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R H Doi

Publications and source records attributed to R H Doi.

161 records · Page 9Linked to original sources
PubMed1968

Presence and function of sulur-containing transfer ribonucleic acid of Bacillus subtilis.

Bacillus subtilis transfer ribonucleic acid (tRNA) was analyzed for the occurrence of thionucleotides by in vivo labeling with (35)S and fractionation by methylated albumin kieselguhr column chromatography. Alkaline hydrolysates of tRNA were also examined by column chromatography and paper electrophoresis, and the amino acid-accepting ability of thionucleotide-containing tRNA was tested after iodine oxidation. The results showed that B. subtilis tRNA contains 4-thiouridylate, a second nucleotide with properties similar to 2-thiopyrimidine, and a third unidentified thionucleotide. The amino acid-accepting ability for serine, tyrosine, lysine, and glutamic acid was markedly inhibited after oxidation of the tRNA with iodine, suggesting the presence of thionucleotides in these tRNA species. This inhibition could be reversed by thiosulfate reduction. The iodine treatment totally inactivated all lysine tRNA species, partially inactivated the serine tRNA species, and did not affect the accepting ability for valine. A comparison of tRNA from cells in the log and stationary phases and from spores revealed similar iodine inactivation patterns in all cases. The thionucleotide content in B. subtilis tRNA differed from that in Escherichia coli, both in extent and in distribution. A possible function of the thionucleotides in tRNA is discussed.

Bacillus subtilis↗
PubMed1967

Differential expression of bacteriophage genomes in vegetative and sporulating cells of Bacillus subtilis.

Two antigenically distinct bacteriophages, beta3 and beta22, have been isolated and characterized with Bacillus subtilis strain W23 as a host. They differ in plaque morphology, single-step growth characteristics, host range, and thermal stability. The deoxyribonucleic acids isolated from beta3 and beta22 differ in base composition, density in CsCl and Cs(2)SO(4), sedimentation coefficient, molecular weight, and thermal denaturation temperature. These phages have been used to analyze the ability of B. subtilis to sporulate despite infection by virulent phages. When development of phages beta3 and beta22 in sporulating cultures was compared with that in log cultures, an increase in the latent periods of infection and a decrease in the burst sizes for the two phages were observed. Sporulating cultures infected with beta3 yielded the usual percentage (85%) of mature spores; 80% of these contained phage determinants and 20% were uninfected. However, cultures infected with beta22 lysed. Of the small fraction (0.01%) which sporulated, 83% were uninfected and 17% were infected. Phage beta3-infected and uninfected spores were examined to distinguish any chemical or physical differences. Preparations of both types of spore contained 81.4 mug of dipicolinic acid per mg (dry weight), and examination by phase-contrast microscopy gave no evidence of any difference in outward appearance. A 20% decrease in infected spore count was observed upon heating at 80 C for 10 min. Differences in the infection processes of the two phages prompted an analysis of the transcription process after infection. Deoxyribonucleic acid-ribonucleic acid hybrid analysis of relative amounts of phage-specific and host-specific messenger ribonucleic acid (mRNA) present in infected cells suggested that beta3 was unable to repress the synthesis of host mRNA and that beta3-specific mRNA synthesis was repressed in sporulation-phase cultures. Phage beta22, in contrast, was able to repress host-specific mRNA synthesis in both log-infected and sporulation-infected cells. The results suggest that the differential expression of the phage genomes is due to the relative ability of the phages to repress the host genome.

Bacillus subtilis↗
PubMed1966

Comparison of two serologically distinct ribonucleic acid bacteriophages. I. Properties of the viral particles.

Overby, L. R. (University of Illinois, Urbana), G. H. Barlow, R. H. Doi, Monique Jacob, and S. Spiegelman. Comparison of two serologically distinct ribonucleic acid bacteriophages. I. Properties of the viral particle. J. Bacteriol. 91:442-448. 1966.-Two ribonucleic acid (RNA) coliphages, MS-2 and Qbeta, have been characterized physically and serologically. MS-2 has an S(20, w) value of 79, a molecular weight of 3.6 x 10(6), a density of 1.422, and pH 3.9 as its isoelectric point. Qbeta has an S(20, w) of 84, a molecular weight of 4.2 x 10(6), a density of 1.439, and an isoelectric point at pH 5.3. One host (Escherichia coli A-19) permits a distinction between the two on the basis of a marked difference in plaque size. They are distinct immunochemically, no serological cross-reaction being detectable.

Centrifugation↗
PubMed1966

Isolation and characterization of ribosomes from Bacillus subtilis spores.

