The actinobacteria Actinomadura hibisca synthesizes the natural products pradimicin A-C through a type II polyketide biosynthetic pathway. Eight tailoring enzymes in pradimicin biosynthesis have been investigated in this work, including PdmJ, PdmW, PdmN, PdmT, PdmO, PdmS, PdmQ and PdmF. PdmJ and PdmW were characterized as cytochrome P450 hydroxylases that catalyze the incorporation of two hydroxyl groups at C-5 and C-6, respectively. These enzymes worked synergistically and their co-expression significantly improved the efficiency of the hydroxylation steps. PdmN is an amino acid ligase that accepts a variety of substrates and ligates a D-alanine moiety to C-16 to form the corresponding derivatives. PdmS and PdmQ were functionally identified as Oglycosyltransferases. Disruption of pdmS in the genome of A. hibisca generated a biosynthetic precursor without sugar moieties, which validated that PdmS is the first glycosyltransferase that attaches the first sugar to the 5-OH of pradimicins. In contrast, disruption of pdmQ led to the synthesis of pradimicin B, confirming that PdmQ was responsible for attaching the D-xylose moiety to the 3'-OH of the first sugar portion in pradimicins. Naturally, the first sugar moiety 4',6'-dideoxy-4'-amino-D-galactose of pradimicin A and B is methylated at 2'-NH. When the expression of PdmO was compromised, the mutant strain produced mainly pradimicin C, which contains the 4',6'- dideoxy-4'-amino-D-galactose in its structure. This suggested that PdmO was responsible for the N-methylation of the amino sugar. PdmF was identified as the C-11 Omethyltransferase. Moreover, PdmT was confirmed to be an O-methyltransferase through gene disruption and in vitro biochemical reactions. PdmT methylates the 7-OH to form a methoxy group that in a later step is removed to generate the pradimicin aglycon. In summary, this research has identified eight important pradimicin biosynthetic enzymes that are involved in various tailoring steps in pradimicin biosynthesis. Several new pradimicin analogues has been generated by manipulating these enzymes. Their enzymatic properties and collaborative actions were investigated. These results not only provide new insights into type II polyketide biosynthetic pathways, but also enable rational engineering of the pradimicin biosynthetic pathway to create new analogues for drug development.

<p>Nonribosomal peptides, polyketides, and fatty acids comprise a distinct subset of microbial secondary metabolites produced by similar biosynthetic methods and exhibit broad structural diversity with a high propensity for biological activity. Dedicated studies of these specific microbial small molecules have identified numerous potent actions towards human cells with many clinical translations. Interestingly, most therapeutically used nonribosomal peptides and polyketides were discovered from soil bacteria, meanwhile, bacteria that have co-evolved within a human context, the human microbiota, have barely been explored for secondary metabolites. The central goal of this thesis is to explore the secondary metabolome of human microbiota for nonribosomal peptides and polyketides, which are hypothesized to possess biological activities significant within the human host context. Candidate organisms were chosen for their established connections to human health and evidence suggestive of secondary metabolite production. Specifically, questions about gene to molecule prediction capability, metabolite production, structural diversity, and biological activity were explored from studies of the dental caries linked Streptococcus mutans UA159, from the probiotic Lactobacillus plantarum WCFS1, and the Crohn’s disease associated Faecalibacterium prausnitzii.</p> / Master of Science (MSc)

Polyketide products are useful compounds to research and industry but can be difficult to access due to their richness in stereogenic centers. Type I polyketide synthases offer unique engineering opportunities to access natural stereocontrol and resultant complex compounds. The development of a controlled in vitro platform based around type I polyketide synthases is described. It has been used to produce a small library of polyketide fragments on an unprecedented and synthetically-relevant scale and explore polyketide synthase enzymology. / text

Os microrganismos atraem considerável atenção por serem uma fonte de compostos biotecnológicos e farmacêuticos. Diversos produtos naturais peptídicos produzidos por fungos e bactérias são sintetizados por grandes enzimas, conhecidas como peptídeo sintetase não ribossômica (NRPS) e policetídeo sintase (PKS). A bioprospecção dos microrganismos isolados do solo de Terra Preta Antropogênica (TPA) da Amazônia Ocidental é de grande importância para o conhecimento deste bioma tropical. Este estudo correlacionou a presença de sideróforos e de compostos antimicrobianos produzidos pelos microrganismos isolados de TPA e dos solos adjacentes com a presença dos genes que codificam para NRPS e PKS. Linhagens bacterianas foram isoladas das amostras do solo coletadas de 10, 20 e 40 cm de profundidade. Os isolados foram cultivados em meio líquido específico por 2 dias a 28oC. Um total de 143 isolados foi testado para a atividade de sideróforo e para isso, as linhagens foram inoculadas em um meio com baixa concentração de ferro (MM9) contendo o complexo cromoazurol S-Fe3. Do total, 72 isolados apresentaram reação positiva para a produção de sideróforo. O DNA genômico dos isolados foi extraído e a amplificação por PCR foi realizada usando iniciadores específicos para NRPS e PKS. Os resultados mostraram que quinze isolados apresentaram o gene que codifica para NRPS, vinte isolados para PKS e somente dez isolados apresentaram ambos os genes. A presença de genes de NRPS e PKS em 31% dos isolados testados sugere que a produção dos sideróforos possa ocorrer pela via não ribossomal. Dois isolados foram selecionados para estudos de identificação e caracterização dos compostos. O isolado TP11 foi