Nucleotide distribution in bacterial DNA's differing in G + C content

Summary The DNA's ofMicrococcus lysodeikticus andClostridium perfringens were fragmented to about 7 000 nucleotide pairs long by shear and fractionated with respect to buoyant density of mercury complexes in Cs₂SO₄. The distribution of G + C content in both DNA's was characteristically asymmetric. InM. lysodeikticus DNA, low G + C fragments were more numerous than high G + C fragments, whereas inC. perfringens DNA, high G + C fragments were more numerous than low G + C fragments. The G + C content of fragments ofM. lysodeikticus DNA varied from 70 to 77%, with a mean and standard deviation of 73.7 ± 1.92% G + C and that ofC. perfringens DNA varied from 27 to 34%, with a mean and standard deviation of 29.8 ± 1.34% G + C. The standard deviation was smaller than that ofEscherichia coli DNA fragments of similar size. Biological meanings of relatively low heterogeneity in nucleotide composition inM. lysodeikticus andC. perfringens are discussed.     

Key interaction modes of dynamic +TIP networks

Dynamic microtubule plus-end tracking protein (+TIP) networks are implicated in all functions of microtubules, but the molecular determinants of their interactions are largely unknown. Here, we have explored key binding modes of +TIPs by analyzing the interactions between selected CAP-Gly, EB-like, and carboxy-terminal EEY/F-COO(-) sequence motifs. X-ray crystallography and biophysical binding studies demonstrate that the beta2-beta3 loop of CAP-Gly domains determines EB-like motif binding specificity. They further show how CAP-Gly domains serve as recognition domains for EEY/F-COO(-) motifs, which represent characteristic and functionally important sequence elements in EB, CLIP-170, and alpha-tubulin. Our findings provide a molecular basis for understanding the modular interaction modes between alpha-tubulin, CLIPs, EB proteins, and the dynactin-dynein motor complex and suggest that multiple low-affinity binding sites in different combinations control dynamic +TIP networks at microtubule ends. They further offer insights into the structural consequences of genetic CAP-Gly domain defects found in severe human disorders.     

Enhancement of oxytetracycline production in a Streptomyces rimosus strain after treatment with acriflavine

Summary A strain ofStreptomyces rimosus was treated with acriflavine as curing agent; morphological and physiologically altered variants were isolated, and changes in sporulation, aerial and substrate mycelia, pigment formation, oxytetracycline (OTC) resistance and biosynthesis are discussed.     

Solitonlike and nonsoliton modes of interaction of taxis waves (illustrated with an example of bacterial population waves)

It was shown earlier that during collisions bacterial population waves may either penetrate one another or stop. In this communication, the mechanism of these two interaction modes is considered in detail. It is shown on the basis of theoretical and experimental results that this interaction is a graphic example confirming one of the characteristic properties of waves in cross-diffusion systems.     

Distribution of ultraviolet-induced lesions in simian virus 40 DNA

In order to analyze the molecular mechanisms of mutagenesis in mammalian cells, we devised an analytical assay using Simian Virus 40 as biological probe. To study the possible correlations between the distribution of the lesions on the treated DNA and the distribution of mutations, we have located and quantified the lesions induced by ultraviolet light (254 nm) on a SV40 DNA fragment. At a fluence of 2,000 J/m2, our results show that the formation frequency of thymine-thymine dimers (TT) is three to four times higher than the formation frequency of the other types of dimers (TC, CT, CC). On the other hand, the formation frequency of a dimer is influenced by the adjacent sequence. In particular, a pyrimidine in the 5' position of a thymine-thymine dimer enhances its formation frequency. At the dose used the formation frequency of the pyrimidine (6-4) pyrimidone photoproducts is twenty times less than the formation frequency of pyrimidine dimers. This paper shows the distribution of the major lesions induced by UV-light on a defined fragment of SV40 genome after UV irradiation. This work is necessary to get an insight into the molecular mechanisms of UV-mutagenesis.     

