Representative unit transposons

A unit transposon carries a core transposition module, which can be mainly divided into Tn3 1, Tn7 2, 3 and Tn554 4 families. Each family can be further divided into various subfamilies based on the amino acid sequences of transposases. The Tn3-family core transposition module is composed of the transposase and resolvase genes and a resolution (res) site. A Tn7-family transposon typically encodes the core transposition determents TnsA (endonuclease), TnsB (transposase), TnsC (transposition regulator), and TnsD plus TnsE (target-site selection proteins), and uses a "cut-and-paste" transposition mechanism. Tn3- and Tn7-family transposons have terminal IRL/IRR pairs. A Tn554-family transposon encodes multiple transposases and transposes preferentially to a single chromosomal site (e.g. att554 for Tn554), generating flanking DRs (e.g. GATGTA for Tn554), but it carries no IRL/IRR pairs.

Table 1|List of representative Tn3-family unit transposons

CategorySub-categoryDesignationAccession numberSynonymResistance genesDRFASTA sequenceGene listGBK-annotationSQN-annotationManual annotationGene organization
Tn3 family Tn3 subfamily Tn3 HM749966 blaTEM-1
Tn3 family Tn3 subfamily Tn1331 KC354802 aacA4, aadA1, blaOXA-9, and blaTEM-1 AATTA
Tn3 family Tn3 subfamily Tn5046 MF344568 mer CTGTA
Tn3 family Tn3 subfamily Tn5401 U03554 None AATTA
Tn3 family Tn3 subfamily Tn5563 U88088 mer
Tn3 family Tn3 subfamily Tn6736 MN423365 ars
Tn3 family Tn3 subfamily Tn6756a CP043513 None
Tn3 family Tn21 subfamily Tn21 AF071413 aadA1, and sul1
Tn3 family Tn21 subfamily Tn1403 AF313472 blaCARB-2, cmlA1d, aadA1a, strA, and strB
Tn3 family Tn21 subfamily Tn1696 U12338 aacC1, aadA2, cmlA1, qacED1, and sul1
Tn3 family Tn21 subfamily Tn1721 X61367 tetA(A)
Tn3 family Tn21 subfamily Tn1722 X61367 None
Tn3 family Tn21 subfamily Tn4658a AB238971 None
Tn3 family Tn21 subfamily Tn4663 AB434906 None
Tn3 family Tn21 subfamily Tn6187 JQ010984 blaOXA-21, aadB, qacED1, sul1, and mer TTCTG
Tn3 family Tn21 subfamily Tn6296 FJ628167 blaKPC-2 GAATTC
Tn3 family Tn21 subfamily Tn6346 EU696790 mer
Tn3 family Tn21 subfamily Tn6358 JX141473 qacH4, blaOXA-10, aadA1, qacED1, sul1, catA2, tetA(A), and mer TTGTA
Tn3 family Tn21 subfamily Tn6382 MN423363 blaIMP-38, mer, blaTEM-1B, blaCTX-M-3, aacA4, and qacG2
Tn3 family Tn21 subfamily Tn6384 MF344563 blaVIM-1, aacA4', aphA15, aadA1b, catB2, qacED1, catA2, aacA4cr, blaOXA-1, and mer TTTCA
Tn3 family Tn21 subfamily Tn6395 MF344573 aacA7, qacED1, sul1, and mer TTGTA
Tn3 family Tn21 subfamily Tn6399a AP004237 glo TTCAT
Tn3 family Tn21 subfamily Tn6403 CP030075 aadA2, mph(E), blaVIM-4, aacA7, sul1, and mer CTCAA
Tn3 family Tn21 subfamily Tn6414 KC340960 dfrA5, blaTEM-1, sul2, strA, strB, aphA1a, and mer
Tn3 family Tn21 subfamily Tn6427 KC543497 None TAGAG
Tn3 family Tn21 subfamily Tn6535 CP009706 ars AATAGA
Tn3 family Tn21 subfamily Tn6558 MH917284 blaCTX-M-14 AGGTC
Tn3 family Tn21 subfamily Tn6567 LT969519 qacG14
Tn3 family Tn21 subfamily Tn6570 CP043397 mer TTT
Tn3 family Tn21 subfamily Tn6595 CP017181 None TTGATC
Tn3 family Tn21 subfamily Tn6603a MT043136 None
Tn3 family Tn21 subfamily Tn6727 CP047346 aadA2, lnuF, qacED1, sul1, mph(E), and mer TA
