DNA-DNA homology studies among strains of Arthrobacter and Brevibacterium

Sixteen named strains of Arthrobacter and two strains of Brevibacterium were investigated by nucleic acid hybridisation. The Arthrobacter strains show homology values ranging between 11 and 55% to the type strain A. globiformis DSM 20124 (ATCC 8010), indicating only a low to moderate relationship. Two strains of A. globiformis, DSM 20124 and DSM 20125, exhibit only poor relationship to one another (30%). Among all the Arthrobacter strains the homology data range between 10 to 70% demonstrating separate status of almost all species. Only A. polychromogenes DSM 20136 was found to be a subspecies of A. oxydans DSM 20119. The type strain of A. citreus, DSM 20133 shows a remarkable lack of homology to four other strains of A. citreus, deposited as ATCC 15170, ATCC 17775, ATCC 21040 and ATCC 21348 (11–13%) which themselves can be separated into two groups according to the homology data (24–31%). Each of the two strains of Brevibacterium share high genetic relatedness with one of these A. citreus groups (71 and 73%, respectively). According to the DNA-DNA homology data, most of the species of Arthrobacter can actually be ranged taxonomically as species.Abbreviation DSM German Collection of Microorganisms, Menzinger Strasse 67, D-8000 Munich 19, FRG - ATCC American Type Culture Collection, Rockville, Maryland, U.S.A. - CCM Czechoslovak Collection of Microorganisms, J. E. Purkyne University, Tr. Obracu miru 10, Brno, CSSR - NCIB National Collection of Industrial Bacteria Aberdeen, Scotland     

DNA-DNA homology among lactose- and sucrose-fermenting transconjugants from Lactococcus lactis strains exhibiting reduced bacteriophage sensitivity

DNA-DNA homology between a reduced bacteriophage sensitivity (Rbs+) probe and DNA from both Rbs+ and Rbs- Lactococcus lactis strains was examined. Homology was detected between the probe and five plasmids (pCI750, pCC34, pEB56, pNP2, and pJS88) isolated from lactose-positive Rbs+ transconjugants and between the probe and genomic DNA of a sucrose-positive Rbs+ transconjugant. Additionally, hybridizations conducted between the probe and plasmids reported to encode abortive bacteriophage infection indicated homology with pTR2030 but not with pBF61 and pGBK17. The results suggest that a common genetic determinant(s) may be present in a variety of lactococcal plasmids coding for Rbs+.     

DNA-DNA homology among lactose- and sucrose-fermenting transconjugants from Lactococcus lactis strains exhibiting reduced bacteriophage sensitivity.

DNA-DNA homology between a reduced bacteriophage sensitivity (Rbs+) probe and DNA from both Rbs+ and Rbs- Lactococcus lactis strains was examined. Homology was detected between the probe and five plasmids (pCI750, pCC34, pEB56, pNP2, and pJS88) isolated from lactose-positive Rbs+ transconjugants and between the probe and genomic DNA of a sucrose-positive Rbs+ transconjugant. Additionally, hybridizations conducted between the probe and plasmids reported to encode abortive bacteriophage infection indicated homology with pTR2030 but not with pBF61 and pGBK17. The results suggest that a common genetic determinant(s) may be present in a variety of lactococcal plasmids coding for Rbs+.     

DNA-rRNA hybridization studies on Halococcus saccharolyticus and other halobacteria

Abstract Several representative extremely halophilic archaea (formerly archaebacteria) were studied with respect to their genetic relatedness by using a DNA-rRNA hybridization approach. Our results confirm the phylogenetic relatedness of Halococcus morrhuae and Halococcus saccharolyticus but support their separation as two different taxa, at least at species level. In addition, this phylogenetic relatedness was significantly lower than that between species belonging to the genera Haloferax and Haloarcula .     

