Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33B.

A cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021bp circular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant similarity with the phage integrase protein from Pseudomonas putida GB-1. The ORF2 product showed some similarity with the hypothetical protein Shal_1786 from Shewanella halifaxensis HAW-EB4. The ORF-3 product revealed high amino acid sequence homology with the Escherichia coli replication initiation protein similar to pi protein of R6K plasmid. Five repeat regions (three perfect 22-bp repeats and two imperfect motifs), a putative ribosome binding site, and -10 and -35 promotor sequences were identified upstream of the ORF-3 (rep). The rep module is very similar to several theta replicating iteron family plasmids, suggesting that pSFKW33 replication follows the same course. The ORF-5 product revealed significant identity with the entry exclusion protein 1 of plasmid pIS2 from enteropathogenic strain E. coli 0111:H. The ORF-6 product showed significant identity with the putative transcriptional regulator protein from Shewanella benthica KT99 belonging to HTH-XRE-family protein. The ORF-8 encoded protein that showed some similarity with the hypothetical protein KT99_00146 from Shewanella benthica KT99. The ORF-4 and ORF-7 encoded putative proteins of 189 and 118 amino acid residues, respectively, with no homologies to any known proteins. The absolute copy number of pSFKW33 was estimated to be five copies per chromosome by real-time PCR.

Molecular characterization of a cryptic plasmid from the psychrotrophic antarctic bacterium Pseudoalteromonas sp. 643A.

We report the identification and nucleotide sequence analysis of pKW1, a plasmid of the psychrotrophic bacterium Pseudoalteromonas sp. 643A isolated from the stomach of Antarctic krill Euphasia superba. pKW1 consists of 4583 bp, has a G+C content of 43% and seven putative open reading frames (ORFs). The deduced amino acid sequence from ORF-1 shared significant similarity with the plasmid replicase protein of Psychrobacter cryohalolentis, strain K5. The DNA region immediately downstream of the ORF-1 showed some homology with the Rep-binding sequence of the theta-replicating ColE2-type plasmids. The ORF-3 amino acid sequence revealed amino acid sequence homology with the mobilization protein of Psychrobacter sp. PRwf-1 and Moraxella catarrhalis, with identities of 28% and 25%, respectively. The ORF-4 showed 46% amino acid sequence homology with the putative relaxase/mobilization nuclease MobA of Hafnia alvei and 44% homology with the putative mobilization protein A of Pasterulla multocida. The copy number of pKW1 in Pseudoalteromonas sp. 643A was estimated of 15 copies per chromosome.