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PubMed1999

A data analysis of the irradiation parameter D10 for bacteria and spores under various conditions.

This paper provides approximate estimates for the irradiation parameter D10 to globally predict the effectiveness of any irradiation process. D10 is often reported to depend on many specific factors, implying that D10 cannot be estimated without exact knowledge of all factors involved. For specific questions these data can of course be useful but only if the conditions reported exactly match the specific question. Alternatively, this study determined the most relevant factors influencing D10, by quantitatively analyzing data from many references. The best first step appeared to be a classification of the data into vegetative bacteria and spores. As expected, spores were found to have significantly higher D10 values (average 2.48 kGy) than vegetative bacteria (average 0.762 kGy). Further analyses of the vegetative bacteria confirmed the expected extreme irradiation resistance of nonpathogenic Deinococcus radiodurans (average 10.4 kGy). Furthermore the analysis identified Enterococcus faecium, Alcaligenes spp., and several members of the Moraxella-Acinetobacter group as having very high resistance at very low temperatures (average 3.65 kGy). After exclusion of high- and low-resistance spores and some specific conditions showing relevant high or low D10 values, the average for spores was estimated to be 2.11 kGy. For vegetative bacteria this average was estimated to be 0.420 kGy. These approximate estimates are not definite, as they depend on the data used in the analyses. It is expected that inclusion of more data will not change the estimates to a great extent. The approximate estimates are therefore useful tools in designing and evaluating irradiation processes.

Acinetobacter↗
PubMed2000

Resistance to apoptosis in prostate cancer cells.

Androgen-independent prostate cancer cells are remarkably resistant to therapeutic agents that work by triggering apoptosis via the caspase cascade. The recent sequencing of the entire genome of one of the most radiation-resistant organisms known, Deinococcus radiodurans, yields some insight into how prostate cancer cells might mount such resistance to apoptosis. Rather than being attributable to any one mechanism, the extreme radiation resistance of D. radiodurans appears to reflect the expression of a large number of different systems capable of preventing, repairing, or tolerating DNA damage and a very high degree of redundancy in these systems. Many molecular alterations that may influence the threshold for apoptosis have already been described in advanced prostate cancer; changes in bcl-2, p53, and the androgen receptor have been the most extensively studied. Current information is consistent with the concept that individual prostate cancer cells express multiple antiapoptotic mechanisms. This conclusion implies that it will not be possible to enhance cellular sensitivity to therapeutics that activate apoptosis by disabling just one target in a pathway, because other proteins are likely to be available to assume its function. Likewise, even elimination of a whole pathway may have little effect on sensitivity because cellular viability is protected by so many different mechanisms. However, where molecular changes have a phenotypic consequence, they offer a window of opportunity for the development of novel therapeutic strategies. One such example is a recently identified small organic compound that can inhibit p53 function and thus protect normal tissues against radiation-induced apoptosis without impairing killing of p53-deficient tumor cells.

Androgen Antagonists↗
PubMedDate not supplied

[Unique properties of highly radioresistant bacteria].

In connection with the Chernobyl Nuclear Power Plant (ChNPP) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. The analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. The extreme radioresistant bacteria are represented by the Deinococcus species, which form a group phylogenetically close to the line Thermus-Meiothermus. Other radioresistant bacteria are the representatives of the genera Rubrobacter, Methylobacterium, Kocuria, Bacillus and some archebacteria. Data on natural habitats, of radioresistant bacteria are not numerous. In a number of cases it is difficult to distinguish their natural habitats, as they were isolated from the samples which were previously exposed to X-ray or gamma-irradiation, or from the ecosystems with the naturally raised radioactivity. To understand the strategy of survival of radioresistant bacteria, we briefly reviewed the mechanism of action of various species of radiation on cells and macromolecules; physiological signs of the cell damage caused by radiation; mechanisms eliminating (repairing) these damages. More details on mechanisms of the DNA repair in D. radiodurans are described. The extreme resistance of D. radiodurans to the DNA damaging factors is defined by 1) repair mechanisms which fundamentally differ from those in other procaryotes; 2) ability to increase the efficiency of a standard set of the DNA repairing proteins. Literary and own data on the effect of radiation on survival of various groups of bacteria in natural ecosystems are summarized. The ecological consequences of the ChNPP accident for soil bacteria in this region were estimated. The reduction of the number of soil bacteria and recession of microbial diversity under the effect of anthropogenic radiation was shown.

Bacteria↗
PubMed1995

ERA-experiment "Space Biochemistry".

