La morphogénèse des ovocoques, dont fait partie le pathogène humain Streptococcus pneumoniae, implique des processus d’élongation et de division associés à la synthèse de la paroi bactérienne. Le composant majeur de cette paroi est le peptidoglycane, un polymère de sucre réticulé par des chaines peptidiques, qui confère la forme de la bactérie et est essentiel à sa survie. La synthèse de peptidoglycane nécessaire à l’élongation et la division bactérienne est effectuée par des complexes protéiques appelés respectivement « élongasome » et « divisome ». Les mécanismes d’assemblage et l’activité de ces complexes dans la cellule bactérienne restent encore non élucidés. Pour imager l’activité des complexes de synthèse du peptidoglycane in vivo à l’échelle du nanomètre, j’ai développé une méthode faisant appel à des dérivés de D-amino acides, à la chimie click et à la microscopie de localisation de molécules uniques (dSTORM ou direct Stochastic reconstruction microscopy). Cette méthode a permis d’obtenir des images à une résolution d’environ 20 nm, révélant des aspects inattendus de la synthèse du peptidoglycane et remettant en question le rôle de certaines protéines dans la morphogenèse du pneumocoque. En combinant ces observations avec les données de la littérature, un modèle simplifié de la morphogénèse des ovocoques est proposé. / The morphogenesis of ovovcocci, which include the human pathogen Streptococcus pneumoniae, involves elongation and division processes associated with cell wall synthesis. The main component of the cell wall is the peptidoglycan, a polymer made of glycan chains cross-linked by peptide chains, which confers the bacterial shape and is essential for cell survival. Peptidoglycan synthesis required for cell elongation and division is performed by large protein complexes called “elongasome” and “divisome”, respectively. The assembly mechanisms and activity of these complexes in the bacterial cell remain mysterious. To image the activity of the peptidoglycan synthesis complexes in vivo at the nanoscale, I developed a method combining D-amino acid derivatives, click chemistry and single-molecule localization microscopy (dSTORM or direct Stochastic reconstruction microscopy). This method allowed obtaining images at a resolution of about 20 nm resolution, revealing unexpected features of peptidoglycan synthesis and challenging the role of some proteins in pneumococcus morphogenesis. By combining these observations with data from the literature, a simplified model of ovococci morphogenesis is proposed.

Toll-like receptors (TLRs), named after toll proteins identified in Drosophila melanogaster, are the pattern recognition receptors in the innate immune system that detect microbes. TLRs are mono, membrane-spanning, as well as non-catalytic receptors, which are mainly expressed in sentinel cells, such as the dendritic cells, neutrophils and macrophages. While humans have ten TLRs (TLR 1 to 10), the mouse has another three (TLRs 11, 12, 13). TLRs are made up of glycoproteins, which have luminal ligand-binding sites consisting of leucine-rich repeat (LRR) for detection of pathogens leading to activation of immune cells. TLR1, 2, 4, and 6 are responsible for recognition of lipids (such as triacetylated lipopeptide), peptidoglycan, and lipopolysaccharide (LPS). However, the TLR3, 7, 8, and 9 mainly recognize nucleic acids, such as double-stranded RNA (dsRNA) and CpG DNA, while the TLR13 detects ribosomal RNA sequences. So far, there are no data on the localization and immunological functions of TLR10. I studied the expression, localization and role of TLR10 in S. pneumoniae infection. First, I examined the expression of TLR10 in lungs of pig, cattle, dog, rat, and chickens. The light and electron microscopic data show TLR10 expression in vascular endothelium and smooth muscles in lungs of control and inflamed animals. Further, we found altered basal level of expression and localization of TLR10 in bovine neutrophils treated with E. coli lipopolysaccharide. These data show the expression of TLR10 in the lungs of tested animal species, and its alteration by LPS in bovine neutrophils. The next study was designed to investigate the regulation of TLR10 expression and to address its role in neutrophil chemotaxis. E. coli LPS activated human neutrophils showed temporal and spatial change in TLR10 expression. Confocal