Determination of 16S ribosomal RNA gene copy number in Streptococcus uberis, S. agalactiae, S. dysgalactiae and S. parauberis

Abstract Species-specific oligonucleotide probes and a universal oligonucleotide probe derived from sequences of 16S rRNA were hybridised to chromosomal DNA from Streptococcus agalactiae, S. dysgalactiae, S. parauberis and S. uberis following digestion with Eco RI. Due to the presence of a unique Eco RI site in each 16S rRNA gene, the number of hybridised fragments was indicative of the number of 16S rRNA genes. Southern hybridisation indicated six 16S rRNA genes in ten isolates of S. agalactiae , five genes in ten isolates of S. uberis , five genes in six isolates and six in another isolate of S. dysgalactiae , and six genes in four isolates of S. parauberis . For a fifth isolate of S. parauberis , six 16S rRNA genes were indicated by the universal probe but only five when hybridised to the species-specific probe, indicating sequence variation (microheterogeneity) within the probe target region.     

栽培高粱、甜高粱和拟高粱比较基因组原位杂交分析

用一种植物的总基因组DNA与近缘或远缘物种的染色体杂交,可以研究植物近缘或远缘物种基因组进化关系。以拟高粱总基因组DNA为探针,对栽培高粱、甜高粱基因组进行杂交,结果表明栽培高粱、甜高粱和拟高粱基因组中重复序列存在很大的同源性,基因组进化关系表现出保守性。栽培高粱与拟高粱基因组间重复序列的同源性要比甜高粱与拟高粱间重复序列的同源性高。     

Six newSalmonella types,isolated in ghana (S. volta,S. agona,S. wa,S. techimani,S. mampong andS. tafo)

Summary Six newSalmonella types isolated in Ghana are described.S. volta, 11: 4: 1,z₁₃, z₂₈ was isolated from a swine;S.agona 4,12: fgs:—,S.wa, 16: b: 1,5S.technimani, 28: c: z₆ andS.tafo, 1, 4 12, 27: z₃₅: 1,7 were isolated from cattle;S.mampong, 13,22: z₃₅: 1,6, was isolated from a lizzard.     

Apparent association constants for E. coli ribosomal proteins S4, S7, S8, S15, S17 and S20 binding to 16S RNA.

We have previously reported the development of a technique utilizing nitrocellulose filters, which rapidly separates ribosomal protein-ribosomal RNA complexes from unbound protein. We have used this technique to obtain binding data for the association of proteins S4, S7, S8, S15, S17, and S20 with 16S RNA. With the exception of protein S17, the association behavior for each of these proteins exhibits a single binding site with a unique binding constant. The apparent association constants have been calculated and have been found to have a range from 1.6 x 10(6) M-1 for protein S7 to 7.1 x 10(7) M-1 for protein S17. The Scatchard plot for the protein S17 binding data is biphasic, suggesting that within the RNA population two different binding sites exist, each with a different apparent association constant.     

Sequence Analysis of 18S-28S rRNA Spacer Regions from Saccharomyces kunashirensis, S. martiniae, S. rosinii, and S. transvaalensis

Sequences of two internal transcribed spacer regions between 18S and 28S rRNA for recently described yeasts species, Saccharomyces kunashirensis, S. martiniae, S. rosinii, and S. transvaalensis, were determined to assess their phylogenetic relationship to the other Saccharomyces species. In the two phylogenetic trees constructed by the neighbor-joining method, independent branches reflected that delimitation of the four new species was valid. Received: 17 June 1998 / Accepted: 7 August 1998     

TRS-based PCR as a potential tool for inter-serovar discrimination of Salmonella Enteritidis,S. Typhimurium,S. Infantis,S. Virchow,S. Hadar,S. Newport and S. Anatum

Salmonella enterica subsp. enterica comprises a number of serovars, many of which pose an epidemiological threat to humans and are a worldwide cause of morbidity and mortality. Most reported food infection outbreaks involve the serovars Salmonella Enteritidis and Salmonella Typhimurium. Rapid identification to determine the primary sources of the bacterial contamination is important to the improvement of public health. In recent years, many DNA-based techniques have been applied to genotype Salmonella. Herein, we report the use of a manual TRS-PCR approach for the differentiation of the Salmonella enterica subspecies enterica serovars in a single-tube assay. One hundred seventy Salmonella strains were examined in this work. These consisted of serovars S. Enteritidis, S. Typhimurium, S. Infantis, S. Virchow, S. Hadar, S. Newport and S. Anatum. Five of the TRS-primers, N₆(GTG)₄, N₆(CAC)₄, N₆(CGG)₄, N₆(CCG)₄ and N₆(CTG)₄, perfectly distinguished the S. Enteritidis and S. Typhimurium serovars, and the N₆(GTG)₄ primer additionally grouped the other five frequently isolated serovars. In our opinion, the TRS-PCR methodology could be recommended for a quick and simple DNA-based test for inter-serovar discrimination of Salmonella strains.     

