<p>Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha / /&beta / hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.</p>

Regioselektive Halogenasen sind Enzyme, die für die Biosynthese verschiedener halogenierter Metaboliten verantwortlich sind. Der Stamm Streptomyces rugosporus produziert die bioaktive halogenierte Verbindung Pyrroindomycin B. In dieser Arbeit wurde ein Gen einer Tryptophan-5-Halogenase aus dem Pyrroindomycinproduzenten Streptomyces rugosporus isoliert. Durch gezielte Mutation des Gens konnte die Beteiligung der Halogenase an der Biosynthese von Pyrroindomycin B nachgewiesen werden. Das Tryptophan-5-Halogenase-Gen wurde heterolog exprimiert. In einem spezifischen Enzymtest konnte die Aktivität der Tryptophan-5-Halogenase gezeigt werden. Tryptophan wurde im Enzymtest durch dieses Enzym monobromiert und monochloriert. Das Protein konnte über Nickelaffinitäts-Chromatographie gereinigt werden. / Regioselectively acting halogenases are enzymes which are responsible for the biosynthesis of a large variety of halogenated secondary metabolites. In many cases the biological activity of these metabolites is influenced by the halogen substituents. Isolation and characterization of the genes of specific halogenases and understanding the biochemistry of these enzymes are prerequisites for genetic engineering aiming at the production of novel halogenated compounds by combinatorial biosynthesis. In the work presented here a halogenase with novel regioselectivity was isolated. It is one of only three specific halogenases for which the enzymatic activity and the involvement in the biosynthesis of a halogenated metabolite could be shown. The availability of this specific tryptophan 5-halogenase is expected to open up novel possibilities for combinatorial biosynthesis and the enzymatic production of halogenated compounds.

<p>Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha / /&beta / hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.</p>

Les peptides lasso sont des peptides bioactifs bactériens issus de la voie de biosynthèse ribosomale et subissant des modifications post-traductionnelles, caractérisés par une structure entrelacée dite en lasso. Ils possèdent un cycle macrolactame en position N-terminale, traversé par la queue C-terminale. Cette topologie de type rotaxane, maintenue par piégeage de la queue C-terminale dans le cycle via des acides aminés encombrant et/ou des ponts disulfure, confère à ces peptides une structure compacte et stable. Les actinobactéries recèlent la plus grande diversité et gamme d'activités biologiques parmi les peptides lasso (antibactériens, anti-VIH, antagonistes de récepteurs..), et l'exploration de génomes suggère une diversité encore plus grande, puisque certains clusters portent des gènes codant des enzymes de modifications post-traductionnelles jamais observées auparavant. Cependant, l'expression de ces peptides semble être rigoureusement contrôlée, rendant leur production en laboratoire difficile à partir de la bactérie productrice. Le rôle écologique et les mécanismes de régulation des peptides lasso ne sont pas très documentés. Leur compréhension permettrait d'améliorer la production et de mieux exploiter les activités biologiques des peptides lasso. / Lasso peptides are ribosomally synthesized and post-translationally modified peptides produced by bacteria, characterized by a remarkable mechanically-interlocked structure. The lasso topology, reminiscent to a rotaxane, consists in an N-terminal macrolactam ring threaded by a C-terminal tail. This compact and stable structure is stabilized by steric entrapping of the tail in the ring, through bulky amino acid(s) and/or disulphide bonds. Lasso peptides produced by Actinobacteria display the greatest chemical diversity and a range of biological activities (antibacterial, anti-HIV, receptor antagonist…), therefore are of high pharmaceutical interest. Genome mining revealed that Actinobacteria have enormous potential to biosynthesize novel lasso peptides, e.g. harbouring new post-translational modifications. However, the expression of these peptides is generally controlled by complex regulatory systems, making their production under laboratory conditions difficult. Understanding the ecological role and regulation mechanisms of lasso peptides would help to improve production and better exploit the biotechnological potential of these molecules. The first part of my work deals with the identification of new lasso peptides from Actinobacteria, using heterologous expression in Streptomyces hosts. The second part of my work deals with the regulation mechanism and ecological role of lasso peptides using sviceucin, a lasso peptide produced by Streptomyces sviceus, as the model for study.

