@article{SchulteSchweinlinWestermannetal.2020, author = {Schulte, Leon N. and Schweinlin, Matthias and Westermann, Alexander J. and Janga, Harshavardhan and Santos, Sara C. and Appenzeller, Silke and Walles, Heike and Vogel, J{\"o}rg and Metzger, Marco}, title = {An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection}, series = {mBio}, volume = {11, 2020}, journal = {mBio}, number = {1}, doi = {10.1128/mBio.03348-19}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229428}, year = {2020}, abstract = {A major obstacle in infection biology is the limited ability to recapitulate human disease trajectories in traditional cell culture and animal models, which impedes the translation of basic research into clinics. Here, we introduce a three-dimensional (3D) intestinal tissue model to study human enteric infections at a level of detail that is not achieved by conventional two-dimensional monocultures. Our model comprises epithelial and endothelial layers, a primary intestinal collagen scaffold, and immune cells. Upon Salmonella infection, the model mimics human gastroenteritis, in that it restricts the pathogen to the epithelial compartment, an advantage over existing mouse models. Application of dual transcriptome sequencing to the Salmonella-infected model revealed the communication of epithelial, endothelial, monocytic, and natural killer cells among each other and with the pathogen. Our results suggest that Salmonella uses its type III secretion systems to manipulate STAT3-dependent inflammatory responses locally in the epithelium without accompanying alterations in the endothelial compartment. Our approach promises to reveal further human-specific infection strategies employed by Salmonella and other pathogens. IMPORTANCE Infection research routinely employs in vitro cell cultures or in vivo mouse models as surrogates of human hosts. Differences between murine and human immunity and the low level of complexity of traditional cell cultures, however, highlight the demand for alternative models that combine the in vivo-like properties of the human system with straightforward experimental perturbation. Here, we introduce a 3D tissue model comprising multiple cell types of the human intestinal barrier, a primary site of pathogen attack. During infection with the foodborne pathogen Salmonella enterica serovar Typhimurium, our model recapitulates human disease aspects, including pathogen restriction to the epithelial compartment, thereby deviating from the systemic infection in mice. Combination of our model with state-of-the-art genetics revealed Salmonella-mediated local manipulations of human immune responses, likely contributing to the establishment of the pathogen's infection niche. We propose the adoption of similar 3D tissue models to infection biology, to advance our understanding of molecular infection strategies employed by bacterial pathogens in their human host.}, language = {en} } @article{JaegerPernitzschRichteretal.2012, author = {J{\"a}ger, Dominik and Pernitzsch, Sandy R. and Richter, Andreas S. and Backofen, Rolf and Sharma, Cynthia M. and Schmitz, Ruth A.}, title = {An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains}, series = {Nucleic Acids Research}, volume = {40}, journal = {Nucleic Acids Research}, number = {21}, doi = {10.1093/nar/gks847}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134972}, pages = {10964-10979}, year = {2012}, abstract = {We report on the characterization and target analysis of the small (s) RNA\(_{162}\) in the methanoarchaeon Methanosarcina mazei. Using a combination of genetic approaches, transcriptome analysis and computational predictions, the bicistronic MM2441-MM2440 mRNA encoding the transcription factor MM2441 and a protein of unknown function was identified as a potential target of this sRNA, which due to processing accumulates as three stabile 5' fragments in late exponential growth. Mobility shift assays using various mutants verified that the non-structured single-stranded linker region of sRNA\(_{162}\) (SLR) base-pairs with the MM2440-MM2441 mRNA internally, thereby masking the predicted ribosome binding site of MM2441. This most likely leads to translational repression of the second cistron resulting in dis-coordinated operon expression. Analysis of mutant RNAs in vivo confirmed that the SLR of sRNA\(_{162}\) is crucial for target interactions. Furthermore, our results indicate that sRNA\(_{162}\)-controlled MM2441 is involved in regulating the metabolic switch between the carbon sources methanol and methylamine. Moreover, biochemical studies demonstrated that the 50 end of sRNA\(_{162}\) targets the 5'-untranslated region of the cis-encoded MM2442 mRNA. Overall, this first study of archaeal sRNA/mRNA-target interactions unraveled that sRNA\(_{162}\) acts as an antisense (as) RNA on cis- and trans-encoded mRNAs via two distinct domains, indicating that cis-encoded asRNAs can have larger target regulons than previously anticipated.}, language = {en} } @article{JiangOronClarketal.2016, author = {Jiang, Yuxiang and Oron, Tal Ronnen and Clark, Wyatt T. and Bankapur, Asma R. and D'Andrea, Daniel and Lepore, Rosalba and Funk, Christopher S. and Kahanda, Indika and Verspoor, Karin M. and Ben-Hur, Asa and Koo, Da Chen Emily and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, Sayed M. E. and Martelli, Pier Luigi and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and T{\"o}r{\"o}nen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, David T. and Chapman, Samuel and BKC, Dukka and Khan, Ishita K. and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, Rebecca E. and Hieta, Reija and Legge, Duncan and Lovering, Ruth C. and Magrane, Michele and Melidoni, Anna N. and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, L{\´e}on-Charles and Das, Sayoni and Dawson, Natalie L. and Lee, David and Lees, Jonathan G. and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tam{\´a}s and Romero, Alfonso E. and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sede{\~n}o-Cort{\´e}s, Adriana E. and Pavlidis, Paul and Feng, Shou and Cejuela, Juan M. and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and Piovesan, Damiano and Tosatto, Silvio C. E. and del Pozo, Angela and Fern{\´a}ndez, Jos{\´e} M. and Maietta, Paolo and Valencia, Alfonso and Tress, Michael L. and Benso, Alfredo and Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Rehman, Hafeez Ur and Re, Matteo and Mesiti, Marco and Valentini, Giorgio and Bargsten, Joachim W. and van Dijk, Aalt D. J. and Gemovic, Branislava and Glisic, Sanja and Perovic, Vladmir and Veljkovic, Veljko and Almeida-e-Silva, Danillo C. and Vencio, Ricardo Z. N. and Sharan, Malvika and Vogel, J{\"o}rg and Kansakar, Lakesh and Zhang, Shanshan and Vucetic, Slobodan and Wang, Zheng and Sternberg, Michael J. E. and Wass, Mark N. and Huntley, Rachael P. and Martin, Maria J. and O'Donovan, Claire and Robinson, Peter N. and Moreau, Yves and Tramontano, Anna and Babbitt, Patricia C. and Brenner, Steven E. and Linial, Michal and Orengo, Christine A. and Rost, Burkhard and Greene, Casey S. and Mooney, Sean D. and Friedberg, Iddo and Radivojac, Predrag and Veljkovic, Nevena}, title = {An expanded evaluation of protein function prediction methods shows an improvement in accuracy}, series = {Genome Biology}, volume = {17}, journal = {Genome Biology}, number = {184}, doi = {10.1186/s13059-016-1037-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166293}, year = {2016}, abstract = {Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.}, language = {en} } @article{MietrachSchlosserGeibel2019, author = {Mietrach, Nicole and Schlosser, Andreas and Geibel, Sebastian}, title = {An extracellular domain of the EsaA membrane component of the type VIIb secretion system: expression, purification and crystallization}, series = {Acta Crystallographica Section F}, volume = {75}, journal = {Acta Crystallographica Section F}, number = {12}, doi = {10.1107/S2053230X1901495X}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213681}, pages = {725-730}, year = {2019}, abstract = {The membrane protein EsaA is a conserved component of the type VIIb secretion system. Limited proteolysis of purified EsaA from Staphylococcus aureus USA300 identified a stable 48 kDa fragment, which was mapped by fingerprint mass spectrometry to an uncharacterized extracellular segment of EsaA. Analysis by circular dichroism spectroscopy showed that this fragment folds into a single stable domain made of mostly α-helices with a melting point of 34.5°C. Size-exclusion chromatography combined with multi-angle light scattering indicated the formation of a dimer of the purified extracellular domain. Octahedral crystals were grown in 0.2 M ammonium citrate tribasic pH 7.0, 16\% PEG 3350 using the hanging-drop vapor-diffusion method. Diffraction data were analyzed to 4.0 {\AA} resolution, showing that the crystals belonged to the enantiomorphic tetragonal space groups P41212 or P43212, with unit-cell parameters a = 197.5, b = 197.5, c = 368.3 {\AA}, α = β = γ = 90°.}, language = {en} } @article{MottolaMorschhaeuser2019, author = {Mottola, Austin and Morschh{\"a}user, Joachim}, title = {An intragenic recombination event generates a Snf4-independent form of the essential protein kinase SNF1 in Candida albicans}, series = {mSphere}, volume = {4}, journal = {mSphere}, number = {3}, doi = {10.1128/mSphere.00352-19}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202170}, pages = {e00352-19}, year = {2019}, abstract = {The heterotrimeric protein kinase SNF1 plays a key role in the metabolic adaptation of the pathogenic yeast Candida albicans. It consists of the essential catalytic α-subunit Snf1, the γ-subunit Snf4, and one of the two β-subunits Kis1 and Kis2. Snf4 is required to release the N-terminal catalytic domain of Snf1 from autoinhibition by the C-terminal regulatory domain, and snf4Δ mutants cannot grow on carbon sources other than glucose. In a screen for suppressor mutations that restore growth of a snf4Δ mutant on alternative carbon sources, we isolated a mutant in which six amino acids between the N-terminal kinase domain and the C-terminal regulatory domain of Snf1 were deleted. The deletion was caused by an intragenic recombination event between two 8-bp direct repeats flanking six intervening codons. In contrast to truncated forms of Snf1 that contain only the kinase domain, the Snf4-independent Snf1\(^{Δ311 - 316}\) was fully functional and could replace wild-type Snf1 for normal growth, because it retained the ability to interact with the Kis1 and Kis2 β-subunits via its C-terminal domain. Indeed, the Snf4-independent Snf1\(^{Δ311 - 316}\) still required the β-subunits of the SNF1 complex to perform its functions and did not rescue the growth defects of kis1Δ mutants. Our results demonstrate that a preprogrammed in-frame deletion event within the SNF1 coding region can generate a mutated form of this essential kinase which abolishes autoinhibition and thereby overcomes growth deficiencies caused by a defect in the γ-subunit Snf4.}, language = {en} } @article{MuellerDolowschiakSellinetal.2016, author = {M{\"u}ller, Anna A. and Dolowschiak, Tamas and Sellin, Mikael E. and Felmy, Boas and Verbree, Carolin and Gadient, Sandra and Westermann, Alexander J. and Vogel, J{\"o}rg and LeibundGut-Landmann, Salome and Hardt, Wolf-Dietrich}, title = {An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection}, series = {PLoS Pathogens}, volume = {12}, journal = {PLoS Pathogens}, number = {6}, doi = {10.1371/journal.ppat.1005723}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167429}, pages = {e1005723}, year = {2016}, abstract = {Salmonella Typhimurium (S.Tm) is a common cause of self-limiting diarrhea. The mucosal inflammation is thought to arise from a standoff between the pathogen's virulence factors and the host's mucosal innate immune defenses, particularly the mucosal NAIP/NLRC4 inflammasome. However, it had remained unclear how this switches the gut from homeostasis to inflammation. This was studied using the streptomycin mouse model. S.Tm infections in knockout mice, cytokine inhibition and -injection experiments revealed that caspase-1 (not -11) dependent IL-18 is pivotal for inducing acute inflammation. IL-18 boosted NK cell chemoattractants and enhanced the NK cells' migratory capacity, thus promoting mucosal accumulation of mature, activated NK cells. NK cell depletion and Prf\(^{-/-}\) ablation (but not granulocyte-depletion or T-cell deficiency) delayed tissue inflammation. Our data suggest an NK cell perforin response as one limiting factor in mounting gut mucosal inflammation. Thus, IL-18-elicited NK cell perforin responses seem to be critical for coordinating mucosal inflammation during early infection, when S.Tm strongly relies on virulence factors detectable by the inflammasome. This may have broad relevance for mucosal defense against microbial pathogens.