This thesis describes observations, techniques and strategies, which contribute towards the development of nanoparticle based detection and treatment of cancer. Quantum dots and biorecognition molecules were studied towards applications in detection and microgels were used in the rational design of a targeted drug delivery vehicle. The fluorescence intensity of quantum dots was examined in buffers commonly used in molecular biology. The fluorescence intensity of ZnS-capped CdSe quantum dots (QDs) was found to vary significantly, depending on the amount of ZnS capping on the QDs or the concentration, pH and type of buffer the QDs were in. Since fluorescence cannot reliably be used to quantify QDs, an alternative quantification method was developed, which does not rely on their fluorescence. This method employs phage display to identify nanoparticle-specific bacteriophage which were then applied in an assay to quantify QDs in environments where absorbance or fluorescence spectroscopy are ineffective. Biorecognition molecules, which can direct nanoparticles to a molecular target, were also identified through phage display. Phage display on whole cells was used to identify a peptide, which was conjugated with QDs to stain HeLa (cervical cancer) cells. A high-throughput phage display screening strategy was also developed, which could enable the simultaneous identification of multiple biorecognition molecules from a single library. QD-encoded microbead barcodes were conjugated to protein targets and then used to screen a phage display library. The beads and the binding phage were then separated using flow cytometry and fluorescence assisted cell sorting. Finally, biorecognition molecules were combined with nanoparticles to create drug delivery vehicles, which were designed to protect, deliver and then release chemotherapeutic drugs through an intracellular pH trigger. PolyNIPAAm and chitosan hydrogels, under 200 nm in diameter, were loaded with chemotherapeutic drugs, conjugated to transferrin and tested in vitro on HeLa cells. These projects demonstrate the great potential in this growing field as well as some of the many challenges that have yet to be overcome.

This thesis describes observations, techniques and strategies, which contribute towards the development of nanoparticle based detection and treatment of cancer. Quantum dots and biorecognition molecules were studied towards applications in detection and microgels were used in the rational design of a targeted drug delivery vehicle. The fluorescence intensity of quantum dots was examined in buffers commonly used in molecular biology. The fluorescence intensity of ZnS-capped CdSe quantum dots (QDs) was found to vary significantly, depending on the amount of ZnS capping on the QDs or the concentration, pH and type of buffer the QDs were in. Since fluorescence cannot reliably be used to quantify QDs, an alternative quantification method was developed, which does not rely on their fluorescence. This method employs phage display to identify nanoparticle-specific bacteriophage which were then applied in an assay to quantify QDs in environments where absorbance or fluorescence spectroscopy are ineffective. Biorecognition molecules, which can direct nanoparticles to a molecular target, were also identified through phage display. Phage display on whole cells was used to identify a peptide, which was conjugated with QDs to stain HeLa (cervical cancer) cells. A high-throughput phage display screening strategy was also developed, which could enable the simultaneous identification of multiple biorecognition molecules from a single library. QD-encoded microbead barcodes were conjugated to protein targets and then used to screen a phage display library. The beads and the binding phage were then separated using flow cytometry and fluorescence assisted cell sorting. Finally, biorecognition molecules were combined with nanoparticles to create drug delivery vehicles, which were designed to protect, deliver and then release chemotherapeutic drugs through an intracellular pH trigger. PolyNIPAAm and chitosan hydrogels, under 200 nm in diameter, were loaded with chemotherapeutic drugs, conjugated to transferrin and tested in vitro on HeLa cells. These projects demonstrate the great potential in this growing field as well as some of the many challenges that have yet to be overcome.

