Identification of antibacterial peptides from endophytic microbiome.

Endophytes, microorganisms living inside plant tissues, are promising producers of lead compounds for the pharmaceutical industry. However, the majority of endophytes are unculturable and therefore inaccessible for functional studies. To evaluate genetic resources of endophytes, we analyzed the biodiversity of fungal microbiome of black crowberry (Empetrum nigrum L.) by next-generation sequencing and found that it consists mainly of unknown taxa. We then separated the host and the endophyte genomes and constructed a fosmid expression library from the endophytic DNA. This library was screened for antibacterial activity against Staphylococcus aureus. A unique antibacterial clone was selected for further analysis, and a gene En-AP1 was identified with no similarity to known sequences. The expressed, folded protein En-AP1 was not active against S. aureus, while tryptic digests exhibited antimicrobial activity. Seven out of twelve synthesized peptides, predicted antibacterial in silico, exhibited in vitro activity towards both S. aureus and Escherichia coli. We propose that the En-AP1 protein is degraded in the library host E. coli and antimicrobial fragments are released from the cell, explaining the in vitro antibacterial activity of the clone. This is the first report of a novel gene expressed in vitro derived from an endophytic microbiome, demonstrating the potential of finding novel genes and compounds from unculturable endophytes.

Analysis of in vitro activities and modes of action of synthetic antimicrobial peptides derived from an alpha-helical 'sequence template'.

OBJECTIVES: Cationic antimicrobial peptides (AMPs) are indispensable components of innate immune systems and promising candidates for novel anti-infective strategies. We rationally designed a series of peptides based on a template derived from known alpha-helical AMPs, which were then analysed regarding efficacy against clinical isolates and antibiotic mechanisms. METHODS: Efficacy tests included standard MIC and synergy assays. Whole cell assays with staphylococcal strains included killing kinetics, efflux experiments and determination of membrane depolarization. The transcriptional response of AMP-treated Staphylococcus aureus SG511 was analysed using a Scienion genomic microarray covering (approximately 90% of) the S. aureus N315 genome and AMP P16(6|E). RESULTS: The AMPs showed remarkable broad-spectrum activity against bacteria and fungi regardless of any pre-existing antibiotic resistance mechanism. Whole cell assays indicated that the AMPs target the cytoplasmic membrane; however, significant membrane leakage and depolarization was only observed with a standard laboratory test strain. Transcriptional profiling identified up-regulation of putative efflux pumps and of aerobic energy generation mechanisms as major counter activities. Important components of the staphylococcal cell wall stress stimulon were up-regulated and the lipid metabolism was also affected. CONCLUSIONS: The broad spectrum activity of amphiphilic helical AMPs is based on multiple stresses resulting from interactions with microbial membranes; however, rather than killing through formation of pores, the AMPs appear to interfere with the coordinated and highly dynamic functioning of membrane bound multienzyme complexes such as electron transport chains and cell wall or lipid biosynthesis machineries.

Role of biochemical markers of bone remodeling in clinical practice.

Bone tissue is subject to remodeling throughout the lifetime of an individual. Through a continuous remodeling cycle, actuated via the so-called 'bone remodeling units', old bone is resorbed by osteoclasts with the formation of cavities that are subsequently filled by osteoblasts. Bone loss observed in old age and in women after menopause is due to an imbalance between bone resorption and formation. Biochemical markers provide a dynamic view of the remodeling process, which covers rate of turnover and pathogenesis, and should improve fracture risk prediction. Furthermore, they can be used to monitor the short-term effects of therapy, and indicate if an excessive slowing of the remodeling process is occurring. When searching for markers of bone remodeling, biochemists have focused mainly on skeletal molecules that can be dosed in plasma and/or urine, as indicators of osteoblast function (i.e. bone alkaline phosphatase, osteocalcin, procollagene I C- and N-terminal propeptides) or osteoclast function (i.e. pyridinium crosslinks, collagen I C- and N-terminal telopeptides). The clinical significance of any marker for bone remodeling depends on two fundamental characteristics: specificity and variability. If the objective is to monitor therapeutic efficacy, it seems most rational to use a resorption marker for drugs that act principally on osteoclast, such as estrogens or bisphosphonates, while for drugs that act principally on osteoblast, such as PTH-peptides a marker for bone formation would be more appropriate.