}, language = {en} } @article{Vogel2020, author = {Vogel, J{\"o}rg}, title = {An RNA biology perspective on species-specific programmable RNA antibiotics}, series = {Molecular Microbiology}, volume = {113}, journal = {Molecular Microbiology}, number = {3}, doi = {10.1111/mmi.14476}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214869}, pages = {550 -- 559}, year = {2020}, abstract = {Our body is colonized by a vast array of bacteria the sum of which forms our microbiota. The gut alone harbors >1,000 bacterial species. An understanding of their individual or synergistic contributions to human health and disease demands means to interfere with their functions on the species level. Most of the currently available antibiotics are broad-spectrum, thus too unspecific for a selective depletion of a single species of interest from the microbiota. Programmable RNA antibiotics in the form of short antisense oligonucleotides (ASOs) promise to achieve precision manipulation of bacterial communities. These ASOs are coupled to small peptides that carry them inside the bacteria to silence mRNAs of essential genes, for example, to target antibiotic-resistant pathogens as an alternative to standard antibiotics. There is already proof-of-principle with diverse bacteria, but many open questions remain with respect to true species specificity, potential off-targeting, choice of peptides for delivery, bacterial resistance mechanisms and the host response. While there is unlikely a one-fits-all solution for all microbiome species, I will discuss how recent progress in bacterial RNA biology may help to accelerate the development of programmable RNA antibiotics for microbiome editing and other applications.}, language = {en} } @article{BoesSpiegelVoepeletal.2015, author = {Boes, Alexander and Spiegel, Holger and Voepel, Nadja and Edgue, Gueven and Beiss, Veronique and Kapelski, Stephanie and Fendel, Rolf and Scheuermayer, Matthias and Pradel, Gabriele and Bolscher, Judith M. and Behet, Marije C. and Dechering, Koen J. and Hermsen, Cornelus C. and Sauerwein, Robert W. and Schillberg, Stefan and Reimann, Andreas and Fischer, Rainer}, title = {Analysis of a multi-component multi-stage malaria vaccine candidate—tackling the cocktail challenge}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {7}, doi = {10.1371/journal.pone.0131456}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173092}, pages = {e0131456}, year = {2015}, abstract = {Combining key antigens from the different stages of the P. falciparum life cycle in the context of a multi-stage-specific cocktail offers a promising approach towards the development of a malaria vaccine ideally capable of preventing initial infection, the clinical manifestation as well as the transmission of the disease. To investigate the potential of such an approach we combined proteins and domains (11 in total) from the pre-erythrocytic, blood and sexual stages of P. falciparum into a cocktail of four different components recombinantly produced in plants. After immunization of rabbits we determined the domain-specific antibody titers as well as component-specific antibody concentrations and correlated them with stage specific in vitro efficacy. Using purified rabbit immune IgG we observed strong inhibition in functional in vitro assays addressing the pre-erythrocytic (up to 80\%), blood (up to 90\%) and sexual parasite stages (100\%). Based on the component-specific antibody concentrations we calculated the IC50 values for the pre-erythrocytic stage (17-25 μg/ml), the blood stage (40-60 μg/ml) and the sexual stage (1.75 μg/ml). While the results underline the feasibility of a multi-stage vaccine cocktail, the analysis of component-specific efficacy indicates significant differences in IC50 requirements for stage-specific antibody concentrations providing valuable insights into this complex scenario and will thereby improve future approaches towards malaria vaccine cocktail development regarding the selection of suitable antigens and the ratios of components, to fine tune overall and stage-specific efficacy.}, language = {en} } @article{SchmollHoschuetzkyMorschhaeuseretal.1989, author = {Schmoll, T. and Hosch{\"u}tzky, H. and Morschh{\"a}user, J. and Lottspeich, F. and Jann, K. and Hacker, J{\"o}rg}, title = {Analysis of genes coding for the Sialic acid-binding adhesin and two other minor fimbrial subunits of the S-fimbrial adhesin determinant of Escherichia coli}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59585}, year = {1989}, abstract = {The S flmbrial adhesln (Sfa) enables Esch richla colito attach to slalfc acld-containing receptor molecules of eukaryotJc cells. As prevlously reported, the genetlc determinant coding for the Sfa of an E. co/1 06 strain was cloned, the gene codlng for the major fimbrfal subunit was ldentlfled and sequenced and th.e S speclflc adhesin was detected. Here we present evidence that ln addltlon to the major subunit proteln SfaA three other minor subunit proteins, SfaG (17 kD), SfaS (14kD) and SfaH (31 kD) can be isolated from the S..speclfic flmbrial adhesln complex. The genes coding for these minor subunits were ldenblied, mutagenlzed separately and sequenced. Using haemagglutlnatton tests. electron-microscopy and quantitative ELISA assays with monoclonal anti-SfaA and anti-SfaS antlbodles the functlons of the minor subunlts were determined. lt was determlned that SfaS ls ldentlcal to the S-specific adhesln; whlch also plays a role ln deterrninatlon of the degree of fimbri· ation ofthe cell. The mlnor subunit SfaH also had some Jnfluence on the Ievei of fimbrlation of the cell. while StaG ls necessary for full expression of S·specific binding. lt was further shown that the amino-terminal proteln sequence of the isolated SfaS profein was identJcal to the proteln sequence calculated from the DNA sequence of the sfaS gene locus.}, subject = {Infektionsbiologie}, language = {en} } @article{SunkavalliAguilarSilvaetal.2017, author = {Sunkavalli, Ushasree and Aguilar, Carmen and Silva, Ricardo Jorge and Sharan, Malvika and Cruz, Ana Rita and Tawk, Caroline and Maudet, Claire and Mano, Miguel and Eulalio, Ana}, title = {Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia}, series = {PLoS Pathogens}, volume = {13}, journal = {PLoS Pathogens}, number = {4}, doi = {10.1371/journal.ppat.1006327}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158204}, pages = {e1006327}, year = {2017}, abstract = {MicroRNAs play an important role in the interplay between bacterial pathogens and host cells, participating as host defense mechanisms, as well as exploited by bacteria to subvert host cellular functions. Here, we show that microRNAs modulate infection by Shigella flexneri, a major causative agent of bacillary dysentery in humans. Specifically, we characterize the dual regulatory role of miR-29b-2-5p during infection, showing that this microRNA strongly favors Shigella infection by promoting both bacterial binding to host cells and intracellular replication. Using a combination of transcriptome analysis and targeted high-content RNAi screening, we identify UNC5C as a direct target of miR-29b-2-5p and show its pivotal role in the modulation of Shigella binding to host cells. MiR-29b-2-5p, through repression of UNC5C, strongly enhances filopodia formation thus increasing Shigella capture and promoting bacterial invasion. The increase of filopodia formation mediated by miR-29b-2-5p is dependent on RhoF and Cdc42 Rho-GTPases. Interestingly, the levels of miR-29b-2-5p, but not of other mature microRNAs from the same precursor, are decreased upon Shigella replication at late times post-infection, through degradation of the mature microRNA by the exonuclease PNPT1. While the relatively high basal levels of miR-29b-2-5p at the start of infection ensure efficient Shigella capture by host cell filopodia, dampening of miR-29b-2-5p levels later during infection may constitute a bacterial strategy to favor a balanced intracellular replication to avoid premature cell death and favor dissemination to neighboring cells, or alternatively, part of the host response to counteract Shigella infection. Overall, these findings reveal a previously unappreciated role of microRNAs, and in particular miR-29b-2-5p, in the interaction of Shigella with host cells.}, language = {en} } @article{LueckBenderOttetal.1991, author = {L{\"u}ck, P. Christian and Bender, Larisa and Ott, Manfred and Helbig, J{\"u}rgen H. and Hacker, J{\"o}rg}, title = {Analysis of Legionella pneumophila serogroup 6 strains isolated from a hospital warm water supply over a three-year period by using genomic long-range mapping techniques and monoclonal antibodies}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-40392}, year = {1991}, abstract = {Over a period of 3 years, Legionella pneumophila serogroup 6 strains were isolated from warm water outlets and dental units in the Dental Faculty and from the Surgery and Internal Medicine Clinics at the University of Dresden, Dresden, Germany. In the bacteriological unit of the above-mentioned facility, L. pneumophila serogroups 3 and 12 were grown frl,)m warm water specimens. The medical facilities are located in separate buildings connected with a ring pipe warm water system. All L. pneumophila serogroup 6 strains isolated from the warm water supply reacted with a serogroup-specific monoclonal antibody, but not with two other monoclonal antibodies which are subgroup specific, reacting with other serogroup 6 strains. The NolI genomic profiles obtained by pulsed-field gel electrophoresis of 25 serogroup 6 strains isolated from the Dental Faculty over a 3-year period, 1 isolate from the Internal Medicine Clinic, and 4 strains from the Surgery Clinic were identical. Furthermore, all these strains hybridized with a 3OO-kb NolI fragment when a legiolysin (lIy)-specific DNA probe was used. The NolI pattern, however, differed from those of six serogroup 6 strains of other origins, one serogroup 12 strain from the bacteriological unit, and another six unrelated strains of serogroups other than serogroup 6. L. pneumophila serogroup 6 strains which can be divided into only two subgroups by the use of monoclonal antibodies are differentiated in at least six Noli cleavage types obtained by pulsed-field electrophoresis.}, language = {en} } @phdthesis{Biswas2005, author = {Biswas, Kajal}, title = {Analysis of Nitrogen starvation induced filamentous growth and characterization of putative essential genes in the human fungal pathogen, Candida albicans}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-11554}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {1. Zusammenfassung Candida albicans ist ein opportunistisch pathogener Hefepilz, der sowohl oberfl{\"a}chliche Infektionen der Schleimhaut als auch lebensbedrohliche systemische Infektionen hervorrufen kann. Obwohl die F{\"a}higkeit von C.albicans Infektionen auszul{\"o}sen weitgehend vom Immunstatus des Wirts abh{\"a}ngt, besitzt der Pilz doch auch spezifische Eigenschaften, die eine Kolonisierung, Disseminierung und Anpassung an unterschiedliche Wirtsnischen erm{\"o}glichen und ihn vom harmlosen Kommensalen zum gef{\"a}hrlichen Krankheitsserreger werden lassen. Unter bestimmten Umweltbedingungen geht C.albicans vom Wachstum als sprossende Hefe zum invasiven, filament{\"o}sen Wachstum {\"u}ber, das eine wichtige Rolle in der Pathogenit{\"a}t des Pilzes spielt. Stickstoffmangel ist eines der Signale, die das filament{\"o}se Wachstum in C.albicans induzieren, und die Kontrolle der Morphogenese durch die Verf{\"u}gbarkeit von Stickstoff wurde in dieser Arbeit detailliert untersucht. Ammonium ist f{\"u}r Hefepilze eine bevorzugte Stickstoffquelle, die {\"u}ber spezifische Transporter in die Zelle aufgenommen wird. In der vorliegenden Arbeit konnte gezeigt werden, dass C.albicans zwei Ammoniumpermeasen besitzt, deren Expression durch Stickstoffmangel induziert wird. W{\"a}hrend die Deletion von CaMEP1 oder CaMEP2 keinen Einfluss auf das Wachstum bei limitierenden Ammoniumkonzentrationen hatte, konnten \&\#61508;mep1 \&\#61508;mep2 Doppelmutanten bei Ammoniumkonzentrationen unter 5 mM nicht mehr wachsen. Im Gegensatz zu \&\#61508;mep1 Mutanten bildeten \&\#61508;mep2 Mutanten unter Stickstoffmangel keine Hyphen mehr und wuchsen ausschließlich in der Hefeform. CaMep2p hat also nicht nur eine Funktion als Ammoniumtransporter, sondern spielt auch eine Rolle bei der Induktion des filament{\"o}sen Wachstums. Weitere Experimente zeigten, dass CaMep2p ein weniger effizienter Ammoniumtransporter als CaMep1p ist, daf{\"u}r aber st{\"a}rker exprimiert wird, und dass dieser Unterschied wichtig f{\"u}r die Signalfunktion von CaMep2p ist. Durch Deletionsanalysen konnte bewiesen werden, dass die C-terminale, cytoplasmatische Dom{\"a}ne von CaMep2p essentiell f{\"u}r die Induktion des Hyphenwachstums ist, f{\"u}r den Ammoniumtransport jedoch nicht ben{\"o}tigt wird, und diese beiden Funktionen von CaMep2p daher voneinander getrennt werden k{\"o}nnen. In C.albicans gibt es mindestens zwei Signalwege die das filament{\"o}se Wachstum steuern, eine MAP-Kinase-Kaskade und einen cAMP-abh{\"a}ngigen Signalweg, die in den Transkriptionsfaktoren Cph1p bzw. Efg1p enden. Bei Inaktivierung des einen oder des anderen Signalwegs induziert