein-less recA allele, in the absence or presence of divalent cations. The cleavage was monitored by the conversion of supercoiled pMLR to nicked circular as well as linear duplex DNA. PI-MleI exhibited both single-stranded nicking and double-stranded DNA cleavage activity. PI- MleI exhibits endonuclease activity both in the presence of Mg2+ or Mn2+ through a two step reaction. PI-MleI mediated cleavage though was found to be divalent cation dependent however was nucleotide cofactor independent, unlike PI-MtuI, which cleaves the cognate DNA substrate in the presence of ATP. PI-MleI endonuclease activity was assayed under different conditions and found to display a broad divalent cation, pH and temperature dependence. The kinetic experiments revealed slow turnover rate of PI-MleI suggesting its weak endonuclease activity in contrast to robust cleavage activity displayed by several other known LAGLIDADG homing endonucleases. An intriguing observation emerged from the cleavage site mapping of PI-MleI at singlenucleotide resolution. PI-MleI displayed a staggered double- strand break in the homing site by nicking in the left flanking sequence 44 to 47 bp and in the right flanking sequence 16 to 25 bp, away from the intein insertion site. Similar cleavage patterns have been earlier observed for few GIY-YIG homing endonucleases. To gain further mechanistic insights into the PI-MleI mediated catalysis, we examined the binding of PI-MleI to the cognate DNA by DNase I and (OP)2 Cu footprinting experiments. Both the footprinting approaches revealed interaction of PI-MleI with a region upstream and downstream of its own insertion site, conferring protection to 16 nucleotide residues on the upper and 12 nucleotide residues on the lower strand, respectively. The asymmetric footprints have been earlier observed for some members of LAGLIDADG-type homing endonucleases wherein protection on the complementary strands was found to be out of register by 2 to 3 nucleotides, respectively. In case of PI-MleI, however the footprint formed on the complementary strands of the homing site is non-overlapping, indicating the asymmetric mode of interaction of the enzyme. Surprisingly, PI-MleI footprint was not evident at the cleavage sites and this could be due to the unstable binding of the intein at these regions. To decipher the interaction of PI-MleI at the cleavage sites and to ascertain if these interactions have any functional implications in terms of alterations in base-pairing positioning or strand separation to mediate DNA catalysis, we probed the structure of PI-MleI-DNA complexes with KMnO4. KMnO4 treatment of PI-MleI-cognate DNA complexes revealed the presence of hypersensitive T residues on both the strands at the cleavage sites, but showed no such reactive T residues within the PI-MleI-binding regions. Also, hyper-sensitive T residues were not seen at or near the intein-insertion site or in the region between binding and cleavage sites suggesting that PI-MleI upon binding its cognate DNA induces distortions selectively at the cleavage region. To validate these findings and to test whether such alterations occurred on all substrate DNA molecules or on a small sub-population of target molecules, we used a more sensitive 2-aminopurine fluorescence approach. To this end, six cognate duplex DNA molecules each containing 2-aminopurine (2-AP) at different positions such as at the insertion site, in the DNAbinding region, at or near to the cleavage sites were synthesized to monitor helical distortions in the target DNA. The 2-AP containing cognate DNA duplexes were incubated with increasing concentrations of PI-MleI in the assay buffer and monitored the changes in 2-AP fluorescence intensity in the spectral region from 330 to 450 nm. Out of the 2-AP placed at several positions within the cognate substrate, only the 2-aminopurines at the cleavage site showed enhanced fluorescence with PI-MleI addition, consistent with the hyper-sensitivity of T residues during KMnO4 probing. The findings suggest that DNA distortion might assist PI-MleI in widening the minor groove at the cleavage site and make the scissile phosphates accessible to the enzyme active site similar to what has been seen with other LAGLIDADG homing enzymes. These observations suggest that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage sites and generates two staggered double-strand breaks. Together, these finding indicate the modular structure of PI-MleI having separate domains for DNA target recognition and cleavage and a bipartite structure of its homing site. After demonstrating the endonuclease activity of PI-MleI, we next examined the active site residues of PI-MleI involved in double-stranded DNA cleavage, which would further provide insights into its catalytic mechanism. Previously, sequence alignment analyses of LAGLIDADG enzymes carried out using different alignment programs identified the presence of 115VLGSLMGDGP123 sequence as DOD motif I (Block C) and 185LQRAVYLGDG194 or 210VLAIWYMDDG219C sequences as catalytic DOD motif II (Block E) in M. leprae RecA intein (PI-MleI). The bioinformatics analyses though on one hand identified the catalytic motifs in PI-MleI, on the other hand led to conflicting data in regard to the identity and the specific position of the catalytic DOD motif II within the PI-MleI polypeptide. We therefore, performed site-directed mutagenesis of key residues in these catalytic motifs and examined their effect on PI-MleI mediated catalysis. A wealth of mutagenesis and structural data, which exists concerning HEnases, suggests that catalytic centers carry essential aspartate residues, one in each of the LAGLIDADG motifs Accordingly, we chose to mutate conserved aspartates that have been previously implicated in catalysis. By site-directed mutagenesis, we constructed five mutant proteins, in which Asp122 was mutated to alanine, cysteine and threonine; whereas Asp193 and Asp218 were mutated to alanine. The identity of each mutant was ascertained by determining the complete nucleotide sequence of the mutant gene. Mutant proteins were further purified to >95% homogeneity using the purification strategy developed for wild type PI-MleI and were found to be devoid of any contaminating exonuclease. To study the effect of mutations in PI-MleI active site residues on its DNA-binding affinity, we examined the binding characteristics of the wild type PI-MleI and its aspartate variants with the intein-less recA substrate and the stability of protein-DNA complexes. All the mutants displayed similar binding affinity to the cognate DNA as that of the wild type PI-MleI, as judged by the comparison of their binding constants (Kd) which were found to be of the same order. Comparison of salt titration isotherms of wild type PI-MleI and its aspartate variants further revealed the similar salt titration midpoint for most of the mutants as that of wild type enzyme suggesting similar protein-DNA complexes stability. Although these results indicate the occurrence of stable complexes between PI-MleI variants and target DNA, to further define the DNA-binding properties of each mutant protein, wild-type PI-MleI and its variants were assayed by DNase I footprinting. All the mutants (D122A, D122C, D122T, D193A and D218A) showed an asymmetric footprint and protection of ~16 nucleotide residues on the upper and 12 nucleotide residues on the lower strand, respectively, near the intein-insertion site similar to the wild type PI-MleI. Together, these observations suggest that the aspartate substitutions in the catalytic motifs do not alter DNA recognition specificity of PI-MleI or its variants, and may not play a direct role in protein-DNA interactions, again implicating the existence of a modular structure of PI-MleI with distinct DNA-binding and catalytic domains. Wild-type PI-MleI although binds near the intein insertion site, but however was found to induce helical distortions only at the cleavage sites. To explore, if aspartate substitutions have any effect on the structural modifications in target DNA sequence, we carried out 2-aminopurine fluorescence with wild type PI-MleI and its variants. In agreement with the wild type enzyme, all the mutants showed increase in fluorescence with target DNA containing 2-AP only at the cleavage sites, but not at the binding sites. However, quantitative measurements of fluorescence change suggested that D122A and D193A mutants show nearly two-fold decrease in the magnitudes of spectral change at the cleavage site compared to wild type and other variants suggesting their involvement in the helical distortion process. To study the effect of Asp substitutions on the catalytic activity of PI-MleI, we performed cleavage assays using cognate plasmid pMLR DNA, with increasing concentrations of wild-type PI-MleI, or its variants and measured the double-stranded cleavage activity. Whereas, D122A and D193A mutants were completely inactive in double-stranded DNA cleavage under the conditions of the cleavage assay, D218A showed DNA cleavage activity comparable to that of the wild type PI-MleI. Similarly, D122T showed decrease in doublestranded DNA cleavage activity. Interestingly, D122C variant showed ~2-fold enhanced DNA cleavage, compared to the wild-type enzyme.Together, these findings provide compelling evidence to conclude that 115VLGSLMGDGP123 and 185LQRAVYLGDG194 motifs (Blocks C and E, respectively), but not 210VLAIWYMDDG219 motif (Block E), and that residues Asp122 and Asp193 play a direct role with respect to the catalytic mechanism of PI-MleI. In summary, these results suggest that the structural and mechanistic aspects of PI-MleI catalysis are distinct from other well-characterized LAGLIDADG-type homing endonucleases and thus provide further insights into understanding the function and evolution of LAGLIDADG homing enzymes.

