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At least 19 recordsLinked to original sources
PubMed1978

The DNA . tyrocidine complex and its dissociation in the presence of gramicidin D.

The peptide antibiotic tyrocidine affects transcription in vitro by interfering with the initiation process. The complex formed between tyrocidine and native DNA is stable against nucleolytic enzymes. It is sensitive to variations in the salt concentration. Protection of DNA as a function of the tyrocidine concentration follows a curve suggesting cooperative binding of tyrocidine to DNA. The complex formation at low tyrocidine concentrations is accompanied by the presence of single stranded regions of unknown length. With single-stranded DNA, tyrocidine forms a complex which is relatively insensitive to high salt concentrations. Both native and single-stranded DNAs of the complexes become digestible in the presence of gramicidin D, another peptide antibiotic. Breakdown of the complex as a function of the gramicidin D concentration follows a curve which is the reverse of cooperative binding. Gramicidin D acts more effectively on single-stranded rather than on double-stranded DNA . tyrocidine complexes. The DNA . tyrocidine complex, which is broken down by formamide and dimethyl sulfoxide is stabilized by gramicidin D. The implications of these results are discussed with respect to a possible recognition of DNA sequences by tyrocidine and the interaction between DNA, tyrocidine and gramicidin D.

Bacillus↗
PubMed1975

Some characteristics of the DNA-tyrocidine complex and a possible mechanism of the gramicidin action.

1. The cyclic peptide antibiotic tyrocidine which inhibits RNA synthesis in vitro by forming a complex with the DNA (Schazschneider, B., Ristow, H. and Kleinkauf, H. (1974) Nature 249, 757-759) induces hypochromicity of the DNA. The complex dissociates at elevated temperatures but which are below the melting temperature of the DNA. 2. The linear peptide antibiotic gramicidin which reverses the inhibitory effect of tyrocidine (Ristow, H., Schazschneider, B., Bauer, K. and Kleinkauf, H. (1975) Biochim. Biophys. Acta 390, 246-252) does not bind to DNA and does not induce hypochromicity of the DNA. However, the DNA-tyrocidine complex dissociates at lower temperatures when gramicidin is present. Thus gramicidin weakens the binding of tyrocidine to DNA. 3. The presence of DNA quenches the fluorescence of tyrocidine but not that of gramicidin. This quenching of tyrocidine fluorescence is reduced in the presence of gramicidin. 4. Tyrocidine inhibits transcription of single-stranded DNA as well. This inhibition too can be reversed by gramicidin. Thus the action of the peptides is not dependent on a double-stranded DNA conformation.

Bacillus↗
PubMed1988

Interrelationships between tyrocidine and gramicidin A' in their interaction with phospholipids in model membranes.

(1) The interaction of tyrocidine with different lipids is studied in model membranes and the results are compared to the gramicinid-lipid interaction. (2) The tyrocidine-dielaidoylphosphatidylethanolamine interaction gives rise to a population of phospholipids with a lower gel to liquid-crystalline transition temperature and to an abolition of the bilayer to HII phase transition, resulting in a macroscopic organization with dynamic and structural properties different from those of the pure lipid. (3) Tyrocidine has a strong fluidizing effect on the acyl chains of phosphatidylcholines, manifested by a decrease in enthalpy of the main thermotropic transition. (4) No evidence of a gramicidin A'-like lipid-structure modulating activity was found. However, tyrocidine inhibits the formation by gramicidin of an HII phase in dioleoylphosphatidylcholine model membranes. Instead, a cubic type of lipid organization is observed. (5) Tyrocidine greatly perturbs the barrier properties of dioleoylphosphatidylcholine model membrane. (6) Gramicidin A' reverses the effect of tyrocidine on membrane permeability by forming a complex in the model membrane with an apparent 1:1 stoichiometry. (7) The results suggest that both peptide antibiotics, which are produced by Bacillus brevis ATC 8185 prior to sporulation, show antagonism in their effect on membrane structure similar to their effect on superhelical DNA (Bogh, A. and Ristow, H. (1986) Eur. J. Biochem. 160, 587-591. The possible underlying basic mechanism is indicated.

Algorithms↗
PubMed1977

The peptide antibiotic gramicidin D. A specific reactivator of tyrocidine-inhibited transcription.

