Estudos de permeação e liberação de peptídeos antimicrobianos estruturalmente derivados da toxina CCDB

O uso de peptídeos sintéticos para o desenvolvimento de novas drogas é uma estratégia promissora no campo da biotecnologia. Peptídeos derivados de toxinas bacterianas intracelulares, produzidas por sistemas de morte pós-segregacional (PKS) tais como CcdB e ParE são exemplos dessa estratégia. Porém, moléculas com estrutura peptídica derivadas de toxinas bacterianas apresentam sérios problemas na aplicação terapêutica por apresentarem baixa solubilidade e difícil permeabilidade em membranas bacterianas. O objetivo desse estudo consistiu no desenvolvimento e aprimoramento de sistemas nanoestruturados (lipossomas) que permita a imobilização de análogos peptídicos da toxina CcdB e sua consequente translocação no citosol bacteriano, permitindo que os mesmos atinjam seus alvos celulares, enzimas DNA girase e Topoisomerase IV. Lipossomas do tipo SUV (small unilamellar vesicles), foram preparados pela técnica de extrusão-evaporação variando-se suas formulações. Desta forma, pretendeu-se avaliar a eficiência de encapsulação dos peptídeos através de técnicas de cromatografia líquida de alta eficiência (CLAE) e espectroscopia de UV-Vis e fluorescência. Após testes de eficiência de encapsulação, os lipossomas contendo os análogos peptídicos encapsulados, foram submetidos a ensaio de inibição de crescimento em meio líquido para duas espécies bacterianas: Staphylococcus aureus e Escherichia coli. Resultados demonstraram que a utilização de sistemas nanoestruturados é de grande importância para viabilizar a aplicação desta classe de biomoléculas em estudos terapêuticos, permitindo assim, que tais peptídeos possam ser utilizados como antibióticos promissores, se associados a sistemas de transporte e liberação controlada de moléculas peptídicas.

Síntese e estudos de sistemas de bioencapsulação associados a peptídeos antimicrobianos miméticos da toxina natural CcdB

Pós-graduação em Biotecnologia - IQ

Strain-specific polyketide synthase genes of Aspergillus niger

In silico comparison of 34 putative pks genes in Aspergillus niger strain CBS 513.88 versus A. niger strain ATCC 1015 genome revealed significant nucleotide identity (>95% covering a minimum of 99% of the gene sequence) for 31 of these genes (approximately 91%). A. niger CBS 513.88 harbors three putative pks genes (An01g01130, An11g05940, and An15g07920), for which nucleotide identity was not found in A. niger ATCC 1015. To compare the results of the in silico analysis with the in vivo situation, experimental data were obtained for a large number of A. niger strains obtained from different substrates and geographical regions. Three putative Os genes that were found to be variable between the two A. niger strains using bioinformatics tools were in fact strain-specific genes based on experimental data. The PCR amplification signals for the An01g01130, An11g05940, and An15g07920 pks genes were detected in only 97%, 71%, and 26% of the strains, respectively. Southern blot analyses confirmed the PCR data. Because one of the strain-specific pits genes (An15g07920) is located in a putative ochratoxin cluster, we focused our investigation on that region. We assessed the ochratoxin production capability of the 119 A. niger strains and found a positive association between the presence of this pia gene and the capability of the respective strain to produce ochratoxin. (C) 2012 Elsevier B.V. All rights reserved.

The Diversity of Polyketide Synthase Genes from Sugarcane-Derived Fungi

The chemical ecology and biotechnological potential of metabolites from endophytic and rhizosphere fungi are receiving much attention. A collection of 17 sugarcane-derived fungi were identified and assessed by PCR for the presence of polyketide synthase (PKS) genes. The fungi were all various genera of ascomycetes, the genomes of which encoded 36 putative PKS sequences, 26 shared sequence homology with beta-ketoacyl synthase domains, while 10 sequences showed homology to known fungal C-methyltransferase domains. A neighbour-joining phylogenetic analysis of the translated sequences could group the domains into previously established chemistry-based clades that represented non-reducing, partially reducing and highly reducing fungal PKSs. We observed that, in many cases, the membership of each clade also reflected the taxonomy of the fungal isolates. The functional assignment of the domains was further confirmed by in silico secondary and tertiary protein structure predictions. This genome mining study reveals, for the first time, the genetic potential of specific taxonomic groups of sugarcane-derived fungi to produce specific types of polyketides. Future work will focus on isolating these compounds with a view to understanding their chemical ecology and likely biotechnological potential.