FtsZ, the principal cell-division protein, polymerizes in GTP-dependent manner in vitro (Bramhill and Thompson, 1994; Mukherjee and Lutkenhaus, 1994; Rivas et al., 2000). FtsZ polymerization at the mid-cell site of bacterium leads to formation of a guiding scaffold, the Z-ring, for bacterial cytokinesis (Bi and Lutkenhaus, 1991; Sun and Margolin, 1998). GTP-induced polymerization process of FtsZ can be monitored in vitro Using 90º light scattering (Mukherjee and Lutkenhaus, 1999) and polymers formed can be visualized using transmission electron microscopy (Lu and Erickson, 1998) or quntitated in terms of the amount of FtsZ polymer pelleted during ultracentrifugation (Mukherjee and Lutkenhaus, 1998). The research work presented in this thesis focused on structure-function correlative analysis of Mycobacterium tuberculosis FtsZ(MtFtsZ0 and FtsZ proteins of Mycobacterium leprae (M1FtsZ), Mycobacterium smegmatis(MsFtsZ), and Streptomyces coelicolor (ScFtsZ) (as it is from Actinomycetes family to which mycobacteria belong) in vitro. It was initiated with investigation on the biochemical properties of Mycobacterium leprae FtsZ (M1FtsZ) in vitro. In comparison with those of MtFtsZ. Subsequently, the role of C-terminal stretch of amino acid residues of MtFtsZ in polymerization was investigated. Finally, a comparative analysis of the biochemical properties of MtFtsZ, MsFtsZ, and ScFtsZ was carried out in order to find out whether a correlation exists between the time taken by the FtsZ of a bacterium to polymerise and the generation time of the organism. The thesis is presented in five chapters. First Chapter gives an exhaustive introduction on the structure-function aspects of FtsZ. Second Chapter deals with materials used in this research work and details of various experimental methods [cloning and expression of FtsZ (White et. Al., 2000), decision and point mutagenesis, preparation of His-tag free MtFtsZ and M1FtsZ by thrombin cleavage method, 90º light scattering (Mukherjee and Lutkenhaus, 1999), White, et al., 2000), transmission electron microscopy (Lu and Erickson, 1998), pelleting assay for polymeric FtsZ (Mukherjee and Lutkenhaus, 1998), GTP-binding by UV-crosslinking (RayChaudhuri and Park, 1992; de Boer et al.,) GTPase assay(RayChaudhuri and Park, 1992); de Boer et al., 1992), Circular Dichroism (Saxena and Wetlaufer, 1971) and ANS fluorescence emission spectroscopy (Semisotnov, et al., 1991)]. The Chapters three to five contain all the data related to the research work, the outlines of which are given below. Chapter 3. Biochemical Characterisation of FtsZ Protein of Mycobacterium leprae In Comparison with the Biochemical Properties of FtsZ Protein of Mycobacteriulm tulberculosis In Vitro The major finding in this part of thesis work is on the demonstration that single reciprocal point mutation partially revives polymerization-inactive M1FtsZ and Inactivates polymerization-active MtFtsZ in vitro. In brief, soluble, recombinant M1FtsZ did not show detectable polymerization in vitro, in contrast to MtFtsZ, which showed appreciable polymerization, under standard conditions, when monitored using 90º light scattering assay and transmission electron microscopy. This was a surprising result, as M1FtsZ and MtFtsZ has 96% protein sequence identity. Mutation f T172 in the N-terminal domain of M1FtsZ to A172, as it exists in MtFtsZ, showed dramatic levels of polymerization in vitro. Reciprocal mutation of A172 in MtFtsZ to T172, as it exists in M1FtsZ, abolished polymerization in vitro. Further, M1FtsZ showed weak GTPase activity, in contrast to MtFtsZ, which showed appreciable GTPase activity. While T172A mutation enhanced GTPase activity of MtFtsZ in vitro. Circular dichroism spectroscopy and ANS fluorescence emission spectroscopy showed that there were no major secondary or tertiary structural changes in these point mutants. These observations demonstrate that the residue at position 172 plays a critical role in the polymerization of M1FtsZ and MtFtsZ, without appreciably affecting their respective GTpPase activity. Further, this result might have implications on evolution of a slow polymerizing FtsZ in slow growing bacteria. Further details of evolution related questions are addressed in Chapter 5. Chapter 4. Role of Carboxy Terminal Residues in the Biochemical Properties of FtsZ Protein of Mycobacterium tuberculosis In Vitro The major finding in this part of thesis work is the demonstration that the C-terminal end residues are critically required for polymerization of MtFtsZ in vitro, which is in direct contrast to the dispensability of C-terminal residues of Escherichia coli FtsZ(EcFtsZ), Bacillus subtilis FtsZ (BsFtsZ), and Pseudomonas aeruginosa (PaFtsZ) for polymerization. FtsZ protein from several bacterial species namely, Methanococcus jannaschii (MjFtsZ), Bacillus subtillis(BsFtsZ), Pseudomonas aeruginosa (PaFtsZ), and Aquifex aeolicus (AaFtsZ) (Lowe and Amos, 1998; Oliva et al., 2007), and Mycobacterium tuberculosis H37Rv (mtFtsZl Leung et al., 2004), whose crystal structures have been solved so far, were found to possess an N-terminal domain and a C-terminal domain that were connected to each other through a helix. The extreme C-terminal portion of all these FtsZ proteins is constituted by an unstructured tail (Lowe and Amos, 1998; Oliva et al., 2007l Leung et al., 2004), which is not found in the respective crystal structure of the protein. We examined whether C-terminal residues of soluble recombinant FtsZ of Mycobacterium tuberculosis (mtFtsZ) have any role in MtFtsZ polymerization in vitro. Deletion of C-terminal 66 residues (313-379) was found to abolish polymerization. Replacement of the C-terminal 66 residues with the extreme C-terminal 13-residue stretch (DDDDVDVPPFMRR) did not restore polymerization. Although the terminal R in DDDDVDVPPFMRR is dispensable for full-length MtFtsZ polymerization, the terminal R in DDDDVDVPPFMR is indispensable for polymerization. Neither replacement of this R, in the terminal R deletion mutant DDDDVDVPPFMR, with K/H/D/A residues enabled polymerization. GTP binding and GTPase activities of the mutants were partially affected. The indispensable nature of C-terminal residues for MtFtsZ polymerization in vitro is contrary to the dispensability of the equivalent extreme C-terminal residues of Escherichi coli, Pseudomonas aeruginosa, and Bacillus subtilis FtsZ (Wang et. Al., 1997; Cordell et al., 2003; Singh et al., 2007) for in vitro polymerization. The essentiality of C-terminal extreme residues of BtFtsZ for polymerization offers direction to design anti MtFtsZ polymerization agents. Chapter 5. An attempt to find correlation between Biochemical properties of FtsZ and Generation Time of the Bacterium The clue that there might be a correlation between FtsZ polymeristion and generation time of the bacterium came from the observation mentioned in chapter 3. The presence of polymerization-aversive T172 in the FtsZ of extremely slow-growing M. leprae 913.5 days generation time, Levy, 1970) and polymerization-favouring A172 in the FtsZ of M. tuberculosis(18hrs generation time, Patterson and Youmans, 1970). For a