Batch procedure for thermal elution of DNA from hydroxyapatite

Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes

Bacterial and plasmid homo- and heteroduplexes have been analyzed with a single-strand specific endonuclease, S1, of Aspergillus oryzae. Under appropriate assay conditions, there was a high degree of correlation between the degree of deoxyribonucleic acid (DNA)-DNA homoduplex formation assessed by the S1 endonuclease and by hydroxyapatite (HA). Heteroduplexes which contain extensive regions of polynucleotide sequences in common are similarly recognized by the S1 endonuclease and HA. In instances where there is little or imperfect complementarity between heterologous DNA strands, the S1 endonuclease and the HA method give slightly different estimates. From DNA duplex thermal stability experiments assayed with the S1 endonuclease, there is preliminary evidence that well-matched sequences identified by the enzyme are not similarly recognized by HA. The assay of homo- and heteroduplexes with the S1 endonuclease permits an accurate, reproducible and rapid determination of polynucleotide sequence relationships and may be seriously considered as a method of choice for survey work and for investigations which require a large number of DNA-DNA hybridization assays.

Molecular studies of R factor compatibility groups

Molecular studies of R factors of six groups, F(II), I(1), I(2), N, B, and H, defined on the basis of compatibility, support the conclusions drawn from genetic studies. In general, R factors of a given compatibility group are similar in size. Deoxyribonucleic acid (DNA) reassociation occurs freely between members of the same group but is minimal between heterologous groups. An exception to this was found in group H, of which one factor showed minimal homology with the remaining plasmids of the group. A further exception was found with groups I(1) and B, which, although genetically distinct, show between 18 and 28% of DNA homology. Groups I(1) and I(2) are molecularly distinct, despite the fact that they both stimulate the synthesis of I-fimbriae.

Molecular relationships among the Salmonelleae

Polynucleotide sequence relatedness studies were carried out to determine the extent of divergence present in members of the tribe Salmonelleae and between salmonellae and other enteric bacteria. Typical Salmonella were 85 to 100% related. Two groups of biochemically atypical Salmonella showed somewhat lower binding to typical salmonellae and to each other. Arizona were 70 to 80% related to salmonellae. Two groups of Arizona were detected. These groups correlated with the presence of monophasic or diphasic flagellar antigens. Salmonella and Arizona were no more related to Citrobacter than to Escherichia coli (45-55%). Relatedness of Salmonella and Arizona to other enterobacteria ranged from 20 to 40% with klebsiellae and shigellae, to 20 to 25% with erwiniae, and to less than 20% with edwardsiellae and Proteus mirabilis.

Polynucleotide sequence relationships among Japanese and American strains of Vibrio parahaemolyticus

Polynucleotide sequence relationships between two reference Vibrio parahaemolyticus strains isolated from Japanese and American gastroenteritis patients were investigated by use of (32)P-DNA/DNA reassociation in free solution. In addition, these strains were similarly compared with 22 other strains of estuarine and marine vibrios, including 11 strains previously identified as V. parahaemolyticus (2 Japanese, 1 of unknown location, and 8 American strains obtained from diverse geographical locations and sources in North America), 3 strains of V. alginolyticus, and 8 of Vibrio spp. Deoxyribonucleic acid (DNA) from the Japanese and American gastroenteritis isolates showed high relative levels of intraspecific duplex formation (92 to 93%) when reassociated, reciprocally, at 60 C. Heterologous DNA duplexes exhibited thermal elution midpoint [Tm(e)] values comparable to those obtained from homologous duplexes (88.0) when thermally eluted from hydroxyapatite, thus indicating high base-pair complementarity. Other V. parahaemolyticus strains showed DNA homologies of 85% or greater, with correspondingly high Tm(e) values (86.0 to 88.0) for the heteroduplexes formed. DNA of two of three V. alginolyticus strains (ATCC 17749 and 166-70) was 55 to 60% homologous to reference V. parahaemolyticus DNA preparations; Vibrio sp. strain 5144 (originally classified as V. parahaemolyticus biotype 2 and subsequently as V. alginolyticus strain 5144) showed only 24 to 26% DNA homology to the same reference DNA. These data provide evidence that Vibrio sp. strain 5144 is genetically distinct from the other V. alginolyticus strains used in this study. Three bioluminescent strains thought to be closely related to V. parahaemolyticus demonstrated only 24 to 31% DNA homology to the reference V. parahaemolyticus DNA. These data firmly establish the existence in some Atlantic and Gulf Coast estuaries of organisms genetically very similar to V. parahaemolyticus, the causative agent of "shirasu" food poisoning in Japan.

