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PubMed2004

Radiation response mechanisms of the extremely radioresistant bacterium Deinococcus radiodurans.

Effect of microgravity on recovery of bacterial cells from radiation damage was examined in IML-2, S/MM-4 and S/MM-9 experiments using the extremely radioresistant bacterium Deinococcus radiodurans. The cells were irradiated with gamma rays before the space flight and incubated on board the Space Shuttle. The survival of the wild type cells incubated in space increased compared with the ground controls, suggesting that the recovery of this bacterium from radiation damage was enhanced under the space environment. No difference was observed between the survivals of radiosensitive mutant rec30 cells incubated in space and on the ground. The amount of DNA-repair related RecA protein induced under microgravity was similar to those of ground controls, however, induction of PprA protein, product of a unique radiation-inducible gene (designated pprA) responsible for loss of radiation resistance in repair-deficient mutant, KH311, was enhanced under microgravity compared with ground controls. Recent investigation in vitro showed that PprA preferentially bound to double-stranded DNA carrying strand breaks, inhibited Escherichia coli exonuclease III activity, and stimulated the DNA end-joining reaction catalyzed by DNA ligases. These results suggest that D. radiodurans has a radiation-induced non-homologous end-joining (NHEJ) repair mechanism in which PprA plays a critical role.

Bacterial Proteins↗
PubMed2005

[Characterization of the changes in protease of Deinococcus radiodurans following irradiation].

The activity of protease from Deinococcus radiodurans R1 (DRR1) recovered from UV light and gamma-ray irradiation were characterized by SDS-PAGE zymography or FITC-labeled casein as substrate. It was demonstrated that proteases with large molecular weight were abundantly and constitutively expressed in DRR1, which consistent with the hypothesis that proteases were among the PHX (predicted highly expressed) proteins in DRR1. A broad range of gelatinolytic protease with molecular mass more than 140 kD and caseinolytic protease with molecular mass more than 120 kD were present in DRR1 cell. The prominent gelatinolytic protease of 174 kD was also active when denatured by SDS and displayed different operation dynamics during the repair process post UV-irradiation and gamma-irradiation, the protease showed its highest activity during gamma-irradiation and in the late recovery stage post-irradiation. Some proteases were demonstrated to be induced specifically by irradiation which suggests that these proteases may regulate breakdown of proteins responsible in sequential pathway, and an elaborate and fine tuning protease system may exist in D. radiodurans during the repair process post irradiation. The expression of protease was also influenced by the nutrition of the culture. A rod-shaped and radiation resistant bacterium RR533.2 isolated from soil in Beijing, China was revealed to display similar zymography pattern using gelatin or casein as substrate.

Deinococcus↗
PubMed2006

[Construction of the recQ double mutants and analysis of adversity in Deinococcus radiodurans].

As a subfamily member of SF1 superfamily, the RecO helicases are highly conserved in evolution and are required for maintaining genome stability in all organisms. Loss of RecO helicase function leads to a breakdown in the maintenance of genome integrity, in particular hyper-recombination. Named after the recQ gene of Escherichia coli, lower eukaryotic species generally only contain a single RecQ family representative; for example, Sgsl in the budding yeast, Saccharomyces cerevisiae, and Rqhl in the fission yeast, Schizosaccharomyces pombe. There are, however, multiple members in most higher organisms, with five being present in humans. Defects in three of these human RecQ helicases give rise to defined clinical disorders associated with cancer predisposition and variable aspects of premature aging. Deinococcus radiodurans encodes two recQ genes with unusual domain: DR1289 and DR2444, whose functions, however, remain obscure currently. DR1289 contains three tandem copies of the C-terminal helicase-RNase D (HRDC) domain, instead of the single copy present in all other bacteria except Neisseria that similarly possesses three copies. DR2444 contains a HRDC domain and a domain homologous to cystathionine gamma-lyase; this is the first example of an HRDC domain that is not associated with either a helicase or a nuclease. In this study, a fusion DNA fragment carrying kanamycin resistance gene with the D. radiodurans groEL promoter, chloramphenicol resistance gene with KAT promoter was cloned by PCR amplification and reversely inserted into the recQ locus in the genome of the wild-type strain RI. Three resulting recQ-deficient strains, designated deltaDR1289, deltaDR2444 and deltarecQ (double mutation), were constructed. Results show that deltaDR1289 and delta recQ were very sensitive to ionizing radiation and H2O2, while delta DR2444 and wild strain R1 were not. The phenotype of delta DR1289 was similar to many RecQ helicase mutants. Therefore, it was presumed that DR1289 was the necessary gene in maintaining the extreme resistance to DNA damaging agents, whereas DR2444 was not. Further research based on genetic and biochemical approaches should help to gain a better understanding of the genes involved in DNA repair.

