Fitness effects of chromosomal toxin-antitoxin systems in Pseudomonas putida
Kuupäev
2023-06-05
Autorid
Ajakirja pealkiri
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Kirjastaja
Abstrakt
Enamiku bakterite kromosoomides leidub mitmeid toksiin-antitoksiin (TA) lookusi, mis kodeerivad bakterile kahjulikku toksiini ning seda neutraliseerivat antitoksiini. Selliste potentsiaalselt surmavate geenide laialdane levik bakterite genoomides on üllatav ning võiks viidata, et TA süsteemid on bakterile mingit moodi kasulikud. Kuigi TA süsteeme on põhjalikult uuritud, pole seni jõutud üksmeelele nende tähtsuses bakteritele. On näidatud, et mõned TA süsteemid stabiliseerivad genoomis leiduvat mobiilset DNA-d, samas kui teised kaitsevad baktereid faagirünnaku korral. Arvatakse, et mõned TA süsteemid võivad olla olulised bakteri stressivastuses. Samas leidub ka uuringuid, mis viitavad, et TA süsteemid võivad olla isekad DNA elemendid, millest pole bakterile mingit kasu. Käesolev doktoritöö keskendub mullabakteri Pseudomonas putida kromosoomis leiduvatele TA süsteemidele, millest kõige põhjalikumalt on seni uuritud GraTA süsteemi. Toksiin GraT on vaid mõõdukalt toksiline ribosoom-sõltuv mRNaas, mis põhjustab külmatundlikku kasvu- ja ribosoomi biogeneesi defekti. Üllatuslikult leiti, et GraT põhjustatud ribosoomi biogeneesi defekti mõjutab bakteri peamine šaperonvalk DnaK, kuid varasemates katsetes jäi DnaK täpne roll selgusetuks. Kuigi GraT on funktsionaalne toksiin ja mõjutab antitoksiini GraA puudumisel P. putida stressitaluvust, ei ole kogu TA süsteemi deleteerimisel P. putida’le mingit efekti. See tõstatas küsimuse, et milline on graTA lookuse ning teiste TA süsteemide tähtsus P. putida’le. Kasutades proteoomi analüüsi, kirjeldab käesolev doktoritöö P. putida vastust toksiinile GraT. Samuti selgitati DnaK šaperoni rolli GraT toksilisuse reguleerimisel. Selgus, et DnaK soodustab GraT toksilisust, abistades ilmselt GraT-d voltumisel. Doktoritöö näitab, et uuritud tingimustes pole 13 TA süsteemist P. putida’le kasu. Pigem võivad nad teatud tingimustes, nagu konkurentsikatsetes ja faagirünnaku korral, bakteri kohasust vähendada. Käesoleva doktoritöö tulemused avardavad teadmisi TA süsteemide bioloogilise tähtsuse kohta ja viitavad selgelt TA süsteemide isekale olemusele.
Most bacteria encode small genetic modules called toxin-antitoxin (TA) systems in their chromosome, which consist of a poisonous toxin and its antidote. It is puzzling why such potentially lethal genetic elements are so widely distributed among bacteria and this could indicate that TA systems benefit their host in some way. The functions of chromosomal TA systems have been intensely studied, but no consensus regarding their importance to bacteria has been reached. Some TA systems have been shown to stabilize mobile genomic DNA, while others can protect bacteria against phages, and some have been proposed to participate in bacterial stress response regulation. However, there are also studies that cannot detect any beneficial effect of TA systems and propose that they are generally selfish DNA elements. This thesis focuses on the chromosomal TA systems of the soil bacterium Pseudomonas putida. The most thoroughly studied P. putida TA system is GraTA. While the toxin GraT is a ribosome-dependent mRNAse, it is conditionally toxic and causes cold-sensitive ribosome biogenesis defect. Interestingly, the major cellular chaperone DnaK was implicated in GraT-caused ribosome biogenesis defect, yet the exact role of DnaK in GraT toxicity has remained unclear. Even though the toxin GraT is functional and can affect the stress tolerance of P. putida in the absence of the antitoxin GraA, the whole TA system deletion has no fitness effects. This raises the question about the importance of GraTA along with other TA systems encoded in P. putida genome. This thesis describes the cellular changes that take place in P. putida cells lacking the antitoxin GraA and shows that DnaK enhances GraT toxicity, probably by helping GraT attain its proper fold. This work shows that TA systems are not beneficial to P. putida. Instead, they can be costly to P. putida in competition assays and during phage invasion. The results of this thesis shed light onto the biological importance of TA systems and clearly point to the selfish nature of TA systems.
Most bacteria encode small genetic modules called toxin-antitoxin (TA) systems in their chromosome, which consist of a poisonous toxin and its antidote. It is puzzling why such potentially lethal genetic elements are so widely distributed among bacteria and this could indicate that TA systems benefit their host in some way. The functions of chromosomal TA systems have been intensely studied, but no consensus regarding their importance to bacteria has been reached. Some TA systems have been shown to stabilize mobile genomic DNA, while others can protect bacteria against phages, and some have been proposed to participate in bacterial stress response regulation. However, there are also studies that cannot detect any beneficial effect of TA systems and propose that they are generally selfish DNA elements. This thesis focuses on the chromosomal TA systems of the soil bacterium Pseudomonas putida. The most thoroughly studied P. putida TA system is GraTA. While the toxin GraT is a ribosome-dependent mRNAse, it is conditionally toxic and causes cold-sensitive ribosome biogenesis defect. Interestingly, the major cellular chaperone DnaK was implicated in GraT-caused ribosome biogenesis defect, yet the exact role of DnaK in GraT toxicity has remained unclear. Even though the toxin GraT is functional and can affect the stress tolerance of P. putida in the absence of the antitoxin GraA, the whole TA system deletion has no fitness effects. This raises the question about the importance of GraTA along with other TA systems encoded in P. putida genome. This thesis describes the cellular changes that take place in P. putida cells lacking the antitoxin GraA and shows that DnaK enhances GraT toxicity, probably by helping GraT attain its proper fold. This work shows that TA systems are not beneficial to P. putida. Instead, they can be costly to P. putida in competition assays and during phage invasion. The results of this thesis shed light onto the biological importance of TA systems and clearly point to the selfish nature of TA systems.
Kirjeldus
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Märksõnad
bacteria, Pseudomonas putida, toxin-antitoxin systems