Chlamydia is a clinically significant organism that exhibits a unique stage-specific developmental cycle, involving the interconversion between two metabolically distinct forms. The completion of eight chlamydial genome sequences identified three different RNA polymerase sigma factor (ó) genes. Temporal gene expression analysis has predicted that each ó may play an integral role in controlling the development cycle. This thesis examines the role of the chlamydial alternate sigma factor, ó54 (rpoN) and the potential mechanism for the control the developmental cycle and disease pathogenesis. To achieve this, we searched the genome for putative ó54 promoters, validated the findings by DNA-binding assays, and examined the roles of the genes predicted to be regulated by ó54. This study applied a bioinformatics approach to search for additional ó54 regulated genes in C. trachomatis L2. A reduced consensus sequence (TGGCACnnnnnTTGC) identified two previously published ó54 promoter sequences upstream of CT652.1 and CT683. A modified consensus sequence (TGG-N9-TGC) was applied to the C. trachomatis D genome in Findpatterns yielded 512 potential targets of which 20 by virtue of sequence orientation and distance upstream of the predicted ORF start codon Primer extension analysis of total RNA isolated at 24 hours post-infection mapped the 5' RNA end upstream for acpS (CT100), yhf0_1 (CT258), SAM (CT404), lpxA (CT531), hypothetical proteins CT652.1 and CT683, and htrA (CT823) to the predicted ó54 promoters. Three candidates (CT291, CT404, and CT847) were mapped to putative ó70-like ó66 promoters. No transcript start sites were detected for the remaining ó54 promoter candidates. Two transcripts were detected from predicted ó66 and ó54 tandem promoters upstream of CT404. Primer extension analysis of the CT404 transcripts from RNA isolated at 4, 8, 12, 24 and 32 hours post-infection showed a decrease between 12 hours and 24 hours post-infection in transcripts thought to be generated from the predicted ó66 promoter. Transcripts from the predicted ó54 promoter were identified throughout development. Temporal gene expression profiles of the candidate genes with predicted ó54 promoters (CT652.1, CT683, CT100, CT258, CT531 and CT823) were resolved throughout the C. trachomatis L2 developmental cycle using real-time PCR. Transcripts for CT608 and CT609 were detected early in the cycle, while strong transcript levels were detected for CT258, CT531 and CT823 after the appearance of CT609 (rpoN). Low levels of CT652.1 and CT683 were measured, in the mid to late phase of the cycle, and transcripts for CT100 appeared at lower levels during the middle phase of the cycle. The functional assay of the predicted ó54 promoters required the generation of recombinant C. trachomatis L2 ó54 (rRpoN). The C. trachomatis rpoN was cloned into a bacterial expression system (pQE70) and the recombinant proteins purified for subsequent DNA mobility shift assays. Expression of rRpoN was hampered by low copy numbers, and unusual physical characteristics. DNA binding and mobility shift assays using rRpoN extracts against the chlamydial CT652.1 ó54 promoter, plus two characterised E. coli ó54 promoters (hypA and hycA), were successful if E. coli core RNA polymerase was added to the assay. All 20 candidates with predicted ó54 promoters were analysed with EMSA using rRpoN extract. The promoters upstream of CT100, CT223, CT258, CT322, CT652.1 and CT683 showed affinity towards the recombinant rRpoN-E. coli core RNA polymerase holoenzyme complex. Searches for potential chlamydial ó54 transcription initiation activators were made using the Multiple Em for Motif Elucidation (MEME) software, looking to identify the DNA binding motifs. The upstream promoter regions of CT100, CT223, CT258, CT322, CT531, CT652.1, CT683 and CT823 in C. trachomatis L2 and orthologs found in other species of Chlamydia were analysed. The software identified a near palindromic sequence upstream of CT100 orthologs in C. trachomatis D and C. trachomatis MoPn (CAACCCAAC and CACCACAAC) where as a CT531- and CT823-specific motif was also discovered (CCGTTGTAGAATCTC). It is beginning to emerge that ó54 may regulate the expression of proteins required for the formation of the cell wall. Since the expression of the ó54 transcript, rpoN, coincides with the morphological change from the non-infectious RB to the infectious EB, predictions could be made concerning which genes are potentially regulated by ó54.

