Polyketides are a large group of structurally diverse natural products that have shown a variety of biological activities. These molecules are synthesized by polyketide synthases (PKSs). PKSs are classified into three types based on their sequence, primary structure, and catalytic mechanism. Because of the bioactivities of polyketide natural products, this study is focused on the engineering of PKS pathways for efficient production of useful bioactive molecules or structural modification to create new molecules for drug development. One goal of this research is to create an efficient method to produce pharmaceutically important molecules. Seven biosynthetic genes from plants and bacteria were used to establish a variety of complete biosynthetic pathways in Escherichia coli to make valuable plant natural products, including four phenylpropanoid acids, three bioactive natural stilbenoids, and three natural curcuminoids. A curcumin analog dicafferolmethane was synthesized by removing a methyltransferase from the curcumin biosynthetic pathway. Furthermore, introduction of a fungal flavin-dependent halogenase into the resveratrol biosynthetic pathway yielded a novel chlorinated molecule 2-chloro-resveratrol. This demonstrated that biosynthetic enzymes from different sources can be recombined like legos to make various plant natural products, which is more efficient (2-3 days) than traditional extraction from plants (months to years). Phenylalanine ammonia-lyase (PAL) is a key enzyme involved in the first biosynthetic step of some plant phenylpropanoids. Based on the biosynthetic pathway of curcuminoids, a novel and efficient visible reporter assay was established for screening of phenylalanine ammonia-lyase (PAL) efficiency in Escherichia coli. The other goal of this research is to characterize and engineer natural product biosynthetic pathways for new bioactive molecules. The biosynthetic gene cluster of the antibacterial compound dutomycin was discovered from Streptomyces minoensis NRRL B-5482 through genome sequencing. Confirmation of the involvement of this gene cluster in dutomycin biosynthesis and creation of a series of new molecules were successfully conducted by rationally modifying the biosynthetic pathway. More importantly, a new demethylated analog of dutomycin was found to have much higher antibacterial activity against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus.

In sea urchin development, cell fate specification appears by the 60-cell stage embryo when several embryonic territories are recognized: the small micromeres, the large micromeres which will generate primary mesenchyme cells, the vegetal2 layer that will give rise to pigment cells, immunocytes, and muscle cells, the vegetal1 layer, as well as the oral and aboral ectoderm. A Delta-Notch signaling event is required for the differential specification of mesodermal cells that will give rise to secondary mesenchyme cells (SMCs). SMCs produce four cell types: pigment cells, blastocoelar cells, circumesophageal muscle cells, and coelomic pouch cells. Pigment cells are the first to be specified. During primary invagination at the gastrula stage, eight pigment cell progenitors delaminate from the archenteron into the blastocoel. By the pluteus stage, approximately 30 pigment cells are embedded in the ectoderm. Pigment cells produce echinochrome, a napthoquinone pigment. Previously, several genes in the sea urchin embryo were isolated that are expressed specifically in pigment cell precursors during the blastula stage. The goal of this research was to characterize a subset of these genes, which are highly similar to: the polyketide synthase gene (Pks), a sulfotransferase gene (Sult), three different members of the flavin-containing monooxygenase gene family (Fmo), and the transcription factor glial cells missing (Gcm). Polyketide synthases (PKSs) are a large family of multifunctional proteins mainly found in bacteria, fungi, and plants. They are responsible for the biosynthesis of a variety of polyketide compounds including antibiotics and mycotoxins. In the sea urchin, SpPks is required for echinochrome biosynthesis. Flavin-containing monooxygenases (FMOs) are NADPH-dependent flavoproteins mainly found in bacteria, plants, and higher metazoan. They are responsible for catalyzing the oxidation of several compounds including the detoxification of xenobiotics and activation of numerous metabolites. It is known that SpFmo1 is required for echinochrome biosynthesis. Sulfotransferases are found from bacteria through higher eukaryotes. These enzymes catalyze the sulfate conjugation of several substrates resulting in either compound detoxification or bioactivation.

