Perpendicular Subcritical Shock Structure in a Collisional Plasma Experiment.

We present a study of perpendicular subcritical shocks in a collisional laboratory plasma. Shocks are produced by placing obstacles into the supermagnetosonic outflow from an inverse wire array z pinch. We demonstrate the existence of subcritical shocks in this regime and find that secondary shocks form in the downstream. Detailed measurements of the subcritical shock structure confirm the absence of a hydrodynamic jump. We calculate the classical (Spitzer) resistive diffusion length and show that it is approximately equal to the shock width. We measure little heating across the shock (<10% of the ion kinetic energy) which is consistent with an absence of viscous dissipation.

'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation.

Certain restriction endonucleases recognise target sequences that contain the stop triplet TAG and are commonly either 4 or 6 bp in length. Interestingly, these restriction targets do not occur at the frequency expected on the basis of base composition and size. For example, the tetranucleotide MaeI recognition sequence (CTAG) occurs considerably less commonly (5-8-fold) in the genome of Escherichia coli (and many other eubacteria) than expected from mononucleotide frequencies. This surprising rarity is particularly evident in protein-encoding genes and is largely dictated by codon usage. Thus, amber (TAG) nonsense mutations frequently give rise to novel MaeI (CTAG) sites which are unique within a translated region. Such amber/MaeI sites, whether arising spontaneously or created in vitro by site-directed mutagenesis, act as a useful physical marker for the presence of the nonsense mutation and are a convenient startpoint for a range of diverse procedures. These features provide a useful supplement to protein engineering methods which use nonsense suppression to mediate amino acid replacements.

Genetic studies of the phs locus of Escherichia coli, a mutation causing pleiotropic lesions in metabolism and pH homeostasis.

In Escherichia coli a pleiotropic mutation, phs, has been reported to affect Na+-linked metabolic functions and pH homeostasis. The phs mutation was previously mapped by its proximity to a met marker, presumed to be metB at 89 min. We have shown that a second mutation to auxotrophy, cymX, which is satisfied by either methionine or cysteine, is closely linked to phs. The cymX and phs lesions map close to trkB and rpsL at 73.5 min and we postulate that they are alleles of cysG and crp, respectively. The basis of the pH sensitivity of DZ3 is discussed in the light of this new information.

Roles of the trkB and trkC gene products of Escherichia coli in K+ transport.

Mutations at the trkB and trkC loci of Escherichia coli produce an abnormal efflux of K+. The mutations are partially dominant in diploids and revert frequently by what appears to be intragenic suppression to the null state. The mutations can be reverted by insertion of Tn10 into the mutated gene, and spontaneous revertants are fully recessive to the mutant allele in diploids. K+ efflux produced by NEM* and by DNP* persists in strains with presumed null mutations at either locus, indicating neither gene product is the primary target for the effect of these inhibitors on K+ efflux. The results are consistent with the view that trkB and trkC encode independent systems for K+ efflux. Mutations at these loci alter regulation of the process so that K+ efflux occurs inappropriately. A second mutation to the null state abolishes this abnormal K+ efflux. These genes may encode K+/H+ antiporters, an activity postulated to mediate K+ efflux and demonstrated to exist in E. coli and other bacteria.

Nucleotide and deduced amino acid sequence of the gene for a novel protein with a possible regulatory function encoded in the beta operon of Staphylococcus aureus.

Although considerable homology exists between the translation products of the rplL, rpoB and rpoC genes of the beta operons of the Gram-negative organism Escherichia coli and the Gram-positive Staphylococcus aureus the region between the rplL and rpoB genes is quite different in the two bacterial species. In E. coli the 324 bp has three centres of dyad symmetry in the first half of the sequence and multiple nonsense codons in all three reading frames. By contrast, the corresponding region in S. aureus consists of 1000 bp capable of forming a similar arrangement of stem-loop structures but with an open reading frame, sited 177 bp downstream of the end of rplL and 217 bp upstream of the beginning of the rpoB gene, with consensus initiation and termination signals, which if translated would generate a 22,665 Da protein with 202 amino acids. In view of the inability to find any significant homology with other proteins in the data bank and because the evidence suggests, as in E. coli, that the rplL-rpoB intergenic sequence is involved in regulation it is proposed that the expression product of orf202 may be a further element of control in the S. aureus beta operon.

In vivo cloning of a carboxy-terminal rpoB allele which confers altered transcriptional properties.

A 3'-terminal mutation of the gene encoding the beta subunit of Escherichia coli RNA polymerase was isolated using an in vivo polA(Ts) technique. Cloning of the allele was monitored by virtue of the fact that the deletion delta(rpoB)1570-1 resulted in an altered-size restriction fragment. DNA sequencing confirmed the predicted nature and location of the mutation: delta(rpoB)1570-1 involved an in-frame deletion of 186 bp (62 codons) encoding amino acid residues 967-1028. The phenotype conferred by delta(rpoB)1570-1 is discussed with respect to conserved domains within the beta polypeptide.

phs Locus of Escherichia coli, a mutation causing pleiotropic lesions in metabolism, is an rpoA allele.

The phs mutation, which causes a pleiotropic growth defect, has been mapped and shown to be an allele of rpoA, the gene for the alpha subunit of RNA polymerase. The mutation is shown to cause a transcription defect in the arabinose operon, araBAD.

Phenotypic properties of a unique rpoA mutation (phs) of Escherichia coli.

The phs mutation of Escherichia coli has been suggested to affect the Na+/H+ antiport (D. Zilberstein, E. Padan, and S. Schuldiner, FEBS Lett. 168:327-330, 1980). We have recently shown that the mutation affects the rpoA gene and thus affects transcription. The extent of the pleiotropy of the phs mutation was investigated. In addition to the previously reported growth defect on L-glutamate and melibiose, the mutation also affects at least two other metabolic systems. The transport and metabolism of arabinose is impaired and the transport of sulfate is reduced. The extent to which the effects of the phs mutation on metabolism are due to a defect in the Na+/H+ antiport was investigated, and no causal role for this transport system in the metabolic defects was found.

Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the beta subunit of Escherichia coli RNA polymerase.

We have mapped principal sites in the Escherichia coli RNA polymerase molecule that are exposed to attack by trypsin under limited proteolysis conditions. The 1342-amino acid-long beta subunit is alternatively cleaved at Arg903 or Lys909. The cleavage occurs adjacent to a dispensable domain (residues 940-1040) that is absent in the homologous RNA polymerase subunits from chloroplasts, eukaryotes, and archaebacteria. In E. coli, this region can be disrupted with genetic deletions and insertions without the loss of RNA polymerase function. Insertion of 127 amino acids into this region introduces a new highly labile site for trypsin proteolysis. The dispensable domain carries the epitope for monoclonal antibody PYN-6 (near residue 1000), which can be used for anchoring the catalytically active enzyme on a solid support. We also report the identification of a secondary trypsin cleavage at Arg81 of the beta' subunit within a putative zinc-binding domain that is conserved in prokaryotes and chloroplasts.