DNA base composition of planktonic species of Anabaena (Cyanobacteria) and its taxonomic value

Fifty axenic strains of planktonic Anabaena, including 24 strains of the straight form and 26 strains of the coiled form, were examined for their DNA base composition (GC content). The taxonomic value of their GC content at species level was evaluated by comparing their morphological, physiological and biochemical properties. The DNA base composition determined for all fifty strains ranged from 35.9 to 56.4 mol% GC. The straight-form strains were in the range of 35.9-56.4 mol% GC, while coiled forms were in the range of 38.1-50.3 mol% GC. In general, strains assigned to the same species showed similar DNA base composition. However, of three strains of A. affinis Lemmermann that were separated into two categories, two had 40.6-40.9 mol% GC, and the third strain 45.6 mol% GC. It is noteworthy that the DNA base composition of the newly established species A. eucompacta Li et Watanabe was 45.5 mol% GC, which differed from 39.5 mol% GC of the morphologically close species, A. compacta (Nygarrd) Hickel.     

Reexamination of the Association Between Melting Point, Buoyant Density, and Chemical Base Composition of Deoxyribonucleic Acid

The equations currently used for the calculation of the chemical base composition of deoxyribonucleic acid (DNA), expressed as moles per cent guanine plus cytosine (% GC), from either buoyant density (rho) or midpoint of thermal denaturation (T(m)) were recalculated by using only sets of data on DNA determined with the same strains. All available information from the literature was screened and supplemented by unpublished data. The results were calculated by regression and correlation analysis and treated statistically. From the data on 96 strains of bacteria, it was calculated that% GC = 2.44 (T(m) - 69.4). T(m) appears to be unaffected by the substitution of cytosine by hydroxymethylcytosine. This equation is also valid for nonbacterial DNA. From the data on 84 strains of bacteria, the relation% GC = 1038.47 (-1.6616) was calculated. The constants in this equation are slightly modified when data on nonbacterial DNA are included. Both correlations differ only slightly from those currently used, but now they lean on a statistically sound basis. As a control, the relation between rho and T(m) was calculated from data of 197 strains; it agrees excellently with the above two equations.     

Use of Lysostaphin in the Isolation of Highly Polymerized Deoxyribonucleic Acid and in the Taxonomy of Aerobic Micrococcaceae

By use of the staphylolytic enzyme lysostaphin, a method was devised for isolating and purifying highly polymerized deoxyribonucleic acid (DNA) from lysostaphinsusceptible Micrococcaceae. Staphylococcus aureus DNA isolated by this procedure gave an estimated molecular weight of ca. 2 x 10(8) and a residual protein content of 2.3%. The mole percentage of guanine + cytosine (GC) present in the DNA from 21 strains of aerobic Micrococceae was determined by buoyant density in cesium chloride. DNA from 12 biochemically typical members of the genus Staphylococcus gave a mean GC composition of 35.2 +/- 0.5 mole per cent. Four biochemically atypical Staphylococcus strains and one biochemically typical strain of the genus Micrococcus (M. candicans) were found to be susceptible to lysostaphin and gave typical Staphylococcus spp. GC base ratios. One biochemically atypical member of the genus Micrococcus (M. varians) was not susceptible to lysostaphin and gave a typical Micrococcus spp. GC base ratio. Lysostaphin susceptibility is an easy test to perform, and the results of this test appear to correlate with GC base ratio studies of the genera of Micrococcaceae.     

Deoxyribonucleic Acid Base Composition in the Taxonomy of Staphylococcus

Twenty-four strains of Staphylococcus aureus, including eight known mutants of S. aureus and strains growing under a variety of environmental conditions or exposed to a number of physical and chemical agents, maintained a remarkably narrow range of guanine plus cytosine (GC) content (32.4 to 35.1%). The wide range of GC content (30.7 to 40%) reported in the literature was due to the variety of methods and calculations used rather than to any substantial variation in base composition. The UV-2 "mutant" (ATCC 13680) with a GC content of 67.6% reported to be derived from S. aureus (ATCC 13679) was a species of Corynebacterium. The data presented were consistent with the concept that base composition changes only to a very slight degree by mutation.     

Agreement Between Deoxyribonucleic Acid Base Composition and Taxometric Classification of Gram-Positive Cocci.

