Comparison of the Potency of the Lipid II Targeting Antimicrobials Nisin, Lacticin 3147 and Vancomycin Against Gram-Positive Bacteria

While nisin (lantibiotic), lacticin 3147 (lantibiotic) and vancomycin (glycopeptides) are among the best studied lipid II-binding antimicrobials, their relative activities have never been compared. Nisin and lacticin 3147 have been employed/investigated primarily as food preservatives, although they do have potential in terms of veterinary and clinical applications. Vancomycin is used exclusively in clinical therapy. We reveal a higher potency for lacticin 3147 (MIC 0.95?C3.8???g/ml) and vancomycin (MIC 0.78?C1.56???g/ml) relative to that of nisin (MIC 6.28?C25.14???g/ml) against the food-borne pathogen Listeria monocytogenes. A comparison of the activity of the three antimicrobials against nisin resistance mutants of L. monocytogenes also reveals that their susceptibility to vancomycin and lacticin 3147 changed only slightly or not at all. A further assessment of relative activity against a selection of Bacillus cereus, Enterococcus and Staphylococcus aureus targets revealed that vancomycin MICs consistently ranged between 0.78 and 1.56???g/ml against all but one strain. Lacticin 3147 was found to be more effective than nisin against B. cereus (lacticin 3147 MIC 1.9?C3.8???g/ml; nisin MIC 4.1?C16.7???g/ml) and E. faecium and E. faecalis targets (lacticin 3147 MIC from 1.9 to 3.8???g/ml; nisin MIC ??8.3???g/ml). The greater effectiveness of lacticin 3147 is even more impressive when expressed as molar values. However, in agreement with the previous reports, nisin was the more effective of the two lantibiotics against S. aureus strains. This study highlights that in many instances the antimicrobial activity of these leading lantibiotics are comparable with that of vancomycin and emphasizes their particular value with respect to use in situations including foods and veterinary medicine, where the use of vancomycin is not permitted.     

Sequence similarities among monkey ori-enriched (ors) fragments

Nucleotide sequences have been determined for eight ors (ori-enriched sequence) fragments isolated from monkey DNA by a method that was designed to enrich for origins of DNA replication [Kaufmann et al., Mol. Cell. Biol. 5 (1985) 721-727]. Evidence has been presented that some or possibly all of these sequences can serve, albeit inefficiently, as oris in vivo [Frappier and Zannis-Hadjopoulos, Proc. Natl. Acad. Sci. USA 84 (1987) 6668-6672]. Two of the fragments were found to contain the long terminal repeat-like elements of the 'O-family' of moderately repetitive sequences that are present in human DNA as a transposon-like element [Paulson et al., Nature 315 (1985) 359-361]. Extensive pair-wise comparisons of the sequences failed to detect any statistically significant common sequences, except for long asymmetrically distributed A + T-rich stretches. Nonetheless, when the ors fragments were examined for the presence of published consensus sequences, seven of eight were found to contain the control sequence described by Dierks et al. [Cell 32 (1983) 695-706], and the same seven of eight were found to contain both the scaffold attachment region T consensus [Gasser and Laemmli, Cell 46 (1986) 521-530] and the minimal Saccharomyces cerevisiae autonomously replicating sequence consensus [e.g., Palzkill and Newlon, Cell 53 (1988) 441-450].     

Conjugal transfer of nisin plasmid genes from Streptococcus lactis 7962 to Leuconostoc dextranicum 181.

Acriflavine-generated mutants of Streptococcus lactis 7962 with various combinations of plasmid molecular masses were screened for nisin production. Nisin was produced by both the wild type and mutants that contained a 17.5-megadalton plasmid, which was obscured by chromosomal fragments. No nisin was produced by plasmid-free mutants. Sucrose fermentation and nisin production were simultaneously expressed. A transconjugant obtained from nisin-producing donor S. lactis 7962 and recipient Leuconostoc dextranicum 181 was a "supernisin" producer. The L. dextranicum Nis+ transconjugant was resistant to S. lactis 7962 phage and vancomycin (greater than 1,000 micrograms/ml), and it contained an extra 17.5-megadalton plasmid.     