identificado como Pseudomonas putida através de seqüenciamento do 16S rRNA e apresentou resultado negativo para hidroxamato e catecol, sugerindo que o tipo de sideróforo não possui nenhum destes grupos funcionais. O isolado TP16 foi identificado como Pseudomonas putida e apresentou produção de sideróforo do tipo catecol e hidroxamato, sugerindo a produção de mais de um sideróforo. Além disso, esta linhagem produziu um composto antimicrobiano, com atividade de sideróforo identificado por espectrometria de massas como pseudomonina com massa molar de 330 Da. / Microorganisms have attracted considerable attention as a source for biotechnological and pharmaceutical agents. Several peptidic natural products synthesized by fungi and bacteria are assembled by large enzymes, referred as nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). Bioprospection of microorganisms isolated from Anthropological Dark Earth soil of Brazilian Occidental Amazon is of great importance to the knowledge of this tropical biome. This study aimed to correlate the presence of siderophores and antimicrobial compounds produced by microorganisms isolated from Dark Earth and adjacent soils of Brazilian Amazon with the presence of genes encoding NRPS and PKS. Bacterial strains were isolated from soil samples collected at 10, 20 and 40 cm depth. The isolates were grown in specific liquid medium for 2 d at 28oC. A total of 143 isolates were screened for siderophore activity and for this, bacterial strains were inoculated on plates containing an iron-limited medium (MM9) amended with a chromeazurol S-Fe3 complex. From the total, seventy-two isolates showed positive reaction for siderophore production. Genomic DNA of the isolates was extracted and PCR amplification was carried out using specific primers for NRPS and PKS. The results showed that fifteen isolates presented NRPS, twenty isolates presented PKS and only ten isolates showed both genes. The presence of NRPS and PKS genes in 31% of the isolates tested suggests that production of siderophores may occur by a nonribosomal pathway. Two isolates were selected for further studies. Isolate TP11 was identified as Pseudomonas putida by 16S rDNA sequencing analysis and was negative for hydroxamate and catechol, suggesting that the siderophore type has no hydroxamate- or catechol-type functional groups. The isolate TP16 was identified as Pseudomonas putida and showed the production of catechol and hydroxamate siderophore-type, suggesting the production of more than one siderophore. In addition, this strain produced an antimicrobial compound, with siderophore activity identified through mass spectrometry as pseudomonine with a molar mass of 330 Da.

Les polykétides sont des molécules complexes possédant des rôles thérapeutiques divers (antibiotiques, anticancéreux, immunosuppresseurs, etc..). Ces composés sont synthétisés par les polykétides synthases (PKS) qui présentent donc un intérêt certain. Une stratégie prometteuse et en développement, appelée biologie synthétique, consiste en l’ingénierie protéique des PKS pour produire de nouveaux polykétides. Cependant, un prérequis au succès de cette méthode est la compréhension du fonctionnement des PKS. En effet, les PKS sont des systèmes complexes composés de plusieurs sous-unités. Celles-ci comportent chacune un ou plusieurs modules responsable d’un cycle d’extension du polykétide. Les modules sont composés également de plusieurs domaines assurant chacun un rôle biosynthétique. Il est ainsi nécessaire de comprendre comment s’opère la communication entre domaines au sein d’un module. Pour cela, nous avons étudié le module 5 de la PKS synthétisant la virginiamycine M par une approche combinant la diffusion des rayons X aux petits angles (SAXS), la résonance magnétique nucléaire (RMN) et la modélisation par homologie. Ainsi nous sommes parvenus à caractériser la structure en solution du module 5, mais également à positionner les structures à haute résolution des domaines à l’intérieur de l’enveloppe SAXS. De plus, notre étude de la dynamique du module 5 a montré que les deux domaines acyl carrier protein (ACP) composant le module semblent non-équivalents, et que l’ACP5b doit être doté d’une certaine mobilité afin d’être fonctionnel, ceci dû à la flexibilité du linker reliant les deux ACP. L’interaction entre les sous-unités consécutives est également primordiale pour assurer la fidélité de la synthèse des polykétides. Ces interactions sont assurées, au moins en partie, par des domaines de petite taille appelés « domaine de docking (DD) ». Jusqu’alors, les DD avaient été caractérisés uniquement chez les PKS de type cis-AT. Nous avons caractérisé une nouvelle classe de DD, la première chez les PKS trans-AT. Grâce à une approche pluridisciplinaire, nous avons montré que l’un des DD constitue probablement une protéine intrinsèquement désordonnée (IDP) : son interaction avec le DD partenaire induirait son repliement. Nous avons résolu la structure RMN d’une protéine de fusion entre les deux DD, affichant une nouvelle topologie pour une interaction protéine-protéine. Cette interface de docking a ensuite été replacée dans son contexte modulaire par SAXS. Contrairement aux autres DD qui ne forment qu’une seule interface de docking, ces DD forment deux complexes de docking à l’intersection des deux sous-unités. Nos données SAXS nous avons également permis de proposer un modèle de l’interface créée entre deux sous-unités PKS dans laquelle une chambre réactionnelle est formée, qui pourrait servir à protéger des intermédiaires réactifs de polykétide. Des enzymes post-PKS interviennent suite à la synthèse du polykétide pour maturer ce dernier. Cette étape est d’une importance considérable puisqu’elle confère la structure et l’activité finale du polykétide. Dans ce contexte, nous avons mené une étude structure/fonction de l’enzyme post-PKS catalysant la macrocyclisation de l’antibiotique lankacidine C. Après un phasage par SAD sur la protéine séléniée, nous avons résolu la