Convergent evolution of [D-Leucine1] microcystin-LR in taxonomically disparate cyanobacteria

Abstract Background Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS secondary metabolic pathway. They are produced by a variety of cyanobacteria and are responsible for the poisoning of humans as well as the deaths of wild and domestic animals around the world. The chemical diversity of the microcystin family is attributed to a number of genetic events that have resulted in the diversification of the pathway for microcystin assembly. Results Here, we show that independent evolutionary events affecting the substrate specificity of the microcystin biosynthetic pathway have resulted in convergence on a rare [D-Leu1] microcystin-LR chemical variant. We detected this rare microcystin variant from strains of the distantly related genera Microcystis, Nostoc, and Phormidium. Phylogenetic analysis performed using sequences of the catalytic domains within the mcy gene cluster demonstrated a clear recombination pattern in the adenylation domain phylogenetic tree. We found evidence for conversion of the gene encoding the McyA2 adenylation domain in strains of the genera Nostoc and Phormidium. However, point mutations affecting the substrate-binding sequence motifs of the McyA2 adenylation domain were associated with the change in substrate specificity in two strains of Microcystis. In addition to the main [D-Leu1] microcystin-LR variant, these two strains produced a new microcystin that was identified as [Met1] microcystin-LR. Conclusions Phylogenetic analysis demonstrated that both point mutations and gene conversion result in functional mcy gene clusters that produce the same rare [D-Leu1] variant of microcystin in strains of the genera Microcystis, Nostoc, and Phormidium. Engineering pathways to produce recombinant non-ribosomal peptides could provide new natural products or increase the activity of known compounds. Our results suggest that the replacement of entire adenylation domains could be a more successful strategy to obtain higher specificity in the modification of the non-ribosomal peptides than point mutations.

Harmful algae and their potential impacts on the coastal ecosystem: growth and toxin production dynamics

