Convenient broad-host-range unstable vectors for studying stabilization cassettes in diverse bacteria

Bartosik, Aneta Agnieszka; Glabski, Krzysztof; Kulinska, Anna; Lewicka, Ewa; Godziszewska, Jolanta; Markowska, Aleksandra; Jagura-Burdzy, Grażyna

doi:10.1186/s12866-016-0674-y

Cited by 9 publications

(8 citation statements)

References 55 publications

(73 reference statements)

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“…Segregational stability of pIGRK plasmid derivatives was tested by replica plating following growth under non-selective conditions for approx. Eighty generations, as described previously [40]. The incompatibility characteristics of two plasmids (residing and introduced) were examined by testing the stability of the residing replicon (pRK-1) in the presence of ampicillin in the growth medium (antibiotic selection for introduced pUC18 vector derivatives containing putative determinants of incompatibility of pIGRK).…”

Section: Methodsmentioning

confidence: 99%

Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions

et al. 2019

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BackgroundGene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called “trivial overlapping”, there are significant implications of such genetic arrangements, including regulation of gene expression and modification of protein activity. It is also postulated that, besides gene duplication, the appearance of overlapping genes (OGs) is one of the most important factors promoting a genome’s novelty and evolution. OGs coding for in-frame proteins with different functions are a particularly interesting case. In this study we identified and characterized two in-frame proteins encoded by OGs on plasmid pIGRK from Klebsiella pneumoniae, a representative of the newly distinguished pHW126 plasmid family.ResultsA single repR locus located within the replication system of plasmid pIGRK encodes, in the same frame, two functional polypeptides: a full-length RepR protein and a RepR’ protein (with N-terminal truncation) translated from an internal START codon. Both proteins form homodimers, and interact with diverse DNA regions within the plasmid replication origin and repR promoter operator. Interestingly, RepR and RepR’ have opposing functions – RepR is crucial for initiation of pIGRK replication, while RepR’ is a negative regulator of this process. Nevertheless, both proteins act cooperatively as negative transcriptional regulators of their own expression.ConclusionsRegulation of the initiation of pIGRK replication is a complex process in which a major role is played by two in-frame proteins with antagonistic functions. In-frame encoded Rep proteins are uncommon, having been described in only a few plasmids. This is the first description of such proteins in a plasmid of the pHW126 family.

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Section: Methodsmentioning

confidence: 99%

Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions

et al. 2019

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“…To evaluate the contribution of each functional module to plasmid maintenance, a set of highly unstable broad-host-range plasmid vectors based on the RK2 replicon of the IncP-1 group has been constructed [ 70 ]. For example, the functionality of the partition module of a IncU plasmid ( Table 1 ), the chromosome partitioning system of Pseudomonas aeruginosa , and the hipAB TA system of the Paracoccus kondratievae plasmid have been confirmed using these vectors [ 70 ].…”

Section: Key Factors In Plasmid Designmentioning

confidence: 99%

Reconsidering plasmid maintenance factors for computational plasmid design

Yano

Shintani

Tomita

et al. 2019

Computational and Structural Biotechnology Journal

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Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

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“…It was shown that some TA systems can promote stability of plasmid maintenance due to toxin-mediated growth inhibition of plasmid-less cells [ 34 , 35 ]. Although this phenomenon is specific for plasmid-encoded TA modules, it has been also reported for several chromosomal TA systems, suggesting that their biological functions could be similar (reviewed in [ 35 ]).…”

Section: Resultsmentioning

confidence: 99%

Identification of Three Type II Toxin-Antitoxin Systems in Model Bacterial Plant Pathogen Dickeya dadantii 3937

Boss

Górniak

Lewańczyk

et al. 2021

IJMS

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Type II toxin-antitoxin (TA) systems are genetic elements usually encoding two proteins: a stable toxin and an antitoxin, which binds the toxin and neutralizes its toxic effect. The disturbance in the intracellular toxin and antitoxin ratio typically leads to inhibition of bacterial growth or bacterial cell death. Despite the fact that TA modules are widespread in bacteria and archaea, the biological role of these systems is ambiguous. Nevertheless, a number of studies suggests that the TA modules are engaged in such important processes as biofilm formation, stress response or virulence and maintenance of mobile genetic elements. The Dickeya dadantii 3937 strain serves as a model for pathogens causing the soft-rot disease in a wide range of angiosperm plants. Until now, several chromosome-encoded type II TA systems were identified in silico in the genome of this economically important bacterium, however so far only one of them was experimentally validated. In this study, we investigated three putative type II TA systems in D. dadantii 3937: ccdAB2Dda, phd-docDda and dhiTA, which represents a novel toxin/antitoxin superfamily. We provide an experimental proof for their functionality in vivo both in D. dadantii and Escherichia coli. Finally, we examined the prevalence of those systems across the Pectobacteriaceae family by a phylogenetic analysis.

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Convenient broad-host-range unstable vectors for studying stabilization cassettes in diverse bacteria

Cited by 9 publications

References 55 publications

Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions

Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions

Reconsidering plasmid maintenance factors for computational plasmid design

Identification of Three Type II Toxin-Antitoxin Systems in Model Bacterial Plant Pathogen Dickeya dadantii 3937

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