Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group

Several group I introns have been previously found in strains of the Bacillus cereus group at three different insertion sites in the nrdE gene of the essential nrdIEF operon coding for ribonucleotide reductase. Here, we identify an uncharacterized group IA intron in the nrdF gene in 12 strains of the B. cereus group and show that the pre-mRNA is efficiently spliced. The Bacillus thuringiensis ssp. pakistani nrdF intron encodes a homing endonuclease, denoted I-BthII, with an unconventional GIY-(X)₈-YIG motif that cleaves an intronless nrdF gene 7 nt upstream of the intron insertion site, producing 2-nt 3′ extensions. We also found four additional occurrences of two of the previously reported group I introns in the nrdE gene of 25 sequenced B. thuringiensis and one B. cereus strains, and one non-annotated group I intron at a fourth nrdE insertion site in the B. thuringiensis ssp. Al Hakam sequenced genome. Two strains contain introns in both the nrdE and the nrdF genes. Phylogenetic studies of the nrdIEF operon from 39 strains of the B. cereus group suggest several events of horizontal gene transfer for two of the introns found in this operon.     

Semiquinone-induced Maturation of Bacillus anthracis Ribonucleotide Reductase by a Superoxide Intermediate

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides, and represent the only de novo pathway to provide DNA building blocks. Three different classes of RNR are known, denoted I-III. Class I RNRs are heteromeric proteins built up by α and β subunits and are further divided into different subclasses, partly based on the metal content of the β-subunit. In subclass Ib RNR the β-subunit is denoted NrdF, and harbors a manganese-tyrosyl radical cofactor. The generation of this cofactor is dependent on a flavodoxin-like maturase denoted NrdI, responsible for the formation of an active oxygen species suggested to be either a superoxide or a hydroperoxide. Herein we report on the magnetic properties of the manganese-tyrosyl radical cofactor of Bacillus anthracis NrdF and the redox properties of B. anthracis NrdI. The tyrosyl radical in NrdF is stabilized through its interaction with a ferromagnetically coupled manganese dimer. Moreover, we show through a combination of redox titration and protein electrochemistry that in contrast to hitherto characterized NrdIs, the B. anthracis NrdI is stable in its semiquinone form (NrdI_sq) with a difference in electrochemical potential of ∼110 mV between the hydroquinone and semiquinone state. The under anaerobic conditions stable NrdI_sq is fully capable of generating the oxidized, tyrosyl radical-containing form of Mn-NrdF when exposed to oxygen. This latter observation strongly supports that a superoxide radical is involved in the maturation mechanism, and contradicts the participation of a peroxide species. Additionally, EPR spectra on whole cells revealed that a significant fraction of NrdI resides in its semiquinone form in vivo, underscoring that NrdI_sq is catalytically relevant.     

Assembly of a fragmented ribonucleotide reductase by protein interaction domains derived from a mobile genetic element

Ribonucleotide reductase (RNR) is a critical enzyme of nucleotide metabolism, synthesizing precursors for DNA replication and repair. In prokaryotic genomes, RNR genes are commonly targeted by mobile genetic elements, including free standing and intron-encoded homing endonucleases and inteins. Here, we describe a unique molecular solution to assemble a functional product from the RNR large subunit gene, nrdA that has been fragmented into two smaller genes by the insertion of mobE, a mobile endonuclease. We show that unique sequences that originated during the mobE insertion and that are present as C- and N-terminal tails on the split NrdA-a and NrdA-b polypeptides, are absolutely essential for enzymatic activity. Our data are consistent with the tails functioning as protein interaction domains to assemble the tetrameric (NrdA-a/NrdA-b)(2) large subunit necessary for a functional RNR holoenzyme. The tails represent a solution distinct from RNA and protein splicing or programmed DNA rearrangements to restore function from a fragmented coding region and may represent a general mechanism to neutralize fragmentation of essential genes by mobile genetic elements.     