The main goal of the present thesis was to study some harmful algal species which cause blooms in Italian coastal waters, leading to consequences for human health, coastal ecosystem, fishery and tourism. In particular, in the first part of this thesis the toxicity of Adriatic strains of the raphidophyte Fibrocapsa japonica was investigated. Despite several hypotheses have been proposed for the toxic mechanism of the raphidophytes, especially for the species Chattonella antiqua and C. marina, which have been studied more extensively, just a few studies on the toxic effects of these species for different organisms were reported. Moreover, a careful reading of the literature evidenced as any ichthyotoxic events reported worldwide can be linked to F. japonica blooms. Although recently several studies were performed on F. japonica strains from the USA, Japan, Australia, New Zealand, the Netherlands, Germany, and France in order to characterize their growth and toxicity features, the work reported in this thesis results one of the first investigation on the toxic effects of F. japonica for different organisms, such as bacteria, crustaceans and fish. Mortality effects, together with haemolysis of fish erythrocytes, probably due to the relatively high amount of PUFAs produced by this species, were observed. Mortality for fish, however, was reported only at a high cell density and after a long exposition period (9-10 days); moreover a significant increase of H2O2 obtained in the tanks where sea basses were exposed to F. japonica was also relevant. This result may justify the absence of ichthyotoxic events in the Italian coasts, despite F. japonica blooms detected in these areas were characterized by high cell densities. This work reports also a first complete characterization of the fatty acids produced and extracellularly released by the Adriatic F. japonica, and results were also compared with the fatty acid profile of other strains. The absence of known brevetoxins in F. japonica algal extracts was also highlighted, leading to the hypothesis that the toxicity of F. japonica may be due to a synergic effect of PUFAs and ROS. Another microalgae that was studied in this thesis is the benthic dinoflagellate Ostreopsis cf. ovata. This species was investigated with the aim to investigate the effect of environmental parameters on its growth and toxicity. O. cf. ovata, in fact, shows different blooming periods along the Italian coasts and even the reported toxic effects are variable. The results of this work confirmed the high variability in the growth dynamic and toxin content of several Italian strains which were isolated in recent years along the Adriatic and Tyrrhenian Seas. Moreover, the effects of temperature and salinity on the behaviour of the different isolates are in good agreement with the results obtained from field surveys, which evidence as the environmental parameters are important factors modulating O. cf. ovata proliferation. Another relevant result that was highlighted is the anomaly in the production of palytoxin-like compounds reported by one of the studied isolate, in particular the one isolated in 2008 in Ancona (Adriatic Sea). Only this strain reported the absence of two (ovatoxin-b and –c) of the five ovatoxins so far known in the toxin profile and a different relative abundance of the other toxins. The last aspect that was studied in this thesis regards the toxin biosythesis. In fact, toxins produced (palytoxin-like compounds) or supposed to be produced (brevetoxin-like compounds) by O. cf. ovata and F. japonica, respectively, are polyketides, which are highly oxygenated compounds synthesized by complex enzymes known as polyketide synthase (PKS) enzymes. These enzymes are multi-domain complexes that structurally and functionally resemble the fatty acid synthases (FASs). This work reports the first study of PKS proteins in the dinoflagellates O. cf. ovata, C. monotis and in the raphidophyte F. japonica. For the first time some PKSs were identified in these species, confirming the presence of PKS proteins predicted by the in silico translation of the transcripts found in K. brevis also in other species. The identification of O. cf. ovata PKSs and the localization of the palytoxin-like compounds produced by this dinoflagellate in a similar location (chloroplast) as that observed for other dinoflagellate and cyanobacterial toxins provides some indication that these proteins may be involved in polyketide biosynthesis. However, their potential function as fatty acid synthases cannot be ruled out, as plant fatty acid synthesis also occurs within chloroplasts. This last hypothesis is also supported by the fact that in all the investigated species, and in particular in F. japonica, PKS proteins were present. Therefore, these results provide an important contribution to the study of the polyketides and of the involvement of PKS proteins in the toxin biosynthesis.

The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning

In Arabidopsis (Arabidopsis thaliana), the blue light photoreceptor phototropins (phot1 and phot2) fine-tune the photosynthetic status of the plant by controlling several important adaptive processes in response to environmental light variations. These processes include stem and petiole phototropism (leaf positioning), leaf flattening, stomatal opening, and chloroplast movements. The PHYTOCHROME KINASE SUBSTRATE (PKS) protein family comprises four members in Arabidopsis (PKS1-PKS4). PKS1 is a novel phot1 signaling element during phototropism, as it interacts with phot1 and the important signaling element NONPHOTOTROPIC HYPOCOTYL3 (NPH3) and is required for normal phot1-mediated phototropism. In this study, we have analyzed more globally the role of three PKS members (PKS1, PKS2, and PKS4). Systematic analysis of mutants reveals that PKS2 (and to a lesser extent PKS1) act in the same subset of phototropin-controlled responses as NPH3, namely leaf flattening and positioning. PKS1, PKS2, and NPH3 coimmunoprecipitate with both phot1-green fluorescent protein and phot2-green fluorescent protein in leaf extracts. Genetic experiments position PKS2 within phot1 and phot2 pathways controlling leaf positioning and leaf flattening, respectively. NPH3 can act in both phot1 and phot2 pathways, and synergistic interactions observed between pks2 and nph3 mutants suggest complementary roles of PKS2 and NPH3 during phototropin signaling. Finally, several observations further suggest that PKS2 may regulate leaf flattening and positioning by controlling auxin homeostasis. Together with previous findings, our results indicate that the PKS proteins represent an important family of phototropin signaling proteins.

