Characterization of the polydisperse closed circular deoxyribonucleic acid molecules of Bacillus megaterium

LC-HRMS based approach to identify novel sphingolipid biomarkers in breast cancer patients

Perturbations in lipid metabolic pathways to meet the bioenergetic and biosynthetic requirements is a principal characteristic of cancer cells. Sphingolipids (SPLs) are the largest class of bioactive lipids associated to various aspects of tumorigenesis and have been extensively studied in cancer cell lines and experimental models. The clinical relevance of SPLs in human malignancies however is still poorly understood and needs further investigation. In the present study, we adopted a UHPLC-High resolution (orbitrap) Mass spectrometry (HRMS) approach to identify various sphingolipid species in breast cancer patients. A total of 49 SPLs falling into 6 subcategories have been identified. Further, integrating the multivariate analysis with metabolomics enabled us to identify an elevation in the levels of ceramide phosphates and sphingosine phosphates in tumor tissues as compared to adjacent normal tissues. The expression of genes involved in the synthesis of reported metabolites was also determined in local as well as TCGA cohort. A significant upregulation in the expression of CERK and SPHK1 was observed in tumor tissues in local and TCGA cohort. Sphingomyelin levels were found to be high in adjacent normal tissues. Consistent with the above findings, expression of SGMS1 in tumor tissues was downregulated in TCGA cohort only. Clinical correlations of the selected metabolites and their performance as biomarkers was also evaluated. Significant ROC and positive correlation with Ki67 index highlight the diagnostic potential and clinical relevance of ceramide phosphates in breast cancer.

Distribution of Bacillus megaterium QM B1551 plasmids among other B. megaterium strains and Bacillus species

Bacillus megaterium QM B1551 contains seven plasmids. Two are small rolling circle plasmids and five are theta-replicating plasmids with cross-hybridizing replicons that define a new family of very homologous yet compatible theta replicons. Previous sequencing of several of the plasmids has shown genes with high similarity to those on the genomes and plasmids of other Gram-positive bacteria. To test the possible distribution of these plasmids, nine other B. megaterium strains and 20 other Bacillus or related species were tested for the presence of similar replicons, and specific flanking DNA by both hybridization and PCR. The theta replicons were widespread among the B. megaterium strains, and two had one or more of the rolling circle plasmids, but none of the plasmid replicon regions were observed in the other Bacillus or related species. It appears from the data that even though some plasmids carry genes suggesting horizontal transfer, their replicons seem to be unique to B. megaterium, or rarely present in related species.

A new bacteriocinogenic activity: megacin BII encoded by plasmid pSE 203 in strains of Bacillus megaterium

Mesophilic strains producing a new bacteriocin: Megacin BII, have been isolated from strains of Bacillus megaterium. Facultatively thermophilic strains producing Megacin BI were less sensitive to this new activity than non-producing mesophiles and strains producing Megacin BII were also more resistant to Megacin BI. Strains producing Megacin BII contained a large plasmid of 36.10(6):pSE 203. This plasmid was introduced into non-megacinogenic acceptor strains by protoplast transformation, they then became megacin producers and immune to Megacin BII. Plasmid pSE 203 has been mapped with endonucleases. No similarity to the Megacin A plasmids pBM 309 [Rostás et al. (1980) and pBM 113 (von Tersch and Carlton (1983 b)] was evident.

Megacinogenic plasmid from Bacillus megaterium 216

Ability to produce megacin A, a bacteriocin of B. megaterium, was transferred from the strain B. megaterium 216 into auxotrophic derivatives of the strain B. megaterium KM via protoplast fusion and polyethylene-glycol-induced protoplast transformation by plasmid DNA, respectively. A 30.9 megadalton plasmid was detected in cells with MegA phenotype, and the loss of this phenotype was accompanied in each case with the elimination of that plasmid. The megacinogenic plasmid pBM309 has a single site for both BamHI and XhoI. It is cleaved by the endonucleases SalI, BglII, PstI, PvuII, and EcoRI into 3, 3, 4, 4, and 9 fragments, respectively. The physical map of this plasmid is presented.