Immunochemical accessibility of ribosomal protein S4 in the 30 S ribosome. The interaction of S4 with S5 and S12

The reactivity of protein S4-specific antibody preparations with 30 S ribosomal subunits and intermediates of in vitro subunit reconstitution has been characterized using a quantitative antibody binding assay. Anti-S4 antibody preparations did not react with native 30 S ribosomal subunits; however, they did react with various subunit assembly intermediates that lacked proteins S5 and S12. The inclusion of proteins S5 and S12 in reconstituted particles resulted in a large decrease in anti-S4 reactivity, and it was concluded that proteins S5 and S12 are primarily responsible for the masking of S4 antigenic determinants in the 30 S subunit. The effect of S5 and S12 on S4 accessibility is consistent with data from a variety of other approaches, suggesting that these proteins form a structural and functional domain in the small ribosomal subunit.     

Genetic differentiation of U.S.S.R. house mice: electrophoretic study of proteins

Protein electrophoresis at 24 loci was used to characterize house mice from 56 localities in the U.S.S.R., concentrating on samples from Moldavia to Primorye (extreme south-east of the U.S.S.R.). Mus -2A is the most widespread form, extending over the European part of the U.S.S.R., Middle Asia and Siberia as far east as the Pacific Ocean. In Moldavia the group is sympatric with Mus-iB . It is found with Mus -4A in Transcaucasus, where it may hybridize with Mus -1. In Primorye Mus -2A and M. raddei have a wide zone of hybridization with Mus -2C.     

Positions of proteins S10, S11 and S12 in the 30 S ribosomal subunit of Escherichia coli.

The results of 17 new neutron distance measurements on protein pairs within the 30 S ribosomal subunit are reported. A partial map of the structure is presented giving the locations of S3, S4, S5, S7, S8, S9, S10, S11 and S12. This map is compared to other information on ribosomal organization and function.     

RNA--protein interactions in the ribosome. IV. Structure and properties of binding sites for proteins S4, S16/S17 and S20 in the 16S RNA

Proteins S4, S16/S17 and S20 of the 30 S ribosomal subunit of Escherichia coli+ associate with specific binding sites in the 16 S ribosomal RNA. A systematic investigation of the co-operative interactions that occur when two or more of these proteins simultaneously attach to the 16 S RNA indicate that their binding sites lie near to one another. The binding site for S4 has previously been located within a 550-nucleotide RNA fragment of approximately 9 S that arises from the 5′-terminal portion of the 16 S RNA upon limited hydrolysis with pancreatic ribonuclease. The 9 S RNA was unable to associate with S20 and S16/S17, however, either alone or in combination. A fragment of similar size and nucleotide sequence, termed the 9 S¹ RNA, has been isolated following ribonuclease digestion of the complex of 16 S RNA with S20 and S16/S17. The 9 S¹ RNA bound not only S4, but S20 and S16/S17 as well, although the fragment complex was stable only when both of the latter protein fractions were present together. Nonetheless, measurements of binding stoichiometry demonstrated the interactions to be specific under these conditions. A comparison of the 9 S and 9 S¹ RNAs by electrophoresis in polyacrylamide gels containing urea revealed that the two fragments differ substantially in the number and distribution of hidden breaks. Contrary to expectation, the RNA in the ribonucleoprotein complex appeared to be more accessible to ribonuclease than the free 16 S RNA as judged by the smaller average length of the sub-fragments recovered from the 9 S¹ RNA. These results suggest that the binding of S4, S16/S17 and S20 brings about a conformational alteration within the 5′ third of the 16 S RNA.To delineate further the portions of the RNA chain that interact with S4, S16/S17 and S20, specific fragments encompassing subsequences from the 5′ third of the 16 S RNA were sought. Two such fragments, designated 12 S-I and 12 S-II, were purified by polyacrylamide gel electrophoresis from partial T₁ ribonuclease digests of the 16 S RNA. The two RNAs, which contain 290 and 210 nucleotides, respectively, are contiguous and together span the entire 5′-terminal 500 residues of the 16 S RNA molecule. When tested individually, neither 12 S-I nor 12 S-II bound S4, S16/S17 or S20. If heated together at 40 °C in the presence of Mg²⁺ ions, however, the two fragments together formed an 8 S complex which associated with S4 alone, with S16/S17 + S20 in combination, and with S4 + S16/S17 + S20 when incubated with an un fractionated mixture of 30 S subunit proteins. These results imply that each fragment contains part of the corresponding binding sites.     

