Bacterial infections are again becoming difficult to treat because the microbes are growing increasingly resistant to the antibiotics in use today. The need for novel antimicrobial compounds is urgent and to achieve this new targets are crucial. In this thesis we present a strategy for identification of such targets via a bioinformatics approach. In our first study we compared proteins with unknown and hypothetical function of the spirochete Treponema pallidum to five other pathogens also causing chronic or persistent infections in humans (Yersinia pestis, Neisseria gonorrhoeae, Helicobacter pylori, Borrelia burgdorferi and Streptococcus pneumoniae). T. pallidum was used as a starting point for the comparisons since this organism has a condensed genome (1.1 Mb). As we aimed at identifying conserved proteins important for in vivo survival or virulence of the pathogens we reasoned that T. pallidum would have deleted genes not important in the human host. This comparison yielded 17 ORFs conserved in all six pathogens, these were deleted in our model organism, Yersinia pseudotuberculosis, and the virulence of these mutant strains was evaluated in a mouse model of infection. Five genes were found to be essential for virulence and thus constitute possible antimicrobial drug targets. We have studied one of these virulence associated genes (vags), vagH, in more detail. Functional and phenotypic analysis revealed that VagH is an S-adenosyl-methionine dependent methyltransferase targeting Release factor 1 and 2 (RF1 and RF2). The analysis also showed that very few genes and proteins were differentially expressed in the vagH mutant compared to wild-type Yersinia. One major finding was that expression of the Type III secretion system effectors, the Yops, were down regulated in a vagH mutant. We dissected this phenotype further and found that the down regulation was due to lowered amounts of the positive regulator LcrF. This can be suppressed either by a deletion of yopD or by over expression of the Ribosomal Recycling Factor (RRF). These results indicate that YopD in addition to its role in translational regulation of the Yops also plays a part in the regulation of LcrF translation. We suggest also that the translation of LcrF is particularly sensitive to the amount of translation competent ribosomes and that one effect of a vagH mutation in Y. pseudotuberculosis is that the number of free ribosomes is reduced; this in turn reduces the amount of LcrF produced thereby causing a down regulation of the T3SS. This down regulation is likely the cause of the attenuated virulence of the vagH mutant. Finally, we set up a high throughput screening assay to screen a library of small molecules for compounds with inhibiting the VagH methyltransferase activity. Five such compounds were identified and two were found to inhibit VagH also in bacterial culture. Furthermore, analogues to one of the compounds showed improved inhibitory properties and inhibited the T3SS-dependent cytotoxic response induced by Y. pseudotuberculosis on HeLa cells. We have successfully identified five novel targets for antimicrobial compounds and in addition we have discovered a new class of molecules with antimicrobial properties.

Antibiotic resistance challenges the practice and development of modern medicine. The aim of this thesis was to test the hypothesis that antibiotic resistance is reversible once the selection pressure of an antibiotic is removed. A decisive reduction (85%) in trimethoprim and trimethoprim-sulfamethoxazole over 24 months in Kronoberg County, Sweden, is described. The resistance baseline prior to the intervention and the effects of the intervention on resistance levels, trimethoprim resistance genes (dfr-genes) and population structure in Escherichia coli were studied. The effects of different algorithms for excluding patient duplicate isolates were small but systematic. An identical algorithm was used throughout. The drastic decrease in the use of trimethoprim containing drugs did not result in a corresponding decrease in trimethoprim resistance. This was true both for total trimethoprim resistance and for trimethoprim mono-resistance. The distributions of E. coli phenotypes, dfr-genes and E. coli sequence types were stable. The marginal effect on resistance rates was explained by a low fitness cost of trimethoprim resistance observed in vitro and the high levels of associated resistance in trimethoprim resistant isolates. Trimethoprim resistance was, although widespread in the E. coli population, more common in certain E. coli sequence types. The distributions of dfr-genes were different in E. coli and K. pneumoniae and between different E. coli sequence types. These results indicate mechanisms related to the genetic back-bone of E coli to be important for the acquisition and persistence of antibiotic resistance. The findings of this thesis indicates that, at least for some classes of antibiotics, we may have overestimated the usefulness of a strategy for reversing antimicrobial resistance based on the fitness cost of resistance. We have equally underestimated the conserving effects of associated resistance. The stability of the dfr-genes and E. coli sequence types underlines the importance of associated resistance and successful lineages in the spread and maintenance of antibiotic resistance in E. coli.