Herkunft und Kriminalität - Ergebnisse der polizeilichen Kriminalstatistik

Im Rahmen von Abstimmungskampagnen zu Migrationsfragen wurde in der schweizerischen Presse und in politischen Diskussionen wiederholt auf die vermeintlich divergierende Kriminalitätsrate zwischen Personen unterschiedlicher Staatszugehörigkeit hingewiesen. Die weit verbreitete Auffassung, dass "Ausländer" ein erhöhtes Kriminalitätspotenzial aufweisen, wurde dabei kaum in Frage gestellt, obwohl verlässliche Zahlen zu dem Thema nur spärlich sind. Um die Wissenslücke zumindest teilweise zu schliessen, werden in diesem Beitrag Ergebnisse einer systematischen Analyse der Daten der polizeilichen Kriminalstatistik (PKS) des Jahres 2011 vorgestellt. Für verschiedene Arten von Straftaten werden rohe und standardisierte Beschuldigtenbelastungsraten (BBR) nach Herkunft und Aufenthaltsstatus berichtet. Zur Berechnung der BBR wird die Anzahl der im Referenzjahr beschuldigten Personen ins Verhältnis zum jeweiligen Bevölkerungstotal gemäss der Bevölkerungsstatistik des Bundesamtes für Statistik gesetzt. Die Standardisierung erfolgt nach Alter und Geschlecht. Es zeigt sich, dass für Ausländer insgesamt eine erhöhte Belastungsrate zu beobachten ist, sich die Differenz zu den Schweizern durch eine Standardisierung nach Alter und Geschlecht jedoch um rund ein Drittel verringert. Weiterhin sind die Ergebnisse sehr unterschiedlich je nach Art der Straftaten und vor allem nach Herkunftsregion.

Herkunft und Kriminalität. Soziologische Determinanten

Im Rahmen von Abstimmungskampagnen zu Migrationsfragen wurde in der schweizerischen Presse und in politischen Diskussionen wiederholt auf die vermeintlich divergierende Kriminalitätsrate zwischen Personen unterschiedlicher Staatszugehörigkeit hingewiesen. Die weit verbreitete Auffassung, dass "Ausländer" ein erhöhtes Kriminalitätspotenzial aufweisen, wurde dabei kaum in Frage gestellt, obwohl verlässliche Zahlen zu dem Thema nur spärlich sind. Um die Wissenslücke zumindest teilweise zu schliessen, werden in diesem Beitrag Ergebnisse einer systematischen Analyse der Daten der polizeilichen Kriminalstatistik (PKS) der Jahre 2010 und 2011 vorgestellt. Für verschiedene Arten von Straftaten werden rohe und standardisierte Beschuldigtenbelastungsraten (BBR) nach Herkunft und Aufenthaltsstatus berichtet. Zur Berechnung der BBR wird die Anzahl im Referenzjahr beschuldigte Personen ins Verhältnis zum jeweiligen Bevölkerungstotal gemäss STATPOP gesetzt. Eine Standardisierung erfolgt in einem ersten Schritt nach Alter und Geschlecht; in einem zweiten Schritt werden Kontextmerkmale der Wohngemeinden der beschuldigten Personen hinzugezogen. Es zeigt sich, dass für Ausländer insgesamt eine erhöhte BRR zu beobachten ist, sich die Differenz zu den Schweizern durch eine Standardisierung nach Alter und Geschlecht jedoch um fast 40 Prozent verringert. Weiterhin sind die Ergebnisse stark heterogen je nach Art der Straftaten und vor allem nach Herkunftsregion. Auch die Hinzunahme von Kontextmerkmalen fördert schliesslich einige interessante Ergebnisse zutage.

