Šiame darbe tirta TetA ir AcrAB siurblių veikla Escherichia coli ląstelėse, panaudojant lipofilinius tetrafenilfosfonio (TPP+) jonus bei mikrobiologiniais ląstelių gyvybingumo tyrimo metodais įvertintas pasirinktų E. coli padermių jautrumas tetraciklinui. Buvo nustatyta, kad atspariausios tetraciklinui yra IQ86 ląstelės, transpozone Tn10 turinčios TetA siurblį koduojančius genus. Registruodami TPP+ pasiskirstymą tarp ląstelių ir jų inkubacinės terpės, nustatėme, kad tetraciklinas didina E. coli ląstelių išorinės membranos (IM) laidumą lipofiliniams junginiams. EDTA pagalba pralaidinus E. coli ląstelių IM, tetraciklinas lengviau patenka į ląstelę. Tai rodo, kad šis antibiotikas į ląstelę patenka ne tik per porinus, bet ir prasiskverbdamas per IM lipidinį dvisluoksnį. TPP+ jonus iš E.coli ląstelių išmetinėjantys DVA siurbliai taip pat sąveikauja ir su tetraciklinu bei chloramfenikoliu. Inkubuojant ląsteles su tetraciklinu, indukuojama šį antibiotiką išstuminėjančio TetA siurblio genų raiška. Vienok, inkubacija su tetraciklinu gali sutrikdyti kitų E. coli ląstelėse esančių DVA siurblių veiklą. Rezerpinas ir chlorpromazinas efektyviai slopina tetracikliną iš ląstelių išstuminėjančių siurblių veiklą, o fenilalanin-arginin- naftilamidas E. coli ląstelių atveju nepasižymi DVA siurblius slopinančiu poveikiu. Nustatyta, kad DVA siurblių slopiklių poveikis stipresnis, kai jie sąveikauja su ląstelėmis terpėje be antibiotikų. / We used lipophilic tetraphenilphosphonium (TPP+) ions for functional analysis of multidrug resistance (MDR) pumps TetA and AcrAB in Escherichia coli cells. We have found that tetracycline increases the cell outer membrane permeability to lipophilic compounds. Tetracycline entered the cells faster when the bacterial outer membrane was permeabilized using EDTA. These results indicate that tetracycline enters the cell not only through the porins, but also it penetrates the lipid bilayer of the outer membrane. MDR pumps extruding TPP+ ions from E. coli cells, also interact with tetracycline and chloramphenicol. Genes of TetA pump are induced, when the cells are incubated with low concentrations of tetracycline. On the other hand, incubation of the cells with tetracycline disturbs the activity of others MDR pumps in E. coli. Reserpine and chlorpromazine effectively inhibit activity of tetracycline-extruding MDR pumps, but Phe-Arg-β-naphtylamide does not show any inhibitory activity. Finally, it has been shown that action of the MDR pump inhibitors is stronger, when they are added to the bacterial suspension in the absence of antibiotics.

