Molecular characterization of functional modules of plasmid pWKS1 of Paracoccus pantotrophus DSM 11072 The GenBank accession number for the sequence reported in this paper is AF482428.

Bartosik, Dariusz; Baj, Jadwiga; Sochacka, Marta; Piechucka, E; Włodarczyk, Michał

doi:10.1099/00221287-148-9-2847

Cited by 31 publications

(25 citation statements)

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“…and, to our knowledge, is the largest TE that has ever been identified by transposition to an entrapment vector. The results summarized in Table 2 show that it was not possible to capture TnPpa1 using the previously constructed entrapment vector pMEC1 carrying the ori region of a small plasmid pWKS1 that naturally resides in strain DSM 11072 (Bartosik et al, 2002). This observation indicates that the nature of the vector replicator region acts as a natural selection for the size of the integrated elements.…”

Section: Discussionmentioning

confidence: 99%

Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

et al. 2006

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A novel shuttle entrapment vector, pMMB2, was used to identify a large transposable element, TnPpa1 (44?3 kb), of Paracoccus pantotrophus DSM 11072. TnPpa1 has a composite structure with divergently oriented copies of a cryptic transposon, Tn3434 (Tn3 family), located at both termini. The core region of the element contains a large set of putative genes, whose products show similarity to enzymes involved in central intermediary metabolism (e.g. tricarboxylic acid cycle or 2-methylcitrate cycle), transporters, transcriptional regulators and conserved proteins of unknown function. A 4?2 kb DNA segment of TnPpa1 is homologous to a region of chromosome cII of Rhodobacter sphaeroides 2.4.1, which exemplifies the mosaic structure of this element. TnPpa1 is bordered by 5 bp long directly repeated sequences and is located within a mega-sized replicon, pWKS5, in the DSM 11072 genome. Spontaneous inversion of the core region of TnPpa1 was detected in the host genome. Analysis of the distribution of TnPpa1 in three other strains of P. pantotrophus revealed that this element was present exclusively within DSM 11072, which suggests its relatively recent acquisition by lateral transfer. The identification of TnPpa1 (which may be considered a transposable genomic island) provides evidence for the transposition and lateral transfer of large DNA segments of chromosomal origin (carrying various housekeeping genes), which may have a great impact on the evolution of bacterial genomes.

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Section: Discussionmentioning

confidence: 99%

Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

et al. 2006

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“…The underlying 454 titanium run resulted in high sequence coverage for each plasmid ranging from 120-to 373-fold. Paracoccus pantotrophus or Rhodobacter blasticus (Bartosik et al, 2002;Inui et al, 2003) and seems to be restricted to cryptic plasmids. The smallest cryptic plasmid pSG4 contains just five genes including a putative mobilization protein and a RepB-type replicase (RepB-V; Fig.…”

Section: Molecular Analyses Of the Three S Guttiformis Plasmidsmentioning

confidence: 99%

Think pink: photosynthesis, plasmids and the Roseobacter clade

Petersen

Brinkmann

Bunk

et al. 2012

Environmental Microbiology

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Summary Aerobic anoxygenic photosynthesis providing additional ATP for a photoheterotrophic lifestyle is characteristic for several representatives of the marine Roseobacter clade. The patchy distribution of photosynthesis gene clusters (PGCs) within this lineage probably results from horizontal transfers and this explanation is supported by two cases of plasmid‐located PGCs. In this study sequencing of the three Sulfitobacter guttiformis plasmids (pSG4, pSG53, pSG118) was initiated with the objective to analyse the 118 kb‐sized photosynthetic replicon, but our annotation revealed several additional important traits including key genes of the primary metabolism. The comparison of the two photosynthesis plasmids from S. guttiformis and Roseobacter litoralis showed that their replication modules are located at precisely the same position within the 45 kb‐sized PGC. However, comprehensive phylogenetic analyses of the non‐homologous replicases (RepB‐III, DnaA‐like I) and the two ParAB partitioning proteins unequivocally document an independent origin of their extrachromosomal replicons. The analogous positioning within the two photosynthesis super‐operons can be explained by a two‐step recombination scenario and seems to be the ultimate result of stabilizing selection. Our exemplary analyses of ‘pink’ plasmids document that chromosomal outsourcing is a common phenomenon in the Roseobacter clade and subsequent horizontal exchanges offer rapid access to the marine pan‐genome.