The general goal of the experiment was to study the response of anhydrobiotic (metabolically dormant) microorganisms (spores of Bacillus subtilis, cells of Deinococcus radiodurans, conidia of Aspergillus species) and cellular constituents (plasmid DNA, proteins, purple membranes, amino acids, urea) to the extremely dehydrating conditions of open space, in some cases in combination with irradiation by solar UV-light. Methods of investigation included viability tests, analysis of DNA damages (strand breaks, DNA-protein cross-links) and analysis of chemical effects by spectroscopic, electrophoretic and chromatographic methods. The decrease in viability of the microorganisms was as expected from simulation experiments in the laboratory. Accordingly, it could be correlated with the increase in DNA damages. The purple membranes, amino acids and urea were not measurably effected by the dehydrating condition of open space (in the dark). Plasmid DNA, however, suffered a significant amount of strand breaks under these conditions. The response of these biomolecules to high fluences of short wavelength solar UV-light is very complex. Only a brief survey can be given in this paper. The data on the relatively good survival of some of the microorganisms call for strict observance of COSPAR Planetary Protection Regulations during interplanetary space missions.

Argon↗
PubMed2001

The emerging impact of genomics on the development of biological weapons. Threats and benefits posed by engineered extremophiles.

During the past decades, representatives of Archaea, Bacteria, and Protista have been found thriving in many newly discovered extremely hostile habitats, which hitherto were regarded as too harsh to harbor life. To illustrate how an extremophile could be targeted for development as a biowarfare agent, an example is presented describing current advances in engineering Deinococcus radiodurans. Using a generally applicable combination of conventional genetic engineering and genomic informatics, this extremely radiation-resistant and environmentally robust bacterium is being developed for biotechnology.

Archaea↗
PubMed2002

Synergistic cell-killing effect of a combination of hyperthermia and heavy ion beam irradiation: in expectation of a breakthrough in the treatment of refractory cancers (review).

We studied the sensitivity against heavy ion beam and hyperthermia on radioresistant procaryote, Deinococcus radiodurans, for the purpose of cancer therapy. First, we examined the decrease of the survival rate and molecular weight of DNA purified from this cell by acid heat treatment. These decreases were recognized by heating at 55 degrees C below pH 5.0. Then, 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 purine rings from the phosphodiester backbone of DNA molecules, i.e., depurination. Second, we investigated the relation between LET (linear energy transfer) and RBE (relative biological effectiveness) on D. radiodurans dry and wet cells using AVF cyclotron at the TIARA facility of JAERI-Takasaki, Japan. These cells were irradiated with carbon (12C5+) ion beam at LET of about 100 keV/microm, neon (20Ne8+) ion beam at LET of about 300 keV/microm and oxygen (16O6+) ion beam at LET of about 400 keV/microm. The peak in the figure of the relation between LET and RBE value was found to increase according to the increase of LET value from 100 keV/microm. Third, we conducted combination treatment with 4.8 kGy of alpha-particles, i.e., boron 10 neutron captured beam induced by Kyoto University Research Nuclear Reactor operated at 5 MW, and hyperthermia at 52 degrees C, which caused the synergistic killing effect on D. radiodurans wet cells. However, being dissimilar to the case of gamma-irradiation, the interval incubation at 30 degrees C in the medium between both treatments could inhibit the recovery of survival.

Combined Modality Therapy↗
PubMed2002

An inventory of genes encoding RNA polymerase sigma factors in 31 completely sequenced eubacterial genomes.

Sigma factors are important elements involved in transcriptional regulation of gene expression by conferring promoter specificity to RNA polymerase. The number of sigma factor encoding genes in 31 completely sequenced bacterial genomes were compared. Two unrelated families of sigma factors, the sigma70- and the sigma54-family were identified previously. The sigma70-family can be further subdivided into two distantly related groups: the sigma70 subfamily and the poorly characterized ECF subfamily. A total of 215 sigma factors could be attributed to these subfamilies. The construction of phylogenetic trees allows subclassifications of sigma factor encoding genes within the subfamilies. With the exception of Deinococcus radiodurans, all species possess a housekeeping primary sigma factor. Free-living species possess a higher number of both sigma70-type and ECF alternative sigma factors than pathogens or symbionts associated with animals. Different bacterial species exhibit large differences in the number of alternative sigma factor encoding genes and consequently huge flexibility in their transcriptional regulatory patterns. Transcriptional regulation in terms of regulons controlled by alternative sigma factors is a late evolving phenomenon. The current nomenclature for sigma factor encoding genes is confusing and should be revised.

Bacteria↗
PubMed2002

A phylogenomic study of the general stress response sigma factor sigmaB of Bacillus subtilis and its regulatory proteins.

