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The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1.

Crowley DJ, Boubriak I, Berquist BR, Clark M, Richard E, Sullivan L, DasSarma S, McCready S - Saline Syst. (2006)

Bottom Line: The UV sensitivity of the uvr mutants is greatly attenuated following incubation under visible light, emphasizing that photoreactivation is highly efficient in this organism.Phylogenetic analysis of the Halobacterium uvr genes indicates a complex ancestry.Phylogenetic analysis provides no clear evidence for lateral transfer of these genes from bacteria to archaea.

View Article: PubMed Central - HTML - PubMed

Affiliation: Natural Sciences Department, Assumption College, 500 Salisbury Street, Worcester, Massachusetts 01609 USA. dacrowle@assumption.edu

ABSTRACT

Background: Sequenced archaeal genomes contain a variety of bacterial and eukaryotic DNA repair gene homologs, but relatively little is known about how these microorganisms actually perform DNA repair. At least some archaea, including the extreme halophile Halobacterium sp. NRC-1, are able to repair ultraviolet light (UV) induced DNA damage in the absence of light-dependent photoreactivation but this 'dark' repair capacity remains largely uncharacterized. Halobacterium sp. NRC-1 possesses homologs of the bacterial uvrA, uvrB, and uvrC nucleotide excision repair genes as well as several eukaryotic repair genes and it has been thought that multiple DNA repair pathways may account for the high UV resistance and dark repair capacity of this model halophilic archaeon. We have carried out a functional analysis, measuring repair capability in uvrA, uvrB and uvrC deletion mutants.

Results: Deletion mutants lacking functional uvrA, uvrB or uvrC genes, including a uvrA uvrC double mutant, are hypersensitive to UV and are unable to remove cyclobutane pyrimidine dimers or 6-4 photoproducts from their DNA after irradiation with 150 J/m2 of 254 nm UV-C. The UV sensitivity of the uvr mutants is greatly attenuated following incubation under visible light, emphasizing that photoreactivation is highly efficient in this organism. Phylogenetic analysis of the Halobacterium uvr genes indicates a complex ancestry.

Conclusion: Our results demonstrate that homologs of the bacterial nucleotide excision repair genes uvrA, uvrB, and uvrC are required for the removal of UV damage in the absence of photoreactivating light in Halobacterium sp. NRC-1. Deletion of these genes renders cells hypersensitive to UV and abolishes their ability to remove cyclobutane pyrimidine dimers and 6-4 photoproducts in the absence of photoreactivating light. In spite of this inability to repair UV damaged DNA, uvrA, uvrB and uvrC deletion mutants are substantially less UV sensitive than excision repair mutants of E. coli or yeast. This may be due to efficient damage tolerance mechanisms such as recombinational lesion bypass, bypass DNA polymerase(s) and the existence of multiple genomes in Halobacterium. Phylogenetic analysis provides no clear evidence for lateral transfer of these genes from bacteria to archaea.

No MeSH data available.


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Quartet puzzling consensus maximum likelihood phylogenetic analysis of Uvr proteins encoded in archaeal genomes and representative bacteria. Phylogenetic analysis of UvrA (A), UvrB (B) and UvrC (C) protein sequences from haloarchaea, mesophilic methanogenic archaea, and representative bacteria.
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Figure 5: Quartet puzzling consensus maximum likelihood phylogenetic analysis of Uvr proteins encoded in archaeal genomes and representative bacteria. Phylogenetic analysis of UvrA (A), UvrB (B) and UvrC (C) protein sequences from haloarchaea, mesophilic methanogenic archaea, and representative bacteria.

Mentions: The uvrA, uvrB, and uvrC genes are found in the halophilic archaea and mesophilic methanogenic archaea but are absent from the genome sequences of all other archaea sequenced to date. Given this distribution, we examined the phylogenetic relationships between the core archaeal-encoded proteins (for all archaea known to contain them) and protein sequences found in a few diverse families of bacteria. Phylogenetic analysis of each of the Uvr sequences gave star topologies at the root, indicating that origins of the protein sequences cannot be uncovered. Haloarchaeal UvrA, UvrB, and UvrC always formed a monophyletic clade. Sequences from the mesophilic methanogenic archaea, however, were paraphyletic, with sequences from Methanosarcina acetivorans being quite different from the sequences encoded in the genomes of Methanothermobacter thermoautotrophicus and Methanosphaera stadtmanae. For UvrA, the haloarchaea were found to group with the UvrA sequence from the extremely radiation resistant bacterium Deinococcus radiodurans, while M. thermoautotrophicum and M. stadtmanae formed their own unique clade. M. acetivorans UvrA branched with the enterobacteria Camphylobacter jejuni and Helicobacter pylori (Figure 5A). For UvrB, the haloarchaea, M. thermoautotrophicum, and M. stadtmanae formed a major monophyletic clade together, while UvrB from M. acetivorans branched off on its own (Figure 5B). For UvrC, the haloarchaea formed a unique monophyletic clade, M. thermoautotrophicum and M. stadtmanae formed a clade with the cyanobacterium Synechocystis sp. PCC, and M. acetivorans claded with the spirochetes Borrelia burgdorferi and Treponema pallidum (Figure 5C).


The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1.

