@article{DejungSubotaBuceriusetal.2016,
  author    = {Dejung, Mario and Subota, Ines and Bucerius, Ferdinand and Dindar, G{\"u}lcin and Freiwald, Anja and Engstler, Markus and Boshart, Michael and Butter, Falk and Janzen, Chistian J.},
  title     = {Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei},
  series = {PLoS Pathogens},
  volume    = {12},
  journal   = {PLoS Pathogens},
  number    = {2},
  doi       = {10.1371/journal.ppat.1005439},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146362},
  pages     = {e1005439},
  year      = {2016},
  abstract  = {Developmental differentiation is a universal biological process that allows cells to adapt to different environments to perform specific functions. African trypanosomes progress through a tightly regulated life cycle in order to survive in different host environments when they shuttle between an insect vector and a vertebrate host. Transcriptomics has been useful to gain insight into RNA changes during stage transitions; however, RNA levels are only a moderate proxy for protein abundance in trypanosomes. We quantified 4270 protein groups during stage differentiation from the mammalian-infective to the insect form and provide classification for their expression profiles during development. Our label-free quantitative proteomics study revealed previously unknown components of the differentiation machinery that are involved in essential biological processes such as signaling, posttranslational protein modifications, trafficking and nuclear transport. Furthermore, guided by our proteomic survey, we identified the cause of the previously observed differentiation impairment in the histone methyltransferase DOT1B knock-out strain as it is required for accurate karyokinesis in the first cell division during differentiation. This epigenetic regulator is likely involved in essential chromatin restructuring during developmental differentiation, which might also be important for differentiation in higher eukaryotic cells. Our proteome dataset will serve as a resource for detailed investigations of cell differentiation to shed more light on the molecular mechanisms of this process in trypanosomes and other eukaryotes.},
  language  = {en}
}
@phdthesis{Zude2014,
  author    = {Zude, Ingmar},
  title     = {Characterization of virulence-associated traits of Escherichia coli bovine mastitis isolates},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-100934},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {Bacterial mastitis is caused by invasion of the udder, bacterial multiplication and induction of inflammatory responses in the bovine mammary gland. Disease severity and the cause of disease are influenced by environmental factors, the cow's immune response as well as bacterial traits. Escherichia coli (E. coli) is one of the main causes of acute bovine mastitis, but although pathogenic E. coli strains can be classified into different pathotypes, E. coli causing mastitis cannot unambiguously be distinguished from commensal E. coli nor has a common set of virulence factors been described for mastitis isolates. This project focussed on the characterization of virulence- associated traits of E. coli mastitis isolates in comprehensive analyses under conditions either mimicking initial pathogenesis or conditions that E. coli mastitis isolates should encounter while entering the udder. Virulence-associated traits as well as fitness traits of selected bovine mastitis or faecal E. coli strains were identified and analyzed in comparative phenotypic assays. Raw milk whey was introduced to test bacterial fitness in native mammary secretion known to confer antimicrobial effects. Accordingly, E. coli isolates from bovine faeces represented a heterogeneous group of which some isolates showed reduced ability to survive in milk whey whereas others phenotypically resembled mastitis isolates that represented a homogeneous group in that they showed similar survival and growth characteristics in milk whey. In contrast, mastitis isolates did not exhibit such a uniform phenotype when challenged with iron shortage, lactose as sole carbon source and lingual antimicrobial peptide (LAP) as a main defensin of milk. Reduced bacterial fitness could be related to LAP suggesting that bacterial adaptation to an intramammary lifestyle requires resistance to host defensins present in mammary secretions, at least LAP. E. coli strain 1303 and ECC-1470 lack particular virulence genes associated to mastitis isolates. To find out whether differences in gene expression may contribute to the ability of E. coli variants to cause mastitis, the transcriptome of E. coli model mastitis isolates 1303 and ECC-1470 were analyzed to identify candidate genes involved in bacterium-host interaction, fitness or even pathogenicity during bovine mastitis. DNA microarray analysis was employed to assess the transcriptional response of E. coli 1303 and ECC-1470 upon cocultivation with MAC-T immortalized bovine mammary gland epithelial cells to identify candidate genes involved in bacterium-host interaction. Additionally, the cell adhesion and invasion ability of E. coli strain 1303 and ECC-1470 was investigated. The transcriptonal response to the presence of host cells rather suggested competition for nutrients and oxygen between E. coli and MAC-T cells than marked signs of adhesion and invasion. Accordingly, mostly fitness traits that may also contribute to efficient colonization of the E. coli primary habitat, the gut, have been utilized by the mastitis isolates under these conditions. In this study, RNA-Seq was employed to assess the bacterial transcriptional response to milk whey. According to our transcriptome data, the lack of positively deregulated and also of true virulence-associated determinants in both of the mastitis isolates indicated that E. coli might have adapted by other means to the udder (or at least mammary secretion) as an inflammatory site. We identified traits that promote bacterial growth and survival