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

Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M - PLoS ONE (2010)

Bottom Line: This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction.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.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium. pjanssen@sckcen.be

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.

Show MeSH

Related in: MedlinePlus

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.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2864759&req=5

pone-0010433-g001: 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.

Mentions: The total genome of C. metallidurans CH34, of 6,913,352 bp, comprises four circular replicons: Chromosome 1 (CHR1) (3,928,089 bp); chromosome 2 (CHR2) (2,580,084 bp); and two megaplasmids pMOL28 (171,459 bp), and pMOL30 (233,720 bp). Since the two megaplasmids are detailed by Monchy et al. [10] and Mergeay et al. [7] this report mainly covers the sequencing and expert annotation of the two large replicons. Nonetheless, in a separate subsection below, we give a brief update on the megaplasmids. Table 1 lists the general features of all four replicons. There are four sets of 5S, 16S, and 23S rRNA genes and 12 structural RNA genes that include one RNAaseP RNA (rnpB; Rmet_R0004), one tmRNA (ssrA; Rmet_R0007), one SRP RNA (ffs; Rmet_R0026), and nine riboswitches as predicted by Rfam (http://rfam.sanger.ac.uk/) (Rmet_R0001, Rmet_R0012, Rmet_R0043, Rmet_R0047, Rmet_R0067, Rmet_R0068, Rmet_R0083, Rmet_R0084, and Rmet_R0085). Sixty-two transfer RNA (tRNA) genes with specificities for all 20 amino acids were identified, most located on CHR1. Five tRNA genes are duplicated on CHR2 (two genes once, and three genes twice) (Table 1). Genome analysis using the MaGe system [48] predicts 6,717 coding sequences (CDS). Of those, 4,518 CDS were assigned a function using one of five evidence classes, while 1,274 and 611 CDS remained, respectively, ‘conserved hypothetical’ or ‘hypothetical’. Using the automated COGnitor module [49] imbedded in the MaGe system 5,133 CDS were assigned to one or more COG functional classes (COGs are Clusters of Orthologous Groups of proteins generated by comparing the protein sequences of complete genomes - each cluster contains proteins or groups of paralogs from at least three lineages). (Figure 1; Table 1). The G+C content of the replicons all are very similar to each other, with an average of 63.7% for the large chromosomes, and of 60.3% for the two plasmids (Table 1).


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

Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M - PLoS ONE (2010)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2864759&req=5

pone-0010433-g001: 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.
Mentions: The total genome of C. metallidurans CH34, of 6,913,352 bp, comprises four circular replicons: Chromosome 1 (CHR1) (3,928,089 bp); chromosome 2 (CHR2) (2,580,084 bp); and two megaplasmids pMOL28 (171,459 bp), and pMOL30 (233,720 bp). Since the two megaplasmids are detailed by Monchy et al. [10] and Mergeay et al. [7] this report mainly covers the sequencing and expert annotation of the two large replicons. Nonetheless, in a separate subsection below, we give a brief update on the megaplasmids. Table 1 lists the general features of all four replicons. There are four sets of 5S, 16S, and 23S rRNA genes and 12 structural RNA genes that include one RNAaseP RNA (rnpB; Rmet_R0004), one tmRNA (ssrA; Rmet_R0007), one SRP RNA (ffs; Rmet_R0026), and nine riboswitches as predicted by Rfam (http://rfam.sanger.ac.uk/) (Rmet_R0001, Rmet_R0012, Rmet_R0043, Rmet_R0047, Rmet_R0067, Rmet_R0068, Rmet_R0083, Rmet_R0084, and Rmet_R0085). Sixty-two transfer RNA (tRNA) genes with specificities for all 20 amino acids were identified, most located on CHR1. Five tRNA genes are duplicated on CHR2 (two genes once, and three genes twice) (Table 1). Genome analysis using the MaGe system [48] predicts 6,717 coding sequences (CDS). Of those, 4,518 CDS were assigned a function using one of five evidence classes, while 1,274 and 611 CDS remained, respectively, ‘conserved hypothetical’ or ‘hypothetical’. Using the automated COGnitor module [49] imbedded in the MaGe system 5,133 CDS were assigned to one or more COG functional classes (COGs are Clusters of Orthologous Groups of proteins generated by comparing the protein sequences of complete genomes - each cluster contains proteins or groups of paralogs from at least three lineages). (Figure 1; Table 1). The G+C content of the replicons all are very similar to each other, with an average of 63.7% for the large chromosomes, and of 60.3% for the two plasmids (Table 1).

Bottom Line: This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction.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.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium. pjanssen@sckcen.be

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.

Show MeSH
Related in: MedlinePlus