title: Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes.
abstract: Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.
authors.affiliation: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies-IBEST, University of Idaho, Moscow, ID 83844-3051, USA.
authors.forename: Diya
authors.initials: D
authors.lastname: Sen
authors.forename: Geraldine A
authors.initials: GA
authors.lastname: Van der Auwera
authors.forename: Linda M
authors.initials: LM
authors.lastname: Rogers
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Thomas
authors.forename: Celeste J
authors.initials: CJ
authors.lastname: Brown
authors.forename: Eva M
authors.initials: EM
authors.lastname: Top
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D005798:Genes, Bacterial; D014644:Genetic Variation; D058507:Host Specificity; D054643:INDEL Mutation; D054892:Metagenome; D008969:Molecular Sequence Data; D009664:Norway; D010802:Phylogeny; D010957:Plasmids / Q000302:isolation & purification*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012987:Soil
chemical_list: D004269:DNA, Bacterial; D012987:Soil