Bacteria have the ability to sense different environmental signals. When an environmental stress is detected, bacteria rapidly adjust their gene expression profile to be able to survive and thrive. The transduction of such environmental signals often requires the coordinated involvement of several factors that constitute complex regulatory networks. Hence, depending on the combination of signals, a unique gene expression profile required to adapt to the specific stress conditions is generated. Proteins are the best-known regulatory factors. However, non-proteinaceous molecules are also important in signal-responsive control of bacterial gene expression. Alarmones are low molecular weight non-proteinaceous regulatory factors which can characteristically be rapidly turned-over to mediate instant changes in gene expression. One such alarmone is the modified nucleotide ppGpp, which directly binds to RNA polymerase to alter its activity. The levels of this alarmone are expected to rapidly increase in response to any environmental stress that result in slow proliferation. DksA, a putative ppGpp co-regulator that likewise directly targets RNA polymerase, has been suggested to be required for both the positive and negative regulation mediated by ppGpp in Escherichia coli. This thesis describes dissection of the role of ppGpp and DksA on transcriptional regulation, primarily using the fim genetic determinant that encodes for the type 1 fimbriae. Type 1 fimbriae are involved in adhesion to abiotic surface and initial adhesion/invasion of bladder cells, as well as in biofilm formation. We found that ppGpp regulates phase variation by increasing the sub-population of cells that express the fimbriae. The effect of ppGpp was ultimately traced to its role in transcription of the fimB gene that encodes a recombinase involved in the phase variation process (paper 1). In contrast, we unexpectedly found that lack of DksA causes an increase, rather than a decrease, in transcription from the fimB P2 promoter in vivo. However, in vitro transcription studies demonstrated that ppGpp and DksA, both independently and co-dependently, stimulate transcription from the fimB P2 promoter. These seemingly contradictory results from the in vivo and in vitro transcriptional studies were shown to be, at least in part, a consequence of the increased association of Gre-factors with RNA polymerase that can occur in the absence of DksA in vivo (paper 2). The results outlined above have implications for the role of ppGpp and/or DksA in global gene expression. Using gene expression profile (microarray analysis) during the transition from logarithmic to stationary phase of E. coli, we found that while most of the genes regulated by ppGpp and DksA are regulated in the same direction by the two factors, many were not. In addition to the fim genes, genes involved in flagella functioning, taxis responses, and a few genes encoding different transport systems are also differentially regulated in ppGpp- and DksA-deficient strains in vivo. Our results clearly indicate that the effect of deficiencies in ppGpp and DksA is far more complex than phenotypic similarity of the corresponding mutants anticipated by the proposed concerted action of ppGpp and DksA on gene expression (paper 2 & 3).

Lipoprotein lipase (LPL) is the main enzyme hydrolyzing triglyceride-rich lipoproteins in plasma. Proteoglycan-bound LPL on the vascular endothelium represent the functional pool of active enzyme. LPL is regulated in a tissue specific manner according to metabolic demands. Rapid regulation of LPL activity is necessary to provide free fatty acids for storage or energy production. This regulatory mechanism appears to be post-translational and requires synthesis of other protein/proteins. Recently it was demonstrated that angiopoietin-like protein 4 (ANGPTL4) is involved in the metabolism of plasma triglycerides and that it is able to inhibit LPL activity in vitro. These properties were linked to the N-terminal coiled-coil domain of ANGPTL4 (ccd-ANGPTL4), but the mechanism for the inhibition was not known. The aim of this thesis was to investigate the molecular mechanism for inhibition of LPL by ccd-ANGPTL4, to characterize regions in ccd-ANGPTL4 that are important for inactivation of LPL and to study the role of ANGPTL4 for regulation of LPL in vivo. Binding of ccd-ANGPTL4 to LPL was demonstrated by several methods, including surface plasmon resonance. The interaction was transient and resulted in conversion of the enzyme from catalytically active dimers to inactive monomers with decreased affinity for heparin. We have shown that ANGPTL4 mRNA in rat adipose tissue turns over rapidly and that changes in the ANGPTL4 mRNA abundance were inversely correlated to LPL activity, both during the fed to fasted and the fasted to fed transitions. We conclude that ANGPTL4 is a fasting-induced controller of LPL in adipose tissue, acting extracellularly on the native conformation of LPL in an unusual fashion, like an unfolding molecular chaperone. Site directed mutagenesis was used to explore regions in ccd-ANGPTL4 important for inactivation of LPL, and for binding of ANGPTL4 to heparin. Others had shown that ccd-ANGPTL4 forms higher oligomers. Structure prediction analyses demonstrated that the coiled-coil domain of ccd-ANGPTL4 probably forms three consecutive α-helices with strong hydrophobic faces, and that there are clusters of positively charged residues both on the helices and in intervening sequences. We made replacements of hydrophobic