Evidence for alternative binding modes in the interaction of benzylamine analogues with bovine liver monoamine oxidase B

The interaction of purified bovine liver MAO B with the benzylamine analogues N,N-dimethylbenzylamine and alpha-methylbenzylamine has been investigated. Both classes of analogues are competitive inhibitors of benzylamine oxidase activity. The K(i) values were determined for nine different para-substituted N, N-dimethylbenzylamine analogues. Analysis of the binding affinities demonstrate the deprotonated forms of the tertiary amines are preferentially bound to MAO B and the affinity decreases with increasing van der Waals volume of the para-substituent. The correlation for this relation is:Log K(i)=-0.97+/-(0.28)sigma+(0. 75+/-0.11)(0.1xV(w))-4.24+/-(0.16)alpha-Methyl benzylamine analogues are also found to be competitive inhibitors of MAO B-catalyzed benzylamine oxidation. Similar K(i) values were determined using either the S or R stereoisomers. Analysis of the binding affinities of five para-substituted alpha-methylbenzylamine analogues to MAO B shows the deprotonated form also to be preferentially bound and the affinity is marginally increased with increasing van der Waals volume of the para-substituent:Log K(i)=-0.71sigma-(0.32)(0. 1xV(w))-3.50Comparison of these data with that previously published for para-substituted benzylamine binding to MAO B (Walker and Edmondson, Biochemistry 33 (1994) 7088-7098) demonstrates that these benzylamine analogues exhibit differing modes of binding to the active site of MAO B. The presence of an electronic substituent effect in the binding of these two classes of analogues compared with the lack of an observable electronic effect in the binding of benzylamine to MAO B is consistent with the proposal that orientation of the benzyl ring of the bound substrate is responsible for the absence of an electronic substituent effect on the rate of the reductive half reaction (Miller and Edmondson, Biochemistry 38 (1999) 13670-13683).     

Evidence for an interaction of lipoprotein lipase with artery wall proteoglycans

1. Artery wall proteoglycans-lipoprotein lipase binding characteristics were studied using bovine milk 125I-labelled lipoprotein lipase (LPL) and chondroitin sulphate-dermatan sulphate proteoglycans (PGs) purified from pig aorta. 2. The binding process was studied either by a soluble assay (gel filtration) or by an immobilized proteoglycan assay (ELISA). 3. The binding process was reversible, saturable and occurred at a stoichiometry 1:1. 4. The binding process involved ionic interactions between the positively charged groups of LPL and the negatively charged groups of PG carbohydrate chains. 5. The complex PG-LPL may lead to the production of remnant lipoproteins and, thereby, contribute to cholesteryl ester accumulation in the arterial wall.     

Evidence for repair of ultraviolet-induced damage in Cystobacter species (Myxobacterales).

Cystobacter species strain CK 1 does not grow with more than 0.2 microgram/ml acriflavine. Spontaneous two-step mutants growing with 2 microgram acriflavine per ml have been selected. One mutant (strain CK3) was used to investigate the effect of repair inhibitors. Both strains exhibit pronounced shoulders in their UV dose curves of inactivation. Acriflavine (AF), coumarin (CU), and caffeine (CA) when incorporated in the post-irradiation plating medium decreased survival of irradiated cells. Post-treatment with 2 microgram acriflavine/ml abolished the shoulder of the curve. Caffeine (1600 microgram/ml) and coumarin (350 microgram/ml) reduced it only to about 40%. It is concluded that probably two repair mechanisms are present. Pre-treatment of the cells with 2 microgram acriflavine/ml for two hours before UV-irradiation resulted in a constant dose enhancement factor of 1.9. The protective effect is increased with the time of treatment with acriflavine. This may indicate that pyrimidine dimers are responsible for UV-inactivation.     