Rayons ionisants, dessiccation, ou encore métabolites secondaires exogènes sont autant de facteurs qui peuvent engendrer des dommages à l’ADN chez les bactéries du sol, notamment en provoquant la formation de cassures double-brin (DSB), préjudice majeur pour une cellule. Chez les procaryotes, l’évolution a sélectionné deux principaux mécanismes de réparation des DSB, à savoir la recombinaison homologue (RH) et le non-homologous end joining (NHEJ). La RH est un mécanisme quasi-ubiquiste dans le monde bactérien qui repose sur l’utilisation d’une copie intacte de la molécule endommagée comme matrice pour la réparation de la DSB. Contrairement à la RH, le NHEJ n’est présent que chez 20 à 25% des bactéries et est considéré comme un mécanisme mutagène puisque la réparation de la DSB se fait sans matrice homologue et peut entrainer l’ajout ou la délétion de nucléotides au site de cassure. Chez la bactérie modèle Mycobacterium, seuls deux acteurs sont nécessaires pour la réparation par NHEJ. Ainsi, un dimère de protéine Ku se fixe sur la cassure puis recrute la protéine multifonctionnelle LigD, qui catalyse le traitement puis la ligation des extrémités grâce à ses domaines polymérase, nucléase et ligase. Les mécanismes de réparation des DSB chez les Streptomyces étaient peu connus à l’initiation de ce travail. Cette bactérie présente des caractéristiques génomiques remarquables avec notamment un chromosome linéaire de grande taille (6 à 12 Mb). En ce qui concerne la RH, nous avons focalisé nos recherches sur les étapes tardives (post-synaptiques) et étudié le rôle du complexe RuvABC et de RecG impliqués chez Escherichia coli dans la migration de la croix de Holliday et de sa résolution. La construction de mutants simples et multiples a montré que bien que les gènes codant ces protéines soient très conservés chez les Streptomyces, leur déficience ne se traduit chez Streptomyces ambofaciens que par une faible baisse de la recombinaison suite à un événement de conjugaison. Aucune baisse de l’efficacité de recombinaison intrachromosomique n’a en revanche été observée. Ces résultats suggèrent que des acteurs alternatifs majeurs sont encore à découvrir chez les Streptomyces. Le décryptage du mécanisme de NHEJ chez S. ambofaciens constitue une première dans ce genre bactérien. Une étude génomique exhaustive a permis de révéler la très grande diversité du nombre d’acteurs potentiels de ce mécanisme (Ku, LigDom, PolDom, NucDom) et de l’organisation des gènes qui les codent.. L’analyse fonctionnelle a révélé que l’ensemble des acteurs étaient impliqués dans la réponse à l’exposition à un faisceau d’électrons accélérés, connus pour induire, entre autre, la formation de DSB. La génération de DSB, par coupure endonucléasique I-SceI, a par ailleurs permis de mettre en évidence au niveau moléculaire des réparations de type NHEJ (délétions ou insertions de quelques nucléotides, intégration de fragments d’ADN). Les cassures dans les régions terminales du chromosome sont accompagnées de grandes délétions (jusqu’à 2,1 Mb) et de réarrangements de grande ampleur incluant circularisations du chromosome et amplifications d’ADN. Les conséquences de la réparation de DSB chez S. ambofaciens sont en tous points similaires aux réarrangements observés spontanément ou par comparaison des génomes des espèces types. Ainsi, il est possible de lier la plasticité du génome à la réparation de DSB. En outre, l’intégration de matériel génétique exogène serait favorisée au cours de la réparation NHEJ ce qui donnerait à ce système de réparation une place importante dans le processus de transfert horizontal, mécanisme d’évolution majeur chez les bactéries / Ionizing radiation, desiccation or exogenous secondary metabolites are all factors that can cause DNA damage in soil bacteria, especially by triggering double strand breaks (DSB), the most detrimental harm for the cell. In prokaryotes, evolution selected two main DSB repair pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ). HR is almost ubiquitous in bacteria and relies on an intact copy of the damaged DNA molecule as a template for DSB repair. In contrast to HR, NHEJ is only present in 20 to 25% of bacteria and is considered as a mutagenic pathway since DSB repair is performed without the need of any template and can lead to nucleotide addition or deletion at DSB site. In the bacterial model Mycobacterium, two partners are sufficient for a functional NHEJ pathway. Thus, Ku protein dimer recognizes and binds the DSB and then recruits the multifunctional LigD protein for extremities treatment and ligation thanks to its polymerase, nuclease and ligase domains. At the beginning of this work, few informations on DSB repair in Streptomyces were available. This bacteria exhibits remarkable genomic features including a large linear chromosome (6 to 12 Mb). Regarding HR, we focused on the late stage (post-synaptic step) in studying the role of RuvABC complex and RecG, involved in branch migration and Holliday junction resolution in E. coli. Construction of single and multiple mutants showed that although the genes encoding these proteins are highly conserved in Streptomyces, their deficiency in Streptomyces ambofaciens only results in a mild decrease of recombination after conjugation events. Besides, no decrease of intrachromosomal recombination efficiency could be observed. These results suggest that major alternative factors are still to be discovered in Streptomyces. This work was also the first occasion to decipher a NHEJ pathway in Streptomyces. An exhaustive genomic study revealed a great diversity in the number of factors potentially implicated in this pathway (Ku, LigDom, PolDom, NucDom) and in the organization of their encoding genes. Functional analyses revealed that all the factors, whatever they are conserved or not between species, were involved in the response to electron beam exposure, known to induce, amongst other things, DSB formation. Generation of DSB by I-SceI endonuclease cleavage was also used to evidence at a molecular level NHEJ type DSB repair (deletions or insertions of several nucleotides, integration of DNA fragments). Targeted breaks in the terminal regions of the chromosome were accompanied by large deletions (up to 2.1 Mb) and major rearrangements including chromosome circularizations and DNA amplifications. Consequences of DSB repair in S. ambofaciens are in all points similar to chromosome rearrangements observed spontaneously or by comparing genomes of different species. Thus, it is possible to link the genome plasticity to DSB repair. In addition, the integration of exogenous genetic material would be favoured during NHEJ repair which would give this repair system a major role in the horizontal transfer process, known to be a main evolution mechanism in bacteria

Orientador: Hélia Harumi Sato / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-16T16:22:18Z (GMT). No. of bitstreams: 1 Lima_EvandroAntoniode_M.pdf: 2108461 bytes, checksum: 6b52a40625238916bf0ef94067896ee2 (MD5) Previous issue date: 2010 / Resumo: A transglutaminase microbiana (MTGase; EC 2.3.2.13) é uma enzima capaz de catalisar a formação de ligações covalentes cruzadas entre proteínas, peptídeos e várias aminas primárias através da reação de acil transferência entre resíduos de glutamina e lisina. A incorporação de ligações covalentes cruzadas entre proteínas por ação da transglutaminase vem sendo empregada pela indústria alimentícia para modificar principalmente a textura, a viscosidade e a capacidade de formação de gel de alimentos. Este trabalho teve como principal objetivo estudar a estabilidade térmica, o efeito de inibidores e ativadores, a concentração e a purificação da transglutaminase microbiana produzida pela linhagem Streptomyces sp. CBMAI 837. No estudo da estabilidade térmica da enzima verificou-se que a transglutaminase de Streptomyces sp. CBMAI 837 é uma enzima termossensível, estável