>Magister Scientiae - MSc / Tuberculosis (TB) is a global health problem and rated as the second leading cause of death after HIV/AIDS. Transmission of TB from one person to the next is very rapid in crowded communities. Therefore, it is crucial to identify people who are infected as quickly as possible not only to provide treatment but also to prevent the spread of the disease. Current TB diagnostic tests such as the culture and sputum smear tests are time-consuming, while rapid tests make use of antibodies that are costly and have low sensitivity and stability. Great improvement has been observed when aptamers are used in place of antibodies in rapid diagnostic tests such as lateral flow devices (LFDs). Therefore, the current study aims to synthesize and identify aptamers against serum biomarkers for development of rapid TB diagnostic tests such as a lateral flow assay. Several TB serum biomarkers have been identified and can be used for the diagnosis of TB. TB biomarkers expressed in serum samples were identified through in silico approach. The biomarkers were expressed in bacterial systems using recombinant DNA technology. The recombinant proteins were purified by affinity chromatography and further used as targets for the selection of aptamers using Systemic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers for the selected biomarkers were synthesized based on magnetic-bead based SELEX and characterized by electrophoretic mobility shift assay (EMSA), Surface Plasmon resonance (SPR) and MicroScale Thermophoresis (MST). Six putative TB serum biomarker proteins were selected from literature, namely, Insulin-like Growth Factor Binding Protein 6 (IGFBP6), Interferon-stimulated Gene 15 (ISG15), Calcium Binding Protein (S100A9), Retinol Binding Protein 4 (RBP4), Granzyme A (GrA), and Transgelin-2 (TAGLN2). The biomarkers were recombinantly expressed and purified after which they were used as targets in SELEX for aptamers synthesis. Aptamers were analysed by in silico method and the ones with highly conserved motifs were selected. The selected aptamers were synthesized and later characterized. The aptamers that show high affinity and specificity for the biomarkers will be used for the fabrication of a rapid lateral flow device for TB screening. Such a test would allow for a short diagnostic turnaround time, and hence expedite treatment.

Exopolysaccharides are essential for the establishment of the symbiosis between Sinorhizobium meliloti and Medicago sativa (alfalfa). The ExoS/ChvI two-component regulatory system is known as a regulator of succinoglycan production but the genes that are directly regulated by ChvI have not been determined. Difficulty isolating exoS and chvI null mutants has prompted the suggestion that these genes are essential for S. meliloti viability. We have successfully isolated exoS and chvI null mutants using a merodiploid facilitated strategy. We present evidence that the S. meliloti ExoS/ChvI two-component regulatory system is essential for symbiosis with alfalfa. Phenotypic analyses of exoS and chvI null mutant strains demonstrate that ExoS/ChvI controls both succinoglycan and galactoglucan production and is required for growth on over 21 different carbon sources. These new findings suggest that the ExoS/ChvI regulatory targets might not be the exo genes that are specific for succinoglycan biosynthesis but rather genes that have common influence on both succinoglycan and galactoglucan production. To obtain further insight into the nature of the ChvI regulon, we obtained a purified His•Tag-ChvI and used it to perform modified electrophoretic mobility shift assays. These assays were done using genomic DNA and were followed by cloning of DNA fragments having the highest affinity for ChvI. Sequencing of these fragments revealed that ChvI has a diverse regulon, it affects transcription of genes encoding enzymes that are involved in different pathways. Transcriptional gene fusion assays confirmed that ChvI is important for the activation of the transcription of the msbA2 operon, as well as repression of the transcription of the rhizobactin 1021 operon and genes SMc00262-61. ChvI-regulation of genes that are part of the connected thiamine and histidine biosynthesis pathways suggest that ChvI could act in a concerted manner to avoid limitation of important intermediates in these pathways. This study presents for the first time genes directly regulated by ChvI and this includes none of the exo genes. This work opens new avenues in the understanding of the global regulatory role of the symbiotically important ExoS/ChvI two-component regulatory system.

