Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial

Abstract

Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance when overexpressed supports the hypothesis of TA systems being associated with stress adaptation. However, the deletion of TA genes has usually no effects on stress tolerance, supporting the selfish elements hypothesis. Here, we aimed to evaluate the cost and benefits of chromosomal TA systems to Pseudomonas putida. We show that multiple TA systems do not confer fitness benefits to this bacterium as deletion of 13 TA loci does not influence stress tolerance, persistence or biofilm formation. Our results instead show that TA loci are costly and decrease the competitive fitness of P. putida. Still, the cost of multiple TA systems is low and detectable in certain conditions only. Construction of antitoxin deletion strains showed that only five TA systems code for toxic proteins, while other TA loci have evolved towards reduced toxicity and encode non-toxic or moderately potent proteins. Analysis of P. putida TA systems' homologs among fully sequenced Pseudomonads suggests that the TA loci have been subjected to purifying selection and that TA systems spread among bacteria by horizontal gene transfer. Bacterial chromosomes contain multiple copies of toxin-antitoxin (TA) gene pairs which code for a toxic protein and an antagonist of the toxin. Chromosomal TA systems most probably originate from plasmids 1-3 , where they contribute to plasmid maintenance during host replication 4. The mechanism behind the plasmid stabilization by TA modules is the unequal stability of the toxin and antitoxin, with the latter being usually less stable than the toxin 5,6. Loss of plasmid and termination of antitoxin production therefore results in release of toxin from the antitoxin-mediated control which ultimately leads to toxin-caused cell death or growth arrest and plasmid-free bacteria are outcompeted from the population 7,8. While the role of TA systems in plasmid addiction is highly recognized, the biological importance of chromosomal TA loci has remained enigmatic despite years of extensive research. Several functions have been attributed to the chromosomal TA systems including stabilization of genomic mobile elements 9,10 , defence against bacteriophages 11,12 as well as other invading mobile DNA 13 and modulation of bacterial stress tolerance 14. However, there are also a lot of contradictions and discrepancy between different studies. For example, chromosomal TA loci were considered to be the major players in formation of metabolically dormant and antibiotic tolerant persister cells but recently this concept was rebutted 15-17. Also, despite multiple studies show that TA toxins can affect the stress tolerance 18-22 , these studies mostly involve artificial overexpression of the toxin which will likely never occur from the single-copy chromosomal TA locus. It is also important to note...

Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies

“…It has been argued that TASs do not necessarily provide an advantage to the producing bacterial strain. For example, chromosomal TASs of Pseudomonas putida were reported to be rather selfish than beneficial, and an indirect positive effect for plants cannot be ruled out ( 43 ). This example on TASs illustrates the need for further functional studies of particular genes and shows the difficulty of assigning them to a unique purpose.…”

Two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies

“…It has been argued that TASs do not necessarily provide an advantage to the producing bacterial strain. For example, chromosomal TASs of Pseudomonas putida were reported to be rather selfish than beneficial, and an indirect positive effect for plants cannot be ruled out [66]. This example on TAS illustrates the need for further functional studies of particular genes, and shows the difficulty to assign them to a unique purpose.…”

eDNA-stimulated cell dispersion fromCaulobacter crescentusbiofilms upon oxygen limitation is dependent on a toxin-antitoxin system

“…TAS have often been reported to play a direct and crucial role in adaptation to different stresses. However, the physiological role of TAS-regulated cell death has been challenged in recent years (Harms et al ., 2017, Goormaghtigh et al ., 2018, Fraikin et al ., 2019, Wade & Laub, 2019, Fraikin et al ., 2020, Rosendahl et al ., 2020). Even if a TAS operon is transcribed under stress conditions, it does not necessarily mean that the toxin is liberated, and transcription might not always reflect TAS activity (LeRoux et al ., 2020).…”