Abstract Hypericum perforatum L. (St. John’s wort) is a medicinal plant widely utilized for the treatment of depression. The antidepressant activity is mainly attributed to the phenolic compounds hypericins and hyperforins, which also have a wide range of other pharmacologically interesting properties. The biosynthetic routes leading to hypericins and hyperforins are poorly understood, although a polyketide pathway including type III polyketide synthases (PKSs) has been suggested to be involved. Furthermore, a gene called hyp-1 is assumed to attend to the final stages of the hypericin biosynthesis. In the present work, the biosynthesis of hypericins and hyperforins in H. perforatum was further studied by focusing on the elucidation of the precursors and genes involved. The incorporation of isotopically labelled branched-chain amino acids into hyperforins was investigated as well as the possibilities to enhance the production of hyperforins in H. perforatum in vitro cultures by feeding them with amino acid precursors. Furthermore, two novel cDNAs encoding for type III PKSs were isolated from H. perforatum. The functions of these new genes, designated HpPKS1 and HpPKS2, as well as the role of hyp-1 were elucidated by comparing their expression with the levels of hypericins and hyperforins in H. perforatum tissues. The enzymatic activity of the recombinant HpPKS2 protein was also analyzed. To study Hyp-1 at a protein level, a protein extraction method was optimized for tissues of Hypericum species. The results show the incorporation of valine and isoleucine into the acyl side chain of hyperforin and adhyperforin, respectively. Through the biotransformation of the amino acid precursors, it is possible to enhance the levels of adhyperforin, but not hyperforin, in H. perforatum shoot cultures, which demonstrates the tight regulation of the hyperforin biosynthesis. A correlation between HpPKS1 expression and hyperforins was detected in H. perforatum tissues. The localization of HpPKS2 mRNA in dark glands in which hypericins accumulate as well as the octaketide synthase activity of the recombinant HpPKS2 suggest that HpPKS2 is associated with possible co-operating tailoring enzymes in the biosynthesis of hypericins. The presence of both hyp-1 mRNA and Hyp-1 protein in distinct places compared with hypericins in H. perforatum tissues does not support the idea that Hyp-1 would be involved in the biosynthesis of hypericins in dark glands, although mobility of the Hyp-1 protein was shown to be possible. The present thesis extends knowledge about the biosynthesis of hypericins and hyperforins in H. perforatum by providing new candidate genes for their biosynthesis and by identifying precursors for hyperforins. Moreover, new information was obtained about the role of hyp-1 in H. perforatum.

Orientador: Fabiana Fantinatti-Garboggini / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T12:39:46Z (GMT). No. of bitstreams: 1 Mantovani_CristinaKampus_M.pdf: 1137189 bytes, checksum: 2db8a522e2d39a0ae80a5e302d4d79e8 (MD5) Previous issue date: 2011 / Resumo: Nas últimas décadas um grande número de compostos de interesse biotecnológico, como por exemplo, citotoxinas, agentes antifúngicos, antimicrobianos, antivirais e anticancerígenos têm sido isolados de esponjas marinhas. Entretanto, estudos comprovam que, em muitos casos, os compostos ativos desses animais são oriundos de micro-organismos associados, que podem compor até 60% do volume tecidual das esponjas. A presente proposta teve por objetivo a caracterização taxonômica da diversidade de bactérias cultiváveis associadas às esponjas coletadas no litoral norte do estado de São Paulo, Brasil, e a avaliação da atividade antimicrobiana a partir de extratos orgânicos brutos dessas bactérias. Um total de 86 bactérias foi recuperado das esponjas Axinella corrugata, Dragmacidon reticulata, Chelonaplysilla erecta e Petromica citrina utilizando diferentes meios de cultivo. A diversidade das bactérias foi caracterizada utilizando dados de morfologia, ARDRA (Amplified Ribossomal Restriction Analysis) e sequenciamento do gene RNA ribossomal 16S, cuja análise permitiu a identificação de membros pertencentes aos filos Proteobacteria, Actinobacteria, Bacteroidetes e Firmicutes num total de 15 gêneros distintos. O gênero Pseudovibrio foi o único presente em todas as esponjas amostradas, e os gêneros Bacillus, Ruegeria, Vibrio, Staphylococcus e Erythrobacter estavam presentes em mais de uma esponja. A esponja Dragmacidon reticulata apresentou a maior diversidade bacteriana, englobando oito diferentes gêneros, dentre eles, um representate do gênero Cyclobacterium, o qual até onde se sabe, foi isolado pela primeira vez de uma esponja marinha. O gênero Bacillus esteve presente em três esponjas, mas na Petromica citrina, endêmica do Brasil, o gênero ficou representado em 74% dos isolados obtidos. Este estudo foi o primerio relato sobre a diversidade de bactérias cultiváveis da esponja Petromica critrina. Todos os isolados foram avaliados quanto à presença ou ausência dos fragmentos dos genes PKS (Polyketide Synthases) e NRPS (Non Ribossomal Peptide Synthetases), visando à investigação do potencial biotecnológico das bactérias, e mais da metade delas apresentaram pelo menos um dos genes estudados. Uma