Polynucleotide sequence relatedness among three groups of pathogenic Escherichia coli strains

Escherichia coli strains that cause dysentery-like disease, parenteral infection, and infantile diarrhea form specific groups based on mobility of O and K antigens in immunoelectrophoresis. Members from each of these groups were assayed for gross nucleotide sequence relatedness. The method used was interspecific deoxyribonucleic acid (DNA) reassociation reactions carried out free in solution. Reassociated DNA was separated from unreacted DNA by passage through hydroxyapatite. DNA relatedness between these groups was approximately 80%. The groups containing those strains causing parenteral infection and those responsible for dysentery-like disease showed preferentially high intragroup DNA relatedness. The group containing strains responsible for infantile diarrhea did not show preferentially high intragroup DNA relatedness with the reference strain employed. These strains, however, did exhibit preferentially high DNA relatedness to a second reference strain.

Deoxyribonucleic acid relatedness among species of Erwinia and between Erwinia species and other enterobacteria

Relatedness in species of Erwinia was assessed by determining the extent of reassociation in heterologous deoxyribonucleic acid preparations. Thermal elution chromatography on hydroxyapatite was used to separate reassociated nucleotide sequences from nonreassociated sequences and to determine the thermal stability of related nucleotide sequences. An apparent 15% core of relatedness is present between fire blight, soft-rot, and "atypical" Erwinia species. All Erwinia species showed low to moderate reaction with representative enteric bacteria.

Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms

Polynucleotide sequence similarity tests were carried out to determine the extent of divergence present in a number of Escherichia coli strains, obtained from diverse human, animal, and laboratory sources, and closely related strains of Shigella, Salmonella, and the Alkalescens-Dispar group. At 60 C, relative reassociation of deoxyribonucleic acid (DNA) from the various strains with E. coli K-12 DNA ranged from 100 to 36%, with the highest level of reassociation found for three strains derived from K-12, and the lowest levels for two "atypical" E. coli strains and S. typhimurium. The change in thermal elution midpoint, which indicates the stability of DNA duplexes, ranged from 0.1 to 14.5 C, with thermal stability closely following the reassociation data. Reassociation experiments performed at 75 C, at which temperature only the more closely related DNA species form stable duplexes, gave similar indications of relatedness. At both temperatures, Alkalescens-Dispar strains showed close relatedness to E. coli, supporting the idea that they should be included in the genus Escherichia. Reciprocal binding experiments with E. coli BB, 02A, and K-12 yielded different reassociation values, suggesting that the genomes of these strains are of different size. The BB genome was calculated to be 9% larger than that of K-12, and that of 02A 9% larger than that of BB. Calculation of genome size for a series of E. coli strains yielded values ranging from 2.29 x 10(9) to 2.97 x 10(9) daltons. E. coli strains and closely related organisms were compared by Adansonian analysis for their relatedness to a hypothetical median strain. E. coli 0128a was the most closely related to this median organism. In general, these data compared well with the data from reassociation experiments among E. coli strains. However, anomalous results were obtained in the cases of Shigella flexneri, S. typhimurium, and "atypical" E. coli strains.