microscopy showed cytosolic and nuclear distribution of TLR10 in normal and activated neutrophils. TLR10 in E. coli LPS-activated neutrophils colocalized with flotallin-1, a lipid raft marker, and EEA-1, an early endosomal marker, suggested its endocytosis. Live cell imaging of LPS activated neutrophils showed TLR10 translocation to the leading edge. Neutrophils upon TLR10 knockdown were unable for fMLP-induced migration. TLR10 knockdown reduced the number of membrane pseudopods in activated neutrophils without altering the expression of key proteins of actin nucleation process, ARP-3 and Diap1. These data show TLR4-mediated pathway for regulation of TLR10 expression, and that TLR10 may have a role in neutrophil chemotaxis. Next, I examined the role of TLR10 in innate immune response to S. pneumoniae infection in U937 human macrophage cell line. S. pneumoniae are major causative agents of pneumonia, meningitis and bacteremia. A significant increase in TLR10 mRNA expression was found in S. pneumoniae (107 cfu for 6hr) challenged macrophages. TLR10 knockdown significantly reduced production of IL-1β, IL-8, IL-17 and TNF-α and no significant change in IL-10 expression, and also significantly diminished nuclear translocation of NF-κB but without affecting the phagocytosis of S. pneumoniae. Altogether, I report the that TLR10 is expressed in the normal and inflamed lungs in cattle, pigs, dogs, rats, chickens and humans. The expression of TLR10 is altered in activated neutrophils, and it plays a role in neutrophils chemotaxis and production of pro-inflammatory cytokines in macrophages infected with S. pneumoniae.

Streptococcus pneumoniae is a commensal inhabitant of the human nasopharynx that can sometimes become pathogenic and cause diseases such as pneumonia, otitis media and meningitis. Carbohydrate metabolism is a critical component of S. pneumoniae virulence. Among the myriad of carbohydrate-specific pathways involved in the host-pneumococcus interaction, the N-glycan foraging pathway stands out because of its direct implication in numerous aspects of virulence such as fitness, adhesion/invasion and impairment of the host immune response. Much of the literature has been focussed on the importance of step-wise depolymerisation of N-glycans by the enzymes NanA, BgaA and StrH. However, the importance of the liberation of N-glycans from host glycoconjuguates and their intake by the bacterium has yet to be examined. We have identified a Carbohydrate Processing Locus (CPL) that is highly conserved throughout a large number of Firmicutes and whose individual components appear widespread in bacteria that we hypothesize is active on host N-glycans. This locus encodes for two putative α-mannosidases GH92 and GH38, a characterised α-mannosidase GH125, a putative β-hexosaminidase GH20C, a putative α-fucosidase GH29 and a ROK (Repressor, Open reading frame, Kinase) protein. The genomic context of CPL orthologues suggests that an endo-β-N-acetylglucosaminidase (EndoD) and an ABC transporter (ABCN-glycan) are functionally associated with this locus. Based on our bioinformatic analyses and known functions of these proteins we hypothesize that the CPL encodes a concerted pathway responsible for the liberation, transport, and processing of N-glycans. The objective of this research is to characterize the putative components of this pathway and assess their implication in virulence. Specific focus on ABCN-glycan demonstrated its specificity for a range of N-glycans liberated by EndoD, shedding light on a novel import system for branched N-glycans. Furthermore, we provided evidence that GH92 is an α-1,2-mannosidase that likely removes the terminal mannose residues found on high-mannose N-glycans. EndoD and GH92 are shown to participate in virulence in mice; however, their role in virulence has yet to be determined. This work will significantly advance the construction and validation of a model of N-glycan processing by S. pneumoniae. As the components of this model pathway are conserved amongst a wide variety of bacteria, this work is of fundamental relevance to understanding how microbes from various environments degrade and metabolize N-glycans. / Graduate