em temperaturas abaixo de 40°C e rapidamente inativada acima de 50°C. Parâmetros cinéticos e termodinâmicos da desnaturação térmica da enzima foram determinados para as seis temperaturas estudadas. Os tempos de meia-vida da enzima a 55 e 60°C foram estimados em 3,5 e 1,9 minutos, respectivamente. A influência de alguns compostos no aumento da estabilidade térmica da enzima foi investigada, sendo verificado que a adição de EDTA e KCl na concentração de 1% e de cisteína e glutationa na concentração de 0,1% aumentaram a estabilidade térmica da transglutaminase durante incubação a 45°C por 30 minutos. O efeito de compostos como etanol, ativadores e inibidores enzimáticos na atividade da MTGase de Streptomyces sp. CBMAI 837 foi estudado. O etanol na concentração de 10% (v:v) apresentou pouco efeito na atividade enzimática, enquanto que concentrações acima de 40% (v:v) provocaram rápida inativação da enzima. A MTGase foi ativada na presença de EDTA e cisteína e inativada na presença de iodoacetamida e ácido cloromercuribenzóico, sugerindo que esta é uma enzima cálcio independente com um resíduo de cisteína no sítio ativo. No estudo da concentração da MTGase foram avaliados diferentes métodos, sendo verificado que a precipitação com sulfato de amônio a 80% de saturação foi o método mais efetivo, possibilitando a concentração do sobrenadante de cultivo cerca de 4,5 vezes com rendimento de 142%. A aplicação da preparação enzimática bruta concentrada de MTGase de Streptomyces sp. CBMAI 837 em proteína texturizada de soja apresentou efeito similar ao da enzima comercial Activa® TG-BP quando aplicada nas mesmas condições. Na purificação da MTGase de Streptomyces sp. CBMAI 837 em coluna de afinidade Blue Sepharose CL-6B foram separadas 3 frações com atividade de transglutaminase (TG-BS1, TG-BS2 e TG-BS3), indicando a presença de isoenzimas. A massa molecular da MTGase presente nas frações purificadas TG-BS2 e TG-BS3 foi estimada em cerca de 35 KDa por SDS-PAGE. As três frações obtidas foram caracterizadas quanto ao pH ótimo de atividade enzimática. Foi observado que a fração parcialmente purificada TG-BS1 apresentou atividade ótima em pH 10,0 e um segundo pico de atividade em pH 6,0, enquanto as frações purificadas TG-BS2 e TG-BS3 apresentaram pH ótimo de atividade em pH 6,5 e também um segundo pico de atividade em pH 10,0 / Abstract: The microbial transglutaminase (MTGase, EC 2.3.2.13) is an enzyme capable of catalyzing the formation of covalent cross-links among proteins, peptides and various primary amines by reaction of acyl transfer between glutamine and lysine residues. The incorporation of covalent cross-links between proteins by the action of transglutaminase has been used by the food industry to modify especially the texture, viscosity and gel forming ability of foods. This work aimed to study the thermal stability, effect of inhibitors and activators, concentration and purification of microbial transglutaminase produced by strain Streptomyces sp. CBMAI 837. It was observed in the study of thermal stability of the enzyme that the transglutaminase from Streptomyces sp. CBMAI 837 is a thermosensitive enzyme, stable at temperatures below 40°C and rapidly inactivated above 50°C. Kinetic and thermodynamic parameters of thermal denaturation of the enzyme were determined for six temperatures. It was estimated that the half-life times of the enzyme at 55 and 60°C were 3.5 and 1.9 minutes, respectively. The influence of compounds to increase the thermal stability of the enzyme was investigated, and it was found that the addition of EDTA and KCl at a concentration of 1% and cysteine and glutathione at a concentration of 0.1% increased the thermal stability of transglutaminase during the incubation at 45°C for 30 minutes. The effect of compounds such as ethanol, activators and inhibitors on enzymatic activity of MTGase from Streptomyces sp. CBMAI 837 was studied. The ethanol concentration 10% (v/v) had little effect