Roles of Long and Short Replication Initiation Proteins in the Fate of IncP-1 Plasmids

Yano, Hirokazu; Deckert, Gail E.; Rogers, Linda; Top, Eva M.

doi:10.1128/jb.06395-11

Cited by 21 publications

(27 citation statements)

References 70 publications

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“…First, a mini-Tn7 region containing a zeocin resistance gene and eyfp was moved from pUC18T-mini-Tn7T-zeo-P A1/04/03 -ecfp into an R6K replicon pHY835 (29). Then, the resulting plasmid, pHY956, and Tn7 transposase expression plasmid pTNS2 were simultaneously introduced into E. coli EC100 by electroporation.…”

Section: Methodsmentioning

confidence: 99%

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

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Sen

Yano

et al. 2013

Appl Environ Microbiol

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c Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.

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Section: Methodsmentioning

confidence: 99%

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

Brown

Sen

Yano

et al. 2013

Appl Environ Microbiol

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“…TrfA2 pBP136 was purified by affinity chromatography from the cell lysate of E. coli Rosetta 2 (DE3) harbouring pHY925 as described previously (Yano et al, 2012). Quantitative Western blotting for whole-cell extracts was conducted using the same anti-TrfA2 pBP136 rabbit antiserum as described previously (Yano et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

“…Electrocompetent cells of P. putida were prepared from overnight culture by washing cells with 300 mM sucrose. Electrocompetent cells of S. japonicum were prepared from bacterial colonies grown for 2 days as described previously (Yano et al, 2012). Cell suspensions (100 ml) containing 10 8 -10 9 cells were mixed with plasmid DNA for electroporation.…”

Section: Methodsmentioning

confidence: 99%

“…Currently, it is recognized that the IncP-1 plasmids are ubiquitous in environmental bacteria residing in soil, sewage, marine sediments and manure (Dahlberg et al, 1997;Schlüter et al, 2007;Binh et al, 2008;Bahl et al, 2009;Gomes et al, 2010;. IncP-1 plasmids are generally considered to have a broad host range because representative plasmids of this group are able to transfer and replicate in hosts belonging to three proteobacterial subclasses, namely Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria (Schmidhauser & Helinski, 1985;De Gelder et al, 2005;Shintani et al, 2010;Yano et al, 2012). Since Yakobson & Guiney (1983) proposed to separate plasmids RP4 and R751 as different subgroups (a, b) based on the sequence similarity in the transfer origin (Yakobson & Guiney, 1983), six IncP-1 subgroups (a, b, c, d, e and j, see Fig.…”

Section: Introductionmentioning

confidence: 99%

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Host range diversification within the IncP-1 plasmid group

et al. 2013

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Broad-host-range plasmids play a critical role in the spread of antibiotic resistance and other traits. In spite of increasing information about the genomic diversity of closely related plasmids, the relationship between sequence divergence and host range remains unclear. IncP-1 plasmids are currently classified into six subgroups based on the genetic distance of backbone genes. We investigated whether plasmids from two subgroups exhibit a different host range, using two IncP1c plasmids, an IncP-1b plasmid and their minireplicons. Efficiencies of plasmid establishment and maintenance were compared using five species that belong to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The IncP-1b plasmid replicated and persisted in all five hosts in the absence of selection. Of the two IncP-1c plasmids, both were unable to replicate in alphaproteobacterial host Sphingobium japonicum, and one established itself in Agrobacterium tumefaciens but was very unstable. In contrast, both IncP-1c minireplicons, which produced higher levels of replication initiation protein than the wild-type plasmids, replicated in all strains, suggesting that poor establishment of the native plasmids is in part due to suboptimal replication initiation gene regulation. The findings suggest that host ranges of distinct IncP-1 plasmids only partially overlap, which may limit plasmid recombination and thus result in further genome divergence.

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“…Multiple studies on eukaryotic viruses indicate that growth in novel hosts leads to evolution in the viral-encoded polymerases to improve their interactions with host proteins such as RNA helicase and importin α [60], [61]. Another example of evolution of a foreign replication protein that interacts with a host helicase is found in bacterial host switching experiments with plasmids [62], [63]. These experiments lead to evolution of the plasmid replication initiation protein, especially in the region that interacts with the host helicase, leading to increased plasmid copy number, which is analogous to evolution in the replication initiation protein of φX174.…”

Section: Discussionmentioning

confidence: 99%

Selection Affects Genes Involved in Replication during Long-Term Evolution in Experimental Populations of the Bacteriophage φX174

et al. 2013

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Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.

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Roles of Long and Short Replication Initiation Proteins in the Fate of IncP-1 Plasmids

Cited by 21 publications

References 70 publications

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

Host range diversification within the IncP-1 plasmid group

Selection Affects Genes Involved in Replication during Long-Term Evolution in Experimental Populations of the Bacteriophage φX174

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