Bacteriophage Lambda (λ) has played a historical role as an essential model contributing to our current understanding of molecular genetics. Lambda’s major capsid protein “gpD” occurs on each capsid at 405 to 420 copies per phage in homotrimeric form and functions to stabilize the head and likely to compact the genomic DNA. The interesting conformation of this protein allows for its exploitation through the genetic fusion of peptides or proteins to either the amino or carboxy terminal end of gpD, while retaining phage assembly functionality and viability. The lytic nature of λ and the conformation of gpD in capsid assembly makes this display system superior to other display options. Despite previous reports of λ as a phage display candidate, decorative control of the phage remains an elusive concept. The primary goal of this study was to design and construct a highly controllable head decoration system governed by two genetic conditional regulation systems; plasmid-mediated temperature sensitive repressor expression and bacterial conditional amber mutation suppression. The historical λ Dam15 conditional allele results in a truncated gpD fragment when translated in nonsuppressor, wild-type E. coli cells, resulting in unassembled, nonviable progeny. I sequenced the Dam15 allele, identifying an amber (UAG) translational stop at the 68th codon. Employing this mutant in combination with a newly created isogenic cellular background utilizing the amber suppressors SupD (Serine), SupE (Glutamine), SupF (Tyrosine) and Sup— (wild type), we sought to control the level of incorporation of undecorated gpD products. As a second dimension, I constructed two separate temperature-inducile plasmids whereby expression of either D or D::eGFP was governed by the λ strong λ CI[Ts]857 temperature-sensitive repressor and expressed from the λ PL strong promoter. Our aim was to measure the decoration of the λ capsid by a D::gfp fusion under varying conditions regulated by both temperature and presence of suppression. This was achieved utilizing this controllable system, enabling the measurement of a variable number of fusions per phage based on diverse genetic and physical environments without significantly compromising phage viability. Surprisingly, both SupE and SupF showed similar levels of Dam15 suppression, even though sequencing data indicated that only SupE could restore the native gpD sequence at amino acid 68 (Q). In contrast, SupD (S), conferred very weak levels of suppression, but imparted an environment for very high decoration of gpD::eGFP per capsid, even at lower (repressed) temperatures. The presence of albeit few wild-type gpD molecules allowed for an even greater display than that of the perceived “100%” decoration scenario provided by the nonsuppressor strain. It appears that the lack of wild-type gpD does not allow for the space required to display the maximum number of fusions and in turn creates an environment that affects both phage assembly and therefore phage viability. Finally, the use of Western blotting, confirmed the presence of gpD::eGFP fusion decoration by employing a polyclonal anti-eGFP antibody. The significance of this work relates to the unique structure of λ’s capsid and its ability to exploit gpD in the design of controlled expression, which is guiding future research examining the fusion of different therapeutic peptides and proteins. Furthermore this approach has important implications specifically for the design of novel vaccines and delivery vehicles for targeted gene therapy in which steric hindrance and avidity are important concerns. The execution of this project employed basic bacterial genetics, phage biology and molecular biology techniques in the construction of bacterial strains and plasmids and the characterization of the phage display system.

Durch die wachsende Anzahl von multiresistenten Bakterien, die auch durch den Mißbrauch von Antibiotika als Masthilfsmittel in der Tierzucht entstanden sind, erlangen alternative Methoden zur Bekämpfung bakterieller Infektionen ihre Bedeutung zurück. Diese Arbeit befaßt sich mit zwei Substanzen, um Infektionen mit Yersinia (Y.) enterocolitica einzudämmen. Es wurde in dieser Arbeit ein Bacteriocin aus Y. enterocolitica isoliert und charakterisiert. Das Reinigungschema folgte den Strategien der Phagenaufreinigung, angeschlossen wurde zur Überprüfung der Reinheit ein Gelfiltrationsschritt. Die Eigenschaften des gereinigten Enterocoliticins wurden in vitro und in vivo getestet. Im Zellkulturversuch zeigte sich das Enterocoliticin in der Abtötung von an eukaryonte Zellen adhärierten Bakterien als sehr wirksam, in eukaryonte Zellen eingewanderte Bakterien wurden hingegen nicht