Conjugal transfer of nisin plasmid genes from Streptococcus lactis 7962 to Leuconostoc dextranicum 181

Acriflavine-generated mutants of Streptococcus lactis 7962 with various combinations of plasmid molecular masses were screened for nisin production. Nisin was produced by both the wild type and mutants that contained a 17.5-megadalton plasmid, which was obscured by chromosomal fragments. No nisin was produced by plasmid-free mutants. Sucrose fermentation and nisin production were simultaneously expressed. A transconjugant obtained from nisin-producing donor S. lactis 7962 and recipient Leuconostoc dextranicum 181 was a "supernisin" producer. The L. dextranicum Nis+ transconjugant was resistant to S. lactis 7962 phage and vancomycin (greater than 1,000 micrograms/ml), and it contained an extra 17.5-megadalton plasmid.     

Beta(Leu121-Lys122) segment of fibrinogen is in a region essential for plasminogen binding by fibrin fragment E

It was shown previously that two sequentially nonidentical regions of human fibrin(ogen), present in fragments D and E, carry specific plasminogen-binding sites [V aradi , A., & Patthy , L. (1983) Biochemistry 22, 2440-2446]. Comparison of the affinity of a variety of fragment E species for immobilized Lys-plasminogen revealed that fragment E3e [(alpha 20/24-78, beta 54-122, gamma 1-53)2] possesses a strong plasminogen-binding site, whereas fragment E3t [(alpha 20/24-78, beta 54-120, gamma 1-53)2] has 30-fold lower affinity for the affinant . Since the two fragments differ only in the beta ( Leu121 - Lys122 ) segment, this suggests that residues beta ( Leu121 - Lys122 ), present in the triple-helical connector region of fibrin(ogen), are essential for plasminogen binding by fragment E. Reduction and alkylation of fragment E3e lead to the destruction of the plasminogen-binding site, indicating that none of the separated, alkylated polypeptide chains of the fragment are able to bind to plasminogen and probably the coiled-coil superstructure of the connector region is necessary for the maintenance of the plasminogen-binding site of fragment E.     

Protein-kinase-C-catalyzed phosphorylation of the microtubule-binding domain of microtubule-associated protein 2 inhibits its ability to induce tubulin polymerization

It has previously been demonstrated that microtubule-associated protein 2 (MAP2) is a good substrate for the purified protein kinase C [Tsuyama, S., Bramblett, G. T., Huang, K.-P. & Flavin, M. (1986) J. Biol. Chem. 261, 4110-4116; Akiyama, T., Nishida, E., Ishida, J., Saji, N., Ogawara, H., Hoshi, M., Miyata, Y. & Sakai, H. (1986) J. Biol. Chem. 261, 15648-15651]. We have shown here that phosphorylation of MAP2, catalyzed by protein kinase C, reduces the ability to induce tubulin polymerization. MAP2 is divided into two domains by digestion with alpha-chymotrypsin; the microtubule-binding and the non-binding (projection) domains. The limited chymotryptic digestion following phosphorylation of MAP2 by protein kinase C has shown that both the domains of MAP2 were phosphorylated by protein kinase C, 50-60% of the incorporated phosphates being detected in the microtubule-binding domain. Polypeptide fragments, containing the microtubule-binding domain of MAP2, were purified by DEAE-cellulose column chromatography after chymotryptic digestion of MAP2. The purified microtubule-binding fragments were competent to polymerize tubulin, and served as good substrates for protein kinase C. The phosphorylation of the microtubule-binding fragments by protein kinase C reduced their ability to induce tubulin polymerization. These results suggest that the ability of MAP2 to induce tubulin polymerization is inhibited by phosphorylation of the microtubule-binding domain catalyzed by protein kinase C.     

Intramolecular cross-linking of myosin subfragment 1 with bimane

We previously showed that the fluorescent inter-thiol cross-linker dibromobimane (DBB) [Kosower, N. S., Kosower, E. M., Newton, G. L., & Ranney, H. M. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 3382-3386] cross-links two [50 and 20 kilodaltons (kDa)] of the three major fragments of myosin subfragment 1 (S-1); on intact S-1, DBB quenches tryptophans and inhibits all ATPases [Mornet, D., Ue, K., & Morales, M. F. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 1658-1662]. Here we characterize the modification chemically: DBB cross-links Cys-522 (50 kDa) with Cys-707 (20 kDa), thereby sealing a large preexisting heavy-chain loop containing important functionalities. Cross-linking rate is insensitive to nucleotides, but apparently sterically, either monobromobimane or DBB reduces Ca2+-ATPase to low, nonzero levels.     