Ausländerkriminalität in der polizeilichen Kriminalstatistik: Sozialstrukturelle Determinanten herkunftsspezifischer Beschuldigtenbelastungsraten

Herkunftsspezifische Kriminalitätsraten stehen immer wieder im Fokus des gesellschaftlichen und politischen Diskurses, belastbare empirische Zahlen zu dem Thema finden sich für die Schweiz jedoch nur spärlich. Um einen Beitrag zur Schliessung dieser Wissenslücke zu leisten, werden im vorliegenden Artikel einige Analysen der polizeilichen Kriminalstatistik (PKS) des Jahres 2011 präsentiert. In einem ersten Schritt werden anhand der PKS 2011 und der Statistik der Bevölkerung und der Haushalte des Bundesamts für Statistik (STATPOP 2010 und 2011) so genannte Beschuldigtenbelastungsraten (BBR; Anzahl Beschuldigte pro 1000 Einwohner) bezüglich Strafgesetzbuch und Betäubungsmittelgesetz berechnet und nach Herkunft und Aufenthaltsstatus verglichen. Es zeigt sich, dass Ausländer v.a. im Strafgesetz deutlich höhere BBR aufweisen als Schweizer. Ein guter Teil der Differenz ist jedoch der unterschiedlichen Altersstruktur der beiden Bevölkerungsgruppen geschuldet. Zudem bestehen enorme Unterschiede in den BBR je nach Herkunftsregion. In einem zweiten Schritt wird ausgehend von den Strukturerhebungen 2010 und 2011 eine Abschätzung vorgenommen, welcher Teil der Differenz in den BBR zwischen Schweizern und Ausländern auf Unterschiede in der sozialen Position zurückgeführt werden kann. Diese Analysen deuten darauf hin, dass unter Kontrolle einer Reihe von Statusmerkmalen (Bildung, berufliche Stellung, Stellung des Haushalts, familiäre Situation) kaum Unterschiede in den BBR zwischen Schweizern und Ausländern bestehen.

Ectopic expression of the minimal whiE polyketide synthase generates a library of aromatic polyketides of diverse sizes and shapes

The single recombinant expressing the Streptomyces coelicolor minimal whiE (spore pigment) polyketide synthase (PKS) is uniquely capable of generating a large array of well more than 30 polyketides, many of which, so far, are novel to this recombinant. The characterized polyketides represent a diverse set of molecules that differ in size (chain length) and shape (cyclization pattern). This combinatorial biosynthetic library is, by far, the largest and most complex of its kind described to date and indicates that the minimal whiE PKS does not independently control polyketide chain length nor dictate the first cyclization event. Rather, the minimal PKS enzyme complex must rely on the stabilizing effects of additional subunits (i.e., the cyclase whiE-ORFVI) to ensure that the chain reaches the full 24 carbons and cyclizes correctly. This dramatic loss of control implies that the growing polyketide chain does not remain enzyme bound, resulting in the spontaneous cyclization of the methyl terminus. Among the six characterized dodecaketides, four different first-ring cyclization regiochemistries are represented, including C7/C12, C8/C13, C10/C15, and C13/C15. The dodecaketide TW93h possesses a unique 2,4-dioxaadamantane ring system and represents a new structural class of polyketides with no related structures isolated from natural or engineered organisms, thus supporting the claim that engineered biosynthesis is capable of producing novel chemotypes.

Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products

The structures of complex polyketide natural products, such as erythromycin, are programmed by multifunctional polyketide synthases (PKSs) that contain modular arrangements of functional domains. The colinearity between the activities of modular PKS domains and structure of the polyketide product portends the generation of novel organic compounds—“unnatural” natural products—by genetic manipulation. We have engineered the erythromycin polyketide synthase genes to effect combinatorial alterations of catalytic activities in the biosynthetic pathway, generating a library of >50 macrolides that would be impractical to produce by chemical methods. The library includes examples of analogs with one, two, and three altered carbon centers of the polyketide products. The manipulation of multiple biosynthetic steps in a PKS is an important milestone toward the goal of producing large libraries of unnatural natural products for biological and pharmaceutical applications.