residues, positively charged residues, cysteine residues and negatively charged residues in ccd-ANGPTL4. In addition, helix-breaking proline residues were introduced in all three helices. We found that hydrophobic residues are important for oligomer formation. The higher oligomers appeared to be stabilized by disulfide bonds, but cysteines are not crucial for oligomerization. Introduction of Pro-residues in the first and second helix prevented formation of higher oligomers and reduced the ability of ccd-ANGPTL4 to inactivate LPL. We found that negatively charged residues in ccd-ANGPTL4 are important for inactivation of LPL. A heparin binding site was localized in the C-terminal end of ccd-ANGPTL4 (amino acid residues 114-140). To investigate whether LPL is differently processed in different depots of adipose tissue we measured the levels of LPL mRNA, protein and activity in omental and subcutaneous adipose tissue in human subjects undergoing elective surgery. Our results show that, although the expression level of LPL was higher in subcutaneous adipose tissue, the specific LPL activity (ratio of activity over the LPL protein mass) was higher in omental adipose tissue. Interestingly, the levels of ANGPTL4 mRNA were lower in omental compared to subcutaneous adipose tissue in most of the studied subjects. This difference can possibly explain the higher specific activity of LPL in omental adipose tissue and indicated that ANGPTL4 is involved in regulation of LPL activity also in humans. LPL produced by macrophages in the artery wall promotes local accumulation of lipids in these cells, and thereby plays an important role in development of atherosclerosis. The known association between type 2 diabetes and atherosclerosis forwarded us to study production of LPL by THP-1 macrophages under hyperglycemic conditions and under treatment with a peroxisome proliferator-activated receptor delta (PPARδ) agonist (GW501516). We found that LPL activity (but not LPL mass) produced by macrophages was decreased by GW501516. The loss of LPL activity coincided with increased level of ANGPTL4 mRNA, indicating that the agonist regulates LPL activity through expression of ANGPTL4. This effect was even more pronounced in cells grown under hyperglycemic conditions. Our data suggest that a suitable PPARδ agonist, like GW501516, may have protective effects against development of atherosclerosis in subjects with diabetes type 2.

Background Coagulase-negative staphylococci (CoNS) and in particular Staphylococcus epidermidis have emerged as major pathogens primarily causing nosocomial infections in patients with indwelling medical devices. These infections are often caused by multidrug-resistant strains of S. epidermidis (MDRSE). Other clinical entities due to CoNS are lower urinary tract infections (UTI) in women and native valve endocarditis. The purpose of this work was to investigate the frequency of antibiotic resistance and the molecular epidemiology of both hospital and community-associated isolates of S. epidermidis in order to examine if certain clones are related to MDRSE infections. Furthermore, we aimed to explore if specific clones of S. saprophyticus are associated with UTI in women. Methods A total of 359 hospital-associated methicillin-resistant isolates of CoNS obtained from 11 hospitals in northern Europe and 223 community-associated staphylococcal isolates were examined. Furthermore, 126 isolates of S. saprophyticus isolated from women with uncomplicated UTI from five different locations in northern Europe were analyzed. Pulsed-field gel electrophoresis (PFGE) was used for genotyping. Additionally, some of the S. epidermidis isolates were analyzed with multilocus sequence typing (MLST). Antibiotic susceptibility was determined for all isolates by the disc diffusion test. Results 293 of the 359 (82%) hospital-associated and 124 of the 223 (56%) community-associated isolates belonged to the species S. epidermidis. Among the hospital-associated S. epidermidis isolates, two dominating PFGE types (type A and B) were distinguished, comprising 78 (27%) and 51 (17%) isolates, respectively. Type A, which was detected in a Norwegian and eight Swedish hospitals, corresponded with a novel sequence type (ST215). Type B was discovered in a German, a Danish and seven Swedish hospitals and corresponded with ST2. In contrast, community-associated isolates of S. epidermidis were genetically extremely diverse with no predominating genotype, and showed a low rate of antibiotic resistance; only two (1.6%) methicillin-resistant strains were detected. Among 126 analyzed isolates of S. saprophyticus, 47 different PFGE profiles were identified. Several clusters of genetically highly related isolates were detected among isolates obtained from different locations and periods of time. Conclusion We have demonstrated the occurrence, persistence and potential dissemination of two multidrug-resistant S. epidermidis (MDRSE) genotypes, including a novel sequence type (ST215), within hospitals in northern Europe. Community-associated isolates of S. epidermidis showed a low rate of methicillin-resistance and were genetically heterogeneous. These results indicate that MDRSE by large are confined to the hospital setting in our region. Moreover, although the S. saprophyticus population was quite heterogeneous, indistinguishable isolates of S. saprophyticus causing lower UTI in women were identified in different countries 11 years apart, indicating the persistence and geographical spread of some clones of S. saprophyticus.