Exopolysaccharides are essential for the establishment of the symbiosis between Sinorhizobium meliloti and Medicago sativa (alfalfa). The ExoS/ChvI two-component regulatory system is known as a regulator of succinoglycan production but the genes that are directly regulated by ChvI have not been determined. Difficulty isolating exoS and chvI null mutants has prompted the suggestion that these genes are essential for S. meliloti viability. We have successfully isolated exoS and chvI null mutants using a merodiploid facilitated strategy. We present evidence that the S. meliloti ExoS/ChvI two-component regulatory system is essential for symbiosis with alfalfa. Phenotypic analyses of exoS and chvI null mutant strains demonstrate that ExoS/ChvI controls both succinoglycan and galactoglucan production and is required for growth on over 21 different carbon sources. These new findings suggest that the ExoS/ChvI regulatory targets might not be the exo genes that are specific for succinoglycan biosynthesis but rather genes that have common influence on both succinoglycan and galactoglucan production. To obtain further insight into the nature of the ChvI regulon, we obtained a purified His•Tag-ChvI and used it to perform modified electrophoretic mobility shift assays. These assays were done using genomic DNA and were followed by cloning of DNA fragments having the highest affinity for ChvI. Sequencing of these fragments revealed that ChvI has a diverse regulon, it affects transcription of genes encoding enzymes that are involved in different pathways. Transcriptional gene fusion assays confirmed that ChvI is important for the activation of the transcription of the msbA2 operon, as well as repression of the transcription of the rhizobactin 1021 operon and genes SMc00262-61. ChvI-regulation of genes that are part of the connected thiamine and histidine biosynthesis pathways suggest that ChvI could act in a concerted manner to avoid limitation of important intermediates in these pathways. This study presents for the first time genes directly regulated by ChvI and this includes none of the exo genes. This work opens new avenues in the understanding of the global regulatory role of the symbiotically important ExoS/ChvI two-component regulatory system.

Submitted by Jonatas Erick Maimoni Campanella null (jemcampanella@gmail.com) on 2018-03-23T19:20:54Z No. of bitstreams: 1 Dissertação FINAL.pdf: 3123007 bytes, checksum: 93be4f3b9e7d1e13ef2550b233a4fa94 (MD5) / Approved for entry into archive by Ana Carolina Gonçalves Bet null (abet@iq.unesp.br) on 2018-03-26T20:34:53Z (GMT) No. of bitstreams: 1 campanella_jem_me_araiq_int.pdf: 3024672 bytes, checksum: 3aeefce6e97b29e1c03b4f8d62b6146c (MD5) / Made available in DSpace on 2018-03-26T20:34:53Z (GMT). No. of bitstreams: 1 campanella_jem_me_araiq_int.pdf: 3024672 bytes, checksum: 3aeefce6e97b29e1c03b4f8d62b6146c (MD5) Previous issue date: 2018-03-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Trabalhos anteriores realizados pelo nosso grupo levaram à identificação da proteína RVB-1 de Neurospora crassa como capaz de se ligar a um fragmento de DNA contendo o motif STRE (Stress Responsive Element). Este elemento de DNA, em Saccharomyces cerevisiae, é descrito estar presente na região promotora de genes responsivos a estresse, incluindo o estresse térmico. Uma busca nos bancos de dados de proteínas mostrou que a RVB-1 apresenta homologia estrutural à proteína RuvBL1 de