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“…Our group has already obtained the sequences of 18 plasmids, ranging in size from 2.7 to 40 kb, that originate from different Paracoccus spp. : P. methylutens DM12 (2 plasmids) [10], P. pantotrophus DSM 11072 (1 plasmid) [11] and four carotenoid producers, P. aestuarii DSM 19484 (5 plasmids) ([GenBank:JQ041633], [GenBank:JQ065021], [GenBank:JQ066766], [GenBank:JQ684025], [GenBank:JQ796370]), P. haeundaensis LMG P-21903 (2 plasmids) ([GenBank:JQ066767], [GenBank:JQ684024]), P. marcusii DSM 11574 (5 plasmids) ([GenBank: KC542384], [GenBank:KC561053], [GenBank:KC561054], [GenBank:KC561055], [GenBank:JQ796371) and P. marcusii OS22 (3 plasmids) ([GenBank:JQ664550], [GenBank:JQ678602], [GenBank:JQ684023]). We have also sequenced the basic replicons of three other plasmids from P. alcaliphilus JCM 7364 (pALC1) and P. versutus UW1 (pTAV1 and pTAV3) [12-14].…”

Section: Introductionmentioning

confidence: 99%

Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids

et al. 2014

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BackgroundParacoccus aminophilus JCM 7686 is a methylotrophic α-Proteobacterium capable of utilizing reduced one-carbon compounds as sole carbon and energy source for growth, including toxic N,N-dimethylformamide, formamide, methanol, and methylamines, which are widely used in the industry. P. aminophilus JCM 7686, as many other Paracoccus spp., possesses a genome representing a multipartite structure, in which the genomic information is split between various replicons, including chromids, essential plasmid-like replicons, with properties of both chromosomes and plasmids. In this study, whole-genome sequencing and functional genomics approaches were applied to investigate P. aminophilus genome information.ResultsThe P. aminophilus JCM 7686 genome has a multipartite structure, composed of a single circular chromosome and eight additional replicons ranging in size between 5.6 and 438.1 kb. Functional analyses revealed that two of the replicons, pAMI5 and pAMI6, are essential for host viability, therefore they should be considered as chromids. Both replicons carry housekeeping genes, e.g. responsible for de novo NAD biosynthesis and ammonium transport. Other mobile genetic elements have also been identified, including 20 insertion sequences, 4 transposons and 10 prophage regions, one of which represents a novel, functional serine recombinase-encoding bacteriophage, ϕPam-6. Moreover, in silico analyses allowed us to predict the transcription regulatory network of the JCM 7686 strain, as well as components of the stress response, recombination, repair and methylation machineries. Finally, comparative genomic analyses revealed that P. aminophilus JCM 7686 has a relatively distant relationship to other representatives of the genus Paracoccus.ConclusionsP. aminophilus genome exploration provided insights into the overall structure and functions of the genome, with a special focus on the chromids. Based on the obtained results we propose the classification of bacterial chromids into two types: “primary” chromids, which are indispensable for host viability and “secondary” chromids, which are essential, but only under some environmental conditions and which were probably formed quite recently in the course of evolution. Detailed genome investigation and its functional analysis, makes P. aminophilus JCM 7686 a suitable reference strain for the genus Paracoccus. Moreover, this study has increased knowledge on overall genome structure and composition of members within the class Alphaproteobacteria.

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Molecular characterization of functional modules of plasmid pWKS1 of Paracoccus pantotrophus DSM 11072 The GenBank accession number for the sequence reported in this paper is AF482428.

Cited by 31 publications

References 50 publications

Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

Think pink: photosynthesis, plasmids and the Roseobacter clade

Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids

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