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2. Experimental evolution of plasmid genomes

Author

Ilhan, Judith, Prof. Dr. Tal Dagan, PD Dr. Charles M.A.P. Franz, Dagan, Tal, and Franz, Charles M. A. P.

Subjects
doctoral thesis, Abschlussarbeit, Experimental evolution, plasmid, ddc:570, Experimental evolution, plasmid, ddc:5XX, Mathematisch-Naturwissenschaftliche Fakultät, Faculty of Mathematics and Natural Sciences
Abstract

The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. The multi-copy state of plasmids leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. Consequently, I hypothesize that genetic drift of plasmid alleles during cell division has implication for the evolutionary rates of plasmids by lowering the number of accumulating mutations that are expected from the mutational supply. To test this hypothesis, I performed an experimental evolution experiment of low- and high-copy non-mobile plasmids in an Escherichia coli host. The results of the experiment revealed that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. The results further suggest that many plasmid mutations are quickly lost due to genetic drift during cell division. Here I term this special type of allele dynamics in the population as ‘segregational drift’. Thus, segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. In conclusion, depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. Plasmid copy number is thus an important determinant of plasmid evolvability due to the manifestation of segregational drift.

Published
2019

5. Additional file 3: Table S2. of Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria

Author

Koch, Robin, Kupczok, Anne, Stucken, Karina, Ilhan, Judith, Hammerschmidt, Katrin, and Dagan, Tal

Subjects
genetic structures
Abstract

Orthologous TSS conservation. For each pair of TSS-classes we compare the ratio of orthologous TSSs to the total frequency of TSSs (using Fisher's exact test). The class with a larger ratio includes more positional orthologs and is therefore more conserved. TSSs that fit into more than one class (i.e., gaTSS, giTSS, aiTSS and gaiTSS) were excluded from the analysis. (PDF 52Â kb)

Published
2017
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6. Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V)

Author

Weissenbach, Julia, Ilhan, Judith, Bogumil, David, Hülter, Nils, Stucken, Karina, Dagan, Tal, Weissenbach, Julia, Ilhan, Judith, Bogumil, David, Hülter, Nils, Stucken, Karina, and Dagan, Tal

Abstract

Chaperonins promote protein folding and areknown to play a role in themaintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a single-copy bicistronic operon, whereas in cyanobacteria up to three groES/groEL paralogs have been documented. Here we study the evolution and functional diversification of chaperonin paralogs in the heterocystous, multi-seriate filament forming cyanobacterium Chlorogloeopsis fritschii PCC 6912. The genome of C. fritschii encodes two groES/groEL operons (groESL1, groESL1.2) and amonocistronic groEL gene (groEL2). A phylogenetic reconstruction reveals that the groEL2 duplication is as ancient as cyanobacteria, whereas the groESL1.2 duplication occurred at the ancestor of heterocystous cyanobacteria. A comparison of the groEL paralogs transcription levels under different growth conditions shows that they have adapted distinct transcriptional regulation. Our results reveal that groEL1 and groEL1.2 are upregulated during diazotrophic conditions and the localization of their promoter activity points towards a role in heterocyst differentiation. Furthermore, protein-protein interaction assays suggest that paralogs encoded in the two operons assemble into hybrid complexes. The monocistronic encoded GroEL2 is not forming oligomers nor does it interact with the co-chaperonins. Interaction between GroES1.2 and GroEL1.2 could not be documented, suggesting that the groESL1.2 operon does not encode a functional chaperonin complex. Functional complementation experiments in Escherichia coli show that only GroES1/GroEL1 and GroES1/GroEL1.2 can substitute the native operon. In summary, the evolutionary consequences of chaperonin duplication in cyanobacteria include the retention of groESL1 as a housekeeping gene, subfunctionalization of groESL1.2 and neofunctionalization of

Published
2017
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10. Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability.

Author

Ilhan, Judith, Kupczok, Anne, Woehle, Christian, Wein, Tanita, Hülter, Nils F, Rosenstiel, Philip, Landan, Giddy, Mizrahi, Itzhak, and Dagan, Tal

Abstract

The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. We investigate the implications of random genetic drift of multicopy plasmids during cell division—termed here "segregational drift"—to plasmid evolution. Performing experimental evolution of low- and high-copy non-mobile plasmids in Escherichia coli, we find that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. In addition, simulated evolution of multicopy plasmid alleles demonstrates that segregational drift leads to increased loss frequency and extended fixation time of plasmid mutations in comparison to haploid chromosomes. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. Our study demonstrates that segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. We suggest that plasmid copy number is an important determinant of plasmid evolvability due to the manifestation of segregational drift. [ABSTRACT FROM AUTHOR]

Published
2019
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