humanos. Além disso, esta proteína é descrita possuir uma proteína paráloga, RuvBL2 ou Rvb2 de humano e S. cerevisiae, respectivamente, cuja proteína ortóloga em N. crassa foi denominada RVB-2. As proteínas RuvBLs foram encontradas estarem associadas a vários processos celulares, muito provavelmente devido as suas capacidades de formar grandes complexos proteicos e possuírem atividade ATPásica. Neste trabalho, estas proteínas foram parcialmente caracterizadas do ponto de vista funcional, bioquímico e biofísico. Os resultados obtidos por microscopia de fluorescência mostraram que ambas apresentam localização nuclear quando o fungo foi exposto a estresse térmico. A análise da expressão da proteína RVB-V5 mostrou estar aumentada, nessa mesma condição ambiental, quando analisada por Western blot. As duas proteínas foram produzidas na forma recombinante em Escherichia coli, tanto isoladamente quanto juntas, e a análise da expressão mostrou alta estabilidade em solução quando ambas foram produzidas em uma mesma célula de bactéria. Ambas mostraram interagir in vitro por análise de pulldown e o complexo RVB-1/2 mostrou ser formado principalmente por α-hélices através de espectropolarimetria de dicroísmo circular. Análise em gel filtração analítica sugeriu que o complexo apresenta diferentes estruturas oligoméricas, quando analisado na ausência e na presença de ATP. O complexo apresentou atividade ATPásica in vitro, o que fortemente sugere que ambas pertencem à família AAA+. Resultados de retardamento em gel de agarose (EMSA), mostraram que tanto separadamente, como na forma de complexo, essas proteínas são capazes de se ligar a fragmentos de DNA dupla fita independentemente de ATP. / Previous work by our group identified the Neurospora crassa RVB - 1 protein as able of binding to a DNA fragment containing the Stress Responsive Element (STRE). In Saccharomyces cerevisiae, this element is present in the promoter region of genes responsive to stress, including heat stress. RVB - 1 shows structural homology to human RuvBL1 protein, and is described to have a paralog, the RuvBL2 or Rvb2 protein in human and S. cerevisiae , respect ively. The N. crassa orthologous protein was identified and named RVB - 2. The RuvBLs proteins have been found to be associated with diverse cellular processes, most likely due to their ability to form large protein complexes and to have ATPase activity. In this work, these proteins were functional, biochemical and biophysically characterized. The fluorescence microscopy results showed that both proteins present nuclear localization in the fungus exposed to heat stress. Analyses of protein expression by Weste rn blot showed an increased expression of the RVB - 1 - v5 protei n in this same condition . The two proteins were produced in Escherichia coli, and expression analyses showed higher stability in solution when both were produced together. Both proteins showed in vitro interaction by pulldown analysis. The RVB - 1/2 complex has the secondary structure mostly formed by α - helices as analysis by CD. The size - exclusion chromatography suggested that the complex present different oligomeric structures when analyzed in the absence and presence of ATP. They present in vitro ATPase activity, which strongly suggest that both belong to the AAA + family. Electrophoresis Mobility Shift Assay (EMSA) showed that both proteins are able to bind to dsDNA fragments, in an ATP - independently manner.

