A febre reumática é um bom exemplo de uma doença auto-imune deflagrada por um processo infeccioso. Num prazo de uma a quatro semanas após a resolução de uma faringite não tratada por cepas reumatogênicas de S. pyogenes, o organismo de um hospedeiro susceptível desencadeia uma resposta imune contra grandes articulações, coração, tecidos subcutâneos e cérebro. Acredita-se que elementos presentes na bactéria e reconhecidos durante a infecção na orofaringe, sejam confundidos com estruturas próprias do organismo, num processo denominado mimetismo molecular. Entre as proteínas envolvidas na reação cruzada, encontram-se a miosina cardíaca, pelo lado do hospedeiro, e a proteína M do microorganismo invasor. Esta última (proteína M) tem sido extensamente estudad. É a base da classificação das cepas de S. pyogenes e importante fator de virulência. Também tem sido explorada como imunógeno em várias estratégias vacinais. O estudo desta patologia tem sido dificultado pela ausência de um modelo animal que reproduza aspectos fundamentais da patologia humana, entre estes as lesões cardíacas. Uma das razões é o fato de que animais não contraem infecção pelo S. pyogenes. Portanto, produzimos a proteína M1 recombinante e mostramos que a imunização de 28 ratos Lewis por um período de 21 dias ou 14 ratos por 41 dias, com esta proteína foi capaz de induzir resposta inflamatória na maioria dos animais com intensidade variável. Células similares aos nódulos de Aschoff e células de Anitschkow, sugestivas das lesões patognomônicas da febre reumática foram observadas em dias e também de um em quatro dos animais controles que receberam PBS e adjuvantes. Estes resultados sugerem a presença de células auto-reativas no miocárdio dos animais imunizados. Em conclusão, o uso de proteína M1 recombinante como imunógeno em modelo animal de ratos Lewis é capaz de desencadear reação inflamatória em miocárdio e tecido valvular e lesões similares às da febre reumática. O modelo do rato Lewis é até o momento o que apresenta maior semelhança com a doença humana e pode ajudar a esclarecer a imunopatologia da febre reumática. Além disso, certamente será importante para a avaliação do potencial de proteção e de segurança em modelos de vacinas contra o S. pyogenes. / Rheumatic fever is a good example of an autoimmune disease triggered by an infectious process. One to four weeks after the resolution of a non treated pharyngitis caused by rheumatogenic strains of S. pyogenes, the susceptible host unravels an immune response targeting joints, heart, conective tissues and brain. It is thought that molecules present in the bacteria and recognized during the infection at the pharynx are confounded with the organism self structure in a process called ?molecular mimicry?. Amongst the proteins involved in the cross reaction, it may be found cardiac myosin, on the host side, and M protein on the invading organism?s side. The latter (Mprotein) has been extensively studied. It is the basis of the S. pyogenes strains classification, and also an important virulence factor. It has also been explored as an immunogen in several vaccine strategies. The nderstanding of this disease has been hampered by the absence of an animal model that reproduces fundamental aspects of the human pathology, specially cardiac lesions. One of the reasons is the fact that animals do not get infected by S. pyogenes. Hence we have produced the recombinant M1 protein and shown that either the immunization of 28 Lewis rats for a period of 21 days or 14 rats for a period of 41 days, was capable of inducing an inflammatory response in most of the animals with variable intensity. Aschoff nodules-like or Anitschkow-like cells resembling rheumatic fever pathognomonic lesions were seen in 50% of the animals immunized subcutaneously and sacrificed on day 21. We have observed an humoral and cellular response (spleen and lymph node derived cells) specifically targeting M1 protein and the amino (M1AB) and carboxy (M1C) terminus of the protein. However, cross reactions with cardiac myosin were not observer. We have derived T lymphocyte lineages obtained from myocardium infiltrating mononuclear cells from 6 of the 10 animals immunized with M1ABC protein subcutaneously and sacrificed on day 41 and also from one out of four PBS - adjuvant immunized animals. These results suggest the presence of autoreactive cells in the myocardium of the immunized animals. In conclusion, the use of the M1 protein as an immunogen on the Lewis rat model is capable of triggering an inflammatory reaction in the myocardium and valvular tissue and it can produce rheumatic fever like lesions. The Lewis rat model is up to this moment the one to present the highest similarity with human disease. Besides, it will certainly be important on the evaluation of the protection and safety of S. pyogenes vaccines.