Regulation of expression of the general stress regulon of Bacillus subtilis is mediated by the activation of the alternative sigma factor sigmaB. Activation of sigmaB is accomplished by a complex regulatory network involving protein-protein interactions and reversible protein phosphorylation. PSI-BLAST searches were performed and phylogenetic trees for sigmaB and its regulatory proteins were constructed. Occurrence of sigmaB is restricted to a small group of gram-positive bacteria (Bacillus, Staphylococcus, Listeria). Related sigma factors also involved in stress responses are present in Mycobacterium tuberculosis, Streptomyces species and even in cyanobacteria (Synechocystis species). Putative regulatory proteins found in several other bacterial species can be broadly catagorized into three categories: Anti sigma factors, anti-anti sigma factors and phosphatases. Anti sigma factors are able to bind to sigma factors and are also kinases of anti sigma factor antagonists. Only in their nonphosphorylated state, these antagonists are able to bind to the anti sigma factor. Phosphorylated antagonists can be dephosphorylated by PP2C phosphatases. These phosphatases are of pivotal importance for activation of the sigma factor. Different phosphatases identified in this search contain a wide variety of domains found in signal transducing proteins (PAS/PAC, GAF, REC, HATase_c, HAMP). The HATPase_c domain found in several phosphatases most probably constitutes a serine/threonine kinase domain of anti sigma factors. Such proteins are most probably bifunctional anti-anti sigma factor kinases and phosphatases. The regulatory network of anti-anti sigma factors anti sigma factors and phosphatases is probably ancient and most likely evolved from a structurally similar network found in the Deinococcus radiodurans genome. In completely sequenced genomes of several bacterial species, some elements of the network are missing. The N-terminus of RsbU, a phosphatase activated in response to environmental stress exhibits similarities to a region in the beta chain of phenylalanyl-tRNA synthetases.

Amino Acid Sequence↗
PubMed1998

Studies on Etching and Damage Action of Low Energy Ion Beam on icrobial Cells.

The action of 20 keV N(+) ion on Deinococcus radiodurans and E. coli was investigated by means of scanning electron microscope(SEM) and electron spin resonance(ESR). The results showed that ion implantation exerted direct etching damage and indirect free radicals action by energy deposition on the cells of the two microbes. The DNA damage and biological mutation resulted mainly from the etching action of injected ions; the free radicals resulted chiefly in the damage of peroxidation of biological macromolecule and membrane lipids except of DNA. Moreover, the damages in D. radiodurans and E. coli by etching and free radicals action aggravated gradually with increasing doses. The sedimentation patterns of tritiated DNA materials in D. radiodurans by neutral sucrose gradient(50-200 g/L) indicated that DNA sedimentation peak of cells incubated for 4 h did not resume control state after the implantation of 60x10(15) N(+) ions injection per cm(2), proving that the direct action of implanted ions led to DNA damage. The survival rate of the implanted D. radiodurans and E. coli lowered after 2 mol/L caffeine and 0.5 mmol/L EDTA treatment, confirming that the etching action of implanted ions was the direct cause resulting in DNA damage and organism mutation.

Journal Article↗
PubMedDate not supplied

[Specificity of bacterial response to variation of isotopic composition of water].

Culture growth of bacteria with different membrane lipid composition was studied in liquid media with different isotope content of water. The concentration of deuterium in water was varied from 0.01 to 90%. It was shown that large concentrations of deuterium cause the inhibition of all cultures except Deinococcus radiodurans, the most stable living cell. Two cultures, Methylobacterium organophilum and Hyphomonas jannaschiana, showed a pronounced activation at a deuterium concentration of 0.01%. At higher deuterium concentrations, the inhibition of culture growth was observed. The strains Renobacter vacuolatum, Arcocella aquatica NO502 and Caulobacter crescentus did not show any significant effect at low concentrations of deuterium.

Bacterial Physiological Phenomena↗
PubMed2004

Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.