on enzyme activity, while concentrations above 40% (v/v) resulted in rapid inactivation of the enzyme. The MTGase was activated in the presence of EDTA and cysteine and inactivated in the presence of iodoacetamide and chloromercuribenzoic acid, suggesting that this is a calcium independent enzyme with a cysteine residue at the active site. Different methods were evaluated in the study of the concentration of MTGase, confirming that the precipitation with ammonium sulfate at 80% saturation of the culture supernatant was the method more effective, being concentrated this enzyme about 4.5 fold with a yield of 142%. The application of crude enzyme preparation of MTGase from Streptomyces sp. CBMAI 837 concentrated by ammonium sulfate in texturized soy protein showed a similar effect to the one of commercial enzyme Activa® TG-BP when applied under the same conditions. Three fractions with transglutaminase activity (TG-BS1, TG-BS2 e TG-BS3) were separated in the purification of MTGase from Streptomyces sp. CBMAI 837 in column affinity Blue Sepharose CL-6B, indicating the presence of isoenzymes. The molecular mass of MTGase present in the purified fractions TG-BS2 e TG-BS3 was estimated at about 35 KDa by SDS-PAGE. The three fractions were characterized by optimum pH of enzymatic activity. It was observed that the partially purified fraction TG-BS1 showed optimal activity at pH 10.0 and a second peak of activity at pH 6.0, while the purified fractions TG-BS2 e TG-BS3 showed optimum pH activity at pH 6.5 and also a second peak of activity at pH 10.0 / Mestrado / Mestre em Ciência de Alimentos

Ácido clavulânico (AC) é um potente inibidor de &beta;-lactamases, produzido por Streptomyces clavuligerus, usado clinicamente em combinação com antibióticos &beta;-lactâmicos para tratar infecções bacterianas resistentes. Apesar da produção industrial de AC já ser bem estabelecida muitos aspectos importantes relacionados com sua biossíntese permanecem carentes de estudo. Sabe-se que a via de síntese do AC envolve no mínimo 8 passos enzimáticos sendo os primeiros passos mais abordados. Por exemplo, as enzimas N2-(2-carboxietil) arginina sintase (CEAS), &beta;-lactama sintase (BLS) e proclavaminato amidino hidrolase (PAH) são as responsáveis pela primeira, segunda e quarta reações enzimáticas respectivamente. Estudos mutagênicos recentes em S.clavuligerus relacionaram cópias extras dos genes ceas, bls e pah (ceas1, bls1 e pah1) com essa via porém nenhum ensaio enzimático foi relatado. Embora os passos finais da via ainda não estejam completamente estabelecidos, a ação de algumas enzimas putativas, como a codificada por orf12, mostraram ser essenciais a produção do AC. Assim, com o objetivo de aumentar a informação disponível sobre a biossíntese do AC estudamos quatro de seus membros: CEAS1, BLS1, PAH1 e a proteína putativa codificada pela orf12. Os genes foram isolados a partir do DNA genômico de S. clavuligerus por PCR e clonados em vetores para produção das proteínas recombinantes em E.coli. Os protocolos de expressão foram estabelecidos para CEAS1, PAH1 e ORF12 e as proteínas recombinantes foram purificadas por cromatografia de afinidade por metal. BLS foi obtida de forma isolúvel. As proteínas solúveis foram caracterizadas por meio de técnicas bioquímicas e estruturais. As análises de CEAS1 e PAH1 foram comparadas com informações já obtidas para as isozimas CEAS2 e PAH2, respectivamente. Assim, as análises de oligomerização das proteínas resultaram em uma mistura de oligômeros (monômero, dímero e tetrâmero) para CEAS1, na forma hexamérica para PAH1 e na forma dimérica para ORF12, estando de acordo com as formas solúvel e cristalográfica de CEAS2 (dímero e tetrâmero) e PAH2 (hexâmero). Espectros de dicroísmo circular mostraram que CEAS1 e PAH1 possuem um enovelamento do tipo &alpha;/&beta; sendo estáveis até 35ºC e numa ampla faixa de pH. Os parâmetros termodinâmicos da interação entre CEAS1 e o cofator Mg+2 foram