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PubMed2001

Molecular cloning and functional analysis of the MutY homolog of Deinococcus radiodurans.

The mutY homolog gene (mutY(Dr)) from Deinococcus radiodurans encodes a 39.4-kDa protein consisting of 363 amino acids that displays 35% identity to the Escherichia coli MutY (MutY(Ec)) protein. Expressed MutY(Dr) is able to complement E. coli mutY mutants but not mutM mutants to reduce the mutation frequency. The glycosylase and binding activities of MutY(Dr) with an A/G-containing substrate are more sensitive to high salt and EDTA concentrations than the activities with an A/7,8-dihydro-8-oxoguanine (GO)-containing substrate are. Like the MutY(Ec) protein, purified recombinant MutY(Dr) expressed in E. coli has adenine glycosylase activity with A/G, A/C, and A/GO mismatches and weak guanine glycosylase activity with a G/GO mismatch. However, MutY(Dr) exhibits limited apurinic/apyrimidinic lyase activity and can form only weak covalent protein-DNA complexes in the presence of sodium borohydride. This may be due to an arginine residue that is present in MutY(Dr) at the position corresponding to the position of MutY(Ec) Lys142, which forms the Schiff base with DNA. The kinetic parameters of MutY(Dr) are similar to those of MutY(Ec). Although MutY(Dr) has similar substrate specificity and a binding preference for an A/GO mismatch over an A/G mismatch, as MutY(Ec) does, the binding affinities for both mismatches are slightly lower for MutY(Dr) than for MutY(Ec). Thus, MutY(Dr) can protect the cell from GO mutational effects caused by ionizing radiation and oxidative stress.

Adenine↗
PubMed2002

Genetic evidence that the uvsE gene product of Deinococcus radiodurans R1 is a UV damage endonuclease.

An in vitro transposition system, developed to facilitate gene disruption in Deinococcus radiodurans R1, has been used to inactivate the gene designated dr1819 in uvrA-1(+) and uvrA-1 backgrounds. dr1819 encodes a protein with homology to a UV DNA damage endonuclease expressed by Schizosaccharomyces pombe. Interruption of dr1819 greatly sensitizes the uvrA-1 strain but not the uvrA-1(+) strain to UV light, indicating that the dr1819 gene product is a component in a DNA repair pathway that can compensate for the loss of nucleotide excision repair in this species. Clones of dr1819 will restore UV resistance to UVS78, a uvrA-1 uvsE strain, indicating that dr1819 and uvsE are the same locus.

Bacterial Proteins↗
PubMed1981

Isolation and characterization of the plasma membrane and the outer membrane of Deinococcus radiodurans strain Sark.

Deinococcus radiodurans strain Sark, although gram-positive, has a complex cell wall profile that includes an outer membrane-like structure. The outer cell envelope layers formed blebs throughout the growth cycle, which were shed as large vesicles (0.5-3.5 micron m in diameter) from approximately 5% of the cell population. Instability was accentuated by treatment with 10% NaCl, which released the outer membrane from all cells without disrupting the peptidoglycan layer, and provided an outer membrane fraction uncontaminated by plasma membrane. Cells so treated formed protoplasts after sequential treatment with 6 M urea, trypsin, and the supernatant from batch cultures of Lysobacter enzymogenes 495. The plasma membrane was isolated from lysed protoplasts. The absence of presence of catalase activity, and differences in lipid composition, were used to differentiate between plasma membrane and outer membrane.

Bacteria↗
PubMed1983

Cell division in Deinococcus radiodurans and a method for displaying septa.

The study of sections, freeze-cleaved, and whole-cell preparations of Deinococcus radiodurans supported the contention that septa close assymmetrically and originate from discrete opposing locations on the cell surface. Tetrads and the larger associations (sheets) of cells in some strains were formed by alternate and synchronized divisions in two planes. The polarity initiating the second division in cells of the Sark strain, in particular, was often expressed in slower growing cells before completion of the first division so that the advancing margins of the first septum were diverted towards the nearest new pole; the resulting gap was closed later on, and consequently, the cell compartments of this coccus were in communication for some time after two rounds of nuclear segregation. Freeze cleaving showed that the initial generation of septa involved a short sulcus in the plasma membrane and not a circumferential infolding. The shape and form of the developing septum was inferred from sections but was displayed in whole-cell preparations by a technique which selectively and positively stained a septal component. Positive staining of the septum with uranyl salts was appreciable when the relative stainability of the peripheral wall (mainly peptidoglycan) was reduced by pretreatment with salts of low atomic weight metals (0.01-1.0%, w/v) such as cobalt, copper, iron, or zinc. Examination of these whole-cell preparations by stereoscopy showed that the septal diaphragm closes as a slit or long oval, and the advancing margin shows curvature towards the next axis of division. The mechanism and exact site of this positive staining was not elucidated; vancomycin blocking of the uncross-linked peptides of peptidoglycan was almost as effective as the transition metal salts as a foretreatment for staining septa.

Cell Division↗
PubMed1997

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.