Peroxyl adduct radicals formed in the iron/oxygen reconstitution reaction of mutant ribonucleotide reductase R2 proteins from Escherichia coli

Catalytically important free radicals in enzymes are generally formed at highly specific sites, but the specificity is often lost in point mutants where crucial residues have been changed. Among the transient free radicals earlier found in the Y122F mutant of protein R2 in Escherichia coli ribonucleotide reductase after reconstitution with Fe2+ and O2, two were identified as tryptophan radicals. A third radical has an axially symmetric EPR spectrum, and is shown here using 17O exchange and simulations of EPR spectra to be a peroxyl adduct radical. Reconstitution of other mutants of protein R2 (i.e. Y122F/W48Y and Y122F/W107Y) implicates W48 as the origin of the peroxyl adduct. The results indicate that peroxyl radicals form on primary transient radicals on surface residues such as W48, which is accessible to oxygen. However, the specificity of the reaction is not absolute since the single mutant W48Y also gives rise to a peroxyl adduct radical. We used density functional calculations to investigate residue-specific effects on hyperfine coupling constants using models of tryptophan, tyrosine, glycine and cysteine. The results indicate that any peroxyl adduct radical attached to the first three amino acid alpha-carbons gives similar 17O hyperfine coupling constants. Structural arguments and experimental results favor W48 as the major site of peroxyl adducts in the mutant Y122F. Available molecular oxygen can be considered as a spin trap for surface-located protein free radicals.     

Bipolar resistivity profiling of 3D tissue culture

We describe a new low-cost technique for continuous monitoring of the thickness of biofilms and tissue cultures, and we demonstrate the advantage of using electrodes of different dimensions to probe different depths of a sample. We have used electric impedance spectroscopy to monitor keratinocyte stem cells (YF29) growing on an array of Ti/Pt coplanar microelectrodes. The thickness of the sample was reconstructed by fitting the measurements to theoretical curves. We have developed an algorithm for the rapid calculation of the resistance through a multilayered sample. This algorithm is based on conformal mapping and the serial partial capacitance technique. The validity of the technique was tested by measuring the sedimentation rate of an alumina powder. Sample thicknesses between 10 and 80 microm could be measured with a resolution of a few microns using the device.     

Comparing ambient, air-convection, and fluid-convection heating techniques in treating hypothermic burn patients, a clinical RCT

Background

Hypothermia in burns is common and increases morbidity and mortality. Several methods are available to reach and maintain normal core body temperature, but have not yet been evaluated in critical care for burned patients. Our unit's ordinary technique for controlling body temperature (Bair Hugger^®+ radiator ceiling + bed warmer + Hotline^®) has many drawbacks e.g.; slow and the working environment is hampered. The aim of this study was to compare our ordinary heating technique with newly-developed methods: the Allon?2001 Thermowrap (a temperature regulating water-mattress), and Warmcloud (a temperature regulating air-mattress).

Methods

Ten consecutive burned patients (> 20% total burned surface area and a core temperature < 36.0°C) were included in this prospective, randomised, comparative study. Patients were randomly exposed to 3 heating methods. Each treatment/measuring-cycle lasted for 6 hours. Each heating method was assessed for 2 hours according to a randomised timetable. Core temperature was measured using an indwelling (bladder) thermistor. Paired t-tests were used to assess the significance of differences between the treatments within the patients. ANOVA was used to assess the differences in temperature from the first to the last measurement among all treatments. Three-way ANOVA with the Tukey HSD post hoc test and a repeated measures ANOVA was used in the same manner, but included information about patients and treatment/measuring-cycles to control for potential confounding. Data are presented as mean (SD) and (range). Probabilities of less than 0.05 were accepted as significant.

Results

The mean increase, 1.4 (SD 0.6°C; range 0.6-2.6°C) in core temperature/treatment/measuring-cycle highly significantly favoured the Allon?2001 Thermowrap in contrast to the conventional method 0.2 (0.6)°C (range -1.2 to 1.5°C) and the Warmcloud 0.3 (0.4)°C (range -0.4 to 0.9°C). The procedures for using the Allon?2001 Thermowrap were experienced to be more comfortable and straightforward than the conventional method or the Warmcloud.

Conclusions

The Allon?2001 Thermowrap was more effective than the Warmcloud or the conventional method in controlling patients' temperatures.     

