Isolation ofBacillus schlegelii,a thermophilic,hydrogen oxidizing,aerobic autotroph,from geothermal and nongeothermal environments

Thermophilic hydrogen-oxidizing strains forming round, terminal endospores were isolated from geothermal areas. They were neutrophilic and facultatively autotrophic. They resembledBacillus schlegelii, a thermophilic hydrogen bacterium found so far only in cold environments. Phenotypic similarities, as well as DNA G+C content and DNA:DNA homologies, clearly revealed that the isolated strains belonged to the taxospeciesB. schlegelii. Hence, the strains ofB. schlegelii found in cold environments are probably allochthonous, their origin being geothermal and volcanic areas.     

Nuclear and Organelle DNA Replication during Spore Germination in Bryophytes and Equisetum

In contrast to ferns, the spore nuclei of the moss, Funaria hygrometrica, are in the G₂ phase. They do not incorporate the thymidine analogue BUdr before the first mitosis. When spores germinate in the presence of aphidicolin, an inhibitor of the (nuclear) DNA polymerase alpha, they give rise to two-celled, negatively phototropic protonemata, consisting of relatively long and thin cells. Determinations of nuclear DNA content further confirm the presence of G₂-nuclei in Funaria spores. Spores of Pogonatum urnigerum and of Equisetum hyemale likewise contain G₂-nuclei, as shown by BUdr incorporation or experiments with aphidicolin, respectively. In germinating Funaria spores, the organelle DNA is synthesized very early and independent of nuclear DNA. A gradient in replication of organelle DNA is found only in the long tip cells which are formed in the presence of aphidicolin.     

Deoxyribonucleic acid relatedness of some menaquinone-producing Flavobacterium and Cytophaga strains

Nine menaquinone-forming strains of the Flavobacterium-Cytophaga complex with DNA base compositions between 35 and 45 moles percent guanineplus-cytosine were investigated for genome sizes and DNA relatedness by DNA: DNA hybridization in vitro, using the optically recorded initial reassociation kinetics. Two strains representing C. hutchinsonii and C. marinoflava proved to be related on the 50 percent binding level, i.e. on a level of DNA relatedness commonly found within well-classified conventional genera of bacteria. Strains of C. johnsonae, F. heparinum, F. meningosepticum, F. odoratum, F. pectinovorum, and an unnamed Flavobacterium-Cytophaga strain were found to be interrelated, and linked to the genus Cytophaga, on the 30, or 20 percent binding levels, respectively. These findings indicate that the organisms in question are related to Cytophaga. They therefore should be transferred into the family Cytophagaceae.     

Structural mechanism of ATP‐dependent DNA binding and DNA end bridging by eukaryotic Rad50

The Mre11–Rad50–Nbs1 (MRN) complex is a central factor in the repair of DNA double‐strand breaks (DSBs). The ATP‐dependent mechanisms of how MRN detects and endonucleolytically processes DNA ends for the repair by microhomology‐mediated end‐joining or further resection in homologous recombination are still unclear. Here, we report the crystal structures of the ATPγS‐bound dimer of the Rad50^NBD (nucleotide‐binding domain) from the thermophilic eukaryote Chaetomium thermophilum (Ct) in complex with either DNA or CtMre11^RBD (Rad50‐binding domain) along with small‐angle X‐ray scattering and cross‐linking studies. The structure and DNA binding motifs were validated by DNA binding experiments in vitro and mutational analyses in Saccharomyces cerevisiae in vivo. Our analyses provide a structural framework for the architecture of the eukaryotic Mre11–Rad50 complex. They show that a Rad50 dimer binds approximately 18 base pairs of DNA along the dimer interface in an ATP‐dependent fashion or bridges two DNA ends with a preference for 3′ overhangs. Finally, our results may provide a general framework for the interaction of ABC ATPase domains of the Rad50/SMC/RecN protein family with DNA.     

