Recessiveness and dominance in barley mutants deficient in Mg-chelatase subunit D, an AAA protein involved in chlorophyll biosynthesis

Mg-chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX at the first committed step of the chlorophyll biosynthetic pathway. It consists of three subunits: I, D, and H. The I subunit belongs to the AAA protein superfamily (ATPases associated with various cellular activities) that is known to form hexameric ring structures in an ATP-dependant fashion. Dominant mutations in the I subunit revealed that it functions in a cooperative manner. We demonstrated that the D subunit forms ATP-independent oligomeric structures and should also be classified as an AAA protein. Furthermore, we addressed the question of cooperativity of the D subunit with barley (Hordeum vulgare) mutant analyses. The recessive behavior in vivo was explained by the absence of mutant proteins in the barley cell. Analogous mutations in Rhodobacter capsulatus and the resulting D proteins were studied in vitro. Mixtures of wild-type and mutant R. capsulatus D subunits showed a lower activity compared with wild-type subunits alone. Thus, the mutant D subunits displayed dominant behavior in vitro, revealing cooperativity between the D subunits in the oligomeric state. We propose a model where the D oligomer forms a platform for the stepwise assembly of the I subunits. The cooperative behavior suggests that the D oligomer takes an active part in the conformational dynamics between the subunits of the enzyme.     

Production of a truncated soluble human semicarbazide-sensitive amine oxidase mediated by a GST-fusion protein secreted from HEK293 cells

Elevated levels of semicarbazide-sensitive amine oxidase (SSAO) activity have been observed in several human conditions such as congestive heart failure, diabetes mellitus, and inflammation. The reactive aldehydes and hydrogen peroxide produced by SSAO have been suggested to contribute to the progression of vascular complications associated with these conditions. In addition, SSAO activity has been shown to be involved in the leukocyte extravasation process at sites of inflammation. To facilitate characterization and development of specific and selective inhibitors of SSAO, we have developed a method for production of recombinant human SSAO. The extracellular region (residues 29-763) of human SSAO was expressed in HEK293 cells in fusion with a mutated Schistosoma japonicum glutathione S-transferase (GST) and secreted to the culture medium. The mutGST-SSAO fusion protein was purified in a single step by glutathione-affinity chromatography followed by site-specific cleavage using a GST-3C protease fusion protein to remove the mutGST fusion partner. A second glutathione-affinity chromatography step was then used to capture both the mutGST fusion partner and the GST-3C protease, resulting in milligram quantities of pure, enzymatically active, and soluble recombinant human SSAO.     

Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA

Efforts to correlate genetic variations with phenotypic differences are intensifying due to the availability of high-density maps of single nucleotide polymorphisms (SNPs) and the development of high throughput scoring methods. These recent advances have led to an increased interest for improved multiplex preparations of genetic material to facilitate such whole genome analyses. Here we propose a strategy for the parallel amplification of polymorphic loci based on a reduced set of nucleotides. The technique denoted Tri-nucleotide Threading (TnT), allows SNPs to be amplified via controlled linear amplification followed by complete removal of the target material and subsequent amplification with a pair of universal primers. A dedicated software tool was developed for this purpose and variable positions in genes associated with different forms of cancer were analyzed using sub-nanogram amounts of starting material. The amplified fragments were then successfully scored using a microarray-based PrASE technique. The results of this study, in which 75 SNPs were analyzed, show that the TnT technique circumvents potential problems associated with multiplex amplification of SNPs from minute amounts of material. The technique is specific, sensitive and can be readily adapted to equipment and genotyping techniques used in other research laboratories without requiring changes to the preferred typing method.     

A proposal for re-defining the way the aetiology of schizophrenia and bipolar human psychiatric diseases is investigated

“The two big problems — the nature of development and the nature of the mind — are being subdued. I don’t know whether there will be beautiful, general theories to come out of this — something really nice like Watson and Crick’s double helix — or whether there will be an accumulation of more and more details. I’ll confess to a secret hope for the former” (Crow 2000).     

Carbon source dependent dynamics of the Ccr4-Not complex in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

We have investigated the composition of the conserved Ccr4-Not complex during different physiological states of Saccharomyces cerevisiae. Major changes were found, most notably in the expression of the central scaffold protein Not1p, which was strongly reduced in the absence of glucose. The low expression of Not1p was also evident from the inability of Pop2p to co-purify Not1p in cells from cultures lacking glucose. However, Not1p was still essential under conditions of low expression. The downregulation of Not1p indicates that many of the Ccr4-Not complex components are likely to have roles outside of the complex. We suggest that the use of different carbon sources will be a good starting point to unravel these functions.     

F-spondin and mindin: two structurally and functionally related genes expressed in the hippocampus that promote outgrowth of embryonic hippocampal neurons.

Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. F-spondin and Mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Genes for both proteins contain a thrombospondin type I repeat(s) at the C terminus and an FS1-FS2 (spondin) domain. Both the vertebrate F-spondin and the zebrafish mindins are expressed on the embryonic floor plate. In the current study we have cloned the rat homologue of mindin and studied its expression and activity together with F-spondin in the developing rodent brain. The two genes are abundantly expressed in the developing hippocampus. In vitro studies indicate that both F-spondin and Mindin promote adhesion and outgrowth of hippocampal embryonic neurons. We have also demonstrated that the two proteins bind to a putative receptor(s) expressed on both hippocampal and sensory neurons.     