Bacterial Proteins↗
PubMed2006

[Construction and functional analysis of the crtl gene disruptant in Deinococcus radiodurans].

With the method of Polymerase Chain Reaction and homologous genetic recombination in vivo, the key gene encoding bacterial-type phytoene desaturase (Crtl) which controls the carotenoids biosynthesis pathway in the non-photosynthetic and extremely radioresistant bacterium Deinococcus radiodurans was deleted from the genome. The colorless mutant obtained was designated as M61. Survival rates of mutant strain and wild type strain were investigated under different doses of gamma-radiation and hydrogen peroxide. The results showed that the radioresistant activity of M61 reduced rapidly under ionization radiation, and it became more sensitive to the treatment of hydrogen peroxide especially to high concentration of hydrogen peroxide compared to that of wild type R1. Reverse Phase High Performance Liquid Chromatography (RP-HPLC) was used to investigate the carotenoid composition of wild type R1 and mutant M61. HPLC results exhibited that the deficient of crtl gene had important effect on pigment biosynthesis pathway, leading to inhibition of the biosynthesis of lycopene and other carotenoids in D. radiodurans. All the results indicated that crtl gene was a key gene controlling the biosynthesis of red carotenoid including lycopene in D. radiodurans. The roles of carotenoids in protecting the bacterial cell from damage by ionization radiation and hydrogen peroxide suggest that the carotenoids contribute to the defense system in D. radiodurans. This study is important for elucidating the radioresistant and antioxidant mechanism in which carotenoids are involved, and it will supply some ideas to the further investigation on the biosynthesis pathway and functions of carotenoids in D. radiodurans.

Bacterial Proteins↗
PubMed2006

[Effects of PprI and RecX on antioxidant activity of Deinococcus radiodurans].

Effects of mutations of Pprl (Dr0167) and RecX (Dr1310), which are relative to radioresistance, on reactive oxygen species scavenging activities in Deinococcus radiodurans were investigated using gene mutation, chemiluminescence measurement and enzyme activity analysis. Their possible regulating functions on the activities of antioxidant enzymes was evaluated. Results show that mutant that lacks PprI is remarkably sensitive to reactive oxygen species and its enzyme activities of catalase and superoxide dismutase decrease significantly. On the other hand, RecX has a "negative" effect on reactive oxygen species scavenging activities of this bacterium, i.e., mutation of recX enhances the scavenging activities on reactive oxygen species, and the enzyme activities of catalase and superoxide dismutase in mutant that lacks RecX are significantly increased. These results indicate that these two genes are relative to the regulation of antioxidant system of this bacterium. It presents some idea to the further investigation on the antioxidant mechanism of this bacterium.

Antioxidants↗
PubMed2006

Analysis of double stranded DNA-dependent activities of Deinococcus radiodurans RecA protein.

In this study, the double-stranded DNA-dependent activities of Deinococcus radiodurans RecA protein (Dr RecA) were characterized. The interactions of the Dr RecA protein with double-stranded DNA were determined, especially dsDNA-dependent ATP hydrolysis by the Dr RecA protein and the DNA strand exchange reaction, in which multiple branch points exist on a single RecA protein-DNA complex. A nucleotide cofactor (ATP or dATP ) was required for the Dr RecA protein binding to duplex DNA. In the presence of dATP, the nucleation step in the binding process occurred more rapidly than in the presence of ATP. Salts inhibited the binding of the Dr RecA protein to double-stranded DNA. Double-stranded DNA-dependent ATPase activities showed a different sensitivity to anion species. Glutamate had only a minimal effect on the double-stranded DNA-dependent ATPase activities, up to a concentration of 0.7 M. In the competition experiment for Dr RecA protein binding, the Dr RecA protein manifested a higher affinity to double-stranded DNA than was observed for single-stranded DNA.