Tn3 family Tn21 subfamily Tn6758 JX448550 mer ACCTT
Tn3 family Tn21 subfamily Tn6806 CP059346 tetA(B), lnuF3, catB8, blaIMP-1, blaOXA-1, aacA4', and dfrA1t
Tn3 family Tn21 subfamily Tn6811 CP029148 None
Tn3 family Tn21 subfamily Tn6896 CP059346 tetA(B), aadA16, dfrA27, arr3, catB3, blaOXA-1, and aacA4cr
Tn3 family Tn21 subfamily Tn6909 CP032168 blaVIM-1, aacA7, dfrA1b, mph(A), qnrA1, aadA2, and dfrA12 TACAA
Tn3 family Tn21 subfamily Tn6910 CP041301 mph(A), qnrA1, aadA2, and dfrA12
Tn3 family Tn21 subfamily Tn6911 KT033469 qacED1, sul1, and mer TGGTA
Tn3 family Tn163 subfamily Tn163 L14931 None ATATT
Tn3 family Tn163 subfamily Tn5403 KJ958926 None
Tn3 family Tn163 subfamily Tn5393c AF262622 strA, and strB TGAAA
Tn3 family Tn4401 subfamily Tn4401b EU176014 blaKPC-2 ATTAC
Tn3 family Tn4401 subfamily Tn4662a KJ920396 None
Tn3 family Tn4401 subfamily Tn5501 Y09450 None
Tn3 family Tn4430 subfamily Tn4430 X13481 None AGCAA
Tn3 family Tn4430 subfamily Tn1546 M97297 van AGGAC
Tn3 family Tn4651 subfamily Tn4651 AJ344068 xyl TACA
Tn3 family Tn4651 subfamily Tn4661a KY494864 None GAGTT
Tn3 family Tn4651 subfamily Tn5041 X98999 mer
Tn3 family Tn4651 subfamily Tn6830 CP045552 cus
Tn3 family Tn21 subfamily Tn6846 CP096924 blaPER-1, blaOXA-101, aacA4-12, aadA5, qacED1, and sul1
Tn3 family Tn21 subfamily Tn7483 CP096964 aacA3, aadA13, qacED1, sul1, aacC2, rmtB, strA, blaOXA-246, blaPER-1, blaTEM-1, and strB
Tn3 family Tn21 subfamily Tn7484 CP096945 aadB, aacA3, blaCARB-2, qacED1, strA, and strB
Tn3 family Tn21 subfamily Tn7485 CP096941 aadA6, qacED1, and sul1
Tn3 family Tn21 subfamily Tn6913a CP064831 aadB, catB5, aadA1a, qacED1, sul1, qnrVC1, qacED1, tetA(B), and blaOXA-10
Tn3 family Tn21 subfamily Tn6913b CP064827 aadB, catB5, aadA1a, qacED1, sul1, qnrVC1, qacED1, tetA(B), and blaOXA-10
Tn3 family Tn21 subfamily Tn6914 CP064828 aadA13, qacED1, and sul1
Tn3 family Tn21 subfamily Tn6505 MK036884 blaIMP-8
Tn3 family Tn21 subfamily Tn6915 CP043955 aadA13, qacED1, sul1, sul3, qacH2, aadA1a, cmlA1a, aadA2, floR, sul2, aph(4)-Ia, aacA4cr, blaOXA-1, catB3, arr-3, qacED1, blaOXA-10, and sul1
Tn3 family Tn21 subfamily Tn6971 CP064830 catA1, aadA1a, qacED1, and sul1
Tn3 family Tn21 subfamily Tn6972 CP064827 catB3, dfrA27, aadA16, qacED1, and sul1
Tn6963-related transposable prophages Tn6963 CP033056 dfrA12, aadA2, aphA1, aacC4, aph(4)-Ia, sul2, floR, aacA4cr12, blaOXA-10, and catB3, dfrA27, aadA16, qacED1, sul1, and tetA(B)
Tn6964-related transposable prophages Tn6964 CP064832 dfrA12, aadA2, aphA1, aacC4, aph(4)-Ia, sul2, floR, aacA4cr12, blaOXA-10, and catB3, dfrA27, aadA16, qacED1, sul1, tetA(B)
Tn6965-related transposable prophages Tn6965 CP064832 dfrA12, aadA2, aphA1, aacC4, aph(4)-Ia, sul2, floR, aacA4cr12, blaOXA-10, and catB3, dfrA27, aadA16, qacED1, sul1, tetA(B)

Fig. 1|Phylogenetic tree of Tn3-family unit transposons

The transposase sequences of indicated transposons were aligned using Clustal Omega 1.2.2 5. A maximum-likelihood tree was constructed using MEGA X 10.1.8 6 with a bootstrap iteration of 500. Shown in the tree are a total of 94 representative Tn3-family transposons, which are derived from a previous grouping scheme 1, and 49 of them are included in REMED.