structure de l’enzyme en complexe avec des analogues de substrats, puis procéder à la conception de mutants pour résoudre la structure de l’enzyme avec son substrat naturel / Polyketides are structurally complex molecules which exhibit diverse therapeutic activities (antibiotic, antitumor, immunosuppressant…). These compounds and the enzymes responsible for their synthesis, the polyketide synthases (PKSs), are thus of significant biomedical interest. An emerging though promising strategy for the generation of novel polyketides is the engineering of the PKS proteins, an approach called synthetic biology. Nevertheless, a fundamental understanding of the mode of operation of the PKS enzymes is directly correlated with the success of this methodology. Indeed, PKSs are molecular-scale assembly lines which are composed of several subunit, each of which includes one or several modules catalyzing a polyketide elongation cycle. The module themselves are composed of several domains each with a specific role in the biosynthesis. It is therefore necessary to understand how the domains within a module communicate with each other. To address this question, we studied module 5 of the PKS responsible for virginiamycin M using an approach combining small angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) and homology modeling. This strategy allowed us to characterize the solution structure of module 5, but additionally to position high-resolution domain structures inside the SAXS envelopes. We also studied the dynamics of module 5, demonstrating that the two component acyl carrier proteins (ACPs) appear to be non-equivalent, and that the function of ACP5b is likely dependent on the mobility conferred on it by the flexible linker between the two domains. The interaction between the consecutive subunits is also critical to ensuring the fidelity of polyketide synthesis. This communication is assured, at least in part, by small domains called docking domains (DD), which have to date only been characterized from cis-AT PKS. Here, we have identified a new class of DD, the first shown to be present in trans-AT PKSs. Using a multidisciplinary approach, we have demonstrated that the N-terminal DD (VirFG NDD) is likely to be an intrinsically disordered protein (IDP), whose interaction with its partner DD (VirA CDD) induces its folding. We have solved the NMR structure of a fusion protein between the two DD, revealing a new topology for a protein-protein interaction. This docking interface was then placed into its modular context by SAXS. In contrast to the other classes of DD which form a single docking complex, this new type of DD gives rise to two docking interfaces at the intersubunit junction. Finally, our SAXS data have allowed us to propose a model for the complete interface between two PKS subunits in which a reaction chamber is formed, which may allow reactive polyketide intermediates to be protected. Post-PKS enzymes catalyze maturation of the polyketide after its release from the last module of the PKS. This processing is critical as it yields the final structure and activity of the polyketide. In this context, we conducted a structure/function study of the post-PKS enzyme catalyzing the macrocyclisation of the antibiotic lankacidine C. After phasing by SAD using a seleniated protein, we solved the structure of the enzyme in complex with substrate analogues. We then proceeded to site-directed mutagenesis of specific residues, in order to solve the structure of the enzyme in complex with its natural substrate

La grande majorité des colorants alimentaires naturels, utilisés dans la formulation des aliments et des boissons, proviennent des pigments extraits de matières premières végétales. Plusieurs couleurs dérivées de plantes peuvent entraîner des problèmes de formulation. Des facteurs, comme par exemple, la région, le climat, l'environnement, la variété cultivée, ont un effet de nuances de couleurs, de résistance et surtout de stabilité dans le produit final. Par ailleurs, les champignons filamenteux du genre Monascus, Penicillium et Talaromyces sont connus comme d'excellents producteurs de pigments rouges. Ces pigments intéressent de ce fait les industries car ils sont stables, non-toxiques et peuvent être utilisés comme colorants alimentaires.La recherche présentée dans le cadre de cette thèse de doctorat concerne la description des propriétés du pigment rouge que produit la souche de Talaromyces albobiverticillius isolée du milieu marin tropical autour de l'île de La Réunion. Les plans d’expérience (DOE) et la méthodologie des surfaces de réponses (RSM) ont été utilisés pour optimiser les conditions de culture et la formulation du milieu de fermentation, dans le but d'accroître les teneurs en polykétides colorés. Douze structures différentes ont été identifiées dans des extraits intracellulaires et extracellulaires des cultures fongiques, à l'aide de séparations et d'analyses spectroscopiques (HPLC-PDA-ESI/MS et RMN). Les pigments N-thréonine-monascorubramine, N-glutaryl-rubropunctamine et PP-O figurent ainsi parmi les 12 composants.Avec la demande croissante de composés colorés naturels dans le secteur industriel, les champignons isolés du milieu marin semblent présenter de nombreux intérêts. Des essais ont ainsi été menés afin d'étudier 1) l'amélioration des conditions de fermentation en fioles agitées ou en fermenteur de 2 litres; 2) les effets de la teneur en sel marin sur la synthèse des pigments; 3) des méthodes d'extraction respectueuses de l'environnement. Globalement, ces résultats font ressortir le grand potentiel des champignons marins produisant ce colorant rouge et la possibilité d'obtenir les colorants alimentaires adaptés. / It is well known that the vast majority of food colorants used in food and beverage applications comes from the pigments synthesized by plant materials. Besides, stability of many plant-derived colors can create formulation problems. Factors such as the region, the climate, the environment, the