determinados mostrando que é entropicamente dirigida, com uma estequiometria de ligação de 4 : 1, com uma constante de afinidade na ordem de micromolar (KD = 1,76 &plusmn; 0.23 &micro;M). Análises realizadas com as técnicas de reação acoplada, de Cromatografia Líquida de Alta Pressão acoplada a Espectrometria de Massas (LC-MS) e de Calorimetria de Titulação Isotérmica mostraram que CEAS1, assim como CEAS2, apresenta atividade sob o substrato gliceraldeído-3-fosfato, porém sem a formação do produto final N2-(2-carboxietil)arginina. Por outro lado, a proteína recombinante PAH1 mostrou ser inativa sobre o substrato análogo, N-&alpha;-acetil-L-arginina. Assim, apesar das isozimas manterem um padrão estrutural, podem ter mecanismos de ação distintos. Em relação a ORF12 esta proteína foi classificada com uma &beta;-lactamase com atividade esterase de acordo com nossos estudos realizados com os substratos cefalosporina C e p-nitrofenil acetato. / Clavulanic acid (CA) is a potent inhibitor of &beta;-lactamases, produced by Streptomyces clavuligerus, clinically used in combination with &beta;-lactam antibiotics to treat resistant bacterial infections. Although CA industrial production is well-established, many important aspects related to its biosynthesis remains under study. It is known that CA pathway involves at least 8 enzymatic steps, being the earliest stages more addressed. For instance, N2-(2-carboxyethyl) arginine synthase (CEAS), &beta;-lactam synthase (BLS) and proclavaminate amidinohydrolase (PAH) are responsible for the first, second and fourth enzymatic reaction, respectively. Recent mutagenic studies in S.clavuligerus have related extra copies of ceas, bls and pah genes ((ceas1, bls1 e pah1) to this pathway but none enzymatic assay was further reported. Although later stages the pathway remain unclear, the action of some putative enzymes like the codified by orf12 showed essential to CA production. Thus, aiming to increase the information available about CA biosynthesis we studied four of its members: CEAS1, BLS1, PAH1, and the putative protein codified by orf12. The genes were isolated from S.clavuligerus genomic DNA by PCR and further cloned into expression vectors in order to produce recombinant proteins in E.coli. Protocols of protein expression were established to CEAS1, PAH1 and ORF12 and recombinant proteins were purified by metal affinity chromatography. BLS was obtained as an insoluble form. Soluble proteins were characterized by means of biochemical and structural approaches. Analyses of CEAS1 and PAH1 were compared with information ever conducted to the isozymes CEAS2 and PAH2, respectively. Thus, oligomerization analysis of proteins resulted respectively in a mix of oligomers forms (monomer, dimer, tetramer) to CEAS1, hexameric form to PAH1 and dimeric form to ORF12, according to the soluble and crystallographic form of CEAS2 (dimer and tetramer) and PAH2 (hexamer). Circular Dichroism spectra showed that CEAS1 and PAH1 have an &alpha;-&beta; conformation and were stable up to 35ºC over a wide pH range. Thermodynamic parameters of CEAS1 cofactor (Mg+2) binding were determined showing that is entropic driven, with a 4:1 binding stoichiometry, with a micro-molar affinity (KD = 1.76 &plusmn; 0.23 &micro;M). Analyses by coupled assay, High Pressure Liquid Chromatography coupled to Mass Spectroscopy (LC-MS) and Isothermal Titration Calorimetry showed that CEAS1, as well as the CEAS2, presents activity at the substrate glyceraldehydes-3-phosphate, however without formation of final product, N2-(2-carboxyethyl)arginine. Meanwhile recombinant PAH1 showed none activity at analogous substrate, N-&alpha;-acetil-L-arginine. Thus despite isozymes maintain a structural pattern, they may have distinct action mechanism. Regards to ORF12, this protein was classified as a &beta;-lactamase with an esterase activity according to our studies performed with the substrates cephalosporin C and p-nitrophenyl acetate.

