RadB acts in homologous recombination in the archaeon Haloferax volcanii,consistent with a role as recombination mediator

Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination – it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination mediator, which it does by inducing a conformational change in RadA and thereby promoting its polymerisation on DNA.     

Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations

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Rapid Analysis of Protein Structure and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

An automated approach for the rapid analysis of protein structure has been developed and used to study acid-induced conformational changes in human growth hormone. The labeling approach involves hydrogen/deuterium exchange (H/D-Ex) of protein backbone amide hydrogens with rapid and sensitive detection by mass spectrometry (MS). Briefly, the protein is incubated for defined intervals in a deuterated environment. After rapid quenching of the exchange reaction, the partially deuterated protein is enzymatically digested and the resulting peptide fragments are analyzed by liquid chromatography mass spectrometry (LC-MS). The deuterium buildup curve measured for each fragment yields an average amide exchange rate that reflects the environment of the peptide in the intact protein. Additional analyses allow mapping of the free energy of folding on localized segments along the protein sequence affording unique dynamic and structural information. While amide H/D-Ex coupled with MS is recognized as a powerful technique for studying protein structure and protein–ligand interactions, it has remained a labor-intensive task. The improvements in the amide H/D-Ex methodology described here include solid phase proteolysis, automated liquid handling and sample preparation, and integrated data reduction software that together improve sequence coverage and resolution, while achieving a sample throughput nearly 10-fold higher than the commonly used manual methods.     

Correlation between the order parameter and the steady-state fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene and an evaluation of membrane fluidity

In this paper it is shown that for 1,6-diphenyl-1,3,5-hexatriene there exists a simple analytical relation between the orientational order parameter and the steady-state fluorescence anisotropy. This relation is derived on semi-empirical grounds. The order parameter and the true microviscosity for membranes as calculated from steady-state measurements are evaluated. For biological membranes the estimation of the order parameter from steady-state experiments is feasible, but the evaluation of the true microviscosity is not reliable. Also, the physiological relevance of the order parameter is discussed.     

Permeability of the foetal capillary endothelium of the guinea-pig placenta to haem proteins of various molecular sizes

Summary Haem proteins of different molecular sizes were perfused into the foetal circulation of the guinea-pig placenta to study the permeability of the foetal endothelium.The smallest molecules tested, microperoxidase (a_e 1.0 nm) and cytochrome C (a_e 1.5 nm), readily penetrated the endothelium; tracer-reaction product was found in the subendothelial space of the capillaries. However, there was no uptake of these two tracers into the syncytiotrophoblast layer of the placenta. An intermediate-sized molecule, myoglobin (a_e 1.7 nm), produced only a weak reaction product in the subendothelial space even when perfused at high concentration. The largest molecule tested, haemoglobin (a_e 2.8 nm), did not penetrate the foetal endothelium at any of the concentrations employed.The foetal capillary endothelium thus provided a barrier to protein penetration from the foetal circulation, dependent on molecular size. There was evidence that the site of this barrier was located in the lateral intercellular spaces between the endothelial cells.The syncytiotrophoblast of this haemomonochorial placenta provided an almost absolute barrier to protein penetration from the foetal circulation. As other workers have described maternal-to-foetal transmission of proteins across this layer in the guinea-pig, a working hypothesis of the role of endothelium and syncytiotrophoblast in maternal/foetal protein exchange is discussed.     

Genetic variation for foot-rot and Fusarium head-blight resistances among full-sib families of a self-incompatible winter rye (Secale cereale L.) population

The amount of genetic variation for resistance to foot rot caused by Pseudocercosporella herpotrichoides, Fusarium spp., and Microdochium nivale and for resistance to head blight caused by Fusarium culmorum are important parameters when estimating selection gain from recurrent selection in winter rye. One-hundred and eighty-six full-sib families of the selfincompatible population variety Halo, representing the Petkus gene pool, were tested for foot-rot resistance at five German location-year combinations (environments) and for head-blight resistance in three environments with artificial inoculation in all but one environment. Foot-rot rating was based on 25 stems per plot scored individually on a 1–9 scale. Head-blight resistance was plotwise scored on a 1–9 scale and, additionally, grain-weight per spike was measured relative to the non-inoculated control plots. Significant estimates of genotypic variance and medium-sized heritabilities (h ²=0.51–0.69) were observed in the combined analyses for all resistance traits. In four out of five environments, the amount of genetic variance was substantially smaller for foot-rot than for head-blight rating. Considerable environmental effects and significant genotype-environment interactions were found for both foot-rot and head-blight resistance. Coefficients of error-corrected correlation among environments were considerably closer than phenotypic correlations. No significant association was found between the resistances to both diseases (r=-0.20 to 0.17). In conclusion, intra-population improvement by recurrent selection should lead to substantial higher foot-rot and head-blight resistances due to significant quantitative genetic variation within Halo. Selection should be carried out in several environments. Lack of correlation between foot-rot and head-blight resistance requires separate infection tests for improving both resistances.     

The Bioutilization of Thiodiglycol (a Detoxication Product of Mustard Gas): Isolation of Degrading Strains and Investigation of Degradation Conditions

The Alcaligenes xylosoxydans subsp.denitrificans strain TD1 capable of degrading thiodiglycol (TDG), a product of mustard gas hydrolysis, was isolated from soil contaminated with breakdown products of this chemical warfare agent. The selected stable variant of TD1 (strain TD2) can grow on TDG with a lag phase of 4–8 h and a specific growth rate of 0.04–0.045 h^–1. Optimal conditions for the biodegradation of TDG (pH, the concentration of TDG in the medium, and specific substrate loading) were determined. TDG was found to be degraded with the formation of diglycolsulfoxide and thiodiglycolic acid as intermediate products. The data obtained can be used to develop approaches to the bioremediation of mustard gas–contaminated soils.