Chromosomes, Bacterial↗
PubMed1996

Recovery of Deinococcus radiodurans from radiation damage was enhanced under microgravity.

Effect of microgravity on recovery of bacterial cells from radiation damage was examined on the IML-2 mission in 1994 using extremely radioresistant bacterium Deinococcus radiodurans. The cells were lyophilized and exposed to 60Co gamma-rays with doses 2 to 12 kGy before the space flight. At the end of the mission, the cells were mixed on board with liquid nutrient medium to allow the cells to start recovery process from the radiation damage. Afterwards the cells were stored at 4 degrees C until landing. The influence of cosmic radiation was negligible, because total absorbed dose of space radiation measured during the mission was less than 2 mGy and this bacterium does not decrease its viability after both gamma-rays and high-LET heavy charged particles irradiation with doses up to 5 kGy. The survival of the cells incubated in space increased significantly compared with the ground controls, suggesting that the recovery of this bacterium from radiation damage was enhanced under microgravity.

Colony Count, Microbial↗
PubMed1999

Damage to DNA purified from the radioresistant prokaryote, Deinococcus radiodurans, by acid heating.

Using a highly radioresistant bacterium, Deinococcus radiodurans, the mechanism of degradation of the purified DNA molecules by heating was examined under acidic conditions. Setting the treatment temperature at 55ûC with a duration of 0 to 20 min and adjusting the pH of the cell suspension to 3, 5 or 7, cell viabilities after the treatment were compared. The survival rate decreased in proportion to the reduction of pH. DNA purified from D. radiodurans was then damaged by irradiation with gamma-rays at 0.22 kGy or 1 kGy. It was considered that the radioresistance of D. radiodurans was due to its high repair capability, rather than any specificity of DNA structure. Purified D. radiodurans DNA was resistant to heating up to 90ûC at neutral pH. However, marked DNA damage occurred when it was heated at pH values below 5.0. Then, DNA labeled with [3H]adenine was examined. Treatment at lower pH and higher temperature resulted in release of more adenine base, i.e., the purine ring, from the DNA molecules. Therefore, we assumed that the decrease in survival of D. radiodurans in vivo and damage to its DNA in vitro by acid heating were due to the release of adenine and guanine from the DNA, i.e., depurination.

Acids↗
PubMed2003

Production of superoxide dismutase by Deinococcus radiophilus.

The production of superoxide dismutase (SOD) varied in Deinococcus radiophilus, the UV resistant bacterium, depending upon different phases of growth, UV irradiation, and superoxide treatment. A gradual increase in total SOD activity occurred up to the stationary phases. The electrophoretic resolution of the SOD in cell extracts of D. radiophilus at each growth phase revealed the occurrence of MnSOD throughout the growth phases. The SOD profiles of D. radiophilus at the exponential phase received oxidative stress by the potassium superoxide treatment or UV irradiation also revealed the occurrence of a single SOD. However, these treatments caused an increase in SOD activity. The data strongly suggest that D. radiophilus has only one species of SOD as a constitutive enzyme, which seems to be a membrane-associated protein.

Cell Membrane↗
PubMed2000

Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation.

The genome of the radiation-resistant eubacterium Deinococcus radiodurans contains an ortholog of an RNA-binding protein known as the Ro 60-kD autoantigen. This protein, which was previously identified only in higher eukaryotes, is normally bound to small RNAs known as Y RNAs. We show that the Ro protein ortholog Rsr contributes to the resistance of D. radiodurans to UV irradiation. Rsr binds several small RNAs, encoded upstream of rsr, that accumulate following UV irradiation. One of these RNAs resembles a Y RNA. These results suggest that Ro RNPs could similarly contribute to the recovery of higher cells following UV irradiation.

Amino Acid Sequence↗
PubMed1991

Evidence against enhancement of the radioresistance of Escherichia coli by cloned Deinococcus radiodurans DNA.

Deinococcus radiodurans genomic DNA, introduced to Escherichia coli in cloning vectors, has been reported to produce radioresistant E. coli that can be selected by gamma irradiation. In this report prior results are reassessed experimentally, and additional studies are presented. Results to date suggest that the acquired radioresistance of E. coli selected by gamma irradiation does not stem from expression of stable plasmid-encoded D. radiodurans sequences, and that acquired radioresistance is not readily transmitted to naive (unirradiated) E. coli by transformation of plasmid recovered from the radioresistant isolates. Several interpretations are discussed.

DNA, Bacterial↗
PubMed1989

Deinococcus radiodurans DNA increases the radiation resistance of Escherichia coli.

A genomic DNA library of Deinococcus radiodurans DNA has been prepared using the plasmid vector pBR322. The recombinant plasmid was used to transform a more radiation-sensitive organism, Escherichia coli RR1. Following selection of transformed organisms by their ability to grow on ampicillin, radiation-resistant organisms were selected by irradiation with 137Cs gamma radiation. Increased radiation resistance correlates with the presence of a 3-kb fragment of DNA in these cells which is derived from D. radiodurans.