Ziel der Arbeit war es, die regulatorischen Mechanismen von Virulenz-assoziierten Genen in den Pathogenen Francisella novicida und Streptococcus pyogenes zu untersuchen. Kapitel eins befasst sich mit der Regulation des Virulenzfaktors Streptolysin S (SLS) von S. pyogenes. Wir untersuchten die Rolle der Ribonuklease (RNase) Y in der transkriptionellen und posttranstrikptionellen Regulation des Gens sagA. RNase Y begünstigte die Produktion einer kleinen RNA (sRNA) vom sagA Transkript, war jedoch nicht an der posttranskriptionellen Regulierung der sagA RNA beteiligt. Dennoch förderte RNase Y die Transkription von sagA indirekt. Wir konnten weiterhin zeigen, dass die 5′- untranslatierte Region (UTR) der sgaA RNA eine Sekundärstruktur besitzt, die möglicherweise einen Liganden bindet und damit die Zugänglichkeit der ribosomalen Bindungsstelle beeinflusst. Die Deletion einzelner Abschnitte der 5′ UTR hat einen negativen Effekt auf die sagA Expression. Wir haben eine Methode entwickelt um die Aktivität von Riboswitches, (u.a. die sagA 5‘ UTR) zu analysieren und konnten damit drei putative Riboswitches in S. pyogenes validieren. In Kapitel zwei charakterisierten wir den Mechanismus mit dem CRISPR-Cas9 aus F. novicida (FnoCas9) die Expression bakterieller Lipoproteine (BLPs) unterdrückt, um dem Immunsystem des Wirtes zu entgehen. Wir zeigen, dass FnoCas9 eine duale Funktion besitzt, die es dem Protein ermöglicht nicht nur DNA zu schneiden, sondern auch Transkription zu regulieren. In dieser erstmals beschriebenen Aktivität bindet FnoCas9 an den tracrRNA:scaRNA Duplex, wodurch der Protein-RNA Komplex an einen DNA Abschnitt hinter dem Promoter der blp Gene bindet und somit deren Transkription verhindert. Diese Bindungsstelle besitzt ein protospacer-adjacent motif (PAM) und eine scaRNA-komplementäre Sequenz, an die der FnoCas9-RNA Komplex bindet, allerdings nicht schneidet. Dieses System könnte in Zukunft das Repertoire an CRISPR-basierten Anwendungsmöglichkeiten erweitern. / The aim of this thesis was to study regulatory mechanisms of virulence-related genes in the bacterial pathogens Francicella novicida and Streptococcus pyogenes. Chapter one focuses on the regulation of the virulence factor streptolysin S (SLS) in S. pyogenes. First, we investigated the role of the ribonuclease (RNase) Y in the transcriptional and post-transcriptional regulation of SLS-coding gene, sagA. We found that RNase Y promotes the production of a small RNA (sRNA) from the sagA transcript but we observed no regulation at the post-transcriptional level. Yet, RNase Y promotes sagA transcription indirectly and affects hemolysis levels. We next showed that the sagA 5′ untranslated region (UTR) contains a secondary structure that is is possibly modulated by direct binding to a ligand and may affect the accessibility to the ribosomal binding site (RBS). Our results indicate that removing fragments of the 5′ UTR has a negative effect on sagA expression. We developed a method for testing the activity of putative riboswitches, including sagA 5′ UTR. Using this method, we validated three predicted riboswitches in S. pyogenes. In chapter two, we characterized the mechanism by which F. novicida CRISPR-Cas9 (FnoCas9) represses the expression of bacterial lipoproteins (BLPs), allowing evasion of the host immune system. We show that FnoCas9 is a dual-function protein that, in addition to its canonical DNA nuclease activity, evolved the ability to regulate transcription. In this newly-described mechanism, the non-canonical RNA duplex tracrRNA:scaRNA guides FnoCas9 to the DNA target located downstream of the promoter of the BLP-coding genes, causing transcriptional interference. The endogenous targets contain a protospacer-adjacent motif (PAM) and a sequence that is complementary to scaRNA, promoting FnoCas9 binding but not DNA cleavage. Engineering this system expands the toolbox of CRISPR applications by allowing repressing other genes of interest.