Proteolytic degradation routes for turkey beta 1-adrenoceptor probed with antipeptide antibodies against the N-terminal sequence of the receptor

Anti-peptide antibodies, raised against the N-terminal sequence (amino acids 2-10) of the turkey beta 1-adrenoceptor [Yarden et al., Proc. Natl. Acad. Sci. USA (1986) 83, 6795-6799] recognized the 50 kDa- but not the 40 kDa-form of the receptor, thus confirming the previous assumption that the N-terminus of the 50 kDa form is lost during its conversion to the 40 kDa-form [Jür beta, R., Hekman, M. & Helmreich, E.J.M. (1985) Biochemistry 24, 3349-3354]. By in situ proteolysis small amounts of receptor fragments were formed, which could be recognized by the N-terminus specific antibody. Therefore, although the production of the stable 40 kDa receptor species by proteolytic removal of a portion of the N-terminal appears to be the predominant route, there exists an additional pathway of degradation which must involve the initial cleavage of the carboxyl terminal.     

Nisin resistance of Streptococcus bovis

The growth of Streptococcus bovis JB1 was initially inhibited by nisin (1 microM), and nisin caused a more than 3-log decrease in viability. However, some of the cells survived, and these nisin-resistant cells grew as rapidly as untreated ones. To see if the nisin resistance was merely a selection, nisin-sensitive cells were obtained from agar plates lacking nisin. Results indicated that virtually any nisin-sensitive cell could become nisin-resistant if the ratio of nisin to cells was not too high and the incubation period was long enough. Isolates obtained from the rumen were initially nisin sensitive, but they also developed nisin resistance. Nisin-resistant cultures remained nisin resistant even if nisin was not present, but competition studies indicated that nisin-sensitive cells could eventually displace the resistant ones if nisin was not present. Nisin-sensitive, glucose-energized cells lost virtually all of their intracellular potassium if 1 microM nisin was added, but resistant cells retained potassium even after addition of 10 microM nisin. Nisin-resistant cells were less hydrophobic and more lysozyme-resistant than nisin-sensitive cells. Because the nisin-resistant cells bound less cytochrome c, it appeared that nisin was being excluded by a net positive (i.e., less negative) charge. Nisin-resistant cells had more lipoteichoic acid than nisin-sensitive cells, and deesterified lipoteichoic acids from nisin-resistant cells migrated more slowly through a polyacrylamide gel than those from nisin-sensitive cells. These results indicated that lipoteichoic acids could be modified to increase the resistance of S. bovis to nisin. S. bovis JB1 cultures were still sensitive to monensin, tetracycline, vancomycin, and bacitracin, but ampicillin resistance was 1,000-fold greater.     

DSC studies of a family of natively disordered fragments from Escherichia coli thioredoxin: surface burial in intrinsic coils

The accumulating data from proteome analysis indicates that numerous proteins have segments and/or domains, involved in regulatory functions of the eukaryotic cell, which are entirely unstructured under physiological conditions, challenging the structure-function paradigm. Although many such natively unfolded proteins have been structurally analyzed by NMR spectroscopy, little is known about solvent inaccessible surfaces in premolten globules and intrinsic coils. Recent DSC studies of two protein fragments have shown a promising way to estimate the predominantly hydrophobic buried surfaces [Georgescu, R. E., García-Mira, M. M., Tasayco, M. L., and Sánchez-Ruiz, J. M. (2001) Eur. J. Biochem. 268, 1-10]. Here we report a systematic heat capacity analysis of a family of natively disordered complementary fragments of oxidized Escherichia coli thioredoxin (1-31/32-108, 1-37/38-108, 1-50/51-108, and 38-73) which provides insights into the local and nonlocal interactions contributing to the burial of predominantly hydrophobic surface in intrinsic coils.     

Scalable purification of the lantibiotic nisin and isolation of chemical/enzymatic cleavage fragments suitable for semi‐synthesis

Herein, we describe a scalable purification of the lantibiotic nisin via an extraction/precipitation approach using a biphasic system, which can be carried out up to 40–80 gram scale. This approach results in an at least tenfold enrichment of commercially available preparations of nisin, which usually contain only 2.5% of the desired peptide, to allow further purification by preparative HPLC. As a follow‐up study, the enriched nisin sample was digested either by trypsin or chymotrypsin, or treated by CNBr, and these reactions were monitored by LC‐MS to identify and characterize the obtained fragments. Two previously unknown cleavage sites have been identified: Asn20–Met21 and Met21–Lys22 for trypsin and chymotrypsin, respectively. Furthermore, a novel and convenient enzymatic approach to isolate the native nisin C‐ring [nisin fragment (13–20)] was uncovered. Finally, by means of preparative HPLC, nisin fragments (1–12), (1–20), (22–34), and (22–31) could be isolated and will be used in a semi‐synthesis approach to elucidate the role of each fragment in the mode of action of nisin as an antimicrobial peptide. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Construction and diversification of yeast cell surface displayed libraries by yeast mating: application to the affinity maturation of Fab antibody fragments