abgetötet. Aufgrund dieser vielversprechenden Ergebnisse wurde der Therapieansatz im Mausmodell angewendet. Das Mausmodell ist für Y. enterocolitica ein bereits erprobtes Modell. Die Tiere wurden oral infiziert, um den natürlichen Infektionsweg nachzustellen, das Enterocoliticin wurde ebenfalls oral verabreicht. Die Infektion wurde durch die Enterocoliticingabe nur unwesentlich beeinflußt, auch gelang der Nachweis des Enterocoliticins weder im Gastrointestinaltrakt noch in den Faeces. Die Therapie der infizierten Mäuse gelang auf diese Weise nicht. Weiterhin wurde ein Yersinia-Phage aus Schweinegülle isoliert, gereinigt und charakterisiert. Es handelt sich um einen T4-ähnlichen, virulenten Phagen mit einer Genomgröße von ca. 50 kbp und einem weiten Wirtsspektrum in Yersinia, das sogar speziesübergreifend ist. Da der Phage bei 37°C die Wirtszelle lysiert und durch seine hohe Wirksamkeit in vitro erschien der Phage von seinen Eigenschaften her zur Phagentherapie als geeignet. Es wurden analog zum Enterocoliticin-Tierexperiment Mäuse mit Y. enterocolitica oral infiziert, diesen Tieren wurde der Phage auf unterschiedlichen Wegen und zu unterschiedlichen Zeitpunkten appliziert. Die Tiere zeigten bei der parenteralen Gabe keinerlei Unverträglichkeitserscheinungen, bei der oralen Gabe wurde der Magensaft zuvor abgepuffert. Der Therapieerfolg im Vergleich zur Kontrollgruppe war wenig vielversprechend, es zeigten sich sehr ähnliche Infektionsverläufe in Kontroll-und Therapiegruppe. Diese beiden untersuchten Alternativwege zur Behandlung von Yersiniosen erwiesen sich bei den angewendeten Methoden bislang als nicht erfolgreich, dennoch muß auf diesem Gebiet weitergeforscht werden, wie erfolgreiche Therapieansätze aus anderen Tiermodellen zeigen. Es wirken nur wenige Phagen im Organismus als Therapeutikum, dennoch müssen diese Untersuchungen unternommen werden, um im Organismus wirksame, antibakterielle Substanzen zu finden und um einen Alternativweg zur Antibiotikumtherapie zu entwickeln. / The increasing number of multi-resistant bacteria, which resulted also from the abuse of antibiotics as mast additives in animal breeding, alternative methods regain importance for the combat at bacterial infections back. In this work two substances were investigated to restrict infections with Yersinia (Y.) enterocolitica. In this study a bacteriocin from Y. enterocolitica, designated enterocoliticin, was isolated and characterized. The purification strategy followed protocols of phage isolation. The purified preparations were examined by final gel filtration step. The properties of the purifed enterocoliticin were tested in vitro and in vivo. In a cell culture assay enterocoliticin was able to kill bacteria adherent to eukaryontic cells very effectively, however, bacteria invaded into eukaryotic cells were not affected. Due to these results enterocoliticin was applied in a mouse-infection-model in a therapeutic attempt. The mouse infection model is a well established system for infections with Y. enterocolitica. The animals were orally infected with Yersinia, and the enterocoliticin was orally applied, too. The infection was only insignificantly influenced by enterocoliticin. In addition of enterocoliticin was not detected succeeded in the gastro-intestinal-tract or in the faeces. The therapy of the infected mice did not succeed in this way. Furthermore, a Yersinia phage from pig manure was isolated and characterized. It is a T4 phage like virulent phage, containing a genom of approx. 50 kbp and posessing a wide host-range in Yersinia. Because of lytic properties of the phage at 37°C and his high effectiveness in vitro the phage appeared to be for phage therapy experiments. Similarly to the enterocoliticin experiment mice were infected with Y. enterocolitica orally, these animals were treated with the phage on different application routes and different time points. The animals did not show any incompatibilities upon parenteral gift. Before oral administration of the phage the gastric juice was buffered. Therapy outcome in comparison to the control group was little promising, it revealed a very similar infection process in control group and therapy group. These two investigated alternative ways for the control of Yersinia infections did not prove successful with the applied methods, however, further research must be carried out as successful therapeutical experiments from other animal models showed. It has to be considered that not all phages are appropriate as therapeutical agent however, more studies must be conducted to find more appropriate substances, which may work as effective antibacterial substances to develop alternative ways to antibiotic therapy.