triagem da atividade antimicrobiana utilizando o método da difusão em bloco de ágar demonstrou que 21 isolados foram promissores para produção de antimicrobianos. Destes isolados foram obtidos os extratos orgâncios brutos, os quais foram testados quanto à determinação da concentração inibitória mínima contra oito micro-organismos indicadores. Um total de 13 extratos orgânicos brutos, em sua maioria respresentantes do gênero Bacillus, demonstraram ação contra o micro-organismo Bacillus subtilis ATCC 6051 e um deles demonstrou ação contra o micro-organismo Escherichia coli ATCC 11775. A numerosa inibição de estirpes de Bacillus por outros Bacillus sugere que a atividade possa ser gerada por bacteriocinas, polipeptídeos produzidos pela via ribossomal que atuam na inibição de crescimento de grupos próximos de micro-organismos. Sua possível função no meio ambiente é prover vantagem seletiva através da eliminação de um competidor relativamente próximo. Ainda, um representante do gênero Exiguobacterium apresentou atividade antimicrobiana contra B. subtilis, resultado este não descrito até o presente na literatura / Abstract: In recent decades a large number of compounds of biotechnological interest, such as cytotoxins, antifungal, antimicrobial, antiviral and anticancer substances have been isolated from marine sponges, however, studies show that, in many cases, the active compounds are actually produced by associated microorganisms, which can comprise up to 60% of the volume of sponge tissue. This proposal aimed to characterize the taxonomic diversity of culturable bacteria associated with sponges collected in the northern coast of São Paulo, Brazil, and to evaluate the antimicrobial activity from crude organic extracts of these bacteria. A total of 86 bacteria were recovered from sponges the Axinella corrugata, Dragmacidon reticulata, Petromica citrina and Chelonaplysilla erecta using different culture media. The diversity of bacteria was characterized using data from morphology, ARDRA (Amplified Ribossomal Restriction Analysis) and sequencing of 16S ribosomal RNA gene, whose analysis allowed the identification of members belonging to the phyla Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, in a total of 15 distinct genera. The genus Pseudovibrio was the only one present in all sponges sampled, and the genera Bacillus, Ruegeria, Vibrio, Staphylococcus and Erythrobacter were present in more than one sponge sampled. The sponge Dragmacidon reticulata showed the highest bacterial diversity, encompassing eight different genera, among which the genus Cyclobacterium, which, as far as is known, was first isolated from a marine sponge. The genus Bacillus was present in three sponges, but in Petromica citrina, endemic to Brazil, the genus accounted for 74% of the isolates. This study was the first report on the diversity of culturable bacteria from the sponge Petromica critrina. All isolates were evaluated for the presence or absence of NRPS (non ribossomal peptide synthetases) and PKS (polyketide synthase) genes in order to investigate the biotechnological potential of bacteria, and over half of the isolates had at least one of these genes. A screening of antimicrobial activity using the diffusion agar disk method showed that 21 isolates were promising for the production of antibiotics. Crude organic extracts from these isolates were produced and tested against eight indicator microorganisms to determine the minimum inhibitory concentration (MIC). A total of 13 crude organic extracts, most of the genus Bacillus, showed inhibitory activity against the microorganism Bacillus subtilis ATCC 6051, and one of them showed activity against the microorganism Escherichia coli ATCC 11775. The large inhibition of Bacillus strains to other Bacillus strains suggests that the activity can be generated by bacteriocins produced through ribosomal polypeptides that inhibit close groups of microorganisms. Its possible role in the environment is to provide a selective advantage by eliminating a relatively close competitor. Still, a representative of the genus Exiguobacterium showed antimicrobial activity against B. subtilis, which was not described in the literature up to date / Mestrado / Microbiologia / Mestre em Genética e Biologia Molecular

Orientadores: Fabiana Fantinatti Garboggini, Marta Cristina Teixeira Duarte / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T21:03:15Z (GMT). No. of bitstreams: 1 Franca_Paula_M.pdf: 7905078 bytes, checksum: 6735b6d77cec7c206090abaa6e56fdfc (MD5) Previous issue date: 2015 / Resumo: Os micro-organismos associados ao continente Antártico apresentam populações diversas e metabolicamente ativas, porém o potencial farmacológico dos compostos obtidos pelos micro-organismos é pouco conhecido. As bactérias são importante fonte de compostos utilizados atualmente como antimicrobianos, e as principais vias de biossíntese de muitos antibióticos são catalisadas pelos genes PKS (Polyketide Synthases) e NRPS (Non Ribosomal Peptide Synthetases). O presente estudo teve como objetivo a avaliação genética e funcional da produção de compostos antimicrobianos obtidos de bactérias isoladas na Baía do Almirantado, Antártica, a identificação taxonômica das bactérias que apresentaram tal potencial e a identificação