Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1

Dolowy, Patrycja; Mondzelewski, Jakub; Zawadzka, Renata; Baj, Jadwiga; Bartosik, Dariusz

doi:10.1016/j.plasmid.2004.11.005

Cited by 5 publications

(6 citation statements)

References 30 publications

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“…strain TM1040 together harbor four of its five rRNA operons ( Table 1). Designation of pSTM1 and pSTM2 as plasmids rather than chromosomes is based on the finding that none of 11 single-copy genes essential for bacterial growth (51) is found on either and that each contains a plasmid-type replication origin (rep and parAB) (12). The relatively small plasmids of Silicibacter sp.…”

Section: Resultsmentioning

confidence: 99%

Ecological Genomics of Marine Roseobacters

Moran

Belas

Schell

et al. 2007

Appl Environ Microbiol

342

299

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Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.In surface waters of the open ocean, 1 in 10 bacterial cells is a member of the Roseobacter group (17). In coastal waters, the number of Roseobacter cells increases to 1 in 5 (11, 19). Despite their obvious ecological success, however, roseobacters do not fit the stereotype of a small, metabolically conservative, "oligotrophic" bacterium (8, 18). Instead, they are large (0.08 m 3 ) (38), easily cultured (19), and respond readily to increased substrate availability (7). Analysis of the first Roseobacter genome sequence, that of Silicibacter pomeroyi, revealed a fairly large genome (4.5 Mb) housing abundant and diverse transporters, complex regulatory systems, and multiple pathways for acquiring carbon and energy in seawater. Roseobacters thus appear to be quite versatile from metabolic and ecological standpoints (43), with an assortment of strategies for obtaining carbon and nutrients and, directly or indirectly, affecting the biogeochemical status of seawater.The availability of two additional closed genome sequences of cultured roseobacters provides the opportunity for an ecologically based analysis of the genetic capabilities of this bacterial taxon. The three organisms are assumed to have different niches in the surface ocean based on the conditions of their isolation: S. pomeroyi is a free-living heterotrophic bacterioplankter obtained from coastal seawater (43), congener Silicibacter sp. strain TM1040 (96% 16S rRNA sequence identity to S. pomeroyi [ Fig. 1]) is an associate of the marine dinoflagellate Pfiesteria piscicida (1, 40), and Jannaschia sp. strain CCS1 (with 94% 16S rRNA sequence identity to the two Silicibacter species) represents a recently discovered class of marine aerobic bacteriochlorophyll a-based phototrophs (4). Our comparative an...

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Section: Resultsmentioning

confidence: 99%

Ecological Genomics of Marine Roseobacters

Moran

Belas

Schell

et al. 2007

Appl Environ Microbiol

342

299

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“…C58 has a larger circular chromosome, a linear chromosome (2.1 Mb), the Ti plasmid pTiC58 (0.2 Mb) and a second plasmid (0.5 Mb) 27,28 ; both plasmids and the linear chromo some replicate using repABC cassettes. The genome of P. versutus has not been sequenced in its entirety, but it appears to have one circular chromosome and two plasmids, pTAV1 (107 Kb) and pTAV3 (~400 Kb) 29 . Of these, pTAV1 has two replication loci, a complete repABC cassette and a second copy of repC 24,30 , whereas pTAV3 encodes a different type of replication system 31 .…”

Section: Distribution Of Repabc-type Systemsmentioning

confidence: 99%

The ABCs of plasmid replication and segregation

2012

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To ensure faithful transmission of low-copy plasmids to daughter cells, these plasmids must replicate once per cell cycle and distribute the replicated DNA to the nascent daughter cells. RepABC family plasmids are found exclusively in alphaproteobacteria and carry a combined replication and partitioning locus, the repABC cassette, which is also found on secondary chromosomes in this group. RepC and a replication origin are essential for plasmid replication, and RepA, RepB and the partitioning sites distribute the replicons to predivisional cells. Here, we review our current understanding of the transcriptional and post-transcriptional regulation of the Rep proteins and of their functions in plasmid replication and partitioning.

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“…Following a further 2 h incubation, the cells were harvested by centrifugation and the His-tagged recombinant protein was purified from a cell lysate using a metal affinity resin (Ni-NTA agarose; Novagen) as described by Dolowy et al (2005). The resulting culture was incubated at 37°C until the OD 600 nm reached 0.8 and then R.PamI(His) 6 protein expression was induced by the addition of arabinose to 0.2%.…”

Section: Purification Of Recombinant Rpami(his) 6 Endonucleasementioning

confidence: 99%

“…The resulting culture was incubated at 37°C until the OD 600 nm reached 0.8 and then R.PamI(His) 6 protein expression was induced by the addition of arabinose to 0.2%. Following a further 2 h incubation, the cells were harvested by centrifugation and the His-tagged recombinant protein was purified from a cell lysate using a metal affinity resin (Ni-NTA agarose; Novagen) as described by Dolowy et al (2005).…”

Section: Purification Of Recombinant Rpami(his) 6 Endonucleasementioning

confidence: 99%

Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilusJCM 7686

Dziewit

Kuczkowska

Adamczuk

et al. 2011

FEMS Microbiol Lett

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Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) encodes a functional type II restriction-modification (R-M) system designated PamI. Homologous systems were identified in the genomes of distinct taxonomic groups of Bacteria and Archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of R-M modules - even between domains. Analysis of the cleavage specificity of the R.PamI endonuclease revealed that this protein is an isoschizomer of restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest that R.PamI and NcoI are accompanied by methyltransferases of different methylation specificities (C5-methylcytosine and N4-methylcytosine methyltransferases, respectively), which possibly exemplifies recombinational shuffling of genes coding for individual components of R-M systems. The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level. Therefore, it functions in an analogous manner to plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of pAMI7 is nonfunctional, it is highly probable that this lack is compensated by the stabilizing activity of PamI. This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria.

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Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1

Cited by 5 publications

References 30 publications

Ecological Genomics of Marine Roseobacters

Ecological Genomics of Marine Roseobacters

The ABCs of plasmid replication and segregation

Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilusJCM 7686

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