L’objet de ces recherches était de trouver de nouveaux EPIs du système d’efflux AcrAB-TolC dans les groupes de dérivés d’amine de la 5-arylidenehydantoine et de la 5-arylideneimidazolone. Dans la première étape de recherche, 32 nouveaux dérivés ont été obtenus après modification de la structure lead P2.Un screening théorique du risque toxique et la prédiction des propriétés médicamenteuses des composés ont été réalisés en utilisant le programme OSIRIS qui calcule différentes propriétés médicamenteuses pertinentes basées sur la structure planaire de la molécule.Dans l’étape suivante de la recherche, l’activité des composés a été évaluée par des études microbiologiques sur souches d’Enterobacter aerogenes avec différentes expressions de la pompe d’efflux AcrAB. La première étude effectuée était un test de sensibilité pour déterminer les CMI des composés afin de trouver une concentration à laquelle les utiliser avec des antibiotiques sans avoir l’influence de leur activité intrinsèque. Puis l’effet des composés sur la sensibilité des antibiotiques tels que l’acide nalidixique, le chloramphénicol, la doxycycline et l’érythromycine a été étudié. Après, le type de coopération avec les antibiotiques a été déterminé par la construction d’isobologrammes et le calcul de l’index de FIC. Les dernières études microbiologiques réalisées sont des tests d’efflux en temps réel qui utilisent un colorant fluorescent 1,2’-dinaphthylamine et ont permis de suivre directement le fonctionnement de la pompe. L’étude des relations structure-activité souligne le rôle essentiel de la nature amphiphile des EPIs dérivés de groupes arylidene de l’hydantoine et de l’imidazolone. / The purpose of this research was to find new EPIs of the AcrAB-TolC efflux system in groups of amine derivatives of 5-arylidenehydantoin and 5-arylideneimidazolone. In the first stage of the research 32 new derivatives of 5-arylidenehydantoin were obtained as a result of modifications of the lead structure P2. Theoretical screening of the toxicity risk as well as the prediction of drug-like properties of hydantoins/imidazolones synthesised were performed by using the OSIRIS program which calculates various drug-relevant properties based on a planar structure of the molecule.In the next stage of the research the activity of compounds was evaluated in microbiological studies. Strains of Enterobacter aerogenes with different expressions of the AcrAB efflux pump were used. The first study carried out was a susceptibility test determining the MICs of compounds in order to find a concentration that could be used in combination with antibiotics without the influence of an intrinsic antibacterial activity of the compounds. Then the effect of the compounds on bacterial susceptibility to antibiotics such as nalidixic acid, chloramphenicol, doxycycline and erythromycin was examined. After, the type of cooperation with antibiotics was determined based on isobolograms and the FIC index calculated. The last of microbiological studies was the real-time efflux (RTE) assay which used the fluorescent dye 1,2’-dinaphthylamine and allowed the functioning of the pump to be monitored directly. The structure-activity relationship (SAR) analysis emphasized the essential role of the amphiphilic nature of the EPIs from the group of arylidene derivatives of hydantoin and imidazolone.

abstract: Synechocystis sp. PCC 6803 is a readily transformable cyanobacteria used to study cyanobacterial genetics, as well as production of biofuels, polyesters, and other industrial chemicals. Free fatty acids are precursors to biofuels which are used by Synechocystis cells as a means of energy storage. By genetically modifying the cyanobacteria to expel these chemicals, costs associated with retrieving the products will be reduced; concurrently, the bacteria will be able to produce the products at a higher concentration. This is achieved by adding genes encoding components of the Escherichia coli AcrAB-TolC efflux system, part of the resistance-nodulation-division (RND) transporter family, to Synechocystis sp. PCC 6803. AcrAB-TolC is a relatively promiscuous multidrug efflux pump that is noted for expelling a wide range of substrates including dyes, organic solvents, antibiotics, and free fatty acids. Adding components of the AcrAB-TolC multidrug efflux pump to a previously created high free fatty acid producing strain, SD277, allowed cells to move more free fatty acids to the extracellular environment than did the parent strain. Some of these modifications also improved tolerance to antibiotics and a dye, rhodamine 6G. To confirm the function of this exogenous efflux pump, the genes encoding components of the AcrAB-TolC efflux pump were also added to Synechocystis sp. PCC 6803 and shown to grow on a greater concentration of various antibiotics and rhodamine 6G. Various endogenous efflux systems have been elucidated, but their usefulness in expelling products currently generated in Synechocystis is limited. Most of the elucidated pumps in the cyanobacteria are part of the ATP-binding cassette superfamily. The knowledge of the resistance-nodulation-division (RND) family transporters is limited. Two genes in Synechocystis sp. PCC 6803, slr2131 and sll0180 encoding homologs to the genes that encode acrB and acrA, respectively, were removed and the modifications resulted in changes in resistance to various antibiotics and a dye and also had an impact on free fatty acid secretion. Both of these deletions were complemented independently with the homologous E. coli gene and the resulting cyanobacteria strains had some of the inherent resistance restored to chloramphenicol and free fatty acid secretion was modified when compared to the wild-type and a high free fatty acid producing strain. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2018

