Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase.

BACKGROUND: The rpoS, nlpD, pcm, and surE genes are among many whose expression is induced during the stationary phase of bacterial growth. rpoS codes for the stationary-phase RNA polymerase sigma subunit, and nlpD codes for a lipoprotein. The pcm gene product repairs damaged proteins by converting the atypical isoaspartyl residues back to L-aspartyls. The physiological and biochemical functions of surE are unknown, but its importance in stress is supported by the duplication of the surE gene in E. coli subjected to high-temperature growth. The pcm and surE genes are highly conserved in bacteria, archaea, and plants. RESULTS: The structure of SurE from Thermotoga maritima was determined at 2.0 A. The SurE monomer is composed of two domains; a conserved N-terminal domain, a Rossman fold, and a C-terminal oligomerization domain, a new fold. Monomers form a dimer that assembles into a tetramer. Biochemical analysis suggests that SurE is an acid phosphatase, with an optimum pH of 5.5-6.2. The active site was identified in the N-terminal domain through analysis of conserved residues. Structure-based site-directed point mutations abolished phosphatase activity. T. maritima SurE intra- and intersubunit salt bridges were identified that may explain the SurE thermostability. CONCLUSIONS: The structure of SurE provided information about the protein's fold, oligomeric state, and active site. The protein possessed magnesium-dependent acid phosphatase activity, but the physiologically relevant substrate(s) remains to be identified. The importance of three of the assigned active site residues in catalysis was confirmed by site-directed mutagenesis.     

Mechanisms underlying shoal composition in the Trinidadian guppy, Poecilia reticulata

Free-ranging groups are frequently assorted by phenotypic characters. However, very little is known about the underlying processes that determine this structuring. In this study, we investigate the mechanisms underlying the phenotypic composition of shoals of guppies ( Poecilia reticulata ) in a high-predation stream in Trinidad's Northern Mountain Range. We collected 57 entire wild shoals, which were strongly assorted by body length. Shoal encounters staged within an experimental arena showed shoal fission (but not fusion) events to be an important mechanism in generating phenotypic assortment. In the wild, fission and fusion between guppy shoals occurred extremely frequently and thus are unlikely to constrain the opportunities for shoal assortment. However, fission and fusion processes occur under the restrictions imposed by the distribution of individuals within the environment. We observed size specific segregation within the habitat in three dimensions, providing a passive mechanism that contributes to the maintenance of the observed homogeneity of group composition. Furthermore sex differences were found in social behaviour. Individual male guppies switched between shoals more frequently than females and left a shoal more often than females. We argue that shoal composition is determined by habitat segregation on a medium spatial scale and by fission/fusion processes on a small spatial scale (with sex-specific shoal dynamics adding a additional layer of complexity).     

PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase

PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36.     

A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research

Post-translational modifications of histones serve as docking sites and signals for effector proteins and chromatin-remodeling enzymes, thereby influencing many fundamental cellular processes. Nevertheless, there are huge gaps in the knowledge of which proteins read and write the 'histone code'. Several techniques have been used to decipher complex histone-modification patterns. However, none is entirely satisfactory owing to the inherent limitations of in vitro studies of histones, such as deficits in the knowledge of the proteins involved, and the associated difficulties in the consistent and quantitative generation of histone marks. An alternative technique that could prove to be a useful tool in the study of the histone code is the use of synthetic peptide arrays (SPOT blot analysis) as a screening approach to characterize macromolecules that interact with specific covalent modifications of histone tails.     

Proof-of-concept human laboratory study for protracted abstinence in alcohol dependence: effects of gabapentin

There is a need for safe medications that can effectively support recovery by treating symptoms of protracted abstinence that may precipitate relapse in alcoholics, e.g. craving and disturbances in sleep and mood. This proof-of-concept study reports on the effectiveness of gabapentin 1200 mg for attenuating these symptoms in a non-treatment-seeking sample of cue-reactive, alcohol-dependent individuals. Subjects were 33 paid volunteers with current Diagnostic and Statistical Manual of Mental Disorders-IV alcohol dependence and a strength of craving rating 1 SD or greater for alcohol than water cues. Subjects were randomly assigned to gabapentin or placebo for 1 week and then participated in a within-subjects trial where each was exposed to standardized sets of pleasant, neutral and unpleasant visual stimuli followed by alcohol or water cues. Gabapentin was associated with significantly greater reductions than placebo on several measures of subjective craving for alcohol as well as for affectively evoked craving. Gabapentin was also associated with significant improvement on several measures of sleep quality. Side effects were minimal, and gabapentin effects were not found to resemble any major classes of abused drugs. Results suggest that gabapentin may be effective for treating the protracted abstinence phase in alcohol dependence and that a randomized clinical trial would be an appropriate next step. The study also suggests the value of cue-reactivity studies as proof-of-concept screens for potential antirelapse drugs.