High-throughput three-dimensional protein structure determination.

In the wake of finished genomic sequencing projects, high-throughput analysis techniques are being developed in various fields of functional genomics. Of special interest in this regard is the three-dimensional structure analysis of proteins by X-ray crystallography and NMR spectroscopy, which has been characterized by distinctly low-throughput in the past. A number of recent advances in instrumentation and software are promising to radically change this situation, leaving the production of suitable protein samples as the sole rate-limiting step in structural analyses.

An integrated approach to structural genomics.

Structural genomics aims at determining a set of protein structures that will represent all domain folds present in the biosphere. These structures can be used as the basis for the homology modelling of the majority of all remaining protein domains or, indeed, proteins. Structural genomics therefore promises to provide a comprehensive structural description of the protein universe. To achieve this, a broad scientific effort is required. The Berlin-based "Protein Structure Factory" (PSF) plans to contribute to this effort by setting up a local infrastructure for the low-cost, high-throughput analysis of soluble human proteins. In close collaboration with the German Human Genome Project (DHGP) protein-coding genes will be expressed in Escherichia coli or yeast. Affinity-tagged proteins will be purified semi-automatically for biophysical characterization and structure analysis by X-ray diffraction methods and NMR spectroscopy. In all steps of the structure analysis process, possibilities for automation, parallelization and standardization will be explored. Major new facilities that are created for the PSF include a robotic station for large-scale protein crystallization, an NMR center and an experimental station for protein crystallography at the synchrotron storage ring BESSY II in Berlin.

Intravenous coronary angiography with dichromography using synchrotron radiation.

Dichromography represents a digital subtraction angiography mode based on energy substraction which allows imaging of fast moving subjects like the heart. For logarithmic subtraction 2 images with X-rays just below and above the iodine K-edge (33.17 keV) are simultaneously obtained in a line scan mode. Monochromatic X-rays of sufficient intensity to visualize coronary arteries of 1 mm diameter with extremely low iodine concentrations (1 mg/cm2) after venous injection is only provided by synchrotron radiation. The system NIKOS (non-invasive coronary arteriography with synchrotron radiation) at the Deutsches Elektronen Synchrotron (DESY) consists of 6 components: a wiggler, a monochromator, a safety system, a scanning device, a detector and a computer system. After experimental studies in dogs patients are imaged since 1990. Initial results demonstrate feasibility and safety of synchrotron radiation coronary angiography. Large scale studies are designed to further evaluate sensitivity and specificity. When compact synchrotron radiation sources become available, this technique could be used for follow-up studies and for evaluation of certain high coronary risk populations.

Purification and properties of the RuvA and RuvB proteins of Escherichia coli.

The RuvA and RuvB proteins of Escherichia coli play important roles in the post-replicational repair of damaged DNA, genetic recombination and cell division. In this paper, we describe the construction of over expression vectors for RuvA and RuvB and detail simple purification schemes for each protein. The purified 22 kDa RuvA polypeptide forms a tetrameric protein (M(r) ca. 100,000) as observed by gel filtration. The tetramer is stabilised by strong disulphide bridges that resist denaturation during SDS-PAGE (in the absence of boiling and beta-mercaptoethanol). In contrast, purified RuvB polypeptides (37 kDa) weakly associate to form a dimeric protein (M(r) ca. 85,000). At low protein concentrations, the RuvB dimer dissociates into monomers. The multimeric forms of each protein may be covalently linked by the bifunctional cross-linking reagent dimethyl suberimidate. Addition of purified RuvA and RuvB to a RecA-mediated recombination reaction was found to stimulate the rate of strand exchange leading to the rapid formation of heteroduplex DNA.

Molecular and functional analysis of the ruv region of Escherichia coli K-12 reveals three genes involved in DNA repair and recombination.

Recombinant plasmids carrying ruvA, ruvB, or both were constructed and used to investigate the genetic defects in a collection of UV-sensitive ruv mutants. The results revealed that efficient survival of UV-irradiated cells depends on both ruvA and ruvB, and on a third gene, ruvC, located upstream of the ruvAB operon. Southern blotting analysis was used to locate insertions in ruv and to examine putative deletion mutants. Two Tn10 insertions were located to the region encoding ruvA. Since these insertions caused a deficiency in the activities of both ruvA and ruvB, we concluded that they must exert a polar effect on ruvB. Two putative ruv deletion mutants were shown to be the result of deletion-inversion events mediated during imprecise excision of Tn10. The relevant inversion breakpoints in these mutants were located to ruvA and ruvC.

Protoplast isolation and regeneration in Streptomyces clavuligerus.

The regeneration of streptomycete protoplasts is a major step following genetic manipulations such as fusion and DNA-mediated transformation. Reports of studies on the regeneration of protoplasts from Streptomyces clavuligerus are limited and for this reason the experiments described in this paper were carried out. An investigation of protoplast formation and cytology was made to gain further insight into the loss of protoplast viability in osmotically stabilized support media. Protoplasts with the highest regeneration frequency were isolated from mycelium, grown in a two-stage culture system (without glycine), using lysozyme dissolved in a sucrose osmoticum containing 1% bovine serum albumin. The latter promoted improved protoplast viability. A systematic survey was made of the components of regeneration medium R5, previously used for S. clavuligerus, and other potentially advantageous components and conditions, in an attempt to raise the regeneration frequency of the protoplasts. An improved regeneration medium (R6) and protocol which supported higher and more consistent levels of regeneration of S. clavuligerus protoplasts resulted from these experiments. These improved procedures for protoplast isolation and regeneration proved to be suitable for other streptomycete species.

Genetic mapping in Streptomyces clavuligerus by protoplast fusion.

The development of a protoplast manipulation protocol for the industrially important bacterium Streptomyces clavuligerus, which produces the beta-lactamase inhibitor clavulanic acid, made possible a preliminary genetic mapping study based on protoplast fusion crosses. A preliminary position for 11 markers on the S. clavuligerus genetic map is proposed. Fusion progeny were characterized by random spore analysis because the markers present in the strains were not amenable to the conventional four-on-four selection procedure. Whilst the resulting map is similar to that derived by conjugation for S. clavuligerus and S. coelicolor, further analysis of the markers is required to confirm these observations.

Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes.

The nucleotide sequence of a 2505 bp region of the Escherichia coli chromosome containing the LexA regulated ruv gene has been determined. A sequence of 1631 bp encoding two non-overlapping open reading frames that constitute a single operon and which specify polypeptides with predicted molecular weights of 22172 daltons and 37177 daltons respectively, was identified as the most probable sequence for ruv. Each of the two open reading frames, designated ruvA and ruvB, is preceded by a reasonable Shine-Dalgarno sequence. Two 16 bp sequences (SOS boxes) that match the consensus sequence for binding LexA protein are located 5' to ruvA in a region that provides a possible single promoter for expression of both ruvA and ruvB, with the second SOS box overlapping the putative -35 region. A possible transcriptional terminator is located 137 bp downstream of ruvB. The amino acid sequence predicted for RuvB contains a region that matches a highly conserved sequence found in several DNA repair and recombination proteins that bind ATP.