Flow-cytometric identification and follow-up of mice exposed to x-irradiation: Evaluation of a model system

An experimental model system is presented that allows the identification and follow-up of mice exposed to ionizing radiation using flow-cytometric measurements of peripheral blood cells. In an experiment, properties of peripheral blood cells were analysed with flow cytometry for a rapid identification of individuals exposed to radiation. Individuals were then followed longitudinally in an attempt to identify those developing neoplasias. Male CBA mice, 25 days old, were subjected to fractionated x-irradiation (4 × 1.31 Gy) to induce haematopoietic malignancies. By repeated blood sampling followed by flow cytometry, frequencies of micronucleated erythrocytes and of proliferating nucleated cells were determined. Neoplasias were diagnosed by histopathology. Five days after the end of radiation exposure, increased frequencies of proliferating cells, polychromatic erythrocytes and micronucleated normochromatic erythrocytes clearly distinguished the exposed group from the control group. Increased cell proliferation in peripheral blood cells could be used to identify animals with manifest tumours, although these animals were at a late stage of tumour development. Animals with thymic lymphoma (not generalized) could not be identified with the flow-cytometric parameters used. We consider that this model system has a potential use when a small number of risk individuals need to be identified and monitored within a large population.     

Heparin/Heparan sulfate domains in binding and signaling of fibroblast growth factor 8b

The role of heparin and heparan sulfate in the binding and signaling of fibroblast growth factors (FGFs) has been subject to intense investigation, but the studies have largely been confined to two species (FGF1 and FGF2) of the family with approximately 20 members. We have investigated the structural requirements for heparin/heparan sulfate in binding and activation of FGF8 (splice variant b). We present evidence that the minimal FGF8b-binding saccharide domain encompasses 5-7 monosaccharide units. The N-, 2-O-, and 6-O-sulfate substituents of heparin/heparan sulfate (HS) are all involved in the interaction, preferentially in the form of trisulfated IdoUA(2-OSO(3))-GlcNSO(3)(6-OSO(3)) disaccharide constituents. These structural characteristics resemble those described earlier for FGF1. By contrast, the saccharide structures required for the biological activity of FGF8b differed significantly from those characteristic for FGF1 and FGF2. Experiments with cells lacking active HS indicated that extended >/=14-mer heparin domains were needed to enhance cell proliferation and Erk phosphorylation by FGF8b, whereas in cells stimulated with FGF1 or FGF2 the corresponding responses were achieved by much shorter, 6-8-mer, oligosaccharides. Furthermore, still longer domains were needed to activate FGF8b in cells with "non-optimal" FGF receptor expression. Collectively, our data suggest that the heparin/HS structures enhancing the biological activity of FGFs were influenced by the FGF species involved as well as by the cellular composition of FGF receptors.     

Effects of pulsed magnetic fields on the developing mouse embryo

The influence of a pulsed magnetic field (PMF; sawtooth with 45-μs linear rise time and 5-μs decay time, peak strength of 15 μT, and frequency 20 pps) on the embryogenesis of CBA/S mice was investigated in five experiments based on a total of 707 exposed and 543 unexposed primigravidas. Sham and PMF exposures began on day 1 of gestation (experiments 1 and 2), on day 2 (experiment 3), on day 5 (experiment 4). and on day 7 (experiment 5): all exposures continued until day 19 post conception (p.c.) when they were terminated, at which time the following variables were measured: number of implants; number of placental resorptions; number of living fetuses; number of dead fetuses; number of malformations in living and dead fetuses; and length and body mass of living fetuses. Control dams were sham-exposed concurrently with corresponding. PMF-exposed dams. With the exception of experiment 5, in which exposure to PMF started on day 7 p.c., all groups of exposed mice had significantly more placental resorptions when compared with concurrent controls. The increased resorption rate was not reflected in a reduction in litter size or in the number of litters. A significant increase in malformed fetuses was not seen in any of the exposed groups, or when groups were pooled. Only in experiment 1 was the number of dead fetuses affected by exposure to PMF. The effect of PMF on the implantation rate was not significant. Body mass and length of exposed fetuses were significantly reduced only when the PMF treatment began on day 7 p.c. That PMF-treated mice had significantly more placental resorptions when exposure began on day 5 p.c. or earlier (before implantation), but not when exposure began on day 7 (after implantation), may indicate a causative pre-implantation effect. Because a PMF-induced increase in the number of resorptions has not been observed in other strains of mice, the effect might be strain-related. © 1993 Wiley-Liss, Inc.     

Ribonucleotide reduction - horizontal transfer of a required function spans all three domains

Background  

Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes. Each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class I RNRs have been identified in archaeal genomes, and classes II and III likewise appear rare across eukaryotes. In this study, we examine whether this distribution is best explained by presence of all three classes in the Last Universal Common Ancestor (LUCA), or by horizontal gene transfer (HGT) of RNR genes. We also examine to what extent environmental factors may have impacted the distribution of RNR classes.