title: 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.
authors.affiliation: Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium. pjanssen@sckcen.be
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Janssen
authors.forename: Rob
authors.initials: R
authors.lastname: Van Houdt
authors.forename: Hugo
authors.initials: H
authors.lastname: Moors
authors.forename: Pieter
authors.initials: P
authors.lastname: Monsieurs
authors.forename: Nicolas
authors.initials: N
authors.lastname: Morin
authors.forename: Arlette
authors.initials: A
authors.lastname: Michaux
authors.forename: Mohammed A
authors.initials: MA
authors.lastname: Benotmane
authors.forename: Natalie
authors.initials: N
authors.lastname: Leys
authors.forename: Tatiana
authors.initials: T
authors.lastname: Vallaeys
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Sébastien
authors.initials: S
authors.lastname: Monchy
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Safiyh
authors.initials: S
authors.lastname: Taghavi
authors.forename: Sean
authors.initials: S
authors.lastname: McCorkle
authors.forename: John
authors.initials: J
authors.lastname: Dunn
authors.forename: Daniël
authors.initials: D
authors.lastname: van der Lelie
authors.forename: Max
authors.initials: M
authors.lastname: Mergeay
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001692:Biological Transport / Q000187:drug effects / Q000235:genetics; D049921:Cupriavidus / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D004777:Environment; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D019216:Metals, Heavy / Q000633:toxicity; D050296:Microbial Viability / Q000187:drug effects / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D001426:Bacterial Proteins; D019216:Metals, Heavy
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