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The number of sequenced genomes increases rapidly due to the development of faster, better and new technologies. Thus, there is a great interest in automation, and standardization of the subsequent processing and analysis stages of the generated enormous amount of data. In the current work, genomes of clones, strains and species of Streptococcus were compared, which were sequenced, annotated and analysed with several technologies and methods. For sequencing, the 454- and Illumina-technology were used. The assembly of the genomes mainly was performed by the gsAssembler (Newbler) of Roche, the annotation was performed by the annotation pipeline RAST, the transfer tool RATT or manually. Concerning analysis, sets of deduced proteins of several genomes were compared to each other and common components, the so-called core-genome, of the used genomes of one or closely related species determined. Detailed comparative analysis was performed for the genomes of isolates of two clones to gather single nucleotide variants (SNV) within genes.
This work focusses on the pathogenic organism Streptococcus pneumoniae. This species is a paradigm for transformability, virulence and pathogenicity as well as resistance mechanisms against antibiotics. Its close relatives S. mitis, S. pseudopneumoniae and S. oralis have no pathogenicity potential as high as S. pneumoniae available and are thus of high interest to understand the evolution of S. pneumoniae. Strains of two S. pneumoniae clones were chosen. One is the ST10523 clone, which is associated with patients with cystic fibrosis and is characterized by long-term persistence. This clone is lacking an active hyaluronidase, which is one of the main virulence factors. The lack of two phage clusters possibly contributed to the long persistence in the human host. The clone ST226 shows a high penicillin resistance but interestingly one strain is sensitive against penicillin. Here it could be seen that the penicillin resistance mainly arose from the presence of mosaic-PBPs, while special alleles of MurM and CiaH - both genes are associated with penicillin-resistance – were present in resistant and sensitive strains as well. Penicillin resistance of S. pneumoniae is the result of horizontal gene transfer, where DNA of closely related species, mainly S. mitis or S. oralis, served as donor. The transfer of DNA from the high-level penicillin-resistant strain S. oralis Uo5 to the sensitive strain S. pneumoniae R6 was intentioned to reveal the amount of transferred DNA and whether it is possible to reach the high resistance level of S. oralis Uo5. Altogether, about 19kb of S. oralis DNA were transferred after three successive transformation steps, about 10-fold less than during transfer from S. mitis, which is more closely related to S. pneumoniae, as donor. MurE was identified as new resistance determinant. Since the resistance level of the donor strain could not be reached, it is assumed, that further unknown factors are present which contribute to penicillin resistance. The comparison of S. pneumoniae and its close relatives was performed using deduced protein sequences. 1.041 homologous proteins are common to the four complete genomes of S. pneumoniae R6, S. pseudopneumoniae IS7493, S. mitis B6 and S. oralis Uo5. Most of the virulence and pathogenicity factors described for S. pneumoniae could also be found in commensal species. These observations were confirmed by further investigations by Kilian et al. (Kilian, et al., 2019). After adding 26 complete S. pneumoniae genomes to the analysis, only 104 gene products could be identified as specific for this species. Investigations of a larger number of related streptococci, which were isolated from human and several primates, confirmed the presence of most of the virulence factors of human pneumococci in S. oralis and S. mitis strains from primates. While NanBC is common among S. pneumoniae and is missing in all S. oralis, all S. oralis contain a ß-N-acetyl-hexosaminidase which vice versa is missing in S. pneumoniae. The occurrence of S. oralis also in free-living chimpanzees suggests the assumption, that this species is part of the commensal flora of these Old-World monkeys unlike S. pneumoniae which has evolved with its human host. Compared to S. pneumoniae, S. oralis shows an amazing variability in factors important for biosynthesis of peptidoglycan and teichoic acid (PBP, MurMN, lic-cluster). Some streptococci contain a second PGP3 homologue. Additional analyses with further isolates, especially of wild animals, are necessary to determine host-specific components.