cultivar all impact colors shade, strength and overall stability in the final product. As an alternate, fungi of the genus Monascus, Penicillium and Talaromyces are known as excellent producers of red pigments. These red pigments are of industrial interest as they are stable and non-toxic and can be used as food colorants.This present research deals with the selection of high throughput red pigment producing Talaromyces albobiverticillius as a source of polyketide based natural food colorants. Design of Experiments (DoE) and Response Surface Methodology (RSM) have been used to optimize culture conditions and media formulation of fermentation process. Using Box Behnken Design (BBD), the influence of different physical factors on pigment and biomass production was studied using potato dextrose broth as culture media. The best optimal conditions were found to be with initial pH of 6.4, temperature of 24 °C, agitation speed of 164 rpm and fermentation time of 149 h gave 47.93 ± 0.58 mg /L of orange pigment, 196.28 ± 0.76 mg / L of red pigment and 12.58 ± 0.41 g /L of dry biomass. With the application of Plackett- Burman Design (PBD), 16 different media formulations were optimized using various carbon and nitrogen sources. When Sucrose and Yeast extract was used as a basal medium at 24° C, high pigment yield was observed: 695.93 ± 0.29 mg /L of orange pigment, 738.28 ± 0.51 mg / L of red pigment and 6.80 ± 0.37 g /L of dry biomass.Twelve different compounds were detected from the HPLC-PDA-ESI/MS analysis of intracellular and extracellular pigmented extracts. In particular, N-threonine-monascorubramine, N-glutaryl-rubropunctamine and PP-O were tentatively identified among these twelve compounds; further, this work reports for the first time on the PDA, MS and NMR characterization of the here named as N-GABA-monascorubramine derivative (6-[(Z)-2-Carboxyvinyl]-N-GABA-monascorubramine) pigment bearing a cis configuration at the C10-C11 double bond, in Talaromyces albobiverticillius 30548. Attempts were made to study the effects of sea salts on pigment synthesis; sustainable green extraction methods for pigments; upscaling of fermentation from shake flasks to laboratory fermenter. All these experiments with their results were discussed briefly as individual chapters. Overall, these findings bring out the potential of marine-derived red pigment producing fungi and its possibility of obtaining tailor made food colorants.

This thesis entitled ‘ Unusual Acylation Properties of Type II Fatty Acid Biosynthesis Acyl Carrier Proteins’ describes the discovery of self-acylation and malonyl transferase activity in acyl carrier proteins involved in type II fatty acid biosynthesis and assigns a physiological role to these processes inside the cellular milieu. Acyl carrier protein (ACP) is one of the most abundant proteins present inside the cell and almost 4% enzymes require it as a cofactor. Acyl carrier proteins can exist either as discrete proteins or as domains of large functional proteins. They function in a variety of synthases as central molecules to which growing acyl intermediates and nascent product molecules are covalently tethered during the elongation and modification steps required to produce the final product. A prototypical bacterial ACP is composed of 70-80 amino acids and is generally expressed in the apo form. It is post-translationally modified to active holo form by the addition of 4'-phosphopantetheine moiety to an absolutely conserved serine residue in a reaction catalyzed by holo-ACP synthase or 4'-phosphopantetheine transferase. Chapter 1 surveys literature related to carrier proteins inside the cell and describes the thesis objective. It also presents an overview of the acyl carrier proteins and their involvement in various metabolic pathways inside the cell. The chapter details the structural organization of acyl carrier proteins from various sources revealing the conservation in their structure and also details the molecular basis of interaction of ACP with other enzymes inside the cell. The discovery of unusual self-acylation property in acyl carrier proteins involved in polyketide biosynthesis and its absence in acyl carrier proteins involved in fatty acid biosynthesis prompted me to investigate the reasons for this selective behavior. Discovery of self-acylation property in acyl carrier proteins Plasmodium falciparum and chloroplast targeted Brassica napus acyl carrier proteins involved in type II fatty acid biosynthesis and the mechanism of this reaction forms the basis of Chapter 2. In this chapter it has been shown that self-acylation property is intrinsic to a given acyl carrier protein and is not dependent on the pathway in which it is involved. Based on primary sequence analysis and site directed mutagenesis studies presence of an aspartate/glutamate has been identified to be critical for the self-acylation event. Furthermore, it has also been shown that the self-acylation event in type II fatty acid biosynthesis acyl carrier proteins is highly specific in nature employing only dicarboxylic acid –CoAs as substrates unlike the polyketide biosynthesis acyl carrier proteins which utilize both dicarboxylic acid and β-keto acid thiol ester -CoAs as substrates. The detailed kinetics of these reactions has also been worked out. Combining all the results a plausible mechanism for the self-acylation reaction has been proposed. Chapter 3 describes the discovery of a novel malonyl transferase behavior in acyl carrier proteins involved in type II fatty acid biosynthesis. Malonyl transferase property in ACPs of type II FAS from a bacterium (Escherichia coli), a plant (Brassica napus) and a parasitic protozoon (Plasmodium falciparum) were investigated to present a unifying paradigm for the mechanism of malonyl transferase behavior in ACPs. Identification of malonyl transferase property in Plasmodium falciparum ACP and Escherichia coli ACP (EcACP) and the absence of this property in Brassica napus ACP has been