The sialidases are a group of glycosyl hydrolases that specifically remove terminal sialic acid (Neu5Ac) residues from various glycans. In the two common human pathogenic bacteria Streptococcus pneumoniae and Pseudomonas aeruginosa, these enzymes have been shown to be key virulence factors directly involved in bacterial colonization and infection. However, little is known about their detailed structural and mechanistic features and lack of this information significantly slows down the progress of new drug discovery targeting these enzymes. Therefore, we embarked structural and kinetic studies towards the three distinct sialidases (designated as NanA, NanB and NanC) from S. pneumoniae, as well as the putative sialidase (designated as PaNA) from P. aeruginosa. Full-length NanA failed to crystallize due to the presence of some natively disordered regions. The catalytic domain of NanA (CNanA) was therefore subcloned, which was crystallized and the structure was determined to 1.5 Å. CNanA exists as a dimer with close contacts between the two monomers. The second pneumococcal sialidase NanB only shares 24% sequence identity with NanA. Crystal structure of NanB was also determined to 1.7 Å, which exhibits a multi-domain monomeric architecture. In general, the core catalytic domain of both CNanA and NanB adopts the classic six- bladed β-propeller fold (or called sialidase fold), with a set of highly conserved residues stacking around the proposed active sites. NanC is a close homologue of NanB, sharing over 50% sequence identity. However, NanC crystallization is not successful so far. To compare the three sialidases in more detail, a computational NanC model was made based on the structure of NanB. Mapping of the active sites of CNanA and NanB was achieved using Neu5Ac2en, a general sialidase inhibitor as the probe. Although sharing many common features, NanA, NanB and NanC present different topologies around the catalytic centre, give these enzymes a high level of diversity in enzymatic kinetics, substrate specificity and catalytic properties. NMR studies show that NanA acts as a classic hydrolytic sialidase; while NanB is found to be an intermolecular trans-sialidase like the leech sialidase; NanC, however, handles multiple catalytic roles efficiently, which include releasing Neu5Ac2en from α2,3- sialyllactose and hydration of Neu5Ac2en to Neu5Ac with high efficiency. S. pneumoniae thus expresses NanA, NanB and NanC for disparate but cooperative roles. Such a working pattern of three sialidases in one microbe is unusual in nature, which might be essential for pneumococcal pathogenesis at various stages. Based on the crystal structures of CNanA and NanB, preliminary work towards S. pneumoniae sialidases inhibitor design is under way, in which, a variety of techniques, such as the fluorescence-based thermal shift assay, NMR spectroscopy, computational docking and X-ray crystallography, are incorporated in. The crystal structure of PaNA was determined to 1.9 Å. This protein appeared to be a unique trimer in crystal that is associated, in part, by the immunoglobulin-like trimerization domain around a three-fold crystallographic axis. The core catalytic domain of PaNA also presents the conserved sialidase fold. Surprisingly, no sialidase activity was detected with this enzyme. In addition, two key catalytic residues including one of the arginine in the arginine triad and the acid/base catalyst aspartic acid are missing in PaNA. In silico docking suggests that Phe129 may confer substrate selectivity towards pseudaminic acid, which is a specific carbohydrate superficially similar to Neu5Ac, but with different stereochemistry at the C-5 position. Site-directed mutagenesis further confirmed that mutation of Phe129 to alanine could turn PaNA into a poor sialidases. Moreover, the crystal structure of PaNA also indicates that His45, Tyr21 and Glu315 may form a charge relay to compensate the missing aspartic acid. Subsequent mutagenesis and NMR kinetic studies proved His45-Tyr21-Glu315 to be a novel charge relay taking the role of the acid/base catalyst. Therefore, PaNA could be a pseudaminidase with structural and mechanistic variations. This enzyme, together some other uncharacterized fellow proteins, might form a novel subclass in the sialidase superfamily. The various findings in the current projects provide meaningful insights towards several sialidases that have been linked to bacterial virulence, which may contribute to a more intensive understanding of S. pneumoniae and P. aeruginosa pathogenesis.