Identification and characterization of a primary antibacterial domain in CAP18, a lipopolysaccharide binding protein from rabbit leukocytes.

Secondary structure prediction studies on CAP18, a lipopolysaccharide binding protein from rabbit granulocytes, identified a highly cationic, 21-residue sequence with the tendency to adopt an amphipathic alpha-helical conformation, as observed in many antimicrobial peptides. The corresponding peptide was chemically synthesized and shown to exert a potent bactericidal activity against both Gram-negative and Gram-positive bacteria, and a rapid permeabilization of the inner membrane of Escherichia coli. Five analogues were synthesized to elucidate structure/activity relationships. It was found that helix disruption virtually eliminates antibacterial activity, while the degree of amphipathicity and the presence of an aromatic residue greatly affect the kinetics of bacterial inner membrane permeabilization.

Chemical synthesis and biological activity of a novel antibacterial peptide deduced from a pig myeloid cDNA.

Several myeloid precursors of antibacterial peptides have recently been shown to share homologous pre- and pro-regions. Taking advantage of this homology, a novel cDNA was cloned from pig bone marrow RNA. This encodes a 166-residue polypeptide with highly conserved pre- (29 residues) and pro- (101 residues) sequences, followed by a unique, 36-residue C-terminal sequence. Structure analyses of this C-terminal region have identified a highly cationic sequence predicted to adopt an amphipathic alpha-helical conformation. A peptide corresponding to this sequence was chemically synthesized and shown to arrest the growth of both Gram-positive and Gram-negative bacteria. At least for Escherichia coli, the activity of this peptide appears to be mediated by its ability to permeabilize the bacterial membranes.

Molecular diversity in gene-encoded, cationic antimicrobial polypeptides.

Gene-encoded, ribosomally synthesised antimicrobial peptides (AMPs) are an ancient and pervasive component of the innate defence mechanisms used by multicellular organisms to control the natural flora and combat pathogens. Bacteria also produce such AMPs to maintain ecological niches free of rival strains. Several hundred different peptides have been characterised to date, and they show a marked degree of variability in both sequence and structure, having evolved to act against distinct microbial targets in different physiological contexts. Many of these peptides appear to function via a selective, but not receptor-mediated, permeabilisation of microbial membranes, while others interact with specific membrane associated or intracellular targets. This review presents a broad survey of different amp structural classes, emphasising both their molecular diversity and underlying similarities. The mode of action of these peptides and potential for biomedical and other application is also briefly discussed.

A novel [60]fullerene amino acid for use in solid-phase peptide synthesis.

[see structure]. A fullerene derivative containing a free amino group has been condensed with N-Fmoc-L-glutamic acid alpha-tert-butyl ester to give a C60-functionalized amino acid. The carboxylic end of this amino acid has been deprotected in acidic conditions, and the resulting acid has been used for solid-phase peptide synthesis. The final peptide, cleaved from the resin, was very soluble in water solutions and showed antimicrobial activity against two representative bacteria.

A study of some polypyridylruthenium(II) complexes as DNA binders and photocleavage reagents.

The nature of the binding of several ruthenium polypyridyl complexes containing 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (DMB), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline (DPP), 2,2',2"-terpyridine (terpy), 2,2'-biquinoline (biq), 1,4,5,8-tetraazaphenanthrene (TAP) and 1,4,5,8,9,12-hexaazatriphenylene (HAT), with calf thymus DNA, poly[d(A-T)] and poly[d(G-C)] were studied by absorption and emission spectroscopy, DNA melting techniques, and emission lifetime measurements. In low ionic strength phosphate buffer, spectroscopic changes and DNA stabilization depended on the polypyridyl ligands present, and indicated binding that varied from substantially electrostatic to intercalative. Ru(bipy)2(HAT)2+ and Ru(phen)3(2+), which bind by partial intercalation, also show a strong preference for poly[d(A-T)]. The emission quantum yields for most complexes were increased in the presence of DNA. An exception was Ru(TAP)3(2+) which has a markedly reduced emission quantum yield and lifetime in the presence of poly[d(G-C)] or CT-DNA, due to photoredox interaction with quanines. Emission decays of the complexes generally showed multiexponential behaviour. The ability of the ruthenium complexes to sensitise DNA cleavage was determined using pBR322 plasmid DNA. Ru(TAP)3(2+) is the most efficient sensitiser while uncharged complexes and complexes with very short-lived excited states do not cleave DNA.