described in this chapter. Detailed investigations demonstrated that presence of an arginine or a lysine in loop II and an arginine or glutamine at the start of helix III as the residues that are critical for the transferase activity. In order to assign a physiologic function to these unusual acylation properties, fabD(Ts) mutant strain of Escherichia coli was utilized for heterologous complementation by the various wild type and mutant ACPs that are able to catalyze either or both of the activities. Growth of the mutant strain at non-permissive temperature, when complemented with ACPs catalyzing both the reactions confirmed that these properties have a physiologic relevance. Extensive mutagenesis experiments in conjunction with complementation studies allowed me to propose a plausible mechanism on how the self-malonylation and malonyl transferase properties operate in tandem. Chapter 4 describes the thermodynamic characterization of self-acylation process using Isothermal Titration Calorimetry. Isothermal Titration Calorimetric studies on the binding of malonyl, succinyl, butyryl and methylmalonyl –CoA to Plasmodium falciparum and Brassica napus acyl carrier proteins were performed to investigate the role of thermodynamic parameters in the specificity of self-acylation reaction. Calculation of the parameters showed that the thermodynamics does not control the self-acylation reaction. The evolution of self-acylation property in various acyl carrier proteins and its possible significance in the evolution of various metabolic events is described in Chapter 5. Extensive bioinformatics search was performed and phylogenetic analysis on acyl carrier proteins from 60 different taxa was done using the MEGA4 program. Analysis showed that this property was first found in cyanobacterium. Later, during the course of evolution this property was lost in most acyl carrier proteins, and was retained either in acyl carrier proteins that are targeted to organelles of cyanobaterial orgin viz. apicoplast in apicomplexans and chlorplasts in plants or in acyl carrier proteins involved in secondary metabolic events such as polyketide biosynthesis. Chapter 6 summarizes the findings of the thesis. Acyl carrier protein from Plasmodium falciparum, Brassica napus and Escherichia coli were characterized for their self-acylation and malonyl transferase properties and a combined mechanism for these two properties is proposed. The work done also provides an in vivo rationale to these in vitro processes. Furthermore, the evolutionary significance of the self-acylation behavior is also discussed in the thesis. The thesis also probes into the thermodynamics of the self-acylation reaction in Plasmodium falciparum and Brassica napus acyl carrier proteins. Thus, the thesis adds a new dimension to the much unexplored ACP biology and paves the way to study in vivo roles of these processes in detail. Appendix I describes the Isothermal Titration calorimetric characterization of binding of various acyl-PO4 molecules to Escherichia coli PlsX (Acyl-phosphate acyltransferase). PlsX, the first enzyme of phosphatidic acid biosynthesis pathway catalyzes the conversion of acyl-ACP into acyl-PO4, which is further used by other enzymes leading to the formation of phosphatidic acid. ITC results presented in this section show that longer chain length acyl-PO4 molecules show better binding to PlsX, as compared to the smaller ones demonstrating that long chain acyl molecules serve as better substrates for phosphatidic acid synthesis.

Natural products represent an incredibly diverse set of chemical structures and activities. Given this fathomless, ever-evolving diversity, a reasonable approach to designing new molecules entails taking a closer look at the biochemistry that Nature has crafted over billions of years on Earth. In particular, much can be learned by unveiling the architectures of proteins, life’s molecular machines, through methods like X-ray crystallography. Acquiring the blueprints of an enzyme brings us closer to understanding the mechanism by which the enzyme transforms a simple substrate it into a complex product with biological function, and inspires us to engineer such systems to our own ends. With a focus on macromolecular structural characterization, this document elaborates on five Gram-negative bacterial biosynthetic enzymes from two categories: Cell-surface modifiers and polyketide synthases. Among the first category are the glycyl carrier protein AlmF and its ligase AlmE of Vibrio cholerae and the phosphoethanolamine transferase EptC of Campylobacter jejuni. These proteins are responsible for decorating cell-surface molecules (e.g., lipid A) of pathogenic bacteria with small functional groups to promote antibiotic resistance, motility, and host colonization. AlmE and EptC represent potential drug targets and their structures lay the groundwork for the design of therapeutics against food-borne illnesses. Included in the second category are the [4+2]-cyclase SpnF and two ketoreductase-linked dimerization elements, each from the spinosyn biosynthetic pathway in Saccharopolyspora spinosa. The former catalyzes a putative Diels-Alder reaction to form a tricyclic precursor of the insecticide spinosad, while the latter two organize ketoreductase domains within modules of a polyketide synthase. The second category also includes Ralstonia eutropha β-ketoacyl thiolase B, a substrate-permissive enzyme that can make or break carbon-carbon bonds with assistance from Coenzyme A or an analogous thiol. Each of these proteins exhibit intriguing structural features or catalyze reactions that show promise for biochemical engineering. / text