Plasmid-mediated transformation in Bacillus megaterium

A transformation system was developed for Bacillus megaterium by using antibiotic resistance plasmid deoxyribonucleic acid molecules derived from Staphylococcus aureus and Bacillus cereus. Lysozyme-generated protoplasts of B. megaterium allowed uptake of plasmid deoxyribonucleic acid in the presence of polyethylene glycol. Transformants expressed the antibiotic resistance determinants present on the plasmid deoxyribonucleic acid, and reisolated plasmid deoxyribonucleic acid yielded restriction endonuclease digestion patterns identical to those of the donor deoxyribonucleic acid.

New cryptic plasmid of Bacillus subtilis and restriction analysis of other plasmids found by general screening

A new cryptic plasmid, pTA1030 (4.5 megadaltons, copy number 16), was characterized by restriction analysis, together with some other plasmids of Bacillus subtilis.

Isolation and characterization of plasmid from the Bacillus brevis var. G.-B. cells

The plasmid designated pAD1 was isolated from the cells of four variants of Bacillus brevis var. G.-B. The plasmid DNA has a molecular weight of about 47.1 x 10(6) daltons and contains 43.4 mole % G+C. The bulk of pAD1 DNA (96--98%) is associated with the fraction of chromosome DNA and membranes. Restriction endonucleases Sma I, Sal I and Bam HI cleaved the plasmid DNA into two, two and six fragments, respectively. The cleavage map of the pAD1 genome has been constructed for these three endonucleases. Restriction enzymes Eco RI, Hind III, Kpn I and Pst I hydrolized the plasmid DNA into 16, 21, 10 and 9 fragments, respectively. The presence of repeated sequences in the plasmid genome was shown based on pAD1 DNA cleavage by these endonucleases.

Characterization of antigens from type A and B yeast cells of Histoplasma capsulatum

The antigenic composition of cytoplasmic extract and culture filtrate antigens of type A and B yeast cells of Histoplasma capsulatum grown in a synthetic medium was studied. These preparations from type A and B yeast cells contained varying amounts of protein, carbohydrates, and protein-carbohydrate complexes. The antigenic analysis of these preparations was performed by antigen-antiserum absorption with subsequent immunodiffusion and cross-immunoelectrophoresis with absorption in situ in an intermediate gel. All protein antigens observed in culture filtrate of either type A or B yeast cells were also present in the cytoplasmic extracts of the same type. The cytoplasmic extract of type A and B yeast cells each contained certain characteristic antigens that were not shared by the other type. Rocket immunoelectrophoresis with different molecular weight fractions of the antigenic preparations from both types indicated the polydisperse nature of Histoplasma yeast cell antigens.

Physical characterization of a plasmid cointegrate containing an F'his gnd element and the Salmonella typhimurium LT2 cryptic plasmid

A recombinant plasmid (pAS19) isolated from a derivative of Salmonella typhimurium LT2, containing the strain LT2 cryptic plasmid and an F'his gnd element, has been physically characterized. The pAS19 plasmid contour length equals the sum of the contour lengths of the cryptic plasmid and F'his gnd element. Deoxyribonucleic acid (DNA)-DNA hybridization experiments demonstrated that whereas the pAS19 plasmid exhibits extensive DNA homology with both the cryptic plasmid and the F'his gnd element, there is little DNA homology between these latter two plasmids. The DNA fragmentation pattern of the pAS19 plasmid produced by the restriction endonuclease R-EcoRI is consistent with that expected for a composite plasmid cointegrate containing most, if not all, of the DNA sequences present in its two component plasmids.

Production of megacins C and Cx: presumptive evidence extrachromosomal control

Exposure of growing cultures of Bacillus megaterium C4A(-) to ethidium bromide or an elevated growth temperature was found to eliminate megacin C production. Ethidium bromide resulted in a cure rate of up to 13%. Growth at 43 degrees C gave a cure rate of up to 99%. Megacin C production was lost spontaneously at a rate of 4% or less. There was a greater rate of spontaneous loss of megacin Cx production by B. megaterium 337, up to 14%. Growth at 43 degrees C resulted in a cure rate of up to 24% in this organism. Reversion to the Meg(+) state by cured clones has never been demonstrated. These observations support the hypothesis that production of megacins C and Cx is plasmid mediated. Meg(-) clones adsorbed more megacin than either parent strain and were more susceptible to megacin action.

