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Nutritional Control of DNA Replication Initiation through the Proteolysis and Regulated Translation of DnaA
Philipps University Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, Germany.
Philipps University Marburg, Germany, Max Planck Institute for Terrestrial Microbiology, Germany.
Philipps University Marburg, Germany.ORCID iD: 0000-0003-1858-7770
Philipps University Marburg, Germany.
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2015 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, no 7, article id e1005342Article in journal (Refereed) Published
Abstract [en]

Bacteria can arrest their own growth and proliferation upon nutrient depletion and under various stressful conditions to ensure their survival. However, the molecular mechanisms responsible for suppressing growth and arresting the cell cycle under such conditions remain incompletely understood. Here, we identify post-transcriptional mechanisms that help enforce a cell-cycle arrest in Caulobacter crescentus following nutrient limitation and during entry into stationary phase by limiting the accumulation of DnaA, the conserved replication initiator protein. DnaA is rapidly degraded by the Lon protease following nutrient limitation. However, the rate of DnaA degradation is not significantly altered by changes in nutrient availability. Instead, we demonstrate that decreased nutrient availability downregulates dnaA translation by a mechanism involving the 5' untranslated leader region of the dnaA transcript; Lon-dependent proteolysis of DnaA then outpaces synthesis, leading to the elimination of DnaA and the arrest of DNA replication. Our results demonstrate how regulated translation and constitutive degradation provide cells a means of precisely and rapidly modulating the concentration of key regulatory proteins in response to environmental inputs.

Place, publisher, year, edition, pages
2015. Vol. 11, no 7, article id e1005342
National Category
Biological Sciences
Research subject
Molecular Bioscience
Identifiers
URN: urn:nbn:se:su:diva-166028DOI: 10.1371/journal.pgen.1005342OAI: oai:DiVA.org:su-166028DiVA, id: diva2:1287727
Available from: 2019-02-11 Created: 2019-02-11 Last updated: 2019-12-04Bibliographically approved
In thesis
1. Stress response regulation and protein aggregate inheritance in Caulobacter crescentus
Open this publication in new window or tab >>Stress response regulation and protein aggregate inheritance in Caulobacter crescentus
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many stress conditions a cell encounters threaten the continuation of basic biological processes ultimately endangering its survival. Heat shock and antibiotic exposure can lead to a sudden surge of protein un- and misfolding, while nutrient starvation directly causes a lack of energy and molecular building blocks. Our understanding of how cells integrate environmental stress signals, execute protective functions and handle persistent damage is still far from comprehensive. In this thesis the model bacterium Caulobacter crescentus was used to answer basic questions about the regulation and execution of bacterial stress responses and damage clearance.

Persistent larger protein aggregates can be maintained as remnants of a past stress exposure and in all of the few bacteria studied to date these particles collect at the poles. In the symmetrically dividing bacterium E. coli this aggregate localization pattern was shown to lead to an old pole lineage-specific retention. In paper I, we studied aggregate formation and inheritance in an asymmetrically dividing bacterium. While aggregates are dissolved by molecular chaperones following moderate heat stress, intense stress induces the emergence of long-lived aggregates. Surprisingly, we find that the majority of persistent aggregates do not collect at the old poles but instead describe a mechanism by which they are constantly displaced towards the new pole. This causes inheritance of aggregates by old and new pole cells at a stable rate without lineage-specific retention, a previously unknown pattern of aggregate inheritance in bacteria.

While we found that deletion of most chaperones in C. crescentus does not affect viability in the absence of stress, the mechanistic basis for why DnaK, like in other bacteria, is also required in the absence of stress remains unclear. In paper II, we show that DnaK's function as a negative regulator of the heat shock sigma factor σ32 is essential for viability at physiological temperatures and uncover potential new layers of σ32 regulation. We find that the σ32-dependent response comprises a reallocation of resources from proliferative to maintenance functions and in addition to its known function in blocking DNA replication also affects other processes like protein translation, a process vulnerable to proteotoxic stress. Prolonged unrestricted activity of this stress response induced by the absence of DnaK is lethal. We conclude that while DnaK is essential for protein folding at elevated temperatures, its evolutionarily newer function in balancing the cell's proliferative and maintenance programs is a requirement for survival.