Stickstoffmangel kein filament{\"o}ses Wachstum mehr. Ein hyperaktives CaMEP2 Allel konnte den filament{\"o}sen Wachstumsdefekt sowohl von \&\#61508;cph1 als auch \&\#61508;efg1 Mutanten aufheben, nicht jedoch den einer \&\#61508;cph1 \&\#61508;efg1 Doppelmutante oder einer Mutante, der das G-Protein Ras1p fehlte, das beide Signalwege aktiviert. Umgekehrt wurde der filament{\"o}se Wachstumsdefekt von \&\#61472;\&\#61508;mep2 Mutanten durch ein dominant-aktives RAS1 Allel bzw. durch die Zugabe von cAMP aufgehoben. Diese Ergebnisse deuten darauf hin, dass CaMep2p bei Stickstoffmangel sowohl den MAP-Kinase- als auch den cAMP-abh{\"a}ngigen Signalweg aktiviert, um filament{\"o}ses Wachstum zu induzieren. In gen{\"u}gend hohen Konzentrationen reprimierte Ammonium das filament{\"o}se Wachstum selbst wenn die Signalwege artifiziell aktiviert waren. Die bevorzugte Stickstoffquelle Ammonium ist deshalb ein Inhibitor der Morphogenese, der durch denselben Transporter in die Zelle aufgenommen wird, der bei Stickstoffmangel das filament{\"o}se Wachstum von C.albicans induziert. Obwohl ein genaues Verst{\"a}ndnis der Virulenzmechanismen von C.albicans auch neue Ans{\"a}tze zur Bek{\"a}mpfung von Infektionen durch diesen Pilz liefern kann, ist doch die Identifizierung und Charakterisierung von essentiellen Genen als potentielle Ziele f{\"u}r die Entwicklung neuer Antimykotika eine Strategie, die von der pharmazeutischen Industrie favorisiert wird. Aus diesem Grund wurden in Zusammenarbeit mit einem Industriepartner drei Gene von C.albicans ausgew{\"a}hlt, die in anderen Pilzen als essentiell beschrieben wurden, und im Rahmen dieser Arbeit funktionell charakterisiert. RAP1 codiert f{\"u}r das Repressor/Aktivator Protein 1, ein Transkriptionsfaktor und Telomerbindeprotein, das in der B{\"a}ckerhefe Saccharomyces cerevisiae essentiell ist. Die Deletion des RAP1 Gens in C.albicans beeintr{\"a}chtigte jedoch nicht die Lebensf{\"a}higkeit der Mutanten, so dass RAP1 kein vielversprechendes Ziel darstellt. CBF1 (centromere binding factor 1) ist in S.cerevisiae wichtig f{\"u}r die korrekte Chromosomenverteilung w{\"a}hrend der Mitose und außerdem auch f{\"u}r die transkriptionelle Aktivierung der Methioninbiosynthesegene; in den verwandten Hefen Kluyveromyces lactis und Candida glabrata ist CBF1 sogar essentiell. C.albicans \&\#61508;cbf1 Mutanten wiesen jedoch keinen erh{\"o}hten Chromosomenverlust auf, so dass CBF1 hier offensichtlich keine Rolle bei der Chromosomensegregation spielt. Allerdings waren die Mutanten auxotroph f{\"u}r schwefelhaltige Aminos{\"a}uren und generell stark im Wachstum beeintr{\"a}chtigt, was zeigte, dass Cbf1p f{\"u}r das normale Wachstum von C.albicans wichtig ist. YIL19 ist in S.cerevisiae ein essentielles Gen und hat eine Funktion bei der Reifung der 18S rRNA. YIL19 stellte sich auch in C.albicans als essentiell heraus. Konditionale Mutanten, in denen YIL19 durch induzierbare, FLP-vermittelte Rekombination aus dem Genom deletiert wurde, waren nicht lebensf{\"a}hig und akkumulierten rRNA Vorstufen. Durch diese Untersuchungen konnte gezeigt werden, dass YIL19 essentiell f{\"u}r diesen wichtigen zellul{\"a}ren Prozess und f{\"u}r die Lebensf{\"a}higkeit von C.albicans ist und sich m{\"o}glicherweise als Ziel f{\"u}r die Entwicklung antifungaler Substanzen eignet.}, subject = {Candida albicans}, language = {en} } @article{PfefferSchoelGulleetal.1991, author = {Pfeffer, K. and Schoel, H. and Gulle, H. and Moll, Heidrun and Kromer, S. and Kaufmann, S. H. E. and Wagner, H.}, title = {Analysis of primary T cell responses to intact and fractionated microbial pathogens}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-46916}, year = {1991}, abstract = {Freshly isolated human T lymphocytes were tested for their response to mycobacteria, mycobacteriallysates, 2 dimensional (2D) PAGE separated mycobacteriallysates, leishmania and defined leishmanial antigen preparations. While,o T cells proliferated vigourously in the presence of mycobacteria and mycobacteria derived lysates, a significant stimulation from 2 D gel separated lysates was not detected. In addition '10 T cells failed to respond towards leishmania or leishmanial components. In the ab T cell compartment some donors, presumably according to their state of immunity against mycobacteria, responded to mycobacteria, mycobacterial lysates and 2 D gel separated mycobacterial lysates. Neither freshly isolated '10 T cells nor ab T cells from naive donors did mount a significant immune response against leishmania.}, language = {en} } @phdthesis{Maeurer2006, author = {M{\"a}urer, Andr{\´e} Germar Paul}, title = {Analysis of the Chlamydophila pneumoniae and host transcriptome in the acute and iron depletion-mediated persistent infection}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-21415}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {The obligate intracellular gram-negative bacterium, Chlamydophila pneumoniae (Cpn), has a significant impact as an acute and chronic disease-causing pathogen. Its potential to undergo persistent infections has been linked to chronic diseases. Several in vitro cell culture models are used to study persistent conditions, mainly IFN_ stimulation, treatment with antibiotics and iron depletion. Little is known about changes in the Cpn transcriptome during the acute and persistent infection. Therefore, the Cpn transcriptome during its acute developmental cycle and iron depletion-mediated persistence was examined in this study. Based on expression profiles, genes with similar expression changes formed 12 clusters using the self-organizing map algorithm. While other studies define genes based on their onset of transcription, here the important feature for clustering was the expression profile. This turned out to be more appropriate for comparing the time specific relevance of a certain cluster of genes to their proposed functions in the cycle. The Cpn clusters were grouped into the 'Early', 'Mid' and 'Late' classes as described for Ctr. Additionally, a new gene expression class containing genes with steadily increasing expression at the end of the developmental cycle was defined and termed 'Tardy' class. Comparison of the Cpn clusters to published proteomics data showed that genes encoding elementary body (EB) proteins peaked in the 'Late' gene cluster. This indicated that genes of the 'Late' and 'Tardy' class have different roles in RB to EB re-differentiation. Moreover, using lexical comparison the EB mRNA profile was significantly linked to the 'Tardy' cluster class. This provided evidence that initial translation in the cycle might be directed from stable transcripts present in the infectious EB form. Based on these criteria the novel 'Tardy' class was separated from the 'Late' class. The gene ontologies were used to identify specific pathways and physiological functions active during the different phases of development. Additionally, the transcriptome of Cpn in the persistent stage was compared to that of the acute developmental cycle. The Cpn transcriptome was altered in the iron-depletion mediated persistence. Genes upregulated were linked to clusters at the beginning of the developmental cycle, and genes down-regulated were linked to clusters at the end of the developmental cycle. These data provided strong evidence that the Cpn transcriptome during persistence is a gene expression arrest in mid-development. In early acute infection convergently or divergently oriented gene pairs preferentially had an antagonistic expression profile, whereas tandemly oriented gene pairs showed a correlated expression profile. This suggests that the Cpn genome is organized mainly in tandemly arranged operons and in convergently or divergently oriented genes with favored antagonistic profiles. The microarray studies done with the Cpn strain CWL029 also showed expression signals for several genes annotated only for the Cpn strains AR39 and J138. BLAST comparison verified that these genes are also coded in the CWL029 genome. Several of these genes were convergently arranged with their neighboring gene and shared overlapping genome information. Among these were parB, involved in DNA segregation and rpsD, an alternative sigma factor responsible for the transcription at late stages of the developmental cycle. Both genes have been described to have major roles in the chlamydial cycle. These genes had an antagonistic expression profile at the beginning of the acute developmental cycle and in persistence, as described before to be predominant for convergently oriented genes. Real time RT-PCR analysis showed that full-length rpsD mRNA transcripts were down-regulated, whereas short-length rpsD mRNA transcripts were up-regulated during the persistent infection. This demonstrated that the rpsD promoter is activated during the persistent infection and that because of the collision of the RNA polymerases full length transcripts were down-regulated. This sigma factor-independent mechanism is known as 'Transcriptional Interference'. This is the first description on how the alternative sigma factor rpsD might be down-regulated during persistent infections. Finally, the host cell transcriptome was analyzed in the acute and persistent infection mediated by the depletion of iron. Cpn infection triggered the upregulation of relB, involved in an alternative NF-KB signaling pathway. Several genes coding for cell cycle proteins were triggered, including cyclin G2 and cyclin D1 and inhibitors of CDK4. Taken together, this work provides insights into the modulation of the pathogen and the host transcriptome during the acute infection and the iron mediated persistent infection.}, subject = {Chlamydia pneumoniae}, language = {en} } @article{KnappThenWelsetal.1985, author = {Knapp, S. and Then, I. and Wels, W. and Michel, W. and Tsch{\"a}pe, H. and Hacker, J{\"o}rg and Goebel, W}, title = {Analysis of the flanking regions from different hemolysin determinants of Escherichia coli}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59374}, year = {1985}, abstract = {The haemolysin (hly) determinant of the plasmid pHly152 contains an IS2 element at 469 bp upstream of the hlyC gene. The sequence at the other (right-hand) end (RS) also shows multiple hybridization with the plasmid pHly152 and the chromosome of some Escherichia coli strains but the nucleotide sequence of this region does not reveal the typical properties of an IS element. Similar arrangements in the regions flanking the hly determinant are also found on various Hly plasmids from uropathogenic E. coli strains. Chromosomal hly determinants Iack both flanking sequences (IS2 and RS) in the immediate vicinity of the hly genes. The sequences immediately upstream of the hlyC gene have been determined from several chromosomal hly determinants and compared with the corresponding sequence of the hly determinant of the plasmid pHly152. We show that these sequences, which contain one promoter (left promoter, phlyL) in all hly determinants tested, vary considerably although common sequence elements can still be identified. In contrast, only relatively few nucleotide exchanges have been detected in the adjacent structural hlyC genes. The A + T content of the 200 bp sequence upstream of hlyC is very high (72 mol\% A + T) but even the structural hly genes show a considerably higher A + T content (about 60 mol\%) than the E. coli chromosome on average (50 mol\% A+T) suggesting that the hly determinant may not have originated in E. coli.}, subject = {Infektionsbiologie}, language = {en} } @article{OttHackerSchmolletal.1986, author = {Ott, M. and Hacker, J{\"o}rg and Schmoll, T. and Jarchau, T. and Korhonen, T. K. and Goebel, W}, title = {Analysis of the genetic determinants coding for the S fimbrial adhesin (sfa) in different Escherichia coli strains causing meningitis or urinary tract infections}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59432}, year = {1986}, abstract = {Recently we have described the molecular cloning of the genetic determinant coding for the S-fimbrial adhesin (Sfa), a sialic acid-recognizing pilus frequently found among extraintestinal Eschenchili coli isolates. Fimbriae from the resulting Sfa + E. coli K-12 clone were isolated, and an Sfa-specific antiserum was prepared. Western blots indicate that S fimbriae isolated from different uropathogenic and meningitis-associated E. coli strains, including 083:Kl isolates, were serologically related. The Sfa-specific antibodies did not cross-react with P fimbriae, but did cross-react with FlC fimbriae. Furthermore the sja+ recombinant DNAs and some cloned s/a-flanking regions were used as probes in Southem experiments. Chromosomal DNAs isolated from 018:Kl and 083:Kl meningitis strains with and without S fimbriae and from uropathogenic 06:K + strains were hybridized against these sfa-specific probes. Only one copy of the sfa determinant was identified on the chromosome of these strains. No sfa-specific sequences were observed on the chromosome of E. coli K-12 strains and an 07:Kl isolate. With the exception of small alterations in the sfa-coding region the genetic determinants for S fimbriae were identical in uropathogenic 06:K + and meningitis 018:Kl and 083:Kl strains. The sfa determinant was also detected on the chromosome of Kl isolates with an Sfa-negative phenotype, and specific cross-hybridization signals were visible after blotting against FlC-specific DNA. In addition homology among the different strains was observed in the sfa-flanking regions.