Photosensitized reactions of poly(U) with tris(2,2'-bipyridyl)ruthenium(II) and peroxydisulfate.

The reactions of polyuridylic acid [poly(U)] with Ru(bpy)3(3+) [Ru(III)] and SO4.-, following UV and visible light irradiation of Ru(bpy)3(2+) [Ru(II)] in the presence of S2O8(2-), were studied in an argon-saturated aqueous solution using time-resolved absorption and conductivity methods. The kinetics of the Ru(III) conversion to Ru(II) in the presence of poly(U) was monitored spectroscopically either in the absence of SO4.- [rapid mixing with Ru(III)] or in its presence (after laser flash excitation, lambda exc = 353 nm). The conversion of Ru(III) to Ru(II) is complete at a [nucleotide]/[sensitizer] (N/S) ratio greater than or equal to 10 (rate constant k = 12 s-1) for rapid mixing and at N/S greater than or equal to 6 (k = 15 s-1 at N/S = 10) after laser pulsing. Conductivity measurements following the laser pulse revealed a fast conductivity increase (risetime less than 10 micros), due to the formation of charged species and protons. A slower increase in the 0.1-0.5 s range was observed for poly(U) but it is considerably smaller for poly(dU) and absent in uracil containing monounits. The slow increase is unaffected by pH changes in the 3.5-7 range, markedly reduced in the 7-9 range and is replaced by a slight decrease in conductivity in buffered solutions. An explanation is that poly(U)-bound excited Ru(II) reacts with S2O8(2-) forming Ru(III) and SO4.- as oxidizing species both of which react with poly(U) bases. The resulting base radicals react with Ru(III) or the ligands in the ruthenium complex, producing protons which give rise to the slow conductivity increase (k = 15 s-1 at N/S = 10). The formation of single-strand breaks and the ensuing release of condensed counterions does not appear to contribute significantly to the slow conductivity signal. At N/S less than 10 the observed rate and extent of Ru(III)--Ru(II) conversion and of the slow proton production vary markedly with the N/S ratio.

Photo-induced electron transfer from nucleotides to ruthenium-tris-1,4,5,8-tetraazaphenanthrene: model for photosensitized DNA oxidation.

The luminescence quenching of ruthenium-tris-1,4,5,8-tetraazaphenanthrene [Ru(tap)3(2+)] by nucleotides approaches the diffusion rate only with guanosine-5'-monophosphate (GMP), the most reducing nucleotide, and leads to an electron transfer with the production of the monoreduced complex and the oxidized base. The resulting deprotonated GMP(-H).radical recombines with the monoreduced complex according to a bimolecular equimolar process. The pH dependence of the decay of the transient reduced complex, in the presence of an oxidant (oxygen or benzoquinone) indicates the formation of Ru(tap)2(tapH)2+, i.e. the reduced protonated species, subsequent to the electron transfer, with a pKa of 7.6 as confirmed from pulse radiolysis experiments. As the non-protonated reduced complex, Ru(tap)2(tap-.)+, has a higher reducing power than the protonated one, oxygen is able to reoxidize only the non-protonated species, whereas benzoquinone reoxidizes both species but with different rate constants. The flash photolysis of Ru(tap)3(2+) in the presence of DNA and the effect of Mg2+ ions and GMP as supplementary additives also show the existence of a photo-induced electron transfer with the nucleic acid, which can be correlated to the photosensitized cleavage of DNA by this complex.

Inhibition of OH radical-induced strand break formation of poly(U) by Ru(bpy)32+ or Ru(phen)32+ attached to the polynucleotide.

Reactions of OH radicals with poly(U) (polyuridylic acid) in the presence of Ru(bpy)32+ or Ru(phen)32+ in aqueous solutions were studied. OH radicals were produced by pulse radiolysis and their reactions with ruthenium complexes were measured spectrophotometrically under conditions were the complexes are attached to the polynucleotide. The OH radical adds to either the uracil moiety or the ruthenium complexes. The ratio of the radicals produced depends only on the ratio of their rate constants and the concentrations of poly(U) and ruthenium complexes. Similar results were obtained with uridine-5'-monosphosphate, where the ruthenium complexes are not attached to the nucleotide. Surprisingly, the yield of single-strand break formation from the OH adducts of uracil in poly(U) is much smaller than that expected on the basis of the yield measured in the absence of ruthenium complexes. Possible reasons for this behaviour are discussed.

