Some applications of deoxyribonucleic acid base composition in bacterial taxonomy

The melting pointT _m, the mean molar (guanine+cytosine) composition and the compositional distribution of purified DNA from several strains ofXanthomonas, Chromobacterium and yellow-pigmented marine bacteria have been determined. These groups were selected because they had been analyzed adansonially. Ten strains ofXanthomonas had an average molar (guanine+cytosine) composition within the range 66.0–68.2%, which was very close to that ofPseudomonas (60–68%), as expected. All strains ofChromobacterium (six of theviolaceum biotype and three of thelividum biotype) had mean molar (guanine+cytosine) compositions within the range 63.4–71.4%. The yellow-pigmented marine flavobacteria had mean molar (guanine+cytosine) compositions of 35.6–40.6%. This suggests that they would not be genetically related to the yellow-pigmentedXanthomonas, nor to facultative aerobic organisms, such asAeromonas and theEnterobacteriaceae. The yellow-pigmented marine swarming bacteria, which resembleCytophaga, fell into two separate groups: some had a mean molar (guanine+cytosine) composition of about 34%, others were around 63%. This suggests genetic heterogeneity. The compositional distribution of DNA molecules was on the whole more narrow in polarly flagellated than in peritrichous organisms.     

The physical base of marine bacterial ecology

Specific affinity theory is compared with traditional ways of understanding the nutrient concentration dependency of microbial growth. It is demonstrated that the Michaelis constant increases with the ratio of metabolic enzyme to membrane permease content of bacteria so that small values can reflect specialization for nutrient collection. When compared to the specific affinity, K_t gives a measure of oligotrophic capacity. Specific affinity, on the other hand, reflects nutrient collection ability directly, and increases with the number of permeases. It can be estimated, along with the other kinetic constant, V_max, by use of isotopes in natural samples. Because of systematic errors in estimating V_max, specific affinity is the preferred measure of substrate accumulation ability. The advantage of simultaneous collection of multiple substrates in dilute solution is demonstrated. The structural basis of this advantage is computed from collision frequency and recollision probability, computations that further show that multisubstrate usage is essential for bacterial growth under low-nutrient conditions. Computed growth rates from specific affinities require that several substrates be used simultaneously for growth at measured concentrations. Formulations anticipate that the surface of oligobacteria should be occupied by a diversity of transporter types, that each type of transporter should occupy only a small portion of the cell surface, and the number of cytoplasmic enzymes can be small, allowing small cell size to give a large surface-to-volume ratio for high specific affinity. The large number of substrate types that may be accumulated by a single oligobacterial species is consistent with extensive species diversity.     

The importance of dispersal for bacterial community composition and functioning

We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into.     

The evolution of base composition and phylogenetic inference

Base composition varies at all levels of the phylogenetic hierarchy and throughout the genome, and can be caused by active selection or passive mutation pressure. This variation can make reconstructing trees difficult. However, recent tree-based analyses have shed light on the forces responsible for the evolution of base composition, forces that might be very general. More explicit tree-based work is encouraged.     

The relationship of DNA base composition and individual protein composition in micro-organisms

Summary To investigate the dependence of protein composition on DNA base composition, a set of data on individual proteins with known amino acid compositions from a spectrum of bacterial species has been compiled. It is found that similar relationships of amino acid frequency to G + C content exist for these proteins as for the bulk proteins studied by Sueoka (1961). The data are analysed by linear and cubic regression, and a measure of the proportions of A + T-rich and G + C-rich codons in the underlying messenger RNAs is put forward. The theoretical limits on the G + C content of coding DNA are discussed, and inference are made about the various selective forces acting on DNAs of different G + C contents.     

The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences

Bacterial genes that code for proteins appear to possess a codon usage characteristic of their overall base composition. This results in different but predictable non-random distributions of nucleotides within codons, permitting the recognition of protein-coding sequences in a wide range of bacterial species. The nature of this distribution depends on the base composition of the coding sequence. The position-specific differences are especially conspicuous in genes of extreme G + C content, allowing the particularly reliable prediction of the reading frame and coding strand of experimentally determined DNA sequences. This fmding has been exploited to identify the coding sequence of the viomycin phosphotransferase (vph) gene of Streptomyces vinaceus. An easily applied computer program (“Frame”) has been written to carry out and display such analyses.     

The relationship between the base composition of bacterial DNA and its intracellular melting temperature as determined by differential scanning calorimetry

The correlation between the melting temperature of intracellular DNA, determined by differential scanning calorimetry (DSC) of whole bacteria, and its guanine + cytosine (G + C) content, was examined for 58 species of bacteria. Samples of vegetative cells were heated in a Perkin-Elmer DSC-2C at 10 degrees C min-1 from 5 to 130 degrees C, cooled to 5 degrees C and then re-heated as before. Literature values for the mole fraction of G + C, XGC, were linearly related to the temperature, Tmax, at which the reversible peak, pr, observed on the second heating run was at a maximum, via the equation XGC = (Tmax -73.8)/41.0. This equation accounted for 91.9% of the variance in XGC with 95% confidence limits of +/- 7.3%, approximately 1.6 times the corresponding uncertainty (+/- 4.5%) quoted by De Ley (Journal of Bacteriology 101, 738-754, 1970) for estimates based on the spectroscopically determined melting temperature of purified DNA. Random errors of measurement of Tmax did not greatly limit the precision of the prediction and it was concluded that factors additional to base composition affected the temperature of DNA melting within the bacterial cell. Displacement of Tmax values from the fitted line was particularly noticeable in Campylobacter, Corynebacterium and Bacterionema species and part of the residual variation appeared to be species specific, possibly caused by differences in intracellular solute concentration.     