Orientador: Luciana Gonzaga de Oliveira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-19T08:47:55Z (GMT). No. of bitstreams: 1 Cruz_PedroLuisRochada_M.pdf: 2656746 bytes, checksum: 52eb866ff62a51e20e65bc5b01101aeb (MD5) Previous issue date: 2011 / Resumo: Actinobactérias são fontes importantes para a descoberta de novas moléculas com atividades biológicas destacadas. A este grupo pertencem Streptomyces, micro-organismos que possuem dentre outros, dois grupos de enzimas multimodulares conhecidas como policetídeo sintase (PKS) e peptídeo não ribossomal sintetase (NRPS) que catalisam a produção de policetídeos e peptídeos não ribossomais respectivamente. A biossíntese destas moléculas se dá geralmente seguindo uma relação linear entre o gene, a enzima e a estrutura da molécula. Desta forma, com o conhecimento das sequências do gene é possível prever a molécula a ser produzida e sua manipulação amplia a possibilidade de obter novas moléculas. Neste sentido foi adotada uma estratégia para o mapeamento dos genes biossintéticos sem a necessidade do sequenciamento extensivo do micro-organismo com o objetivo de prever o tipo de policetídeo e peptídeo não ribossomal produzido por linhagens de Streptomyces isoladas de Citrus ssp. Com o objetivo de conhecer os metabólitos produzidos por estes micro-organismos foi feito também o cultivo destes em meios contendo fontes de nutrientes variadas e o monitoramento de metabólitos presentes nos extratos utilizando técnicas de cromatografia líquida acoplada com espectrometria de massas. Ensaios em placas permitiram a visualização da produção de sideróforos e a atividade antibiótica dos meios de cultivo / Abstract: Actinobacteria are important sources of new molecules with biological activities. Streptomyces are the most important genera studied. Such microorganisms carries out among a variety of biosynthetic enzimes, two main groups known as polyketide synthase (PKS) and non ribosomal peptide synthetase (NRPS), both catalyzing the biosynthesis of polyketide and non ribosomal peptides respectively. PKS and NRPS biosynthesis follows a collinear relationship among the gene cluster, the enzyme and the secondary metabolite. Therefore, the knowledge of the gene sequences allows to find new molecules. In this work we adopted a strategy to map the biosynthetic genes without the need of extensive whole genome sequencing in order to predict the metabolite produced by Streptomyces strains isolated from Citrus ssp. The strains were also cultivated and the metabolite production monitored by liquid chromatography coupled with mass spectrometry. In addition, the biological activity of these medium was estimated using qualitative biochemical assays / Mestrado / Quimica Organica / Mestre em Química

Magister Scientiae - MSc / Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha;/&beta; hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted. / South Africa

Les cassures double brin de l’ADN sont des dommages pouvant engendrer la mort cellulaire. Deux mécanismes majeurs sont impliqués dans leur réparation chez les bactéries : la recombinaison homologue et le Non-Homologous End Joining (NHEJ). Streptomyces est une bactérie modèle pour étudier l'impact relatif des mécanismes de recombinaison sur la structure du génome et son évolution ; le chromosome est en effet caractérisé par sa linéarité, son organisation génétique compartimentée et sa plasticité génomique remarquable. L'objectif de cette recherche est d'identifier les acteurs impliqués dans les mécanismes de réparation des cassures double brin qui restent inconnus chez Streptomyces à ce jour. Concernant la recombinaison homologue, la première étape consiste en une maturation des extrémités d’ADN générées par la cassure. Cette première étape est assurée par un complexe à activité hélicase-nuclease : RecBCD (chez Escherichia coli), AddAB (chez Bacillus subtilis) ou AdnAB (chez les mycobactéries). Une analyse in silico des génomes disponibles de Streptomyces a permis d’identifier chez ces organismes, deux gènes conservés et adjacents, nommés adnA et adnB en raison de leur homologie avec les gènes adnAB récemment identifiés chez les mycobactéries. Les tentatives visant à déléter ces gènes chez Streptomyces ambofaciens et Streptomyces