Submitted by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-04-16T14:40:02Z No. of bitstreams: 1 FernandaNomiyamaFigueiredoDissertacao2018.pdf: 2178476 bytes, checksum: 23f38c14567d00ff189eaef20f904495 (MD5) / Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-04-16T14:40:47Z (GMT) No. of bitstreams: 1 FernandaNomiyamaFigueiredoDissertacao2018.pdf: 2178476 bytes, checksum: 23f38c14567d00ff189eaef20f904495 (MD5) / Made available in DSpace on 2018-04-16T14:40:47Z (GMT). No. of bitstreams: 1 FernandaNomiyamaFigueiredoDissertacao2018.pdf: 2178476 bytes, checksum: 23f38c14567d00ff189eaef20f904495 (MD5) Previous issue date: 2018-03-06 / Klebsiella pneumoniae is one of the main bacterial agents that may cause infections related to health care assistance. K. pneumoniae frequently carries the resistance gene K. pneumoniae carbapenemase (KPC). Currently, tigecycline can be considered one of the last therapeutic options for KPC, but reports of tigecycline-resistant KPC isolates are on the rise, being indicated as most common mechanism the increased AcrAB-TolC efflux pump system expression. However, molecular tigecycline resistance mechanisms associated to AcrAB-TolC still remains obscure. Thus, the main goal of this study was to verify if tigecycline resistance can be related to the presence of mutations in the regulatory genes of AcrAB-TolC, AcrR and RamR. Therefore, 32 K. pneumoniae isolates were used, identification and antibiogram performed using Vitek 2 systems. The minimum inhibitory concentrations were confirmed using E-test. Primers were designed in order to verify mutations within AcrR and RamR genes. PCR analysis showed that the mutations found within these genes were transversions (94% for AcrR and 90% for RamR) and transitions (6% for AcrR and 10% for RamR). Nevertheless among the mutations, no distinction between tigecycline susceptible and resistant isolates was found. Some of the transversions caused change in the amino acid encoding 6 in AcrR and 15 in RamR. Presence of these types of mutations evaluation can be seen as the first bacterial resistance study step, as it may be caused by oxidative damage for bacterial DNA, frequently caused by antibiotic selective pressure. Tigecycline resistance found in this study`s clinical isolates may be associated to alterations in another genes that can trigger mechanisms associated to this antibiotic. / Klebsiella pneumoniae consiste em um dos principais agentes bacterianos causadores de infec????es relacionadas ?? assist??ncia ?? sa??de (IRAS). K. pneumoniae carrega frequentemente o gene de resist??ncia K. pneumoniae carbapenemase (KPC). Atualmente, a tigeciclina pode ser considerada uma das ??ltimas op????es terap??uticas para KPC, mas os relatos de isolados de KPC resistentes a tigecilina est??o em ascens??o, sendo a hiperexpress??o da bomba de efluxo AcrAB-TolC indicado como mecanismo mais comum. No entanto, os mecanismos moleculares de resist??ncia ?? tigeciclina associada ao AcrAB-TolC permanecem obscuros. Desta forma o objetivo deste trabalho foi verificar se a resist??ncia a tigeciclina pode estar relacionada ?? presen??a de muta????es nos genes ArcR e RamR, reguladores de AcrAB-TolC. Para tanto, 32 isolados de K. pneumoniae foram utilizados, sendo a identifica????o e o antibiograma feitos utilizando o sistema Vitek 2. A confirma????o das concentra????es inibit??rias m??nimas (CIMs) foram realizadas por E-test. Iniciadores foram desenhados para verifica????o de muta????es nos genes (AcrR e RamR). As an??lises por PCR mostraram que as muta????es encontradas nos genes AcrR e RamR foram substitui????es por transvers??o (94% e 90% para AcrR e RamR respectivamente) e transi????o (6% e 10% para AcrR e RamR respectivamente), por??m n??o foi identificada distin????o da presen??a de muta????es entre isolados sens??veis e resistentes a tigeciclina. Algumas tranvers??es ocasionaram mudan??a na codifica????o do amino??cido, sendo 6 em AcrR e 15 em RamR. A avalia????o da presen??a desses tipos de muta????es consiste em um primeiro passo para o estudo da resist??ncia bacteriana, j?? que pode ser causada por dano oxidativo ao DNA bacteriano, frequentemente ocasionado por press??o seletiva dos antibi??ticos. A resist??ncia a tigeciclina encontrada nos isolados cl??nicos do presente estudo, provavelmente pode estar associada a altera????es em outros genes desencadeadores de mecanismos de resist??ncia a tigeciclina.

