Molecular characterization of the pSinB plasmid of the arsenite oxidizing, metallotolerantSinorhizobiumsp. M14 – insight into the heavy metal resistome of sinorhizobial extrachromosomal replicons

Abstract

Sinorhizobium sp. M14 is an As(III)-oxidizing, psychrotolerant strain, capable of growth in the presence of extremely high concentrations of arsenic and many other heavy metals. Metallotolerant abilities of the M14 strain depend upon the presence of two extrachromosomal replicons: pSinA (∼ 109 kb) and pSinB (∼ 300 kb). The latter was subjected to complex analysis. The performed analysis demonstrated that the plasmid pSinB is a narrow-host-range repABC-type replicon, which is fully stabilized by the phd-vapC-like toxin-antitoxin stabilizing system. In silico analysis showed that among the phenotypic gene clusters of the plasmid pSinB, eight modules are potentially involved in heavy metals resistance (HMR). These modules carry genes encoding efflux pumps, permeases, transporters and copper oxidases, which provide resistance to arsenic, cadmium, cobalt, copper, iron, mercury, nickel, silver and zinc. The functional analysis revealed that the HMR modules are active and have an effect on the minimal inhibitory concentration (MIC) values observed for the heterological host cells. The phenotype was manifested by an increase or decrease of the MICs of heavy metals and it was strain specific. The analysis of distribution of the heavy metal resistance genes, i.e. resistome, in Sinorhizobium spp. plasmids, revealed that the HMR modules are common in these replicons.

Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica)

“…This may be explained by the possibility that some of the identified heavy metal-resistance genes are inactive, either permanently due to the presence of mutation or facultatively (only in a particular host) as a result of genetic incongruity, which was previously shown for several other resistance module-bacterial host systems (Dziewit et al , 2015Romaniuk et al 2017). On the other hand, resistance phenotypes observed for strains without identified resistance genes could be "nonspecific" and resulted from, e.g., altered cell envelope permeability or biofilm formation (Wales and Davies 2015).…”

“…LM20, and Sinorhizobium sp. M14 were used as the positive controls in PCRs, as these strains previously gave positive results for the presence of particular resistance genes (Drewniak et al 2013;Dziewit et al 2015;Romaniuk et al 2017).…”

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14

“…Based on similarity searches of the scaffolds, previous plasmid profiling of Ensifer sp. M14 [ 10 , 12 ], and the finished genomes of related strains [ 33 , 58 ], we predict that the Ensifer sp. M14 genome consists of one chromosome (at least 4.4 Mbp in size), two additional large replicons (chromids and/or large megaplasmids, at least 1.6 Mbp and 0.6 Mbp in size), and the two previously reported smaller megaplasmids (pSinA and pSinB, 109 kbp and 300 kbp, respectively, based on previous papers [ 10 , 12 ]).…”

“…M14 were identified on the basis of the ANI results. These 10 genomes, together with the complete pSinA and pSinB plasmid sequences [ 10 , 12 ], were used as reference genomes for further scaffolding of the assembly using MeDuSa [ 18 ]. The Ensifer sp.…”

“…Structural and functional analysis of this plasmid showed that it carries gene clusters involved in heavy metals resistance. Among these are genes encoding efflux pumps, permeases, transporters, and copper oxidases, which are responsible for resistance to arsenic, cobalt, zinc, cadmium, iron, mercury, nickel, copper, and silver [ 12 ].…”