A new site-specific endonuclease from Streptomyces lavendulae (SlaI)

A new restriction-like endonuclease, SlaI, was found and partially purified from Streptomyces lavendulae ATCC8664. This endonuclease cleaved bacteriophage lambda DNA at only one site, and cytosine-substituted bacteriophage T4 DNA at 16 sites. The recognition sequence was determined by using SlaI fragments of cytosine-substituted bacteriophage T4 DNA. The hexanucleotide recognized by SlaI endonuclease was

$\text{5′-}\text{C}\text{?}\text{T}\text{-}\text{C}\text{-}\text{G}\text{-}\text{A}\text{-}\text{G}\text{-3′}$

$\text{3′-}\text{G}\text{-}\text{A}\text{-}\text{G}\text{-}\text{C}\text{-}\text{A}\text{-↑}\text{C}\text{-5′}$

with the sites of cleavage as indicated by the arrows. Therefore, SlaI endonuclease was an isochizomer of XhoI endonuclease.     

Studies of viable T4 bacteriophage containing cytosine-substituted DNA (T4dC phage)

Summary Digestion of non-glucosylated and cytosine-substituted T4 phage (T4dC) DNA with SalI restriction endonuclease showed that the DNA had nine SalI-sensitive sites. There were eight SalI sites in DNA from a strain which had a deletion in the rII-denB-ndd region. The comparison of two digestion patterns indicated that one of the SalI-sensitive sites was present in the deleted region and that the SalI-F fragment (8.4x10⁶ daltons) was located adjacent to the SalI-C or SalI-D fragment (15.5x10⁶ daltons) on the T4 chromosome. The DNA gave no detectable cleavage product when digested with BamHI endonuclease alone, while, when digested successively with BamHI and SalI, the DNA yielded two new digestion products in place of one fragment formed by SalI alone. The BamHI-sensitive site was in the SalI-A fragment (25.2x10⁶ daltons). The usefulness of this information for making cleavage maps of T4 phage chromosome is discussed.     

Quantitative microarray-based DNA-DNA hybridization assay for measuring genetic distances among bacterial species and its application to the identification of family Enterobacteriaceae

Quantitative DNA-DNA hybridization to measure the genetic distances among bacterial species is indispensable for taxonomical determination. In the current studies, we developed a method to determine bacterial DNA relatedness on a glass microarray. Reference DNAs representing a total 93 species of Enterobacteriaceae were arrayed on a glass microplate, and signal intensities were measured after 2 hr of hybridization with Cy3-labeled bacterial DNAs. All immobilized DNAs from members of the family Enterobacteriaceae were identified by this method except for DNAs from Yersinia pseudotuberculosis and Y. pestis. These results suggest that quantitative microarray hybridization could be an alternative to conventional DNA-DNA hybridization for measuring chromosome relatedness among bacterial species.     

Activity-based in vitro selection of T4 DNA ligase

Recent in vitro methodologies for selection and directed evolution of proteins have concentrated not only on proteins with affinity such as single-chain antibody but also on enzymes. We developed a display technology for selection of T4 DNA ligase on ribosome because an in vitro selection method for DNA ligase had never been developed. The 3' end of mRNA encoding the gene of active or inactive T4 DNA ligase-spacer peptide fusion protein was hybridized to dsDNA fragments with cohesive ends, the substrate of T4 DNA ligase. After in vitro translation of the mRNA-dsDNA complex in a rabbit reticulocyte system, a mRNA-dsDNA-ribosome-ligase complex was produced. T4 DNA ligase enzyme displayed on a ribosome, through addition of a spacer peptide, is able to react with dsDNA in the complex. The complex expressing active ligase was biotinylated by ligation with another biotinylated dsDNA probe and selected with streptavidin-coated magnetic beads. We effectively selected active T4 DNA ligase from a small amount of protein. The gene of the active T4 DNA ligase was enriched 40 times from a mixture of active and inactive genes using this selection strategy. This ribosomal display strategy may have high potential to be useful for selection of other enzymes associated with DNA.     

Conserved portion in bacterial ribosomal RNA

The conserved portion in bacterial ribosomal RNA was studied by the DNA-RNA hybridization method. The hybridization percentages were as follows: Bacillus subtilis DNA and B. subtilis 23S rRNA, 0.16; Escherichia coli DNA and E. coli 23S rRNA, 0.15; B. subtilis DNA and E. coli 23S rRNA, 0.03; E. coli DNA and B. subtilis 23S rRNA, 0.04. The RNA's extracted from the heterologous hybrids could be rehybridized with DNA's of B. subtilis and E. coli. The average chain lengths of the RNA's were estimated by sucrose density gradient centrifugation and Sephadex gel filtration. The results suggested that the size might be larger than 30 nucleotides. Nucleotide compositions of the RNA's in the hybrids were also studied. Both RNA's contained higher molar percentages of guanylic acid and cytidylic acid than the whole rRNA's.     