Efficient hydroxylamine mutagenesis ofHaloferax mediterranei and other extremely halophilic archaebacteria

The lethal and mutagenic effects of hydroxylamine onHaloferax mediterranei and five other extremely halophilic archaebacteria are described for the first time. Although previous studies have shown thatH. mediterranei was very resistant to the lethal action of other DNA-damaging agents, this strain was found to be relatively sensitive to hydroxylamine, but also more successfully mutated by the latter. The efficiency of the mutagenicity obtained with the hydroxylamine treatment was tested under a variety of conditions, and optimal procedures are described that yielded a number of useful auxotrophic mutant strains ofH. mediterranei. Likewise, a strong induced mutagenicity after hydroxylamine mutagenesis was achieved for the majority of the other archaebacteria tested.     

DNA-DNA hybridization studies and phenotypic characteristics of strains within the 'Streptococcus milleri group'

Twenty-five strains resembling 'Streptococcus milleri' were compared by DNA-DNA hybridization, by whole-cell-derived polypeptide patterns on SDS-PAGE, and by biochemical tests. Four homology groups were revealed by DNA-DNA hybridization. DNA homology groups 1, 2 and 3 were closely related and contained the type strains NCDO 2226 (Streptococcus constellatus), NCDO 2227 (Streptococcus intermedius) and NCTC 10713 (Streptococcus anginosus), respectively. DNA homology group 4 consisted of four strains received as variants of Streptococcus intermedius which were found not to be closely related to strains in groups 1-3. The data from SDS-PAGE polypeptide patterns and biochemical tests supported the recognition of three centres of variation within the 'Streptococcus milleri group' corresponding to DNA homology groups 1-3 and indicated that strains of DNA homology group 4 are members of an as yet undescribed species within the viridans streptococci.     

Stringency and relaxation among the halobacteria.

Accumulation of stable RNA and production of guanosine polyphosphates (ppGpp and pppGpp) were studied during amino acid starvation in four species of halobacteria. In two of the four species, stable RNA was under stringent control, whereas one of the remaining two species was relaxed and the other gave an intermediate phenotype. The stringent reaction was reversed by anisomycin, an effect analogous to the chloroamphenicol-induced reversal of stringency in the eubacteria. During the stringent response, neither ppGpp nor pppGpp accumulation took place during starvation. In both growing and starved cells a very low basal level of the two polyphosphates appeared to be present. In the stringent species the intracellular concentration of GTP did not diminish but actually increased during the course of the stringent response. These data demonstrate that (i) wild-type halobacteria can have either the stringent or the relaxed phenotype (all wild-type eubacteria tested have been shown to be stringent); (ii) stringency in the halobacteria is dependent on the deaminoacylation of tRNA, as in the eubacteria; and (iii) in the halobacteria, ppGpp is not an effector of stringent control over stable-RNA synthesis.     

DNA-DNA and rRNA-DNA hybridization studies in the genus Ectothiorhodospira and other purple sulfur bacteria

DNA-DNA hybridization reveals low DNA homologies (about 14%) between the species of Ectothiorhodospira genus and indicate clearly that the degree of divergence within this genus exceeds the interspecific level. The degree of genome similarities of E. mobilis and E. vacuolata (more than 80% homology) is high and characteristic for the strains of one and the same species.The results of rRNA-DNA and secondary DNA-DNA hybridization indicate the following: Ectothiorhodospira and Thiocapsa are far less related than the genera of one and the same family; the genus Ectothiorhodospira is equidistant from both families of purple sulfur and nonsulfur bacteria. Thus Ectothiorhodospira is a taxon of a higher rank than a genus; we agree with Imhoff's proposal of a new family Ectothiorhodospiraceae.     

RNA polymerase subunit homology among cyanobacteria, other eubacteria and archaebacteria.

RNA polymerase purified from vegetative cells of the cyanobacterium Anabaena sp. strain PCC 7120 contains a dissociable sigma factor and a core of five subunits: the beta', beta, and two alpha subunits characteristic of all eubacteria and an additional 66,000-molecular-weight polypeptide called gamma. Fifteen of fifteen strains of unicellular and filamentous cyanobacteria tested contained a serologically related gamma protein. Antiserum to gamma reacted with Escherichia coli beta' and the A subunit of RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Thus the evolution of the RNA polymerase beta' subunit has followed different paths in three groups of procaryotes: cyanobacteria, other eubacteria, and archaebacteria.     