Die heutige Epigenetik erfordert eine evolutionstheoretische Neubewertung zum Verhältnis von Entwicklung, Vererbung und Anpassungsfähigkeit der Lebewesen. Heutige Fragen zur Entstehung und Weitergabe epigenetischer Veränderungen reichen zurück bis in die Anfänge mytho-, theo- und kosmologischer Betrachtungen. Platon, Augustinus und Cusanus lösen metaphysische Probleme des Anfangs durch einen Übergang vom Sein zum Werden. Eine Übertragung kosmologischer Konzepte in die Embryologie findet sowohl bei Aristoteles als auch in der Renaissance statt. Harvey und Wolff beschreiben die Epigenese in Anlehnung an die kosmologische Revolution von Planeten und Gestirnen als epigenetische Revolution von Henne und Ei. Die Transformation von der zeitlosen, natürlichen Ordnung zu einer Genealogie der Natur und der Triumph der Epigenesis-Theorie über die Präformationslehre ermöglichen zu Beginn des 19. Jahrhundert eine Biologie, die in ihren epigenetischen Grundannahmen unterschiedliche Autoren wie Goethe, Schelling, Lamarck, Mendel und Darwin verbindet. Mit der Umdeutung der revolutionären Epigenese bei Lamarck werden onto- und phylogenetische Prozesse unterscheidbar, deren Verhältnis bei Darwin und in den postdarwinschen Debatten durch verschiedene Theorien der Entwicklung, Vererbung und Anpassung bestimmt wird. Schon bei Darwin kommt es zu einer pangenetischen Synthese von neolamarckistischen, selektions- und organisationstheoretischen Mechanismen der Anpassung. In der ersten Hälfte des 20. Jahrhunderts entsteht die heute noch prägende genetische Evolutionstheorie, bei der Entwicklung und Anpassung vererbungs- und selektionstheoretisch verengt werden. Mit Waddingtons Epigenetik wird das Verhältnis von Onto- und Phylogenese durch die epigenetische Landschaft verräumlicht und das Konzept der Anpassungsfähigkeit konkretisiert. Die Molekularisierung von genetischer und epigenetischer Evolution lässt epigenetische Fragen der Biologie des 19. Jahrhunderts und das protobiologische Erbe wieder aktuell werden. Epigenetische Evolution beruht auf einer Synergie von natürlicher Selektion und epigenetischer Systemdynamik. Diese Synergie erzeugt anpassungs- und lernfähige Organismen, die auf ihre eigene Entwicklung, Vererbung und Anpassungsfähigkeit Einfluss nehmen können. Mit den jüngsten theoretischen Entwicklungen der Epigenetik hat eine Temporalisierung des biologischen Informationsverständnisses begonnen. Aufgabe der genealogischen Annäherung ist die Erhellung dieser historischen Entwicklung und ihrer Relevanz für die heutige Theoriebildung.
Cyanobacteria are the only prokaryotes with the ability to conduct oxygenic photosynthesis,
therefore having major influence on the evolution of life on earth. Their diverse morphology
was traditionally the basis for taxonomy and classification. For example, the genus
Chroococcidiopsis has been classified within the order Pleurocapsales, based on a unique
reproduction modus by baeocytes. Recent phylogenetic results suggested a closer
relationship of this genus to the order Nostocales. However, these studies were based
mostly on the highly conserved 16S rRNA and a small selection of Chroococcidiopsis
strains. One aim of this present thesis was to investigate the evolutionary relationships of
the genus Chroococcidiopsis, the Pleurocapsales and remaining cyanobacteria using
16S rRNA, rpoC1 and gyrB gene. Including the single gene, as the multigene analyses of
97 strains clearly showed a separation of the genus Chroococcidiopsis from the
Pleurocapsales. Furthermore, a sister relationship between the genus Chroococcidiopsis
and the order Nostocales was confirmed. Consequently, the monogeneric family
Chroococcidiopsidaceae Geitler ex. Büdel, Donner & Kauff familia nova is justified. The
phylogenetic analyses also revealed the polyphyly of the remaining Pleurocapsales, due to
the fact that the strain Pleurocapsa PCC 7327 was always separated from other strains.
This is supported by differences in their metabolism, ecology and physiology.
A second aim of this study was to investigate the thylakoid arrangement of
Chroococcidiopsis and a selection of cyanobacterial strains. The investigation of 13 strains
with Low Temperature Scanning Electron Microscopy revealed two unknown thylakoidal
arrangements within Chroococcidiopsis (parietal and stacked). This result revised the
knowledge of the thylakoid arrangement in this genus. Previously, only a coiled
arrangement was known for three strains. Based on the data of 66 strains, the feature
thylakoid arrangement was tested as a potential feature for morphological identification of
cyanobacteria. The results showed a strong relationship between the group assignment of
cyanobacteria and their thylakoid arrangements. Hence, it is in general possible to
conclude from this certain phenotypic character the affiliation to a particular family, order
or genus.
The third aim of this study was to investigate biogeographical patterns of the worldwide
distributed genus Chroococcidiopsis. The phylogenetic analysis suggested that the genus do not have biogeographical patterns, which is in contrast with a recent study on hypolithic
living Chroococcidiopsis strains and the majority of phylogeographic analysis of
microorganisms. Further analysis showed no separation of different life-strategies within
the genus. These results could be related to the genetic markers utilized, which may not
contain biogeographical information. Hence the present study can neither exclude nor
prove the possibility of biogeographic and life-strategy patterns in the genus
Chroococcidiopsis.
Future research should be focused on finding appropriate genetic markers investigate of
evolutionary relationships and biogeographical patterns within Chroococcidiopsis.