Spatio-temporal organization of intracellular ATP content and oscillation patterns in response to blue light byPhysarum polycephalum

Summary Phototactic responses in a giant amoeboid cell ofPhysarum plasmodium were studied both by analyzing intracellular ATP content and by applying image processing for recording oscillatory changes in thickness with use of a microcomputer. The ATP content fluctuated and deviated from the initial level upon exposure to light with varying wavelength from 400 to 600 nm. The maximum decrease in the integrated value dt with T=9 minutes occurred at the wavelength 450 nm. The ATP in a migrating plasmodium distributed twice as high in the front as in the rear. This polar pattern became unstable, and a new wavy pattern appeared by stimulating a local frontal part with blue light. In a concentrically extending plasmodium, peripheral and inside regions oscillated in opposite phase to each other. When part of this organism was exposed to light, stimulated and unslimulated regions began to oscillate in opposite phase, and phase waves propagated inward the stimulated region. And the protoplasm there became thinner, the strongest avoidance reaction occurring to 450 nm light as in ATP response. Phototactic behavior inPhysarum is discussed in terms of bifurcation in spatio-temporal organization appearing in a self-organizing system.     

Physico-chemical studies of taste reception. IV. Response of individual phospholipid membrane to a variety of chemical stimuli.

Variations in the membrane potential across model membranes made of Millipore filter paper and various single phospholipids were measured in response to salt, acid and distilled water. The phospholipids used were phosphatidylcholine (c), spingomyelin (SM), phosphatidylethanolamine (PE), and phosphatidylserine (PS). Results were compared with those obtained with the model membrane made of the total lipids extracted from bovine tongue epithelium, which simulated well the receptor potential observed with intact tast organs. The membrane potential of PE- and PS-membranes increased monotonously with increase of the concentration of 1:1 type salt, while that of PC- and SM-membranes exhibited no appreciable change in 1:1 salt solutions. Application of CaC12 to the membranes brought about a varity of response depending on the species of lipids used. PE- and PS-membranes showed a larger change in the membrane potential than PC- and SM-membranes when pH of the solution was varied. Fe-3+ was strongly absorbed on the surface of PC and SM-membranes, while Fe-3+ bound to PE- and PS-membranes was easily removed by an application of salt solution. A transient increase in the membrane potential was observed when distilled water was applied to the membrane adapted to an appropriate salt solution, which was similar to the water response observed in taste cells. PC- and SM-membranes responded to water when the membrane adapted to either NaC1 or CaC12, but PS-membrane responded only when the membrane was adapted to a solution containing CaC12. PE-membrane did not respond to water in any cases examined. The membrane prepared with a mixture of two species of phospholipids responded neither to salt nor to water, while the membranes prepared with the total lipids or a mixture of three species of lipids in appropriate ratio responded to both. The water response of the total lipids membrane vanished in a high temperature medium, while the water response of PC-membrane retained in all temperature ranges examined, i.e. between 20 degrees and 62 degrees C. The results obtained suggest that a mosaic structure, where each domain has different functions against various chemical stimuli, is formed on the surface of the model membrane made of the total lipids.     

Ca(2+)-responsive extensible monolayer membrane of calmodulin-albumin conjugate.

A Ca(2+)-responsive monolayer protein membrane was prepared by developing calmodulin and bovine serum albumin at the air-water interface and by conjugating them with a bifunctional agent. In the case of the BSA monolayer, complex formation with Mg2+ generated a larger change in surface pressure than that with Ca2+. On the other hand, a drastic change in surface pressure was observed for the conjugated thin membrane associated with Ca2+ than that associated with Mg2+. Due to a drastic change in the conformation of calmodulin, the conjugated protein film changes its morphology (STM image), depending on Ca2+ concentration: the extended structure in the presence of Ca2+ transforms to a shrinked structure in the absence of Ca2+. The largest surface pressure change was detected when calmodulin was mixed with an equimolar amount of bovine serum albumin.     

Evaluation of small ligand–protein interaction by ligation reaction with DNA-modified ligand

A method for the evaluation of interactions between protein and ligand using DNA-modified ligands, including signal enhancement of the DNA ligation reactions, is described. For proof of principle, a DNA probe modified by biotin was used. Two DNA probes were prepared with complementary sticky-ends. While one DNA probe was modified at the 5′-end of the sticky-end, the other was not modified. The probes could be ligated together by T4 DNA ligase along the strand without biotin modification. However, in the presence of streptavidin or anti-biotin Fab, the ligation reaction joining the two probes could not occur on either strand.