Bishop, Helen L. (Syracuse University, Syracuse, N.Y.), and Roy H. Doi. Isolation and characterization of ribosomes from Bacillus subtilis spores. J. Bacteriol. 91:695-701. 1966.-The isolation of ribosomes from Bacillus subtilis spores was accomplished by freezing the spores in liquid nitrogen and grinding the spore pellet with an equal weight of levigated alumina. The ribosomes, which were adsorbed to the alumina, were freed by the addition of vegetative-cell ribosomes or bulk ribonucleic acid (RNA) to the crude alumina-ground extract. The spore ribosomes had sedimentation properties and RNA and protein compositions similar to those of vegetative-cell ribosomes. The difficulty encountered in obtaining spore ribosomes by ordinary extraction methods may be the result of nuclease and protease activities which were demonstrated in spore extracts.

Bacillus subtilis↗
PubMed1966

Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis.

Doi, Roy H. (University of California, Davis), and Richard T. Igarashi. Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis. J. Bacteriol. 92:88-96. 1966.-Hybrid formation was demonstrated between Bacillus subtilis ribosomal ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) from various bacterial species. The high degree of complementarity between B. subtilis ribosomal RNA and the DNA from B. cereus and B. stearothermophilus suggested a method to test whether the same RNA sequences were hybridizing with the DNA from these two species. Saturation studies with 16S and 23S RNA preparations from B. subtilis showed that a definite number of complementary sites was present in each DNA. Base composition analyses of the RNA in the hybrid demonstrated that ribosomal RNA sequences were involved. Hybrid competition studies revealed that B. stearothermophilus ribosomal RNA could compete totally against B. subtilis ribosomal RNA for B. stearothermophilus DNA, although it could compete only partially against the B. subtilis ribosomal RNA hybridizing with B. cereus DNA. These observations were made independently with both 16S and 23S ribosomal RNA preparations. These results revealed that different nucleotide sequences of B. subtilis ribosomal RNA were hybridizing with the DNA from B. cereus and B. stearothermophilus. Two possible interpretations of these results are: (i) different nucleotide sequences from a homogeneous ribosomal RNA population are hybridizing with heterologous DNA preparations, and (ii) ribosomal RNA cistrons are heterogeneous.

Adenine↗
PubMed1966

Comparison of two serologically distinct ribonucleic acid bacteriophages. II. Properties of the nucleic acids and coat proteins.

Overby, L. R. (University of Illinois, Urbana), G. H. Barlow, R. H. Doi, Monique Jacob, and S. Spiegelman. Comparison of two serologically distinct ribonucleic acid bacteriophages. II. Properties of the nucleic acids and coat proteins. J. Bacteriol. 92:739-745. 1966.-The ribonucleic acid (RNA) molecules and coat proteins of two RNA coliphages, MS-2 and Qbeta, have been characterized. MS-2 RNA shows an S(20,w) of 25.8 and a molecular weight by light scattering of 10(6). The corresponding parameters for Qbeta-RNA were 28.9 and 0.9 x 10(6). A difference in base composition was reflected in the adenine-uracil ratio, which was 0.95 for MS-2 and 0.75 for Qbeta. The two RNA preparations are readily separated by chromatography on columns of methylated albumin. Both gave identical bouyant densities in cesium sulfate of 1.64 g/ml. The coat protein subunits were of similar molecular weights: 15,500 (Qbeta) and 14,000 (MS-2). They differed, however, in that the Qbeta-protein lacked tryptophan and histidine, whereas the MS-2 protein lacked only histidine.

Adenine↗
PubMedDate not supplied

The interaction between Bacillus subtilis sigma-A (sigma A) factor and RNA polymerase with promoters.

The P2 promoter from Bacillus subtilis sigma-A (sigma A) operon and the strong phi 29 phage G3b promoter were used to study their interactions with free sigma A and with RNA polymerase holoenzymes (E sigma A and E sigma 70). No binding of free sigma A to the tested promoters was observed, suggesting that the B subtilis free sigma A does not bind promoter by itself for the initiation of RNA transcription. Different footprints of B subtilis RNA polymerase holoenzyme (E sigma A) on the P2 and G3b promoters were detected. The footprint on the P2 promoter is mainly in the -10 downstream region of the bottom strand (noncoding strand) DNA and limited on the top strand (coding strand), whereas the footprints on both strands of the G3b promoter are very clear. These results suggest that the footprint regions of RNA polymerase on a promoter and the strength of its binding to the promoter depend on the properties of the specific promoter DNA sequence. It also suggests that the -10 and its downstream regions are more important than the -35 region for the formation of the E sigma A-P2 promoter open complex. Footprints of B subtilis E sigma A and E coli E sigma 70 on the same G3b promoter are very similar on the top strand but different on the bottom strand, with the footprint being about 17 bases wider (-4 to +13) in the case of E coli E sigma 70. Since this region contains most of the bases involved in promoter DNA melting, we suggest that E coli and B subtilis RNA polymerases have different efficiency in forming the open complex with heterologous promoter DNA during initiation of transcription.

Bacillus Phages↗