bacterium, which has short generation time, it might be conducive to have an FtsZ that will also polymerise fast. Conversely, for a bacterium, which has long generation, it might be conducive to have an FtsZ molecule that will polymerise slow. In this respect, a preliminary comparative study was carried out between the generation time of bacterial species, E. coli, Mycobacterium smegmatis, Streptomyces coelicolor, M leprae, and M. tuhberculosis and their respective FtsZ (EcFtsZ, MsFtsZ, M1FtsZ and MtFtsZ). Detailed biochemical characterization of EcFtsZ and MtFtsZ has already been reported in the literature. In this thesis work, biochemical characterisation of M1FtsZ(Chapter 3), ScFtsZ and MsFtsZ (in this Chapter) were carried out. E. coli, which has a generation time of 18-55 min(labrum, 1953), possesses FtsZ (EcFtsZ) that reaches steady state of polymerization in about 10 sec under standard conditions in vitro (Beamhill and Thompson, 1994), using 90º light scattering assay (Mukherjee and Lukenhaus, 1999). On the other hand, M. tuberculosis, which has a generation time of 18hrs in vivo (Patterson and Youmans, 1970) and 24 hrs in vitro (Hiriyanna and Ramakrishnan, 1986) possesses FtsZ (MtFtsZ) that reaches steady state of polymerization in about 6 min post-addiction of GTP in vitro (White et al., 2000). Further, M. leprae, which takes 13.5 days tp divide once in vivo (levy, 1970), possesses an FtsZ (M1FtsZ) that does not even show polymerization under standard conditions in vitro (Chapter 3 of this thesis). The organisms Mycobacterium smegmatis and Streptomyces coelicolor have generation times that fall in between those of the other three organisms mentioned above. While M. smegmatis divides once in 2-3 hrs (Husson, 1998), S. coelicolor has a variable generation time depending on growth condition, which can be as fast as once in 2.31 hours, depending upon growth conditions (Cox, 2004). We found ScFtsZ and MsFtsZ takes around 4 min to reach polymerization saturation after addition of GTP, EcFtsZ( 10 sec), MtFtsZ (10 min) and M1FtsZ (dose not polymerise in vitro) seem to indicate that there exists a correlation between polymerization saturation after addition of GTP, EcFtsZ (10sec), MtFtsZ (10 min) and M1FtsZ (does not polymerise in vitro) seem to indicate that there exists a correlation between polymerization saturation time and the generation time of the respective bacterium. But when we compared polymerization time of ScFtsZ and MsFtsZ (4 min both case) with MtFtsZ ( 6 min), we found that there is no linear correlation with generation time of these bacteria and the time taken by their FtsZ to reach steady state of polymerization. Many more bacterial FtsZ proteins need to be characterized to conclusively state wthether there exist a correlation between generation time of bacteria and the time taken for their FtsZ to reach steady state of polymeristion. Such correlation would simply reveal the fact that the primary structure of an FtsZ protein might have evolved to suit the generation time of the bacterium.

Submitted by Anderson Silva (avargas@icict.fiocruz.br) on 2012-10-15T19:20:49Z No. of bitstreams: 1 amanda_n_b_fontes_ioc_bcm_0050_2011.pdf: 3773109 bytes, checksum: 8933f048c4d79d33efa1313c366344a8 (MD5) / Made available in DSpace on 2012-10-15T19:20:49Z (GMT). No. of bitstreams: 1 amanda_n_b_fontes_ioc_bcm_0050_2011.pdf: 3773109 bytes, checksum: 8933f048c4d79d33efa1313c366344a8 (MD5) Previous issue date: 2011-05-26 / Fundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhães. Recife, PE, Brasil / A hanseníase é uma doença infecto-contagiosa crônica, causada pelo Mycobacterium leprae. Após o sequenciamento do genoma deste patógeno, inúmeros esforços têm sido feitos na busca por sequências repetitivas com potencial para diferenciar isolados de M. leprae. Atualmente, VNTRs têm sido utilizados com o objetivo de compreender a diversidade genética deste patógeno em áreas com alta prevalência da doença. Além disso, SNPs também têm contribuído para elucidar aspectos referentes à disseminação da hanseníase pelo mundo. Neste estudo, a variabilidade genética de 292 isolados de M. leprae oriundos de amostras clínicas de pacientes hansenianos das regiões norte, nordeste e sudeste do país foi avaliada utilizando 16 VNTRs e três SNPs. O polimorfismo dos diferentes VNTRs foi determinado através de MLVA (Multiple-locus VNTR analysis) utilizando FLA (Fragment lenght analysis), enquanto que os SNPs foram analisados através de PCR-RFLP e/ou sequenciamento. O poder discriminatório dos 16 VNTRs foi de 0.999, sendo que as repetições de dinucleotídeos AT e o trinucleotídeo GAA21 apresentaram os maiores índices de discriminação alélica. Além da genotipagem de isolados de M. leprae de biópsias de pele, material de linfa fixado em lâmina de baciloscopia também foi utilizado como uma fonte alternativa para obtenção de DNA deste bacilo. Com relação à genotipagem por SNP, foi possível observar a predominância do genótipo 3, associado à população européia, em Rondônia, Rio de Janeiro e São Paulo. Já o genótipo 4, oriundo da África Ocidental, foi predominante em Pernambuco e Fortaleza. A presença dos diferentes genótipos e sua predominância em determinadas áreas corroboram com o processo de colonização do país que se reflete na atual composição étnica da população brasileira. Com base nos perfis obtidos através dos VNTRs e SNPs, foram identificados seis grupos geneticamente idênticos: quatro do Ceará, um de Rondônia e outro formado entre amostras de Minas Gerais e São Paulo. Nenhuma associação entre os pacientes enquadrados nos grupos da região norte e sudeste do país foi estabelecida. Todavia, foi possível observar que os grupos foram formados entre indivíduos oriundos de mesmo estado ou região geográfica. Com relação aos grupos formados entre as amostras do Ceará, associações entre o gênero masculino e o local de origem das amostras foram estabelecidas com base nos genótipos de M. leprae, sugerindo que estes seriam fatores de risco para a transmissão da hanseníase. Neste estudo, também foi possível avaliar amostras de pacientes com hanseníase recidiva para quatro VNTRs e os achados sugerem que estes pacientes foram re-infectados ou que houve mudança da população bacteriana durante a recidiva da doença. Os resultados comprovam que a genotipagem de M. leprae é uma ferramenta importante na elucidação de aspectos relativos à transmissão e disseminação da doença pelo mundo. / Leprosy is a chronic infectious disease caused by Mycobacterium leprae. After sequencing the genome of this pathogen, numerous efforts have been made to identify repetitive sequences with potential to differentiate isolates of M. leprae. Currently, VNTRs have been used in order to understand the genetic diversity of this pathogen in areas with high prevalence of leprosy. Another form of genetic polymorphism, namely single nucleotide polymorphisms (SNPs), elucidated aspects related to the spread of leprosy in the world. In this study, the genetic variability of 292 M. leprae isolates from clinical leprosy patients from the north, northeast and southeast of the country, were analyzed for composition of 16 VNTRs and