Polyphasic taxonomy of the genus Vibrio: polynucleotide sequence relationships among selected Vibrio species

Polynucleotide relationships among selected Vibrio species were examined by means of deoxyribonucleic acid (DNA) reassociation reactions and chromatography on hydroxyapatite. Relative levels of intraspecific DNA duplex formation (V. cholerae-V. cholerae and V. parahaemolyticus-V. parahaemolyticus) were found to be high at 60 C (>80%), and only minimally reduced at 75 C. Interspecific DNA duplexes between V. cholerae DNA and that of the non-cholera vibrios also exhibited high relative levels of formation at 60 C (>80%) and, with one exception, were only slightly reduced at 75 C. The thermal stability of these duplexes formed at 60 or 75 C was virtually identical to that of homologous V. cholerae DNA duplexes. The degree of reassociation and the thermal stability of V. cholerae-non-cholera vibrio DNA duplexes suggests relatively little evolutionary divergence in these organisms. In all other interspecific DNA reassociation reactions, only low levels of DNA duplex formation were noted at 60 C (<25%), and these were drastically reduced (>50%) at 75 C. The degree of nucleotide sequence divergence indicated by these reactions suggests that these Vibrio species are not significantly related to V. cholerae or V. parahaemolyticus. Reassociation reactions between V. cholerae DNA and the DNA of V. parahaemolyticus indicated these species were not significantly related to each other.

Lack of nucleotide sequence relationship among the temperate bacteriophage SPO2, Bacillus subtilis, and virulent bacteriophages beta 3 and beta 22

Radiolabeled phage SPO2 fragments were tested for the abiity to form interspecies deoxyribonucleic acid (DNA) duplexes with DNA from Bacillus subtilis and from phages beta3 and beta22. No reassociation, above control values, occurred between the DNA of phage SPO2 and that of its host or either of the virulent B. subtilis phages. It appears that extensive nucleotide sequence similarities between portions of host and phage DNA species are not necessary for the formation of the lysogenic state. The thermal elution profile of reassociated SPO2 DNA exhibited a normal distribution, indicating no heterogeneity in base composition. This differs from temperate enterophages whose DNA molecules contain regions of differing base composition.

Polynucleotide sequence relationships among members of Enterobacteriaceae

Polynucleotide relationships were examined among many representatives of the Enterobacteriaceae by means of agar, membrane filter, and hydroxyapatite procedures. The amount of deoxyribonucleic acid (DNA) that reassociated was dependent, especially in interspecific reactions, on the annealing temperature. In only three cases: Escherichia coli-Shigella flexneri, Salmonella typhimurium-S. typhi, and Proteus mirabilis-P. vulgaris, was relative interspecific duplex formation 80% or higher. In most cases interspecies DNA duplex formation was 40% or less of that obtained from intraspecies DNA reassociation reactions. The stability of E. coli-S. flexneri DNA duplexes formed at either 60 or 75 C was virtually identical to that of homologous E. coli DNA duplexes, and the degree of interspecies duplex formation was minimally affected by the temperature increase (86% at 60 C; 77% at 75 C). The thermal stability of DNA duplexes formed at 60 C between DNA from E. coli and DNA from strains of Aerobacter aerogenes, S. typhimurium, S. typhi, and P. mirabilis was about 12 to 14 C below that of reassociated E. coli DNA. At 75 C, the formation of the interspecific DNA duplexes was markedly decreased, but the stability of the DNA able to reassociate at this temperature approximated that of reassociated E. coli DNA. The degree of reassociation and the thermal stability of E. coli-S. flexneri DNA duplexes suggests relatively little evolutionary divergence in these organisms. The other enterobacteria tested, however, have diverged to a point where less than one-half of their DNA can reanneal with E. coli DNA at 60 C and less than 10% reacts at 75 C. The degree of divergence between various enterobacteria does not appear to be uniform along the DNA molecule. Ribosomal ribonucleic acid (RNA)-specific sequences are conserved among most enterobacteria. An examination of messenger RNA relatively specific for the lactose operon suggests that specific chromosomal genes may diverge more or less than the genome as a whole.