}, subject = {Infektionsbiologie}, language = {en} } @phdthesis{Grozdanov2004, author = {Grozdanov, Lubomir Assenov}, title = {Analysis of the genome organization and fitness traits of non-pathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-9304}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2004}, abstract = {In the last years more than one hundred microbial genomes have been sequenced, many of them from pathogenic bacteria. The availability of this huge amount of sequence data enormously increases our knowledge on the genome structure and plasticity, as well as on the microbial diversity and evolution. In parallel, these data are the basis for the scientific "revolution" in the field of industrial and environmental biotechnology and medical microbiology - diagnostics and therapy, development of new drugs and vaccines against infectious agents. Together with the genomic approach, other molecular biological methods such as PCR, DNA-chip technology, subtractive hybridization, transcriptomics and proteomics are of increasing importance for research on infectious diseases and public health. The aim of this work was to characterize the genome structure and -content of the probiotic Escherichia coli strain Nissle 1917 (O6:K5:H31) and to compare these data with publicly available data on the genomes of different pathogenic and non-pathogenic E. coli strains and other closely related species. A cosmid genomic library of strain Nissle 1917 was screened for clones containing the genetic determinants contributing to the successful survival in and colonization of the human body, as well as to mediate this strain's probiotic effect as part of the intestinal microflora. Four genomic islands (GEI I-IVNissle 1917) were identifed and characterized. They contain many known fitness determinants (mch/mcm, foc, iuc, kps, ybt), as well as novel genes of unknown function, mobile genetic elements or newly identified putative fitness-contributing factors (Sat, Iha, ShiA-homologue, Ag43-homologues). All islands were found to be integrated next to tRNA genes (serX, pheV, argW and asnT, respectively). Their structure and chromosomal localization closely resembles those of analogous islands in the genome of uropathogenic E. coli strain CFT073 (O6:K2(?):H1), but they lack important virulence genes of uropathogenic E. coli (hly, cnf, prf/pap). Evidence for instability of GEI IINissle 1917 was given, since a deletion event in which IS2 elements play a role was detected. This event results in loss of a 30 kb DNA region, containing important fitness determinants (iuc, sat, iha), and therefore probably might influence the colonization capacity of Nissle 1917 strain. In addition, a screening of the sequence context of tRNA-encoding genes in the genome of Nissle 1917 was performed to identify genome wide potential integration sites of "foreign" DNA. As a result, similar "tRNA screening patterns" have been observed for strain Nissle 1917 and for the uropathogenic E. coli O6 strains (UPEC) 536 and CFT073. I. Summary 4 The molecular reason for the semi-rough phenotype and serum sensitivity of strain Nissle 1917 was analyzed. The O6-antigen polymerase-encoding gene wzy was identified, and it was shown that the reason for the semi-rough phenotype is a frame shift mutation in wzy, due to the presence of a premature stop codon. It was shown that the restoration of the O side-chain LPS polymerization by complementation with a functional wzy gene increased serumresistance of strain Nissle 1917. The results of this study show that despite the genome similarity of the E. coli strain Nissle 1917 with the UPEC strain CFT073, the strain Nissle 1917 exhibits a specific set of geno- and phenotypic features which contribute to its probiotic action. By comparison with the available data on the genomics of different species of Enterobacteriaceae, this study contributes to our understanding of the important processes such as horizontal gene transfer, deletions and rearrangements which contribute to genome diversity and -plasticity, and which are driving forces for the evolution of bacterial variants. At last, the fim, bcs and rfaH determinats whose expression contributes to the mutlicellular behaviour and biofilm formation of E. coli strain Nissle 1917 have been characterized.}, subject = {Escherichia coli}, language = {en} } @phdthesis{Hampe2018, author = {Hampe, Irene Aurelia Ida}, title = {Analysis of the mechanism and the regulation of histatin 5 resistance in \(Candida\) \(albicans\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159634}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Antimycotics such as fluconazole are frequently used to treat C. albicans infections of the oral mucosa. Prolonged treatment of the fungal infection with fluconazole pose a risk to resistance development. C. albicans can adapt to these stressful environmental changes by regulation of gene expression or by producing genetically altered variants that arise in the population. Adapted variants frequently carry activating mutations in zinc cluster transcription factors, which cause the upregulation of their target genes, including genes encoding efflux pumps that confer drug resistance. MDR1, regulated by the zinc cluster transcription factor Mrr1, as well as CDR1 and CDR2, regulated by the zinc cluster transcription factor Tac1, are well-known examples of genes encoding efflux pumps that extrude the antimycotic fluconazole from the fungal cell and thus contribute to the survival of the fungus. In this study, it was investigated if C. albicans can develop resistance to the antimicrobial peptide histatin 5, which serves as the first line of defence in the oral cavity of the human host. Recently, it was shown that C. albicans transports histatin 5 outside of the Candia cell via the efflux pump Flu1. As efflux pumps are often regulated by zinc cluster transcription factors, the Flu1 efflux pump could also be regulated by a zinc cluster transcription factor which could in a hyperactive form upregulate the expression of the efflux pump, resulting in increased export of histatin 5 and consequently in histatin 5 resistance. In order to find a zinc cluster transcription factor that upregulates FLU1 expression, a comprehensive library of C. albicans strains containing artificially activated forms of zinc cluster transcription factors was screened for suitable candidates. The screening was conducted on medium containing mycophenolic acid because mycophenolic acid is also a substrate of Flu1 and a strain expressing a hyperactive zinc cluster transcription factor that upregulates FLU1 expression should exhibit an easily recognisable mycophenolic acid-resistant phenotype. Further, FACS analysis, quantitative real-time RT-PCR analysis, broth microdilution assays as well as histatin 5 assays were conducted to analyse the mechanism and the regulation of histatin 5 resistance. Several zinc cluster transcription factors caused mycophenolic acid resistance and upregulated FLU1 expression. Of those, only hyperactive Mrr1 was able to confer increased histatin 5 resistance. Finding Mrr1 to confer histatin 5 resistance was highly interesting as fluconazole-resistant strains with naturally occurring Mrr1 gain of function mutations exist, which were isolated from HIV-infected patients with oral candidiasis. These Mrr1 gain of function mutations as well as artificially activated Mrr1 cause fluconazole resistance by upregulation of the efflux pump MDR1 and other target genes. In the course of the study, it was found that expression of different naturally occurring MRR1 gain-of-function mutations in the SC5314 wild type background caused increased FLU1 expression and increased histatin 5 resistance. The same was true for fluconazole-resistant clinical isolates with Mrr1 gain of function mutations, which also caused the overexpression of FLU1. Those cells were less efficiently killed by histatin 5 dependent on Mrr1. Surprisingly, FLU1 contributed only little to histatin 5 resistance, rather, overexpression of MDR1 mainly contributed to the Mrr1-mediated histatin 5 resistance, but also additional Mrr1-target genes were involved. These target genes are yet to be uncovered. Moreover, if a link between the yet unknown Mrr1-target genes contributing to fluconazole resistance and increased histatin 5 resistance can be drawn remains to be discovered upon finding of the responsible target genes. Collectively, this study contributes to the understanding of the impact of prolonged antifungal exposure on the interaction between host and fungus. Drug therapy can give rise to resistance evolution resulting in strains that have not only developed resistance to fluconazole but also to an innate host mechanism, which allows adaption to the host niche even in the absence of the drug.}, subject = {Histatin 5}, language = {en} } @article{OttHacker1991, author = {Ott, M. and Hacker, J{\"o}rg}, title = {Analysis of the variability of S fimbriae expression in an Escherichia coli pathogen.}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59695}, year = {1991}, abstract = {The uropathogenic Escherichia coli wiJd..:type strain 536 produces S-fimbriae, P-related fimbriae and type I fimbriae. Using immuno-colony dot and ELISA techniques, variants were detected showing an increased degree of S-fimbrial production. It was demonstrated by itrtmunofluorescence microscopy that in noimal (wild-type) and hyperS- fimbriated E. coli populaiions non-fimbriated cells also · exist, and that the percentage of Sfinibrlated and non-fimbriated bacteria was roughly identica1 in either population. Hyper-Sfimbriated variants could be stably maintained. The transition from wild-type to hyper-S-fimbriation, which occurs spontaneously, is markedly higher than vice versa. Southern blot analysis of the S fimbrial adhesin (sfa) determinants of normal and hyper-fimbriated strains revealed no marked difference in the gene structure.}, subject = {Infektionsbiologie}, language = {en} } @article{MollMitchell1988, author = {Moll, Heidrun and Mitchell, Graham F.}, title = {Analysis of variables associated with the promotion of resistance, and its abrogation, in T cell-reconstituted nude mice infected with Leishmania major}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-30949}, year = {1988}, abstract = {No abstract available}, language = {en} } @article{HackerOttWintermeyeretal.1993, author = {Hacker, J{\"o}rg and Ott, Manfred and Wintermeyer, Eva and Ludwig, Birgit and Fischer, Gunter}, title = {Analysis of virulence factors of Legionella pneumophila.}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70620}, year = {1993}, abstract = {Legionella pneumophila, the causative agent of Legionnaires' disease is a facultative intracellular bacterium, which in the course of human infection multiplies in lung macrophages predominantly manifesting as pneumonia. The natural habitat of Legionella is found in sweet water reservoirs and man-made water systems. Virulent L. pneumophila spontaneously convert to an avirulent status at a high frequency. Genetic approaches have led to the identification of various L. pneumophila genes. The mip (macrophage infectivity potentiator) determinant remains at present the sole established virulence factor. The Mip protein exhibits activity of a peptidyl prolyl cis trans isomerase (PPiase), an enzyme which is able to bind the immunosuppressant FK506 and is involved in protein folding. The recently cloned major outer membrane protein (MOMP) could play a role in the uptake of legionellae by macrophages. Cellular models are useful in studying the intracellular replication of legionellae in eukaryotic cells. Human celllines and protozoan models are appropriate for this purpose. By using U 937 macrophage-like cells and Acanthamoeba castellanii as hosts, we could discriminate virulent and avirulent L. pneumophila variants since only the virulent strain was capable of intracellular growth at 37 oc. By using these systems we further demonstrated that a hemolytic factor cloned and characterized in our laboratory, legiolysin (lly), had no influence on the intracellular growth of L. pneumophila.}, subject = {Legionella pneumophila}, language = {en} } @article{YuVogelFoerstner2018, author = {Yu, Sung-Huan and Vogel, J{\"o}rg and F{\"o}rstner, Konrad U.}, title = {ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes}, series = {GigaScience}, volume = {7}, journal = {GigaScience}, doi = {10.1093/gigascience/giy096}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178942}, year = {2018}, abstract = {To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.