three SNPs. The genetic variability of different VNTRs was evaluated by MLVA (Multiple-locus VNTR analysis) using FLA (Fragment length analysis) while the SNPs were analyzed by RFLP-PCR and/or sequencing. The discriminatory power of 16 VNTRs was 0.999 and the AT dinucleotides and the GAA21 trinucleotide demonstrated the higher rates of allelic discrimination. In addition to the genotyping of isolates of M. leprae derived from skin biopsy samples, lymph fixed in ZN slides was also used as an alternative source to obtain DNA. By SNP typing, we observed the high prevalence of genotype 3, previously associated with Europeans, in the states of Rondônia, Rio de Janeiro and São Paulo. On the other hand, genotype 4, originating from Western Africa, was predominant in Pernambuco and Fortaleza. The presence of different genotypes and their prevalence in certain areas of Brazil is in accordance to the country’s history of colonization which reflects in the current ethnic composition of the population. Based on the VNTR and SNP profiles, six identical groups of two isolates each were identified: four from Ceará, one from Rondônia and another composed of samples from Minas Gerais and São Paulo. No association between patients from north and southeast of the country was established, however, most groups were composed by patients from the same state or geographic region. When performing an analysis of genotype similarity with patient data in groups from Ceará, we observed association of male gender and place of origin with M. leprae genotype grouping, suggesting these could be risk factors for transmission of leprosy. In this analysis, patients with leprosy relapse were also analyzed for four VNTRs and the results suggest the occurrence of re-infection or of bacterial population shift during disease relapse. The results of this study demonstrate that genotyping of M. leprae is an important tool to elucidate aspects of transmission and spread of disease in the world.

Leprosy is slowly progressive, chronic infectious disease, caused by the bacillus Mycobacterium leprae (M. leprae), with a potentially severe, mutilating and stigmatizing evolution. It represents a major public health problem in a lot of the countries around the world. Since 1982, the World Health Organization (WHO) recommended multidrug therapy (MDT) for the treatment of the disease with the combination of three drugs (rifampicin, clofazimine and dapsone) in multibacillary cases, and two, for the paucibacillary (rifampicin and dapsone). When more than one drug is used, the risks of adverse effects are increased. Retrospective papers reveal that adverse effects of drugs of MDT are one of the causes of irregularity or noncompliance with treatment, which make difficult the combat against the disease as a public heath problem. Furthermore, the occurrence of these events in an economically active age group may cause work absenteeism and be onerous. On other hand, spontaneous reports of adverse effects systems are at risk of subnotification, demanding the elaboration of specific forms of notification. Therefore, this paper aimed: 1) To verify the frequency and types of adverse effects to the drugs used on multidrug treatment (MDT) in two centers of reference in leprosy treatment, as well as the occurrence of serious adverse events leading to change in the treatment and its correlation with the presence of other diseases; 2) To identify clinical and epidemiological aspects of risk associated with the occurrence of adverse reactions and the instant of its appearance. 3) To analyze the risk of adverse effects interfere with treatment adherence, therapeutic response and the occurrence of leprosy reaction in patients followed in two referral centers treating leprosy. We designed a prospective study, after approval of the ethics committee, with monthly evaluation of the patients in two centers of leprosy treatment during the period of November 2011 and May 2014: in the ambulatory of (Des)Mancha-Sergipe Project, Universiy Hospital, Universidade Federal de Sergipe, and Reference Center of Leprosy, CEMAR (Centro de Especialidades Médicas de Aracaju). We applied a questionnaire to collect demographic, clinic, epidemiologic parameters such as sex, age, Body Mass Index (BMI), operational form of disease and adverse effects information in monthly evaluation, and analyzed their relationship to the therapeutic response, occurrence of leprosy reactions and treatment adherence. After the inclusion and exclusion criteria, we followed 119 of 245 patients that initiated the MDT between November 2011 and May 2013 in two centers. Adverse effects to MDT treatment were common, with a predominance of cutaneous related ones associated to clofazimina, such as ichthyosis/ xerosis (70.6%) and skin pigmentation (65.5%), followed by anemia related to dapsone (62.2 %). Although most adverse events to MDT were mild, severe adverse effects were detected, such as Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS) in 3 patients, who required the suspension of MDT and replacement of dapsone for another drug, besides haemolytic anemia and drug hepatitis. Therapy was replaced in 13 patients, of whom 12 had at least 1 disease, which indicates probable use of other medications and suggests possible drug interaction as influence on adverse reactions, especially in the more severe. It was observed association of adverse effects to MDT with gender, age group, body mass index (BMI), operational classification and occurrence of leprosy reaction. The adverse effects did not impact on the adherence to treatment or therapeutic response. Thus, although retrospective papers show that adverse effects to drugs of MDT are important cause of irregularity or noncompliance with treatment, this present study was prospective, revealing that the active search for patients and specific adverse effect investigation forms can prevent leprosy treatment dropout. / A Hanseníase é uma doença infecciosa crônica, lentamente progressiva, causada pelo bacilo Mycobacterium leprae (M. leprae), de evolução potencialmente grave, mutilante e estigmatizante. Representa um grande problema de saúde pública em vários países do mundo. Desde 1982, a Organização Mundial de Saúde (OMS) preconizou a poliquimioterapia (PQT) para o tratamento da doença com a combinação de três drogas (rifampicina, clofazimina e dapsona) nos casos multibacilares, e de duas, para os paucibacilares (rifampicina e dapsona). Quando se utiliza mais de uma droga, existe o risco da soma de efeitos adversos. Estudos retrospectivos, transversais e de série de casos revelam que as reações adversas às drogas utilizadas na poliquimioterapia (PQT) constituem uma das causas de irregularidade ou abandono do tratamento, dificultando o combate da doença como problema de saúde pública. Além disso, a ocorrência desses eventos em faixa etária economicamente ativa pode levar ao absenteísmo ao trabalho e tornar-se onerosa. Por outro lado, os sistemas de relato espontâneo das reações adversas são prejudicados pela subnotificação, demandando a elaboração de formulários específicos de notificação. Diante disso, o presente estudo teve como objetivos: 1) Verificar a frequência e tipos de efeitos adversos às drogas usadas na poliquimioterapia (PQT), bem como a ocorrência de eventos adversos graves que levem à mudança no esquema terapêutico e sua correlação com a presença de comorbidades. 