DNA base composition ofKlebsiella rubiacearum

The base composition of pure DNA from a strain of a nitrogen-fixing leaf-nodule bacterium was determined. The mean molar (guanine + cytosine) composition of 55.5% is in agreement with previous conclusions that this bacterium belongs in the genusKlebsiella.     

Risk factors for bacterial catheter colonization in regional anaesthesia

BACKGROUND: Although several potential risk factors have been discussed, risk factors associated with bacterial colonization or even infection of catheters used for regional anaesthesia are not very well investigated. METHODS: In this prospective observational trial, 198 catheters at several anatomical sites where placed using a standardized technique. The site of insertion was then monitored daily for signs of infection (secretion at the insertion site, redness, swelling, or local pain). The catheters were removed when clinically indicated (no or moderate postoperative pain) or when signs of potential infection occurred. After sterile removal they were prospectively analyzed for colonization, defined as > 15 colony forming units. RESULTS: 33 (16.7%) of all catheters were colonized, and 18 (9.1%) of these with additional signs of local inflammation. Two of these patients required antibiotic treatment due to superficial infections. Stepwise logistic regression analysis was used to identify factors associated with catheter colonization. Out of 26 potential factors, three came out as statistically significant. Catheter placement in the groin (odds-ratio and 95%-confidence interval: 3.4; 1.5-7.8), and repeated changing of the catheter dressing (odds-ratio: 2.1; 1.4-3.3 per removal) increased the risk for colonization, whereas systemic antibiotics administered postoperatively decreased it (odds ratio: 0.41; 0.12-1.0). CONCLUSION: Colonization of peripheral and epidural nerve catheter can only in part be predicted at the time of catheter insertion since two out of three relevant variables that significantly influence the risk can only be recorded postoperatively. Catheter localisation in the groin, removal of the dressing and omission of postoperative antibiotics were associated with, but were not necessarily causal for bacterial colonization. These factors might help to identify patients who are at increased risk for catheter colonization.     

Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition

We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC --> AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC --> AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC --> AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.     

Theoretical models for heterogeneity of base composition in DNA

Data on DNA base composition heterogeneity and molecular size, mainly from bacteria, are compiled from the literature. A series of theoretical models of increasing complexity is put forward, and it is concluded that the data support a model in which the DNA consists of a sequence of “segments” with different underlying base compositions. Estimates of mean segment length and variance of G + C content are made. The possibility that the excess heterogeneity above random results from variation in the composition of coded proteins is considered and rejected. It is concluded that the heterogeneity is probably caused by variations in the relative use of synonymous codons in different genes.     

Spectral analysis for base composition of DNA undergoing melting

A microcomputer-controlled spectrophotometer is described for obtaining the base composition of melting domains in DNA from derivative melting curves. Values have been determined for the differential molar extinction coefficients for the A-T and G-C base pair at the three wavelengths most useful for spectral analysis of base composition, 260, 270 and 282 nm. The average RMS error for these values was 29 l(mol X cm)-1 for the melting of 14 DNA specimens ranging in base composition from 0-0.72 F(G + C). A precision of approximately 1% in base composition of domains is possible. Such analysis is useful for confirming or establishing assignments of domains to particular subtransitional features in high resolution melting curves.     

The amino acid composition of mammalian and bacterial cells

Summary High performance liquid chromatography was used to analyze the amino acid composition of cells. A total of 17 amino acids was analyzed. This method was used to compare the amino acid compositions of the following combinations: primary culture and established cells, normal and transformed cells, mammalian and bacterial cells, andEscherichia coli andStaphylococcus aureus. The amino acid compositions of mammalian cells were similar, but the amino acid compositions ofEscherichia coli andStaphylococcus aureus differed not only from mammalian cells, but also from each other. It was concluded that amino acid composition is almost independent of cell establishment and cell transformation, and that the amino acid compositions of mammalian and bacterial cells differ. Thus, it is likely that changes in amino acid composition due to cell transformation or species differences between mammalian cells are negligible compared with the differences between mammalian and bacterial cells, which are more distantly related.     

The quick approximation of DNA base composition from absorbancy ratios

The approximate base composition of pure deoxyribonucleic acid (DNA) can be quickly estimated from the absorbancy ratio E₂₆₀/E₂₈₀ in 0.1n acetic acid according to the empirical relation % GC=168.6–87.4 (E₂₆₀/E₂₈₀), valid in the range 40 to 70% GC (molar per cent guanine ... cytosine). The method is only accurate to within + 3% GC. It can be used when a quick, rough estimate of DNA base composition is required, e.g., to check the correct taxonomic position of new isolates or to give an approximation of the melting point T_m or buoyant density of an unknown DNA sample. The method can not be recommended for distinguishing between two genera with closely related % GC values, or for finer distinction within one genus.     

Deoxyribonucleic acid base composition of simonsiellaceae

The molar percentages of guanine plus cytosine in the DNA of 51 strains of Simonsiellaceae were determined by buoyant density ultracentrifugation of cell lysates in CsCl. The DNA base ratios ranged from 41–55 mole-% guanine plus cytosine. These values fall within the range known for the Order Cytophagales, the non-fruiting gliding bacteria, and are out-side the range of the Order Myxobacterales, the fruiting myxobacteria. Among the strains of the genus Simonsiella, four distinct groups can be delineated on the basis of source of origin (sheep, dog, cat, human) and GC content. The neotype of Alysiella filiformis has a GC content of 45.4 mole-%.