TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis

Abstract

We describe here the structure and organization of TnCentral (https://tncentral.proteininformationresource.org/ [or the mirror link at https://tncentral.ncc.unesp.br/]), a web resource for prokaryotic transposable elements (TE). TnCentral currently contains ∼400 carefully annotated TE, including transposons from the Tn3, Tn7, Tn402, and Tn554 families; compound transposons; integrons; and associated insertion sequences (IS). These TE carry passenger genes, including genes conferring resistance to over 25 classes of antibiotics and nine types of heavy metal, as well as genes responsible for pathogenesis in plants, toxin/antitoxin gene pairs, transcription factors, and genes involved in metabolism. Each TE has its own entry page, providing details about its transposition genes, passenger genes, and other sequence features required for transposition, as well as a graphical map of all features. TnCentral content can be browsed and queried through text- and sequence-based searches with a graphic output. We describe three use cases, which illustrate how the search interface, results tables, and entry pages can be used to explore and compare TE. TnCentral also includes downloadable software to facilitate user-driven identification, with manual annotation, of certain types of TE in genomic sequences. Through the TnCentral homepage, users can also access TnPedia, which provides comprehensive reviews of the major TE families, including an extensive general section and specialized sections with descriptions of insertion sequence and transposon families. TnCentral and TnPedia are intuitive resources that can be used by clinicians and scientists to assess TE diversity in clinical, veterinary, and environmental samples. IMPORTANCE The ability of bacteria to undergo rapid evolution and adapt to changing environmental circumstances drives the public health crisis of multiple antibiotic resistance, as well as outbreaks of disease in economically important agricultural crops and animal husbandry. Prokaryotic transposable elements (TE) play a critical role in this. Many carry "passenger genes" (not required for the transposition process) conferring resistance to antibiotics or heavy metals or causing disease in plants and animals. Passenger genes are spread by normal TE transposition activities and by insertion into plasmids, which then spread via conjugation within and across bacterial populations. Thus, an understanding of TE composition and transposition mechanisms is key to developing strategies to combat bacterial pathogenesis. Toward this end, we have developed TnCentral, a bioinformatics resource dedicated to describing and exploring the structural and functional features of prokaryotic TE whose use is intuitive and accessible to users with or without bioinformatics expertise.

Keywords: antibiotic resistance; database; genome evolution; insertion sequence; integrons; mobile genetic elements; plasmid-mediated resistance; transposition mechanisms; transposons; virulence.

FIG 1

Structural arrangement of prokaryotic transposable elements. The TE is indicated by a pale-yellow horizontal bar at the top of each section. ORFs are shown as horizontal arrows with arrowheads indicating the direction of expression: purple, transposition-associated genes; red, antibiotic resistance genes; and green, other passenger genes. The inverted terminal repeats found at the ends of the majority of TE are shown as gray arrows, and the direct target repeats generally produced by insertion are indicated by small black arrows. (A) Insertion sequence (IS), a short DNA segment encoding only the mobilization protein (transposase, TnpA), flanked by two imperfect inverted repeats (IRs) and generally containing a short flanking directly repeated duplication (DR) on the target of insertion. (B) The tIS (transporter IS) is structurally similar to an IS but contains passenger genes. These are presently restricted to the IS1595 and IS66 families. (C) Compound transposons are formed by two IS in either a direct or an inverted orientation, flanking a variety of passenger genes, including those for antibiotic resistance. (D) Transposons are more heterogeneous structures and include different sets of transposition-related genes that are specific to each transposon family and multiple antibiotic resistances, virulence, and other passenger genes. This is an example of a Tn3 family transposon with transposon, tnpA, and resolvase genes, tnpR.

FIG 2

(A) TnCentral homepage showing clickable links to various TnCentral sections in the box on the left. (B) TnCentral search interface showing search choices for TE on the left and for transposition-related and passenger genes on the left.

FIG 3

TnCentral TE entry page. Numbers 1 to 10 indicate various sections of the entry page (see the text for details).

FIG 4

Main sections of TnPedia, a TnCentral-related wiki compiling information on prokaryotic transposable elements. Only three of four sections (general information, IS families, and transposon families) are illustrated. A fourth section, the transposition glossary, is under construction.

FIG 5

Comparing protein coding genes in Tn554 family members. (A) TnCentral transposon search interface, showing a search for Tn554 in the TE family field. (B) Interface for customizing the columns in the search results display. Clicking on “customize display” (red box) opens the interface. (C) Partial Tn554 family search results after customization to show information on protein coding genes (All Gene Fields).

FIG 6

Exploring toxin/antitoxin genes in TnCentral. (A) Partial results of searching TnCentral for toxin genes. The settings used to obtain these results are shown in the red box. Links to entry pages for the TE carrying the indicated genes are provided in the MGE accession column (e.g., TnSku1-CP002358.1, yellow box). (B) Partial search results for antitoxin genes in TnCentral. Settings are shown in the red box. (C) ORF Summary section of the entry page for TnSku1-CP002358.1, showing the presence of a toxin/antitoxin gene pair (Gp49 toxin/HTH antitoxin).

FIG 7

Analysis of ABR in Tn21 Relatives. (A) TnCentral sequence search using the sequence of Tn5060, the proposed ancestor of Tn21, as a query. The query entry box and the customizable BLAST parameters are shown. The display of the parameters can be hidden/shown by clicking on the red double arrowhead. (B) Sequence search results. The query sequence is represented by the width of the alignment column. The red bars represent regions of the matched transposons that are highly similar to regions of Tn5060. (C) ABR genes and targeted antibiotic classes in Tn21 relatives. Red shading in the table cells indicates that the transposon carries at least one gene targeting the antibiotic class; blue shading indicates that it does not. The ABR genes found in each transposon are indicated in the table cells.

FIG 8

TnCentral curation workflow (see the text for a description).