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Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F - PLoS ONE (2015)

Bottom Line: CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes.We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7).Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France.

ABSTRACT
Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

No MeSH data available.


Related in: MedlinePlus

Schematic diagram of ICE19 in CB2.This figure shows one part of the arsenic island of CB2 (RGP19) that has the characteristics of an ICE (called ICE19) (A) Alignment of ICE19 of Thiomonas sp. CB2 with its cognate portion found in the strain 3As (ThGEI-O). The arsenic island RGP19 of CB2 is localized in a different genomic region that ThGEI-O in 3As. The ThGEI-O of 3As (upper portion of the figure) is localized in a gene encoding a 4Fe-4S ferredoxin which is intact in CB2. Direct repeat sequences are indicated. (B) Sequence comparison of the almost perfect direct repeat flanking the ICE19. attL: left DR; attR: right DR. (C) Schematic representation of the integrated and circular form of the ICE19 of CB2, which were detected by PCR. The sequence attI is identical to attR and attB identical to attL. The % of nucleotide identity is expressed along a grey scale. Figures were generated with Easyfig [50].
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pone.0139011.g005: Schematic diagram of ICE19 in CB2.This figure shows one part of the arsenic island of CB2 (RGP19) that has the characteristics of an ICE (called ICE19) (A) Alignment of ICE19 of Thiomonas sp. CB2 with its cognate portion found in the strain 3As (ThGEI-O). The arsenic island RGP19 of CB2 is localized in a different genomic region that ThGEI-O in 3As. The ThGEI-O of 3As (upper portion of the figure) is localized in a gene encoding a 4Fe-4S ferredoxin which is intact in CB2. Direct repeat sequences are indicated. (B) Sequence comparison of the almost perfect direct repeat flanking the ICE19. attL: left DR; attR: right DR. (C) Schematic representation of the integrated and circular form of the ICE19 of CB2, which were detected by PCR. The sequence attI is identical to attR and attB identical to attL. The % of nucleotide identity is expressed along a grey scale. Figures were generated with Easyfig [50].

Mentions: RGP19 is 338.7 kb long and contains genes implicated in resistance to various heavy metals (As, mercury, copper, zinc, and cadmium). Genes involved in sulfate assimilation (cys genes) and biotin synthesis (bio genes), were also present in this genomic island. In fact, many integrases are also located on RGP19, as well as genes involved in conjugation, including phage integrase and relaxase. 49 bp nearly perfect direct repeats are located at the left extremity of RGP19 and between gene THICB2v3-780013 and -780014, and the region between these two repeats contains tra and trb genes involved in conjugation (Fig 5). The excision and circularization of this part have been confirmed by PCR in CB2 (Fig 5C and data not shown). All these observations emphasized the fact that this region has been acquired after insertion and is or, at some point, was mobile. Consequently, this part of RGP19 (from 3533461 to 3796598, 185,5 Kb) has the characteristics of an integrative and conjugative element (ICE) [36], and has been designated ICE19 and the repeats designed attL and attR (Fig 5). We observed that the arsenic island is not syntenic in 3As as compared to CB2 and only part of this ICE19 is found in 3As (in the genomic island previously named ThGEI-O [16], Fig 5). In particular, the tra and trb genes were not found in the ThGEI-O and therefore this island has not the characteristics of an ICE. In 3As, ThGEI-O is located in the middle of a gene encoding a 4Fe-4S ferredoxin, whereas in CB2, ICE19 is found near the fbp gene encoding fructose-1,6-bisphosphatase and the Thr tRNA. The presence of direct repeats (DR) at the both sides of the ThGEI-O (RGP19-like island) in 3As was previously described [16] and indicates a probable insertion by site-specific recombination in the gene encoding a 4Fe-4S ferredoxin. Interestingly, similar repeats are also found in the ICE19 of CB2, although one is slightly different, perhaps due to punctual mutations occurred after the insertion or rearrangement of genes in this region (Fig 5). These observations suggest that the two islands, ThGEI-O in 3As and RGP19 in CB2, may have similar origin but evolved differently in the two strains.


Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F - PLoS ONE (2015)

Schematic diagram of ICE19 in CB2.This figure shows one part of the arsenic island of CB2 (RGP19) that has the characteristics of an ICE (called ICE19) (A) Alignment of ICE19 of Thiomonas sp. CB2 with its cognate portion found in the strain 3As (ThGEI-O). The arsenic island RGP19 of CB2 is localized in a different genomic region that ThGEI-O in 3As. The ThGEI-O of 3As (upper portion of the figure) is localized in a gene encoding a 4Fe-4S ferredoxin which is intact in CB2. Direct repeat sequences are indicated. (B) Sequence comparison of the almost perfect direct repeat flanking the ICE19. attL: left DR; attR: right DR. (C) Schematic representation of the integrated and circular form of the ICE19 of CB2, which were detected by PCR. The sequence attI is identical to attR and attB identical to attL. The % of nucleotide identity is expressed along a grey scale. Figures were generated with Easyfig [50].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589449&req=5

pone.0139011.g005: Schematic diagram of ICE19 in CB2.This figure shows one part of the arsenic island of CB2 (RGP19) that has the characteristics of an ICE (called ICE19) (A) Alignment of ICE19 of Thiomonas sp. CB2 with its cognate portion found in the strain 3As (ThGEI-O). The arsenic island RGP19 of CB2 is localized in a different genomic region that ThGEI-O in 3As. The ThGEI-O of 3As (upper portion of the figure) is localized in a gene encoding a 4Fe-4S ferredoxin which is intact in CB2. Direct repeat sequences are indicated. (B) Sequence comparison of the almost perfect direct repeat flanking the ICE19. attL: left DR; attR: right DR. (C) Schematic representation of the integrated and circular form of the ICE19 of CB2, which were detected by PCR. The sequence attI is identical to attR and attB identical to attL. The % of nucleotide identity is expressed along a grey scale. Figures were generated with Easyfig [50].
Mentions: RGP19 is 338.7 kb long and contains genes implicated in resistance to various heavy metals (As, mercury, copper, zinc, and cadmium). Genes involved in sulfate assimilation (cys genes) and biotin synthesis (bio genes), were also present in this genomic island. In fact, many integrases are also located on RGP19, as well as genes involved in conjugation, including phage integrase and relaxase. 49 bp nearly perfect direct repeats are located at the left extremity of RGP19 and between gene THICB2v3-780013 and -780014, and the region between these two repeats contains tra and trb genes involved in conjugation (Fig 5). The excision and circularization of this part have been confirmed by PCR in CB2 (Fig 5C and data not shown). All these observations emphasized the fact that this region has been acquired after insertion and is or, at some point, was mobile. Consequently, this part of RGP19 (from 3533461 to 3796598, 185,5 Kb) has the characteristics of an integrative and conjugative element (ICE) [36], and has been designated ICE19 and the repeats designed attL and attR (Fig 5). We observed that the arsenic island is not syntenic in 3As as compared to CB2 and only part of this ICE19 is found in 3As (in the genomic island previously named ThGEI-O [16], Fig 5). In particular, the tra and trb genes were not found in the ThGEI-O and therefore this island has not the characteristics of an ICE. In 3As, ThGEI-O is located in the middle of a gene encoding a 4Fe-4S ferredoxin, whereas in CB2, ICE19 is found near the fbp gene encoding fructose-1,6-bisphosphatase and the Thr tRNA. The presence of direct repeats (DR) at the both sides of the ThGEI-O (RGP19-like island) in 3As was previously described [16] and indicates a probable insertion by site-specific recombination in the gene encoding a 4Fe-4S ferredoxin. Interestingly, similar repeats are also found in the ICE19 of CB2, although one is slightly different, perhaps due to punctual mutations occurred after the insertion or rearrangement of genes in this region (Fig 5). These observations suggest that the two islands, ThGEI-O in 3As and RGP19 in CB2, may have similar origin but evolved differently in the two strains.

Bottom Line: CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes.We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7).Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France.

ABSTRACT
Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

No MeSH data available.


Related in: MedlinePlus