Yeast display is a powerful technology for the affinity maturation of human antibody fragments. However, the technology thus far has been limited by the size of antibody libraries that can be generated, as using current transformation protocols libraries of only between 10(6) and 10(7) are typically possible. We have recently shown that Fab antibodies can be displayed on the cell surface of Saccharomyces cerevisiae [van den Beucken, T., Pieters, H., Steukers, M., van der Vaart, M., Ladner, R.C., Hoogenboom, H.R., Hufton, S.E., 2003. Affinity maturation of Fab antibody fragments by fluorescent-activated cell sorting of yeast-displayed libraries. FEBS Lett. 546, 288-294]. This discovery and the knowledge that Fab antibodies are heterodimeric suggest that independent repertoires of heavy chain (HC) and light chain (LC) can be constructed in haploid yeast strains of opposite mating type. These separate repertoires can then be combined by highly efficient yeast mating. Using this approach, we have rapidly generated a naive human Fab yeast display library of over 10(9) clones. In addition, utilizing error-prone polymerase chain reaction, we have diversified Fab sequences and generated combinatorial and hierarchical chain shuffled libraries with complexities of up to 5 x 10(9) clones. These libraries have been selected for higher affinity using a repeating process of mating-driven chain shuffling and flow cytometric sorting.     

Event-driven simulation of cerebellar granule cells

Around half of the neurons of a human brain are granule cells (approximately 10(11)granule neurons) [Kandel, E.R., Schwartz, J.H., Jessell, T.M., 2000. Principles of Neural Science. McGraw-Hill Professional Publishing, New York]. In order to study in detail the functional role of the intrinsic features of this cell we have developed a pre-compiled behavioural model based on the simplified granule-cell model of Bezzi et al. [Bezzi, M., Nieus, T., Arleo, A., D'Angelo, E., Coenen, O.J.-M.D., 2004. Information transfer at the mossy fiber-granule cell synapse of the cerebellum. 34th Annual Meeting. Society for Neuroscience, San Diego, CA, USA]. We can use an efficient event-driven simulation scheme based on lookup tables (EDLUT) [Ros, E., Carrillo, R.R., Ortigosa, E.M., Barbour, B., Ags, R., 2006. Event-driven simulation scheme for spiking neural networks using lookup tables to characterize neuronal dynamics. Neural Computation 18 (12), 2959-2993]. For this purpose it is necessary to compile into tables the data obtained through a massive numerical calculation of the simplified cell model. This allows network simulations requiring minimal numerical calculation. There are three major features that are considered functionally relevant in the simplified granule cell model: bursting, subthreshold oscillations and resonance. In this work we describe how the cell model is compiled into tables keeping these key properties of the neuron model.     

A small plasmid for recombination-based screening.

We reported recently the construction of the 4.4-kb R6K-derived pMAD1 plasmid carrying supF [Stewart et al., Gene 106 (1991) 97-101] that does not share nt sequences with ColE1 and therefore permits recombination-based screening of lambda libraries that contain ColE1 sequences. Here we describe the construction of the 2.5-kb R6K-derived plasmid, pMAD3, that lacks the pi-encoding pir gene required for R6K replication. To supply pi [Inuzuka and Helinski, Proc. Natl. Acad. Sci. USA 75 (1978) 5381-5385] in trans, we employed pPR1 delta 22pir116, referred to henceforth as pPR1 [McEachern et al., Proc. Natl. Acad. Sci. USA 86 (1989) 7942-7946; Dellis and Filutowicz, J. Bacteriol. 173 (1991) 1279-1286]. Plasmid pMAD3 is small enough to be amplified readily by PCR [Saiki et al., Science 230 (1985) 1350-1354]. This permits the insertion of larger fragments and the retrieval of larger lambda inserts, as well as the use of a simplified PCR-based cloning protocol which utilizes annealing rather than ligation to create recombinants in pMAD3 [Nisson et al., PCR Methods and Applications 1 (1991) 120-123].     

Degradation of basement membranes by human matrix metalloproteinase 3 (stromelysin).