Crowley DJ, Boubriak I, Berquist BR, Clark M, Richard E, Sullivan L, DasSarma S, McCready S - Saline Syst. (2006)

Quartet puzzling consensus maximum likelihood phylogenetic analysis of Uvr proteins encoded in archaeal genomes and representative bacteria. Phylogenetic analysis of UvrA (A), UvrB (B) and UvrC (C) protein sequences from haloarchaea, mesophilic methanogenic archaea, and representative bacteria.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590041&req=5

Figure 5: Quartet puzzling consensus maximum likelihood phylogenetic analysis of Uvr proteins encoded in archaeal genomes and representative bacteria. Phylogenetic analysis of UvrA (A), UvrB (B) and UvrC (C) protein sequences from haloarchaea, mesophilic methanogenic archaea, and representative bacteria.
Mentions: The uvrA, uvrB, and uvrC genes are found in the halophilic archaea and mesophilic methanogenic archaea but are absent from the genome sequences of all other archaea sequenced to date. Given this distribution, we examined the phylogenetic relationships between the core archaeal-encoded proteins (for all archaea known to contain them) and protein sequences found in a few diverse families of bacteria. Phylogenetic analysis of each of the Uvr sequences gave star topologies at the root, indicating that origins of the protein sequences cannot be uncovered. Haloarchaeal UvrA, UvrB, and UvrC always formed a monophyletic clade. Sequences from the mesophilic methanogenic archaea, however, were paraphyletic, with sequences from Methanosarcina acetivorans being quite different from the sequences encoded in the genomes of Methanothermobacter thermoautotrophicus and Methanosphaera stadtmanae. For UvrA, the haloarchaea were found to group with the UvrA sequence from the extremely radiation resistant bacterium Deinococcus radiodurans, while M. thermoautotrophicum and M. stadtmanae formed their own unique clade. M. acetivorans UvrA branched with the enterobacteria Camphylobacter jejuni and Helicobacter pylori (Figure 5A). For UvrB, the haloarchaea, M. thermoautotrophicum, and M. stadtmanae formed a major monophyletic clade together, while UvrB from M. acetivorans branched off on its own (Figure 5B). For UvrC, the haloarchaea formed a unique monophyletic clade, M. thermoautotrophicum and M. stadtmanae formed a clade with the cyanobacterium Synechocystis sp. PCC, and M. acetivorans claded with the spirochetes Borrelia burgdorferi and Treponema pallidum (Figure 5C).

Bottom Line: The UV sensitivity of the uvr mutants is greatly attenuated following incubation under visible light, emphasizing that photoreactivation is highly efficient in this organism.Phylogenetic analysis of the Halobacterium uvr genes indicates a complex ancestry.Phylogenetic analysis provides no clear evidence for lateral transfer of these genes from bacteria to archaea.

View Article: PubMed Central - HTML - PubMed

Affiliation: Natural Sciences Department, Assumption College, 500 Salisbury Street, Worcester, Massachusetts 01609 USA. dacrowle@assumption.edu

ABSTRACT

Background: Sequenced archaeal genomes contain a variety of bacterial and eukaryotic DNA repair gene homologs, but relatively little is known about how these microorganisms actually perform DNA repair. At least some archaea, including the extreme halophile Halobacterium sp. NRC-1, are able to repair ultraviolet light (UV) induced DNA damage in the absence of light-dependent photoreactivation but this 'dark' repair capacity remains largely uncharacterized. Halobacterium sp. NRC-1 possesses homologs of the bacterial uvrA, uvrB, and uvrC nucleotide excision repair genes as well as several eukaryotic repair genes and it has been thought that multiple DNA repair pathways may account for the high UV resistance and dark repair capacity of this model halophilic archaeon. We have carried out a functional analysis, measuring repair capability in uvrA, uvrB and uvrC deletion mutants.

Results: Deletion mutants lacking functional uvrA, uvrB or uvrC genes, including a uvrA uvrC double mutant, are hypersensitive to UV and are unable to remove cyclobutane pyrimidine dimers or 6-4 photoproducts from their DNA after irradiation with 150 J/m2 of 254 nm UV-C. The UV sensitivity of the uvr mutants is greatly attenuated following incubation under visible light, emphasizing that photoreactivation is highly efficient in this organism. Phylogenetic analysis of the Halobacterium uvr genes indicates a complex ancestry.

Conclusion: Our results demonstrate that homologs of the bacterial nucleotide excision repair genes uvrA, uvrB, and uvrC are required for the removal of UV damage in the absence of photoreactivating light in Halobacterium sp. NRC-1. Deletion of these genes renders cells hypersensitive to UV and abolishes their ability to remove cyclobutane pyrimidine dimers and 6-4 photoproducts in the absence of photoreactivating light. In spite of this inability to repair UV damaged DNA, uvrA, uvrB and uvrC deletion mutants are substantially less UV sensitive than excision repair mutants of E. coli or yeast. This may be due to efficient damage tolerance mechanisms such as recombinational lesion bypass, bypass DNA polymerase(s) and the existence of multiple genomes in Halobacterium. Phylogenetic analysis provides no clear evidence for lateral transfer of these genes from bacteria to archaea.

No MeSH data available.


Related in: MedlinePlus