Streptococcus pyogenes ist ein humanpathogenes Bakterium, welches verschiedene Gewebe besiedeln kann und dadurch unterschiedliche Krankheiten verursacht. Die enorme Anpassungsfähigkeit des Bakteriums beruht auf dessen Fähigkeit, verschiedene, vom Wirt induzierte Stresskonditionen zu ertragen. Genetische Faktoren, die in diesem Zusammenhang eine Rolle spielen, sind Toxin-Antitoxin (TA) Systeme. Typ II TA Systeme kodieren für zwei Proteine, ein Toxin und ein Antitoxin, die einen stabilen TA Komplex bilden. Verschlechtern sich die Wachstumsbedingungen, kann das Antitoxin proteolytisch abgebaut werden, wodurch das freigesetzte Toxin essentielle zelluläre Prozesse des Bakteriums inhibiert. In dieser Studie charakterisierte ich zwei chromosomal kodierte ParDE TA Systeme des pathogenen Bakteriums S. pyogenes. Ähnlich zu anderen Systemen werden das Toxin und das Antitoxin beider hier charakterisierten Systeme co-transkribiert und durch Stresseinwirkung (z.B. Aminosäure-mangel) induziert. Zudem konnten weitere posttranskriptionelle bzw. posttranslationale Mechanismen zur Regulierung der Genexpression beider Systeme nachgewiesen werden. Die extrachromosomale Expression der Toxine ParE1 und ParE2 führten in S. pyogenes und Escherichia coli zum Zelltod, wobei die Co-expression der entsprechenden Antitoxine ParD1 und ParD2 die Toxizität minderte. Allerdings verursachte die Überexpression der Antitoxine allein ebenfalls eine Inhibierung des Zellwachstums. ParD1 hemmte die Zellteilung in E. coli, wobei der N-Terminus des Proteins entscheidend für diesen Effekt zu sein schien. Zusammengefasst erweitern die Ergebnisse dieser Arbeit unser Verständnis von ParE Toxinen und verdeutlichen die diversen Mechanismen, welcher sich TA Systeme bedienen, um die bakterielle Physiologie zu beeinflussen. Zusätzlich gibt diese Arbeit einen Einblick in mögliche Mechanismen, die S. pyogenes implementiert, um Stresskonditionen im Wirt zu überdauern. / Streptococcus pyogenes is a human pathogen with a remarkable ability to colonize different tissues and to endure diverse host-induced stress conditions through mechanisms that have yet to be fully understood. One strategy employed by bacteria to cope with changing environments are toxin-antitoxin (TA) genetic modules. Under non-ideal conditions, the antitoxin is subject to proteolysis and thus the freed toxin protein can target crucial pathways in the cell modulating bacterial growth. This study, describes the characterization of two chromosomally encoded ParDE-like TA systems from the human pathogen S. pyogenes. The antitoxin-toxin genes of the parDEF1 and parDE2 TA systems are co-transcribed and triggered by stress-induced conditions. The parDE2 TA showed an inspected mRNA processing under amino acid starvation which suggest a putative post-transcriptional regulation. At the post-translational level, both systems are controlled by ClpXP antitoxin-protein degradation in vivo, an important factor for TA triggering. Furthermore, bacterial plasmid-based expression of the toxins ParE1 and ParE2 resulted in effects in cell viability while the antitoxin molecules ParD1 and ParD2 were able to prevent the toxins lethality, respectably. Unlike canonical antitoxins, both ParD1 and ParD2 molecules also displayed deleterious effects, which seemed to be exclusive and related with the N-terminus domain potentially involved in DNA-interaction. Finally, the ParE toxins presented remarkable plasticity, able to harm not only gyrase but also topoisomerase IV, two important bacterial drug targets that modulate DNA-topology. These results expand the view on the ParE molecular targets and highlight the diverse mechanisms TAs employ to modulate bacterial physiology. We also provide more insights into possible mechanisms that S. pyogenes employs to endure stress in the host and efficiently cause disease.