}, language = {en} } @article{WenckerMarincolaSchoenfelderetal.2021, author = {Wencker, Freya D. R and Marincola, Gabriella and Schoenfelder, Sonja M. K. and Maaß, Sandra and Becher, D{\"o}rte and Ziebuhr, Wilma}, title = {Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay}, series = {Nucleic Acids Research}, volume = {49}, journal = {Nucleic Acids Research}, number = {4}, doi = {10.1093/nar/gkaa1277}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259029}, pages = {2192-2212}, year = {2021}, abstract = {In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5′ untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5′-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3′-end. The obtained data suggest that coordinated RNA decay represents another checkpoint in a complex regulatory network that adjusts costly methionine biosynthesis to current metabolic requirements.}, language = {en} } @article{GlaserSchurigtSuzukietal.2015, author = {Glaser, Jan and Schurigt, Uta and Suzuki, Brian M. and Caffrey, Connor R. and Holzgrabe, Ulrike}, title = {Anti-Schistosomal Activity of Cinnamic Acid Esters: Eugenyl}, series = {Molecules}, volume = {20}, journal = {Molecules}, doi = {10.3390/molecules200610873}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125712}, pages = {10873-10883}, year = {2015}, abstract = {Bornyl caffeate (1) was previously isolated by us from Valeriana (V.) wallichii rhizomes and identified as an anti-leishmanial substance. Here, we screened a small compound library of synthesized derivatives 1-30 for activity against schistosomula of Schistosoma (S.) mansoni. Compound 1 did not show any anti-schistosomal activity. However, strong phenotypic changes, including the formation of vacuoles, degeneration and death were observed after in vitro treatment with compounds 23 (thymyl cinnamate) and 27 (eugenyl cinnamate). Electron microscopy analysis of the induced vacuoles in the dying parasites suggests that 23 and 27 interfere with autophagy.}, language = {en} } @article{GlaserSchultheisHazraetal.2014, author = {Glaser, Jan and Schultheis, Martina and Hazra, Sudipta and Hazra, Banazri and Moll, Heidrun and Schurigt, Uta and Holzgrabe, Ulrike}, title = {Antileishmanial Lead Structures from Nature: Analysis of Structure-Activity Relationships of a Compound Library Derived from Caffeic Acid Bornyl Ester}, doi = {10.3390/molecules19021394}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-112835}, year = {2014}, abstract = {Bioassay-guided fractionation of a chloroform extract of Valeriana wallichii (V. wallichii) rhizomes lead to the isolation and identification of caffeic acid bornyl ester (1) as the active component against Leishmania major (L. major) promastigotes (IC50 = 48.8 µM). To investigate the structure-activity relationship (SAR), a library of compounds based on 1 was synthesized and tested in vitro against L. major and L. donovani promastigotes, and L. major amastigotes. Cytotoxicity was determined using a murine J774.1 cell line and bone marrow derived macrophages (BMDM). Some compounds showed antileishmanial activity in the concentration range of pentamidine and miltefosine which are the standard drugs in use. In the L. major amastigote assay compounds 15, 19 and 20 showed good activity with relatively low cytotoxicity against BMDM, resulting in acceptable selectivity indices. Molecules with adjacent phenolic hydroxyl groups exhibited elevated cytotoxicity against murine cell lines J774.1 and BMDM. The Michael system seems not to be essential for antileishmanial activity. Based on the results compound 27 can be regarded as new lead structure for further structure optimization}, language = {en} } @article{MarincolaLiongSchoenetal.2021, author = {Marincola, Gabriella and Liong, Olivia and Schoen, Christoph and Abouelfetouh, Alaa and Hamdy, Aisha and Wencker, Freya D. R. and Marciniak, Tessa and Becker, Karsten and K{\"o}ck, Robin and Ziebuhr, Wilma}, title = {Antimicrobial Resistance Profiles of Coagulase-Negative Staphylococci in Community-Based Healthy Individuals in Germany}, series = {Frontiers in Public Health}, volume = {9}, journal = {Frontiers in Public Health}, issn = {2296-2565}, doi = {10.3389/fpubh.2021.684456}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-240881}, year = {2021}, abstract = {Coagulase-negative staphylococci (CoNS) are common opportunistic pathogens, but also ubiquitous human and animal commensals. Infection-associated CoNS from healthcare environments are typically characterized by pronounced antimicrobial resistance (AMR) including both methicillin- and multidrug-resistant isolates. Less is known about AMR patterns of CoNS colonizing the general population. Here we report on AMR in commensal CoNS recovered from 117 non-hospitalized volunteers in a region of Germany with a high livestock density. Among the 69 individuals colonized with CoNS, 29 had reported contacts to either companion or farm animals. CoNS were selectively cultivated from nasal swabs, followed by species definition by 16S rDNA sequencing and routine antibiotic susceptibility testing. Isolates displaying phenotypic AMR were further tested by PCR for presence of selected AMR genes. A total of 127 CoNS were isolated and Staphylococcus epidermidis (75\%) was the most common CoNS species identified. Nine isolates (7\%) were methicillin-resistant (MR) and carried the mecA gene, with seven individuals (10\%) being colonized with at least one MR-CoNS isolate. While resistance against gentamicin, phenicols and spectinomycin was rare, high resistance rates were found against tetracycline (39\%), erythromycin (33\%) and fusidic acid (24\%). In the majority of isolates, phenotypic resistance could be associated with corresponding AMR gene detection. Multidrug-resistance (MDR) was observed in 23\% (29/127) of the isolates, with 33\% (23/69) of the individuals being colonized with MDR-CoNS. The combined data suggest that MR- and MDR-CoNS are present in the community, with previous animal contact not significantly influencing the risk of becoming colonized with such isolates.}, language = {en} } @article{SharanFoerstnerEulalioetal.2017, author = {Sharan, Malvika and F{\"o}rstner, Konrad U. and Eulalio, Ana and Vogel, J{\"o}rg}, title = {APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {11}, doi = {10.1093/nar/gkx137}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157963}, pages = {e96}, year = {2017}, abstract = {RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot.}, language = {en} } @article{GuptaSrivastavaOsmanogluetal.2021, author = {Gupta, Shishir K. and Srivastava, Mugdha and Osmanoglu, {\"O}zge and Xu, Zhuofei and Brakhage, Axel A. and Dandekar, Thomas}, title = {Aspergillus fumigatus versus genus Aspergillus: conservation, adaptive evolution and specific virulence genes}, series = {Microorganisms}, volume = {9}, journal = {Microorganisms}, number = {10}, issn = {2076-2607}, doi = {10.3390/microorganisms9102014}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-246318}, year = {2021}, abstract = {Aspergillus is an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genus Aspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows us to investigate the selection pressure driving the adaptive evolution in the pathogenic species A. fumigatus. Among single-copy orthologs (SCOs) for A. fumigatus and the closely related species A. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be positively selected and thus important for adaption. A. fumigatus PSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory and virulence-related pathways, such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein-coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation, such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives of A. fumigatus as an ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution of A. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, antimycotic targeting and understanding fundamental virulence processes.}, language = {en} } @phdthesis{Froehlich2012, author = {Fr{\"o}hlich, Kathrin}, title = {Assigning functions to Hfq-dependent small RNAs in the model pathogen Salmonella Typhimurium}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85488}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Non-coding RNAs constitute a major class of regulators involved in bacterial gene expression. A group of riboregulators of heterogeneous size and shape referred to as small regulatory RNAs (sRNAs) control trans- or cis-encoded genes through direct base-pairing with their mRNAs. Although mostly inhibiting their target mRNAs, several sRNAs also induce gene expression. An important co-factor for sRNA activity is the RNA chaperone, Hfq, which is able to rearrange intramolecular secondary structures and to promote annealing of complementary RNA sequences. In addition, Hfq protects unpaired RNA from degradation by ribonucleases and thus increases sRNA stability. Co-immunoprecipitation of RNA with the Hfq protein, and further experimental as well as bioinformatical studies performed over the last decade suggested the presence of more than 150 different sRNAs in various Enterobacteria including Escherichia coli and Salmonellae. So-called core sRNAs are considered to fulfill central cellular activities as deduced from their high degree of conservation among different species. Approximately 25 core sRNAs have been implicated in gene regulation under a variety of environmental responses. However, for the majority of sRNAs, both the riboregulators' individual biological roles as well as modes of action remain to be elucidated. The current study aimed to define the cellular functions of the two highly conserved, Hfq-dependent sRNAs, SdsR and RydC, in the model pathogen Salmonella Typhimurium. SdsR had been known as one of the most abundant sRNAs during stationary growth phase in E. coli. Examination of the conservation patterns in the sdsR promoter region in combination with classic genetic analyses revealed SdsR as the first sRNA under direct transcriptional control of the alternative σ factor σS. In Salmonella, over-expression of SdsR down-regulates the synthesis of the major porin OmpD, and the interaction site in the ompD mRNA coding sequence was mapped by a 3'RACE-based approach. At the post-transcriptional level, expression of ompD is controlled by three additional sRNAs, but SdsR plays a specific role in porin regulation during the stringent response. Similarly, RydC, the second sRNA adressed in this study, was initially discovered in E. coli but appeared to be conserved in many related γ-proteobacteria. An interesting aspect of this Hfq-dependent sRNAs is its secondary structure involving a pseudo-knot configuration, while the 5' end remains single stranded. A transcriptomic approach combining RydC pulse-expression and scoring of global mRNA changes on microarrays was employed to identify the targets of this sRNA. RydC specifically activated expression of the longer of two versions of the cfa mRNA encoding for the phospholipid-modifying enzyme cyclopropane fatty acid synthase. Employing its conserved single-stranded 5' end, RydC acts as a positive regulator and masks a recognition site of the endoribonuclease, RNase E, in the cfa leader.}, subject = {Small RNA}, language = {en} } @article{BarthelsMarincolaMarciniaketal.2020, author = {Barthels, Fabian and Marincola, Gabriella and Marciniak, Tessa and Konh{\"a}user, Matthias and Hammerschmidt, Stefan and Bierlmeier, Jan and Distler, Ute and Wich, Peter R. and Tenzer, Stefan and Schwarzer, Dirk and Ziebuhr, Wilma and Schirmeister, Tanja}, title = {Asymmetric Disulfanylbenzamides as Irreversible and Selective Inhibitors of Staphylococcus aureus Sortase A}, series = {ChemMedChem}, volume = {15}, journal = {ChemMedChem}, number = {10}, doi = {10.1002/cmdc.201900687}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214581}, pages = {839 -- 850}, year = {2020}, abstract = {Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with drug-resistant strains being responsible for tens of thousands of deaths per year. S. aureus sortase A inhibitors are designed to interfere with virulence determinants. We have identified disulfanylbenzamides as a new class of potent inhibitors against sortase A that act by covalent modification of the active-site cysteine. A broad series of derivatives were synthesized to derive structure-activity relationships (SAR). In vitro and in silico methods allowed the experimentally observed binding affinities and selectivities to be rationalized. The most active compounds were found to have single-digit micromolar Ki values and caused up to a 66 \% reduction of S. aureus fibrinogen attachment at an effective inhibitor concentration of 10 μM. This new molecule class exhibited minimal cytotoxicity, low bacterial growth inhibition and impaired sortase-mediated adherence of S. aureus cells.