Streptococci resident in the oral cavity have been linked to infective endocarditis (IE). While viridans streptococci are commonly studied and associated with IE, less research has been focused on Streptococcus pneumoniae. Two-component systems (TCSs), consisting of a histidine kinase (HK) protein and response regulator (RR) protein, are bacterial signaling systems that may mediate S. pneumoniae TIGR4 strain virulence in IE. To test this hypothesis, TCS RR mutants of TIGR4 were examined in vivo through use of rabbit models. There were 14 RR proteins identified and 13 RR mutants synthesized because SP_1227 was found to be essential. The requirement of the 13 RRs for S. pneumoniae growth in IE models was assessed by quantifying mutants after overnight inoculation in IE infected rabbits through use of real time PCR (qPCR), colony enumeration on antibiotic selection plates, and competitive index assays. Real time PCR pinpointed several candidate virulence factors. Candidate RR SP_0798 was selected to be further examined. In the in vivo model, mutant SP_0798 grew significantly less than our control mutant SP_1678, which encodes a hypothetical protein and grew at a comparable rate to wild-type TIGR4 strains. Literature and databases identified SP_0798 as the ciaR gene, which has roles in regulating many diverse cellular functions. Our data suggests that RR SP_0798 is a virulence factor of S. pneumoniae TIGR4 strain in IE. This research may place more emphasis on virulence factors and lead to novel methods to combat pneumococcal endocarditis.

Due to the development of multidrug resistance in Streptococcus pneumoniae, research has begun to define new drug targets for pneumonia therapy. Different research groups have identified a lipoprotein, PsaA that is important for pneumonia virulence. PsaA is a manganese transporter that is required for bacterial virulence and growth. We have employed computer modeling to virtually screen a small-molecule database for inhibition of PsaA function by targeting the metal binding pocket, performing receptor-based virtual screening and molecular docking and scoring to identify potential inhibitors of PsaA function. We have developed an assay for screening compounds, including the use of a PsaA mutant, testing of multiple compounds, and identification of compounds that inhibit Streptococcus pneumoniae growth at concentrations less than 20 μM. We experimentally tested the effect on Mn uptake and their PsaA dependence for 42 compounds, but these experiments suggested that these compounds were affecting bacterial growth by a different mechanism.

Orientador: Edison Iglesias de Oliveira Vidal / Resumo: Introdução: O Streptococcus Pneumoniae é o agente infeccioso mais frequentemente associado à ocorrência de pneumonia bacteriana e a vacinação é considerada a principal estratégia para a prevenção dessa doença. De acordo com o Programa Nacional de Imunização (PNI) a vacina pneumocócica polissacarídica 23-valente (Pn23) não faz parte do calendário básico de vacinação e deve ser dispensada a indivíduos a partir de 2 anos de idade desde que portadores de um conjunto de doenças e condições de alto risco para infecções pneumocócicas. A forma de operacionalização atual do PNI em relação à Pn23 se dá de modo que essa vacina não se encontra disponível nas Unidades Básicas de Saúde (UBS) e sua liberação se dá mediante solicitação aos Centros de Referência em Imunobiológicos Especiais (CRIEs), através de uma ficha de Solicitação de Imunobiológicos Especiais (SIBE). Acredita-se que tal formatação da logística de dispensação da vacina constitui um elemento limitador do acesso da população adulta à mesma. O objetivo da presente pesquisa foi avaliar a efetividade de uma intervenção piloto no município de Jahu de caráter multifatorial sobre a frequência de dispensação da Pn23 para a população adulta com indicação clínica conforme definida pelo PNI. Métodos: A intervenção foi composta por um componente caracterizado pela descentralização do fluxo de dispensação da vacina, de modo que esta passasse a estar disponível diretamente nas UBS, como é feito com as demais vacinas do calendário básico ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: Streptococcus Pneumoniae is the infectious agent most commonly associated with bacterial pneumonia and vaccination against it is considered the main strategy to prevent its occurrence. According to the Brazilian National Immunization Program (NIP) the 23-valent pneumococcal polysaccharide vaccine (Pn23) is not part of the country’s basic vaccination program and is recommended only for individuals aged 2 years and older who suffer from a variety of high-risk diseases and conditions for pneumococcal infections. The current operationalization of the NIP regarding the Pn23 vaccine determines that that vaccine is not available at Primary Healthcare Units (PHU) and that its distribution to those units