The research detailed in this dissertation is focused on the use of biomolecules (i.e., peptides and proteins) to form non-biologically produced materials under mild reaction conditions (i.e, neutral pH, aqueous solutions, and room temperature). The peptides utilized in the studies detailed in this dissertation were identified through the screening of single crystal rutile TiO2 substrates or Ge powder with a phage-displayed peptide library. Twenty-one peptides were identified which possessed an affinity for Ge. Those peptides possessing a basic isoelectric point as well as hydroxyl- and imidazole-containing amino acid residues were found to be the most effective in precipitating amorphous germania from an alkoxide precursor. The phage-displayed peptide library screening of TiO2 substrates yielded twenty peptides. The titania formation activity of these peptides was found to correlate with the number of positive charges they carried. The titania materials generated by the library-identified and designed peptides were found to be composed of amorphous titania as well as <10 nm anatase and/or monoclinic TiO2 crystallites. Four recombinant proteins, derived from the amino acid sequences of proteins (silaffins) associated with biosilicification in diatoms, were also investigated for titania precipitation activity. The two most basic of these recombinant silaffins, rSil1L and rSilC, were able to induce the formation of titania. The titania precipitates generated by rSil1L were found to be similar to those produced by the phage-displayed library identified peptides. The second recombinant silaffin, rSilC, was found to produce hollow spheres of titania, which, following dehydration, were observed to transform into larger, solid spheres composed of radially aligned columns of rutile TiO2. The highly repetitive nature of the rSilC s amino acid sequence is believed to be responsible for the differences in TiO2 polymorph generated by the different recombinant silaffins and peptides. This dissertation also details research conducted on the formation of titania utilizing rSilC conjugated to synthetic and biogenic silica surfaces. These silica surfaces were functionalized with a newly developed drendritic growth technique. The dendritic functional-group amplification process was demonstrated to increase the loading of hexahisitidine tagged proteins on silica surfaces by more than 40%, as compared to traditional immobilization procedures.

The recent development of methods for constructing andhandling large collections (libraries) of proteins, from whichvariants with desired traits can be isolated, hasrevolutionized the field of protein engineering. Key elementsof such methods are the various ways in which the genotypes(the genes) and the phenotypes (the encoded proteins) arephysically linked during the process. In one section of thework underlying this thesis, one such technique (phagedisplay), was used to isolateand identify protein librarymembers based on their catalytic or target molecule-bindingproperties. In a first study, phage display libraries of the lipolyticenzyme Lipolase from Thermomyces lanuginosa were constructed,the objective being to identify variants with improvedcatalytic efficiency in the presence of detergents. Toconstruct the libraries, nine positions were targeted for codonrandomization, all of which are thought to be involved in theconformational change-dependent enzyme activation that occursat water-lipid interfaces. The aim was to introduce two tothree amino acid mutations at these positions per lipase gene.After confirming that the wt enzyme could be functionallydisplayed on phage, selections with the library were performedutilizing a mechanism-based biotinylated inhibitor in thepresence of a detergent formulation. According to rhodamineB-based activity assays, the fraction of active clonesincreased from 0.2 to 90 % over three rounds of selection.Although none of the variants selected using this approachshowed increased activity, in either the presence or absence ofdetergent compared to the wild type enzyme, the resultsdemonstrated the possibility of selecting variants of theenzyme based on catalytic activity. In the following work, phage libraries of the StaphylococcalProtein A (SPA)-derived Z-domain, constructed by randomizationof 13 surface-located positions, were used to isolate Z domainvariants (affibodies) with novel binding specificities. Astargets for selections, the parental SPA domains as well as twopreviously selected