Bakterien haben eine Vielzahl an Strategien entwickelt, um sich an ständig wechselnde Umweltbedingungen anzupassen, darunter auch post-transkriptionelle regulatorische Mechanismen. Die Genexpression kann hierbei durch gezielten Abbau oder Stabilisierung von RNA durch Ribonukleasen (RNasen) reguliert werden. RNasen weisen je nach Spezies allerdings unterschiedliche Effekte auf Genexpression und bakterielle Physiologie, sowie verschiedene Strategien der Substraterkennung auf. Dies zeigt, dass unser Verständnis des RNA-Abbaus bei weitem nicht vollständig ist. Ziel dieser Arbeit ist es, die Eigenschaften und Funktionen der endoRNase Y des humanpathogenen Bakteriums Streptococcus pyogenes zu studieren. Um Einblick in Funktion und Spezifität dieser RNase zu gewinnen, wurden deren genomweite Schnittpositionen (“targetome”) mit Hilfe von RNA-Sequenzierung identifiziert. Zur weiteren Analyse des RNase Y-abhängigen RNA-Abbaus wurde dieses Ergebnis mit dem “targetome” der drei 3′-5′-Exoribonukleasen (ExoRNasen) PNPase, YhaM und RNase R verglichen. Schließlich wurden die Anforderungen für die Prozessierung durch RNase Y und deren Rolle in der Regulation von Virulenzgenen in vivo anhand der speB mRNA, die einen wichtigen Virulenzfaktor codiert, untersucht. Wir konnten in dieser Arbeit zeigen, dass RNase Y Substrate bevorzugt nach einem Guanosin schneidet und dieses Nukleosid essenziell für die Prozessierung der speB mRNA in vivo ist. Obwohl RNase Y die speB mRNA schneidet, unterstützen die Daten ein Modell nach dem RNase Y die Expression von speB auf transkriptioneller Ebene reguliert. Mit Hilfe des “targetome”-Vergleichs konnten wir ferner zeigen, dass RNase Y den RNA-Abbau in S. pyogenes initiiert und die dabei generierten 3′-Enden der RNA hauptsächlich von den 3′-5′-exoRNasen PNPase und/oder YhaM prozessiert werden. Zusammenfassend erweitern diese Erkenntnisse unser Verständnis der Funktionalität von RNase Y und des RNA-Abbaus in Gram-positiven Bakterien. / Bacteria have developed a plethora of strategies to cope with constantly changing environmental conditions, including post-transcriptional regulatory mechanisms. With this regard, regulation of gene expression can be achieved by either the rapid removal or stabilization of RNA molecules by ribonucleases (RNases). RNases exhibit species-specific effects on gene expression, bacterial physiology and different strategies of target recognition, indicating that our understanding of the RNA degradation machinery is not yet complete. The aim of this thesis was to investigate the features and functions of endoRNase Y from the strict human pathogen Streptococcus pyogenes. To gain insight into the role and specificity of this RNase, we identified RNase Y cleavage positions (i.e. targetome) genome-wide by RNA sequencing. Next, to investigate the RNA degradation pathway depending on RNase Y, we compared the RNase Y targetome with the ones of the three 3′-to-5′ exoribonuclease (exoRNases), namely PNPase, YhaM and RNase R. Finally, to dissect the requirements for RNase Y processing and to decipher the role of RNase Y in virulence gene regulation, we studied the impact of RNase Y on speB mRNA, encoding a major virulence factor. This study reveals that RNase Y preferentially cleaves RNAs downstream of a guanosine and for the first time we were able to show that the presence of a guanosine residue is essential for the processing of speB mRNA, in vivo. Although RNase Y cleaves the speB mRNA, our data underpin a model in which RNase Y-mediated regulation of speB expression occurs at the transcriptional level. Using the targetome comparative approach, we demonstrated that RNase Y initiates RNA decay in S. pyogenes and that the RNase Y-generated RNA 3′ ends are usually further trimmed by PNPase and/or YhaM. Overall, these findings increase our understanding of RNase Y functionality and RNA degradation in Gram-positive bacteria.