Plasmid deoxyribonucleic acid in Bacillus subtilis and Bacillus pumilus

Two of eighteen strains of Bacillus subtilis examined contained covalently closed circular duplex deoxyribonucleic acid (DNA) of homogeneous size and buoyant density. Strain ATCC 15841 contained about 16 copies per chromosome of plasmid pPL1, a circular DNA element having a molecular weight of about 4.7 times 10(6) and a buoyant density of 1.700. Strain ATCC 7003 contained about one to two copies per chromosome of plasmid pPL2. pPL2 had a molecular weight of about 46 times 10(6) and a buoyant density of 1.696. Strain ATCC 7003 appeared to be closely related to B. subtilis 168 by genetic, physiological, and biochemical criteria. Strain ATCC 15841 appeared to be much less closely related. B. pumilus ATCC 12140 contained two size classes of covalently closed circular duplex DNA. The plasmids pMB1 and pMB2 had molecular weights of about 6.8 times 10(6) and 5.3 times 10(6), respectively, and were present in several copies per chromosome.

Evidence for a nonrandom base sequence in a Bacillus pumilus plasmid: EcoR1 endonuclease digestion of pPL576

EcoR1 endonuclease digested the Bacillus pumilus plasmid pPL576 (molecular weight similar to 28 X 10-6) into three distinct size classes of linear fragments. The molecular weights of the fragments are 13.0 X 10-6, 0.5 X 10-6, and 6.5 X 10-6 by sucrose gradient analysis. By electron microscope analysis the three fragments account for about 99% of the intact plasmid. These results indicate that pPL576 molecules contain a nonrandom base sequence, and are consistent with the interpretation that pPL576 is autonomous and not the result of cyclization of random chromosome fragments.

Biochemical studies of two Bacillus pumilus plasmids

Bacillus pumilus NRS 576 harbored an estimated two copies per chromosome of a covalently closed, circular (CCC) deoxyribonucleic acid (DNA) molecule, the 576 plasmid. The 576 plasmid has a buoyant density of 1.698 g/cm(3) and a molecular weight of about 28 x 10(6). Plasmid copy number remained about the same in both exponentially growing and stationary-phase cells. Spontaneous variants of NRS 576 that formed spores at an elevated frequency were designated as W mutants. W mutants appeared to have lost the 576 plasmid on the basis of the following: W mutants (38 tested) lacked detectable CCC DNA, and the majority of the plasmid homologous sequences in bulk NRS 576 DNA were absent from bulk W mutant DNA. B. pumilus ATCC 7065 harbored at least 10 copies per chromosome of a CCC DNA element, the 7065 plasmid. The 7065 plasmid has a buoyant density of 1.696 g/cm(3) and a molecular weight of about 6 x 10(6). Although the copy number of the plasmid appeared to remain the same in exponentially growing and stationary-phase cells, an additional CCC form of higher molecular weight was detected in stationary-phase cells.

Size distribution of the closed circular deoxyribonucleic acid molecules of Bacillus megaterium: sedimentation velocity and electron microscope measurements

The circular deoxyribonucleic acid (DNA) of Bacillus megaterium was fractionated by sedimentation velocity on preparative zonal gradients. The fractions obtained were characterized by analytical sedimentation velocity analysis on neutral and alkaline sucrose gradients, and by contour length measurement by electron microscopy. Each fraction was found to contain circular molecules of one to three discrete sizes, in various combinations of covalently closed and open circular forms. Estimations of the molecular masses of these sizes gave values of 3.9, 6.2, 16.0, 31, and 60 million daltons for the major molecular species. Minor amounts of molecules of 7.6, 11.7, 47, 89, and 112 million daltons were observed in the electron microscope analyses. Length measurements of almost 600 molecules from the various fractions showed that all except six could be placed in distinct size classes. The distribution of molecular sizes in unfractionated circular DNA was shown to consist primarily of the two smallest size classes, although the relative proportions by weight of five of the classes were roughly equivalent.