abstract: Emergence of multidrug resistant (MDR) bacteria is a major concern to global health. One of the major MDR mechanisms bacteria employ is efflux pumps for the expulsion of drugs from the cell. In Escherichia coli, AcrAB-TolC proteins constitute the major chromosomally-encoded drug efflux system. AcrB, a trimeric membrane protein is well-known for its substrate promiscuity. It has the ability to efflux a broad spectrum of substrates alongside compounds such as dyes, detergent, bile salts and metabolites. Newly identified AcrB residues were shown to be functionally relevant in the drug binding and translocation pathway using a positive genetic selection strategy. These residues—Y49, V127, D153, G288, F453, and L486—were identified as the sites of suppressors of an alteration, F610A, that confers a drug hypersensitivity phenotype. Using site-directed mutagenesis (SDM) along with the real-time efflux and the classical minimum inhibitory concentration (MIC) assays, I was able to characterize the mechanism of suppression. Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression. To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A. / Dissertation/Thesis / Masters Thesis Biology 2016

Antibiotic resistance is an ongoing global medical crisis and we are in great need of new antibacterial agents to combat rapidly emerging resistant pathogens. Tigecycline is one of few drugs that have been introduced into medicine during the last two decades. It is a broad-spectrum third generation tetracycline that is active against multidrug-resistant bacteria that cause complicated infections. In this thesis I examined the development of tigecycline resistance in Escherichia coli and associated in vitro and in vivo fitness effects. Selections of spontaneous E. coli mutants revealed relatively high accumulation rates of changes in the multidrug efflux system AcrAB-TolC regulation network and in heptose biosynthesis and transport pathways important for lipopolysaccharide (LPS) synthesis. Both groups of mutations led to reduced susceptibility to tigecycline and slower growth compared to the wild-type bacteria. Additional in vitro fitness assays and in vivo competitions showed that LPS mutants were less fit than efflux mutants, providing a possible explanation for why up-regulation of multidrug efflux pumps is the main tigecycline resistance mechanism reported in clinical isolates. Tigecycline was designed to evade the two most common tetracycline resistance mechanisms conferred by Tet proteins, efflux and ribosomal protection. However, tigecycline is a substrate for the tetracycline modifying enzyme Tet(X). Screening of Tet protein mutant libraries showed that it is possible to select Tet mutants with minimal inhibitory concentrations of tigecycline that reach clinically relevant levels. Mutations in Tet proteins that permitted a better protection from tigecycline frequently exhibited reduced activity against earlier generations of tetracyclines, except for the Tet(X) enzyme mutants, which were better at inactivating all tested tetracyclines. This is particularly worrisome because different variants of Tet(X) have recently spread to multidrug-resistant pathogens through horizontal gene transfer. Therefore, Tet(X) mutants with improved activity threaten the medical future of tetracyclines. Multidrug resistance is easily disseminated through horizontally spreading conjugative plasmids. pUUH239.2 is an example of a successful conjugative plasmid that caused the first clonal outbreak of extended spectrum β-lactamase-producing Klebsiella pneumoniae in Scandinavia. This plasmid was formed after rearrangements between two different plasmid backbones and it carries resistance genes to multiple antibiotic classes, heavy metals, and detergents.