Development and Application of Random DIG-Labelled Probes Based on Total Genomic Lactobacillus DNA

Summary Nine Lactobacillus-specific and non-isotopically (digoxygenin) labelled probes were developed on the basis of Lactobacillus total chromosomal DNA. Their specificity and applicability for Lactobacillus discrimination was proven by DNA–DNA hybridization to reference strains from the American Type Culture Collection (ATCC). The DNA probes were divided into three groups depending on the ability to hybridize to DNA from the same and/or from a group of related Lactobacillus strains. They were assayed in the species-specific detection of vaginal strains from the genus Lactobacillus. Six DNA probes were successfully applied for characterization of 21 newly isolated vaginal Lactobacilli. The species affliation of some isolates was determined. The developed DNA probes were evaluated for usage as a qualitative hybridization test for detection of Lactobacillus species in mixed cultures, obtained directly from vaginal samples without strain isolation.     

Isolation and genetic analysis of temperature-sensitive mutants of B. subtilis defective in DNA synthesis

Summary Fifty temperature-sensitive mutants defective in DNA synthesis at high temperature have been identified among 655 temperature-sensitive mutants isolated at random from a mutagenised population of B. subtilis. They are distributed in a non-random fashion in 9 genetic linkage groups, located in different regions of the B. subtilis genome. It is suggested that at least 14 genes are involved in B. subtilis DNA replication.     

Analysis ofDrosophila chromosome4 using pulsed field gel electrophoresis

Previous estimates of the size ofDrosophila melanogaster chromosome4 have indicated that it is 1% to 4% of the genome or 6 Mb. We have used pulsed field gel electrophoresis (PFGE) to separate megabase-sized molecules ofD. melanogaster chromosomal DNA. Southern blots of these gels were probed with DNA fragments from thecubitus interruptus andzfh-2 genes, which are located on chromosome4. They each identify the same-sized distinct band that migrates at approximately 5.2 Mb in DNA preparations from the Kc cell line. We interpret this band to be intact chromosome4. In DNA obtained from embryos of variousD. melanogaster wild-type strains, this chromosome band showed strain-specific size variation that ranged from 4.5 to 5.2 Mb. TheD. melanogaster chromosome4 probes also identified a single, 2.4 Mb band in embryonic DNA fromDrosophila simulans. We conclude thatD. simulans chromosome4 is substantially smaller than that ofD. melanogaster, presumably owing to diffirences in the amount of heterochromatic DNA sequences. Our simple DNA preparation from embryos and PFGE conditions should permit preparative isolation of chromosome4 DNA and will facilitate the molecular mapping of this chromosome.     

Polymerase chain reaction in situ: an appraisal of an emerging technique

Summary Polymerase chain reaction (PCR)in situ is a new technique which promises to enhance considerably our ability to detect a few copies of target nucleic acid sequences in fixed tissues and cells. It has an enormous potential for application in diagnostic histopathology of viral diseases and in the study of gene expression. PCRin situ is, however, technically difficult, and amplification of the target DNA is only 30–300 fold. In this article we present an overview of PCRin situ techniques used to amplify both DNA and RNA targets (RT-PCRin situ). We also identify problems which can reduce the efficiency of the technique or which can give rise to false-positive results. They include (1) the inhibitory effects of cross-linking of histones to DNA or PCR amplification, (2) abstraction of PCR reagents by tissue-bonding agents which are used to coat glass slides, (3) poor denaturation of target DNA and subsequent DNA renaturation due to extensive cross-linking of histones to DNA, or because of incorrect temperature regulation of thermal cyclers, (4) false-positive results which arise from end-labelling of DNA strand breaks byTaq polymerase, and (5) diffusion of PCR products into and out of cells leading to false-positive results. We present some of the approaches that have been used to overcome some of these difficulties and suggest new avenues for investigation to improve this technique further.     

Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment

Acidobacterium is proposed as a new genus for the acidophilic, chemoorganotrophic bacteria containing menaquinone isolated from acidic mineral environments.Acidobacterium capsulatum is proposed for the singleAcidobacterium species which consists of eight strains (Biogroup 5). The members of this species are gram-negative, aerobic, mesophilic, non-spore-forming, capsulated, saccharolytic, and rod-shaped bacteria. They are motile by peritrichous flagella. They can grow between pH 3.0 and 6.0, but not at pH 6.5. They give positive results in tests for esculin hydrolysis, catalase, and -galactosidase. Oxidase and urease are negative. They can use glucose, cellobiose, starch, maltose, or -gentiobiose as a sole carbon source, but cannot use elemental sulfur and ferrous iron as an energy source. The DNA base composition is 59.7–60.8 guanine plus cytosine (G+C) mol%. The major isoprenoid quinone is menaquinone with eight isoprene units (MK-8). The major fatty acid is 13-methyltetradecanoic acid. DNA relatedness between this species and the species ofAcidiphilium, Acidomonas, andDeinobacter was 18 to 2%. From phenotypic and chemotaxonomic characters, these member do not belong to any known taxa of gram-negative bacteria. A culture of the type strain (strain 161) has been deposited in the Japan Collection of Microorganisms as JCM 7670.     

Lack of genetic relatedness betweenYersinia philomiragia (the “philomiragia” bacterium) andYersinia species

Four strains ofYersinia philomiragia were studied biochemically and genetically. They showed a high degree of phenotypic similarity and formed a homogenous DNA relatedness group. We could not demonstrate any significant DNA relatedness between this group and otherYersinia species, other Enterobacteriaceae, orPasteurella multocida. Y. philomiragia is phenotypically quite different from other yersiniae and Enterobacteriaceae. These DNA and phenotypic data indicate thatY. philomiragia is not a member of the genusYersinia or a member of the family Enterobacteriaceae. It is suggested that, pending further study, this organism be referred to as the “Philomiragia” bacterium.     

Long-Range Interactions between Ligands Bound to a DNA Molecule Give Rise to Adsorption with the Character of Phase Transition of the First Kind

Abstract

Influence of long-range interactions between ligands bound to DNA molecule on the character of their adsorption is studied using computer modeling. For this investigation, two calculation procedures are developed. They are based upon the method of the free energy minimum and on the partition function method. The both procedures demonstrate that in the case of a strong enough attraction between all the bound ligands their binding to DNA has the character of phase transition of the first kind. There is a break in the binding curve c(c₀) where c—relative concentration of bound ligands, c ₀—molar concentration of free ligands. The break occurs because there is an interval of central degrees of binding (～50% of the maximum c value) that are prohibited for individual DNA molecules. Such a transition might be caused by some types of DNA condensation. Attraction between the neighboring ligands only, adjacent or/and separated by double helix regions, does not cause this effect.     

A hybrid DNA sequence containing the replication origin of the multicopy yeast plasmid 2 micron circle and an additional repeated sequence can convert maltose-negative into maltose-positive strains

Summary Yeast DNA pools were prepared by ligating partial Sau3A genomic digests from strains carrying various MAL genes into the BamHI site of the yeast-Escherichia coli shuttle vector YRp7. They were used to transform recipient yeast strains that could not utilize maltose since they lacked a classical MAL gene. Transformants were obtained that could use maltose and also formed normal levels of maltase. They were unstable. They would lose the selective marker TRP1 of YRp7 alone, together with the ability to utilize maltose or only the ability to utilize maltose. The insertion of one of the plasmids was used as a hybridization probe for the others and found to share homologous sequences with all. They were then shown to contain the replication origin of the yeast 2 m circle plasmid and additional genomic digests of total yeast DNA. They hybridized at various degrees of efficiency with several bands, indicating that they were part of a family of repeated sequences. Apparently, it was the combination of the replication origin of the 2 m circles with the additional sequences that promoted maltose utilization.     