2) Identificar as variáveis de risco clínicas e epidemiológicas associadas à ocorrência das reações adversas e ao instante de seu aparecimento. 3) Analisar o risco das reações adversas interferirem na adesão ao tratamento, na resposta terapêutica e na ocorrência de reação hansênica em pacientes acompanhados em dois centros de referência do tratamento de hanseníase. Foi realizado estudo prospectivo, com avaliação mensal dos pacientes de dois centros de tratamento de hanseníase, o ambulatório do projeto (Des)Mancha-Sergipe do Hospital Universitário da Universidade Federal de Sergipe e no Centro de Referência em Hanseníase do CEMAR (Centro de Especialidades Médicas de Aracaju), no período de Novembro de 2011 a Maio de 2014. Dados demográficos, clínicos, epidemiológicos e laboratoriais foram coletados em avaliações mensais, para investigação de efeitos adversos e sua relação com forma clínica da doença, resposta terapêutica, ocorrência de reações hansênicas e aderência ao tratamento. Após os critérios de inclusão de exclusão, foram acompanhados 119 de 245 pacientes que iniciaram a PQT entre Novembro de 2011 e Maio de 2013 nos 2 centros. As reações adversas ao tratamento da PQT mostraram-se frequentes, com predomínio dos efeitos cutâneos relacionados à clofazimina, como ictiose/ xerose (70,6%) e pigmentação da pele (65,5%), seguidos pela anemia relacionada à dapsona (62,2%). Embora a maioria dos eventos adversos laboratoriais tenham sido leves, efeitos adversos graves foram detectados, a exemplo da síndrome de reação à droga com eosinofilia e sintomas sistêmicos (DRESS), observada em 3 pacientes, que requereu suspensão da PQT e substituição da Dapsona por outra droga, além de anemia hemolítica e hepatite medicamentosa. A terapêutica foi substituída em 13 pacientes, dos quais 12 tinham pelo menos 1 comorbidade, o que denota provável uso de outras medicações e sugere possível interação medicamentosa como influência nas reações adversas, especialmente nas mais graves. Observou-se associação de eventos adversos à PQT com o sexo feminino, faixa etária, Índice de Massa Corpórea (IMC), classificação operacional e ocorrência de reação hansênica. Não se observou repercussão dos eventos adversos na aderência ao tratamento ou na resposta terapêutica. Dessa forma, embora estudos retrospectivos apontem as reações adversas às drogas da PQT como importante causa de tratamento incompleto, o presente estudo foi prospectivo, revelando que a busca ativa dos pacientes e a utilização de formulário de investigação de eventos adversos podem prevenir o abandono terapêutico.

Pathogenic bacteria such as M.tuberculosis have evolved several mechanisms to aid their intracellular survival and subvert host defenses. One of the contributing factors is thought to be the production and secretion of large amount of cAMP, Mycobacterial genomes encode a large number of adenylyl cyclases distinct in their structure and regulatory mechanisms. The roles of these enzymes in the physiology and pathogenesis of virulent mycobacteria are only now being elucidated. The roles of phosphodiesterases (PDEs), which serve to lower cAMP levels through degradation are, however, relatively unexplored. The Rv0805 gene was previously shown to code for an active phosphodiesterase from Mycobacterium tuberculosis. Bioinformatics analysis revealed that orthologs of Rv0805 were found even in eukaryotes. Biochemical and structural characterization of Rv0805 revealed that it was a class III cAMP phosphodiesterase. Comparative genomics identified a close ortholog of Rv0805 in M. leprae (ML2210). The genome of M. leprae Encodes only 1,604 predicted proteins and possesses the highest number of pseudogenes, 1,116. The retention of a functional PDE, the ortholog of Rv0805, in the minimal genome of M. leprae is indicative of its importance in cellular physiology. Biochemical characterization of proteins from M. leprae and use of heterologous hosts will help understand this human pathogen better, since there are no tools currently available to genetically manipulate this bacterium. Sequence analysis of ML2210 revealed the presence of conserved motifs and residues known to be critical for catalysis and unique to class III phosphodiesterases. ML2210 shares 83% sequence identity with Rv0805 and 24% sequence identity with the phosphodiesterase from E. coli (cpdA). In vitro biochemical characterization of ML2210 using non-nucleotide colorigenic and cyclic nucleotide substrates revealed that it was an enzymatically active phosphodiesterase. Kinetic parameters of ML2210 with respect ot colorigenic substrates revealed that its catalytic properties were similar to that of Rv0805. However, with respect to hydrolysis of 3’, 5’-cAMP, ML2210 was catalytically more efficient than Rv0805, suggesting that in spite of being orthologs, these enzymes have evolved distinct specificities at their active site. A parallel of monoclonal antibodies raised to Rv0805 was also used understand the differences in the biochemical properties of Rv0805 and ML2210 better. It was observed that only one monoclonal antibody was able to recognize ML2210 by ELISA and not by Western blot analysis. These results revealed that conformational differences between ML2210 and Rv0805 exist. Over-expression of ML2210 in M. smegmatis resulted in a modest decrease in intracellular cAMP levels. Despite the absence of a predicted transmembrane region or a membrane-targeting signal, ML2210 localized to the cell envelop fraction upon over expression in M. smegmatis. Moreover, like Rv0805, over-expression of ML2210 also resulted in perturbation of the cell wall of M. smegmatis, arguing for additional cellular roles of this protein. Orthologs of Rv0805 or ML2210 are found only in slow growing mycobacteria suggesting that other cyclic nucleotide phosphodiesterases could regulate cAMP levels in fast growing mycobacteria like M. smegmatis. Since BLAST results did not retrieve an ortholog of Rv0805 or ML2210, COG1409 (COG database) containing Rv0805 was examined for the presence of other mycobacterial phosphodiesterases. Bioinformatics analysis identified Rv2795c as another PDE from M. tuberculosis. Sequence analysis of Rv2795c revealed the presence of all the motifs conserved in the class III PDEs but Rv2795c shared only 22% sequence identity with Rv0805 and 19% sequence identity with CpdA. Importantly, an ortholog of Rv2795c was identified in M. leprae. Interestingly. Rv2795c and its orthologs branched away from Rv0805, making it phylogenetically distinct and hence warranting further characterization. Recombinant, purified MSMEG_2647 (the Rv2795c ortholog from M. smegmatis) was able to hydrolyze cyclic nucleotides and other phosphodiester substrates in vitro. The Km for colorigenic substrates was higher when compared to the Km of ML2210 or Rv0805 for these substrates. However, the kinetic parameters of MSMEG_2647 for cyclic nucleotides