The sporulating bacterial strain Bacillus brevis (ATCC 8185) produces two types of peptide antibiotics, the linear gramicidins and the cyclic tyrocidines. Their effects on transcription in vitro were studied: 1. RNA synthesis catalized by RNA polymerase and DNA as template, both from B. brevis cells, is inhibited by the addition of gramicidin maximally to 50% as compared to controls without gramicidin. This inhibition is dependent on the concentration of gramicidin as well as on that of RNA polymerase. 2. Transcription of DNA is also inhibited by tyrocidine. This inhibition is partially compensated by the addition of gramicidin. Here, the action of gramicidin is again dependent on its concentration and on that of RNA polymerase. 3. This counteraction of gramicidin occurs only with RNA polymerase from B. brevis. Enzyme preparations of other origin are additively inhibited by gramicidin when previously inhibited by tyrocidine. The specific action pattern of gramicidin and tyrocidine in connection with the B. brevis RNA polymerase supports the notion that the two peptide antibiotics may be involved in a gene regulatory mechanism during sporogenesis.

Bacillus↗
PubMed1990

Suppression of tyrocidine production by purine nucleotides and related substances in Bacillus brevis.

Bacillus brevis (ATCC 8185) produces an antibiotic peptide, tyrocidine. We found that adenosine or 5'-AMP suppressed the production of tyrocidine with half-maximum inhibition at 100-300 microM. This inhibition was specific to the production of tyrocidine since neither adenosine nor 5'-AMP showed any effect on bacterial growth. Cyclic nucleotides had no effect. These results suggest that adenosine, 5'-AMP or its metabolite was specifically involved in the regulation of tyrocidine production.

Adenosine↗
PubMed1979

Determination of individual side-chain conformations, tertiary conformations, and molecular topography of tyrocidine A from scalar coupling constants and chemical shifts.

We report for the decapeptide tyrocidine A: (a) H alpha and H beta chemical shifts and scalar coupling constants for most residues of tyrocidine A in methanol-d4 and dimethyl-d6 sulfoxide (Me2so-d6) and the H alpha and H beta chemical shifts for other residues; (b) scalar coupling constants 3J alpha beta for nine side chains in methanol-d4 but only seven side chains in Me2SO-d6, due to chemical shift degeneracy; the Gln9 and Tyr10 side chains in methanol-d4 were only approximately analyzed; (c) a total spin-spin analysis of Pro5 in Me2SO-d6 and, partly by comparison, also in methanol-d4; (d) conversion of 3J alpha beta values to side-chain conformations for all residues in methanol-d4; comparisons, where possible, led to the conclusion that side-chain conformations are similar in methanol-d4 and Me2SO-d6; (e) an absolute conformational analysis of Pro5 from 3J values and a method of assigning all pro-R,S protons; Pro5 has a Ramachandran B, C2-Cexo-Cendo conformation; (f) chi 1, chi 2 conformations of several aromatic residues based upon proton-chromophore distance measurement from anomalous chemical shifts and Johnson-Bovey diagrams; (g) pro-R and pro-S assignments of H beta's from anomalous chemical shifts, high-temperature dependence of anomalous chemical shifts, and backbone side-chain nuclear Overhauser effects; (h) most tertiary conformations of the whole tyrocidine A molecule possessing residues 4--8 and 10 in highly preferred (ca. 90%) chi 1 conformations, but residues 1--3 and 9 having at least two chi 1 rotamers; (2) description of three topographical regions of the molecule--a hydrophobic region, a flat hydrophilic surface on the other side of the molecule, and a hydrophilic region consisting of two peptide backbone units and the side chains of Asn8, Gln9, and Tyr10; (j) proposed side chain, beta-turn, and beta-pleated sheet conformations that readily account for all "normal" and anomalous chemical shifts.

Amino Acids↗
PubMed1986

DNA-supercoiling is affected in vitro by the peptide antibiotics tyrocidine and gramicidin.

Tyrocidine, a peptide antibiotic produced by Bacillus brevis (ATCC 8185), relaxes superhelical DNA in a biphasic manner and induces 'packaging' of the DNA at higher concentrations. This was concluded from studies using the sensitive 4,5',8-trimethylpsoralen photobinding technique [Sinden, R. R., Carlson, J. O. & Pettijohn, D.-E. (1980) Cell 21, 773-783]. Relaxed DNA is not affected by tyrocidine whereas linearized molecules become packaged. The linear gramicidin synthesized by the same strain reverses the tyrocidine-induced relaxation as well as the packaging, an observation which might be of biological relevance.

