Sirvi Märksõna "bacteriophages" järgi

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Characterising a Novel HNH-Domain Containing Bacterial Immunity System From Escherichia coli
(Tartu Ülikool, 2025) Aliyeva, Elfi; Mets, Toomas, juhendaja; Abdullah, Minhal, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Bioinseneeria instituut
Bacteria are constantly in danger of being attacked by bacterial viruses - bacteriophages. To combat the threat, bacteria have developed a wide array of intricate and diverse immune systems. Phage therapy’s growing popularity has led to increased interest in bacterial immunity. My thesis investigates one such potential immunity system from Escherichia coli, discovered by our colleagues at Lund University, named Bogomol. It is predicted to be comprised of an HNH-containing endonuclease domain and a C-terminal domain of unknown function. I validated Bogomol as an immunity system acting against certain phages of Straboviridae. This was done by performing efficiency of plating assays and liquid culture experiments against the BASEL phage library. As an attempt to further investigate the triggers of Bogomol, escape mutant experiments were also conducted.
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Stringent response in the infection of lytic phages of Pseudomonas putida
(Tartu Ülikool, 2025) Rikberg, Roger; Tamman, Hedvig, juhendaja; Lewańczyk, Alicja Cecylia, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Molekulaar- ja rakubioloogia instituut
As the most abundant group of organisms on Earth, bacteria inhabit nearly every environment and are therefore frequently exposed to stress, including bacteriophage infection. Stringent response, induced by the alarmone molecule (p)ppGpp, is a common stress response in bacteria to overcome different stressful conditions. Pseudomonas putida, known for its versatile metabolism, is widely used in environmental studies and biotechnology. However, the role of stringent response in phage defence remains poorly understood. Therefore, this thesis aims to ascertain whether the stringent response influences the infection of lytic phages in P. putida, focusing on phage adsorption and burst size. The results of this study show that, in general, phage infection in liquid media are consistent with solid media results. While the stringent response does not notably affect adsorption, it can influence the length of latent period and reduce the burst size of infecting phages.
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The opposite effects of stringent response on phage infection of Pseudomonas putida
(2026-01-02) Lewańczyk, Alicja Cecylia; Hinnu, Mariliis; Mägi, Elise; Rikberg, Roger; Brauer, Age; Tamman, Hedvig
Guanosine tetra- and pentaphosphate ((p)ppGpp) are one of the key players in the stress response of bacteria. Accumulation of these alarmones activates the stringent response, usually triggered by different nutritional stresses. For Pseudomonas putida, there is only limited data available on the importance of the stringent response in stress situations. Also, in recent years, different specific phage defence systems have received much attention, but little is known about the involvement of stringent response in phage infection. Here, we show that P. putida PaW85 (p)ppGpp0 is prototrophic and tolerates chemical stress well. However, in the stationary phase P. putida cells deprived of (p)ppGpp have impaired membrane integrity. In addition, we conducted a large-scale screening of stringent response effects on phage infections using the CEPEST phage collection. We tested 67 phages of 22 different species and revealed that the lack of (p)ppGpp has opposing effects on phage infection with nearly half of the tested phages showing higher infection efficiency on the (p)ppGpp0 cells, whereas the other half shows reduced infection. We show that the differences in phage infection efficiency for phages Aura and Amme-3 are not caused by adsorption rate differences, but alterations in downstream steps of the infection cycle—prolonged latent period in the absence of (p)ppGpp or unproductive infection in the presence of (p)ppGpp. Altogether, results indicate that the role of stringent response in phage infection is highly diverse, and over half of the times the presence of (p)ppGpp facilitates phage infections rather than protects the cells.
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Validating Three Anti-Phage Defense Systems in Pseudomonas putida
(Tartu Ülikool, 2025) Polekauskaite, Ilze; Ainelo, Andres, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Bacteriophages (phages) are viruses that infect bacteria, causing significant mortality. Due to this selective pressure, bacteria contain anti-phage defense systems, proteins which help to abrogate or reduce the effects of infection. As biotechnology employs genetic editing techniques to optimize microbial strains, understanding their genome is necessary to guide these decisions. Aside from efficient performance or production, anti-phage defense systems are an important consideration for minimizing risks to bacterial survival. The soil bacterium Pseudomonas putida prominently figures in synthetic biology research due to its favourable characteristics. Despite this, the anti-phage defense systems of P. putida, and the biotechnological PaW85 strain, are not studied extensively due to the lack of isolated phages. In this study, we use the CEPEST P. putida phage collection to verify three predicted anti-phage defense systems, PD-T7-1, HerA/DUF4297 and RMII. Mutant strains lacking the respective systems were constructed and phage susceptibility assays were conducted to test the function of each system in anti-phage defense. Ultimately, the roles of PD-T7-1 and RMII could not be verified with the phages available, while HerA/DUF4297 was seen to have defensive function. Further, using a strain with an active site mutation in DUF4297 showed that the enzyme likely functions as a nuclease in the complex. In the future, the expansion of the CEPEST collection will enable to further test the potential anti-phage defense roles of PD-T7-1 and RMII. Additionally, the validation of defensive function initiates future research in characterizing the activation mechanisms of HerA/DUF4297 in P. putida. Together, the findings expand the current body of knowledge of the anti-phage defense systems in P. putida and may improve future biotechnology applications.