Reconsidering plasmid maintenance factors for computational plasmid design

Yano, Hirokazu; Shintani, Masaki; Tomita, Masaru; Suzuki, Haruo; Oshima, Taku

doi:10.1016/j.csbj.2018.12.001

Cited by 26 publications

(21 citation statements)

References 187 publications

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“…The shuttle vector pMMGK brings new proteins (RepA, RepB, RepC, eGFP and Kan R ) and new RNAs to C. burnetii . The potential effects of these proteins and RNAs on bacterial physiology are impossible to predict (25, 26). The RSF1010 ori -based shuttle vectors are commonly used for C. burnetii transformation (27, 28).…”

Section: Discussionmentioning

confidence: 99%

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

Luo

Sun

et al. 2019

Preprint

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20Coxiella burnetii is a Gram-negative, facultative intracellular microorganism that can 21 cause acute or chronic Q fever in human. It was recognized as an obligate intracellular 22 organism until the revolutionary design of an axenic cystine culture medium (ACCM). 23Present axenic culture of C. burnetii strictly requires a hypoxic condition (<10% 24 oxygen). Here we investigated the normoxic growth of C. burnetii strains in ACCM-2 25 with or without tryptophan supplementation. Three C. burnetii strains -Henzerling 26 phase I, Nine Mile phase II and a Nine Mile phase II transformant, were included. The 27 transformant contains a pMMGK plasmid that is composed of a RSF1010 ori, a 28 repABC operon, an eGFP gene and a kanamycin resistance cassette. We found that, 29 under normoxia if staring from an appropriate concentration of fresh age inocula, 30 Nine Mile phase II can grow significantly in ACCM-2 with tryptophan, while the 31 transformant can grow robustly in ACCM-2 with or without tryptophan. In contrast, 32 long-term frozen stocks of phase II and its transformant, and Henzerling phase I of 33 different ages had no growth capability under normoxia under any circumstances. 34 Furthermore, frozen stocks of the transformant consistently caused large 35 splenomegaly in SCID mice, while wild type Nine Mile phase II induced a lesser 36 extent of splenomegaly. Taken together, our data show that normoxic cultivation of 37 phase II C. burnetii can be achieved under certain conditions. Our data suggests that 38 tryptophan and an unknown temperature sensitive signal are involved in the 39 expression of genes for normoxic growth regulated by quorum sensing in C. burnetii. 40 129 Mile phase II and NMIIpMMGK were used. In the second experiment, 9 five weeks 130 old mice were averaged into three infection groups: one month old Nine Mile phase II, 131 one-month old NMIIpMMGK and 19 months old NMIIpMMGK. At indicated days 132 post-infection, mice were weighted and sacrificed to harvest spleens to determine 133 splenomegaly (spleen weight/body weight). Each spleen was homogenized in 2 mL 134 PBS. Total DNAs from 20 μL of each tissue homogenate were purified with DNeasy 135

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Section: Discussionmentioning

confidence: 99%

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

Luo

Sun

et al. 2019

Preprint

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“…This allows more accurate comparisons between the evolutionary host range and replication/transfer host range of the plasmid. In addition, various factors have been found that determine or affect the host range of a plasmid within itself and/or in its host chromosome, including DNA polymerase, helicase, gyrase, and nucleoid associated proteins involved in the capability of replication, maintenance, and/or conjugation of a plasmid (Shintani et al, 2015;Shintani and Suzuki, 2019;Yano et al, 2019). Therefore, it is necessary to consider the absence or presence of these factors on the plasmid or chromosomes for the prediction of plasmid host range.…”

Section: Comparisons Of Predicted Hosts Of Psn1216-29 With Experimentally Obtained Transconjugantsmentioning

confidence: 99%

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

et al. 2020

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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).

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“…In summary, our use of both deletion and synthetic biology approaches (35) in this study revealed a unique and novel feature of IncP-9 plasmids in that mpfK and kikA pWW0 are indispensable for the conjugative transfer of the two IncP-9 plasmids. On the other hand, R751 and R388 did not require the MpfK-like proteins for their conjugative transfer.…”

Section: Discussionmentioning

confidence: 80%

Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK , Whose Homologs Are Conserved in Various MPF _T -Type Plasmids

Kishida

Nonoyama

Lukas

et al. 2019

Appl Environ Microbiol

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Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPFT type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPFT-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPFT-type plasmids. IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.

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Reconsidering plasmid maintenance factors for computational plasmid design

Cited by 26 publications

References 187 publications

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

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

Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK , Whose Homologs Are Conserved in Various MPF _T -Type Plasmids

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Reconsidering plasmid maintenance factors for computational plasmid design

Cited by 26 publications

References 187 publications

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector

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

Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK , Whose Homologs Are Conserved in Various MPF T -Type Plasmids

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Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK , Whose Homologs Are Conserved in Various MPF _T -Type Plasmids