Mechanisms of ultraviolet-induced mutation. Mutational spectra in the Escherichia coli lacI gene for a wild-type and an excision-repair-deficient strain

We have analyzed the DNA sequence changes in a total of 409 ultraviolet light-induced mutations in the lacI gene of Escherichia coli: 227 in a Uvr+ and 182 in a UvrB- strain. Both differences and similarities were observed. In both strains the mutations were predominantly (60 to 75%) base substitutions, followed by smaller contributions of single-base frameshifts, deletions and frameshift hotspot mutations. The base substitutions proved largely similar in the two strains but differences were observed among the single-base frameshifts, the deletions and the hotspot mutations. Among the base substitutions, both transitions (72.5%) and transversions (27.5%) were observed. The largest single group was G.C----A.T (60% of all base substitutions). The sites where G.C----A.T changes occurred were strongly correlated (97.5%) with sequences of adjacent pyrimidines, indicating mutation targeted ultraviolet photoproducts. Comparable amounts of mutation occurred at cytosine/cytosine and (mixed) cytosine/thymine sites. From an analysis of the prevalence of mutation at either the 5' or 3' side of a dipyrimidine, we conclude that both cyclobutane dimers and (6-4) lesions may contribute to mutation. Despite the general similarity of the base-substitution spectra between the wild-type and excision-defective strains, a number of sites were uniquely mutable in the UvrB- strain. Analysis of their surrounding DNA sequences suggested that, in addition to damage directly at the site of mutation, the potential for nearby opposite-strand damage may be important in determining the mutability of a site. The ultraviolet light-induced frameshift mutations were largely single-base losses. Inspection of the DNA sequences at which the frameshifts occurred suggested that they resulted from targeted mutagenesis, probably at cyclobutane pyrimidine dimers. The prevalence of frameshift mutations at homodimers (TT or CC) suggests that their formation involves local misalignment (slippage) and that base-pairing properties are partially retained in cyclobutane dimers. While the frameshift mutations in the Uvr+ strain were distributed over many different sites, more than half in the UvrB- strain were concentrated at a single site. Ultraviolet light-induced deletions as well as frameshift hotspot mutations (+/- TGGC at positions 620 to 632) are considered to be examples of untargeted or semitargeted mutagenesis. Hotspot mutations in the Uvr+ strain showed an increased contribution by (-)TGGC relative to (+)TGGC, indicating that ultraviolet light may specifically promote the loss of the four bases.(ABSTRACT TRUNCATED AT 400 WORDS)     

Replication and repair of UV-induced mutational lesions in chemostat cultures of Escherichia coli WP2 Hcr

Mutation to resistance to bacteriophage T5 was studied in chemostat cultures of Escherichia coli strain WP2 Hcr exposed to ultraviolet radiation (UV). The results are in generally good agreement with those obtained earlier by Bridges and Munson for UV-induced reversion to tryptophan independence in exponentially growing cultures of the same strain: expressed mutant yields followed a dose-squared response, mutations were not expressed before approximately one generation after exposure to UV, there was a slow disappearance of dimers especially noticeable in slowly growing and stationary cultures, and the first replication gave rise to duplex mutants in both strands. Several new results were also obtained. In addition to expressed mutant yields, induction of mutational capacity was also observed to follow a dose-squared response, indcating that the response is not an artifact of selection or repair. Induction also increased with growth rate, apparently as the square of the number of genes for T5-sensitivity per cell. It is suggested that mutagenesis is proportional to the number of genes per cell, that recombination is also proportional to the number of genes per cell, and that the number of mutational lesions is proportional to the product of the two. These results also provide evidence that DNA replication occurs near the end of the cell cycle in slowly growing cultures. Under all growth conditions, latent mutant concentrations mutational capacity) decreased by a factor of two with each successive division. Latent mutants were, however, photoreversible for only the first two generations. If mutagenesis occurs as a recombinant event between two mutational lesions, then the results also indicate that these lesions are separated, on the average, by no more than a single cistron.     

