The Tn 3 -family of Replicative Transposons

Abstract

Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.

Toxin-Antitoxin Gene Pairs Found in Tn 3 Family Transposons Appear To Be an Integral Part of the Transposition Module

“…Numbers above the lines of each clade indicate the maximum likelihood bootstrap values. The subgroups adhere closely to those defined by Nicolas et al (1) with some minor variations resulting from the significantly larger Tn sample. The majority of members carry tnpR, serine resolvases (purple circles).…”

“…3. Note that, with minor exceptions, the entire Tn3 library conforms closely to the previously defined Tn3 family subgroups (1). The majority of Tn3 family members encode a TnpR resolvase (Fig.…”

“…A similar situation is found in the unrelated Tn4651 subgroup member TnPosp1_p, which has the configuration TϾ AϾ tnpRϾ tnpAϾ. We extracted Tn3 family members from the ISfinder database which served to generate the subgroups defined in the work of Nicolas et al (1). Many others were drawn from the literature and have been given official names (Tn followed by digits, e.g., Tn1234; https://transposon.lstmed.ac.uk/tn-registry), while others were identified using Tn3_finder software (TnCentral, https://tncentral .proteininformationresource.org/TnFinder.html) and given temporary names.…”

“…Identification of TA gene pairs in Tn3 family members. As a first step, we undertook a detailed annotation of available Tn3 family members in the ISfinder database (23) and also those listed in the work of Nicolas et al (1). We also searched NCBI for previously annotated Tn3 family members (March 2018) and made use of an in-house script which searches for tnpA, tnpR, and TA genes located in proximity to each other (Tn3finder, https://tncentral.proteininformationresource.org/TnFinder.html; Tn3ϩTA_finder, https://github.com/danillo-alvarenga/tn3-ta_finder) to search complete bacterial genomes in the RefSeq database at NCBI.…”

Frequent Tn 2 Misannotation in the Genetic Background of rmtB

“…The absence of these sequences upstream of rmtB suggests the nonmobilization of rmtB by Tn2. For this mobilization to occur, the IRL upstream bla TEM-1b gene would have been inactivated by a new passenger gene (in this case, rmtB) and a more distant "surrogate" IR sequence recruited (13). This kind of mobilization had occurred with Tn4401, a derivate transposon of Tn3 that carries bla KPC-2 (14).…”