Photoinduced interaction of Ru(bpy)3 2+ with nucleotides and nucleic acids in the presence of S2O8 2-; a transient conductivity study.

The photochemical reactions of Ru(bpy)3(2+) with single- and double-stranded DNA, polynucleotides and purine-containing nucleotides in argon-saturated aqueous solution in the presence of S2O8(2-) were studied using time-resolved absorption and conductivity methods. The conversion of Ru(bpy(3(3+) to Ru(bpy)3(2+), monitored spectroscopically either after rapid mixing with substrate or after laser flash excitation (lambda exc = 353 nm) is quantitative at nucleotide-to-sensitizer ratios [N]/[S] of 1-2 for DNA and other guanine-containing compounds. Conductivity measurements following the laser pulse revealed a fast conductivity increase (rise time, less than 0.1 ms) due to the formation of protons and, to a lesser degree, to charged species of much lower ion mobility. A slower component in the 0.01-1 s range was observed for nucleic acids; its amplitude is markedly reduced at pH 6-9. In buffered neutral solution the signal is replaced by a slight decrease in conductivity. Electronically excited Ru(bpy)3(2+) bound to DNA reacts with S2O8(2-) to form Ru(bpy)3(3+) and SO4(.-) as primary oxidizing species both of which react with bases. The resulting base radicals react subsequently with Ru(bpy)3(3+) and Ru(bpy)3(2+) or the ligands in the ruthenium complex, producing protons which give rise to the slower conductivity increase. The formation of single-strand breaks and the ensuing release of condensed counterions does not appear to contribute significantly to the slow component. The transient conductivity behaviour is sensitive to the single- or double-stranded nature of DNA.

Binding of Ru(bpy)3(2+) and Ru(phen)3(2+) to polynucleotides and DNA: effect to added salts on the absorption and luminescence properties.

The interactions of tris(2,2'-bipyridyl)ruthenium(II) chloride and tris-(1,10-phenanthroline)ruthenium(II) chloride, Ru(bpy)3Cl2 and Ru(phen)3Cl2 respectively, with nucleic acids were studied by means of absorption spectroscopy and time-resolved and steady state luminescence techniques in unbuffered aqueous solution at room temperature as a function of added salt, oxygen and the [nucleotide]/[sensitizer] ratio (N/S). The hypochromicity of the visible absorption band of Ru(ligand)3(2+) and the changes in the luminescence intensity and luminescence decay kinetics are considerably larger in the presence of double-stranded calf thymus DNA (dsDNA) than in the presence of single-stranded DNA and polynucleotides. This is suggested to be the result of partial intercalation of the ruthenium complex into the dsDNA rather than just its higher charge density with respect to ssDNA. Spectral changes in the presence of dsDNA increase with increasing N/S ratio (maximum changes reached at N/S = 10-12, half-value 3-4). This is postulated to be due to a transition from mainly electrostatic binding to a binding in which partial intercalation plays an increased role. Addition of alkali or alkaline earth salts at very low concentrations stabilizes partial intercalation whereas higher salt concentrations lead to a release of the ruthenium complex from the strand. This effect of the salt cation increases in the order Cs less than Rb less than K less than Na less than Li less than Ba less than Sr less than Ca less than Mg less than Be. For Ru(bpy)3(2+) the presence of 0.5 mM Mg(ClO4)2 or 6 mM NaClO4 are sufficient to release 50% of the ruthenium complexes which are bound to the dsDNA (N/S = 10); the corresponding half-concentrations for Ru(phen)3(2+) are 0.8 mM and 40 mM respectively. The half-concentrations for release increase with increasing N/S ratio and decrease with the ionic radius of the added salt.

Photoaddition of ruthenium(II)-tris-1,4,5,8-tetraazaphenanthrene to DNA and mononucleotides.