Silvestri, L. G. (Università Statale, Milan, Italy), and L. R. Hill. Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci. J. Bacteriol. 90:136-140. 1965.-It had been previously proposed, from taxometric analyses, that gram-positive, catalase-positive cocci be divided into two subgroups. Thirteen strains, representative of both subgroups, were examined for deoxyribonucleic acid (DNA) base composition, determined from melting temperatures. Per cent GC (guanine + cytosine/total bases) values fell into two groups: 30.8 to 36.5% GC and 69 to 75% GC. Strains with low per cent GC values belonged to the Staphylococcus aureus-S. saprophyticus-S. lactis taxometric subgroups, and those with high per cent GC values belonged to the S. roseus-S. afermentans subgroup. The hypothetical nature of any classification is emphasized, and, in the present work, the hypothesis derived from taxometric analyses of division into two subgroups is confirmed by the study of DNA base ratios. The two subgroups correspond, respectively, to the genera Staphylococcus and Micrococcus.     

Genetic heterogeneity among Lactobacillus acidophilus strains

Physiological characteristics, DNA base composition (% GC) and DNA-DNA reassociation values were determined for 138 Lactobacillus acidophilus strains. Twenty seven strains were received from various culture collections and 111 strains were freshly isolated during a study on the composition of the intestinal lactic microflora of piglets and suckling calves.All strains had physiological characteristics which were substantially similar. The strains isolated from pigs were unable to ferment trehalose. The % GC ranged from 35.8 to 43.4.On the basis of the results of DNA-DNA hybridization the strains were divided into four genetic groups.This study was partially supported by grants from the Consiplio Nazionale Ricerche (C.N.R.).     

Deoxyribonucleic Acid Base Composition of Rothia dentocariosa as Determined by Thermal Denaturation

The moles per cent guanine plus cytosine (GC) of 10 filamentous strains of Rothia dentocariosa ranged from 65.4 to 69.7. Major differences were not observed in the base composition of a filamentous form (69.7 moles% GC) and its coccal variant (68.0 moles% GC).     

Classification of the genus Humicola Traaen: II. The DNA base composition of some strains within the genus

The base composition of DNA (GC content) of 25 strains, morphologically referred to the genusHumicola Traaen, is studied. The range of GC% variation is about 23 % (from 28,5 % to 51,6). Two prominent groups of strains with similar GC content may be distinguished: one ranging from 28 % to 37 % and the other ranging from 40 % to 49 %. The aleuriospore size is not related to the DNA base composition, but a group of strains with prevalently coloured hyphae, with aleuriospores of similar size and with high GC content is recognized. Several previous literature reports on the taxonomy ofHumicola are discussed.     

DNA Base Composition and Esterase Patterns of Bacteria Isolated from Deep Sea Sediments

Electrophoretic patterns of esterase isozymes and DNA base compositions were determined for 38 marine bacteria, 31 strains of which were from sediment samples collected at depths of 9400–10,400 in in the Philippine and Marianas Trenches of the Pacific Ocean, and 7 from seawater samples collected at various depths of surface–4000 m and from several locations in the Pacific Ocean. Previous numerical taxonomic analysis indicated 5 distinct phenetic clusters; 4 identified as Pseudomonas and 1 as aerogenic Aeromonas. In this study, the DNA base composition range for the entire sample set was found to be 41–59 moles % of GC. However, 32 of the 38 strains possessed a GC of c. 57%. In general, strains belonging to the same phenon possessed nearly identical DNA base composition and demonstrated similar esterase patterns.     

Deoxyribonucleic Acid Base Composition of Some Members of the Subgenera Betabacterium and Streptobacterium

The base composition of deoxyribonucleic acid (DNA) prepared from four Betabacterium strains and four Streptobacterium strains was determined. Per cent GC values (guanine + cytosine/total bases) of the DNA were evaluated from the “melting-temperatures” (Tm) of the nucleic acids. For the Betabacterium strains, these values ranged from 44 to 51.5% GC, and those for the Streptobacterium strains ranged from 43 to 47.5% GC. The taxonomic division into these two subgenera is not, therefore, supported by these findings.     

Deoxyribonucleic acid base composition ofMicrococcus roseus

The percentage guanine + cytosine (GC) in the DNA of 13 strains ofMicrococcus roseus has been determined. Two methods were used to analyse the base composition, namely determination of T _m value and determination of the ratio E₂₆₀/E₂₈₀ at pH 3. The percentage GC in the strains ofM. roseus ranged from 66.2 to 73.8 and was in agreement with their present taxonomic position.     

