Site-Specific Recombination System Encoded by Toluene Catabolic Transposon Tn<i>4651</i>

Genka, Hiroyuki; Nagata, Yasunobu; Tsuda, Masashi

doi:10.1128/jb.184.17.4757-4766.2002

Cited by 19 publications

(12 citation statements)

References 40 publications

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“…As shown in Figure 1, the homologous C. litoralis region differs slightly, since it contains two additional ORFs (encoding a putative DoxD-like membrane protein and a truncated transposase) that are absent in pZM3H1 (Figure 1). Further in silico sequence analysis revealed that this region of the C. litoralis genome represents part of a putative Tn 3 family transposon (coordinates 155,646-171,707 [GenBank:NZ_AAOA01000001]) (Figure 1), related to Tn 4651 identified in plasmid pWW0 of Pseudomonas putida [51]. Plasmid pZM3H1 carries a large portion of this C. litoralis transposon (17 ORFs; orf8-orf23 ), although it lacks the 5.3 -kbterminal region of the element, which contains three genes coding for a putative NADP-specific glutamate dehydrogenase, a conserved membrane protein and a transposase (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

“…Plasmid pZM3H1 carries a large portion of this C. litoralis transposon (17 ORFs; orf8-orf23 ), although it lacks the 5.3 -kbterminal region of the element, which contains three genes coding for a putative NADP-specific glutamate dehydrogenase, a conserved membrane protein and a transposase (Figure 1). This truncated transposon contains (i-ii) two heavy metal resistance cassettes – a Co/Zn/Cd efflux system ( orf11 , orf12 ) and mercury resistance determinants ( orf16 - orf22 ), (iii) an ORF encoding a protein of the metallo-beta-lactamase family ( orf15 ), (iv) a site-specific resolution system (composed of two genes tnpS and tnpT , and a putative resolution site with a hairpin structure) homologous to the MRS system of Tn 4651 [51], as well as (v) four ORFs encoding hypothetical proteins with unknown functions ( orf8 , orf13 , orf14 and orf23 ) (Figure 1). …”

Section: Resultsmentioning

confidence: 99%

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Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

et al. 2013

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BackgroundHalomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.ResultsThe analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.ConclusionsThis study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

et al. 2013

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“…Several class II transposons carry tyrosine recombinases to resolve their cointegrates (3,30), and we have also identified and characterized a tyrosine recombinase, TnpS, in the smaller toluene-catabolic transposon Tn4651 from pWW0 ( Fig. 3B) (15).…”

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confidence: 99%

Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn 4655 Suggests Catabolic Gene Spread by a Tyrosine Recombinase

et al. 2006

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The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic determinants for bacterial aerobic catabolism of aromatic hydrocarbons. In contrast to the detailed studies of its catabolic cascade and enzymatic functions, the biological characteristics of plasmid NAH7 have remained unclear. Our sequence determination in this study together with the previously deposited sequences revealed the entire structure of NAH7 (82,232 bp). Comparison of NAH7 with two other completely sequenced IncP-9 catabolic plasmids, pDTG1 and pWW0, revealed that the three plasmids share very high nucleotide similarities in a 39-kb region encoding the basic plasmid functions (the IncP-9 backbone). The backbone of NAH7 is phylogenetically more related to that of pDTG1 than that of pWW0. These three plasmids carry their catabolic gene clusters at different positions on the IncP-9 backbone. All of the NAH7-specified nah genes are located on a class II transposon, Tn4655. Our analysis of the Tn4655-encoded site-specific recombination system revealed that (i) a novel tyrosine recombinase, TnpI, catalyzed both the intra-and intermolecular recombination between two copies of the attI site, (ii) the functional attI site was located within a 119-bp segment, and (iii) the site-specific strand exchange occurred within a 30-bp segment in the 41-bp CORE site. Our results and the sequence data of other naphthalene-catabolic plasmids, pDTG1 and pND6-1, suggest a potential role of the TnpI-attI recombination system in the establishment of these catabolic plasmids.

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“…Finally, transposon TnHdN1.1 ( Figure 7C) is the only example in our collection of a tnpS+tnpT transposon carrying a TA module. The res site and relevant promoter elements for the divergently expressed tnpS+tnpT have been identified between the tnpS and tnpT genes in transposon Tn4651 (8,11). In TnHdN1.1, the TA gene pair is located to the right of tnpS, between tnpS and tnpA and all three genes are oriented in the same direction.…”

Section: Regulation Of Ta Gene Expressionmentioning

confidence: 99%

“…TnpR is a classic serine (S)-site-specific recombinase (e.g., (9)); TnpI is a tyrosine (Y) recombinase (10)(see (1)) and TnpS+TnpT is a heteromeric resolvase combining a tyrosine recombinase, TnpS, and a divergently expressed helper protein, TnpT, with no apparent homology to other proteins (8,11). The tnpR gene can be either co-linear with tnpA or divergent.…”

Section: Introductionmentioning

confidence: 99%

Toxin-antitoxin gene pairs found in Tn3family transposons appear to be an integral part of the transposition module

Lima‐Mendez

Alvarenga

Ross

et al. 2019

Preprint

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Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tn). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase (TnpR/I/S+T) and transposase (TnpA). We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes.Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself. ImportanceTransposable Elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, moulding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence) and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role 3 of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tn during transposition. 4

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Site-Specific Recombination System Encoded by Toluene Catabolic Transposon Tn4651

Cited by 19 publications

References 40 publications

Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn 4655 Suggests Catabolic Gene Spread by a Tyrosine Recombinase

Toxin-antitoxin gene pairs found in Tn3family transposons appear to be an integral part of the transposition module

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