}, language = {en} } @article{FrankMarcudeOliveiraAlmeidaPetersenetal.2015, author = {Frank, Benjamin and Marcu, Ana and de Oliveira Almeida Petersen, Antonio Luis and Weber, Heike and Stigloher, Christian and Mottram, Jeremy C. and Scholz, Claus J{\"u}rgen and Schurigt, Uta}, title = {Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210}, series = {Parasites \& Vectors}, volume = {8}, journal = {Parasites \& Vectors}, number = {404}, doi = {10.1186/s13071-015-0974-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124997}, year = {2015}, abstract = {Background Autophagy participates in innate immunity by eliminating intracellular pathogens. Consequently, numerous microorganisms have developed strategies to impair the autophagic machinery in phagocytes. In the current study, interactions between Leishmania major (L. m.) and the autophagic machinery of bone marrow-derived macrophages (BMDM) were analyzed. Methods BMDM were generated from BALB/c mice, and the cells were infected with L. m. promastigotes. Transmission electron microscopy (TEM) and electron tomography were used to investigate the ultrastructure of BMDM and the intracellular parasites. Affymetrix® chip analyses were conducted to identify autophagy-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The protein expression levels of autophagy related 5 (ATG5), BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3), cathepsin E (CTSE), mechanistic target of rapamycin (MTOR), microtubule-associated proteins 1A/1B light chain 3B (LC3B), and ubiquitin (UB) were investigated through western blot analyses. BMDM were transfected with specific small interfering RNAs (siRNAs) against autophagy-related genes and with mimics or inhibitors of autophagy-associated miRNAs. The infection rates of BMDM were determined by light microscopy after a parasite-specific staining. Results The experiments demonstrated autophagy induction in BMDM after in vitro infection with L. m.. The results suggested a putative MTOR phosphorylation-dependent counteracting mechanism in the early infection phase and indicated that intracellular amastigotes were cleared by autophagy in BMDM in the late infection phase. Transcriptomic analyses and specific downregulation of protein expression with siRNAs suggested there is an association between the infection-specific over expression of BNIP3, as well as CTSE, and the autophagic activity of BMDM. Transfection with mimics of mmu-miR-101c and mmu-miR-129-5p, as well as with an inhibitor of mmu-miR-210-5p, demonstrated direct effects of the respective miRNAs on parasite clearance in L. m.-infected BMDM. Furthermore, Affymetrix® chip analyses revealed a complex autophagy-related RNA network consisting of differentially expressed mRNAs and miRNAs in BMDM, which indicates high glycolytic and inflammatory activity in the host macrophages. Conclusions Autophagy in L. m.-infected host macrophages is a highly regulated cellular process at both the RNA level and the protein level. Autophagy has the potential to clear parasites from the host. The results obtained from experiments with murine host macrophages could be translated in the future to develop innovative and therapeutic antileishmanial strategies for human patients.}, language = {en} } @article{RaschigRamirez‐ZavalaWiestetal.2023, author = {Raschig, Martina and Ram{\´i}rez-Zavala, Bernardo and Wiest, Johannes and Saedtler, Marco and Gutmann, Marcus and Holzgrabe, Ulrike and Morschh{\"a}user, Joachim and Meinel, Lorenz}, title = {Azobenzene derivatives with activity against drug-resistant Candida albicans and Candida auris}, series = {Archiv der Pharmazie}, volume = {356}, journal = {Archiv der Pharmazie}, number = {2}, doi = {10.1002/ardp.202200463}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-312295}, year = {2023}, abstract = {Increasing resistance against antimycotic drugs challenges anti-infective therapies today and contributes to the mortality of infections by drug-resistant Candida species and strains. Therefore, novel antifungal agents are needed. A promising approach in developing new drugs is using naturally occurring molecules as lead structures. In this work, 4,4'-dihydroxyazobenzene, a compound structurally related to antifungal stilbene derivatives and present in Agaricus xanthodermus (yellow stainer), served as a starting point for the synthesis of five azobenzene derivatives. These compounds prevented the growth of both fluconazole-susceptible and fluconazole-resistant Candida albicans and Candida auris strains. Further in vivo studies are required to confirm the potential therapeutic value of these compounds.}, language = {en} } @article{BeckerOelschlaegerWullaertetal.2013, author = {Becker, Svetlana and Oelschlaeger, Tobias A. and Wullaert, Andy and Pasparakis, Manolis and Wehkamp, Jan and Stange, Eduard F. and Gersemann, Michael}, title = {Bacteria Regulate Intestinal Epithelial Cell Differentiation Factors Both In Vitro and In Vivo}, series = {PLoS ONE}, volume = {8}, journal = {PLoS ONE}, number = {2}, doi = {10.1371/journal.pone.0055620}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131168}, pages = {e55620}, year = {2013}, abstract = {Background: The human colon harbours a plethora of bacteria known to broadly impact on mucosal metabolism and function and thought to be involved in inflammatory bowel disease pathogenesis and colon cancer development. In this report, we investigated the effect of colonic bacteria on epithelial cell differentiation factors in vitro and in vivo. As key transcription factors we focused on Hes1, known to direct towards an absorptive cell fate, Hath1 and KLF4, which govern goblet cell. Methods: Expression of the transcription factors Hes1, Hath1 and KLF4, the mucins Muc1 and Muc2 and the defensin HBD2 were measured by real-time PCR in LS174T cells following incubation with several heat-inactivated E. coli strains, including the probiotic E. coli Nissle 1917+/- flagellin, Lactobacilli and Bifidobacteria. For protein detection Western blot experiments and chamber-slide immunostaining were performed. Finally, mRNA and protein expression of these factors was evaluated in the colon of germfree vs. specific pathogen free vs. conventionalized mice and colonic goblet cells were counted. Results: Expression of Hes1 and Hath1, and to a minor degree also of KLF4, was reduced by E. coli K-12 and E. coli Nissle 1917. In contrast, Muc1 and HBD2 expression were significantly enhanced, independent of the Notch signalling pathway. Probiotic E. coli Nissle 1917 regulated Hes1, Hath1, Muc1 and HBD2 through flagellin. In vivo experiments confirmed the observed in vitro effects of bacteria by a diminished colonic expression of Hath1 and KLF4 in specific pathogen free and conventionalized mice as compared to germ free mice whereas the number of goblet cells was unchanged in these mice. Conclusions: Intestinal bacteria influence the intestinal epithelial differentiation factors Hes1, Hath1 and KLF4, as well as Muc1 and HBD2, in vitro and in vivo. The induction of Muc1 and HBD2 seems to be triggered directly by bacteria and not by Notch.}, language = {en} } @article{SchefferKoenigHackeretal.1985, author = {Scheffer, J. and K{\"o}nig, W. and Hacker, J{\"o}rg and Goebel, W.}, title = {Bacterial adherence and hemolysin production from Escherichia coli induces histamine and leukotriene release from various cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59361}, year = {1985}, abstract = {We investigated the role of bacterial adherence and hemolysin production from Escherichia coli parent and genetically cloned strains as to their eft'ects on bistaJidne release from rat mast cells and leukotriene generation from human polymorphonuclear granulocytes. These mediators were involved in the induction of inftammatory disease processes and led, for example, to enhancement of vascular permeability, chemotaxis (leukotriene 84 [LTB4]), chemoaggregation, lysosomal enzyme release, and smooth muscle contraction, (LTC4, LTD4 , and LTE4). Washed bacteria (E. coli K-12 Ms+ my=; E. coli 536 Ms+ MR= my=) as weil as their culture supematants were analyzed. Washed E. coli K-12 (Hiy+), unlike Hly- strains, induced high amounts of histamine release from rat mast cells and chemotactic activity from human polymorphonuclear granulocytes. Significant leukotriene releasewas obtained with washed E. coli K-12 my+ strains and their bacterial culture supematants. Leukotriene induction was dependent on the amount of hemolysin activity present in the supematant. However, additional soluble factors should also be considered. The presence of hemolysin appeared to aceeierate and enhance the rate of phagocytosis of bacteria by neutrophUs. When E. coli 536 (MS+ MR= Hly=) strains were analyzed, the simultaneous presence of MR+ pili and hemolysin production led to an increase in histamine release as compared with MR- my+ strains. The genetically cloned MR+ my+ E. coli 536 strain induced higher amounts of IeukotrieDes as compared with the wUd-type strain. Our data soggest a potent role for adhesins and hemolysin as virulence factors in inducing the release of inftammatory mediators.}, subject = {Infektionsbiologie}, language = {en} } @phdthesis{Zdziarski2008, author = {Zdziarski, Jaroslaw Maciej}, title = {Bacterial Genome Plasticity and its Role for Adaptation and Evolution of Asymptomatic Bacteriuria (ABU) Escherichia coli Strains}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-32879}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {Asymptomatic bacteriuria (ABU) represents the long term bacterial colonization of the urinary tract, frequently caused by Escherichia coli (E. coli), without typical symptoms of a urinary tract infection (UTI). To investigate characteristics of ABU E. coli isolates in more detail, the geno- and phenotypes of eleven ABU isolates have been compared. Moreover, consecutive in vivo re-isolates of the model ABU strain 83972 were characterized with regard to transcriptomic, proteomic and genomic alterations upon long term in vivo persistence in the human bladder. Finally, the effect of the human host on bacterial adaptation/evolution was assessed by comparison of in vitro and in vivo-propagated strain 83972. ABU isolates represent a heterologous group of organisms. The comparative analysis of different ABU isolates elucidated the remarkable genetic and phenotypic flexibility of E. coli isolates. These isolates could be allocated to all four major E. coli phylogenetic lineages as well as to different clonal groups. Accordingly, they differed markedly in genome content, i.e., the genome size as well as the presence of typical UPEC virulence-associated genes. Multi locus sequence typing suggested that certain ABU strains evolved from UPEC variants that are able to cause symptomatic UTI by genome reduction. Consequently, the high E. coli genome plasticity does not allow a generalized view on geno- and phenotypes of individual isolates within a clone. Reductive evolution by point mutations, DNA rearrangements and deletions resulted in inactivation of genes coding for several UPEC virulence factors, thus supporting the idea that a reduced bacterial activation of host mucosal inflammation promotes the ABU lifestyle of these E. coli isolates. Gene regulation and genetic diversity are strategies which enable bacteria to live and survive under continuously changing environmental conditions. To study adaptational changes upon long term growth in the bladder, consecutive re-isolates of model ABU strain 83972 derived from a human colonisation study and from an in vitro long term cultivation experiment were analysed with regard to transcriptional changes and genome rearrangements. In this context, it could be demonstrated that E. coli, when exposed to different host backgrounds, is able to adapt its metabolic networks resulting in an individual bacterial colonisation strategy. Transcriptome and proteome analyses demonstrated distinct metabolic strategies of nutrients acquisition and energy production of tested in vivo re-isolates of strain 83972 that enabled them to colonise their host. Utilisation of D-serine, deoxy- and ribonucleosides, pentose and glucuronate interconversions were main up-regulated pathways providing in vivo re-isolates with extra energy for efficient growth in the urinary bladder. Moreover, this study explored bacterial response networks to host defence mechanisms: The class III alcohol dehydrogenase AdhC, already proven to be involved in nitric oxide detoxification in pathogens like Haemophilus influenzae, was shown for the first time to be employed in defending E. coli against the host response during asymptomatic bacteriuria. Consecutive in vivo and in vitro re-isolates of strain 83972 were also analysed regarding their genome structure. Several changes in the genome structure of consecutive re-isolates derived from the human colonisation study implied the importance of bacterial interactions with the host during bacterial microevolution. In contrast, the genome structure of re-isolates from the in vitro long term cultivation experiment, where strain 83972 has been propagated without host contact, was not affected. This suggests that exposure to the immune response promotes genome plasticity thus being a driving force for the development of the ABU lifestyle and evolution within the urinary tract.