Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

Abstract

Plasmids are important “vehicles” for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

Manipulating Bacterial Communities by in situ Microbiome Engineering

“…Recent sequencing efforts have demonstrated that plasmids are prevalent in microbial communities [61]. However, the host ranges of most plasmids remain unknown, and their associated proteins and modes of regulation are poorly characterized [62].…”

Acinetobacter baumannii: biology and drug resistance — role of carbapenemases

“…Plasmids are circular or linear double-stranded DNA molecules distinct from chromosomal DNA, often transferred by means of conjugation [90,91]. Studies concerning the sequence analysis of A. baumannii plasmid replicons revealed the differences comparing to other prokaryotic species, suggesting that A. baumannii strains may carry distinct set of plasmid types [92,93].…”

“…Moreover, the MIC values of doripenem are lower than presented by imipenem and meropenem for A. baumannii. The studies concerning analysis of carbapenems MIC 90 values among Acinetobacter spp., revealed more than eightfold higher MIC 90 for ertapenem, comparing to other carbapenems [45][46][47].…”

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

“…The former plasmids encode all genes required for transfer (namely genes for a relaxase, a coupling protein (T4CP) and a mating-pair formation system (MPF), while the latter generally encode only the relaxase gene but lack VirB4 and MPF and then need a helper plasmid for transfer293031323334. Analysis of the phylogenetic relationships among the relaxases allows the classification of transmissible plasmids into eight (MOB) families2930323334.…”

“…45.7%) (see Supplementary Table S4). In this regard, based on genomic data Nishida47 and Shintani et al 31. reveled that the GC contents of the majority of plasmids is lower than the GC contents of its host chromosome.…”