Cat gene frequencies in cities of the U.S.S.R.

Analyses of mutant gene frequencies have been completed for the cities of Armavir, Khabarovsk and Vladivostok of the U.S.S.R. These are compared with previous work and the overall picture briefly summarised and discussed. The prospects for future investigations are stressed.     

Ribosomal protein-nucleic acid interactions. I. Isolation of a polypeptide fragment from 30S protein S8 which binds to 16S rRNA.

Within the bacterial ribosome a large number of specific protein and rRNA interactions appear to be required for assembly of the particle and its subsequent function in protein synthesis. In this communication it is shown that it is possible to isolate cyanogen bromide digestion products from ribosomal 30S protein S8 which will interact stoichiometrically with 16S rRNA. In addition to this a small binding polypeptide was generated from S8-16S rRNA complexes which were treated with proteinase K. The digestion of the complex yields a "protected" fragment of protein S8 which binds to 16S-rRNA. The isolated fragment will reassociate with 16S rRNA. It is not displaced by other 30S ribosomal proteins and blocks the binding of intact S8 to 16S rRNA. The size the possible structure of the S8 protein binding site are discussed and compared with the binding of cyanogen bromide digestion products which bind to 16S rRNA.     

The subunit interface of the Escherichia coli ribosome. Crosslinking of 30 S protein S9 to proteins of the 50 S subunit.

Purified 50 S ribosomal subunits were found to contain significant amounts of protein coincident with the 30 S proteins S9 and/or S11 on two-dimensional polyacrylamide/urea electropherographs. Peptide mapping established that the protein was largely S9 with smaller amounts of S11. Proteins S5 and L6 were nearly coincident on the two-dimensional polyacrylamide/urea electropherographs. Peptide maps of material from the L6 spot obtained from purified 50 S subunits showed the presence of significant amounts of the peptides corresponding to S5. Experiments in which ³⁵S-labelled 30 S subunits and non-radioactive 50 S subunits were reassociated to form 70 S ribosomes showed that some radioactive 30 S protein was transferred to the 50 S subunit. Most of the transferred radioactivity was associated with two proteins, S9 and S5. Sulfhydryl groups were added to the 50 S subunit by amidination with 2-iminothiolane (methyl 4-mercaptobutyrimidate). These were oxidized to form disulfide linkages, some of which crosslinked different proteins of the intact 50 S ribosomal subunit. Protein dimers were partially fractionated by sequential salt extraction and then by electrophoresis of each fraction in polyacrylamide gels containing urea. Slices of the gel were analysed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Final identification of the constituent proteins in each dimer by two-dimensional polyacrylamide/urea gel electrophoresis showed that 50 S proteins L5 and L27 were crosslinked to S9. The evidence suggests that proteins S5, S9, S11, L5 and L27 are located at the interface region of the 70 S ribosome.     

A comparison of fertilization envelope development in three species of Strongylocentrotus (S. franciscanus, S. droebachiensis, and S. purpuratus)

The ultrastructure of fertilization envelope (FE) development and the polypeptide spectra of Strongylocentrotus franciscanus and S. droebachiensis envelopes were compared to S. purpuratus. In S. franciscanus, the FE reached its maximum thickness of 67 nm by 3 minutes postinsemination (PI), and final structuralization was observed by 40 minutes PI. The fully formed FE did not have microvillar impressions (casts) and was symmetrical, with outer double laminar elements surrounding an amorphous central region. Isolated S. franciscanus FEs were soluble in reducing and denaturing solvents and the same set of 33 polypeptides ranging from 18.5 to 260 kD was detected in FEs isolated from 10 to 180 minutes PI. The S. droebachiensis FE retained microvillar casts, assumed its definitive form by 3 minutes PI, and was 70 nm thick between microvillar impressions. Isolated S. droebachiensis FEs were partially soluble in reducing and denaturing solvents, and the polypeptide spectra of FEs isolated between 10 and 60 minutes PI were identical and showed 14 polypeptides from 18.5 to 265 kD. Antisera against extracted FEs and the FE extract from S. purpuratus were immunologically cross-reactive (using an enzyme-linked immunosorbent assay) with S. franciscanus and S. droebachiensis FE preparations; immunoblots identified 13 and 5 cross-reactive polypeptides, respectively. Most of the cross-reactive polypeptides were of slightly different molecular weight. Based on comparative ultrastructural, solubility, and electrophoretic data, we suggest that S. droebachiensis FE development is most like that observed in S. purpuratus.     