Escherichia coli↗
PubMed1989

Evidence for the cloning of Deinococcus radiodurans DNA fragments that render Escherichia coli radiation resistant.

DNA from the radiation-resistant bacterium Deinococcus radiodurans was isolated and used to generate a cosmid library. This cosmid library was grown in Escherichia coli and radiation-resistant E. coli were isolated. Following exposure to 1000 Gy the radiation-resistant transformants exhibited a survival of approximately 10(-1) instead of the 10(-11) exhibited by the nontransformed E. coli. Smaller fragments of DNA were subcloned from the radiation-resistant E. coli; these fragments bestow similar levels of radiation resistance (ratio of slopes = 6.8) to native E. coli upon transfection.

Cloning, Molecular↗
PubMed1989

Structure of a novel glucosamine-containing phosphoglycolipid from Deinococcus radiodurans.

The structure of a major novel lipid from Deinococcus radiodurans has been determined to be 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(alpha-N-acetylglucosaminyl) -N- glyceroyl alkylamine. The lipid was shown to contain a phosphatidic acid backbone by digestion with phospholipase A2 and by hydrolysis with hydrofluoric acid. Using a combination of chemical and NMR spectroscopic techniques, the structure of this lipid was elucidated and compared with that of a similar phosphoglycolipid reported earlier (Anderson, R., and Hansen, K. (1985) J. Biol. Chem. 260, 12219-12223) in which galactose was found in place of N-acetylglucosamine. The fatty acid compositions of the two lipids were similar.

Acetylation↗
PubMed1985

Structure of a novel phosphoglycolipid from Deinococcus radiodurans.

The chemical structure of a major phosphoglycolipid from Deinococcus radiodurans has been shown to be 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(alpha-galactosyl)-N-D-gl yceroyl alkylamine. By infrared spectroscopy, the lipid was shown to contain both carbonyl ester and amide linkages. Chemical analysis demonstrated a molar ratio of fatty acid, carbohydrate, and phosphorus of 2:1:1. The lipid was shown to contain an sn-3-phosphatidic acid backbone by digestion with phospholipase A2. Phosphodiester bond cleavage of the lipid with hydrofluoric acid liberated a component which contained galactose, glyceric acid, and alkylamines. Using NMR and permethylation/hydrolysis procedures, galactose was shown to be linked alpha-glycosidically to the 3-O-position of glyceric acid.

Chemical Phenomena↗
PubMed1994

Plasmids in several strains of Deinococcus radiodurans.

Deinococcus radiodurans is known as a radioresistant bacterium. For the construction of the shuttle vector, plasmids of this bacterium were isolated and investigated. At least two new plasmids in the cells of D. radiodurans MR1, KR1 and Sark were found in this experiment. However, a common plasmid among MR1, KR1 and Sark strains could not be found. These plasmids would be useful for the construction of the shuttle vector for cloning radioresistant genes of this bacterium.

DNA, Bacterial↗
PubMed1994

DNA deoxyribophosphodiesterase and an activity that cleaves DNA containing thymine glycol adducts in Deinococcus radiodurans.

Deinococcus radiodurans is the most radioresistant bacterium discovered to date. Recently it has been demonstrated that this organism contains the DNA repair enzyme uracil-DNA glycosylase and an apurinic/apyrimidinic (AP) endonuclease that may function as part of a DNA base excision repair pathway. We demonstrate here that a DNA deoxyribophosphodiesterase activity that acts on incised AP sites in DNA to remove deoxyribose-phosphate groups is found in lysates prepared from D. radiodurans cells. The partially purified activity was found to be smaller in size than the E. coli dRpase activity, with an estimated molecular weight of 25-30 kDa. In addition, an activity that recognizes and cleaves DNA containing thymine glycols was also detected, with a molecular weight of approximately 30 kDa. This enzyme may be analogous to the thymine glycol glycosylase/AP lyase endonuclease III of E. coli.

Chromatography, High Pressure Liquid↗
PubMedDate not supplied

Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans.

The results of previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groESL and dnaKJ operons and proteases such as clpB are induced in response to elevated temperature. In addition, previous qualitative whole-cell mass spectrometric studies conducted under heat shock conditions indicated global changes in the D. radiodurans proteome. To enable the discovery of novel heat shock inducible proteins as well as gain greater biological insight into the classical heat shock response at the protein level, we undertook the global whole-cell FTICR mass spectrometric proteomics study reported here. We have greatly increased the power of this approach by conducting a large number of replicate experiments in addition to taking a semiquantitative approach to data analysis, finding good reproducibility between replicates. Through this analysis, we have identified with high confidence a core set of classical heat shock proteins whose expression increases dramatically and reproducibly in response to elevated temperature. In addition, we have found that the heat shock proteome includes a large number of induced proteins that have not been identified previously as heat responsive, and have therefore been designated as candidate responders. Finally, our results are consistent with the hypothesis that elevated temperature stress could lead to cross-protection against other related stresses.

Adaptation, Physiological↗