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Table 2|List of representative Tn7-family unit transposons

CategorySub-categoryDesignationAccession numberSynonymResistance genesDRFASTA sequenceGene listGBK-annotationSQN-annotationManual annotationGene organization
Tn7 family Tn7 subfamily Tn7 KX117211 aadA1, sat2, and dfrA1 GGGCT
Tn7 family Tn7 subfamily Tn6411 CP024477 blaIMP-1, aacA7, aacC2, and tmrB AAGCC
Tn7 family Tn7 subfamily Tn6726 AP018750 aadA2, aphA6, armA, blaNDM-1, bleMBL, msr(E), mph(E), qacED1, and sul1 GCTGC
Tn7 family Tn552 subfamily Tn552 X52734 blaZ AGCCC
Tn7 family Tn5053 subfamily Tn5053 L40585 mer
Tn7 family Tn5053 subfamily Tn402=Tn5090 X72585 None
Tn7 family Tn5053 subfamily Tn512 EU306744 mer
Tn7 family Tn5053 subfamily Tn5058a Y17897 mer
Tn7 family Tn6022 subfamily Tn6022 CP038644 None ACCGC
Tn7 family Tn6022 subfamily Tn6509 JN676148 TnAbaR23 ars, mer, tetA(A), aadA1a, qacED1, and sul1
Tn7 family Tn6022 subfamily Tn6519 NC025109 TnAbaR4 blaOXA-23 CCATT
Tn7 family Tn6230 subfamily Tn6230 CP038601 sil, cop GCGGC
Tn7 family Tn6230 subfamily Tn6725 CP012999 mcr-9.1, and sil CGCGC
Tn7 family Tn6800 CP064830 lnu(F)1b, catB2, and aadA1

Fig. 2|Phylogenetic tree of Tn7-family unit transposons

The transposase sequences of indicated transposons were aligned using Clustal Omega 1.2.2 5. A maximum-likelihood tree was constructed using MEGA X 10.1.8 6 with a bootstrap iteration of 500. Shown in the tree are a total of 13 representative Tn7-family transposons, which are based on a previous grouping scheme 7, and all of them are included in REMED.

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Table 3|List of representative Tn554-family unit transposons

CategorySub-categoryDesignationAccession numberSynonymResistance genesDRFASTA sequenceGene listGBK-annotationSQN-annotationManual annotationGene organization
Tn554 family Tn554 subfamily Tn554 X03216 aad9, and erm(A) GATGTA
Tn554 family Tn554 subfamily Tn5406 AF186237 None GATGTA
Tn554 family Tn6488 subfamily Tn6488 MF344569 None ACAACGA
Tn554 family Tn6571 subfamily Tn6571 CP000058 None GAGCC

Fig. 3|Phylogenetic tree of Tn554-family unit transposons

The transposase (TnpA or GinA) sequences of indicated transposons were aligned using Clustal Omega 1.2.2 5. A maximum-likelihood tree was constructed using MEGA X 10.1.8 6 with a bootstrap iteration of 500. Shown in the tree are a total of 10 representative Tn554-family transposons, and four (Tn554, Tn5406, Tn6488 and Tn6571) of them are included in REMED.

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References

1.    Nicolas E, Lambin M, Dandoy D et al. The Tn3-family of replicative transposons. Microbiology spectrum 2015; 3.
2.    Peters JE, Fricker AD, Kapili BJ et al. Heteromeric transposase elements: generators of genomic islands across diverse bacteria. Mol Microbiol 2014; 93: 1084-92.
3.    Peters JE. Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond. Mol Microbiol 2019; 112: 1635-44.
4.    Haroche J, Allignet J, El Solh N. Tn5406, a new staphylococcal transposon conferring resistance to streptogramin A and related compounds including dalfopristin. Antimicrob Agents Chemother 2002; 46: 2337-43.
5.    Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sciences. Protein Sci 2018; 27: 135-145.
6.    Kumar S, Stecher G, Li M et al. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35 (6): 1547-9.
7.    Peters JE, Fricker AD, Kapili BJ et al. Heteromeric transposase elements: generators of genomic islands across diverse bacteria. Mol Microbiol 2014; 93: 1084-92.