Functions of the peptide antibiotics tyrocidine and gramicidin. Induction of conformational and structural changes of superhelical DNA

The Multifaceted Antibacterial Mechanisms of the Pioneering Peptide Antibiotics Tyrocidine and Gramicidin S

Cyclic β-sheet decapeptides, such as tyrocidines and gramicidin S, were among the first antibiotics in clinical application. Although they have been used for such a long time, there is virtually no resistance to them, which has led to a renewed interest in this peptide class. Both tyrocidines and gramicidin S are thought to disrupt the bacterial membrane. However, this knowledge is mainly derived from in vitro studies, and there is surprisingly little knowledge about how these long-established antibiotics kill bacteria. Our results shed new light on the antibacterial mechanism of β-sheet peptide antibiotics and explain why they are still so effective and why there is so little resistance to them.

Cyclic β-sheet decapeptides from the tyrocidine group and the homologous gramicidin S were the first commercially used antibiotics, yet it remains unclear exactly how they kill bacteria. We investigated their mode of action using a bacterial cytological profiling approach. Tyrocidines form defined ion-conducting pores, induce lipid phase separation, and strongly reduce membrane fluidity, resulting in delocalization of a broad range of peripheral and integral membrane proteins. Interestingly, they also cause DNA damage and interfere with DNA-binding proteins. Despite sharing 50% sequence identity with tyrocidines, gramicidin S causes only mild lipid demixing with minor effects on membrane fluidity and permeability. Gramicidin S delocalizes peripheral membrane proteins involved in cell division and cell envelope synthesis but does not affect integral membrane proteins or DNA. Our results shed a new light on the multifaceted antibacterial mechanisms of these antibiotics and explain why resistance to them is virtually nonexistent.

Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

BACKGROUND

Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species.

RESULTS

We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales.

CONCLUSIONS

Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.

Inhibition of malaria parasite blood stages by tyrocidines, membrane-active cyclic peptide antibiotics from Bacillus brevis

Tyrothricin, a complex mixture of antibiotic peptides from Bacillus brevis, was reported in 1944 to have antimalarial activity rivalling that of quinine in chickens infected with Plasmodium gallinaceum. We have isolated the major components of tyrothricin, cyclic decapeptides collectively known as the tyrocidines, and tested them against the human malaria parasite Plasmodium falciparum using standard in vitro assays. Although the tyrocidines differ from each other by conservative amino acid substitutions in only three positions, their observed 50% parasite inhibitory concentrations (IC(50)) spanned three orders of magnitude (0.58 to 360 nM). Activity correlated strictly with increased apparent hydrophobicity and reduced total side-chain surface area and the presence of ornithine and phenylalanine in key positions. In contrast, mammalian cell toxicity and haemolytic activities of the respective peptides were considerably less variable (2.6 to 28 microM). Gramicidin S, a structurally analogous antimicrobial peptide, was less active (IC(50)=1.3 microM) and selective than the tyrocidines. It exerted its parasite inhibition by rapid and selective lysis of infected erythrocytes as judged by fluorescence and light microscopy. The tyrocidines, however, did not cause an overt lysis of infected erythrocytes, but an inhibition of parasite development and life-cycle progression.

Probing the interaction of the multidrug-resistance phenotype with the polypeptide ionophore gramicidin D via functional channel formation

It has been proposed that the multidrug resistance (MDR) transporter, P-glycoprotein (P-170), may be physiologically involved in the transport of polypeptides. As a step towards understanding the interaction of P-170 with polypeptides, we isolated various gramicidin-D-resistant mammalian cell lines. Gramicidin D is a hydrophobic pentadecapeptide ionophore that forms proton and alkali metal cation-permeable channels in lipid bilayers. Gramicidin-D-resistant cells displayed a prominent MDR gene amplification, P-170 overexpression, reduced drug accumulation, and consequent resistance to MDR-type cytotoxic agents. Modulators of the MDR phenotype, including verapamil, reserpine and quinidine, rendered these cells sensitive to gramicidin D. Using these cell lines, we established an assay that probes for the intra-membranal interaction between P-170 and gramicidin D. Gramicidin-D channel formation was followed by cellular accumulation of 86Rb+. Ionophore-resistant cells, and other MDR cells, did not show an appreciable increase in 86Rb+ influx rates, in the presence of increasing gramicidin-D concentrations. In contrast, parental cells displayed a dose-dependent increase in the 86Rb+ influx rates. Interestingly, in the absence of serum, gramicidin-D-resistant cells resumed the wild-type, ionophore-dose-dependent increase in 86Rb+ influx rates. MDR modulators caused a resumption of channel formation in ionophore-resistant cells. We conclude that acquisition of the MDR phenotype is an efficient means of cellular protection against gramicidin D. Hence, a new approach is offered in which P-170 interaction with gramicidin D is quantitatively followed by a rapid assessment of the biological activity (i.e. channel formation) of the substrate itself. Possible mechanisms of P-170 interaction with free ionophore monomers, and membrane-associated gramicidin D are discussed.