DNA, Superhelical↗
PubMed1989

Structure of tyrocidine micelles in isotropic aqueous solution.

Aqueous solutions of tyrocidine B, iodoacetyltyrocidine B, and diiodotyrocidine B in 40% H2O:60% ethanol (w/w) were investigated by analytical ultracentrifugation, light scattering, and small-angle X-ray scattering techniques. A reasonable hydrodynamic description of the aggregates of molecular weight 28,600 is a rod with a length of 170 A and a diameter of 30 A; this description is consistent with the X-ray scattering data. Over a broad range of concentrations, inelastic light scattering measurements and small-angle X-ray scattering experiments provide the same hydrodynamic values (e.g., Stokes radii and frictional ratios). The positions of the iodines were resolved and found at a radius (R) of 16 A. So, the iodine-iodine distance across the cross section is 34 A, indicating that labeled tyrocidine B is not affected during the aggregational process.

Chemical Phenomena↗
PubMed1979

Total assignments, including four aromatic residues, and sequence confirmation of the decapeptide tyrocidine A using difference double resonance. Qualitative nuclear overhauser effect criteria for beta turn and antiparallel beta-pleated sheet conformations.

The complete assignments of all the proton magnetic resonance signals from each NH-CalphaH-CbetaH2 moiety in a complex peptide containing several residues of the same type has not yet been achieved without specific or stereospecific isotopic enrichment. We report the sequencing and proton magnetic resonance spectral assignments, including those of 4 aromatic residues, of tyrocidine A, an analog of the decapeptide gramicidin S. Two complementary methods, proton-proton nuclear Overhauser enhancements and scalar decoupling, evaluated by two distinct forms of difference double resonance, were used. All chemical shifts, scalar coupling constants, and [1H:1H] nuclear Overhauser enhancements for the backbone protons are reported. The [1H:1H] nuclear Overhauser enhancements are consistent with tyrocidine A possessing a beta-I turn/beta-II' turn/antiparallel beta-pleated sheet conformation. In addition to the previously proposed nuclear Overhauser enhancement criteria for beta turns and antiparallel beta sheets, another criterion for identifying the antiparallel beta sheet is demonstrated; namely, the nuclear Overhauser enhancement between 2 CalphaH protons of the central resisdues, in this case the Phe7CalphaH and Orn2CalphaH.

Amino Acid Sequence↗
PubMed1975

Studies of individual amino acid residues of the decapeptide tyrocidine A by proton double-resonance difference spectroscopy in the correlation mode.

The cyclic decapeptide antibiotic tyrocidine A was studied by two relatively new methods, viz., correlation proton magnetic resonance (pmr) spectroscopy and double-resonance difference pmr spectroscopy. The correlation method of spectral accumulation provided pmr spectra of good resolution, and in addition the signal-to-noise ratio achieved per unit time of accumulation was much higher than that achieved by use of the conventional continuous wave (cw) method. Furthermore, when protonated solvents are used, the correlation mode of accumulation has a distinct advantage over pulse and fast Fourier transform (fft) methods currently in use. Double-resonance difference (drd) spectra of individual amino acid residues in tyrocidine A were obtained by the correlation method when the decoupling frequency was maintained at the center frequency of the appropriate C-alpha proton multiplet and at a level of power that totally decoupled vicinal C-alpha and C-beta protons; the resolution of these spectra was good, and the signal-to-noise ratio was high. The distinct patterns and spectral positions of the drd spectra were characteristic of the particular type of amino acid residue and, therefore, could be used as the basis for making assignments. Furthermore, the drd spectra revealed the spectral positions of individual C-alpha and C-beta proton transitions and therefore, upon spectral analysis, could provide the chemical shifts and coupling constants of these protons. Positions of transitions were revealed even though they were hidden by overlap in the corresponding conventional single- or double-resonance spectra.

Amino Acids↗
PubMed1989

Gene cluster containing the genes for tyrocidine synthetases 1 and 2 from Bacillus brevis: evidence for an operon.