The Aquificales species are presently believed to be the earliest branching lineage within Bacteria. However, the branching order of this group in different phylogenetic trees is highly variable and not resolved. In the present work, the phylogenetic placement of Aquificales was examined by means of a cladistic approach based on the shared presence or absence of definite signature sequences (consisting of conserved inserts or deletions) in many highly conserved and important proteins, e.g. RNA polymerase beta (RpoB), RNA polymerase beta (RpoC), alanyl-tRNA synthetase (AlaRS), CTP synthase, inorganic pyrophosphatase (PPase), Hsp70 and Hsp60. For this purpose, fragments of the above genes that contained the signature regions were cloned from different Aquificales species (Calderobacterium hydrogenophilum, Hydrogenobacter marinus, and Thermocrinis ruber) and the sequence data were compared with those available from all other species. The presence in Aquificales species of distinctive inserts in Hsp70 and Hsp60 that are not found in any Firmicutes, Actinobacteria, or Thermotoga-Clostridium species excluded them from these groups of Bacteria. The shared presence of prominent indels in the RpoB (>100 amino acids), RpoC (>100 amino acids) and AlaRS (4 amino acids) proteins, which are only found in the various Aquificales species, the Chlamydiae, the CFBG (Cytophaga-Flavobacteria-Bacteroides-green sulfur bacteria) group, and Proteobacteria, strongly suggests their placement within these groups of Bacteria. A specific relationship between Proteobacteria and Aquificales is suggested by the presence in inorganic pyrophosphatase of a 2-amino-acid insert that is uniquely found in these phyla. However, the Aquificales species lacked a number of other protein signatures (e.g. indels in CTP synthase and Hsp70) that are characteristic of Proteobacteria, indicating that they constitute a distinct phylum related to Proteobacteria. These results provide strong and consistent evidence that the Aquificales diverged after the branching of Firmicutes, Actinobacteria, Thermotoga, Deinococcus-Thermus, green nonsulfur bacteria, Cyanobacteria, Spirochetes, Chlamydiae, and CFBG group, but before the emergence of the Proteobacteria.

Alanine-tRNA Ligase↗
PubMed2004

[Analysis of bacterial composition of the pink mat from spectacles hot spring in Tengchong by culture-independent approach].

The bacterial composition of the pink mat was studied by culture-independent approach. 23 complete 16S rDNA sequences were obtained. According to the sequences alignment and analysis of comparability, the bacteria of the pink mat was consisted of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacter, Deinococcus-thermus, Aquificals. And compared with bacterial composition of the mats from Octopus spring in Yellowstone Park and Haegindi and Fluidir spring, Olkelduhals, Grensdalur spring in Iceland, the pink mat in spectacles spring had highest bacterial diversity among them because it perhaps included lots of bacteria at lower temperature. And the result indicated the same community lived in the same niche and Aquficales was dominant group among bacterial composition of the mat in higher temperature and near-neutral hot spring.

Bacteria↗
PubMedDate not supplied

Physiological changes induced in four bacterial strains following oxidative stress.

In order to study the behaviour and resistance of bacteria under extreme conditions, physiological changes associated with oxidative stress were monitored using flow cytometry. The study was conducted to assess the maintenance of membrane integrity and potential as well as the esterase activity, the intracellular pH and the production of superoxide anions in four bacterial strains (Ralstonia metallidurans, Escherichia coli, Shewanella oneidensis and Deinococcus radiodurans). The strains were chosen for their potential usefulness in bioremediation. Suspensions of R. metallidurans, E. coli, S. oneidensis and D. radiodurans were submitted to 1 h oxidative stress (H2O2 at various concentrations from 0 to 880 mM). Cell membrane permeability (propidium iodide) and potential (rhodamine-123, 3,3'-dihexyloxacarbocyanine iodide), intracellular esterase activity (fluorescein diacetate), intracellular reactive oxygen species concentration (hydroethidine) and intracellular pH (carboxyflurorescein diacetate succinimidyl ester (5(6)) were monitored to evaluate the physiological state and the overall fitness of individual bacterial cells under oxidative stress. The four bacterial strains exhibited varying sensitivities towards H2O2. However, for all bacterial strains, some physiological damage could already be observed from 13.25 mM H2O2 onwards, in particular with regard to their membrane permeability. Depending on the bacterial strains, moderate to high physiological damage could be observed between 13.25 mM and 220 mM H2O2. Membrane potential, esterase activity, intracellular pH and production of superoxide anion production were considerably modified at high H2O2 concentrations in all four strains. In conclusion, we show that a range of significant physiological alterations occurs when bacteria are challenged with H2O2 and fluorescent staining methods coupled with flow cytometry are useful for monitoring the changes induced not only by oxidative stress but also by other stresses like temperature, radiation, pressure, pH, etc....

Bacteria↗
PubMedDate not supplied

[Polyamines in representative taxa of coryneform and other bacteria].