Tyrocidine-induced modulation of the DNA conformation in Bacillus brevis

Using the [3H]trimethylpsoralen photobinding method [Sinden, R.R., Carlson, J.O. & Pettijohn, D.E. (1980) Cell 21, 773-783], a decrease in unrestrained torsional tension of DNA was detected in Bacillus brevis cells when they had entered the sporulation phase. This decrease in superhelicity was found in cells which synthesized the peptide antibiotic tyrocidine and which were stimulated to sporulate. Fluctuations in superhelicity probably reflect a highly complicated picture of tension-relaxing and tension-inducing activities. Addition of tyrocidine to vegetative cells reduced by one-half the torsional tension from DNA, whereas ethidium bromide relaxes DNA completely. Cross-links between DNA and tyrocidine were introduced with ultraviolet light in vitro and in vivo indicating that the modulation of the DNA conformation in the cell may in fact be due to a DNA-tyrocidine interaction. In a growing B. brevis culture exogenous [3H]tyrocidine could only be photobound to DNA after the cells had entered the sporulation phase. Our results could mean that the peptide antibiotic tyrocidine is active in B. brevis on the DNA level as one regulatory factor controlling DNA functions.

The GTP pool in Bacillus brevis and its significance for sporulation

The GTP pool of Bacillus brevis as well as that of other nucleotides is highly sensitive to all kinds of environmental changes like the cell transfer procedures or nutrient depletion of the cells. In growing cultures, as well as in cells transferred from rich to nitrogen-deficient medium, the nucleotide pool decreases significantly. This decrease is followed by the onset of sporulation only when cells are allowed to produce the peptide antibiotic tyrocidine or if tyrocidine is added to the culture. However, exogenous tyrocidine is active in triggering sporulation only when it is added within a short period of time immediately after shift down, that is when the nucleotide pool is observed to decrease.

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.

Effect of linear gramicidin on sporulation and intracellular ATP pools of Bacillus brevis

When Bacillus brevis ATCC 8185 was subjected to nutritional shiftdown from a rich medium to one completely devoid of a nitrogen source, sporulation could be stimulated by the addition of linear gramicidin. Gramicidin-induced sporulation occurred after a considerably longer lag period than the earlier described tyrocidine-induced process (Ristow and Paulus 1982) but involved similar associated biochemical changes, such as extracellular protease production, rapid incorporation of radioactive precursors into RNA, and dipicolinate synthesis. The increased incorporation of [3H]leucine into tyrocidine was a characteristic element in gramicidin-induced sporulation, not being observed when spore formation was accelerated by limited nitrogen supplementation. Nitrogen supplementation (0.02-0.01% nutrient broth) caused a slow and gradual increase in dipicolinate production, in contrast to the sudden, rapid rise of dipicolinate synthesis provoked by the addition of gramicidin or tyrocidine. The induction of sporulation by gramicidin occurred at very low peptide concentrations (0.03 microM), which also brought about an acute depletion of intracellular ATP. In sporulation accelerated by nutrient broth, no depression of ATP level was observed and nonionophoric analogues of gramicidin were unable to substitute for gramicidin in inducing sporulation.

Complexation and phase transfer of nucleic acids by gramicidin S

A novel interaction between gramicidin S (GrS) and nucleic acids is characterized which, like that between GrS and nucleotides, exploits both the dicationic and amphiphilic properties of the peptide. Complex formation between calf thymus DNA and GrS is demonstrated by (i) phase transfer to CHCl3 of ultrasonically irradiated DNA and (ii) inhibition of phase transfer to CHCl3 of adenosine 5'-triphosphate by either native or ultrasonically irradiated DNA. The stoichiometry of the interaction is 2:1 (DNA-P:GrS), which is consistent with a predominantly electrostatic mode of binding. The apparent affinity of GrS for DNA is considerably higher than it is for free nucleotides. The interaction of the monocationic derivative [2-N delta-acetylornithyl]gramicidin S with calf thymus DNA is considerably weaker. DNA binding by GrS provides a rationale for the lag between germination and RNA synthesis exhibited by wild-type spores of producer strains of Bacillus brevis but not by GrS-negative mutants. On the basis of these results in vitro, a protective role is proposed for GrS in the dormant spore.