Growth and cell cycle progression is also regulated in response to nutrient limitation. Like under heat shock conditions, we show in paper III that carbon starvation during entry into stationary phase leads to a block of DNA replication for which, in contrast to heat stress, the molecular basis was not yet understood. We find that downregulation of DnaA levels is achieved by an as yet unknown nutrient availability sensing process involving the 5' untranslated region, inhibiting translation of the dnaA mRNA, which combined with constant degradation of DnaA by the protease Lon results in its elimination. This study provided new mechanistic insight into nutrient-dependent control of DNA replication and shows that the same regulatory outcomes can be achieved through different means depending on the stress response.

In conclusion this thesis describes the discovery of an unanticipated alternative way of protein aggregate inheritance with implications for our view on damage segregation in bacterial populations as well as new mechanistic insight into how cells balance proliferative with protective functions in response to heat shock and nutrient limitation.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 2019. p. 81
Keywords
stress, protein aggregation, cellular aging, molecular chaperones, heat shock response, DnaK, sigma factor, suppressor genes, DNA replication, starvation, Caulobacter crescentus
National Category
Biological Sciences
Research subject
Molecular Bioscience
Identifiers
urn:nbn:se:su:diva-166030 (URN)978-91-7797-586-1 (ISBN)978-91-7797-587-8 (ISBN)
Public defence
2019-03-29, Vivi Täckholmsalen (Q-salen) NPQ-huset, Svante Arrhenius väg 20, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2019-03-06 Created: 2019-02-12 Last updated: 2019-04-12Bibliographically approved
2. Regulation of the bacterial cell cycle in response to starvation
Open this publication in new window or tab >>Regulation of the bacterial cell cycle in response to starvation
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacteria have adapted to diverse environments, which are often unpredictable and constantly changing. In order to survive, bacteria need to make the most of nutrients while they are available, while being prepared to rapidly change their behaviour when conditions take a turn for the worse. One of the most central processes that must be regulated to ensure survival when conditions change is the cell cycle, the succession of DNA replication, chromosome segregation and cell division connecting growth and proliferation.

In this thesis, we investigate how environmental information, specifically nutrient availability, is used to modulate cell cycle progression. In Paper I, we uncover a mechanism used by Caulobacter crescentus to arrest DNA replication in response to nutrient depletion. We find that the essential replication initiator protein DnaA is eliminated under these conditions, and determine that this occurs by a mechanism based on constant degradation of DnaA by the protease Lon. This constant degradation is coupled with regulated translation of the dnaA mRNA to decrease DnaA synthesis as nutrient levels decrease. We found that this regulated translation of dnaA depends on its long 5′ untranslated region.

The replication initiator DnaA is conserved in almost all bacteria, and although some aspects of its regulation are maintained, others work differently in distantly related bacteria. In Paper II, we investigate how the enteric bacterium Escherichia coli regulates DNA replication at the onset of the stationary phase. We found that although DnaA is eliminated as growth slows, this downregulation is not required to arrest replication. We also found that the signalling molecule ppGpp, which is produced in response to starvation, is required for the elimination of DnaA at entry to stationary phase. High ppGpp levels lead to a block of replication initiation, however we found that chromosome content is still dramatically reduced at the onset of stationary phase in the absence of ppGpp, indicating that a ppGpp-independent mechanism is involved.

While bacteria are usually studied over short timeframes and under optimal conditions in the laboratory, in nature, bacteria are often found in environments where only very slow growth is possible. In Paper III, we investigate a change in morphology observed to occur in a small subpopulation of cells in cultures of C. crescentus after extended incubation in the stationary phase. These cells form long, helical filaments. We determined that the filamentation arises as a result of a block of DNA replication and cell division while growth continues, and that this can be induced by a combination of conditions in the medium: low phosphate, high pH and excess ammonium. We find that these conditions occur in freshwater lakes during persistent algal blooms in the summer months, indicating that this response might occur in the wild.

In summary, this thesis provides new insight into the mechanisms bacteria use to adapt their cell cycle, and specifically, DNA replication to changes in their environment, how bacteria are able to change their morphology by disrupting the coupling between growth and the cell cycle, and investigates how this morphological plasticity may be advantageous in natural environments.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 2019. p. 64
National Category
Biological Sciences
Research subject
Molecular Bioscience
Identifiers
urn:nbn:se:su:diva-172600 (URN)978-91-7797-823-7 (ISBN)978-91-7797-824-4 (ISBN)
Public defence
2019-10-18, Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.

Available from: 2019-09-25 Created: 2019-09-04 Last updated: 2019-09-17Bibliographically approved

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