Co-localization of PARP-1 and lamin B in the nuclear architecture: a halo-fluorescence- and confocal-microscopy study

A functional interaction between poly(ADP-ribose) polymerase-1 (PARP-1) and lamin B has recently been proposed by nuclear fractionation, crosslinking, and immunoprecipitation experiments. Here we use fluorescence microscopy to verify and extend these findings. We analyze nuclear halo preparations by fluorescence in situ immuno staining (FISIS), which shares attributes with traditional nuclear fractionation techniques, and by confocal laser scanning microscopy (CLSM). The results agree in that a major part of the enzyme co-localizes with lamin B under physiological conditions, where PARP-1 only has basal activity. After DNA damage and the associated activation of PARP-1, and during the subsequent entry into apoptosis, dramatic changes occur: a gradual release of the enzyme from the lamina, accompanied by its accumulation in nucleoli. Our observations are in line with biochemical evidence for lamin B-PARP-1 interactions under physiological conditions and suggest ways by which these interactions are modified to support PARP-functions in damage and its fate in apoptosis.     

A "gain of function" mutation in a protein mediates production of novel modified nucleosides

The mutation sufY204 mediates suppression of a +1 frameshift mutation in the histidine operon of Salmonella enterica serovar Typhimurium and synthesis of two novel modified nucleosides in tRNA. The sufY204 mutation, which results in an amino-acid substitution in a protein, is, surprisingly, dominant over its wild-type allele and thus it is a "gain of function" mutation. One of the new nucleosides is 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modified by addition of a C(10)H(17) side chain of unknown structure. Increased amounts of both nucleosides in tRNA are correlated to gene dosage of the sufY204 allele, to an increased efficiency of frameshift suppression, and to a decreased amount of the wobble nucleoside mnm(5)s(2)U34 in tRNA. Purified tRNA(Gln)(cmnm(5)s(2)UUG) in the mutant strain contains a modified nucleoside similar to the novel nucleosides and the level of aminoacylation of tRNA(Gln)(cmnm(5)s(2)UUG) was reduced to 26% compared to that found in the wild type (86%). The results are discussed in relation to the mechanism of reading frame maintenance and the evolution of modified nucleosides in tRNA.     

Effects from hydrogen bonding and rigidity on selectivity in tartaric acid-based chiral selectors for enantioselective liquid chromatography

Tartaric acid-based selectors 1 ((R,R)-O,O'-Bis(dimethylbenzoyl)-N,N'-diallyl-N,N'-dimethyl tartaramide) and 2 ((R,R)-N-allyl-O,O'-bis(dimethylbenzoyl) tartarimide) were synthesized, immobilized on silica, and evaluated as chiral stationary phases in enantioselective chromatography. Comparison with the commercially available column Kromasil-CHI-1, based on selector 3 ((R,R)-O,O'-Bis(dimethylbenzoyl)-N,N'-diallyl tartaramide) resulted in the conclusion that amide NH functions are essential to chiral recognition on this sorbent. Furthermore, NH functions contribute significantly to retention of analytes except for alcohols. It was also found that flexibility of the benzoyl moieties is essential to selectivity.     

Flash-induced relaxation changes of the EPR signals from the manganese cluster and YD reveal a light-adaptation process of photosystem II

By exposing photosystem II (PSII) samples to an incrementing number of excitation flashes at room temperature, followed by freezing, we could compare the Mn-derived multiline EPR signal from the S2 oxidation state as prepared by 1, 5, 10, and 25 flashes of light. While the S2 multiline signals exhibited by these samples differed very little in spectral shape, a significant increase of the relaxation rate of the signal was detected in the multiflash samples as compared to the S2-state produced by a single oxidation. A similar relaxation rate increase was observed for the EPR signal from Y(D*). The temperature dependence of the multiline spin-lattice relaxation rate is similar after 1 and 5 flashes. These data are discussed together with previously reported phenomena in terms of a light-adaptation process of PSII, which commences on the third flash after dark-adaptation and is completed after 10 flashes. At room temperature, the fast-relaxing, light-adapted state falls back to the slow-relaxing, dark-adapted state with t(1/2) = 80 s. We speculate that light-adaptation involves changes necessary for efficient continuous water splitting. This would parallel activation processes found in many other large redox enzymes, such as Cytochrome c oxidase and Ni-Fe hydrogenase. Several mechanisms of light-adaptation are discussed, and we find that the data may be accounted for by a change of the PSII protein matrix or by the light-induced appearance of a paramagnetic center on the PSII donor side. At this time, no EPR signal has been detected that correlates with the increase of the relaxation rates, and the nature of such a new paramagnet remains unclear. However, the relaxation enhancement data could be used, in conjunction with the known Mn-Y(D) distance, to estimate the position of such an unknown relaxer. If positioned between Y(D) and the Mn cluster, it would be located 7-8 A from the spin center of the S2 multiline signal.