Use of Shake Cultures in a Semisolid Thioglycolate Medium for Differentiating Staphylococci from Micrococci

The standard diagnostic test for differentiating staphylococci from micrococci is based on the ability of the former to produce acid anaerobically in a glucose-containing growth medium. This test has been modified to provide greater convenience, easier interpretation of results, and better correlation with deoxyribonucleic acid (DNA) base composition. In the modified test, shake cultures in Brewer's fluid thioglycolate medium with 0.3% agar added are observed for growth in the anaerobic zone of the tubes. This test was applied to 125 strains of staphylococci and micrococci, and all except two strains gave results that were consistent with other criteria. Of particular interest were eight strains of Micrococcus saprophyticus and three strains of M. lactis that have a DNA composition of 30 to 37% guanine plus cytosine (GC). All 11 of these cultures produced anaerobic growth and thus would be classified as staphylococci. Strains of M. lactis that have a high GC content in their DNA grew only aerobically. Some cultures of staphylococci produced characteristic band patterns of anaerobic growth and other cultures produced only a few anaerobic colonies from an inoculum of 10(6) to 10(7) cells. These observations suggest some interesting genetic and metabolic capabilities in such cultures.     

DNA base composition of some sheathed bacteria

The DNA base composition of five recently isolated Haliscomenobacter hydrossis strains were compared with those of Sphaerotilus natans, Leptothrix cholodnii and Leptothrix discophora. The DNA base composition of H. hydrossis strains ranged from 48.3 to 49.7% GC, whereas the % GC values of S. natans, L. cholodnii and L. discophora were found to be 69.7, 69.6 and 71.2, respectively. These results indicate that Haliscomenobacter species and the microorganisms of the Sphaerotilus-Leptothrix group should not be classified into the same genus, as they are genetically at best remotely related.The reallocation of some Leptothrix species into the genus Sphaerotilus is not in contradiction with their DNA base composition.     

Deoxyribonucleic Acid Base Composition of Species in the Yeast Genus Kluyveromyces van der Walt emend. van der Walt

The deoxyribonucleic acid base composition (percent guanine + cytosine [GC]) was determined for 29 strains, representing 18 species of the genus Kluyveromyces. It was concluded that on the basis of GC content (47.4%) and other properties K. veronae occupies an uncertain position in the genus Kluyveromyces. The GC content of the remaining 17 species ranged from 35.3 to 43.4%, and three groups of species were recognized. The GC content of the first ranged from 35.3 to 38.0%; that of the second group from 39.5 to 41.7%; that of the third group from 42.4 to 43.4%. Several species revealed a nearly identical GC content. The GC contents do not correspond in all instances with the five groups of species proposed by van der Walt.     

Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis

Base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of Aquifex aeolicus and Bacillus subtilis, having different optimal growth temperatures. These two bacteria do not have significant difference in overall GC composition, but GC(1+2) and GC3 levels were found to vary significantly. Significant increments in purine content and GC3 composition have been observed in the coding sequences of Aquifex aeolicus than its Bacillus subtilis counterparts. Correspondence analyses on codon and amino acid usages reveal that variation in base composition actually influences their codon and amino acid usages. Two selection pressures acting on the nucleotide level (GC3 and purine enrichment), causes variation in the amino acid usage differently in different protein secondary structures. Our results suggest that adaptation of amino acid usages in coil structure of Aquifex aeolicus proteins is under the control of both purine increment and GC3 composition, whereas the adaptation of the amino acids in the helical region of thermophilic bacteria is strongly influenced by the purine content. Evolutionary perspectives concerning the temperature adaptation of DNA and protein molecules of these two bacteria have been discussed on the basis of these results.     

Determination of guanine-plus-cytosine content of bacterial DNA by dual-laser flow cytometry

A dual-laser flow cytometer was used to analyse different species of bacteria for the molar percentage of guanine-plus-cytosine (% G + C) without the need for DNA extraction or purification. Ethanol-fixed bacterial cells were stained with a combination of DNA-specific fluorochromes, Hoechst 33258 and chromomycin A3, which bind to AT- and GC-rich regions of DNA, respectively. A linear relationship (r = 0.99) was demonstrated between the log of the ratio of chromomycin A3 to Hoechst 33258 fluorescence and the log of the % G + C as determined by thermal denaturation (Tm) or buoyant density centrifugation (Bd) methods. Linearity was maintained for all bacterial species tested over the range of 28-67% G + C. A standard curve was constructed using five strains whose % G + C had been determined by other methods. From the equation describing this line, the % G + C values of nine other strains with known DNA base composition, together with the five strains used to construct the curve, were calculated using the chromomycin A3 to Hoechst 33258 ratio and were in agreement with values obtained by Tm, Bd or HPLC. The reproducibility of flow cytometric analysis (mean error 0.7% G + C) compared well with the reproducibility of other methods. Mixtures containing two species were also analysed. Two cell populations could be discerned in mixtures containing two species which differed in base composition by as little as 4% G + C.(ABSTRACT TRUNCATED AT 250 WORDS)     