}, subject = {Escherichia coli}, language = {en} } @article{HessStritzkerHaertletal.2011, author = {Hess, Michael and Stritzker, Jochen and H{\"a}rtl, Barbara and Sturm, Julia and Gentschev, Ivaylo and Szalay, Aladar}, title = {Bacterial glucuronidase as general marker for oncolytic virotherapy or other biological therapies}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69163}, year = {2011}, abstract = {Background: Oncolytic viral tumor therapy is an emerging field in the fight against cancer with rising numbers of clinical trials and the first clinically approved product (Adenovirus for the treatment of Head and Neck Cancer in China) in this field. Yet, until recently no general (bio)marker or reporter gene was described that could be used to evaluate successful tumor colonization and/or transgene expression in other biological therapies. Methods: Here, a bacterial glucuronidase (GusA) encoded by biological therapeutics (e.g. oncolytic viruses) was used as reporter system. Results: Using fluorogenic probes that were specifically activated by glucuronidase we could show 1) preferential activation in tumors, 2) rena l excretion of the activated fluorescent compounds and 3) reproducible detection of GusA in the serum of oncolytic vaccinia virus treated, tumor bearing mice in several tumor models. Time course studies revealed that reliable differentiation between tumor bearing and healthy mice can be done as early as 9 days post injection of the virus. Regarding the sensitivity of the newly developed assay system, we could show that a single infected tumor cell could be reliably detected in this assay. Conclusion: GusA therefore has the potential to be used as a general marker in the preclinical and clinical evaluation of (novel) biological therapies as well as being useful for the detection of rare cells such as circulating tumor cells}, subject = {Virologie}, language = {en} } @article{SchrotenWolskePlogmannetal.1991, author = {Schroten, Horst and Wolske, Anja and Plogmann, Ricarda and Hanisch, Franz-Georg and Hacker, J{\"o}rg and Uhlenbr{\"u}ck, Gerhard and Wahn, Volker}, title = {Binding of cloned S-fimbriated E. coli to human buccal epithelial cells-different inhibition of binding by neonatal saliva and adult saliva.}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-86291}, year = {1991}, abstract = {Investigations were carried out on the adhesion of cloned S-fimbriated E. coli, labelled with fluoresceinisothiocyanate (FITC) to human buccal epithelial cells. Fluorescence microscopic analysis revealed binding of bacteria to 75-95\% of epithelial cells. Inhibition experiments with fetuin, a 1-acid glycoprotein and N-acetyl neuraminic acid confirmed the specificity of bacterial binding to sialoglycoproteins. Further studies using saliva as an inhibitor resulted in a 4-5 times stronger binding inhibition by newborn saliva in comparison to adult saliva coinciding with a 4-5 times higher content of total N-acetyl neuraminic acid in samples of newborn saliva. In Western blot analysis sialoglycoprotein bands with a molecular weight >200 kD reacting with wheat germ agglutinin (WGA), were only identified in samples of newborn saliva. These bands are classified as mucins on account of molecular weight and staining. These data suggest that saliva mucins could represent a major defense mechanism against bacterial infections at a stage of ontogeny where the secretory IgAsystem is not yet developed.}, subject = {Escherichia coli}, language = {en} } @article{KorhonenParkkinenHackeretal.1986, author = {Korhonen, T. K. and Parkkinen, J. and Hacker, J{\"o}rg and Finne, J. and Pere, A. and Rhen, M. and Holth{\"o}fer, H}, title = {Binding of Escherichia coli S fimbriae to human kidney epithelium}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59415}, year = {1986}, abstract = {Purified S fimbriae and an Escherichia coli strain carrying the recombinant plasmid pANN801-4 that encodes S fimbriae were tested for adhesion to frozen sections of human kidney. The fimbrlae and the bacteria bound to the same tissue domains, and in both cases the binding was specifically inhibited by the receptor analog of S fimbria, sialyl(a2-3)1actose. S fimbriae bound specifically to the epithelial elements in the kidneys; to the epithelial cells of proximal and distal tubules as weil as of the collecting ducts and to the visceral and parietal glomerular epithelium. In addition, they bound to the vascular endothelium of glomerull and of the renal Interstitium. No blnding to connective tissue elements was observed. The results suggest that the biological functlon of S fimbriae is to mediate the adheslon of E. coli to human epithelial and vascular endothellal ceUs.}, subject = {Infektionsbiologie}, language = {en} } @article{ParkkinenKorhonenPereetal.1988, author = {Parkkinen, J. and Korhonen, T. K. and Pere, A. and Hacker, J{\"o}rg and Soinila, S.}, title = {Binding sites in the rat brain for Escherichia coli S fimbriae associated with neontal meningitis}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59500}, year = {1988}, abstract = {Escherichia coli strains that cause sepsis and meningitis in neonatal infants carry S fimbriae that bind to sialyl galactoside units of cell surface glycoproteins. To investigate the possible role of S fimbriae in determining the tissue tropism of neonatal menlngitis, we have studied the preselice of binding sites for S fimbriae in different tissues of the neonatal rat which is susceptible to meningitis caused by S-fimbriated E. coli. Purified S fimbriae were incubated on cryostat sections of different rat oipns and their bindina was assessed by indirect immunofluorescence. In the bnin of the neonatal rat, S fimbriae specifically bound to the luminal surfaces of the vascular endothelium and of the epithelium lining the choroid plexuses and bnin ventricles. The · bindlog W.s completely inhibited by the trisaccharide NeuAca2-3Ga)ßl-4Gic, a receptor analogue of S fimbriae, and by a preceding neuraminidase treatment of the sections. A recombinant E. coli strain expressina S fimbriae adhered in large numbers to the same tissue sites in the neonatal brain sections as did the purified fimbriae, · whereas the nonfimbriated host strahi and a recombiiuuit strain expresslog P fi.mbriae did not adhere to brain tissues. The results soggest that adhesion of S-fimbriated bacteria to the binding sites observed in the neonatai bnin has a pathogenetic roJe durlog bacterial Invasion from cii'culation into the cerebrospinal fluid.}, subject = {Infektionsbiologie}, language = {en} } @phdthesis{Sharan2017, author = {Sharan, Malvika}, title = {Bio-computational identification and characterization of RNA-binding proteins in bacteria}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-153573}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {RNA-binding proteins (RBPs) have been extensively studied in eukaryotes, where they post-transcriptionally regulate many cellular events including RNA transport, translation, and stability. Experimental techniques, such as cross-linking and co-purification followed by either mass spectrometry or RNA sequencing has enabled the identification and characterization of RBPs, their conserved RNA-binding domains (RBDs), and the regulatory roles of these proteins on a genome-wide scale. These developments in quantitative, high-resolution, and high-throughput screening techniques have greatly expanded our understanding of RBPs in human and yeast cells. In contrast, our knowledge of number and potential diversity of RBPs in bacteria is comparatively poor, in part due to the technical challenges associated with existing global screening approaches developed in eukaryotes. Genome- and proteome-wide screening approaches performed in silico may circumvent these technical issues to obtain a broad picture of the RNA interactome of bacteria and identify strong RBP candidates for more detailed experimental study. Here, I report APRICOT ("Analyzing Protein RNA Interaction by Combined Output Technique"), a computational pipeline for the sequence-based identification and characterization of candidate RNA-binding proteins encoded in the genomes of all domains of life using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences of an input proteome using position-specific scoring matrices and hidden Markov models of all conserved domains available in the databases and then statistically score them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them according to functionally relevant structural properties. APRICOT performed better than other existing tools for the sequence-based prediction on the known RBP data sets. The applications and adaptability of the software was demonstrated on several large bacterial RBP data sets including the complete proteome of Salmonella Typhimurium strain SL1344. APRICOT reported 1068 Salmonella proteins as RBP candidates, which were subsequently categorized using the RBDs that have been reported in both eukaryotic and bacterial proteins. A set of 131 strong RBP candidates was selected for experimental confirmation and characterization of RNA-binding activity using RNA co-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) experiments. Based on the relative abundance of transcripts across the RIP-Seq libraries, a catalogue of enriched genes was established for each candidate, which shows the RNA-binding potential of 90\% of these proteins. Furthermore, the direct targets of few of these putative RBPs were validated by means of cross-linking and co-immunoprecipitation (CLIP) experiments. This thesis presents the computational pipeline APRICOT for the global screening of protein primary sequences for potential RBPs in bacteria using RBD information from all kingdoms of life. Furthermore, it provides the first bio-computational resource of putative RBPs in Salmonella, which could now be further studied for their biological and regulatory roles. The command line tool and its documentation are available at https://malvikasharan.github.io/APRICOT/.}, language = {en} } @article{McFlederMakhotkinaGrohetal.2023, author = {McFleder, Rhonda L. and Makhotkina, Anastasiia and Groh, Janos and Keber, Ursula and Imdahl, Fabian and Pe{\~n}a Mosca, Josefina and Peteranderl, Alina and Wu, Jingjing and Tabuchi, Sawako and Hoffmann, Jan and Karl, Ann-Kathrin and Pagenstecher, Axel and Vogel, J{\"o}rg and Beilhack, Andreas and Koprich, James B. and Brotchie, Jonathan M. and Saliba, Antoine-Emmanuel and Volkmann, Jens and Ip, Chi Wang}, title = {Brain-to-gut trafficking of alpha-synuclein by CD11c\(^+\) cells in a mouse model of Parkinson's disease}, series = {Nature Communications}, volume = {14}, journal = {Nature Communications}, doi = {10.1038/s41467-023-43224-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357696}, year = {2023}, abstract = {Inflammation in the brain and gut is a critical component of several neurological diseases, such as Parkinson's disease (PD). One trigger of the immune system in PD is aggregation of the pre-synaptic protein, α-synuclein (αSyn). Understanding the mechanism of propagation of αSyn aggregates is essential to developing disease-modifying therapeutics. Using a brain-first mouse model of PD, we demonstrate αSyn trafficking from the brain to the ileum of male mice. Immunohistochemistry revealed that the ileal αSyn aggregations are contained within CD11c+ cells. Using single-cell RNA sequencing, we demonstrate that ileal CD11c\(^+\) cells are microglia-like and the same subtype of cells is activated in the brain and ileum of PD mice. Moreover, by utilizing mice expressing the photo-convertible protein, Dendra2, we show that CD11c\(^+\) cells traffic from the brain to the ileum. Together these data provide a mechanism of αSyn trafficking between the brain and gut.}, language = {en} } @phdthesis{Peterson2008, author = {Peterson, Lisa}, title = {CEACAM3-mediated phagocytosis of human-specific bacterial pathogens involves the adaptor molecule Nck}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-46378}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) are exploited by human-specific pathogens to anchor themselves to or invade host cells. Interestingly, human granulocytes express a specific isoform, CEACAM3, that can direct efficient, opsonin-independent phagocytosis of CEACAM-binding Neisseria, Moraxella and Haemophilus species. As opsonin-independent phagocytosis of CEACAM-binding Neisseria depends on Src-family protein tyrosine kinase (PTK) phosphorylation of the CEACAM3 cytoplasmic domain, we hypothesized that an SH2-containing protein might be involved in CEACAM3-initiated, phagocytosis-promoting signals. Accordingly, we screened glutathione-S-transferase (GST) fusion proteins containing SH2 domains derived from a panel of signaling and adapter molecules for their ability to associate with CEACAM3. In vitro pull-down assays demonstrated that the SH2 domain of the adapter molecule Nck (GST-Nck SH2), but not other SH2 domains such as the Grb2 SH2 domain, interact with CEACAM3 in a phosphotyrosine-dependent manner. Either deletion of the cytoplasmic tail of CEACAM3, or point-mutation of a critical arginine residue in the SH2 domain of Nck (GST-NckSH2R308K) that disrupts phosphotyrosine binding, both abolished CEACAM3-Nck-SH2 interaction. Upon infection of human cells with CEACAM-binding Neisseria, full-length Nck comprising an SH2 and three SH3 domains co-localized with tyrosine phosphorylated CEACAM3 and associated bacteria as analyzed by immunofluorescence staining and confocal microscopy. In addition, Nck could be detected in CEACAM3 immunoprecipitates confirming the interaction in vivo. Importantly, overexpression of a GFP-fusion protein of the isolated Nck SH2 domain (GFP-Nck-SH2), but not GFP or GFP-Nck SH2 R308K reduced CEACAM3-mediated phagocytosis of CEACAM-binding Neisseria suggesting that the adaptor molecule Nck plays an important role in CEACAM3-initiated signaling leading to internalization and elimination of human-specific pathogens.