Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance

Tanaka, Masashi; Earl, Ashlee M.; Howell, Heather A.; Park, Mie Jung; Eisen, Jonathan A.; Peterson, Scott N.; Battista, John R.

doi:10.1534/genetics.104.029249

Cited by 272 publications

(416 citation statements)

References 45 publications

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“…However, in both B. subtilis and D. radiodurans, RecN expression does not rely on a response to DNA damage, suggesting housekeeping roles for RecN in genome maintenance. The B. subtilis ortholog has been directly shown to be constitutively expressed (17,21), and D. radiodurans recN transcripts do not change in response to DNA damage (56), even though the gene is required for DNA damage tolerance (18). Although it is still unclear exactly which step in DSB repair RecN facilitates, the cohesin-like function demonstrated here for the Dr RecN protein suggests a structural role for the protein and represents a first step in understanding the precise function of bacterial RecN proteins.…”

Section: Discussionmentioning

confidence: 99%

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

Reyes

Patidar

Uranga

et al. 2010

Journal of Biological Chemistry

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The bacterial RecN protein is involved in the recombinational repair of DNA double-stranded breaks, and recN mutants are sensitive to DNA-damaging agents. Little is known about the biochemical function of RecN. Protein sequence analysis suggests that RecN is related to the SMC (structural maintenance of chromosomes) family of proteins, predicting globular N-and C-terminal domains connected by an extensive coil-coiled domain. The N-and C-domains contain the nucleotide-binding sequences Walker A and Walker B, respectively. We have purified the RecN protein from Deinococcus radiodurans and characterized its DNA-dependent and DNA-independent ATPase activity. The cellular genome maintenance processes of DNA replication, recombination, and repair are highly interconnected, sharing multiple pathways and common enzymes. A physical understanding of the function of key enzymes involved in genome maintenance processes is critical for elucidating the basic DNA metabolic strategies of cells. The primary function of homologous DNA recombination in mitotic cells as well as bacterial cells is the nonmutagenic repair of replication forks that have stalled or collapsed at noncoding lesions or breaks (1-3). When a replication fork encounters a break in the phosphodiester backbone of one template strand, a double-stranded break (DSB) 2 results (4). Recombinational DSB repair pathways promote strand invasion to regenerate a fork structure. In Escherichia coli, these pathways include the helicase and nuclease functions of the RecBCD complex, and the RecA protein. RecN, among various other proteins, is required for DSB repair in bacteria. Existing DSB repair models do not encompass RecN, because no clear function has been ascribed to the protein as yet.The recN gene of E. coli (also known as radB (5)) was identified by two groups over 20 years ago. Lloyd et al. (6) isolated a mutation (rec-259) that caused increased sensitivity to UV light in a recBC sbcB background. Independently, Sargentini and Smith (7) isolated the radB101 mutation, which caused sensitivity to ␥-irradiation and mitomycin C. Expression of the recN gene is regulated by the LexA repressor (8, 9), and the RecN protein is one of the most abundantly produced proteins induced as part of the SOS response to DNA damage (10). Once produced in response to damage, RecN protein has a very short half-life (ϳ10 min), because it apparently is rapidly proteolyzed by the ClpXP protease system (11).The recN gene product was originally placed in the RecF-dependent gap repair pathway, but substantial evidence suggests that RecN is also involved in the RecBCD DSB repair pathway. Unlike other members of the RecF pathway, recN mutants are quite sensitive to ionizing radiation or mitomycin C, and the repair of multiple, site-specific DSBs does not occur in the absence of RecN (8,12,13). The recN gene is also required for the suppression of chromosomal rearrangements and deletions (12) during the repair of a single DSB. Given this wealth of genetic data, the RecN protein is clearly involve...

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Section: Discussionmentioning

confidence: 99%

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

Reyes

Patidar

Uranga

et al. 2010

Journal of Biological Chemistry

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“…Several DNA-damage-inducible proteins that may be necessary for DNA repair have been detected in cell extracts of D. radiodurans using 2D-PAGE analysis (Hansen, 1980;Tanaka et al, 1996). Recent transcriptome and proteome analyses have revealed the comprehensive expression profiles of radiation-inducible genes and proteins (Lipton et al, 2002;Liu et al, 2003;Tanaka et al, 2004;Zhang et al, 2005). It has therefore been established that D. radiodurans possesses a DNA damage response mechanism.…”

Section: Introductionmentioning

confidence: 99%

Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans

et al. 2006

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The extremely radioresistant bacterium Deinococcus radiodurans contains two LexA homologues (LexA1 and LexA2) that are possible transcriptional regulators associated with the DNA damage response. In this study, resequencing revealed that there was an additional cytosine nucleotide (nucleotide position 612) in the D. radiodurans lexA2 gene. Purified LexA2 possessed proteolytic activity that could be stimulated by RecA. In an effort to gain an insight into the role of LexA2 in the radiation response mechanism, recA, lexA1 and lexA2 disruptant strains were generated and investigated. The intracellular level of RecA increased in lexA1 and lexA2 disruptant strains following γ-irradiation as in the wild-type strain. These results indicated that the two LexA homologues did not possess functional overlap regarding the induction of RecA. The lexA2 disruptant strains exhibited a much higher resistance to γ-rays than the wild-type strain. Furthermore, a luciferase assay showed that pprA promoter activation was enhanced in the lexA2 disruptant strain following γ-irradiation. The pprA gene encoding the novel radiation-inducible protein PprA plays a critical role in the radioresistance of D. radiodurans. The increase in radioresistance of the lexA2 disruptant strain is explained in part by the enhancement of pprA promoter activation.

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“…Only D. radiodurans R 1 T has been studied extensively. Its genome has been sequenced (White et al, 1999), and analyses of the transcriptome (Liu et al, 2003;Tanaka et al, 2004) . For all other tests, bacterial strains were cultivated at 30 u C in TSB/10 or on agar plates containing the same medium.…”

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confidence: 99%

“…Only D. radiodurans R 1 T has been studied extensively. Its genome has been sequenced (White et al, 1999), and analyses of the transcriptome (Liu et al, 2003;Tanaka et al, 2004) and proteome (Lipton et al, 2002) have been The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains VCD115 T and VCD117 are AY876378 and AY876379, respectively. Levels of 16S rRNA gene sequence similarity and DNA-DNA relatedness between strains VCD115 T and VCD117 and rates of survival after gamma and UV irradiation are available as supplementary material in IJSEM Online.…”

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confidence: 99%

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert

Groot

Chapon

Servant

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

147

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Two gamma-and UV-radiation-tolerant, Gram-negative, rod-shaped bacterial strains, VCD115 T and VCD117, were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridizations showed that VCD115 T and VCD117 are members of a novel species belonging to the genus Deinococcus, with Deinococcus grandis as its closest relative. The DNA G+C contents of VCD115 T and VCD117 are 59?8 and 60?6 mol%, respectively. The major fatty acids (straight-chain 15 : 1, 16 : 1, 17 : 1 and 16 : 0), polar lipids (dominated by phosphoglycolipids and glycolipids) and quinone type support the affiliation to the genus Deinococcus. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation of VCD115 T and VCD117 from recognized Deinococcus species. Strains VCD115 T and VCD117 are therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed, with the type strain VCD115 T (=DSM 17065 T =LMG 22923 T ).Various bacterial species have the capacity to survive under conditions that are commonly considered as extreme, for example in environments experiencing high pressure or high salt concentrations. In our laboratory, we are studying bacteria that live in the upper sand layers of deserts, where they are exposed to cycles of high and low temperatures, and to cycles of desiccation and hydration. De-and rehydration may cause DNA damage in these bacteria, and in order to survive they probably possess efficient DNA-repair mechanisms. Ionizing radiation causes similar types of DNA damage including double-strand breaks, which are the most deleterious to the organism (Mattimore & Battista, 1996). Bacteria belonging to the genus Deinococcus, in particular the well-studied Deinococcus radiodurans, have the distinctive feature of being the most radiation-tolerant of vegetative cells. D. radiodurans can withstand doses of radiation a thousand times higher than a human can. It can survive doses of radiation that do not exist naturally on Earth. Therefore, it is likely that this radiation tolerance is related to the bacterial response to natural non-radioactive DNA-damaging conditions such as desiccation (Makarova et al., 2001). At the time of writing, eight recognized species belong to the genus Deinococcus (Ferreira et al., 1997;Rainey et al., 1997;Suresh et al., 2004). Three other species have been described very recently, 'Deinococcus frigens', 'Deinococcus saxicola' and 'Deinococcus marmoris ' (Hirsch et al., 2004). Only D. radiodurans R 1 T has been studied extensively. Its genome has been sequenced (White et al., 1999), and analyses of the transcriptome (Liu et al., 2003;Tanaka et al., 2004) . For all other tests, bacterial strains were cultivated at 30 u C in TSB/10 or on agar plates containing the same m...

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Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance

Cited by 272 publications

References 45 publications

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert

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