Three nth homologs are all required for efficient repair of spontaneous DNA damage in Deinococcus radiodurans

Hua, Xiaoting; Xu, Xin; Li, Mingfeng; Wang, Chao; Teng, Bing; Hua, Yuejin

doi:10.1007/s00792-012-0447-y

Cited by 10 publications

(11 citation statements)

References 49 publications

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“…The nth single, double and triple mutants are as resistant to IR and H 2 O 2 as the wild type, but each single mutant shows slightly elevated levels of spontaneous mutation (Hua et al. 2012). In vitro , enzymatic activity has been detected for DR_0289 and DR_2438, but so far not for DR_0928 (Sarre et al.…”

Section: Dna Repair In Deinococcusmentioning

confidence: 99%

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Lim

Jung

Blanchard

et al. 2018

FEMS Microbiology Reviews

163

140

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Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.

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Section: Dna Repair In Deinococcusmentioning

confidence: 99%

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Lim

Jung

Blanchard

et al. 2018

FEMS Microbiology Reviews

163

140

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“…The total number of colony-forming units (CFU) was determined by plating serial dilutions on LB plates. The frequencies of mutations conferring resistance to Rif were determined by dividing the median number of mutants by the average number of cells [26]. For mutation rates, the maximum-likelihood estimator applying the newton.…”

Section: Measurement Of Mutation Frequency and Mutation Rate In Rif Rmentioning

confidence: 99%

“…The PCR products were purified and sequenced by Biosune biological company (Hangzhou, China). The sequences and trace data were transferred to the SEQMAN program (DNASTAR), which was used for sequence assembly and SNP detection [26].…”

Section: Dna Isolation and Rpob Sequencing Of Rif R Mutantsmentioning

confidence: 99%

The mismatch repair system (mutS and mutL) in Acinetobacter baylyi ADP1

Zhou

Zhang

et al. 2020

BMC Microbiol

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Background: Acinetobacter baylyi ADP1 is an ideal bacterial strain for high-throughput genetic analysis as the bacterium is naturally transformable. Thus, ADP1 can be used to investigate DNA mismatch repair, a mechanism for repairing mismatched bases. We used the mutS deletion mutant (XH439) and mutL deletion mutant (XH440), and constructed a mutS mutL double deletion mutant (XH441) to investigate the role of the mismatch repair system in A. baylyi. Results: We determined the survival rates after UV irradiation and measured the mutation frequencies, rates and spectra of wild-type ADP1 and mutSL mutant via rifampin resistance assay (Rif R assay) and experimental evolution. In addition, transformation efficiencies of genomic DNA in ADP1 and its three mutants were determined. Lastly, the relative growth rates of the wild type strain, three constructed deletion mutants, as well as the rifampin resistant mutants obtained from Rif R assays, were measured. All three mutants had higher survival rates after UV irradiation than wild type, especially the double deletion mutant. Three mutants showed higher mutation frequencies than ADP1 and favored transition mutations in Rif R assay. All three mutants showed increased mutation rates in the experimental evolution. However, only XH439 and XH441 had higher mutation rates than the wild type strain in Rif R assay. XH441 showed higher transformation efficiency than XH438 when donor DNA harbored transition mutations. All three mutants showed higher growth rates than wild-type, and these four strains displayed higher growth rates than almost all their rpoB mutants. The growth rate results showed different amino acid mutations in rpoB resulted in different extents of reduction in the fitness of rifampin resistant mutants. However, the fitness cost brought by the same mutation did not vary with strain background. Conclusions: We demonstrated that inactivation of both mutS and mutL increased the mutation rates and frequencies in A. baylyi, which would contribute to the evolution and acquirement of rifampicin resistance. The mutS deletion is also implicated in increased mutation rates and frequencies, suggesting that MutL may be activated even in the absence of mutS. The correlation between fitness cost and rifampin resistance mutations in A. baylyi is firstly established.

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“…Similarly, homozygous Arabidopsis thaliana arp −/− (AP endonuclease homologous gene) mutant exhibited no sensitivity to H 2 O 2 , but high sensitivity to tert-butyl hydroperoxide, suggesting that ARP is a major plant AP endonuclease that removes the special types of oxidative DNA base damage (Akishev et al, 2016). Meanwhile, the D. radiodurans polX mutant and endonuclease III (nth) mutants showed no significant difference from wild type in H 2 O 2 stress resistance (Khairnar and Misra, 2009;Hua et al, 2012). It has also been shown that mutation of both ttendolVI and ttpolX resulted in a significant decline in activity following exposure to H 2 O 2 in Thermus thermophilus (Nakane et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans

Wang

Chen

et al. 2020

Front. Microbiol.

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Various endogenous and exogenous agents cause DNA damage, including apurinic/apyrimidinic (AP) sites. Due to their cytotoxic effects, AP sites are usually cleaved by AP endonuclease through the base excision repair (BER) pathway. Deinococcus radiodurans , an extraordinary radiation-resistant bacterium, is known as an ideal model organism for elucidating DNA repair processes. Here, we have investigated a unique AP endonuclease (DrXth) from D. radiodurans and found that it possesses AP endonuclease, 3′-phosphodiesterase, 3′-phosphatase, and 3′–5′ exonuclease but has no nucleotide incision repair (NIR) activity. We also found that Mg 2+ and Mn 2+ were the preferred divalent metals for endonuclease and exonuclease activities, respectively. In addition, DrXth were crystallized and the crystals diffracted to 1.5 Å. Structural and biochemical analyses demonstrated that residue Gly198 is the key residue involved in the substrate DNA binding and cleavage. Deletion of the drxth gene in D. radiodurans caused elevated sensitivity to DNA damage agents and increased spontaneous mutation frequency. Overall, our results indicate that DrXth is an important AP endonuclease involved in BER pathway and functions in conjunction with other DNA repair enzymes to maintain the genome stability.

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Three nth homologs are all required for efficient repair of spontaneous DNA damage in Deinococcus radiodurans

Cited by 10 publications

References 49 publications

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

The mismatch repair system (mutS and mutL) in Acinetobacter baylyi ADP1

Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans

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