Genomic and Transcriptomic Changes That Mediate Increased Platinum Resistance in Cupriavidus metallidurans

Abstract

The extensive anthropogenic use of platinum, a rare element found in low natural abundance in the Earth’s continental crust and one of the critical raw materials in the EU innovation partnership framework, has resulted in increased concentrations in surface environments. To minimize its spread and increase its recovery from the environment, biological recovery via different microbial systems is explored. In contrast, studies focusing on the effects of prolonged exposure to Pt are limited. In this study, we used the metal-resistant Cupriavidus metallidurans NA4 strain to explore the adaptation of environmental bacteria to platinum exposure. We used a combined Nanopore–Illumina sequencing approach to fully resolve all six replicons of the C. metallidurans NA4 genome, and compared them with the C. metallidurans CH34 genome, revealing an important role in metal resistance for its chromid rather than its megaplasmids. In addition, we identified the genomic and transcriptomic changes in a laboratory-evolved strain, displaying resistance to 160 µM Pt4+. The latter carried 20 mutations, including a large 69.9 kb deletion in its plasmid pNA4_D (89.6 kb in size), and 226 differentially-expressed genes compared to its parental strain. Many membrane-related processes were affected, including up-regulation of cytochrome c and a lytic transglycosylase, down-regulation of flagellar and pili-related genes, and loss of the pNA4_D conjugative machinery, pointing towards a significant role in the adaptation to platinum.

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

“…This phenomenon of a czc determinant duplication was observed in C. metallidurans BS1 while previously a similar phenomenon was also reported in C. metallidurans NA4 where a large part of the resistance systems was found not to be plasmid-encoded. C. metallidurans NA4 was shown to have similar genome architecture in that the main large metal resistance clusters on pMOL30 were syntenic with gene clusters on NA4's chromid instead of NA4's plasmids (pNA4_A-D) as was also the case in BS1 (Ali et al, 2019) Figure S2). The zntA_czcI 2 B 2 A 2 _S 2 R 2 core-determinant was present (DDF84_RS21985 -DDF84_RS22020) comprising structural and regulatory genes as well as encoding the P IB2 -type ATPase, ZntA (Legatzki et al, 2003;Scherer and Nies, 2009).…”

“…Strain BS1 contained predicted intact prophages [Bacill_SP_15_ (NC_031245; 7), Burkho_phiE255 (NC_009237; 32), and Ralsto_RSA1 (NC_009382; 29)] as well as NA4, H1130 and Ni-2, detailed information of prophages is mentioned Table 5. Previous studies also provided evidence for the presence of prophages in other strains of C. metallidurans than strain CH34 (Van Houdt et al, 2018;Ali et al, 2019).…”

“…However, at genome level, strain NA4 shows a higher degree of kinship to type strain CH34 than strain BS1. This could be an indication of a genetic drift correlating with global distribution and habitat adaptation (Mergeay et al, 1978;Ali et al, 2019). C. metallidurans BS1 conferred resistance to Zn 2+ displaying a MIC of 20 mM, Cd 2+ (2.5 mM), Co 2+ (20mM), Ni 2+ (8 mM), As 3+ (3.5 mM), Cu 2+ (5 mM), Au 3+ (1 µM) and Pb 2+ (1.7 mM) on Mineral salts medium 284 plates.…”

“…Comparative genomic features between BS1, CH34 and NA4 are shown in Table 2 and general genome statistics are given in Table 3. Several genome sequences of different C. metallidurans strains have been analyzed and studied further, including C. metallidurans H1130 (102 contigs), C. metallidurans NA1 (238 contigs), C. metallidurans NA4 (chromosome + chromid + pNA4_A-_D), C. metallidurans NE12 (87 contigs), C. metallidurans NBRC101272 (63 contigs), C. metallidurans NDB3NO24 (38 contigs) and C. metallidurans Ni-2 (chromosome + pNi-2_1-3) (Janssen et al, 2010;Van Houdt et al, 2012;Monsieurs et al, 2013Monsieurs et al, , 2014Mergeay, 2015;Ali et al, 2019). The analyzed strains possess the capability to maintain viability over a wide range of metal (Vandamme and Coenye, 2004;Scherer and Nies, 2009;Van Houdt et al, 2018;Lee et al, 2019).…”

“…Comparison and characteristics of the genomic islands of C. metallidurans strain CH34 and BS1; (*)(Van Houdt et al, 2012;Ali et al, 2019).…”