INRA USC1242, Montpellier, France.
BMC Genomics. 2013 Apr 30;14:292. doi: 10.1186/1471-2164-14-292.
Mesorhizobium 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.
The 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.
The 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.
中慢生根瘤菌 STM 2683T 和 Mesorhizobium sp. 菌株 STM 4661 是从距离遥远的采矿迹地的金属豆科植物 Anthyllis vulneraria 根瘤中分离出来的。与其他中慢生根瘤菌相比，它们能耐受异常高的锌和镉浓度。这项工作旨在研究与锌或镉暴露相关的基因表达谱，并鉴定这两种对矿山植物稳定化有意义的金属中慢生根瘤菌菌株中参与金属耐受的基因。
对这两个 Mesorhizobium 菌株的基因组草图进行了测序，并用于映射锌或镉胁迫后获得的 RNAseq 数据。比较基因组学和转录组学允许快速发现金属特异性或/和菌株特异性基因。STM 2683 和 STM 4661 分别有 1.05%（72/6844）和 0.97%（68/6994）的预测编码 DNA 序列（CDS）在金属暴露时显著差异表达。其中，大量参与运输（STM 2683 和 STM 4661 分别有 13/72 和 13/68）和螯合（STM 2683 和 STM 4661 分别有 15/72 和 16/68）的 CDS 被鉴定出来。有 13 个 CDS 在两个菌株中都有同源物，并受锌和/或镉的差异调控。例如，鉴定了几种 PIB 型 ATP 酶和可能参与金属螯合的基因。在两个分离株中差异调节的保守 CDS 中，我们还发现了编码高亲和力 ABC 型锌输入系统的 znuABC 同源物，该系统可能参与锌稳态。此外，全局分析表明，两种金属也显著抑制了翻译机制。
基于 RNAseq 的比较方法揭示了两个中慢生根瘤菌菌株中相对较少的基因受到显著调控。其中很少有基因参与非特异性金属反应，这表明该方法非常适合鉴定特异性响应锌和镉的基因。在显著上调的基因中，有几个编码金属外排和螯合系统，这可以被认为是根瘤菌金属耐受最广泛的机制。下游功能研究将通过选择合适的金属中慢生根瘤菌伙伴来增加成功的植物稳定化策略。