were comparable to those of ML2210 or Rv0805. MSMEG_2647 was a metal dependent enzyme and among the panel of metals tested, Mn2+ supported the highest in vitro catalytic activity of MSMEG_2647. Zn2+ inhibited the catalytic activity of MSMEG_2647. In order to gain insight into the catalysis of MSMEG_2647, the end products of cAMP hydrolysis by MSMEG_2647 were analysed using reverse phase HPLC. The assay revealed that the end products of cyclic nucleotide hydrolysis by MSMEG_2647 were different when compared to the end products of hydrolysis of the same substrates by Rv0805 or ML2210. This suggests differences in the architecture of the active site residues of the mycobacterial MPEs. A mutational anlaysis of the active site residues in MSMEG_2647 was carried out to identify residues involved in substrate recognition and metal coordination. Although Rv0805 and MSMEG_2647 shared only a 22% sequence identity, MSMEG_2647 displayed strict conservation in the core MPE motifs. Mutation of the active residues N97 and H98 in Rv0805 had led to an abrogation of its catalytic activity. However, corresponding mutations of N76A and H77A in MSMEG_2647, did not lead to a loss in its catalytic activity. A third mutation known to be important for the catalytic activity of Rv0805 (D19) was incorporated. The corresponding residue at D19 position was mutated to an alanine. The catalytic activity of MSMEG_2647D19AN76AH77A mutant was abrogated, suggesting that while the core MPE motifs are conserved between mycobacterial PDEs, differences in the ensemble of the active site residues contributing to their catalytic activity exist. Thus, at least two biochemically diverse PDE clades are found in mycobacterial species. In order to decipher the function of MSMEG_2647, its expression was monitored during the growth of M. Smegmatis. The promoter of MSMEG_2647 displayed maximum activity during the logarithmic phase of M. smegmatis growth after which its activity declined as M. smegmatis entered the stationary phase. However in contrast to this, the transcript corresponding to msmeg_2647 mRNA was found at both logarithmic and stationary phases. The MSMEG_2647 protein was also detected at both logarithmic and stationary phases of M. smegmatis. These results suggest that additional factors may contribute to the stability of msmeg_2647 mRNA and protein levels. Localization studies of MSMEG_2647 revealed that MSMEG_2647 was present in the cytosol as well as in the cell envelope fractions. Interestingly, over-expression of MSMEG_2647 did not result in a significant increase in PDE activity in various subcellular fractions, suggesting tight regulation on the in vivo activity in various subcellular fractions, suggesting tight regulation on the in vivo activity of MSMEG_2647. In addition, over-expression of MSMEG_2647 in M. smegmatis led to only a modest decrease in cAMP levels in M. smegmatis. These results suggested additional roles of MSMEG_2647 in the biology of mycobacteria. Overexpression of MSMEG_2647 peturbed the integrity of cell wall as assessed by the use of lipophillic indicators of cell growth, crystal violet and malachite green, and a cell wall targeting antibiotic, isoniazid. Analyzing the gene neighborhood of MSMEG_2647 provided an insight into its putative function. It was observed that the stop codon of msmeg_2647 overlapped with the start codon of msmeg_2648 and stop codon of msmeg-2648 overlapped with the start codon of msmeg_2649. RT PCR was carried out at logarhtimic and stationary phases of M. smegmatis growth, which revealed that a polycistronic mRNA was being transcribed. These results confirmed that msmeg_2647, msmeg_2648 and msmeg_2649 were a part of an operon. Interestingly, these three genes as a gene cluster were confined to only those actinobacteria that produced mycolic acids. An operon often encodes products that form multiprotein complexes and operate in a common pathway. Since there were a part of an operon, a GST pull-down approach was employed to test if MSMEG_2647, MSMEG_2648 and MSMEG_2649 could physically interact. It was observed that MSMEG_2647 interacted with MSMEG_2648 and MSMEG_2649. MSMEG_2648 in turn interacted with MSMEG_2649. A role for MSMEG_2647 as a scaffold recruiting MSMEG_2648 and MSMEG_2649 is therefore proposed. In turn, a complex formation with these proteins may regulate the activity of MSMEG_2647. Attempts to generate a knock out of msmeg_2647 in M. smegmatis by homologous recombination were not successful suggesting either the gene was essential or a polar effect on msmeg_2648(an essential gene for the viability of M. smegmatis) may not allow msmeg_2647 to be deleted from the genome of M. smegmatis. In summary, this study has identified and characterized two new phosphodiesterases from mycobacteria, one from the pathogenic mycobacterium, M. leprae and the other, a PDE from M. smegmatis that is conserved in all species of mycobacteria. Several, key biochemical differences were observed using biochemical and biological approaches. It appears that the cellular roles of mycobacterial phsophodiesterases may extend beyond cAMP hydrolysis, with these proteins not only regulating cell wall properties but also acting as scaffolding proteins in the cell.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O diagnóstico da hanseníase neural pura baseia-se em dados clínicos e laboratoriais do paciente, incluindo a histopatologia de espécimes de biópsia de nervo e detecção de DNA de Mycobacterium leprae (M. leprae) pelo PCR. Como o exame histopatológico e a técnica PCR podem não ser suficientes para confirmar o diagnóstico, a imunomarcação de lipoarabinomanana (LAM) e/ou Glicolipídio fenólico 1 (PGL1) - componentes de parede celular de M. leprae foi utilizada na primeira etapa deste estudo, na tentativa de detectar qualquer presença vestigial do M. leprae em amostras de nervo sem bacilos. Além disso, sabe-se que a lesão do nervo na hanseníase pode diretamente ser induzida pelo M. leprae nos estágios iniciais da infecção, no entanto, os mecanismos imunomediados adicionam severidade ao comprometimento da função neural em períodos sintomáticos da doença. Este estudo investigou também a expressão imuno-histoquímica de marcadores envolvidos nos mecanismos de patogenicidade do dano ao nervo na hanseníase. Os imunomarcadores selecionados foram: quimiocinas CXCL10, CCL2, CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, e metaloproteinases 2 e 9. O estudo foi desenvolvido em espécimes de biópsias congeladas de nervo coletados de pacientes com HNP (n=23 / 6 BAAR+ e 17 BAAR - PCR +) e pacientes diagnosticados com outras neuropatias (n=5) utilizados como controle. Todas as amostras foram criosseccionadas e submetidas à imunoperoxidase. Os resultados iniciais demonstraram que as 6 amostras de nervos BAAR+ são LAM+/PGL1+. Já entre as 17 amostras de nervos BAAR-, 8 são LAM+ e/ou PGL1+. Nas 17 amostras de nervos BAAR-PCR+, apenas 7 tiveram resultados LAM+ e/ou PGL1+. A detecção de imunorreatividade para LAM e PGL1 nas amostras de nervo do grupo HNP contribuiu para a maior eficiência diagnóstica na ausência recursos a diagnósticos moleculares. Os resultados