Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes

Abstract

Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.

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

“…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).…”

“…ncc resistance determinant such as NreB, NccC, NccB, and NccA (Nickel-Cobalt-Cadmium Resistance Protein), showed a 100% identical AA sequence in both strains, CH34 and BS1. A nonsense/frameshift mutation in NccB, indicated to be present in strain CH34 and NA1, NA4, H1130 (Van Houdt et al, 2018) was also observed to be present in BS1. The smaller segment of NccB is 100% similar to the NccB segment in strain CH34 both by nucleotide and amino acid BLAST analysis but the larger locus was 99% similar, with one arginine replaced with isoleucine in BS1.…”

“…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). 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.…”

“…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). Rfam 7 predicted that both C. metallidurans CH34 and C. metallidurans BS1 contained four sets of 5S, 16S, 23S r RNA genes.…”

DNA-Binding and Transcription Activation by Unphosphorylated Response Regulator AgrR From Cupriavidus metallidurans Involved in Silver Resistance

“…The genome-wide expression analysis of the silver-resistant mutant NA4S was previously performed via the microarray platform of the C. metallidurans type strain CH34 ( Mijnendonckx et al, 2019 ). However, taking into account the strain differences ( Van Houdt et al, 2018 ; Ali et al, 2019 ), we reassessed this more accurately via an RNA-seq approach. As the increased resistance stemmed from natural selection of resistance-conferring mutations ( Lenski, 2017 ), the global shift in transcriptome, resulting from the altered genotype of the evolved strain (NA4S) as compared with the parental strain (NA4), was examined in non-selective conditions ( Sandberg et al, 2014 ; LaCroix et al, 2015 ; McCloskey et al, 2018 ).…”