Sirvi Autor "Rikberg, Roger" järgi

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Isolation and characterization of a phage collection against Pseudomonas putida
(2024-06-11) Brauer, Age; Rosendahl, Sirli; Kängsep, Anu; Lewańczyk, Alicja Cecylia; Rikberg, Roger; Hõrak, Rita; Tamman, Hedvig
The environmental bacterium, Pseudomonas putida, possesses a broad spectrum of metabolic pathways. This makes it highly promising for use in biotechnological production as a cell factory, as well as in bioremediation strategies to degrade various aromatic pollutants. For P. putida to flourish in its environment, it must withstand the continuous threats posed by bacteriophages. Interestingly, until now, only a handful of phages have been isolated for the commonly used laboratory strain, P. putida KT2440, and no phage defence mechanisms have been characterized. In this study, we present a new Collection of Environmental P. putida Phages from Estonia, or CEPEST. This collection comprises 67 double-stranded DNA phages, which belong to 22 phage species and 9 phage genera. Our findings reveal that most phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require an intact lipopolysaccharide for P. putida infection. Furthermore, we show that cryptic prophages present in the P. putida chromosome provide strong protection against the infection of many phages. However, the chromosomal toxin–antitoxin systems do not play a role in the phage defence of P. putida. This research provides valuable insights into the interactions between P. putida and bacteriophages, which could have significant implications for biotechnological and environmental applications.
Poomisvastuse mõju Pseudomonas putida stressitaluvusele
(Tartu Ülikool, 2023) Rikberg, Roger; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Molekulaar- ja rakubioloogia instituut
Poomisvastus on viis, kuidas bakterid tulevad toime mitmesuguste stressitingimustega. Kuigi poomisvastuse mõju on varasemalt põhjalikult kirjeldatud biokile moodustumises, on tagaplaanile jäänud Pseudomonas putida faagikaitse ning antibiootikumi- ja kemikaalitolerantsuse uuringud. Seega puudub selge ülevaade poomisvastuse mõjust P. putida füsioloogiale. Sellest lähtuvalt oli käesoleva töö eesmärgiks välja selgitada, kuidas poomisvastus mõjutab P. putida’t, käsitledes ka selle võimalikku rolli faagivastases kaitses. Tulemused näitasid, et poomisvastus-defektsed tüved on prototroofid ning et poomisvastus mõjutab vähesel määral antibiootikumi- ja kemikaalitolerantsust ning kaitseb nõrgalt bakteriofaagide eest, kuid kaitse tugevus sõltub suuresti konkreetsest bakteriofaagist. Lisaks leiti, et poomisvastus-defektsed tüved on statsionaarses kasvufaasis suuremad kui metsiktüve rakud, moodustavad ahelaid ning neil esinevad tugevad membraanidefektid.
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.