Magister Scientiae - MSc / Ischemic heart disease is a disease which is characterized by the reduced blood supply to the heart. According to WHO 2013, ischemic heart disease is one of the major causes of death globally. For this reason, it is imperative to search for methods whereby heart cells can be protected from cell death. The upregulation of heat shock proteins (Hsps) is one of the major techniques which can be used to protect the heart cells from Hsps cell death and improve the tolerance to ischemic stresses in various models. The increased expression of Hsps during heat shock pre-conditioning is regulated by heat shock transcription factors (HSFs). HSFs orchestrate the initiation of gene expression by binding to sequence motifs, known as cis-acting regulatory elements (CAREs). Since gene expression is regulated at a transcriptional level, it is expected that functionally related genes (e.g. heat shock response genes) might also be regulated by the same transcription factors (TFs). In this study an in silico approach was performed to identify the promoter sequences of 50 known heat shock responsive genes using Genomatix Software. This software was also used to identify transcription factor binding sites that are statistically over represented in the promoter sequences of these genes. The use of the Electrophoretic Mobility Shift Assay was included to confirm that protein cell lysates of stressed cells contain proteins (TFs) that bind to this sequence (SP1F_KLFS_01). Luciferase promoter reporter assay were also used to iii investigate the transcriptional activity of mutant promoter constructs in which the SP1F_KLFS_01 was mutated. SP1F_KLFS_01 is a ±25 base pair sequence that was identified in the promoter sequences of 19 heat shock responsive genes, including the well-known Hsp70 and Hsp90. This sequence is a potential binding site for two TFs, Specificity Protein-1 and Krueppel like TFs. Consequently, the aim of this study is to identify CAREs that are statistically over-represented in the promoter regions of heat shock response genes. In conclusion, in vitro experiments of this study did not support the findings of the in silico experiments, therefore additional methods should be implemented to expand the investigation for the involvement of cis-acting regulatory elements in the regulation of heat shock proteins in cardiomyocytes, prior to heat shock.

No description available.

Dissertation (Ph.D.)--University of South Florida, 2009. / Title from PDF of title page. Document formatted into pages; contains 86 pages. Includes vita. Includes bibliographical references.

Dissertation (Ph.D.)--University of South Florida, 2009. / Includes vita. Includes bibliographical references. Also available online.

Orientadores: Maria Isabel Nogueira Cano, Carlos Henrique Inacio Ramos / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-08T19:46:21Z (GMT). No. of bitstreams: 1 Lira_CristinaBragadeBrito_D.pdf: 9068778 bytes, checksum: 7561201fa37b1109dc7803fb6173aad0 (MD5) Previous issue date: 2007 / Resumo: A leishmaniose é uma doença parasitária que foi considerada pela Organização Mundial de Saúde como uma doença de Categoria 1, pois para a mesma não existem formas de controle, diagnóstico ou terapia eficientes. Os parasitas do gênero Leishmania (família Trypanosomatidae) são agentes etiológicos da leishmaniose e possuem cromossomos lineares com extremidades teloméricas. Os telômeros são complexos nucleoproteicos essenciais para manuntenção da estabilidade do genoma e viabilidade celular. Devido à importância das proteínas teloméricas na manutenção dessas estruturas, elas têm sido considerados bons alvos para a terapia anticâncer e antiparasitária. Sendo assim, o objetivo deste trabalho foi identificar proteínas que se associam aos telômeros de Leishmania amazonensis. Três metodologias diferentes foram utilizadas para antigir este objetivo: (i) purificação de proteínas teloméricas a partir de extratos de L. amazonensis, (ii) busca no banco de dados de Leishmania por proteínas homólogas que apresentassem domínios de ligação ao DNA do tipo Myb, e (iii) seleção genética em levedura (sistema mono-híbrido). A purificação de proteínas teloméricas a partir de extratos nucleares de L. amazonensis resultou no isolamento da proteína LaRbp38. Ensaios in vitro de interação proteína-DNA e ensaios in vivo (imunoprecipitação de cromatina) comprovaram a interação de LaRbp38 com DNA telomérico, DNA rico em GT e DNA do cinetoplasto. LaRbp38 pode ser considerada um bom alvo para a terapia antiparasitária pois é uma proteína exclusiva de tripanosomatídeos e seu homólogo em T. brucei é essencial para a sobrevivência do parasita. Para dar início a experimentos de caracterização da estrutura