Evidence for an anisotropic magnetic interaction between the (bacteriopheophytin) intermediary acceptor and the first quinone acceptor in bacterial photosynthesis

We have investigated electron spin polarization effects occurring in protonated and perdeuterated reaction centers of Rhodospirillum rubrum with electron spin resonance at 9 and 35 GHz (X- and Q-band). As for Rhodopseudomonas sphaeroides strains 2.4.1 and R-26 (Gast, P. and Hoff, A.J. (1979) Biochim. Biophys. Acta 548, 520–535; Gast, P., Mushlin, R.A. and Hoff, A.J. (1982) J. Phys. Chem. 86, 2886–2891), electron spin polarization effects of the prereduced first quinone acceptor Q^?_A in R. rubrum are strongly nonuniform. This nonuniformity is due to an anisotropic magnetic coupling between the intermediary bacteriopheophytin acceptor (I^?) and Q^?_A. It is argued that the anisotropy is too strong to arise solely from an anisotropy in the exchange interaction between I^? and Q^?_A and that dipolar contributions to the magnetic coupling between I^? and Q^?_A are important. The anisotropy in the magnetic coupling for reaction centers of Rps. sphaeroides strains 2.4.1 and R-26 is different from that of R. rubrum wild type. The combination of the 4-fold higher resolution at Q-band and the line narrowing upon deuteration has enabled us to obtain the principal g values and two hyperfine interaction constants of the reduced first quinone acceptor Q^?_A. The principal g values are g_x = 2.0067, g_y = 2.0056 and g_z = 2.0024; the hyperfine constant of the CH₂ group at position 1 is 1.6 G and that of the CH₃ group at position 2 is 2.1 G. These values are close to those found for ubisemiquinone in vitro (Okamura, M.Y., Debus, R.J., Isaacson, R.A. and Feher, G. (1980) Fed. Proc. 39, 1802; Hales, B.J. (1975) J. Am. Chem. Soc. 97, 5993–5997).     

Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems

Gene clusters encoding various type III secretion system (T3SS) injectisomes, frequently code downstream of the conserved atpase gene for small hydrophilic proteins whose amino acid sequences display a propensity for intrinsic disorder and coiled-coil formation. These properties were confirmed experimentally for a member of this class, the HrpO protein from the T3SS of Pseudomonas syringae pv phaseolicola: HrpO exhibits high alpha-helical content with coiled-coil characteristics, strikingly low melting temperature, structural properties that are typical for disordered proteins, and a pronounced self-association propensity, most likely via coiled-coil interactions, resulting in heterogeneous populations of quaternary complexes. HrpO interacts in vivo with HrpE, a T3SS protein for which coiled-coil formation is also strongly predicted. Evidence from HrpO analogues from all T3SS families and the flagellum suggests that the extreme flexibility and propensity for coiled-coil interactions of this diverse class of small, intrinsically disordered proteins, whose structures may alter as they bind to their cognate folded protein targets, might be important elements in the establishment of protein-protein interaction networks required for T3SS function.     

一株蒽降解细菌的分离及降解特性研究

【目的】从盐碱土壤中筛选蒽降解菌株并分析其降解特性。【方法】采用极度稀释结果流式细胞检测法筛选分离纯化菌株,通过16S rRNA基因序列分析对菌株进行初步鉴定,采用气质联用仪(GC-MS)分析蒽的降解特性。【结果】从盐碱土壤中筛选出一株高效蒽降解菌株。经过16S rRNA基因序列分析,鉴定该菌株为Demequina salsinemorus BJ1。菌株可以利用蒽作为唯一碳源生长,降解率可达92%。在一定浓度范围内,随着蒽浓度的降低,细菌生长速率变快,降解率升高。添加外加碳源后,细菌生长速率明显变快,而对蒽降解率变低。对萃取中间代谢产物的质谱分析表明,降解蒽的中间代谢产物主要有9,10-anthracenedione (9,10-蒽醌)和Phthalic acid (邻苯二甲酸)等,说明它可能通过邻苯二甲酸途径降解蒽。【结论】筛选得到一株新的耐盐碱蒽降解菌,该菌降解效率高,对修复石油污染的土壤有一定的现实意义。