The pathogen Streptococcus pyogenes is a significant cause of human morbidity and mortality. Most of the work in this thesis is focused on streptococcal virulence factor IdeS, but the thesis also features work on SpeB, another streptococcal virulence factor. Both IdeS and SpeB are secreted cysteine proteases and both have previously been shown to degrade human IgG. IgG is the only known substrate for IdeS while SpeB is a more promiscuous protease with a larger number of identified substrates. A significant part of the data presented in this thesis is the result of designing and optimizing methods to detect and accurately measure the proteolytic degradation of IgG. Methods aimed at measuring the binding interactions between enzyme and substrate have also been frequently utilized. I show that IdeS is a monomeric protease, as opposed to previously published data that suggested it to be dimeric. IdeS cleaves the two heavy chains of IgG in a two-step reaction and I demonstrate that the first cleavage is magnitudes faster than the second one. This means that IdeS is a more efficient enzyme than previously thought. The difference in rate cannot completely be explained by a loss of affinity between IdeS and IgG after the cleavage of the first heavy chain. The velocity of IdeS is further increased by the presence of human Cystatin C, via an unknown mechanism. Cystatin C is normally a protease inhibitor and it having an opposite effect is puzzling.The synthesis and evaluation of novel inhibitors are also described. Peptide analogues mimicking the sequence surrounding the scissile bond on IgG - with an amino acid replaced with a more rigid motif - act as specific, but low-affinity, inhibitors of IdeS. The peptide analogues’ inhibitory capacity for SpeB and papain was also assayed.When it comes to SpeB, I show that it does not have IgG as a substrate under physiological conditions, in contrast to what was previously thought. This thesis does not only present findings on the IgG degrading capacity of IdeS and SpeB but also include data on fundamental enzymatic properties for these proteases.

Most pathogens gain access to their host through mucosal surfaces. It is therefore desirable to develop mucosal vaccines that elicit an immune response to prevent this crucial first step in infection. Current mucosal vaccines are live attenuated strains of pathogens. More recent efforts have focused on the use of recombinant non-pathogenic gram-positive bacteria as live vaccine delivery vectors. Here I have tested the potential of Lactococcus lactis to be used as a vaccine vector. A recombinant strain of L. lactis has been constructed which expresses and displays on its surface the C repeat region (CRR) of the M6 protein of Streptococcus pyogenes. I show that nasal vaccination of mice with this strain elicited strong salivary IgA and serum lgG response. These responses protected mice against a nasal challenge with S. pyogenes. Subcutaneous vaccination with the same strain of L. lactis produced a strong serum lgG response, but no salivary lgA response. Subcutaneous vaccination did not protect the mice against nasal infections when the mice were challenged with S. pyogenes. The immune response and protection afforded by concomitant vaccination by both nasal and subcutaneous routes were better that that seen in nasal vaccination alone. This study shows that an effective vaccine against S. pyogenes is possible using L. lactis as a vaccine vector. It also opens up the potential of L. lactis to be used in the development of vaccines to other mucosal infections. / Graduation date: 2004

Heme is the major iron source for the deadly human pathogen, Group A Streptococcus (GAS). During infection, GAS lyses host cells releasing hemoglobin and other hemoproteins. This dissertation aims to elucidate the general mechanism by which GAS obtains and utilizes heme as an iron source from the host hemoproteins. GAS encodes a heme relay system consisting of Shr, Shp and the SiaABC transporter. We specifically determine the role of Shr in the heme uptake process, by conducting a detailed functional characterization of its constituent domains. We also undertake to solve the long-standing mystery surrounding the catabolism of heme in streptococci. The studies presented herein established Shr as a prototype of a new family of NEAT-containing hemoproteins receptors. They demonstrate its importance in heme acquisition by GAS and provide a molecular model for heme scavenging and transfer by the protein. We show that Shr modulates heme uptake depending on heme availability by a mechanism where NEAT1 facilitates fast heme scavenging and delivery to Shp, whereas NEAT2 serves as a temporary storage for heme on the bacterial surface. Finally, we identified and characterized for the first time, a heme oxygenase (HO) in the Streptococcus genus which was named HupZ. Sequence comparison between HupZ and several HOs from different structural families indicates that this enzyme is unrelated to any of the previously characterized HOs. However, orthologs of the protein are found in other important pathogens. The structure and the catalytic mechanism of HupZ suggest that it is the representative of a new family of flavoenzymes capable of degrading heme using their reduced flavin cofactor as a source of electrons. Overall, this work contributes significant knowledge to the topic of heme utilization by pathogens and importantly, provides new direct evidence that associates flavins with heme metabolism in bacteria. Thus it sets a new direction in the field and lays the ground for future fundamental and applied discoveries.