is conditional to the receipt of a special vaccine request form by the regional Reference Centers for Special Immunobiologic Products (RCSIP). We believed that such centralized system of distribution of the Pn23 vaccine constituted a barrier for the eligible adult population to have access the vaccine. The aim of the present study was to assess the effectiveness of a multifactorial intervention on the frequency of use of the Pn23 vaccine among adults of the municipality of Jahu with a clinical indication for the vaccine according to the NIP. Methods: The intervention consisted of the decentralization of the Pn23 vaccine distribution so that doses of that vaccine were made available at each PHU as if it were part of the country’s basic vaccination program. Additionally, t... (Complete abstract click electronic access below) / Mestre

Streptococcus pneumoniae (pneumococcus) is commonly found in the nasopharynx of healthy individuals, yet it can be a serious pathogen, particularly in the lower respiratory tract, where it can cause severe pneumonia. During pneumococcal pneumonia, anti-bacterial host defense requires the orchestrated expression of innate immunity mediators, initiated by alveolar macrophages and dependent on transcriptional activity driven by Nuclear Factor-𝜅B (NF-𝜅B). Although the initiation of a pulmonary inflammatory response is critical to anti-pneumococcal defense during pneumonia, how differences in pneumococcal-macrophage interactions can influence this process is unclear. To determine the functional significance of varying macrophage NF-𝜅B activation, we examined macrophage responses to pneumococcal stimulation in culture and in mice. Macrophage-pneumococcal interactions resulted in the induction of varied NF-𝜅B activation. Two main pathways were revealed regarding host response and disease outcome. Pneumococci that induced efficient macrophage NF-𝜅B activation resulted in robust anti-pneumococcal lung defense and bacterial clearance. Conversely, failure to activate effective macrophage NF-𝜅B signaling resulted in an altered macrophage response of necroptosis. Overall, we conclude that varying levels of macrophage NF-𝜅B activation by pneumococcus can directly influence the severity of infection. Furthermore, inefficient macrophage NF-𝜅B activation can also have cytotoxic effects on these critical lung resident cells during pneumonia. The induction of macrophage NF-𝜅B activation by S. pneumoniae is as diverse as the population of pneumococcal isolates in the community. A unique host-pathogen interaction exists between pneumococcus and the alveolar macrophage that plays an important role in anti-pneumococcal defense during pneumonia and in the prevention of cytotoxic consequences induced by virulent pneumococci. This interaction suggests that therapies, which modulate NF-𝜅B activation, hold promise for augmenting resistance and ameliorating deleterious effects during pneumococcal pneumonia that could lead to the development of severe disease.

As infecções do trato respiratório inferior lideram entre as principais causas de morbidade e mortalidade no mundo. Um dos grandes problemas associados ao tratamento das infecções do sistema respiratório, como as pneumonias, advém da crescente resistência aos mais modernos antibióticos adquirida pelos microrganismos. A terapia fotodinâmica, uma técnica baseada na interação da luz com uma substância fotoativa para causar dano oxidativo a células, tem se destacado como uma interessante alternativa para diversas doenças como diferentes tipos de câncer e infecções. Neste trabalho foi realizada, com experimentos in vitro, uma prova de princípio da possibilidade de inativar, com um protocolo eficiente e seguro, uma das bactérias mais comumente encontradas em quadros de pneumonia, a Streptococcus pneumoniae, com terapia fotodinâmica infravermelha mediada pela indocianina verde. Duas fontes de luz, uma a base de lasers emitindo 780 nm e outra construída com LEDs emitindo 850 nm, foram comparadas para avaliar sua eficiência. Experimentos com a bactéria foram realizados para determinação dos melhores parâmetros de inativação microbiana. Em seguida, ensaios de citotoxicidade foram feitos com macrófagos RAW 264.7 com o intuito de averiguar se as condições microbicidas não apresentavam atividade tóxica para células fagocitárias do sistema imune. Foi possível delinear os parâmetros de concentração de indocianina, tempo de incubação e dose de luz que apresentassem atividade microbicida e que não fossem tóxicas para as células. A interação da terapia fotodinâmica com a ação fagocitária dos macrófagos sobre as bactérias foi avaliada pelo estabelecimento de co-cultura dessas espécies. Concluiu-se que, utilizando-se LEDs de 850 nm fornecendo uma dose de luz de 10 J/cm2 as amostras contendo indocianina verde 5μM, é possível inativar S. pneumoniae de modo eficiente e auxiliar a ação fagocitária de