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Natural competence in the Planctomycetes and its use in transforming the Gemmata-related species Tuwongella immobilis
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2019 (English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Place, publisher, year, edition, pages
2019.
National Category
Evolutionary Biology
Research subject
Biology with specialization in Molecular Evolution
Identifiers
URN: urn:nbn:se:uu:diva-378567OAI: oai:DiVA.org:uu-378567DiVA, id: diva2:1294262
Available from: 2019-03-06 Created: 2019-03-06 Last updated: 2019-03-22
In thesis
1. Evolution of cellular complexity and other remarkable features in Gemmataceae: Complex bacterial lineages defy prokaryotic trends
Open this publication in new window or tab >>Evolution of cellular complexity and other remarkable features in Gemmataceae: Complex bacterial lineages defy prokaryotic trends
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacteria of the family Gemmataceae belong the phylum Planctomycetes and are remarkable because of their complex cellular architectures, previously considered to be traits exclusive to eukaryotes. This thesis provides clues to the atypical cell envelope, the enhanced radiotolerance and the amazing cellular complexity of these bacteria.

A comparative genomics study of these bacteria revealed massive duplications and new combinations of structural domains that are highly abundant in eukaryotes but rare in bacteria. These domains are known to facilitate signalling and protein interactions. The proteins of these bacteria also contain long regions with no predicted domains. On average, eukaryotic proteins are longer and more disordered than prokaryotic proteins. Intriguingly, the length and fraction of disordered regions in proteins of some bacteria are higher than in many other prokaryotes, and these bacteria also have complex lifestyles. Many bacteria in the Planctomycetes, including the Gemmataceae, are among these few bacteria. This suggests that there is no sharp boundary between prokaryotes and eukaryotes with respect to protein length and domain composition patterns, as previously thought.

A bioinformatics analysis revealed the loss of genes for the peptidoglycan cell wall in some lineages of the Planctomycetes. Loss of the gene for the FtsZ protein, the major cell division protein in bacteria, may have facilitated the evolution of budding in the Planctomycetales and led to the gradual loss of the cell wall and cell division gene cluster. These changes may have enabled the expansion of the inner membrane and triggered adaptive changes in conserved membrane proteins and transport systems. The loss of the peptidoglycan cell wall may also explain the altered cell morphology. A subcellular proteomics study showed that the DNA replication and repair proteins are associated with the cell envelope, which supports the cell factory model of DNA replication.

T. immobilis, which has the simplest genome of all members of the Gemmataceae, was found to be naturally competent and most suitable for transformation experiments. T. immobilis was transformed to produce mutants in which the gene for DdrA, a double stranded break DNA repair protein, has been inactivated. The DdrA-null mutant showed a major loss in radiotolerance.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 71
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1778
Keywords
Molecular evolution, Planctomycetes, Gemmataceae, functional organization, signalling, protein interaction, peptidoglycan, membranes, cell division, radiation tolerance, Pfam, SCOP, comparative genomics, protein architecture, domain shuffling and orthologous clustering
National Category
Genetics Cell and Molecular Biology Evolutionary Biology
Research subject
Bioinformatics; Biology with specialization in Molecular Evolution; Biology with specialization in Molecular Biology
Identifiers
urn:nbn:se:uu:diva-378405 (URN)978-91-513-0585-1 (ISBN)
Public defence
2019-04-23, B10:2, Biomedicinskt centrum (BMC), Husargatan 3, Uppsala, 09:15 (English)
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Supervisors
Available from: 2019-03-26 Created: 2019-03-05 Last updated: 2019-05-07

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