da segunda parte deste estudo mostraram que foram encontradas imunoreatividade para CXCL10, CCL2, MMP2 e MMP9 nos nervos da hanseníase, mas não em amostras de nervos com outras neuropatias. Além disso, essa imunomarcação foi encontrada predominantemente em células de Schwann e em macrófagos da população celular inflamatória nos nervos HNP. Os outros marcadores de ativação imunológica foram encontrados em leucócitos (linfócitos T e macrófagos) do infiltrado inflamatório encontrados nos nervos. A expressão de todos os marcadores, exceto CXCL10, apresentou associação com a fibrose, no entanto, apenas a CCL2, independentemente dos outros imunomarcadores, estava associada a esse excessivo depósito de matriz extracelular. Nenhuma diferença na frequência da imunomarcação foi detectada entre os subgrupos BAAR+ e BAAR-, exceção feita apenas às células CD68+ e HLA-DR+, que apresentaram discreta diferença entre os grupos BAAR + e BAAR- com granuloma epitelioide. A expressão de MMP9 associada com fibrose é consistente com os resultados anteriores do grupo de pesquisa. Estes resultados indicam que as quimiocinas CCL2 e CXCL10 não são determinantes para o estabelecimento das lesões com ou sem bacilos nos em nervo em estágios avançados da doença, entretanto, a CCL2 está associada com o recrutamento de macrófagos e com o desenvolvimento da fibrose do nervo na lesão neural da hanseníase. / The diagnosis of pure neural leprosy (PNL) is based on clinical and laboratory data, including the histopathology of nerve biopsy specimens and detection of M. leprae DNA by polymerase chain reaction (PCR). Given that histopathological examination and PCR methods may not be sufficient to confirm diagnosis, immunolabeling of lipoarabinomanan (LAM) and/or phenolic glycolipid 1 (PGL1) M. leprae wall components were utilized in the first step of this investigation in an attempt to detect any vestigial presence of M. leprae in AFB- nerve samples. Furthermore, its well known that nerve damage in leprosy can be directly induced by Mycobacterium leprae in the early stages of infection; however, immunomediated mechanisms add gravity to the impairment of neural function in symptomatic periods of the disease. Therefore, this study also investigated the immunohistochemical expression of immunomarkers involved in the pathogenic mechanisms of leprosy nerve damage. These markers selected were CXCL10, CCL2 chemokines and CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, metalloproteinases 2 and 9 in nerve biopsy specimens collected from leprosy (23) and nonleprosy patients (5) suffering peripheral neuropathy. Twenty-three PNL nerve samples (6 AFB+ and 17 AFB-PCR+) were cryosectioned and submitted to LAM and PGL1 immunohistochemical staining by immunoperoxidase; 5 nonleprosy nerve samples were used as controls. The 6 AFB-positive samples showed LAM/PGL1 immunoreactivity. Among the 17 AFB- samples, only 8 revealed LAM and/or PGL1 immunoreactivity. In 17 AFB-PCR+ patients, just 7 had LAM and/or PGL1-positive nerve results. In the PNL cases, the detection of immunolabeled LAM and PGL1 in the nerve samples would have contributed to enhanced diagnostic efficiency in the absence of molecular diagnostic facilities. The results of the second part of this study showed that CXCL10-, CCL2-, MMP2- and MMP9-immunoreactivities were found in the leprosy nerves but not in nonleprosy samples. Immunolabeling was predominantly found in recruited macrophages and Schwann cells composing the inflammatory cellular population in the leprosy-affected nerves. The immunohistochemical expression of all the markers, but CXCL10, was associated with fibrosis; however, only CCL2 was, independently from the other markers, associated with this excessive deposit of extracellular matrix. No difference in the frequency of the immunolabeling was detected between the AFB+ and AFB- leprosy subgroups of nerves, exception made to some statistical tendency to difference in regard to CD68+ and HLA-DR+ cells in the AFB- nerves exhibiting epithelioid granuloma. MMP9 expression associated with fibrosis is consistent with previous results of this research group. The findings conveys the idea that CCL2 and CXCL10 chemokines at least in advanced stages of leprosy nerve lesions are not determinant for the establishment of AFB+ or AFB- leprosy lesions, however, CCL2 is associated with macrophage recruitment and fibrosis.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O diagnóstico da hanseníase neural pura baseia-se em dados clínicos e laboratoriais do paciente, incluindo a histopatologia de espécimes de biópsia de nervo e detecção de DNA de Mycobacterium leprae (M. leprae) pelo PCR. Como o exame histopatológico e a técnica PCR podem não ser suficientes para confirmar o diagnóstico, a imunomarcação de lipoarabinomanana (LAM) e/ou Glicolipídio fenólico 1 (PGL1) - componentes de parede celular de M. leprae foi utilizada na primeira etapa deste estudo, na tentativa de detectar qualquer presença vestigial do M. leprae em amostras de nervo sem bacilos. Além disso, sabe-se que a lesão do nervo na hanseníase pode diretamente ser induzida pelo M. leprae nos estágios iniciais da infecção, no entanto, os mecanismos imunomediados adicionam severidade ao comprometimento da função neural em períodos sintomáticos da doença. Este estudo investigou também a expressão imuno-histoquímica de marcadores envolvidos nos mecanismos de patogenicidade do dano ao nervo na hanseníase. Os imunomarcadores selecionados foram: quimiocinas CXCL10, CCL2, CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, e metaloproteinases 2 e 9. O estudo foi desenvolvido em espécimes de biópsias congeladas de nervo coletados de pacientes com HNP (n=23 / 6 BAAR+ e 17 BAAR - PCR +) e pacientes diagnosticados com outras neuropatias (n=5) utilizados como controle. Todas as amostras foram criosseccionadas e submetidas à imunoperoxidase. Os resultados iniciais demonstraram que as 6 amostras de nervos BAAR+ são LAM+/PGL1+. Já entre as 17 amostras de nervos BAAR-, 8 são LAM+ e/ou PGL1+. Nas 17 amostras de nervos BAAR-PCR+, apenas 7 tiveram resultados LAM+ e/ou PGL1+. A detecção de imunorreatividade para LAM e PGL1 nas amostras de nervo do grupo HNP contribuiu para a maior eficiência diagnóstica na ausência recursos a diagnósticos moleculares. Os resultados da segunda parte deste estudo mostraram que foram encontradas imunoreatividade para CXCL10, CCL2, MMP2 e MMP9 nos nervos da hanseníase, mas não em amostras de nervos com outras neuropatias. Além disso, essa imunomarcação foi encontrada predominantemente em células de Schwann e em macrófagos da população celular inflamatória nos nervos HNP. Os outros marcadores de ativação imunológica foram encontrados em leucócitos (linfócitos T e macrófagos) do infiltrado inflamatório encontrados nos nervos. A expressão de todos os marcadores, exceto CXCL10, apresentou associação com a fibrose, no entanto, apenas a CCL2, independentemente dos outros imunomarcadores, estava associada a esse excessivo depósito de matriz extracelular. Nenhuma diferença na frequência da imunomarcação foi detectada entre os subgrupos BAAR+ e BAAR-, exceção feita apenas às