Determination of Plasmid pSN1216-29 Host Range and the Similarity in Oligonucleotide Composition Between Plasmid and Host Chromosomes

Abstract

Strain or plasmidRelevant characteristics References Bacterial strains Escherichia coliDH5α F − , 80dlacZ M15, (lacZYA-argF) U169, deoR, recA1, endA1, hsdR17(r K − , m K + ), phoA, supE44, λ − , thi-1, gyrA96, relA1DH5α, Tc r This study S17-1 λpir RK2 tra regulon; host for pir-dependent plasmids; recA thi pro hsdR M RP4-2-Tc:Mu-Km:Tn7λpir Tp r Sm r Simon et al., 1983 Pseudomonas putida KT2440 pWW0-free Pseudomonas putida mt-2 Bagdasarian et al., 1981 KT2440(pBBR1MCS-5) pBBR1MCS-5-harboring KT2440 This study KT2440(pSN1216-29, pBBR1MCS-5) pSN1216-29 and pBBR1MCS-5-harboring KT2440 This study SMDBS A dapB-deleted strain of SM1443, Rif r of KT2440 (KT2442) with mini-Tn5-lacI q cassette inserted into the chromosome Shintani et al., 2014 SMDBS(pSN1216-29:gfp) SMDBS bearing pSN1216-29:gfp This study Pseudomonas resinovorans CA10dm4RGFP CA10dm4R (spontaneous rifampicin-resistant CA10dm4), miniTn7(Gm) P A1/O4/O3 -gfp-a was inserted into chromosome (Gm r , Cm r ). Yanagiya et al., 2018 CA10dm4RGFP(pSN1216-29, pBBR1MCS-2) pSN1216-29 and pBBR1MCS-2-harboring CA10dm4RGFP Yanagiya et al., 2018 Plasmids pBBR1MCS-2 Km r , lacZα mob; compatible with IncP, IncQ, and IncW plasmids Kovach et al., 1995 pBBR1MCS-3 Tc r , lacZα mob; compatible with IncP, IncQ, and IncW plasmids Kovach et al., 1995 mini-pBBR1MCS-3 Self-ligated 3020-bp DNA region containing oriV, rep, and Tc r gene of pBBR1MCS-3 This study pBBR1MCS-5 Gm r , lacZα mob; compatible with IncP, IncQ, and IncW plasmids Kovach et al., 1995 pJBA28 Ap r , Km r ; delivery plasmid for mini-Tn5-Km-P A1/O4/O3 -RBSII-gfpmut3*-T 0 -T 1 Andersen et al., 1998 pSN1216-29 Conjugative, broad-host-range plasmid Yanagiya et al., 2018 pSN1216-29:gfp mini-Tn5-Km-P A1/O4/O3 -RBSII-gfpmut3*-T 0 -T 1 was inserted in the end of tivB7 gene (25,653 nt of pSN1216-29). This study Gel/PCR DNA fragments Extraction kit (RBC Bioscience, New Taipei City, Taiwan), NEBuilder Hifi DNA Assembly system (New England Biolabs, Ipswich, MA, United States), and competent E. coli DH5α cells (RBCBioscience) were employed for cloning of DNA fragments. The other procedures were performed according to standard methods (Sambrook and Russell, 2001).

Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan

“…A mini-Tn 5 with P A1/O4/O3 -RBSII- gfpmut3* and Km-resistance gene on pJBA28 ( 54 ) was introduced into plasmid pSN0729-62 ( 5 ) using E. coli S17-1λ pir ( 55 ) as described previously ( 56 ). For pSN1104-11 gfp Tc, P A1/O4/O3 -RBSII- gfpmut3* on pJBA28 were introduced into the plasmid by homologous recombination (Text S1).…”

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

“…This result highlights that conjugal transfer occurs in the field. Plasmid pSN1216-29 has been isolated from cow manure [114] and was demonstrated to be able to conjugate with a broad range of bacterial genera extracted from soil and cow manure [115]; despite the fact that this plasmid does not carry accessory genes, one transposition event can lead to antimicrobial resistance acquisition, followed by horizontal dissemination.…”

Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome

“…The four PromA plasmids (pSN1104-11, pSN0729-62 [30], pMH0613-68, and pYK0414-12) were transferred to P. resinovorans CA10rm4R fromCA10dm4RGFP with pBBRMCS-2 [30]. Then mini-Tn5 (3 859 bp) with P A1/O4/O3 -RBSII-gfpmut3* and the Km-resistance gene was randomly inserted into the four PromA plasmids using pJBA28 [33] and E. coli S17-1 λpir [34] as described previously [17]. The mini-Tn5 was inserted into 38 362 nucleotides (nt) of pSN1104-11, 40 891 nt of pMH0613-68, 35 137 nt of pYK0414-12, and 35 612 nt of pSN0729-62.…”

“…These plasmid host ranges are determined using filter and/or liquid mating assays between donor strain(s) and recipients (transconjugant ranges). Several studies have comprehensively identified the transconjugants of plasmids including members of IncP/P-1 [5][6][7][8][9][10][11][12], IncP-7 [13], IncP-9 [13], IncH1A [14], IncQ/P-4 [15], PromA (only PromAβ−1) [16], and pSN1216-29 [17]. However, the number of plasmids whose host ranges have been analysed is still limited because the analyses are timeconsuming and costly, and it is unfeasible to experimentally identify all plasmid transconjugant ranges.…”

“…Additionally, k-mer compositions are also used to identify the putative evolutionary hosts of plasmids, in which a plasmid has been replicated at some point during its evolutionary history [23]. However, few studies have compared the bacterial taxa of experimentally identified transconjugants (transconjugant range) with the predicted evolutionary host ranges [17,24]. Although the transconjugant range is important for understanding plasmid behaviour in the environment, it is still unclear whether transconjugant ranges can be predicted based on nucleotide sequences of plasmids and bacterial chromosomes.…”