Metabólitos secundários produzidos por espécies vegetais são, há tempos, reconhecidos como moléculas capazes de desempenhar ações farmacológicas. Entre as plantas medicinais mais utilizadas estão espécies do gênero Hypericum, pertencente à família Guttiferae, e que possui 494 espécies. Destas, aproximadamente 20 estão distribuídas no sul e sudeste do Brasil e apresentam o acúmulo de compostos fenólicos como flavonoides, xantonas, benzopiranos e floroglucinois. Como forma de garantia da qualidade e quantidade de plantas medicinais para consumo da indústria farmacêutica, bem como uma alternativa para preservação das espécies, o estabelecimento de protocolos de cultivo apresenta-se como uma opção vantajosa frente ao uso de plantas coletadas diretamente de seus locais de crescimento. Por este motivo, espécies nativas do sul do Brasil como H. polyanthemum, H. ternum, H. myrianthum, H. carinatum e H. campestre tiveram seus protocolos de cultivo in vitro e ex vitro (aclimatização) estabelecidos, verificando-se a possibilidade da produção de biomassa vegetal uniforme e de maneira otimizada, com a manutenção da síntese dos metabólitos de interesse. H. teretiusculum, espécie recém identificada na região central do estado, apresenta o acúmulo de metabólitos secundários e escassos relatos na literatura, focados em seus aspectos botânicos. Estes fatos levaram ao estabelecimento do protocolo de cultivo in vitro e aclimatização da espécie. As plântulas apresentaram crescimento satisfatório quando cultivadas in vitro em meio MΔ apenas ou suplementado com ácido indol butírico. Após 18 semanas de aclimatização, verificou-se o aumento da biomassa e o acúmulo dos derivados do floroglucinol uliginosina B e isohyperbrasilol B, verificados em traços na planta in natura, bem como hiperbrasilol B e japonicina A, não detectados nos extratos das plantas coletadas de seu habitat natural. Este resultado evidencia a relevância do cultivo in vitro como forma de otimização da produção de moléculas bioativas. Entre as espécies nativas estudadas, H. polyanthemum destaca-se por ser a única, até o momento, produtora dos três benzopiranos, HP1, HP2 e HP3. Além deles, a planta também produz o derivado do floroglucinol uliginosina B. A presença de HP1, com atividades analgésica e antidepressiva bem como de uliginosina B, que se classifica como novo protótipo para moléculas antidepressivas, levou ao desenvolvimento de um depósito de patente para o extrato n-hexano da espécie e requer estudos para a investigação da otimização em sua biossíntese. Neste sentido, a influência da imposição de estresse abiótico (ácido salicílico e dano mecânico, sozinhos ou combinados, fertilização e seca, sozinhos ou combinados) em plantas aclimatizadas de H. polyanthemum foi investigada na décima oitava semana de aclimatização. Embora HP2 não tenha apresentado aumento em nenhum dos tratamentos aplicados, o aumento de 40 e 6 vezes na produção de uliginosina B nas folhas e flores, respectivamente, destaca-se entre os resultados obtidos, bem como aumento significativo na síntese de HP1 nas folhas e flores e HP3 nas folhas após a aplicação de seca e seca com fertilização, respectivamente. Os resultados sugerem que a biossíntese dos principais metabólitos de H. polyanthemum pode ser consideravelmente incrementada com a exploração do recurso da imposição de estresse hídrico no mesmo. O estabelecimento do cultivo in vitro de raízes adventícias de H. polyanthemum foi realizado como alternativa de produção rápida e “limpa” dos metabólitos secundários de interesse. No entanto, embora apresentando crescimento satisfatório em meio líquido, a síntese de benzopiranos e floroglucinois não foi verificada, mas a produção de diversas xantonas. Interessante é ressaltar que apenas traços de uma xantona é relatado para plantas in natura da espécie, não sendo detectada em plântulas cultivadas in vitro. Com o objetivo de compreender a produção e regulação na síntese destes compostos, realizou-se a investigação de enzimas poliacetídeo sintases (PKS) do tipo III nos tecidos da espécie, com o objetivo principal da obtenção de uma isobutirofenona sintase, envolvida com a biossíntese de floroglucinois e benzopiranos. Dos screenings realizados com primers de expressão de algumas PKS do tipo III foi possível isolar uma benzofenona sintase (BPS) das culturas de células em suspensão e um fragmento 3’-terminal de uma ORF específica para PKS do tipo III, sem apresentar enzimas funcionalmente relacionadas à BPSs. Estes achados concordam com o perfil fitoquímico das culturas de células em suspensão, que apresentam no mínimo duas xantonas como componentes majoritários, e das plântulas in vitro, que apresentam majoritariamente benzopiranos e derivados do floroglucinol em seus extratos, sem detecção de estruturas relacionadas à xantonas. Considerados em seu conjunto, os resultados do presente trabalho contribuem para a preservação e manutenção da qualidade do material vegetal das espécies de Hypericum com potencial uso na terapêutica, bem como contribui para o entendimento da biosíntese dos principais metabólitos de H. polyanthemum que demonstram variar de acordo com o tecido vegetal. / Plant secondary metabolites are long ago known to be able to perform pharmacological effects. Hypericum genus possesses 494 species distributed around the world and approximately 20 grow in south Brazil and accumulate phenolic compounds such as flavonoids, xanthones, benzopyrans and phloroglucinol derivatives. Aiming plant quantity and quality for pharmaceutical industry purposes, as well as to avoid natural resource exploitation, in vitro and ex vitro (acclimatization) protocols were established for H. polyanthemum, H. ternum, H. myrianthum, H. carinatum e H. campestre, affording uniform and increased vegetal biomass. H. teretiusculum is a species recently found in the state center, demonstrating secondary metabolite accumulation and only few information in literature, most of them directed to botanical aspects. These data leaded to the establishment of in vitro and ex vitro propagation protocols for the species. Plants were successfully micropropagated in MΔ medium with or without IBA supplementation. After 18 weeks of field growth, vegetal biomass increase and phloroglucinol derivatives accumulation was verified, with uliginosin B and isohyperbrasilol