Formation of adducts between Ru(TAP)3(2+) (TAP = 1,4,5,8-tetraazaphenanthrene) and DNA has been monitored by gel electrophoresis, UV-vis spectroscopy and dialysis methods. Adduct formation is found for both single- and double-stranded nucleic acids. The reaction with double-stranded DNA is found to be insensitive to solution pH or aeration. Spectroscopic changes similar to those for DNA are found with GMP in oxygen-free pH 5 solution. However, different reactions occur with GMP at higher pH or when the solution contains oxygen. Comparative experiments with double-stranded poly[d(G-C)] or poly[d(A-T)] indicate that the adduct with DNA involves binding to the guanosine moiety. It is proposed that the product is formed by the reaction of the reduced ruthenium complex and oxidised guanine species produced by photo-induced electron transfer.

Localization of beta-defensin genes in non human primates.

Defensins are a family of host defence peptides that play an important role in the innate immunity of mammalian and avian species. In humans, four beta-defensins have been isolated so far, corresponding to the products of the genes DEFB1 (h-BD1, GenBank accession number NM_005218); DEFB4 (h-Bd2, NM_004942.2), DEFB103 (h-BD3, NM_018661); and DEFB104 (hBD4, NM_080389) mapping on chromosome 8p23.22. We have localized beta-defensin genes on metaphasic chromosomes of great apes and several non-human primate species to determine their physical mapping. Using fluorescent in situ hybridization and BAC probes containing the four beta-defensin genes, we have mapped the homologous regions to the beta-defensin genes on chromosome 8p23-p.22 in non-human primates, while no signals were detected on prosimians chromosomes.

Design of synthetic antimicrobial peptides based on sequence analogy and amphipathicity.

Novel alpha-helical antimicrobial peptides have been devised by comparing the N-terminal sequences of many of these peptides from insect, frog and mammalian families, extracting common features, and creating sequence templates with which to design active peptides. Determination of the most frequent amino acids in the first 20 positions for over 80 different natural sequences allowed the design of one peptide, while a further three were based on the comparison of the sequences of alpha-helical antimicrobial peptides derived from the mammalian cathelicidin family of precursors. These peptides were predicted to assume a highly amphipathic alpha-helical conformation, as indicated by high mean hydrophobic moments. In fact, circular dichroism experiments showed clear transitions from random coil in aqueous solution to an alpha-helical conformation on addition of trifluoroethanol. All four peptides displayed a potent antibacterial activity against selected gram-positive and gram-negative bacteria (minimum inhibitory concentrations in the range 1-8 microM), including some antibiotic resistant strains. Permeabilization of both the outer and cytoplasmic membranes of the gram-negative bacterium, Escherichia coli, by selected peptides was quite rapid and a dramatic drop in colony forming units was observed within 5 min in time-killing experiments. Permeabilization of the cytoplasmic membrane of the gram-positive bacterium, Staphylococcus aureus, was instead initially quite slow, gathering speed after 45 min, which corresponds to the time required for significant inactivation in time-killing studies. The cytotoxic activity of the peptides, determined on several normal and transformed cell lines, was generally low at values within the minimum inhibitory concentration range.

Amphipathic alpha helical antimicrobial peptides.

Antimicrobial peptides (AMPs) that assume an amphipathic alpha helical structure are widespread in nature. Their activity depends on several parameters including the sequence, size, degree of structure formation, cationicity, hydrophobicity and amphipathicity. The analysis of numerous natural AMPs provided representative values for these parameters and led to a sequence template with which to generate potent artificial lead AMPs. Sequences were then varied in a rational manner, using both natural and nonproteinogenic amino acids, to probe the individual roles of each parameter in modulating biological activity. A high cationicity combined with a stabilized amphipathic alpha helical structure conferred enhanced cidal activity towards all the cell types considered, and was a requirement for Gram-positive bacteria and fungi. An elevated helicity also correlated with increased hemolytic activity. The structural requirements for activity against several Gram-negative bacteria were instead considerably less stringent, so that it persisted in peptides in which formation of a helical structure and/or amphipathicity were impeded. Either a reduced charge or a reduced hydrophobicity resulted in generally inactive peptides. These observations, combined with the kinetics of bacterial membrane permeabilization and time-killing are discussed in terms of currently accepted models of action for this type of peptide. The simple guidelines obtained in this study allowed the design of highly active shortened AMPs and may be generally useful in the development of this type of peptides as anti-infective agents.