DNA Base composition of soil arthrobacters and other coryneforms from cheese and sea fish

The DNA base composition of 34 coryneforms isolated from different sources, and those of 20 named cultures of the generaArthrobacter, Brevibacterium,Mycobacterium, Corynebacterium andNocardia has been determined. A preliminary study of the morphological and physiological characteristics of the new isolates, and some named cultures, led to a division into three groups:

1. Soil coryneforms identified as arthrobacters, completed with theArthrobacter globiformis strains ATCC 8602 and 8010.
2. Orange coryneforms and one white isolate from cheese, and orange coryneforms including one yellow isolate from sea fish, completed with twoBrevibacterium linens strains ATCC 9174 and 9175.
3. Non-orange cheese coryneforms.

DNA base composition of group (1) ranges from 65.3 to 67.0 molar % GC, suggesting that this group is genetically homogeneous. % GC values of group (2) range from 62.6 to 64.0 except for one isolate (65.6), suggesting that this group is also homogeneous. DNA base composition of group (3) ranges from 65.5 to 66.9 % GC, except for three isolates (56.5, 60.1, 60.6). It is concluded that as far as their % GC is concerned, the strains of group (3), except the threem entioned ones, may be closely related to the arthrobacters of group (1). The strains of group (2) are probably less closely related to those of the groups (1) and (3).     

Characterization of Deoxyribonucleic Acids from Streptomycetes and Nocardiae

The relationships among selected streptomycetes, nocardiae, and mycobacteria have been determined, based upon the base composition of their deoxyribonucleic acid (DNA) and upon the ability of their denatured DNA to anneal with single-stranded reference DNA. The streptomycetes constituted a homogeneous group whose DNA contained between 69 and 73 mole% guanine + cytosine (% GC). Moreover, the streptomycetes examined showed 37 to 88% homology with the Streptomyces venezuelae and S. rimosus reference DNA. The nocardial and mycobacterial DNA both contained 62 to 69% GC. The nocardial strains studied fell into either a 62 to 64% GC group or a 68 to 69% GC group, indicating that they should not be assigned to a single species. The nocardiae having 68 to 69% GC showed 24 to 44% homology with S. venezuelae reference DNA. In competition experiments, wherein unlabeled heterologous DNA interfered with binding of labeled homologous DNA, the nocardial DNA with 68 to 69% GC showed a greater degree of homology with the streptomycetes than did the nocardial DNA with 62 to 64% GC. In addition, the DNA from spores of S. venezuelae was cursorily examined, and interactions between S. venezuelae denatured DNA and polyribonucleotides were sought. The buoyant density of the DNA from S. venezuelae spores was distinctly less than that from mycelia. Moreover, denatured S. venezuelae DNA formed a dense complex with polyriboguanylate.     

GC-biased segregation of noncoding polymorphisms in Drosophila

The study of base composition evolution in Drosophila has been achieved mostly through the analysis of coding sequences. Third codon position GC content, however, is influenced by both neutral forces (e.g., mutation bias) and natural selection for codon usage optimization. In this article, large data sets of noncoding DNA sequence polymorphism in D. melanogaster and D. simulans were gathered from public databases to try to disentangle these two factors-noncoding sequences are not affected by selection for codon usage. Allele frequency analyses revealed an asymmetric pattern of AT vs. GC noncoding polymorphisms: AT --> GC mutations are less numerous, and tend to segregate at a higher frequency, than GC --> AT ones, especially at GC-rich loci. This is indicative of nonstationary evolution of base composition and/or of GC-biased allele transmission. Fitting population genetics models to the allele frequency spectra confirmed this result and favored the hypothesis of a biased transmission. These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content.     

Physiologische und biochemische Beiträge zur Taxonomie der Gattungen Ankistrodesmus und Scenedesmus

The base composition of the DNA was found to be a species-specific, taxonomically valuable character also in the genera Ankistrodesmus (21 strains) and Scenedesmus (27 strains). As compared to the genus Chlorella, however, the differences between different species are considerably smaller. The GC content is between 63 and 70% in the genus Ankistrodesmus, and between 52 and 62% in the genus Scenedesmus. Obviously, a few strains with a very much different base composition do not belong to the genus Ankistrodesmus.