From a genomic library of the tyrocidine producer Bacillus brevis ATCC 8185 constructed in the bacteriophage vector EMBL3, a recombinant phage which contains the structural genes coding for tyrocidine synthetases 1 and 2, TycA and TycB, was identified. The location of the tycA gene within the 16-kilobase insert of this clone, EMBL25-1, was mapped by hybridization studies by using the previously isolated tycA DNA as a probe. Restriction analyses, the construction of subclones, and the analysis of proteins encoded by the subclones located the tycB gene at the 3' end of the tycA gene and revealed that the two genes are transcribed in the same direction. Nuclease S1 protection studies and DNA sequencing studies of the intergenic region indicated that tycA and tycB are separated by a 94-base-pair noncoding region and suggested that these genes are organized as an operon.

Amino Acid Sequence↗
PubMed1977

Isolation of amino acid activating subunit--pantetheine protein complexes: their role in chain elongation in tyrocidine synthesis.

Dissociation of the multienzymes of tyrocidine synthesis by prolonged incubation of crude extracts of Bacillus brevis (Dubos strain, ATCC 8185) has yielded, on Sephadex G-100 chromatography, two fractions of amino acid activating subunits, a larger one of 70,000 daltons and a smaller one of 90,000 daltons; the latter was a complex consisting of the 70,000 dalton subunit and the pantetheine-carrying protein of about 20,000 daltons. When it dissociated, the intermediate enzyme, which activates three amino acids, contained two-thirds of the subunits in the 70,000 dalton and one-third in the 90,000 dalton fraction; the heavy enzyme, which activates six amino acids, contained five-sixths of the subunits in the former fraction and one-sixth in the latter. Both fractions showed ATP-PP(i) exchange with all amino acids that are activated by the respective polyenzymes. With proline as an example, the 70,000 dalton subunit exhibited a single low-affinity binding site, which should correspond to the peripheral thiol acceptor site, whereas the 90,000 dalton subunit showed both a low-affinity binding site and an additional high-affinity site for proline; the high-affinity site is attributed to the pantetheine present on the pantetheine-carrying protein, and suggests that amino acids are translocated from the peripheral SH to the pantetheine-carrying moiety during chain elongation. This was confirmed by the observation that the 90,000 dalton complex, when incubated with the light enzyme in the presence of phenylalanine and proline, produced DPhe-Pro dipeptide that cyclized into DPhe-Pro diketopiperazine, but the 70,000 dalton activating subunit, when similarly incubated, did not. After subunit dissociation, however, no further elongation occurred after the transfer from phenylalanine to proline.

Aminoacylation↗
PubMed1975

Tyrocidine and the linear gramicidin. Do these peptide antibiotics play an antagonistic regulative role in sporulation?

1. The cyclic peptide antibiotic tyrocidine, synthesized by Bacillus brevis (ATCC 8185), inhibits RNA synthesis in an in vitro transcriptional system by forming a complex with the DNA. 2. The linear peptide antibiotic gramicidin, synthesized by the same strain, reverses at least partly this inhibition. The molecular mechanism of this reactivation is unknown. Gramicidin by itself inhibits transcription in vitro. This inhibition is not due to a complex formation between DNA and the peptide. 4. A possible regulative role of the two peptides in sporulation is discussed.

Bacillus↗
PubMed1991

Nucleotide sequence of the LYS2 gene of Saccharomyces cerevisiae: homology to Bacillus brevis tyrocidine synthetase 1.

The Saccharomyces cerevisiae LYS2 gene, which encodes alpha-aminoadipate reductase, an essential enzyme in the yeast lysine biosynthetic pathway, has been sequenced. A large open reading frame (ORF) has been identified which can specify a 1392-amino acid protein with a deduced Mr of 155,344. A DNA database search using the translated LYS2 ORF as a probe has revealed significant aa sequence homology to the Bacillus brevis enzyme tyrocidine synthetase 1.

Aldehyde Oxidoreductases↗
PubMed1990

N-terminal halves of gramicidin S synthetase 1, and tyrocidine synthetase 1 as novel members of firefly luciferase family.

It was found, by computer-assisted homology search, that the N-terminal halves of gramicidin S synthetase 1 and tyrocidine synthetase 1 are homologous with beetle luciferases and plant 4-coumarate:CoA ligases. The comparison of the reactions catalyzed by these enzymes showed that they are involved in similar reactions; the adenylation of their substrates and the formation of thiolester. Structural and functional implication of the sequence homology and molecular evolution of these proteins are discussed.

Amino Acid Isomerases↗