Two kinds of insertions in bacterial genes

Summary Six insertion mutations in the gal operon of E. coli and two insertion mutations in the xycIIOP operon of bacteriophage lambda were tested for homology by annealing separated strands of lambda dgal DNA carrying the insertions, and inspection in the electron microscope.Class 1, consisting of the gal mutations OP 128, OP 141, T-N 116, OP 306, T-N 102 and the lambda mutation r14 are about 800 nucleotide pairs long, completely homologous and not circularly permuted. The first three insertions of class 1 are integrated in one direction with respect to the adjacent genes, the other three in the opposite direction. The DNA inserted in this class of mutations is called IS1.Class 2 consists of the gal insertion OP 308 and the lambda insertion r32. They are about 1400 nucleotide pairs long. The two are integrated in opposite direction with respect to the chromosome of dgal. The DNA in insertion mutations of class 2 will be called IS 2. IS1 and IS2 do not share any detectable homology.These data are supported by cross-hybridization experiments using RNA transcribed in vitro from lambda dgal or lambda DNA carrying one insertion and DNA carrying either the same or a different insertion.Similar results were obtained by Malamy, Fiandt, Szybalski and Fiandt, Szybalski, Malamy (accompanying papers).     

Interspecific relationships and biogeography of some Bornean tree shrews (Tupaiidae: Tupaia), based on DNA hybridization and morphometric comparisons1

The interspecific relationships and biogeography of seven southeast Asian tree shrew species in the genus Tupaia were examined by DNA hybridization and multivariate morphometric analysis. Urogale everetti served as the outgroup. DNA hybridization data indicate that T. tana is most closely related to T. tnontana, and they form a clade with T. minor. Morphometric comparisons indicate that T. tana and 77 minor, and 7. montana and T palawanensis, form groups that, together, are most similar to T. glis. T. javanica and U. everetti cluster outside the rest of Tupaia. The DNA hybridization data support a model of Bornean speciation driven by sea‐level changes. They also indicate either (1) that there is a large variation in the rate of tree shrew evolution or (2) that U. everetti may in fact be a member of the ingroup. When considered in light of the phylogenetic results, the morphometric data suggest substantial convergence in body size or correlation in character changes.     

Frame-shift mutants induced by quinacrine are recognized by the mismatch repair system in Streptococcus pneumoniae

Summary We describe the isolation of amethopterin-resistant mutants induced by quinacrine treatment of exponentially growing cultures of Streptococcus pneumoniae. Only mutants located by recombination analysis in a few hundred base pairs were further studied. They were cloned and their DNA sequences show that most of them are ±1-base frame-shift mutants. They are excised and repaired to a degree similar to transition mutants (low efficiency class), suggesting that the mismatches resulting from a transition or a ±1-base mutation are similar substrates for the Hex mismatch repair system.     

Synthesis,Characterization, and DNA‐Binding and ‐Cleavage Properties of Dinuclear CuII?Salophen/Salen Complexes

Dinuclear Cu^II complexes, [Cu₂(salophen)₂] ( 1 ) and [Cu₂(salen)₂] ( 2 ), with Schiff bases derived from salicylaldehyde and o‐phenylenediamine (ophen) or ethylenediamine (en) were synthesized and characterized. They exhibit square‐planar geometry with CuN₂O₂ coordination, where the dianionic Schiff base acts as a tetradentate N₂O₂ donor ligand. Calf thymus (CT)‐DNA Binding studies revealed that the complexes possess good binding propensities (K_b=3.13×10⁵ for 1 and K_b=2.99×10⁵ M ⁻¹ for 2 ). They show good DNA‐cleavage abilities under oxidative and hydrolytic conditions. Complex 1 binds and cleaves DNA more efficiently as compared to 2 due to the presence of an extended aromatic phenyl ring which might be involved in an additional stacking interaction with DNA bases. From the kinetic experiments, hydrolytic DNA‐cleavage rate constants were determined as 1.54 for 1 and 0.72 h⁻¹ for 2 . The nuclease activities of 1 and 2 are significant, giving rise to (2.03–2.88)×10⁷‐fold rate enhancement compared to non‐catalyzed DNA cleavage.     