células CD68+ e HLA-DR+, que apresentaram discreta diferença entre os grupos BAAR + e BAAR- com granuloma epitelioide. A expressão de MMP9 associada com fibrose é consistente com os resultados anteriores do grupo de pesquisa. Estes resultados indicam que as quimiocinas CCL2 e CXCL10 não são determinantes para o estabelecimento das lesões com ou sem bacilos nos em nervo em estágios avançados da doença, entretanto, a CCL2 está associada com o recrutamento de macrófagos e com o desenvolvimento da fibrose do nervo na lesão neural da hanseníase. / The diagnosis of pure neural leprosy (PNL) is based on clinical and laboratory data, including the histopathology of nerve biopsy specimens and detection of M. leprae DNA by polymerase chain reaction (PCR). Given that histopathological examination and PCR methods may not be sufficient to confirm diagnosis, immunolabeling of lipoarabinomanan (LAM) and/or phenolic glycolipid 1 (PGL1) M. leprae wall components were utilized in the first step of this investigation in an attempt to detect any vestigial presence of M. leprae in AFB- nerve samples. Furthermore, its well known that nerve damage in leprosy can be directly induced by Mycobacterium leprae in the early stages of infection; however, immunomediated mechanisms add gravity to the impairment of neural function in symptomatic periods of the disease. Therefore, this study also investigated the immunohistochemical expression of immunomarkers involved in the pathogenic mechanisms of leprosy nerve damage. These markers selected were CXCL10, CCL2 chemokines and CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, metalloproteinases 2 and 9 in nerve biopsy specimens collected from leprosy (23) and nonleprosy patients (5) suffering peripheral neuropathy. Twenty-three PNL nerve samples (6 AFB+ and 17 AFB-PCR+) were cryosectioned and submitted to LAM and PGL1 immunohistochemical staining by immunoperoxidase; 5 nonleprosy nerve samples were used as controls. The 6 AFB-positive samples showed LAM/PGL1 immunoreactivity. Among the 17 AFB- samples, only 8 revealed LAM and/or PGL1 immunoreactivity. In 17 AFB-PCR+ patients, just 7 had LAM and/or PGL1-positive nerve results. In the PNL cases, the detection of immunolabeled LAM and PGL1 in the nerve samples would have contributed to enhanced diagnostic efficiency in the absence of molecular diagnostic facilities. The results of the second part of this study showed that CXCL10-, CCL2-, MMP2- and MMP9-immunoreactivities were found in the leprosy nerves but not in nonleprosy samples. Immunolabeling was predominantly found in recruited macrophages and Schwann cells composing the inflammatory cellular population in the leprosy-affected nerves. The immunohistochemical expression of all the markers, but CXCL10, was associated with fibrosis; however, only CCL2 was, independently from the other markers, associated with this excessive deposit of extracellular matrix. No difference in the frequency of the immunolabeling was detected between the AFB+ and AFB- leprosy subgroups of nerves, exception made to some statistical tendency to difference in regard to CD68+ and HLA-DR+ cells in the AFB- nerves exhibiting epithelioid granuloma. MMP9 expression associated with fibrosis is consistent with previous results of this research group. The findings conveys the idea that CCL2 and CXCL10 chemokines at least in advanced stages of leprosy nerve lesions are not determinant for the establishment of AFB+ or AFB- leprosy lesions, however, CCL2 is associated with macrophage recruitment and fibrosis.

La lèpre est une maladie tropicale négligée qui atteint près de 200 000 personnes chaque année et dont l’agent causal est Mycobacterium leprae. La susceptibilité génétique de l’hôte à la maladie est bien établie, et a permis de comprendre certains mécanismes de la physiopathologie de la maladie. Il existe par ailleurs une grande variabilité inter-individuelle des manifestions cliniquesde la maladie, qui s’étendent d’un pôle dit tuberculoïde à un pôle dit lépromateux. Nous avons cherché à identifier les facteurs de susceptibilité génétique à cette polarisation de la maladie. Nous avons tout d’abord décrit que le sexe et l’âge sont des facteurs non-génétiques associés à ce phénotype.Notre travail s’est ensuite appuyé sur les outils classiques de l’épidémiologie génétique, c’est à dire les études de liaison et d’association, pour identifier des variants génétiques qui influencent la polarisation de la lèpre. Nous avons utilisé une puce à ADN pangénomique avec plus de 500 000 marqueurs pour génotyper un échantillon de familles vietnamiennes comprenant 939 malades, dont 692 enfants. Nous avons identifié une liaison de la région 19p12 avec la polarisation de la lèpre. L’étude d’association n’a pas permis d’identifier de signal significatif à l’échelle du génome. Nous avons développé un nouveau test d’association pour des données familiales qui a permis d’améliorer les résultats sans atteindre la significativité. Notre travail sera prolongé par des études d’association dans deux populations cas-témoins du Vietnam et du Brésil. Nous chercherons à identifier les marqueurs causaux au sein de la région de liaison 19p12 d’une part, et à découvrir de nouveaux variants d’autre part. L’identification de marqueurs associés à la polarisation de la lèpre permettra de mieux prévoir l’évolution de la maladie et de proposer des traitements plus ciblés selon le risque génétique individuel. / Leprosy is a neglected tropical disease that affects nearly 200,000 people each year and caused byMycobacterium leprae. Genetic host susceptibility to the disease is well established, and helped to understand some of the mechanisms of the disease’s physiopathology. There is also a wide inter-individual variability of the clinical manifestations of the disease, which runs from a so-said tuberculoid to a so-said lepromatous pole. We sought to identify genetic susceptibility factors for this polarization of the disease. We initially described gender and age as non-genetic factors associated with this phenotype. We then based our analysis on the classical tools from thefield of genetic epidemiology, namely linkage and association studies, to identify genetic variants that influence leprosy polarization. We used a DNA-microarray with 500,000 markers spanning over the whole genome to genotype a sample of Vietnamese families including 939 patients, of which 692 were children. We have found a region linked to leprosy polarization on chromosome 19p12. The association study could not identify a significant signal across the genome. We developed a new test for association designed for familial data that improved the results without reaching significance. Our work will be pursued by association studies in two case-control populations from Vietnam and Brazil. We will try to identify the causal markers within the 19p12 linkage region on the one hand, and to discover new variants on theother hand. The identification of markers associated with leprosy polarization could help us to better predict the evolution of the disease, and to offer more targeted treatments to patients, based on their individual genetic risk.