}, subject = {Adaptorproteine}, language = {en} } @article{GarciaBetancurGoniMorenoHorgeretal.2017, author = {Garc{\´i}a-Betancur, Juan-Carlos and Go{\~n}i-Moreno, Angel and Horger, Thomas and Schott, Melanie and Sharan, Malvika and Eikmeier, Julian and Wohlmuth, Barbara and Zernecke, Alma and Ohlsen, Knut and Kuttler, Christina and Lopez, Daniel}, title = {Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus}, series = {eLife}, volume = {6}, journal = {eLife}, number = {e28023}, doi = {10.7554/eLife.28023}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170346}, year = {2017}, abstract = {A central question to biology is how pathogenic bacteria initiate acute or chronic infections. Here we describe a genetic program for cell-fate decision in the opportunistic human pathogen Staphylococcus aureus, which generates the phenotypic bifurcation of the cells into two genetically identical but different cell types during the course of an infection. Whereas one cell type promotes the formation of biofilms that contribute to chronic infections, the second type is planktonic and produces the toxins that contribute to acute bacteremia. We identified a bimodal switch in the agr quorum sensing system that antagonistically regulates the differentiation of these two physiologically distinct cell types. We found that extracellular signals affect the behavior of the agr bimodal switch and modify the size of the specialized subpopulations in specific colonization niches. For instance, magnesium-enriched colonization niches causes magnesium binding to S. aureusteichoic acids and increases bacterial cell wall rigidity. This signal triggers a genetic program that ultimately downregulates the agr bimodal switch. Colonization niches with different magnesium concentrations influence the bimodal system activity, which defines a distinct ratio between these subpopulations; this in turn leads to distinct infection outcomes in vitro and in an in vivo murine infection model. Cell differentiation generates physiological heterogeneity in clonal bacterial infections and helps to determine the distinct infection types.}, language = {en} } @phdthesis{Lerch2018, author = {Lerch, Maike Franziska}, title = {Characterisation of a novel non-coding RNA and its involvement in polysaccharide intercellular adhesin (PIA)-mediated biofilm formation of \(Staphylococcus\) \(epidermidis\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-155777}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Coagulase-negative staphylococci, particularly Staphylococcus epidermidis, have been recognised as an important cause of health care-associated infections due to catheterisation, and livestock-associated infections. The colonisation of indwelling medical devices is achieved by the formation of biofilms, which are large cell-clusters surrounded by an extracellular matrix. This extracellular matrix consists mainly of PIA (polysaccharide intercellular adhesin), which is encoded by the icaADBC-operon. The importance of icaADBC in clinical strains provoking severe infections initiated numerous investigations of this operon and its regulation within the last two decades. The discovery of a long transcript being located next to icaADBC, downstream of the regulator gene icaR, led to the hypothesis of a possible involvement of this transcript in the regulation of biofilm formation (Eckart, 2006). Goal of this work was to characterise this transcript, named ncRNA IcaZ, in molecular detail and to uncover its functional role in S. epidermidis. The ~400 nt long IcaZ is specific for ica-positive S. epidermidis and is transcribed in early- and mid-exponential growth phase as primary transcript. The promotor sequence and the first nucleotides of icaZ overlap with the 3' UTR of the preceding icaR gene, whereas the terminator sequence is shared by tRNAThr-4, being located convergently to icaZ. Deletion of icaZ resulted in a macroscopic biofilm-negative phenotype with highly diminished PIA-biofilm. Biofilm composition was analysed in vitro by classical crystal violet assays and in vivo by confocal laser scanning microscopy under flow conditions to display biofilm formation in real-time. The mutant showed clear defects in initial adherence and decreased cell-cell adherence, and was therefore not able to form a proper biofilm under flow in contrast to the wildtype. Restoration of PIA upon providing icaZ complementation from plasmids revealed inconsistent results in the various mutant backgrounds. To uncover the functional role of IcaZ, transcriptomic and proteomic analysis was carried out, providing some hints on candidate targets, but the varying biofilm phenotypes of wildtype and icaZ mutants made it difficult to identify direct IcaZ mRNA targets. Pulse expression of icaZ was then used as direct fishing method and computational target predictions were executed with candidate mRNAs from aforesaid approaches. The combined data of these analyses suggested an involvement of icaR in IcaZ-mediated biofilm control. Therefore, RNA binding assays were established for IcaZ and icaR mRNA. A positive gel shift was maintained with icaR 3' UTR and with 5'/3' icaR mRNA fusion product, whereas no gel shift was obtained with icaA mRNA. From these assays, it was assumed that IcaZ regulates icaR mRNA expression in S. epidermidis. S. aureus instead lacks ncRNA IcaZ and its icaR mRNA was shown to undergo autoregulation under so far unknown circumstances by intra- or intermolecular binding of 5' UTR and 3' UTR (Ruiz de los Mozos et al., 2013). Here, the Shine-Dalgarno sequence is blocked through 5'/3' UTR base pairing and RNase III, an endoribonuclease, degrades icaR mRNA, leading to translational blockade. In this work, icaR mRNA autoregulation was therefore analysed experimentally in S. epidermidis and results showed that this specific autoregulation does not take place in this organism. An involvement of RNase III in the degradation process could not be verified here. GFP-reporter plasmids were generated to visualise the interaction, but have to be improved for further investigations. In conclusion, IcaZ was found to interact with icaR mRNA, thereby conceivably interfering with translation initiation of repressor IcaR, and thus to promote PIA synthesis and biofilm formation. In addition, the environmental factor ethanol was found to induce icaZ expression, while only weak or no effects were obtained with NaCl and glucose. Ethanol, actually is an ingredient of disinfectants in hospital settings and known as efficient effector for biofilm induction. As biofilm formation on medical devices is a critical factor hampering treatment of S. epidermidis infections in clinical care, the results of this thesis do not only contribute to better understanding of the complex network of biofilm regulation in staphylococci, but may also have practical relevance in the future.}, subject = {Biofilm}, language = {en} } @article{KramerBinningerSchirrmacheretal.1986, author = {Kramer, Michael D. and Binninger, Linda and Schirrmacher, Volker and Moll, Heidrun and Prester, Marlot and Nerz, Gaby and Simon, Markus M.}, title = {Characterization and isolation of a trypsin-like serine protease from a long-term culture cytolytic t cell line andits expression by functionally distinct T cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-31636}, year = {1986}, abstract = {No abstract available}, subject = {Biologie}, language = {en} } @article{MunoaHackerJuarez1988, author = {Munoa, F. and Hacker, J{\"o}rg and Juarez, A.}, title = {Characterization of a chromosomal mutant that blocks hemolysin excretion in Escherichia coli}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59534}, year = {1988}, abstract = {We analyzed an Escherichia coli strain which harbours a chromosomal mutation that blocks the hemolysin excretion. Compartmentation studies showed that hemolysin accumulates in the cytoplasm and not in the periplasm. The mutation did not affect the SDS-PAGE protein pattern of the outer membrane, although some alterations were apparent in the periplasmic protein pattern. The mutant strain, E. coli Hsb-1 also failed to export a cloned fimbrial adhesin. The mutation maps in the min. 3.5 of the E. coli genetic map.}, subject = {Infektionsbiologie}, language = {en} } @article{MoserOrskovHackeretal.1986, author = {Moser, I. and Orskov, I. and Hacker, J{\"o}rg and Jann, K.}, title = {Characterization of a monoclonal antibody against the fimbrial F8 antigen of Escherichia coli}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59385}, year = {1986}, abstract = {A monoclonal lgG 1 antibody against F8 fimbriae was obtained with the hybridoma technique using spieen cells from C3H/f rnice immunised with a fimbrial preparation of Escherichia coli 2980 (018ac: K5: H-: FIC, F8) and Sp 2/0 Ag8 myeloma cells. The hybrid cells were cloned twice by lirniting dilution and grown in tissue culture. The monoclonal antibody was purified from culture supernatants on Protein A Sepharose. lt reacted with F8 fimbriae in colony blot, enzyme-linked immunosorbent assay (ELISA) and immunoblot after electrotransfer from sodium dodecyl sulphate-polyacrylarnide gel electrophoresis (SOS-PAGE) of fimbrial preparations. The antibody bound to and agglutinated F8-fimbriated bacteria.}, subject = {Infektionsbiologie}, language = {en} } @article{HackerSchrettenbrunnerSchroeteretal.1986, author = {Hacker, J{\"o}rg and Schrettenbrunner, A. and Schr{\"o}ter, G. and Schmidt, G. and D{\"u}vel, H. and Goebel, W.}, title = {Characterization of Escherichia coli wild-type strains by means of agglutination with antisera raised against cloned P-, S- and MS-fimbriae antigens, hemagglutination, serotyping and hemolysin-production}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-72992}, year = {1986}, abstract = {E. coli stcains isolated from patients with urinary tcact infecrions (UTn very often possess mannose"sensitive (MS) and mannose-resistant (MR) adherence facmrs (fimbriae). According to their receptor specificity the mannose-resistant adhesins can be divided inm several types, P, S, M and X. We have cloned rhe determinants of rhree groups of UTI E. coli adhesins, MS, p and S, and prepared specific aorisera against the fimbriae antigens. 189 hernagglutination (HA+) -positive stcains, 96 fecal isolates and 93 strains isoJated from UTI . have been tesred with rhese specific antisera and further characterized by receptor specific : HA, HA parteras and further of rhe "common 0 serogroups" 01, 02, 04, 06, 07, 08, 018, ' 025, 075, most prevalenr in UTI, and hemolysin production. · 68 (73 \%) of the UTI srrains a.nd 50 (52\%) of the fecal isolates showed P-receptor specificiry; 16 (17\%) of the uropathogenic bacteria and 33 (34\%) of the fecal strains exhibited S, M or X-fimbriae antigens. 24\% of rhe P-hemagglutinating (P+) strains reacted wirb P (F8)-specific antiserum. In contrast, more than three quaner of the s+-srrains were agglutinated by S-specific antiserum. HA-pattern VJ and 018 amigen were found to be associared with P-fimbriae strains, wbereas HA-pattern V and VII and the 0 anrigens 02 (M-type), 06 and 018 (5-type) occurred most frequently in p- -strains. A high percentage of P-fimbriated strains showed mannose-sensitive hemagglurination and hemolysin production.}, subject = {Escherichia coli}, language = {en} } @article{WintermeyerRdestLudwigetal.1991, author = {Wintermeyer, E. and Rdest, U. and Ludwig, B. and Debes, A. and Hacker, J{\"o}rg}, title = {Characterization of legiolysin (lly); responsible for hemolytic activity, colour production and fluorescence of Legionella pneumophila}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59706}, year = {1991}, abstract = {No abstract available}, subject = {Infektionsbiologie}, language = {en} } @article{HughesHackerDueveletal.1987, author = {Hughes, C. and Hacker, J{\"o}rg and D{\"u}vel, H. and Goebel, W}, title = {Chromosomal deletions and rearrangements cause coordinate loss of hemolysis, fimbriation and serum resistance in an uropathogenic strain of Escherichia coli}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-59470}, year = {1987}, abstract = {No abstract available}, subject = {Infektionsbiologie}, language = {en} }