Solution conformation of virginiamycin S. II. The conformation of allohydroxy- and deoxyvirginiamycin S.

The experimental results of 1H- and 13C-NMR studies of allohydroxy-, and of deoxyvirginiamycin S strongly confirm the conformation that was proposed earlier for the parent virginiamycin S (Anteunis, Callens and Tavernier (1975) Eur. J. Biochem. 58, 259--268). The changing nature of dipole-induced dipole interaction is responsible for the specific gradually increasing libration of the N-MePhe side chain along the series virginiamycin S, allohydroxy-, deoxyvirginiamycin S. Previous methods for the estimation of rotameric populations around the alpha, beta bonds are critically evaluated and compared to the present results obtained from interpretation of geminal 2J (beta) coupling constants.     

Ribosomal activity of the 16 S.23 S RNA complex

It has been demonstrated in this laboratory that 16 S and 23 S RNAs form a binary complex like 30 S and 50 S ribosomes under certain specific conditions, and 5 S RNA can be incorporated into the complex in stoichiometric amounts in presence of three ribosomal proteins, L5, L18, and L15/25. These studies raised the basic question of whether such complex will have biological activity. Therefore, the following steps in protein synthesis were examined with the complex in place of the ribosomes: (i) poly-U-dependent binding of phenylalanyl tRNA; (ii) EF-G-dependent GTPase activity; (iii) initiation complex formation; (iv) peptidyl transferase activity; and (v) poly-U-dependent polyphenylalanine synthesis. All the steps could be unequivocally demonstrated by the addition of a limited number of proteins although the complex had comparatively much less activity than 70 S ribosomes. It appears that rRNAs are directly involved in various steps of protein synthesis. Furthermore, the 16 S.23 S RNA complex might have acted as a primitive ribosome, as suggested by Crick and Orgel.     

Four newSalmonella types (S. gambaga,S. kumasi,S. pramiso andS. ashanti) isolated in Ghana

Summary Four newSalmonella types isolated in Ghana are described.S.gambaga, 21; z35: enz15,S.kumasi, 30;z10: enz15, andS.pramiso, 3,10;c: 1,7 were isolated from reptiles,S. ashanti, 28; b: 1,6 was isolated from a rat.     

Rotational diffusion of Escherichia coli ribosomes. I. - Free 70 S, 50 S and 30 S particles.

The rotational brownian diffusion of Escherichia coli ribosomes has been studied by following the transient dichroism generated by optical excitation of a covalent probe into its triplet state. The induced absorption anisotropy decays exponentially with characteristic correlation times: 2.5 microseconds, 1.6 microseconds and 1.1 microseconds for the 70S ribosome and the 50S and 30S subparticles respectively. The corresponding Stokes radii are in the same order, 133 A, 115 A and 103 A. The hydrodynamic properties are discussed in terms of an ellipsoidal shape of the ribosome particles.     

Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14

We have used rapid probing methods to follow the changes in reactivity of residues in 16 S rRNA to chemical and enzymatic probes as ribosomal proteins S2, S3, S10, S13 and S14 are assembled into 30 S subunits. Effects observed are confined to the 3' major domain of the RNA and comprise three general classes. (1) Monospecific effects, which are attributable to a single protein. Proteins S13 and S14 each affect the reactivities of different residues which are adjacent to regions previously found protected by S19. S10 effects are located in two separate regions of the domain, the 1120/1150 stem and the 1280 loop; both of these regions are near nucleotides previously found protected by S9. Both S2 and S3 protect different nucleotides between positions 1070 and 1112. In addition, S2 protects residues in the 1160/1170 stem-loop. (2) Co-operative effects, which include residues dependent on the simultaneous presence of both proteins S2 and S3 for their reactivities to appear similar to those observed in native 30 S subunits. (3) Polyspecific effects, where proteins S3 and S2 independently afford the same protection and enhancement pattern in three distal regions of the domain: the 960 stem-loop, the 1050/1200 stem and in the upper part of the domain (nucleotides 1070 to 1190). Proteins S14 and S10 also weakly affect the reactivities of several residues in these regions. We believe that several of the protected residues of the first class are likely sites for protein-RNA contact while the third class is indicative of conformational rearrangement in the RNA during assembly. These results, in combination with the results from our previous study of proteins S7, S9 and S19, are discussed in terms of the assembly, topography and involvement in ribosomal function of the 3' major domain.