affibodies directed against two unrelatedtarget proteins were used. Binders of all three targets wereisolated with affinities (KD) in the range of 2-0.5 µM.One SPA binding affibody (ZSPA-1) was shown to bind to each of the fivehomologous native IgG-binding domains of SPA, as well as theZdomain used as the scaffold for library constructions.Furthermore, the ZSPA-1affibody was shown to compete with one of thenative domains of SPA for binding to the Fc part of humanantibodies, suggesting that the ZSPA-1affibody bound to the Fc-binding surface ofthe Z domain. The majority of the affibodies isolated in theother two selections using two different affibodies as targets,showed very little or no binding to unrelated affibodies,indicating that the binding was directed to the randomizedsurface of their respective targets, analogously toanti-idiotypic antibodies. The structure of the wild type Z domain/ZSPA-1affibody co-complex was determined by x-raycrystallography, which confirmed the earlier findings in thatthe affibody ZSPA-1affibody was shown to bind to the Fc bindingsurface of the Z domain. Further, both the Z domain and the ZSPA-1affibody had very similar three helix-bundletopologies, and the interaction surface involved ten out of thethirteen randomized residues, with a central hydrophobic patchsurrounded by polar residues. In addition, the interactionsurface showed a surprisingly high shape complementarity, giventhe limited size of the library used for selections. The ZSPA-1affibody was further investigated for use invarious biotechnological applications. In one study, the ZSPA-1affibody was successfully recruited as a novelaffinity gene fusion partner for production, purification anddetection of cDNA-encoded recombinant proteins using anSPA-based medium for affinity chromatography. Further, the SPAbinding capability of the ZSPA-1affibody was employed for site-specific andreversible docking of ZSPA-1affibody-tagged reporter proteins onto an SPAfusion protein anchored to a cellulose surface via acellulose-binding moiety. These generated protein complexesresembles the architecture of so-called cellulosomes observedin cellulolytic bacteria. The results suggest it may bepossible to use anti-idiotypic affibody-binding protein pairsas modules to build other self-assembling types of proteinnetworks. Keywords:phage display, selection, mechanism-basedinhibitor, affinity domains, crystal structure, Staphylococcusaureus protein A, affinity chromatography, anti-idiotypicbinding pairs, affibody, combinatorial, protein engineering,lipase, cellulosome, assembly.

Bovine anaplasmosis is caused by Anaplasma marginale and A. centrale. The most pathogenic and important species for cattle production is A. marginale, and is widely distributed in tropical, subtropical and temperate regions of the world. A. marginale is an intra-erythrocyte rickettsia of susceptible ruminants, biological and mechanically transmitted by ticks and hematophagous insects. The tick Rhipicephalus (Boophilus) microplus is the main vector of A. marginale in Brazil. The congenital form of transmission in cattle may occur, causing the neonatal anaplasmosis. The outer membrane of A. marginale includes six well characterized major surface proteins, MSP1a, MSP1b, MSP2, MSP3, MSP4 and MSP5, which play important role in the development of the immune response of infected animals. In this study, we have used the Phage Display technology to identify specific peptides that were immunoreactive to monoclonal antibodies anti-A. marginale proteins. Peptide selection was performed using a subtractive selection of a peptide library with 12 random amino acids, Ph.D.-12, expressed on the surface of the M13 filamentous phage concurrently against the anti-MSP1a and anti-MSP2. After four rounds of selection and validation by ELISA, the selected peptides have recognized only the anti-MSP1. Analysis of bioinformatics identified 45 peptides, which showed the protein consensus sequence STxS that was represented in 78% of selected phages. Due to the multiple motif repeats found in MSP1 protein, the STSSxL motif may become an important biological target, with potential use in diagnostic tests and vaccine for the control of Anaplasma marginale. / Anaplasmose bovina é uma infecção causada por Anaplasma marginale e A. centrale. A espécie mais patogênica e de maior importância para bovinos é a A. marginale e está amplamente distribuída nas regiões tropicais, subtropicais e temperada do mundo. A. marginale é uma rickettsia