Adenosine Triphosphatases↗
PubMed1999

Pharmacologic application of FTIR spectroscopy: effect of ascorbic acid-induced free radicals on Deinococcus radiodurans.

Fourier transform infrared (FTIR) spectroscopy was used as a convenient and easy-to-run method to monitor radical-induced damage on the radiation-resistant Deinococcus radiodurans strain. Increasing concentrations of ascorbic acid added to the culture medium during the stationary phase produced striking changes in the infrared spectra. These changes especially occurred in the 1700-900 cm(-1) region, which is spectroscopically assigned to the amide I and II components, nucleotide bases, phosphodiester backbone and sugar rings, and were correlated with the oxidant effect of ascorbic acid. Thus, FTIR analysis allows a rapid characterization of the changes induced by ascorbic acid in the cell environment, which can be correlated in part with the generation of free radicals. Beyond a critical ascorbic acid concentration of 40 mM, these free radicals can cause severe damage to the biomolecular components, as soon as the antioxidant defenses of the bacterium are overwhelmed.

Ascorbic Acid↗
PubMed1995

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.

DNA Damage↗
PubMed2001

Sensitivity of Deinococcus radiodurans to gamma-irradiation: a novel approach by Fourier transform infrared spectroscopy.

Deinococcus radiodurans is a red-pigmented coccus known to be particularly resistant to both chemical and radiative agents. Fourier transform infrared (FT-IR) spectroscopy was used as a convenient and easy-to-run method to monitor damage induced in this bacterium by ionizing radiations. First, stationary-phase cultures were submitted to increasing doses of gamma-irradiation ((137)Cs source). Beyond a threshold of 11 kGy, striking changes occurred in spectra of irradiated samples compared with unirradiated ones, especially in the 1750-900 cm(-1) region, which is spectroscopically assigned to amide I and II components, nucleotide bases, the phosphodiester backbone, and the sugar ring. Second, bacterial cultures were postirradiation reincubated. After a reincubation time of 15 h, the oxidative stress was in part overwhelmed, and the growth of D. radiodurans again occurred, although some biocellular components remained altered. Consequently, FT-IR analysis is an accurate means to rapidly visualize biomolecular changes undergone by cells both after gamma-irradiation and during the repair mechanism.

Algorithms↗
PubMed2000

Analysis of Drosophila yellow-B cDNA reveals a new family of proteins related to the royal jelly proteins in the honeybee and to an orphan protein in an unusual bacterium Deinococcus radiodurans.

The yellow locus in Drosophila is involved in both cuticle development and behaviour. However, the function of the encoded protein is unknown. Here we have characterised the sequence and expression pattern of a new Drosophila gene, designated yellow-B, encoding a 453-amino-acid protein that is 57% identical to Yellow. High levels of yellow-B mRNA are present in the larval-pupal stages, but the gene is also expressed in the head. Bioinformatics analysis indicates that the Drosophila genome encodes at least 7 members of the Yellow family distributed among chromosomes 2, 3, and X. The Yellow proteins are related to the Royal Jelly proteins and have no relatives in other non-insect metazoan species. Interestingly, a Yellow-like protein is encoded by the genome of a radiation tolerant bacterium, Deinococcus radiodurans.

Amino Acid Sequence↗
PubMed2001

Inactivation of two homologues of proteins presumed to be involved in the desiccation tolerance of plants sensitizes Deinococcus radiodurans R1 to desiccation.

Mutational inactivation of the genes designated DR1172 and DRB0118 in Deinococcus radiodurans R1 greatly sensitizes this species to desiccation, but not to ionizing radiation. These genes encode proteins that share features with the desiccation-induced LEA76 proteins of many plants and the PCC13-62 protein of Craterostigma plantagineum, suggesting that D. radiodurans may serve as a useful model for the study of desiccation tolerance in higher organisms.