Biosynthesis of the Pseudomonas polyketide coronafacic acid requires monofunctional and multifunctional polyketide synthase proteins

Coronafacic acid (CFA) is the polyketide component of the phytotoxin coronatine, a virulence factor of the plant pathogen Pseudomonas syringae. Our current knowledge of polyketide biosynthesis largely is based on the analysis of polyketide synthases (PKSs) in actinomycetes and other Gram-positive bacteria. Consequently, the cloning and characterization of the CFA biosynthetic gene cluster will contribute significantly to our knowledge of polyketide synthesis in Pseudomonas. In this report, we describe two genes in the CFA biosynthetic gene cluster that encode PKSs that are structurally and functionally similar to the multifunctional modular PKSs, which catalyze the synthesis of macrolide antibiotics. The CFA PKS genes were overproduced in Escherichia coli and shown to cross-react with antisera made to a modular PKS involved in erythromycin synthesis. A scheme for CFA biosynthesis is presented that incorporates the activities of all proteins in the CFA PKS. In this report a gene cluster encoding a pseudomonad polyketide has been completely sequenced and the deduced gene functions have been used to develop a biosynthetic scheme.

Deciphering the mechanism for the assembly of aromatic polyketides by a bacterial polyketide synthase.

Aromatic polyketides are assembled by a type 11 (iterative) polyketide synthase (PKS) in bacteria. Understanding the enzymology of such enzymes should provide the information needed for the synthesis of novel polyketides through the genetic engineering of PKSs. Using a previously described cell-free system [B.S. & C.R.H. (1993) Science 262, 1535-1540], we studied a PKS enzyme whose substrate is not directly available and purified the TcmN polyketide cyclase from Streptomyces glaucescens. TcmN is a bifunctional protein that catalyzes the regiospecific cyclization of the Tcm PKS-bound linear decaketide to Tcm F2 and the 0-methylation of Tcm D3 to Tcm B3. In the absence of TcmN, the decaketide formed by the minimal PKS consisting of the TcmJKLM proteins undergoes spontaneous cyclization to form some Tcm F2 as well as SEK15 and many other aberrant shunt products. Addition of purified TcmN to a mixture of the other Tcm PKS components both restores and enhances Tcm F2 production. Interestingly, Tcm F2 but none of the aberrant products was bound tightly to the PKS. The results described support the notion that the polyketide cyclase, not the minimal PKS, dictates the regiospecificity for the cyclization of the linear polyketide intermediate. Furthermore, because the addition of TcmN to the TcmJKLM proteins results in a significant increase of the total yield of decaketide, interactions among the individual components of the Tcm PKS complex must give rise to the optimal PKS activity.

Very-long-baseline radio interferometry (VLBI) observations of gamma-ray blazars: results from millimeter-VLBI observations.

VLBI observations of the extremely gamma-bright blazar PKS 0528+134 at 8, 22, 43, and 86 GHz reveal a strongly bent one-sided-core jet structure with at least three moving and two apparently stationary jet components. At the highest observing frequencies the brightest and most compact jet component (the VLBI core) is unresolved with an upper limit to its size of approximately 50 microarcsec corresponding to approximately 0.2 parsec [H0 = 100 km.s-1.Mpc-1 (megaparsec-1), q0 = 0.5, where H0 is Hubble constant and q0 is the deceleration parameter]. Two 86-GHz VLBI observations performed in 1993.3 and 1994.0 reveal a new jet component emerging with superluminal speed from the core. Linear back-extrapolation of its motion yields strong evidence that the ejection of this component is related to an outburst in the millimeter regime and a preceding intense flare of the gamma-flux density observed in early 1993. This and the radio/optical "light curves" and VLBI data for two other sources (S5 0836+710 and 3C 454.3) suggest that the observed gamma-radiation might be Doppler-boosted and perhaps is closely related to the physical processes acting near the "base" of the highly relativistic jets observed in quasars.