Abstract
BackgroundMesorhizobium metallidurans STM 2683T and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high Zinc and Cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with Zinc or Cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes.ResultsThe draft genomes of the two Mezorhizobium strains were sequenced and used to map RNAseq data obtained after Zinc or Cadmium stresses. Comparative genomics and transcriptomics allowed the rapid discovery of metal-specific or/and strain-specific genes. Respectively 1.05% (72/6,844) and 0.97% (68/6,994) predicted Coding DNA Sequences (CDS) for STM 2683 and STM 4661 were significantly differentially expressed upon metal exposure. Among these, a significant number of CDS involved in transport (13/72 and 13/68 for STM 2683 and STM 4661, respectively) and sequestration (15/72 and 16/68 for STM 2683 and STM 4661, respectively) were identified. Thirteen CDS presented homologs in both strains and were differentially regulated by Zinc and/or Cadmium. For instance, several PIB-type ATPases and genes likely to participate in metal sequestration were identified. Among the conserved CDS that showed differential regulation in the two isolates, we also found znuABC homologs encoding for a high affinity ABC-type Zinc import system probably involved in Zinc homeostasis. Additionally, global analyses suggested that both metals also repressed significantly the translational machinery.ConclusionsThe comparative RNAseq-based approach revealed a relatively low number of genes significantly regulated in the two Mesorhizobium strains. Very few of them were involved in the non-specific metal response, indicating that the approach was well suited for identifying genes that specifically respond to Zinc and Cadmium. Among significantly up-regulated genes, several encode metal efflux and sequestration systems which can be considered as the most widely represented mechanisms of rhizobial metal tolerance. Downstream functional studies will increase successful phytostabilization strategies by selecting appropriate metallicolous rhizobial partners.
Highlights
Mesorhizobium metallidurans STM 2683T and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils
Among our RNA sequencing (RNAseq) data, we identified other Coding DNA Sequences (CDS) significantly up-regulated in the two Mesorhizobium strains under Zn and/or Cd exposure (7 CDS identified in STM 2683 and 8 in STM 4661) that may be involved in the precipitation of metals by phosphates or their reduction as sulfides (Tables 4 and 5)
Identification of candidate genes possibly involved in transport by Cation Diffusion Facilitor proteins (CDFs) efflux systems Among the putative CDS probably involved in metal efflux, we identified a putative CDF-type transporter that presented homologies with ZitB, a Zn-specific transporter identified in E. coli [31] and CzcD involved notably in Cd and Zn resistance in C. metallidurans [32] that was significantly up-regulated (> 2-fold) after Zn treatment in STM 4661 (MESS4v1_360039)
Summary
Mesorhizobium metallidurans STM 2683T and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. Strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils They tolerate unusually high Zinc and Cadmium concentrations as compared to other mesorhizobia. Mining spoils are major sources of pollution as they disperse into the surrounding environment through aerial or water erosion and can be found several kilometers away from their original site of deposit Such sources of pollution pose significant risks to public health [1] and to ecosystem dynamics due to reduced biodiversity resulting from low plant coverage caused by soil toxicity [2]. In highly polluted soils like mining soils, where the removal of metals by phytoextraction using hyperaccumulator plants is not efficient due to the slowness of the process, the best adapted method is phytostabilization [3] This consists in limiting the dissemination of toxic metals by using metallicolous plants, i.e. metal tolerant plants, to establish a persistent plant cover and prevent pollution through erosion. Survival and proliferation of organisms on metal contaminated sites depends on their capacity to tolerate high metal concentrations and requires the acquisition of resistance mechanisms
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