Bacteria↗
PubMed1985

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.

Chromosome Mapping↗
PubMed1996

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.

Amino Acid Sequence↗
PubMed1991

Influence of repeated lyophilization on the survival of Deinococcus proteolyticus, Micrococcus luteus and Escherichia coli.

Repeated lyophilization of Deinococcus proteolyticus, Micrococcus luteus and Escherichia coli cells results in a successive decrease of their survival. The survival curve is exponential with E. coli and M. luteus, and sigmoidal with a broad shoulder with D. proteolyticus both after repeated lyophilization and after UV- or gamma-irradiation. When cells were subjected to gamma-irradiation after a 20-fold freeze-drying, the corresponding survival curve became exponential without the shoulder. Hence we assume that irradiation and repeated lyophilization afflict the same cellular structures and/or functions.

DNA, Bacterial↗
PubMed1989

The action of free radicals on Deinococcus radiodurans carotenoids.

The possible role of carotenoids as free radical scavengers has not been completely elucidated. To gain further insight into the quenching of OH radicals by carotenoids, we used a feasible bacterial model, Deinococcus radiodurans, a red pigmented bacterium. We compared the action of H2O2 which produces in vivo OH radicals by a Fenton-type reaction on the parental and two mutant strains, i.e., a red pigmented and a colorless one. While the red pigmented bacteria were resistant to H2O2 action, the colorless strain was significantly more sensitive and its sensitivity was dose-dependent. In the red pigmented strains, H2O2 induced a significant decrease in one carotenoid (X5), which could be responsible for the antioxidant activity.

Carotenoids↗
PubMed1991

Reconstitution of the Deinococcus radiodurans aposuperoxide dismutase.

Deinococcus radiodurans, a radiation-resistant aerobe, synthesized a 43,000 Mr dimeric superoxide dismutase. The holoenzyme, sp act 3300 U/mg, contained 1.5 g-atoms Mn, 0.6 g-atom Fe, and 0.1 g-atom Zn per mole dimer. Apoprotein, prepared by dialysis of the holoenzyme in denaturant plus chelator and then renatured in chelex-treated Tris chloride buffer, rapidly regained superoxide dismuting activity upon incubation in 1 mM MnCl2. Reconstitution was dependent on Mn concentration and pH. The Mn-reconstituted protein, sp act 3560 U/mg, contained 1.7 g-atoms Mn per mole dimer. The holoenzyme and Mn-reconstituted apoprotein migrated with the same patterns in 10% acrylamide gels and focused to the same pattern upon isoelectric focusing. Fluorescence emission maxima of the holoenzyme, Mn-reconstituted apoprotein, and the renaturated apoprotein were 329 +/- 1 nm but differed from the denatured apoprotein (352 nm). Apoprotein bound 1.7 g-atoms Zn and from 3-7 g-atoms Fe per mole dimer on incubation with 1 mM ZnSO4 and Fe(NH4)2(SO4)2, respectively. Although neither Zn nor Fe restored superoxide dismuting activity, the ferrous and the zinc salt inhibited reconstitution of the apoprotein with manganese. Metal addition to renatured aposuperoxide dismutase offers a novel approach to reconstitution of procaryote superoxide dismutases.

Amino Acids↗
PubMed1986

Three-dimensional structure of the regular surface layer (HPI layer) of Deinococcus radiodurans.

The low-resolution structure of the regular surface layer of Deinococcus radiodurans has been determined from negatively stained specimens by three-dimensional electron microscopy. The layer has P6 symmetry, a lattice constant of 18 nm and a thickness of 6.5 nm. Three-dimensional reconstruction was performed by a hybrid real space/Fourier space approach that incorporates partial compensation of lattice distortions: The model obtained is discussed in the light of independent information about the surface structure of this layer, derived from metal shadowing and surface relief reconstruction. While agreement is quite satisfactory for the apparently more rigid inner surface, the outer surface shows severe flattening effects. The structure of the HPI layer is compared with other bacterial surface layers using a classification scheme that is outlined in the Appendix.

Bacteria↗
PubMed1994

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.

Acriflavine↗