in milk whey. The ability to utilize citrate promotes fitness and survival of E. coli that are thriving in mammary secretions. According to our results, lactoferrin has only weak impact on E. coli in mammary secretions. At the same time bacterial determinants involved in iron assimilation were negatively regulated, suggesting that, at least during the first hours, iron assimilation is not a challenge to E. coli colonizing the mammary gland. It has been hypothesized that cellular iron stores cause temporary independency to extracellular accessible iron. According to our transcriptome data, this hypothesis was supported and places iron uptake systems beyond the speculative importance that has been suggested before, at least during early phases of infection. It has also been shown that the ability to resist extracytoplasmic stress, by oxidative conditions as well as host defensins, is of substantial importance for bacterial survival in mammary secretions. In summary, the presented thesis addresses important aspects of host-pathogen interaction and bacterial conversion to hostile conditions during colonization of the mastitis inflammatory site, the mammary gland.},
  subject      = {Escherichia coli},
  language  = {en}
}
@article{SharmaDugarHerbigetal.2013,
  author    = {Sharma, Cynthia M. and Dugar, Gaurav and Herbig, Alexander and F{\"o}rstner, Konrad U. and Heidrich, Nadja and Reinhardt, Richard and Nieselt, Kay},
  title     = {High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates},
  series = {PLoS Genetics},
  journal   = {PLoS Genetics},
  doi       = {10.1371/journal.pgen.1003495},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96610},
  year      = {2013},
  abstract  = {Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA-seq (dRNA-seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA-seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA-seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA-seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level.},
  language  = {en}
}
@phdthesis{Michaelis2005,
  author    = {Michaelis, Kai},
  title     = {Untersuchungen zur Genomstruktur und Biofilmbildung von pathogenen Escherichia coli Isolaten},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-17593},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Das Kerngenom pathogener Escherichia coli Isolate wird von zahlreichen variablen Regionen unterbrochen, die meist durch horizontalen Gentransfer erworben wurden und {\"u}ber das ganze Chromosom verteilt sind. Diese variablen Bereiche tragen h{\"a}ufig Gene f{\"u}r Virulenz- und Fitnessfaktoren und sind oftmals nur instabil in das Chromosom integriert. Um die Verbreitung variabler Bereiche, die insbesondere Virulenzfaktoren kodieren, innerhalb verschiedener klinischer Isolate n{\"a}her untersuchen zu k{\"o}nnen, wurde im Rahmen dieser Arbeit ein spezieller DNA-Array entwickelt. Dieser enthielt zahlreiche Sonden f{\"u}r Gene, die f{\"u}r die Virulenz von verschiedenen Erregern der Gattung E. coli als auch der Untergruppe Shigella charakteristisch sind. Mit diesem "Pathoarray" wurde die Verbreitung von Virulenzgenen in unterschiedlichen E. coli Isolaten untersucht. Zus{\"a}tzlich wurden Unterschiede im Kerngenom mit Hilfe eines kommerziell erwerbbaren DNA-Arrays bestimmt. Ein Vergleich des Kerngenoms von uropathogenen St{\"a}mmen mit Derivaten, bei denen Pathogenit{\"a}tsinseln deletiert sind, best{\"a}tigte die Auffassung, dass der Deletion von Pathogenit{\"a}tsinseln ein spezieller Mechanismus zu Grunde liegt, von dem das Kerngenom nicht betroffen ist. Das Kerngenom der untersuchten St{\"a}mme war prinzipiell sehr konserviert und unterschied sich lediglich durch wenige Gene aus Bakteriophagen. Die gr{\"o}ßten Unterschiede wurden bei Genen beobachtet, die zum variablen Teil des Genoms geh{\"o}ren und charakteristisch f{\"u}r das jeweilige Isolat waren. Mit Hilfe der DNA-Array Technologie lassen sich auch {\"A}nderungen von Expressionsprofilen studieren, die von Mutationen oder durch Umwelteinfl{\"u}sse bedingt werden. Im zweiten Teil dieser Arbeit wurde durch Transkriptomanalysen das RfaH-abh{\"a}ngige Regulon untersucht, insbesondere im Hinblick auf solche Gene, die die Biofilmbildung beeinflussen. Beim Vergleich der Transkriptome von E. coli 536rfaH mit dem Wildtyp wurde eine signifikant erh{\"o}hte Expression von Antigen 43 festgestellt. Im E. coli K-12 Stammhintergrund konnte dieses Oberfl{\"a}chenprotein als Hauptfaktor f{\"u}r die RfaH-abh{\"a}ngige Biofilmbildung identifiziert werden. Das verk{\"u}rzte LPS-Kernoligosaccharid im Stamm MG1655rfaH hatte ebenfalls einen großen Einfluss auf die verst{\"a}rkte Biofilmbildung. Vermutlich verst{\"a}rkte die verbesserte Pr{\"a}sentation von Agn43 durch ein verk{\"u}rztes LPS die Biofilmbildung signifikant. Andere Oberfl{\"a}chenstrukturen, wie die Colans{\"a}ure-Kapsel, zeigten keinen Effekt auf die Biofilmbildung von E. coli MG1655rfaH. Neben den Expressionsprofilen der St{\"a}mme 536 und 536rfaH bei 37 Grad C wurden auch die Expressionsprofile bei 30 Grad C sowie von Biofilmen analysiert. Prinzipiell konnten bei allen untersuchten Wachstumsbedingungen nur geringe Unterschiede zwischen 536 und 536rfaH festgestellt werden. Beim Vergleich der unterschiedlichen Wachstumsbedingungen (Temperatureffekt und planktonische Zellen vs. Biofilm) wurden jedoch deutliche Unterschiede beobachtet. Sowohl Gene des Kerngenoms als auch Gene von Pathogenit{\"a}tsinseln waren temperaturabh{\"a}ngig reguliert. Bei E. coli Isolaten lassen sich neben genomischen Unterschieden auch ph{\"a}notypische Unterschiede beobachten. Es wurde festgestellt, dass die Biofilmbildung von E. coli Isolaten abh{\"a}ngig von verschiedenen Faktoren und molekularen Mechanismen ist. Zudem konnte dargelegt werden, wie Unterschiede in der Zusammensetzung der {\"a}ußeren Membran durch eine ver{\"a}nderte LPS-Struktur und die Expression von Adh{\"a}sinen die Biofilmbildung beeinflussen k{\"o}nnen.},
  subject      = {Escherichia coli},
  language  = {de}
}