intraeritrocitária de ruminantes susceptíveis, transmitido biológica e mecanicamente por carrapatos e insetos hematófagos. O carrapato Rhipicephalus (Boophilus) microplus é o principal transmissor de A. marginale no Brasil. A forma congênita de transmissão em bovinos pode ocorrer, ocasionando a anaplasmose neonatal. A membrana externa do A. marginale inclui seis proteínas principais de superfície (MSPs) bem caracterizadas, designadas de MSP1a, MSP1b, MSP2, MSP3, MSP4 e MSP5 e desempenham papel importante no desenvolvimento da resposta imune de animais infectados. Para o desenvolvimento deste estudo, foi utilizada a técnica de Phage Display para identificar peptídeos ligantes a anticorpos monoclonais reativos a proteínas de Anaplasma marginale a partir de bibliotecas de peptídeos recombinantes por meio da tecnologia Phage Display. Para seleção dos peptídeos foi realizado uma seleção subtrativa utilizando uma biblioteca de peptídeos com 12 aminoácidos randômicos, Ph.D.-12, expressa na superfície do fago filamentoso M13 concomitantemente contra os anticorpos anti-MSP1a e anti-MSP2. Após quatro ciclos de seleção e validação por ELISA, o conjunto de peptídeos selecionados apresentou ser unicamente reconhecido pelo anticorpo anti- MSP1. Análises de bioinformática identificaram 45 peptídeos, que apresentaram o motivo proteico consenso STxS, representado em 78% dos fagos seqüenciados. Devido aos múltiplos sítios repetidos encontrados na proteína MSP1, o motivo proteíco STSSxL pode ser um importante alvo biológico, com potencial utilização em ensaios diagnósticos e vacinais para o controle de Anaplasma marginale. / Mestre em Genética e Bioquímica

Mu is a temperate bacteriophage which infects Escherichia coli and several other Gram negative enteric bacteria. It is an extraordinary phage in several respects and has carved a special niche for itself both as a genetic tool and a paradigm in phage biology, almost rivaling phage lambda. It is also a predator that has adapted its hunting skills well in order to have an extraordinarily wide host range. While phage Mu finds a mention in almost every genetics textbook for several of its unique and well-studied characteristics, there are a few aspects of its biology that are far from understood. In this thesis, light has been shed on one such less understood feature of Mu biology, namely its anti-restriction function. The enigmatic mom gene of bacteriophage Mu is the center of this thesis work. Bacteriophages, through their sheer number and versatility of attack tactics, constitute an overwhelming threat to bacteria in the natural environment. While it is not always possible to completely prevent the entry of foreign DNA into the cell, it is in the interest of the bacterium to tame the xenogeneic DNA, whose expression may have adverse effects on bacterial fitness. Bacterial nucleoid associated proteins (NAPs) participate in chromosome structuring and global transcriptional regulation. Besides this canonical role, they furnish the job of regulating xenogeneic DNA as well. NAPs are known to regulate the expression of toxin-antitoxin modules, pathogenicity islands and other horizontally transferred DNA and have a profound role in regulating transposon dynamics and the lifestyle of many phages. Chapter 1 introduces the role of bacterial NAPs in silencing foreign DNA, especially after the DNA establishes itself in the host. This thesis examines the role of a bacterial NAP namely Fis in fine-tuning an immune evasion function of bacteriophage Mu. A general introduction to phage Mu and its host expansion strategies, with special focus on its DNA modification function is also presented. Owing to the various immune evasion strategies, phages often have an upper hand on their hosts in the ongoing evolutionary arms race. One such strategy is DNA modification which bacteriophages have evolved as a means to protect their genomes from restriction enzymes of the host. While most phages employ the commonplace methylation modification for their anti-restriction function, phage Mu employs an unusual acetamido modification, catalysed by its protein Mom. Mom modified DNA is refractory to several restriction enzymes from different bacterial species. However, the modification is toxic to the host and thus mom expression needs to be precisely regulated to prevent untimely expression. A crowded multifactorial regulatory circuit has evolved to ensure the expression of mom without jeopardizing the welfare of the bacterial host. Chapter 2 