macrófagos. / The lower respiratory tract infections lead among the main causes of morbidity and mortality worldwide. A major problem associated with respiratory tract infections, e.g. pneumonia, stems from from the increasingly resistance to most modern antibiotics developed by microorganisms. Photodynamic therapy, a technique based on the interaction of light and a photoactive substance to cause oxidative damage to cells, has emerged as an attractive alternative for several diseases such as different kinds of cancer and infections. In this work, with in vitro experiments, we accomplished a proof of concept for the possibility of inactivating, with an efficient and secure protocol, one of the most commonly found bacteria in pneumonia cases, Streptococcus pneumoniae, with infrared photodynamic therapy mediated by indocyanine green. Two light sources, one based on 780 nm lasers and the other built with 850 nm LEDs, were compared to evaluate their efficiency. Experiments with bacteria determined the best parameters microbial inactivation. Then, cytotoxicity assays with RAW 264.7 macrophages analyzed if the microbicidal parameters had toxic effects on immune cells. It was possible to delineate the indocyanine concentration parameters, incubation time and dose of light to obtain microbicidal results that weren´t toxic to the cells. Interaction of photodynamic therapy with the phagocytic action of macrophages on the bacteria was assessed by establishing a co-culture with these species. We concluded that, using 850 nm LEDs providing a light dose of 10 J/cm2 to samples containing 5μM indocyanine green, it is possible to inactivate S. pneumoniae and efficiently assist the phagocytic action of macrophages.

Thesis advisor: Michelle Meyer / The primary bacterial targets for most antibiotics are well known. To survive the stress of an antibiotic a bacterium must decrease the antibiotic to target binding ratio to escape from harmful effects. This can occur through a number of different functions including down-regulation of the target, mutation of the binding site on the target, and decreasing the intake or increasing the efflux of the antibiotic. However, it is becoming more evident that an antibiotic stress response influences more than just the primary target, and that a wave of secondary responses can be triggered throughout the bacterium. As a result resistance mutations may arise in genes that are indirectly affected by the initial interaction between the antibiotic and target. These indirect responses have been found to be associated with metabolism, regulation, cell division, oxidative stress, and other critical pathways. One technique recently developed in our lab, called transposon insertion sequencing (Tn-seq), can be used to further understand the complexity of these indirect responses by profiling growth rates (fitness) of mutants at a genome-wide level. However, Tn-seq is normally performed with large libraries of pooled mutants and thus it remains unclear how this may influence fitness of some independent mutants that may be compensated by others in the population. Additionally, since the original method has only utilized planktonic culture, it is also not clear how higher order bacterial structures, such as biofilms or microcolonies, influence bacterial fitness. To better understand the dynamics of pooled versus individual mutant culture, as well as the effect of community structure in microcolony development on the influence of fitness, we adapted a droplet microfluidics-based technique to encapsulate and culture single mutants. We were able to successfully encapsulate at least 7 different species of bacterial pathogens, including Streptococcus pneumoniae, and culture them planktonically, or as microcolonies, in either monodisperse liquid or agarose droplets. These experiments, however, raised an important challenge: the DNA yield from one encapsulation experiment is insufficient to generate samples for sequencing by means of the traditional Tn-seq method. This led us to develop a novel Tn-seq DNA library preparation method, which is able to generate functional Tn-seq library molecules from picogram amounts of DNA. This method is not ideal yet because fitness data generated through the new method currently does not correlate well with data from traditional Tn-seq library preparation. However, we have identified one major culprit that should be easily solvable. We expect by modifying the binding site of the primer used for linear amplification of transposon ends that the new preparation method will be able recapitulate results from the traditional Illumina preparation method for Tn-seq. This will enable us to prepare robust Tn-seq samples from very small amounts of DNA in order to probe stress responses in single mutants as well as in microcolonies in a high-throughput manner. / Thesis (MS) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.