Plasmid diversity in arctic strains of Psychrobacter spp

Abstract

Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments.

Fig. 1

Phylogenetic tree for 16S rDNA sequences of Psychrobacter spp. The tree was constructed by the neighbor-joining algorithm with Kimura corrected distances. The statistical support for the internal nodes was determined by 1000 bootstrap replicates and values of >50 % are shown. ‘DAB’ strains are denoted by bold text and strains analyzed in this study are indicated by black dots. The types of environment from which particular strains were isolated are indicated in square parenthesis by the numerical code, explained in the legend next to the tree. The 16S rDNA sequence of Moraxella catarrhalis RH4 was used as the outgroup

Fig. 2

Linear maps showing the genetic structure of circular plasmids pP12P1, pP32BP1, pP43BP1, pP43BP2, pP43BP3, pP43BP4, pP60P1, pP60P2 and pP109bwP1. The predicted genetic modules are indicated by gray rectangles: REP _A (REP_B) repA-like (repB-like) replication systems, MOB _P (MOB_Q, MOB_V) system for mobilization for conjugal transfer, TA toxin–antitoxin system, R-M type II restriction-modification system, MRS multimer resolution system, AhpC subunit C of alkyl hydroperoxide reductase module. Gray stars indicate Sel1 domain repeat-containing proteins with slight homology to beta-lactam hydrolases. Arrows indicate the transcriptional orientation of the genes. Areas of gray shading connect genes of different plasmids encoding related proteins

Fig. 3

Structure and alignments of repB-like oriVs and iterons (a) and repA-like oriVs (b) of the analyzed Psychrobacter plasmids. Nucleotides identical to the reference sequence of oriV of ColE2 are shown against a black background and those common to at least 50 % of the analyzed sequences have a gray background

Fig. 4

Structure and alignments of oriTs of the analyzed Psychrobacter plasmids. Nucleotides identical to the reference (oriT of pSW200 and oriT of pBBR1) or consensus sequences (oriT of MOB_Q modules) are shown against a black background and those common to at least 50 % of the analyzed sequences have a gray background. The positions of the predicted oriTs within the sequences of the plasmids are shown in parenthesis. Experimentally determined or predicted (for pSW200) nic-cleavage sites are indicated with a triangle

Fig. 5

Phylogenetic tree for 16S rDNA sequences of psychrophilic bacteria harboring plasmids. The tree was constructed by the neighbor-joining algorithm with Kimura corrected distances, and the statistical support for the internal nodes was determined by 1000 bootstrap replicates. The 16S rDNA sequence of a representative of the Archaea, Ignicoccus hospitalis KIN4/I, was used as the outgroup. Gram-negative and gram-positive bacteria are shown against dark and light gray backgrounds, respectively. The type of replication system of each analyzed plasmid (based on sequence alignments, which are summarized in the Supplementary Materials, Figs. S2, S3 and S4) is indicated by a dot or square: black dot RepB-like, white square RepA-like, black square RepL-like, white dot other types. Dots within square parenthesis represent replication systems of composite replicons, and dots within round parenthesis represent replication modules of plasmids of Pseudomonas sp. MC1, Pseudoalteromonas spp. (Bsi429, PS1M2 and PS1M3) and Flavobacterium sp. KP1 (whose 16S rDNA sequences were not available in the GenBank database). Accession numbers of all plasmids whose replication proteins were used for the analysis are given in the Supplementary Materials, Table S3