The composition of polyamines is studied for the first time in representatives of the genus Micrococcus and taxon "conglomeratus", strains Staphylococcus aureus CCM 209, Deinococcus erythromyxa CCM 706 as well as of Erwinia carotovora ATCC 15713 polyamines, which are not extracted by perchloric acid. Considerable amounts of spermine and rarely of spermidine are revealed in cells of Gram positive microorganisms, that differs them from Gram negative bacteria possessing high concentrations of putrescine, spermidine and their derivatives. A procedure is developed for detection of polyamines in cells of Gram positive microorganisms. It is recommended to use the hydrolysis of their cells by 6N HCl for 4 at 120 degrees C or for 8-10h at 100 degrees C with the subsequent electrophoretic separation. Putrescine, as well as comparable with it amount of agmatine and spermidine traces are found in Erwinia carotovora ATCC 15713 cell hydrolyzates, whereas putrescine and agmatine traces are found in perchloric extracts of intact cells. Spermine is not observed in the cells. The binding of polyamines with biopolymers of cells of Gram positive bacteria and their difference by the given character from the Gram negative procaryotes are under discussion.

Actinomycetales↗
PubMedDate not supplied

[High resistance of some oligotrophic bacteria to ionizing radiation].

The resistance against ionizing radiation of seven cultures of oligotrophic and eutrophic bacteria was investigated in the interval 0-360 Gr/h. It is determine that all of tested bacteria are distributed into three groups according to the lever of their resistance. Most resistant were: Methylobacterium organophilum, Pedodermatophilus halotolerans (LD50 = 270 Cr/h). These organisms are close to Deinococcus radiodurans in the survival. Middle resistance shown water-born ring-forming bacteria Flectobacillus major, Arcocella aquatica (LD50 = 173 and 210 Gr/h respectively). High sensitive were eutrophs: Pseudomonas fluorescens, Escherichia coli (LD50 = 43 and 38 Gr/h respectively). By use of X-ray microanalysis was shown that after the radiation potassium content in cell was increased and calcium content was decreased. The elements content in the cells of eutrophs (Escherichia coli) remains without change. In present paper are also discussed possible mechanisms of the resistance of oligotrophs against gamma-irradiation.

Bacteria↗
PubMed2002

Gene expression profiling using advanced mass spectrometric approaches.

In the era of systems biology, computational and high-throughput experimental biological approaches are increasingly being combined to provide global snapshots of entire genomes and proteomes under tissue- and disease-specific conditions. The aim is to identify proteins changing in concentration and/or post-translational state and/or location, and develop a better molecular level understanding of the operation of biological systems. Here we describe an approach for comparative proteomics that builds upon the combination of high-performance nano-scale separations with the high-mass measurement accuracy, mass-resolving power and sensitivity of Fourier transform ion cyclotron resonance mass spectrometry to provide broad dynamic range, comprehensive and quantitative proteome measurements.

Amino Acid Sequence↗
PubMed2003

Improved peptide sequencing using isotope information inherent in tandem mass spectra.

We demonstrate here the use of natural isotopic 'labels' in peptides to aid in the identification of peptides with a de novo algorithm. Using data from ion trap tandem mass spectrometric (MS/MS) analysis of 102 tryptic peptides, we have analyzed multiple series of peaks within LCQ MS/MS spectra that 'spell' peptide sequences. Isotopic peaks from naturally abundant isotopes are particularly prominent even after peak centroiding on y- and b-series ions and lead to increased confidence in the identification of the precursor peptides. Sequence analysis of the MS/MS data is accomplished by finding sequences and subsequences in a hierarchical manner within the spectra.

Algorithms↗
PubMed2003

Nanoscale proteomics.

Efforts to develop a liquid chromatography (LC)/mass spectrometry (MS) technology for ultra-sensitive proteomics studies (i.e., nanoscale proteomics) are described. The approach combines high-efficiency nanoscale LC (separation peak capacity of approximately 10(3); 15-microm-i.d. packed capillaries with flow rates of 20 nL min(-1), the optimal separation linear velocity) with advanced MS, including high-sensitivity and high-resolution Fourier transform ion cyclotron resonance MS, to perform both single-stage MS and tandem MS (MS/MS) proteomic analyses. The technology enables broad protein identification from nanogram-size proteomics samples and allows the characterization of more abundant proteins from sub-picogram-size samples. Protein identification in such studies using MS is demonstrated from <75 zeptomole of a protein. The average proteome measurement throughput is approximately 50 proteins h(-1) using MS/MS during separations, presently requiring approximately 3 h sample(-1). Greater throughput (approximately 300 proteins h(-1)) and improved detection limits providing more comprehensive proteome coverage can be obtained by using the "accurate mass and time" tag approach developed in our laboratory. This approach provides a dynamic range of at least 10(6) for protein relative abundances and an improved basis for quantitation. These capabilities lay the foundation for studies from single or limited numbers of cells.

Amino Acid Sequence↗