The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments

Abstract

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.

Figure 1. Circular representation of the two main replicons of CH34.

Circles display from the inside outwards: (ring 1) scale in Mb, (ring 2) GC-content using a 2 kb window, (ring 3) GC-skew (G-C/G+C ratio) using a 2 kb window, (rings 4 and 5) predicted CDSs transcribed in a counterclockwise/clockwise direction; genomic islands are indicated in black solid bars and given a numbering; black open triangles represent the IS elements; colored triangles depict transposons: red, Tn6049; blue, Tn6049; and green, Tn6050.

Figure 2. Functional distribution over CHR1 and CHR2 by COG classification.

The scale represents the normalised ratio of CDS numbers per replicon (i.e. the ratio of percentages for each class per replicon); a ration of 1 means that genes classified in a particular COG are, numberwise, evenly distributed over both replicons, taking into account the different total count of genes per replicon. Detailed data are in Table S1.

Figure 3. Shared and unique proteins of Cupriavidus chromosomes.

4-way comparison Venn diagram illustrating the intersection and differences between chromosomal replicons of completed Cupriavidus genomes. Intersections show the number of shared proteins between two or more organisms based on reciprocal best BLAST hits (see Methods). Numbers in parantheses depict the missing overlap sectors due to circular drawing and represent proteins shared between opposite genomes but absent in the other two genomes. Abbreviations: Cmet, C. metallidurans CH34; Cpin, C. pinatubonensis JMP134; Ceut, C. eutrophus; Ctai, C. taiwanensis.

Figure 4. Comparative DNA analysis of Cupriavidus chromosomes.

Nucleotide based comparison of the CHR1 replicons of the four Cupriavidus species (abbreviations as in Figure 3) and R. solanacearum GMI1000 (denoted as Rsol) using the anchor-allignment software Murasaki (http://murasaki.dna.bio.keio.ac.jp/) . Scale in Mb is shown on top.

Figure 5. Distribution of the Bug domain.

Overrepresentation of ‘Bug’ domains in the family Burkholderiales according to MIST data (http://mistdb.com/), with numbers in parantheses. Organisms encoding more then 40 Bug domain-containing proteins are in bold. Only relevant taxa and species are shown (see text). Detailed data are in Table S8.

Figure 6. The bvgSA and kps loci of C. metallidurans CH34.

Genomic region on the CHR2 replicon of C. metallidurans CH34 covering the bvgSA locus encoding a master virulence regulon (Rmet_5710, _5714, _5724) and the kps locus for synthesis and transport of capsular polysaccharides (Rmet_5729 to _5737). Relevant synteny maps are given for 11 organisms. Abbreviations: Cpin, C. pinatubonensis JMP134; Ceut, C. eutrophus H16; Ctai, C. taiwanensis; Bpet, B. petrii DSM 12804; Bbro, Bordetella bronchiseptica RB50; Paer, Pseudomonas aeruginosa PAO1; Bpar, B. parapertussis 12822; Bper, B. pertussis Tohama I; Ecol-A, avian pathogenic Escherichia coli (APEC01); Ecol-U, uripathogenic E. coli (UTI89); Ecol-K, E. coli K12. A nearby IS1088 element (Rmet_5718) is indicated with a blue rectangle in the +1 reading frame (see text).