dessa proteína, LaRbp38 foi expressa em bactérias. Como a proteína permaneceu na fração insolúvel, experimentos preliminares de renovelamento foram feitos mostrando que a proteína necessita da presença de DNA, ou de moléculas análogas, para se renovelar in vitro. As buscas no banco de dados de L. major resultaram no descobrimento de uma lista de proteínas que apresentam domínio de ligação ao DNA do tipo Myb. Uma proteína foi escolhida e sua homóloga em L. amazonensis foi denominada LaTBP1. O domínio Myb de LaTBP1 se localiza na porção central da proteína e apresenta alta similaridade de seqüência com domínios Myb encontrados em fatores de transcrição to tipo TFIIIB, proto-oncogene c-MYB e membros da família de proteínas teloméricas Rap1p. Ensaios de interação proteína-DNA e de imunoprecipitação de cromatina confirmaram que LaTBP1 interage tanto com o DNA telomérico quanto com DNAs ricos em GT. Prefências por estes dois tipos de DNAs são apresentadas pelas proteínas teloméricas Rap1, Taz1 e TEBP1, descritas em leveduras e eucariotos superiores. A utilização do sistema mono-híbrido para identificação de proteínas teloméricas de Leishmania resultou em uma lista de proteínas candidatas. A possível função telomérica das mesmas foi inferida com base na homologia de seqüência com proteínas já descritas e em testes de interação proteína-DNA in vitro utilizando-se extratos das leveduras recombinantes. Apesar desses resultados serem promissores, análises mais detalhadas são necessárias para confirmar estas interações. Concluindo, as três metodologias se mostraram eficazes para a identificação de proteínas teloméricas e a utilização das mesmas resultou na identificação de diversas proteínas teloméricas, algumas delas ainda hipotéticas / Abstract: Leishmaniasis is a parasitic disease that was classified by World Health Organization as a Category 1 disease because there are no effective control programs or therapeutics to this disease. Parasites from the Leishmania genus are the ethiologic agents of leishmaniasis and they possess linear chromosomes with telomeric ends. Telomeres are nucleoprotein specialized nucleoprotein complexes essential for maintaining chromosomal stability and cell viability. Since telomeric proteins are essential for the maintenance of telomeres, they could be considered good targets for anticancer and antiparasitic drugs. Therefore, the goal of this work was to identify Leishmania amazonensis proteins that interact with the telomeric DNA. Three methodologies were used the achive this goal: (i) purification of telomeric proteins from nuclear extracts of L. amazonensis, (ii) Leishmania genome database mining for protein containing a Myb-like domain, and (iii) use of One-hybrid system (Clontech). The search for telomeric proteins in nuclear extracts of L. amazonensis resulted in the identification of LaRbp38. EMSA and immunoprecipitation assays were used to attest LaRbp38 binding to telomeric, GT-rich and kinetoplast DNAs, both in vitro and in vivo. LaRbp38 could be considered a good drug target for antiparasitic therapy since it is exclusive of trypanosomatids and itshomologue in T. brucei is essential for parasite survival. In order to characterize structurally this protein, LaRbp38 was expressed in bacteria. The protein was present in the insoluble fraction of the bacterial lysate. Therefore, preliminary experiments of refolding were done. LaRbp38 seems to need DNA, or analog molecules, in order to correctly refold in vitro. Data-mining in the L. major genome resulted on a list of proteins bearing a Myb-like domain. One protein was chosen and its L. amazonensis homologue was termed LaTBP1. LaTBP1 Myb-like domain is centrally localized and shares sequence similarities with Myb-like domains found on transcription factors TFIIIB and c-MYB, and with the RAP1 telomeric proteins. Competition and chromatin immunoprecipitation assays confirmed the specificity of LaTBP1 for telomeric and GT-rich DNAs. This binding specifities are also found on the telomeric proteins Rap1, Taz1 and TEBP1, described in yeast and higher eukaryotes. A list of proteins with a putative telomeric function was generated after the use of the Onehybrid system. Sequence analysis (search for homologues in other organisms) and EMSA, done with protein extract of recombinant yeast, were used to infer a telomeric function for the proteins found by this methodology. Although the results are encouraging, detailed analysis are necessary to validate the interactions. In conclusion, the three methodologies were usefull for the identification of telomeric proteins. This work resulted in the identification of several telomeric candidate proteins / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular