The resistance of Micrococcus radiodurans to killing and mutation by agents which damage DNA

Development of a gene-coded biosensor to establish a high-throughput screening platform for salidroside production

Metabolic engineering reconfigures cellular networks to produce value-added compounds from renewable substrates efficiently. However, identifying strains with desired phenotypes from large libraries through rational or random mutagenesis remains challenging. To overcome this bottleneck, an effective high-throughput screening (HTS) method must be developed to detect and analyze target candidates rapidly. Salidroside is an aromatic compound with broad applications in food, healthcare, medicine, and daily chemicals. However, there currently needs to be HTS methods available to monitor salidroside levels or to screen enzyme variants and strains for high-yield salidroside biosynthesis, which severely limits the development of microbial cell factories capable of efficiently producing salidroside on an industrial scale. This study developed a gene-encoded whole-cell biosensor that is specifically responsive to salidroside. The biosensor was created by screening a site-saturated mutagenic library of uric acid response regulatory protein binding bags. This work demonstrates the feasibility of monitoring metabolic flux with whole-cell biosensors for critical metabolites. It provides a promising tool for building salidroside high-yielding strains for high-throughput screening and metabolic regulation to meet industrial needs.

DR0022 from Deinococcus radiodurans is an acid uracil-DNA glycosylase

Uracil-DNA glycosylase (UDG) initiates base excision repair (BER) by removing damaged or modified nucleobases during DNA repair or mammalian demethylation. The UDG superfamily consists of at least six families with a variety of catalytic specificities and functions. Deinococcus radiodurans, an extreme radiation resistant bacterium, contains multiple members of UDG enzymes within its genome. The present study reveals that the putative protein, DR0022, is a uracil-DNA glycosylase that requires acidic conditions for its glycosylase activity, which is the first case of such an enzyme within the UDG superfamily. The key residues in the catalytic motifs are investigated by biochemical, enzyme kinetics, and de novo structural prediction, as well as molecular modeling analyses. The structural and catalytic roles of several distinct residues are discussed in light of predicted and modeled DR0022 glycosylase structures. The spontaneous mutation rate analysis performed in a dr0022 deficient D. radiodurans strain indicated that the dr0022 gene plays a role in mutation prevention. Furthermore, survival rate analysis in a dr0022 deficient D. radiodurans strain demonstrated its role in stress resistance, including γ-irradiation. Additionally, the novel acid UDG activity in relationship to its in vivo roles is discussed. This work underscores the functional diversity in the UDG superfamily.

Super-resolution confocal cryo-CLEM with cryo-FIB milling for in situ imaging of Deinococcus radiodurans

Studying bacterial cell envelope architecture with electron microscopy is challenging due to the poor preservation of microbial ultrastructure with traditional methods. Here, we established and validated a super-resolution cryo-correlative light and electron microscopy (cryo-CLEM) method, and combined it with cryo-focused ion beam (cryo-FIB) milling and scanning electron microscopy (SEM) volume imaging to structurally characterize the bacterium Deinococcus radiodurans. Subsequent cryo-electron tomography (cryo-ET) revealed an unusual diderm cell envelope architecture with a thick layer of peptidoglycan (PG) between the inner and outer membranes, an additional periplasmic layer, and a proteinaceous surface S-layer. Cells grew in tetrads, and division septa were formed by invagination of the inner membrane (IM), followed by a thick layer of PG. Cytoskeletal filaments, FtsA and FtsZ, were observed at the leading edges of constricting septa. Numerous macromolecular complexes were found associated with the cytoplasmic side of the IM. Altogether, our study revealed several unique ultrastructural features of D. radiodurans cells, opening new lines of investigation into the physiology and evolution of the bacterium.

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User-friendly, commercially available method for correlative cryo-super resolution light microscopy (LM) and cryo-FIB-milling.

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Cryo-super resolution LM, cryo-FIB milling, cryo-SEM volume imaging, and cryo-electron tomography (cryo-ET) to study Deinococcus radiodurans.

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Unique D. radiodurans cell envelope is composed of two membranes, thick peptidoglycan, an additional layer, and an S-layer.

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Cytoskeletal filaments FtsA and FtsZ were observed at the leading edges of division septa.

Manganese is a Deinococcus radiodurans growth limiting factor in rich culture medium

To understand the effects triggered by Mn²⁺ on Deinococcus radiodurans, the proteome patterns associated with different growth phases were investigated. In particular, under physiological conditions we tested the growth rate and the biomass yield of D. radiodurans cultured in rich medium supplemented or not with MnCl2. The addition of 2.5-5.0 µM MnCl2 to the medium neither altered the growth rate nor the lag phase, but significantly increased the biomass yield. When higher MnCl2 concentrations were used (10-250 µM), biomass was again found to be positively affected, although we did observe a concentration-dependent lag phase increase. The in vivo concentration of Mn²⁺ was determined in cells grown in rich medium supplemented or not with 5 µM MnCl2. By atomic absorption spectroscopy, we estimated 0.2 and 0.75 mM Mn²⁺ concentrations in cells grown in control and enriched medium, respectively. We qualitatively confirmed this observation using a fluorescent turn-on sensor designed to selectively detect Mn²⁺in vivo. Finally, we investigated the proteome composition of cells grown for 15 or 19 h in medium to which 5 µM MnCl2 was added, and we compared these proteomes with those of cells grown in the control medium. The presence of 5 µM MnCl2 in the culture medium was found to alter the pI of some proteins, suggesting that manganese affects post-translational modifications. Further, we observed that Mn²⁺ represses enzymes linked to nucleotide recycling, and triggers overexpression of proteases and enzymes linked to the metabolism of amino acids.

Oxidative stress resistance in Deinococcus radiodurans

Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.

RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans

Deinococcus radiodurans is one of the most radiation-resistant organisms known. It can repair hundreds of radiation-induced double-strand DNA breaks without loss of viability. Genome reassembly in heavily irradiated D. radiodurans is considered to be an error-free process since no genome rearrangements were detected after post-irradiation repair. Here, we describe for the first time conditions that frequently cause erroneous chromosomal assemblies. Gross chromosomal rearrangements have been detected in recA mutant cells that survived exposure to 5kGy γ-radiation. The recA mutants are prone also to spontaneous DNA rearrangements during normal exponential growth. Some insertion sequences have been identified as dispersed genomic homology blocks that can mediate DNA rearrangements. Whereas the wild-type D. radiodurans appears to repair accurately its genome shattered by 5kGy γ-radiation, extremely high γ-doses, e.g., 25kGy, produce frequent genome rearrangements among survivors. Our results show that the RecA protein is quintessential for the fidelity of repair of both spontaneous and γ-radiation-induced DNA breaks and, consequently, for genome stability in D. radiodurans. The mechanisms of decreased genome stability in the absence of RecA are discussed.

A new perspective on radiation resistance based on Deinococcus radiodurans

In classical models of radiation toxicity, DNA is the molecule that is most affected by ionizing radiation (IR). However, recent data show that the amount of protein damage caused during irradiation of bacteria is better related to survival than to DNA damage. In this Opinion article, a new model is presented in which proteins are the most important target in the hierarchy of macromolecules affected by IR. A first line of defence against IR in extremely radiation-resistant bacteria might be the accumulation of manganese complexes, which can prevent the production of iron-dependent reactive oxygen species. This would allow an irradiated cell to protect sufficient enzymatic activity needed to repair DNA and survive.

Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing

The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null rad52 mutation. The repair did not involve Rad51-driven strand invasion, and moreover the suppression of strand invasion increased repair with oligonucleotides. A DSB was shown to activate targeting by oligonucleotides homologous to only one side of the break at large distances (at least 20 kb) from the break in a strand-biased manner, suggesting extensive 5' to 3' resection, followed by the restoration of resected DNA to the double-strand state. We conclude that long resected chromosomal DSB ends are repaired by a single-strand DNA oligonucleotide through two rounds of annealing. The repair by single-strand DNA can be conservative and may allow for accurate restoration of chromosomal DNAs with closely spaced DSBs.

HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans

The HspR protein functions as a negative regulator of chaperone and protease gene expression in a diversity of bacteria. Here we have identified, cloned and deleted the Deinococcus radiodurans HspR homologue, DR0934. Delta hspR mutants exhibit moderate growth defects when shifted to mild heat shock temperatures, but are severely impaired for survival at 48 degrees C. Using quantitative reverse transcription polymerase chain reaction and global transcriptional analysis, we have identified 14 genes that are derepressed in the absence of stress in the delta hspR background, 11 of which encode predicted chaperones and proteases, including dnaKJgrpE, ftsH, lonB, hsp20 and clpB. Promoter mapping indicated that the transcription of these genes initiates from a promoter bearing a sigma70-type consensus, and that putative HspR binding sites (HAIR) were present in the 5'-untranslated regions. Electrophoretic mobility shift assays indicated that HspR binds to these promoters at the HAIR site in vitro. These results strongly suggest that DR0934 encodes the HspR-like global negative regulator of D. radiodurans that directly represses chaperone and protease gene expression by binding to the HAIR site in close proximity to promoter regions.

Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans

The sig1 gene, predicted to encode an extracytoplasmic function-type heat shock sigma factor of Deinococcus radiodurans, has been shown to play a central role in the positive regulation of the heat shock operons groESL and dnaKJ. To determine if Sig1 is required for the regulation of additional heat shock genes, we monitored the global transcriptional and proteomic profiles of a D. radiodurans R1 sig1 mutant and wild-type cells in response to elevated temperature stress. Thirty-one gene products were identified that showed heat shock induction in the wild type but not in the sig1 mutant. Quantitative real-time PCR experiments verified the transcriptional requirement of Sig1 for the heat shock induction of the mRNA of five of these genes-dnaK, groES, DR1314, pspA, and hsp20. hsp20 appears to encode a new member of the small heat shock protein superfamily, DR1314 is predicted to encode a hypothetical protein with no recognizable orthologs, and pspA is predicted to encode a protein involved in maintenance of membrane integrity. Deletion mutation analysis demonstrated the importance in heat shock protection of hsp20 and DR1314. The promoters of dnaKJE, groESL, DR1314, pspA, and hsp20 were mapped and, combined with computer-based pattern searches of the upstream regions of the 26 other Sig1 regulon members, these results suggested that Sig1 might recognize both sigma70-type and sigma(W)-type promoter consensus sequences. These results expand the D. radiodurans Sig1 heat shock regulon to include 31 potential new members, including not only factors with cytoplasmic functions, such as groES and dnaK, but also those with extracytoplasmic functions, like pspA.

HucR, a Novel Uric Acid-responsive Member of the MarR Family of Transcriptional Regulators from Deinococcus radiodurans

The MarR family of transcriptional regulators comprises a subset of winged helix DNA-binding proteins and includes numerous members that function in environmental surveillance of aromatic compounds. We describe the characterization of HucR, a novel MarR homolog from Deinococcus radiodurans that demonstrates phenolic sensing capabilities. HucR binds as a homodimer to a single site within its promoter/operator region with Kd = 0.29 +/- 0.02 nM. The HucR binding site contains a pseudopalindromic sequence, composed of 8-bp half-sites separated by 2 bp. The location of the HucR binding site in the intergenic region between hucR and a putative uricase suggests a mechanism of simultaneous co-repression of these two genes. The substrate of uricase, uric acid, is an efficient antagonist of DNA binding, reducing HucR-DNA complex formation to 50% at 0.26 mM ligand, compared with 5.2 and 46 mM for the aromatic compounds salicylate and acetylsalicylate, respectively. Enhanced levels in vivo of hucR and uricase transcript and increased uricase activity under conditions of excess uric acid further indicate a novel regulatory mechanism of aromatic catabolism in D. radiodurans. Since uric acid is a scavenger of reactive oxygen species, we hypothesize that HucR is a participant in the intrinsic resistance of D. radiodurans to high levels of oxidative stress.

Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans

Two genes bearing similarity to alternative sigma factors were identified in the Deinococcus radiodurans genome sequence and designated sig1 and sig2. These genes were cloned and inactivated, and both were found to be important for survival during heat and ethanol stress, although the sig1 mutants displayed a more severe phenotype than the sig2 mutants. Reporter gene fusions to the groESL and dnaKJ operons transformed into these mutant backgrounds indicated that sig1 is required for the heat shock induction of groESL and dnaKJ, whereas sig2 mutants show a more moderate defect in dnaKJ induction and are not impaired for groESL induction. Essentiality tests suggested that neither sig1 nor sig2 is essential under all conditions. Sequence comparisons demonstrated that the sig1 gene product is classed distinctly with extracytoplasmic function (ECF) sigma factors, whereas Sig2 appears to be a more divergent sigma factor ortholog. These results suggest that sig1 encodes the major ECF-derived heat shock sigma factor in D. radiodurans and that it plays a central role in the positive regulation of heat shock genes. sig2, in contrast, appears to play a more minor role in heat shock protection and may serve to modulate the expression of some heat protective genes.

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.

DNA polymerase I is essential for growth of Methylobacterium dichloromethanicum DM4 with dichloromethane

Methylobacterium dichloromethanicum DM4 grows with dichloromethane as the unique carbon and energy source by virtue of a single enzyme, dichloromethane dehalogenase-glutathione S-transferase. A mutant of the dichloromethane-degrading strain M. dichloromethanicum DM4, strain DM4-1445, was obtained by mini-Tn5 transposon mutagenesis that was no longer able to grow with dichloromethane. Dichloromethane dehalogenase activity in this mutant was comparable to that of the wild-type strain. The site of mini-Tn5 insertion in this mutant was located in the polA gene encoding DNA polymerase I, an enzyme with a well-known role in DNA repair. DNA polymerase activity was not detected in cell extracts of the polA mutant. Conjugation of a plasmid containing the intact DNA polymerase I gene into the polA mutant restored growth with dichloromethane, indicating that the polA gene defect was responsible for the observed lack of growth of this mutant with dichloromethane. Viability of the DM4-1445 mutant was strongly reduced upon exposure to both UV light and dichloromethane. The polA'-lacZ transcriptional fusion resulting from mini-Tn5 insertion was constitutively expressed at high levels and induced about twofold after addition of 10 mM dichloromethane. Taken together, these data indicate that DNA polymerase I is essential for growth of M. dichloromethanicum DM4 with dichloromethane and further suggest an important role of the DNA repair machinery in the degradation of halogenated, DNA-alkylating compounds by bacteria.

Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1

The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.

Why is Deinococcus radiodurans so resistant to ionizing radiation?

When exponential-phase cultures of Deinococcus radiodurans are exposed to a 5000-Gray dose of gamma radiation, individual cells suffer massive DNA damage. Despite this insult to their genetic integrity, these cells survive without loss of viability or evidence of mutation, repairing the damage by as-yet-poorly-understood mechanisms.

Repair of oxidized bases in the extremely radiation-resistant bacterium Deinococcus radiodurans

Deinococcus radiodurans is able to resist and survive extreme DNA damage induced by ionizing radiation and many other DNA-damaging agents. It is believed that it possesses highly efficient DNA repair mechanisms. To characterize the repair pathway of oxidized purines in this bacteria, we have purified, from crude extracts, proteins that recognize these oxidized bases. We report here that D. radiodurans possesses two proteins excising the oxidized purines (formamidopyrimidine and 8-oxoguanine) by a DNA glycosylase-a purinic/apyrimidine lyase mechanism. Moreover, one of those proteins is endowed with a thymine glycol DNA glycosylase activity. One of these proteins could be the homolog of the Escherichia coli Fpg enzyme, which confirms the existence of a base excision repair system in this bacteria.

High sensitivity of Deinococcus radiodurans to photodynamically-produced singlet oxygen

PURPOSE

To study the sensitivity of two bacterial cell systems to photodynamic treatment and X-ray irradiation as part of a project to establish efficient procedures for waste water disinfection.

MATERIALS AND METHODS

Stationary-phase cells of Deinococcus radiodurans (Gram-positive) and Escherichia coli (Gram-negative) were exposed to visible light in a buffer solution containing up to 5 microg/ml sensitizer rose bengal (RB) and to X-rays at dose rates of 32.8 Gy/min or 14.6 Gy/min, respectively.

RESULTS

Survival of both cell types decreased with increasing exposure time to visible light and increasing concentration of RB, and therefore with an increase in singlet oxygen production. Surprisingly, D. radiodurans, the most resistant cell system to ionizing radiation, was more sensitive to photodynamic treatment than E. coli by about a factor of 100.

CONCLUSIONS

The main target of singlet oxygen reaction is the cell membrane. The repair of such damage in D. radiodurans is less effective than in E. coli.

Against all odds: the survival strategies of Deinococcus radiodurans

Bacteria of the genus Deinococcus exhibit an extraordinary ability to withstand the lethal and mutagenic effects of DNA damaging agents-particularly the effects of ionizing radiation. These bacteria are the most DNA damage-tolerant organisms ever identified. Relatively little is known about the biochemical basis for this phenomenon; however, available evidence indicates that efficient repair of DNA damage is, in large part, responsible for the deinococci's radioresistance. Obviously, an explanation of the deinococci's DNA damage tolerance cannot be developed solely on the basis of the DNA repair strategies of more radiosensitive organisms. The deinococci's capacity to survive DNA damage suggests that (a) they employ repair mechanisms that are fundamentally different from other prokaryotes, or that (b) they have the ability to potentiate the effectiveness of the conventional complement of DNA repair proteins. An argument is made for the latter alternative.

Identification and characterization of uvrA, a DNA repair gene of Deinococcus radiodurans

Deinococcus radiodurans is extraordinarily resistant to DNA damage, because of its unusually efficient DNA repair processes. The mtcA+ and mtcB+ genes of D. radiodurans, both implicated in excision repair, have been cloned and sequenced, showing that they are a single gene, highly homologous to the uvrA+ genes of other bacteria. The Escherichia coli uvrA+ gene was expressed in mtcA and mtcB strains, and it produced a high degree of complementation of the repair defect in these strains, suggesting that the UvrA protein of D. radiodurans is necessary but not sufficient to produce extreme DNA damage resistance. Upstream of the uvrA+ gene are two large open reading frames, both of which are directionally divergent from the uvrA+ gene. Evidence is presented that the proximal of these open reading frames may be irrB+.

An alternative pathway of recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcus radiodurans

Deinococcus radiodurans R1 and other members of this genus are able to repair and survive extreme DNA damage induced by ionizing radiation and many other DNA-damaging agents. The ability of R1 to repair completely > 100 double-strand breaks in its chromosome without lethality or mutagenesis is recA dependent. However, during the first 1.5 h after irradiation, recA+ and recA cells show similar increases in the average size of chromosomal fragments. In recA+ cells, DNA continues to enlarge to wild-type size within 29 h. However, in recA cells, no DNA repair is observed following the first 1.5 h postirradiation. This recA-independent effect was studied further, using two slightly different Escherichia coli plasmids forming adjacent duplication insertions in the chromosome, providing repetitive sequences suitable for circularization by non-recA-dependent pathways following irradiation. After exposure to 1.75 Mrad (17,500 Gy), circular derivatives of the integration units were detected in both recA+ and recA cells. These DNA circles were formed in the first 1.5 h postirradiation, several hours before the onset of detectable recA-dependent homologous recombination. By comparison, D. radiodurans strains containing the same E. coli plasmids as nonrepetitive direct insertions did not form circular derivatives of the integration units before or after irradiation in recA+ or recA cells. The circular derivatives of the tandemly integrated plasmids were formed before the onset of recA-dependent repair and have structures consistent with the hypothesis that DNA repair occurring immediately postirradiation is by a recA-independent single-strand annealing reaction and may be a preparatory step for further DNA repair in wild-type D. radiodurans.

Changes in cellular proteins of Deinococcus radiodurans following gamma-irradiation

In order to examine radiation-induced proteins in an extremely radioresistant bacterium, Deinococcus radiodurans R1, changes in cellular proteins after gamma-irradiation were analysed by two-dimensional gel electrophoresis and silver staining. Nine proteins (190, 120, 87,60, 58, 52, 46, 41 and 41 kDa) were increased (or appeared) and more than 13 proteins diminished after gamma-irradiation at 6 kGy. Increase of eight proteins (except for 190-kDa protein) was prevented when the cells were irradiated in the presence of chloramphenicol. Three proteins, 87, 60 and 46 kDa, continued to be synthesized during post-irradiation incubation, and the amounts of these proteins increased with higher doses in a range of 1-12 kGy. Changes in the amount of proteins after irradiation in the R1 strain were compared with those in a moderately radioresistant mutant (rec I) and in a highly radiosensitive mutant (rec30). These three proteins were increased in both R1 and recI, but not in rec 30, suggesting that they are characteristic for radioresistant strains. In addition, from the microsequence analysis, the 46-kDa protein was found to be homologous to the EF-Tu protein of Escherichia coli, whereas the remarkable homologous sequence to the N-terminal of the 60-kDa protein was not found among the known proteins.

Isolation and characterization of a novel Deinococcus radiodurans mutant abnormally susceptible to mutation induction by UV, gamma-ray, and mitomycin C

We isolated and characterized a novel, radiation 'hypermutable' mutant of Deinococcus radiodurans. Compared with the wild-type strain D. radiodurans IR, this mutator strain, designated S101, exhibited sensitivity to UV light, gamma-ray, mitomycin C, and N-methyl-N'-nitro-N-nitrosoguanidine. Spontaneous revertants of S101 that restored wild-type phenotype (non-mutability and resistance to these DNA-damaging agents) were also isolated. Furthermore, the increased susceptibility to DNA-damaging agents and mutability observed in S101 could be mimicked by treating D. radiodurans IR with Mn(II) ions. Our results suggest a putative new pathway of DNA repair in the extremely radioresistant bacterium D. radiodurans.

A model for repair of radiation-induced DNA double-strand breaks in the extreme radiophile Deinococcus radiodurans

The bacterium Deinococcus (formerly Micrococcus) radiodurans and other members of the eubacterial family Deinococaceae are extremely resistant to ionizing radiation and many other agents that damage DNA. Stationary phase D. radiodurans exposed to 1.0-1.5 Mrad gamma-irradiation sustains > 120 DNA double-strand breaks (dsbs) per chromosome; these dsbs are mended over a period of hours with 100% survival and virtually no mutagenesis. This contrasts with nearly all other organisms in which just a few ionizing radiation induced-dsbs per chromosome are lethal. In this article we present an hypothesis that resistance of D. radiodurans to ionizing radiation and its ability to mend radiation-induced dsbs are due to a special form of redundancy wherein chromosomes exist in pairs, linked to each other by thousands of four-stranded (Holliday) junctions. Thus, a dsb is not a lethal event because the identical undamaged duplex is nearby, providing an accurate repair template. As addressed in this article, much of what is known about D. radiodurans suggests that it is particularly suited for this proposed novel form of DNA repair.

Defective transformation of chromosomal markers in DNA polymerase I mutants of the radioresistant bacterium Deinococcus radiodurans

The transformation efficiency of six independently selected chromosomal markers (four for rifampicin resistance and two for acriflavine resistance) was found to be reduced by about 3 logs in a Deinococcus radiodurans strain that was isogenic with wild type except for an insertional mutation in the pol gene that eliminated DNA polymerase I activity (strain 6R1A). D. radiodurans strains UV17 and 303, previously obtained by chemical mutagenesis, were determined to be partially deficient in DNA Pol I activity as assessed in a permeabilized cell system. Both UV17 and 303 demonstrated intermediate transforming efficiencies that correlated with their levels of residual polymerase activity. The transformation efficiency of strain 6R1A could be greatly restored by expression of cloned E. coli DNA Pol I, but not to wild-type levels. Plasmid transfer and chromosomal duplication insertion were not substantially affected by lack of DNA Pol I activity. D. radiodurans is known to possess extraordinarily efficient repair pathways for DNA damage, and is refractory to DNA damage-induced mutagenesis caused by numerous agents, including several that cause base mispairing. We suggest that D. radiodurans may differ from other naturally transformable bacteria in that DNA Pol I is needed to efficiently convert most drug-resistance markers. This unusual mechanism may be required to accomplish chromosomal conversion prior to correction of donor DNA by this organism's efficient repair pathways.

DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans

Deinococcus radiodurans and other members of the same genus share extraordinary resistance to the lethal and mutagenic effects of ionizing and u.v. radiation and to many other agents that damage DNA. While it is known that this resistance is due to exceedingly efficient DNA repair, the molecular mechanisms responsible remain poorly understood. Following very high exposures to u.v. irradiation (e.g. 500 J m-2, which is non-lethal to D. radiodurans), this organism carries out extremely efficient excision repair accomplished by two separate nucleotide excision repair pathways acting simultaneously. One pathway requires the uvrA gene and appears similar to the UvrABC excinuclease pathway defined in Escherichia coli. The other excision repair pathway is specific for u.v. dimeric photoproducts, but is not mediated by a pyrimidine dimer DNA glycosylase. Instead, it is initiated by a second bona fide endonuclease that may recognize both pyrimidine dimers and pyrimidine-(6-4)pyrimidones. After high doses of ionizing-radiation (e.g. 1.5 Mrad), D. radiodurans can mend > 100 double-strand breaks (dsb) per chromosome without lethality or mutagenesis. Both dsb mending and survival are recA-dependent, indicating that efficient dsb mending proceeds via homologous recombination. D. radiodurans contains multiple chromosomes per cell, and it is proposed that dsb mending requires extensive recombination amongst these chromosomes, a novel phenomenon in bacteria. Thus, D. radiodurans may serve as an easily accessible model system for the double-strand-break-initiated interchromosomal recombination that occurs in eukaryotic cells during mitosis and meiosis.

AP endonuclease and uracil DNA glycosylase activities in Deinococcus radiodurans

An endonuclease specific for apurinic/apyrimidinic (AP) sites was identified and purified from extracts of Deinococcus radiodurans. The enzyme is 34.5 kD, has no activity towards normal, alkylated, uracil-containing, or UV-irradiated DNA, and is active in the presence of EDTA. The addition of up to 10 mM Mg2+ or Mn2+ did not affect activity, but higher concentrations were inhibitory. There is no associated exonuclease activity, either in the presence or absence of divalent cation. Optimal reaction conditions were 150 mM NaCl and pH 7.5. A uracil DNA glycosylase was also detected, active in the presence of EDTA, selectively removing uracil from DNA without generating other byproducts. The optimal reaction conditions were 50 mM NaCl and pH 7.5. Implications for base excision repair in D. radiodurans are discussed.

Gene fusions with lacZ by duplication insertion in the radioresistant bacterium Deinococcus radiodurans

Deinococcus radiodurans is the most-studied species of a eubacterial family characterized by extreme resistance to DNA damage. We have focused on developing molecular biological techniques to investigate the genetics of this organism. We report construction of lacZ gene fusions by a method involving both in vitro splicing and the natural transformation of D. radiodurans. Numerous fusion strains were identified by expression of beta-galactosidase. Among these fusion strains, several were inducible by exposure to the DNA-damaging agent mitomycin C, and four of the inducible fusion constructs were cloned in Escherichia coli. Hybridization studies indicate that one of the damage-inducible genes contains a sequence reiterated throughout the D. radiodurans chromosome. Survival measurements show that two of the fusion strains have increased sensitivity to mitomycin C, suggesting that the fusions within these strains inactivate repair functions.

Microbiological safety of irradiated foods

This paper attempts to summarize relevant information on microbiological safety of irradiated foods in the light of previous reports of expert committees and current literature references. After a brief survey of the relative radiation resistance of food-borne microorganisms, the importance of microbial load for dose requirement, and the role of post-irradiation conditions, it addresses the following questions: Could selective changes in the microflora, caused by non-sterilizing radiation doses, make known pathogens more likely to occur, or bring into prominence unfamiliar pathogens? Is it probable that 'mutational' (including adaptive) changes might make pathogens more virulent, more harmful, or more difficult to recognize, and could new pathogens arise in this way? Is it possible that development of radiation-resistant strains might render the antimicrobial irradiation processes ineffective? The present survey of relevant scientific evidence related to these questions reaffirms the basic conclusion of earlier reviews, that microbiological safety of irradiated food is fully comparable with that of foods preserved by other acceptable preservation methods. Similar to other preservation processes, gains in microbiological or keeping quality attained by food irradiation can be and must be safeguarded by proper control in the food irradiation facilities and by proper care of the product before and after processing.

Bacterial genes involved in response to near-ultraviolet radiation

A model of the possible pathways of activities following NUV treatment was presented in Section I and in Fig. 1. Some of the components are firmly established, some are speculative, and many are difficult to evaluate because of insufficient experimental information. Perhaps the most relevant experiments, especially concerning ozone depletion, would be to determine the mutational specificity of NUV. By selecting lacI mutants after exposing cells to NUV, and sequencing the bases of this gene, this is now feasible. There are some problems, however. The mutation frequency is normally so low that it might be difficult to distinguish NUV mutants from spontaneous mutants. However, by irradiating cells having a uvrA or uvrB mutation, the frequency of mutation above background can be increased considerably. There remains the problem as to what fraction of the observed mutations results from oxidative damage. Some of this could be clarified by comparing mutation spectra of cells treated with NUV and cells subjected to excess oxidative damage and determining what fraction results from other avenues of lesion formation in DNA. Different species of reactive oxygen could cause different kinds of DNA lesions, and, fortunately, use of appropriate mutants should allow us to sort out any differences in specificity of lesions. Also, by appropriate manipulation of quantities of endogenous photosensitizers, it might be possible to sort out the specific mutations that are caused by photodynamic action. Another avenue of research is to explore the pathways by which NUV lesions are repaired, and whether such repair is error prone or error free. Again, the use of mutants such as xthA, uvr, and polA should assist in our understanding of the specificity of the mutational events. There are now a number of examples of global control mechanisms whereby cells abruptly shift their protein synthesis pattern under environmental stress. It is important to understand whether NUV stress results in induction of one or more of the known regulatory genes, or whether another regulon might be involved. One particular aspect of regulation that remains unsolved is the role of the katF gene, which is known to regulate the xthA and katE, but it may also regulate other genes as well. A number of striking physiological events occur even at very low fluences of NUV irradiation of cells. In part, this may be related to regulon induction. However, some of these events are in need of special exploration, such as changes at the membrane level.(ABSTRACT TRUNCATED AT 400 WORDS)

The plasmids of Deinococcus spp. and the cloning and restriction mapping of the D. radiophilus plasmid pUE1

Plasmids were found in strains representing all four species of the genus Deinococcus viz. D. radiodurans, D. radiopugnans, D. radiophilus and D. proteolyticus but were not found in the most intensively-investigated strain of the genus, D. radiodurans R1. Their sizes were calculated from electron micrographs. D. radiophilus yielded three size classes of plasmid while D. radiodurans Sark, D. proteolyticus and D. radiopugnans each yielded two. Attempts to cure D. radiophilus and D. radiodurans Sark of any of their plasmids, using a variety of methods, were unsuccessful. A 10.8 kbase pair (kb) plasmid from D. radiophilus, pUE1, was cloned into the PstI site of pAT153 and propagated in Escherichia coli HB101. The recombinant plasmid, pUE109 was subjected to single and double digestion with various restriction endonucleases and its restriction map constructed. The resistance of E. coli HB101 to ultraviolet radiation was not increased when pUE109 was introduced into it. Attempts to transform D. radiodurans with pUE109 failed to detect tetracycline-resistant transformants.

Cloning of the DNA repair genes mtcA, mtcB, uvsC, uvsD, uvsE and the leuB gene from Deinococcus radiodurans

A gene library from Deinococcus radiodurans has been constructed in the cosmid pJBFH. A 51.5-kb hybrid cosmid, pUE40, that transduced Escherichia coli HB101 from leucine dependence to independence was selected, and a 6.9-kb fragment which carried the leuB gene from D. radiodurans was subcloned into the EcoRI site of pAT153. The DNA repair genes mtcA, mtcB, uvsC, uvsD and uvsE, which code for two D. radiodurans UV endonucleases were identified by transforming appropriate repair-deficient mutants of D. radiodurans to repair proficiency with DNA derived from the gene library. Hybrid cosmid pUE50 (37.9 kb) containing an insert carrying both the mtcA and mtcB genes was selected and 5.6- and 2.7-kb DNA fragments carrying mtcA and mtcB, respectively, i.e., the genes that code for UV endonuclease alpha, were subcloned into the EcoRI site of pAT153. The three genes uvsC, uvsD and uvsE, that code for UV endonuclease beta, were all present in the 46.0-kb hybrid cosmid pUE60. The uvsE gene in a 12.2-kb fragment was subcloned into the HindIII site of pAT153 and the size of the insert reduced to 6.1 kb by deletion of a 6.7-kb fragment from the hybrid plasmid pUE62. None of the uvs genes introduced into the UV-sensitive E. coli CSR603 (uvrA-) was able to complement its repair defect. The mtcA, uvsC, uvsD and uvsE genes were found in the 52.5-kb hybrid cosmid pUE70. It is concluded that the DNA repair genes mtcA, mtcB, uvsC, uvsD and uvsE are located within an 83.0-kb fragment of the D. radiodurans genome.

A review of the genetic effects of ethyl methanesulfonate

Ethyl methanesulfonate (EMS) is a monofunctional ethylating agent that has been found to be mutagenic in a wide variety of genetic test systems from viruses to mammals. It has also been shown to be carcinogenic in mammals. Alkylation of cellular, nucleophilic sites by EMS occurs via a mixed SN1/SN2 reaction mechanism. While ethylation of DNA occurs principally at nitrogen positions in the bases, because of the partial SN1 character of the reaction, EMS is also able to produce significant levels of alkylation at oxygens such as the O6 of guanine and in the DNA phosphate groups. Genetic data obtained using microorganisms suggest that EMS may produce both GC to AT and AT to GC transition mutations. There is also some evidence that EMS can cause base-pair insertions or deletions as well as more extensive intragenic deletions. In higher organisms, there is clear-cut evidence that EMS is able to break chromosomes, although the mechanisms involved are not well understood. An often cited hypothesis is that DNA bases ethylated by EMS (mostly the N-7 position of guanine) gradually hydrolyze from the deoxyribose on the DNA backbone leaving behind an apurinic (or possibly an apyrimidinic) site that is unstable and can lead to single-strand breakage of the DNA. Data also exist that suggest that ethylation of some chromosomal proteins in mouse spermatids by EMS may be an important factor in causing chromosome breakage.

Roles of the uvsC, uvsD, uvsE, and mtcA genes in the two pyrimidine dimer excision repair pathways of Deinococcus radiodurans

In Deinococcus radiodurans, the genes uvsC, uvsD, uvsE, and mtcA are all involved in the single-strand incision of UV-irradiated DNA, and mutations in at least two of them were required to produce an incisionless strain. One mutation must be in mtcA and one in uvsC, uvsD, or uvsE. Strains carrying single mutations in any one of the genes can incise DNA to the same extent as the wild-type strain. Neither the presence of EDTA nor the absence of protein synthesis affected the incision step. Strains deficient in DNA incision have greatly reduced DNA degradation after UV irradiation, and upon addition of chloramphenicol to the postirradiation medium, they do not undergo excessive DNA degradation as is seen in the wild-type strain and strains singly mutant in uvsC, uvsD, or uvsE. The strain singly mutant in mtcA also lacked chloramphenicol-enhanced DNA degradation and loss of viability but behaved similarly to the wild-type strain with respect to resumption of DNA synthesis and DNA degradation in the absence of chloramphenicol. It is proposed that two constitutive, cation-independent UV endonucleases are present in D. radiodurans: UV endonuclease alpha (the product of the mtcA gene), which incises in response to pyrimidine dimers, mitomycin C cross-links, bromomethylbenzanthracene adducts, and other alkylation damage, and UV endonuclease beta (the product of the uvsC, uvsD, and uvsE genes), which incises only in response to pyrimidine dimers. Both endonucleases have associated exonuclease activity. The exonucleolytic activity associated with UV endonuclease alpha requires a UV-induced protein to terminate (or control) its activity, whereas the exonucleolytic activity associated with UV endonuclease beta is slower acting and does not require the inducible terminator.

DNA damage, prophage induction and mutation by furazolidone

Ultraviolet absorption data and thermal chromatography through hydroxyapatite (HAP) column revealed that furazolidone treatment of Vibrio cholerae cells produced more than 80% of DNA reversibly bihelical due to the formation of interstrand cross-links and the reaction obeyed a first order relation. Sensitivities of the Escherichia coli strains to the lethal action of the drug were in the order: AB 2480(uvr- rec-) greater than AB 2463(rec-) greater than AB 1886(uvr-) greater than AB 1157(repair proficient) or AB 4401(wild type). Furazolidone was 'Rec test' positive, produced dose-dependent prophage induction in E. coli cells and also dose-dependent streptomycin-resistance forward mutation in V. cholerae cells. The quantitative aspect and also the mode of furazolidone action on DNA were discussed.

Induction of mutation in Micrococcus radiodurans by N-methyl-N'-nitro-N-nitrosoguanidine

Micrococcus radiodurans was highly resistant to the lethal effect of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) but it was sensitive to the mutagenic action of this chemical. The induction of mutation was not significantly modified by the culture growth phase. This last finding leads to the assumption that the mutation takes place at some distance from the replication fork. Moreover, a low concentration of MNNG induced mutations that were added to those subsequently obtained from a second exposure to a higher concentration of the alkylating agent. Thus, M. radiodurans does not seem to have an inducible error-free repair system for alkylation damage. Furthermore, incubation in the presence of chloramphenicol did not modify the mutation rate, indicating that protein synthesis is not involved in the mutagenic process.

Genetic effects of N-methyl-N'-nitro-N-nitrosoguanidine and its homologs

Since the discovery of the mutagenic activity of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) in 1960, this compound has become one of the most widely used chemical mutagens. The present paper gives a survey on the chemistry, metabolism, and mode of interaction of MNNG with DNA and proteins, and of the genotoxic effects of this agent on microorganisms, plants, and animals, including human cells cultured in vitro. Data on the carcinogenicity and teratogenicity of MNNG as well as on the genotoxic effects of homologs of MNNG are also presented.

UV light-induced survival response in a highly radiation-resistant isolate of the Moraxella-Acinetobacter group

A highly radiation-resistant member of the Moraxella-Acinetobacter group, isolate 4, obtained from meat, was studied to determine the effect of preexposure to UV radiation on subsequent UV light resistance. Cultures that were preexposed to UV light and incubated for a short time in plate count both exhibited increased survival of a UV light challenge dose. This response was inhibited in the presence of chloramphenicol. Frequencies of mutation to streptomycin, trimethoprim, and sulfanilamide resistance remained the same after the induction of this survival response and were not altered by treatment with mutagens, with the exception of mutation to streptomycin resistance after gamma-irradiation or nitrosoguanidine or methyl methane sulfonate treatment. The results indicated that isolate 4 has a UV light-inducible UV light resistance mechanism which is not associated with increased mutagenesis. The characteristics of the radiation resistance response in this organism are similar to those of certain other common food contaminants. Therefore, considered as part of the total microflora of meat, isolate 4 and the other radiation-resistant Moraxella-Acinetobacter isolates should not pose unique problems in a proposed radappertization process.

Misrepair mutagenesis in Myxococcus xanthus: induction of rifampicin-resistant mutants by N-methyl-N'-nitro-N-nitrosoguanidine and ultraviolet-irradiation

In the ultraviolet (UV)-mutable bacterium, Myxococcus xanthus, dose response curves for the induction of rifampicin-resistant (Rifr) mutants were compared with dose response curves for Weigle(W)-reactivation of the UV-irradiated phage Mx4 at a phage survival of 5 X 10(-6). In most strains examined, including a uvr mutant, these curves are largely similar. Unexpectedly the UV-sensitive strain M. xanthus Bt, which is unable to perform W-reactivation, is nevertheless UV-mutable. This result may indicate that the repair pathway involved in phage reactivation is only partly responsible for UV-mutagenesis or alternatively is not able to act on phage DNA in M. xanthus Bt cells. N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) treatment of M. xanthus cells also results in marked W-reactivation of the UV-irradiated phage Mx4 at the same survival of 5 X 10(-6). The MNNG-stimulated phage reactivation is of the same order of magnitude as the UV-stimulated phage reactivation. Also the dose response curves for the induction of Rifr mutants by MNNG and the MNNG-stimulated phage reactivation are quite similar. This coincidence may indicate that misrepair mutagenesis is involved in both UV and MNNG-mutagenesis. It is suggested that M. xanthus is a useful organism with which to study misrepair mutagenesis in bacteria.

Defective excision repair in a mutant of Micrococcus radiodurans hypermutable by some monofunctional alkylating agents

The lethal and mutagenic effects of methyl methanesulphonate (MMS), ethyl methanesulphonate (EMS), and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) can be dissociated in a mitomycin C (MTC)-sensitive mutant, strain 302, of Micrococcus radiodurans. As regards lethality 302 is extremely sensitive, compared with the wild type, to MTC and decarbamoyl MTC (DCMTC), slightly sensitive to EMS, MNNG, nitrous acid, 7-bromomethylbenz[alpha]anthracene (BrMBA), and N-acetoxy-N-2-acetylaminofluorene (AAAF), and resistant to MMS, hydroxylamine, and ICR 191G. As regards mutability it is, compared to the wild type, very sensitive to MMS, EMS, and MNNG, and slightly sensitive to hydroxylamine and nitrous acid but not to any other agent examined. Alkaline sucrose gradient studies indicate the 302 does not incise DNA containing BrMBA adducts, although it does incise DNA damaged by AAAF but probably not to the same extent as wild type. We put forward the hypothesis that the hypermutability of 302 is due to the non-removal of bases or nucleotides, modified in exocyclic positions, which have altered base-pairing capabilities, while lethality results from the non-removal of bases or nucleotides, also modified in exocyclic positions, which no longer form hydrogen-bonded base pairs.

An Escherichia coli mutant refractory to nitrosoguanidine mutagenesis

A newly-isolated Escherichia coli mutant suffers only about 10% as many mutations as normal strains on exposure to nitrosoguanidine. The responsible mutation, inm-1, maps at approximately minute 79 in the current E. coli genetic map. The mutant is normal for overall growth, nitrosoguanidine lethality, spontaneous mutagenesis, ultraviolet light lethality and mutagenesis, ethyl methanesulfonate lethality and mutagenesis, and the adaptive repair induced by alkylating agents. The existence of this mutation proves that nitrosoguanidine mutagenesis is not merely the result of reactions between the chemical and DNA, but requires specific cellular function(s), and underscores the peculiarity of nitrosoguanidine as a mutagen.

DNA-membrane complex restoration in Micrococcus radiodurans after X-irradiation: relation to repair, DNA synthesis and DNA degradation

The DNA-membrane complex in Micrococcus radiodurans was shown to be essentially constituted of proteins, lipids and DNA. The complex was dissociated immediately after X-irradiation of cells and restored during post-incubation in complete medium. In X-irradiated protoplasts some DNA remained associated with the complex. Restoration of the complex during post-incubation was only seen in a medium favouring DNA polymerase and ligase activities. Under this condition no DNA synthesis occurred, suggesting that complex restoration may involve ligase activity. The complex restoration in the wild type and the X-ray sensitive mutant UV17 of M. radiodurans was strictly dependent on the X-ray dose. It was correlated with survival and DNA degradation but always preceded the onset of DNA synthesis after X-irradiation. At the same dose the complex restoration was about 2 fold lower in mutant than in wild type cells indicating that the restoration of the complex is related to repair capacity. The results are consistent with the idea that the complex protects X-irradiated DNA of M. radiodurans from further breakdown and, subsequently, permits DNA synthesis and repair to occur.