uncovers a new player in mom regulation. The study shows that the bacterial chromatin architectural protein Fis is a transcriptional repressor of mom promoter and that Fis mediates its repressive effect by denying access to RNA polymerase at mom promoter. Two distinct roles of Fis have been known previously in Mu biology. In addition to bringing about the overall downregulation of transposition events and transcription of early genes of phage Mu, Fis also stimulates tail fiber flipping by aiding the activity of a site-specific recombinase. The present study thus presents a novel facet of Fis function in Mu biology. While the regulation of mom has been a matter of intense investigation over the past few decades, most biochemical and structural aspects of the Mom protein per se have remained mysterious owing to the difficulties in cloning this toxic gene. Chapter 3 describes the expression, purification and biophysical characterization of Mom. A variety of techniques show Mom to be folded and dimeric in solution. SPR studies with Mom indicate its high affinity binding to DNA. Chapter 4 deals with the attempts to identify the elusive co-factor of Mom. To begin with, the in vivo activity of Mom was demonstrated by employing a simple plasmid cleavage assay based on the resistance of Mom modified DNA to certain restriction endonucleases. A variety of disparate in silico structure prediction tools such as I-TASSER, Robetta and PHYRE indicate Mom to be related to the GCN5-related N-acetyltransferase superfamily. Mutation of residues deemed important from this analysis indeed abolished or reduced Mom activity in vivo, validating the bioinformatics based prediction and shed light on the possible active site of Mom. However, acetyltransferases are not known to transfer acetamido groups. It was also necessary to establish beyond doubt, the chemical structure of the Mom modified nucleoside. High resolution mass spectrometry data showed the modification to be acetamido, corroborating the earlier sole report on this aspect. Based on the biochemical reactions that acetyl coenzyme A is known to participate in, it is difficult to explain the involvement of acetyl coenzyme A in acetamido addition. Notwithstanding the converging predictions of different bioinformatics tools, caution is recommended when inferring function from structurally similar family members. It is possible that a different chemistry might have converged on the same (acetyltransferase) fold, given that none of the known pathways utilizing acetyl coenzyme A can explain the Mom modification. Several likely candidates such as carboxy-SAM, glyoxylic acid and glycine were also tested for being donors of the two carbon entity transferred on adenine by Mom. Since these candidates tested negative in our genetic assays, a genome-wide genetic screen was subsequently devised to identify the host genes involved in mom modification. The assay exploited the phenotype of lethality associated with overexpression of Mom in E. coli in order to screen for mutations in the host genome that rescued the toxicity. However, the survivors which were obtained in this assay had emerged through mutations in the mom gene rather than abrogation of the co-factor synthesis pathway of the host. The results point at two possibilities: (i) utilization of essential gene(s) or (ii) existence of redundant pathways for the Mom modification reaction. Chapter 5 is an account of our attempts to trace the lineage of mom and its regulatory region, employing updated DNA and protein sequence databases. Despite the selective advantage conferred on the phage by the anti-restriction function of mom, in many Mu-like phages, mom is either absent or substituted with methyltransferases. However, in Mu-like genomes that do encode mom, in spite of a significant overall sequence divergence from Mu, the core elements of the mom regulatory circuit seem to have either co-evolved or have been selectively conserved. Although Mu appears to be unique in the possession of a regulatory circuit tailored for the purpose of mom regulation, recently discovered Mu-like genomes show that different types of regulatory features evolved several times in closely related genomes. It is very likely that a toxic gene like mom has earned its place in the phage genome by carrying along with itself a baggage of regulatory elements. Failure to sustain sufficient regulatory pressure may trigger the loss or replacement of the advantageous but potentially lethal mom function.

