Synthesis of nickel–iron hydrogenase in Cupriavidus metallidurans is controlled by metal-dependent silencing and un-silencing of genomic islands

Abstract

Cupriavidus metallidurans CH34 is able to grow autotrophically as a hydrogen-oxidizing bacterium and produces nickel-dependent hydrogenases, even under heterotrophic conditions. Loss of its two native plasmids resulted in inability of the resulting strain AE104 to synthesize the hydrogenases and to grow autotrophically in phosphate-poor, Tris-buffered mineral salts medium (TMM). Three of eleven previously identified catabolic genomic islands (CMGIs; Van Houdt et al., 2009), two of which harbor the genes for the membrane-bound (CMGI-2) and the soluble hydrogenase (CMGI-3), were silenced in strain AE104 when cultivated in phosphate-poor TMM, explaining its inability to produce hydrogenases. Production of the soluble hydrogenase from the aut region 1 of CMGI-3, and concomitant autotrophic growth, was recovered when the gene for the zinc importer ZupT was deleted in strain AE104. The transcriptome of the ΔzupT mutant exhibited two up-regulated gene regions compared to its parent strain AE104. Expression of the genes in the aut region 1 increased independently of the presence of added zinc. A second gene region was expressed only under metal starvation conditions. This region encoded a TonB-dependent outer membrane protein, a putative metal chaperone plus paralogs of essential zinc-dependent proteins, indicating the presence of a zinc allocation pathway in C. metallidurans. Thus, expression of the genes for the soluble hydrogenase and the Calvin cycle enzymes on aut region 1 of CMGI-3 of C. metallidurans is under global control and needs efficient ZupT-dependent zinc allocation for a regulatory role, which might be discrimination of nickel.

Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold–Copper Mine

“…metal-resistance super clusters were formed as newly sorted genome islands ( Figure 6 and Supplementary Table S6). The major difference between C. metallidurans BS1 and CH34 is that C. metallidurans BS1 contained three prophages while it does not have the structural and accessory genes for the soluble and membrane-bound hydrogenase present in C. metallidurans CH34 (Mergeay et al, 1985;Janssen et al, 2010;Herzberg et al, 2015). Presence of prophages were also confirmed in C. metallidurans NA1, C. metallidurans NA4, C. metallidurans H1130 and C. metallidurans Ni-2 via PHAST 8 and/or PHASTER (Van Houdt et al, 2018).…”

“…This absence is shown by gaps in the chromosome of strain BS1 ( Figure 5). These genomic gaps also included CMGI-2 and CMGI-3, which carry the genes for hydrogen-dependent facultative chemolithotrophy coupled with carbon dioxide fixation (Mergeay et al, 1985;Van Houdt et al, 2009;Herzberg et al, 2015). This leads to a main characteristic in the phenotypic distinction of these two strains.…”

Synergistic Toxicity of Copper and Gold Compounds in Cupriavidus metallidurans

“…Statistics. A Student t test was used to determine statistical significance, but in most cases the distance (D) has been used several times previously for such analyses (19,33,63). It is a simple, more useful value than the Student t test result because nonintersecting deviation bars of two values (D Ͼ 1) for three repeats always means a statistically relevant (Ն95%) difference provided the deviations are within a similar range.…”

Responses to copper stress in the metal‐resistant bacterium Cupriavidus gilardii CR3: a whole‐transcriptome analysis

“…In contrast, other finished genomes in Cupriavidus species have two or at least one plasmids bearing metal‐resistant genes, which means that C. gilardii CR3 probably possesses distinguishing molecular mechanisms for copper. To date, only C. metallidurans among the genus of Cupriavidus was reported its metal‐resistance mechanisms associated with a total of 16 metals by microarray sequencing .…”