coelicolor ont été infructueuses. Cependant, le fait que leur délétion soit rendue possible par l’ajout d’une copie ectopique du locus sauvage nous a amené à conclure au caractère essentiel d’adnA et adnB chez Streptomyces. La trans-complémentation d’un mutant [delta]recB d’E. coli par le locus adnAB de S. ambofaciens restaure l’activité nucléase cellulaire et la survie en présence ou non d’agent génotoxique, suggérant qu’adnAB code l’homologue fonctionnel de RecBCD d’E. coli. Le rôle central d’adnAB dans la recombinaison homologue et la réplication est discuté. Le mécanisme NHEJ montre une distribution sporadique chez les bactéries et implique les deux protéines Ku et LigD. La protéine Ku se fixe sur les extrémités de l’ADN et recrute la ligase LigD. Cette dernière est une protéine multifonctionnelle présentant, outre une activité ligase, une activité polymérase et parfois une activité nucléase. L’analyse des génomes de Streptomyces a révélé un nombre variable d’homologues de ku (1-3) et d’homologues codant pour l’une ou l’autre des trois activités de LigD. Ces différents gènes définissent deux loci conservés entre espèces de Streptomyces. Chez S. ambofaciens, trois homologues de ku (nommés kuA, kuB et kuC) et deux ligases ATP-dépendantes (nommés ligC et ligD) ont été identifiés. L’exposition de souches déficientes pour ces différents gènes aux agents endommageant l’ADN (la mitomycine C, l’irradiation par faisceau d’électrons) a démontré l’implication de kuA et ligC, deux acteurs conservés, mais aussi des gènes variables kuC et ligD, dans la réparation de l’ADN. Ces résultats ouvrent de nouvelles perspectives pour comprendre le rôle du NHEJ dans l'évolution du génome et la biologie Streptomyces. / Double strand breaks (DSB) constitute the most deleterious form of DNA damage that a bacterial cell can encounter. Two major pathways can carry out DSB repair in bacteria: homologous recombination and Non-Homologous End Joining (NHEJ). Streptomyces is a model bacterium to explore the relative impact of these recombination mechanisms on genome structure and evolution; the chromosome is indeed typified by its linearity, its compartmentalized genetic organization and its remarkable genomic plasticity. The objective of this research is to identify actors involved in DSB repair mechanisms which remain mostly elusive in Streptomyces up to now. The first step of DSB repair by homologous recombination is the resection of broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB and Mycobacterium tuberculosis AdnAB. In silico analysis of Streptomyces genomes allowed to identify homologues for adnA and adnB which constitute a highly conserved locus within the genus. Attempts to disrupt these two genes were unsuccessful in Streptomyces ambofaciens as well as in Streptomyces coelicolor, unless an extra copy of adnAB was inserted in the chromosome. This indicates that AdnA and AdnB are both essential for Streptomyces growth. Complementation of an E. coli [delta]recB mutant by S. ambofaciens adnAB locus restored nuclease activity and cell survival in the presence or absence of DNA damaging agent, strongly suggesting that Streptomyces adnAB encodes a functional homologue of E. coli RecBCD. The key role of adnAB in homologous recombination and DNA replication is discussed. The NHEJ mechanism shows a sporadic distribution in bacteria and is known to involve the two proteins Ku and LigD. The Ku protein binds to the ends of the broken DNA and recruits the ATP-dependent ligase LigD which is a multifunctional protein carrying ligase, polymerase and sometimes nuclease activity. In silico analysis of Streptomyces genomes revealed a complex organization with a variable number of ku homologues (1 to 3) and of homologues encoding one of the three distinct LigD activities. These homologues define two conserved loci. S. ambofaciens possesses 3 ku (named kuA, kuB and kuC) and 2 ATP-dependent ligases (named ligC and ligD). Exposure to DNA damaging agents (mitomycin C, electron beam irradiation) of mutant strains got involved kuA and ligC, two conserved actors, but also variable genes such as kuC and ligD in DNA repair. These results open up new prospects to understand the role of NHEJ in the biology and genome evolution of Streptomyces.