B, just found as traces in in natura plants as well as hyperbrasilol B and japonicin A, not detected in plants harvested directly from the wild. These results attest the relevance of cultivation protocols establishment aiming to optimize bioactive molecules obtainment. Among the native studied species, H. polyanthemum is highlighted for HP1, HP2 and HP3 benzopyrans productions, described just for the species until now. Besides, the phloroglucinol uliginosin B is also produced. The presence of HP1, with antinociceptive and antidepressant activities and uliginosin B, classified as a novel prototype for antidepressant-like molecules, a patent was deposited for n-hexanic extract of the species, claiming for investigations focusing on biosynthesis increment. Guided for this objective, abiotic stresses (SA application and mechanical damage, alone or combined, mild fertilization and drough, alone or combined) was imposed to acclimatized plants of H. polyanthemum on eighteenth week of field growth. Although HP2 was not increased with any of the applied treatments, a 40-fold and 6-fold increase on uliginosin B production in leaves and reproductive parts, respectively are highlighted among the obtained results, as well as significant increase in HP1 in leaves and HP3 in reproductive parts after drought and drought + fertilization treatment, respectively. The data suggest that main H. polyanthemum metabolites might be strongly induced by drought stress modulation. The establishment of in vitro adventitious root cultures of H. polyanthemum was described as alternative for rapid and “clean” secondary metabolites obtainment. Nevertheless, even demonstrating ability for stable in vitro growth, benzopyrans and phloroglucinol derivatives were not detected in this tissue, but a wide array of xanthones was detected instead. It is interesting to point out that only traces of xanthone is related for in natura plants and such class of compounds was not detected in in vitro plants. Aiming to understand biosynthesis of these compound, type III polyketide synthases (type III PKS) were investigated in H. polyanthemum tissue, focusing mainly on BUS discovery, involved in benzopyrans and phloroglucinol biosynthesis. After screening cell suspension cultures cDNA, a benzophenone synthase (BPS) enzyme was isolated and biochemically characterized, while in vitro plants afforded a 3’-end fragment of a type III PKS specific ORF and neither other enzymes related with xanthone biosynthesis. These data are in accordance with phytochemical profile displayed by cells suspensions, presenting at least two xanthones as majoritarian compounds in the extracts, and plants, which just accumulate benzopyrans and uliginosin B. Considered compiled data, the present work direct medicinal plant studies into increment of valuable secondary metabolites.

Metabólitos secundários produzidos por espécies vegetais são, há tempos, reconhecidos como moléculas capazes de desempenhar ações farmacológicas. Entre as plantas medicinais mais utilizadas estão espécies do gênero Hypericum, pertencente à família Guttiferae, e que possui 494 espécies. Destas, aproximadamente 20 estão distribuídas no sul e sudeste do Brasil e apresentam o acúmulo de compostos fenólicos como flavonoides, xantonas, benzopiranos e floroglucinois. Como forma de garantia da qualidade e quantidade de plantas medicinais para consumo da indústria farmacêutica, bem como uma alternativa para preservação das espécies, o estabelecimento de protocolos de cultivo apresenta-se como uma opção vantajosa frente ao uso de plantas coletadas diretamente de seus locais de crescimento. Por este motivo, espécies nativas do sul do Brasil como H. polyanthemum, H. ternum, H. myrianthum, H. carinatum e H. campestre tiveram seus protocolos de cultivo in vitro e ex vitro (aclimatização) estabelecidos, verificando-se a possibilidade da produção de biomassa vegetal uniforme e de maneira otimizada, com a manutenção da síntese dos metabólitos de interesse. H. teretiusculum, espécie recém identificada na região central do estado, apresenta o acúmulo de metabólitos secundários e escassos relatos na literatura, focados em seus aspectos botânicos. Estes fatos levaram ao estabelecimento do protocolo de cultivo in vitro e aclimatização da espécie. As plântulas apresentaram crescimento satisfatório quando cultivadas in vitro em meio MΔ apenas ou suplementado com ácido indol butírico. Após 18 semanas de aclimatização, verificou-se o aumento da biomassa e o acúmulo dos derivados do floroglucinol uliginosina B e isohyperbrasilol B, verificados em traços na planta in natura, bem como hiperbrasilol B e japonicina A, não detectados nos extratos das plantas coletadas de seu habitat natural. Este resultado evidencia a relevância do cultivo in vitro como forma de otimização da produção de moléculas bioativas. Entre as espécies nativas estudadas, H. polyanthemum destaca-se por ser a única, até o momento, produtora dos três benzopiranos, HP1, HP2 e HP3. Além deles, a planta também produz o derivado do floroglucinol uliginosina B. A presença de HP1, com atividades analgésica e antidepressiva bem como de uliginosina B, que se classifica como novo protótipo para moléculas antidepressivas, levou ao desenvolvimento de um depósito de patente para o extrato n-hexano da espécie e requer estudos para a investigação da otimização em sua biossíntese. Neste sentido, a influência da imposição de estresse abiótico (ácido salicílico e dano mecânico, sozinhos ou combinados, fertilização e seca, sozinhos ou combinados) em plantas aclimatizadas de H. polyanthemum foi investigada na décima oitava semana de aclimatização. Embora HP2 não tenha apresentado aumento em nenhum dos tratamentos aplicados, o aumento de 40 e 6 vezes na produção de uliginosina B nas folhas e flores, respectivamente, destaca-se entre os resultados obtidos, bem como aumento significativo na síntese de HP1 nas folhas e flores e HP3 nas folhas após a aplicação de seca e seca com fertilização, respectivamente. Os