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Bacterial genome size reduction by experimental evolution
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
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2005 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, Vol. 102, no 34, 12112-12116 p.Article in journal (Refereed) Published
Abstract [en]

Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.

Place, publisher, year, edition, pages
2005. Vol. 102, no 34, 12112-12116 p.
Keyword [en]
bacterial evolution, genome reduction, serial passage
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-80317DOI: 10.1073/pnas.0503654102PubMedID: 16099836OAI: oai:DiVA.org:uu-80317DiVA: diva2:108231
Available from: 2006-05-05 Created: 2006-05-05 Last updated: 2011-06-30Bibliographically approved
In thesis
1. Dynamics of the Bacterial Genome: Rates and Mechanisms of Mutation
Open this publication in new window or tab >>Dynamics of the Bacterial Genome: Rates and Mechanisms of Mutation
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacterial chromosomes are highly dynamic, continuously changing with respect to gene content and size via a number of processes, including deletions that result in gene loss. How deletions form and at what rates has been the focus of this thesis.

In paper II we investigated how chromosomal location affects chromosomal deletion rates in S. typhimurium. Deletion rates varied more than 100-fold between different chromosomal locations and some large deletions significantly increased the exponential growth rate of the cells. Our results suggest that the chromosome is heterogeneous with respect to deletion rates and that deletions may be genetically fixed as a consequence of natural selection rather than by drift or mutational biases.

In paper I we examined in a laboratory setting how rapidly reductive evolution, i.e. gene loss, could occur. Using a serial passage approach, we showed that extensive genome reduction potentially could occur on a very short evolutionary time scale. For most deletions we observed little or no homology at the deletion endpoints, indicating that spontaneous deletions often form through a RecA independent process.

In paper III we examined further how large spontaneous deletions form and, unexpectedly, showed that 90% of all spontaneous chromosomal deletions required error-prone translesion DNA polymerases for their formation. We propose that the translesion polymerases stimulate deletion formation by allowing extension of misaligned single-strand DNA ends.

In paper IV we investigated how the translesion DNA polymerase Pol IV, RpoS and different types of stresses affect mutation rates in bacteria. Derepression of the LexA regulon caused a small to moderate increase in mutation rates that was fully dependent on functional endonucleases but only partly dependent on translesion DNA polymerases. RpoS levels and growth stresses had only minor effects on mutation rates. Thus, mutation rates appear very robust and are only weakly affected by growth conditions and induction of translesion polymerases and RpoS.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 56 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 509
bacteria, bacterial evolution, genome reduction, gene loss, serial passage, DNA homology, tranlesion DNA polymerase, stress
National Category
Microbiology in the medical area Microbiology in the medical area
Research subject
Evolutionary Genetics; Microbiology
urn:nbn:se:uu:diva-111428 (URN)978-91-554-7687-8 (ISBN)
Public defence
2010-02-05, C10:305, BMC, Husargatan 3, Uppsala, 09:00 (English)
Available from: 2010-01-14 Created: 2009-12-14 Last updated: 2010-01-15

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Nilsson, A IKoskiniemi, SannaAndersson, Dan I
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