Les cyanobactéries sont des micro-organismes qui préoccupent les autorités de santé publique dans le monde entier, en raison de la toxicité des cyanotoxines qu'elles produisent. Certaines cyanotoxines dont les microcystines (MC) sont des hépatotoxines inhibitrices de protéines phosphatases à sérine/thréonine. Aujourd'hui, plus de 200 variants de MCs ont été identifiés. Il s'agit d'heptapeptides monocycliques synthétisés par voie non-ribosomale dont la MC-LR (cyclo- (D-Ala-L-Leu-D-érythro-β-méthylAsp-L-Arg-ADDA-D-Glu-N-méthyl-hydro-Ala) est le variant le plus étudié en raison de sa fréquence et de sa forte toxicité. L’objectif de cette étude est le développement d'une méthode d'immunoanalyse rapide, sensible et fiable pour détecter les MCs. Le projet vise donc à développer un outil alternatif de détection de la MC-LR, qui serait mieux adapté aux analyses sur le terrain que les méthodes analytiques, biologiques ou les méthodes d'inhibition d'activité enzymatique actuellement disponibles. L'originalité de ce projet réside dans l'utilisation de deux approches différentes pour sélectionner de nouveaux anticorps spécifiques de la MC-LR. La première repose sur l'immunisation d'animaux de laboratoire, la technologie d'hybridation cellulaire et la sélection d'hybridomes sécréteurs d'anticorps monoclonaux. Si la méthodologie mise en œuvre a effectivement permis d'obtenir des immun-sérums spécifiques, la sélection des hybridomes d'intérêt reste à optimiser. La seconde stratégie mise en œuvre est basée sur la technologie du phage display pour sélectionner des fragments d'anticorps spécifiques de MC-LR à partir d'une banque de taille d’environ 109 phages, exprimant en surface des anticorps sous un format scFv (Shahsavarian et al., 2014). Plusieurs méthodes de criblage ont été développées et trois scFv ont été sélectionnés et étudiés, parallèlement à un quatrième scFv identifié dans une étude précédente (McElhiney et al., 2002), tous spécifiques à la MC-LR. Ces scFv ont été produits sous forme libre, soluble et leur spécificité à la MC-LR a été évaluée par ELISA et résonance plasmonique de surface. Les résultats obtenus montrent que les scFv sélectionnés sont tous capables de reconnaître la MC-LR. Néanmoins, ces résultats sont peu reproductibles et remettent en question le protocole de renaturation utilisé. Un travail de fond sur l’optimisation du protocole de renaturation s’avèrerait nécessaire pour les scFv ici sélectionnés, afin d’identifier les paramètres précis aboutissant à la perte ou au gain de leur fonctionnalité. / Cyanobacteria are ubiquitous microorganisms that present a worldwide concern to public health authorities because of the toxicity of the cyanotoxins they produce. Some cyanotoxins are hepatotoxins such as microcystins (MCs). At least 200 variants of MCs have been identified till today. In our study, we focus on MC-LR, a monocyclic heptapeptide (cyclo-(D-Ala-L-Leu-D-erythro-β-methylAsp-L-Arg-ADDA-D-Glu-N-methyldehydro-Ala), since it is the most frequently detected and one of the most toxic. In our study, we are interested in developing a fast, sensitive and reliable method to detect MCs. The project aims to develop an alternative pollution detection method that would be better suited to field measurements than the physicochemical methods currently available. The originality of this project lies in the use of two different approaches to select a panel of antibodies suitable for the development of immunodetection tests. The first one is based on the hybridoma technology for the production of monoclonal antibodies. The second one is based on phage display technique to select antibody fragments that are specific to MC-LR from a library of approximately 109 phages, expressing on the surface scFv fragments (Shahsavarian et al., 2014). Two monoclonal antibodies were selected using the first approach, and their specificity was evaluated using ELISA technique. Along with three scFvs selected from phage display approach. An additional scFv was added to this list: 3A8, selected from a previous study (McElhiney et al., 2002) and also specific to MC-LR. The scFvs were cloned into an expression vector in order to get each clone in its scFv soluble form. Then, their specificity to MC-LR was evaluated using ELISA technique and Surface plasmon resonance. The results show a potential specificity to MC-LR. Nevertheless, these results are not very reproducible and call into question the refolding protocol used. A thorough work on this protocol optimization would be necessary, in order to find the key parameters that control the loss or gain of their functionality

No description available.