resultados sugerem que a biossíntese dos principais metabólitos de H. polyanthemum pode ser consideravelmente incrementada com a exploração do recurso da imposição de estresse hídrico no mesmo. O estabelecimento do cultivo in vitro de raízes adventícias de H. polyanthemum foi realizado como alternativa de produção rápida e “limpa” dos metabólitos secundários de interesse. No entanto, embora apresentando crescimento satisfatório em meio líquido, a síntese de benzopiranos e floroglucinois não foi verificada, mas a produção de diversas xantonas. Interessante é ressaltar que apenas traços de uma xantona é relatado para plantas in natura da espécie, não sendo detectada em plântulas cultivadas in vitro. Com o objetivo de compreender a produção e regulação na síntese destes compostos, realizou-se a investigação de enzimas poliacetídeo sintases (PKS) do tipo III nos tecidos da espécie, com o objetivo principal da obtenção de uma isobutirofenona sintase, envolvida com a biossíntese de floroglucinois e benzopiranos. Dos screenings realizados com primers de expressão de algumas PKS do tipo III foi possível isolar uma benzofenona sintase (BPS) das culturas de células em suspensão e um fragmento 3’-terminal de uma ORF específica para PKS do tipo III, sem apresentar enzimas funcionalmente relacionadas à BPSs. Estes achados concordam com o perfil fitoquímico das culturas de células em suspensão, que apresentam no mínimo duas xantonas como componentes majoritários, e das plântulas in vitro, que apresentam majoritariamente benzopiranos e derivados do floroglucinol em seus extratos, sem detecção de estruturas relacionadas à xantonas. Considerados em seu conjunto, os resultados do presente trabalho contribuem para a preservação e manutenção da qualidade do material vegetal das espécies de Hypericum com potencial uso na terapêutica, bem como contribui para o entendimento da biosíntese dos principais metabólitos de H. polyanthemum que demonstram variar de acordo com o tecido vegetal. / Plant secondary metabolites are long ago known to be able to perform pharmacological effects. Hypericum genus possesses 494 species distributed around the world and approximately 20 grow in south Brazil and accumulate phenolic compounds such as flavonoids, xanthones, benzopyrans and phloroglucinol derivatives. Aiming plant quantity and quality for pharmaceutical industry purposes, as well as to avoid natural resource exploitation, in vitro and ex vitro (acclimatization) protocols were established for H. polyanthemum, H. ternum, H. myrianthum, H. carinatum e H. campestre, affording uniform and increased vegetal biomass. H. teretiusculum is a species recently found in the state center, demonstrating secondary metabolite accumulation and only few information in literature, most of them directed to botanical aspects. These data leaded to the establishment of in vitro and ex vitro propagation protocols for the species. Plants were successfully micropropagated in MΔ medium with or without IBA supplementation. After 18 weeks of field growth, vegetal biomass increase and phloroglucinol derivatives accumulation was verified, with uliginosin B and isohyperbrasilol B, just found as traces in in natura plants as well as hyperbrasilol B and japonicin A, not detected in plants harvested directly from the wild. These results attest the relevance of cultivation protocols establishment aiming to optimize bioactive molecules obtainment. Among the native studied species, H. polyanthemum is highlighted for HP1, HP2 and HP3 benzopyrans productions, described just for the species until now. Besides, the phloroglucinol uliginosin B is also produced. The presence of HP1, with antinociceptive and antidepressant activities and uliginosin B, classified as a novel prototype for antidepressant-like molecules, a patent was deposited for n-hexanic extract of the species, claiming for investigations focusing on biosynthesis increment. Guided for this objective, abiotic stresses (SA application and mechanical damage, alone or combined, mild fertilization and drough, alone or combined) was imposed to acclimatized plants of H. polyanthemum on eighteenth week of field growth. Although HP2 was not increased with any of the applied treatments, a 40-fold and 6-fold increase on uliginosin B production in leaves and reproductive parts, respectively are highlighted among the obtained results, as well as significant increase in HP1 in leaves and HP3 in reproductive parts after drought and drought + fertilization treatment, respectively. The data suggest that main H. polyanthemum metabolites might be strongly induced by drought stress modulation. The establishment of in vitro adventitious root cultures of H. polyanthemum was described as alternative for rapid and “clean” secondary metabolites obtainment. Nevertheless, even demonstrating ability for stable in vitro growth, benzopyrans and phloroglucinol derivatives were not detected in this tissue, but a wide array of xanthones was detected instead. It is interesting to point out that only traces of xanthone is related for in natura plants and such class of compounds was not detected in in vitro plants. Aiming to understand biosynthesis of these compound, type III polyketide synthases (type III PKS) were investigated in H. polyanthemum tissue, focusing mainly on BUS discovery, involved in benzopyrans and phloroglucinol biosynthesis. After screening cell suspension cultures cDNA, a benzophenone synthase (BPS) enzyme was isolated and biochemically characterized, while in vitro plants afforded a 3’-end fragment of a type III PKS specific ORF and neither other enzymes related with xanthone biosynthesis. These data are in accordance with phytochemical profile displayed by cells suspensions, presenting at least two xanthones as majoritarian compounds in the extracts, and plants, which just accumulate benzopyrans and uliginosin B. Considered compiled data, the present work direct medicinal plant studies into increment of valuable secondary metabolites.