Some pathogenic bacteria derive significant amounts of iron heme from their hosts. In this study we investigated SiaA, a heme binding protein from Streptococcus pyogenes. The wildtype methionine79 putative axial ligand was mutated to alanine. SiaA M79A was expressed in E. coli in three production runs, lysed by sonication or French press, and purified by fast protein liquid chromatography (FPLC). Nickel affinity FPLC was found to give much purer SiaA when 30 mM imidazole was added to the binding buffer. The protocol using extensive sonication resulted in SiaA weighing 30464 Da. The protocol using French press resulted in SiaA weighting 33358 Da. Despite the difference in masses, the two forms of SiaA interacted with heme similarly.

Group A Streptococcus (GAS) is a common pathogen of the human skin and mucosal surfaces and is capable of producing a variety of diseases. This dissertation investigates the function of a metalloregulator named MtsR in GAS physiology and disease process. An mtsR mutant was constructed and analyzed. Consistent with MtsR role in iron uptake regulation, the mtsR mutant accumulates more iron (80 ± 22.5%) than the wild type strain. Inactivation of mtsR results in constitutive transcription of the sia (Streptococcal Iron Acquisition) operon, which is negatively regulated by iron in the parent strain. We identified the promoter that controls the expression of the sia operon (Pshr) and used it as a model to study MtsR interaction with DNA. Electrophoretic mobility gel shift assays (EMSAs) demonstrated that MtsR binds to the shr upstream region specifically and in an iron and manganese dependent manner. DNase I footprint analysis revealed that MtsR protects a 69 bp segment in Pshr that includes 2 inverted repeats, overlapping the core promoter elements. A global transcriptional analysis determined that MtsR modulates the expression of 64 genes, of which 44 were upregulated and 20 were downregulated in the mtsR mutant. MtsR controls genes with diverse functions including immune evasion, colonization, dissemination, metal homeostasis, nucleic acid and amino acid metabolism, and protein stability. MtsR functions as a dual regulator as it binds to the promoters of the repressed genes ska, aroE, and nrdF.2, as well as the upstream region of the positively regulated genes mga, emm49, and pyrF. A 16 bp MtsR-binding consensus region was identified in all of the promoters that are directly regulated by MtsR. In conclusion, we have demonstrated that MtsR is a global regulator in GAS that controls the expression of vital virulence factors and genes involved in metal transport, virulence and metabolic pathways.

Anthraquinone (AQ) derivatives with relatively high reduction potentials have been synthesized to afford good candidates for electron transfer studies in DNA. Electron withdrawing groups on the anthraquinone ring gave derivatives with less negative reduction potentials. The anthraquinone imide (AQI) derivatives had reduction potentials less negative than AQ derivatives. The AQI ring system was subject to base-induced hydrolysis. Water-soluble sulfonated tetraarylporphyrins have been studied in a wide variety of contexts. Herein, we report the first synthesis of a pentasulfonated porphyrin bearing an internal cyclic sulfone ring. Treatment of 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4) with fuming H2SO4 gave a structure consistent with initial sulfonation followed by dehydration to give a sulfone bridge between an ortho-position of one of the phenyl groups and a β-pyrrole position on the porphine ring (TPPS4Sc). The structure was established by ESI-MS and 1HNMR. The Soret absorption is red shifted by about 32 nm compared to that of TPPS4. Streptococcus pyogenes obtains iron by taking up heme from the environment during infection. One of the heme uptake pathways is the Sia or Hts pathway. The initial protein in this pathway is Shr, which has two heme-binding NEAT domains, NEAT1 nearer the N-terminus, and NEAT2 nearer the C-terminus. We report biophysical characteristics of these two NEAT domains. To assess stability of this domain towards heme release, denaturation studies of the Fe(II) and Fe(III) forms were performed. For each domain, both the Fe(II) and the Fe(III) forms behave similarly in thermal denaturation and guanidinium denaturation. Overall, NEAT2 is more stable than NEAT1. Spectral signatures, sequence alignment and homology modeling for both domains suggest that one of the axial ligands is methionine. NEAT2 autoreduces as the pH increases and autooxidizes as the pH decreases. Heme uptake from the host environment is the only iron acquisition pathway in S. pyogenes; inhibition of this pathway might be an approach to infection control. Compounds that might inhibit the heme uptake pathway were selected via virtual screening.