I-SceI endonuclease: a new tool for DNA repair studies and genetic manipulations in streptomycetes

Actinomycetes are Gram-positive bacteria with a complex life cycle. They produce many pharmaceutically relevant secondary metabolites, including antibiotics and anticancer drugs. However, there is a limited number of biotechnological applications available as opposed to genetic model organisms like Bacillus subtilis or Escherichia coli. We report here a system for the functional expression of a synthetic gene encoding the I-SceI homing endonuclease in several streptomycetes. Using the synthetic sce(a) gene, we were able to create controlled genomic DNA double-strand breaks. A mutagenesis system, based on the homing endonuclease I-SceI, has been developed to construct targeted, non-polar, unmarked gene mutations in Streptomyces sp. Tü6071. In addition, we have shown that homologous recombination is a major pathway in streptomycetes to repair an I-SceI-generated DNA double-strand break. This novel I-SceI-based tool will be useful in fundamental studies on the repair mechanism of DNA double-strand breaks and for a variety of biotechnological applications.     

Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution

Virulence genes of pathogenic bacteria, which code for toxins, adhesins, invasins or other virulence factors, may be located on transmissible genetic elements such as transposons, plasmids or bacteriophages. In addition, such genes may be part of particular regions on the bacterial chromosome, termed‘pathogenicity islands’(Pais). Pathogenicity islands are found in Gram-negative as well as in Gram-positive bacteria. They are present in the genome of pathogenic strains of a given species but absent or only rarely present in those of non-pathogenic variants of the same or related species. They comprise large DNA regions (up to 200 kb of DNA) and often carry more than one virulence gene, the G+C contents of which often differ from those of the remaining bacterial genome. In most cases, Pais are flanked by specific DNA sequences, such as direct repeats or insertion sequence (IS) elements. In addition, Pais of certain bacteria (e.g. uropathogenic Escherichia coli, Yersinia spp., Helicobacter pylori) have the tendency to delete with high frequencies or may undergo duplications and amplifications. Pais are often associated with tRNA loci, which may represent target sites for the chromosomal integration of these elements. Bacteriophage attachment sites and cryptic genes on Pais, which are homologous to phage integrase genes, plasmid origins of replication or IS elements, indicate that these particular genetic elements were previously able to spread among bacterial populations by horizontal gene transfer, a process known to contribute to microbial evolution.     

Cloning of a gene from the fission yeast S. pombe which complements E. coli pyrB, the gene for aspartate transcarbamylase

Summary DNA fragments of the fission yeast Schizosaccharomyces pombe that can complement pyrB mutations in Escherichia coli have been cloned into pBR322. Two contiguous HindIII fragments which are 2.7 kb and 1.5 kb in size are essential for this complementation. The cloned fragments have been proved to derive from yeast DNA by the use of Southern hybridization techniques. They apparently carry the structural gene for aspartate transcarbamylase [EC 2.1.3.2] and a promoter signal that is functional in E. coli. S. pombe is now the fourth eukaryote with a gene shown to be functionally expressed in E. coli. The DNA fragments cloned in this work will be useful in molecular-cloning studies in S. pombe.     

PM2 bacteriophage plaque morphology mutants exhibit differences in DNA length and restriction endonuclease patterns

A large plaque (LP) and a small plaque (SP) variant of PM2 bacteriophage were isolated from a mixture of the two plaque variants and were grown separately in the appropriate host bacterium,Alteromonas espejiana. They have remained pure for approximately one year from the original isolation. Restriction endonuclease analyses revealed differences in theHaeIII restriction profile between the two variants.HaeIII fragment 1 of the SP DNA was found to be smaller than the corresponding fragment from the LP variant DNA, whereas fragment 7 from the SP DNA was slightly larger than the same fragment from LP DNA. Electron microscopy of heteroduplexes formed between the DNAs from the two variants revealed that the deletion in fragment 1 mapped very close to the junction betweenHaeIII fragments 1 and 13 on the physical map of PM2 DNA. The difference in DNA length between the two variants results from addition or deletion mutations.Deceased.