do perfil químico dos compostos antimicrobianos. O total de 153 bactérias foi isolado do ambiente antártico, 127 isolados apresentaram pelo menos um dos genes PKSI, PKSII e NRPS. Estes foram identificados através do sequenciamento parcial do gene RNA ribossomal 16S e pertencem a 28 gêneros distintos, sendo representantes dos Filos Proteobacteria, Firmicutes, Actinobacteria e Bacteroidetes. A avaliação funcional da produção de antimicrobianos foi realizada com o total de 76 isolados dos quais 30 isolados formaram halos de inibição frente a micro-organismos testes. Os extratos brutos obtidos foram avaliados quanto à concentração inibitória mínima (MIC) frente a oito micro-organismos não virulentos, e 18 extratos brutos apresentaram atividade inibitória, onde se destaca o extrato denominado E131, obtido da bactéria do gênero Streptomyces, que apresentou atividade bacteriostática frente S. aureus e M. luteus, e atividade bactericida frente a C. albicans e B. subtilis. Frente a micro-organismos isolados de amostras clínicas, 11 extratos brutos apresentaram atividade inibitória frente a quatro cepas de Neisseria meningitides, com MIC dos extratos brutos variando de 0,0313 mg.mL-1 até 2,0 mg.mL-1. O extrato E46, obtido da bactéria Pseudoalteromonas sp., destacou-se quanto à atividade inibitória observada frente às quatro cepas avaliadas. Frente à cepa B4, destacam-se a atividade antimicrobiana dos extratos brutos obtido das bactérias Pseudoalteromonas sp. e Pseudomonas azotoformans CUG12536. Frente à cepa YUSA, destaca-se a atividade antimicrobiana observada pelo extrato bruto obtido da bactéria Marinilactibacillus sp., cuja atividade antimicrobiana foi relatada pela primeira vez neste gênero de bactéria. Os extratos brutos possuem em sua composição, compostos cuja atividade antimicrobiana é conhecida, como ácidos graxos e compostos cuja atividade antimicrobiana não está descrita na literatura. Os testes de fracionamento dos extratos frente a solventes de diferentes polaridades indicou que os extratos brutos são solúveis, em sua maioria, a solvente polar. Portanto, as bactérias isoladas da Antártica produzem compostos de interesse farmacológico e podem ser utilizadas como fonte de novos compostos. Tais resultados enfatizam a necessidade de mais estudos de bactérias associadas a ambientes extremos, como a Antártica / Abstract: Microorganisms associated with the Antarctic continent have various and metabolically active populations, but the pharmacological potential of compounds obtained by micro-organisms is poorly understood. Bacterias are an important source of compounds currently used as antimicrobial, major biosynthetic pathways of many antibiotics are catalyzed by the PKS genes (Polyketide Synthases) and NRPS (Non Ribosomal Peptide Synthetases). This study had the objective to genetic and functional evaluation of the antimicrobial activity of bacteria isolated in Admiralty Bay, Antarctica, and the taxonomic identification of bacteria that had such potential and identification of the chemical profile of antimicrobial compounds. The total of 153 bacteria was isolated from Antarctic environment, among the isolates, 127 isolates showed at least one of the genes PKSI, PKSII and NRPS. These were identified by partial sequencing of 16S ribosomal RNA gene and belong to 28 different genera, with representatives of the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The functional evaluation of the production of antibiotic was conducted with a total of 76 isolates including 30 isolates that formed inhibition halos against test microorganisms. The crude extracts were evaluated as the minimum inhibitory concentration (MIC) against eight non-virulent microorganisms, and 18 crude extracts showed activity, highlighting the so-called E131 extract, obtained from bacteria of the genus Streptomyces, which showed bacteriostatic activity against S. aureus and M. luteus, and bactericidal activity against C. albicans and B. subtilis. Faced with microorganisms isolated from clinical samples, 11 crude extracts showed inhibitory activity against four strains of Neisseria meningitides, with MIC ranging from 0.0313 mg.mL-1 to 2.0 mg.mL-1. The E46 extract obtained from the bacterium Pseudoalteromonas sp., stood out as the inhibitory activity observed across the four evaluated strains. Faced with the strain B4, stand out the antimicrobial activity of crude extracts obtained from bacteria Pseudoalteromonas sp. and Pseudomonas azotoformans CUG12536. Against YUSA strain, Marinilactibacillus sp. crude extract showed antimicrobial activity, which was the first reported in this bacterial genus. The extracts have in their composition, antimicrobial compounds whose activity is known, such as fatty acids, and compounds whose antimicrobial activity is not described in the literature. Fractionation tests of extracts using solvents of different polarities, indicated that the crude extracts are soluble mostly the polar solvent. Therefore, the bacteria isolated from the Antarctic produce compounds of pharmacological interest and can be used as a source of novel compounds. These results highlight the need for more studies of bacteria associated with extreme environments, such as Antarctica / Mestrado / Microbiologia / Mestra em Genética e Biologia Molecular