Differentiation of lactic streptococcal phages into phage species by DNA-DNA homology

Twenty-five lactic streptococcal bacteriophages were differentiated by DNA homology into four species. Complete correlation was found between DNA homology groups and morphological characteristics of the phages except that two phage types, which differed in only the presence or absence of a collar, were one species by DNA homology. These findings were supported by serological data and differences in DNA molecular weights of the proposed species. The complete lack of homology between these phage species indicates that they are unlikely to have a recent common phage ancestor and that one morphological type of phage has not been derived by mutation from a phage of another morphological type.     

The future of DNA-DNA hybridization studies

Summary This article draws on many vertebrate examples to assess the future of DNA-DNA hybridization studies. I first discuss whether applications of the method have reached the point of diminishing returns, or rather the start of a great leap forward, in our evolutionary understanding. Vertebrate groups whose relationships are especially likely to be illuminated include parrots, pigeons, bats, pinnipeds, mammalian carnivores, frogs, and rodents. There are at least two reasons why classifications based on DNA-DNA hybridization may prove to differ from classifications based on particular character, whether these be noncoding DNA sequences or protein sequences or anatomical characters. Because evolutionary relationships can now be deduced independently of anatomical characters, this should permit a renaissance in comparative anatomical studies of adaptation. The origin of major functional shifts from changes in a small fraction of the genome is illustrated by polar bears, sea otters, warblers, vultures, and especially by humans.     

Antagonistic interactions among halobacteria due to halocin production

Abstract By using 3 different methods for the detection of antagonism, complex patterns of this type of interaction were evident within a group comprising 79 halobacterial strains, which included the most divergent types of culture collection strains available, as well as freshly isolated ones. The experiments carried out showed that such interactions are not due to phages, but to the effects of bacteriocin-like substances, known as halocins. With the exception of only 2 strains, all the remainder caused inhibition to a greater or lesser degree, showing a wide variety of activity spectra. Comparative numerical analysis of these spectra revealed the existence of at least 15 different groups of halocins.     

Variation of virulence and other properties among Sendai virus strains

The virulence of five Sendai virus strains (MN, Z, KN, Mol, and Hm) isolated from laboratory rodents was compared, using 3-week-old female Jcl-ICR mice. The virulence of the strains was Mol, MN, KN, Z, and Hm in decreasing order. The 50% lethal dose and 50% lung consolidation inducing dose of the highest virulent strain differed by the order of more than 10(3) and 10(6), respectively, from those of the lowest virulent one. Other properties such as the growth rate in LLC-MK2 cells, neuraminidase activities, and molecular weights of structural proteins also differed among the virus strains. These results indicate that Sendai virus prevailing in laboratory rodents is not homogenous with respect to virulence and some other properties.     

Differentiation of lactic streptococcal phages into phage species by DNA-DNA homology.

Twenty-five lactic streptococcal bacteriophages were differentiated by DNA homology into four species. Complete correlation was found between DNA homology groups and morphological characteristics of the phages except that two phage types, which differed in only the presence or absence of a collar, were one species by DNA homology. These findings were supported by serological data and differences in DNA molecular weights of the proposed species. The complete lack of homology between these phage species indicates that they are unlikely to have a recent common phage ancestor and that one morphological type of phage has not been derived by mutation from a phage of another morphological type.     

PCR-RFLP and total DNA homology revealed three related genomic species among broad-host-range Frankia strains

Abstract: Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified nif D-K intergenic spacer (IGS) region was used to cluster 22 Frankia strains of the Elaeagnus host specificity group into seven genomic groups and to measure the degree of genetic similarity among them. This PCR-RFLP analysis could assign freshly isolated strains to described genomic species and revealed genomic groups not yet described among Frankia strains of the Elaeagnus specificity group. Six broad-host-range Frankia strains, infective on both Alnus and Elaeagnus , fell into three closely related PCR-RFLP clusters. DNA-DNA hybridization was then used to establish the correlations between PCR-RFLP clusters and total DNA relatedness groups. The three PCR-RFLP clusters agreed with two new and one reference genomic species, indicating that Frankia ability to nodulate with Alnus and Elaeagnus is a monophyletic trait shared by three genomic species.