Connective tissue cells synthesize and secrete a group of matrix metalloproteinases (MMPs), all of which are capable of degrading the extracellular-matrix components. One of them, MMP-3 (stromelysin) has been shown to degrade purified basement-membrane components, collagen IV and laminin [Okada, Y., Nagase, H. & Harris, E. D., Jr. (1986) J. Biol. Chem. 261, 14245-14255]. Here we report that MMP-3 degrades collagen IV and laminin in intact basement membranes from bovine glomeruli (GBM) and bovine anterior-lens capsules (LBM). Degradation products were analysed by SDS/polyacrylamide-gel electrophoresis to determine the number and sizes of polypeptide fragments. Immunoblotting techniques were used to identify the origins of the fragments, i.e. collagen IV or laminin. The fragments of collagen IV were further mapped using specific antibodies that recognize the N-terminal (7 S) domain, the C-terminal (NC-1) domain, or the major triple-helical region between the terminal domains. Degradation of collagen IV was extensive; many fragments were found, from both GBM and LBM, in the Mr range 25,000-380,000. A large fragment of laminin (Mr greater than 380,000) was found in the GBM digests without reduction, but it dissociated into 220,000-Mr chains upon reduction. The results suggest that MMP-3 plays an important role in the catabolism of basement membranes.     

Calmodulin-linked equilibria in smooth muscle myosin light chain kinase

Competition experiments using 9-anthroylcholine, a fluorescent dye that undergoes calmodulin-dependent binding by smooth muscle myosin light chain kinase [Malencik, D. A., Anderson, S. R., Bohnert, J. L., & Shalitin, Y. S. (1982) Biochemistry 21, 4031], demonstrate a strongly stabilizing interaction between the adenosine 5'-triphosphate and myosin light chain binding sites operating within the enzyme-calmodulin complex but probably not in the free enzyme. The interactions in the latter case may be even slightly destabilizing. The fluorescence enhancement in solutions containing 5.0 microM each of the enzyme and calmodulin is directly proportional to the maximum possible concentration of bound calcium on the basis of four calcium binding sites. Evidently, all four calcium binding sites of calmodulin contribute about equally to the enhanced binding of 9-anthroylcholine by the enzyme. Fluorescence titrations on solutions containing 1.0 microM enzyme plus calmodulin yield a Hill coefficient of 1.2 and K = 0.35 +/- 0.08 microM calcium. Three proteolytic fragments of smooth muscle myosin light chain kinase, apparent products of endogenous proteolysis, were isolated and characterized. All three possess calmodulin-dependent catalytic activity. Their interactions with 9-anthroylcholine, in both the presence and absence of calmodulin, are similar to those of the native enzyme. However, the stabilities of their complexes with calmodulin vary. The corresponding dissociation constants range from 2.8 nM for the native enzyme and 8.5 nM for the 96K fragment to approximately 15 nM for the 68K and 90K fragments [0.20 N KCl, 50 mM 3-(N-morpholino)propanesulfonic acid, and 1 mM CaCl2, pH 7.3, 25 degrees C]. A coupled fluorometric assay, modified from a spectrophotometric assay for adenosine cyclic 3',5'-phosphate dependent protein kinase [Cook, P. F., Neville, M. E., Vrana, K. E., Hartl, F. T., & Roskoski, R. (1982) Biochemistry 21, 5794], has provided the first continuous recordings of myosin light chain kinase phosphotransferase activity. The results show that smooth muscle myosin light chain kinase is a responsive enzyme, whose activity adjusts rapidly to changes in solution conditions.     

Electrostatic switches that mediate the pH-dependent conformational change of "short" recombinant human pseudocathepsin D

Human cathepsin D (hCatD) is an aspartic peptidase with a low pH optimum. X-ray crystal structures have been solved for an active, low pH (pH 5.1) form (CatD(lo)) [Baldwin, E. T., Bhat, T. N., Gulnik, S., Hosur, M. V., Sowder, R. C., Cachau, R. E., Collins, J., Silva, A. M., and Erickson, J. W. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6796-6800] and an inactive, high pH (pH 7.5) form (CatD(hi)) [Lee, A. Y., Gulnik, S. V., and Erickson, J. W. (1998) Nat. Struct. Biol. 5, 866-871]. It has been suggested that ionizable switches involving the carboxylate side chains of E5, E180, and D187 may mediate the reversible interconversion between CatD(hi) and CatD(lo) and that Y10 stabilizes CatD(hi) [Lee, A. Y., Gulnik, S. V., and Erickson, J. W. (1998) Nat. Struct. Biol. 5, 866-871]. To test these hypotheses, we generated single point mutants in "short" recombinant human pseudocathepsin D (srCatD), a model kinetically similar to hCatD [Beyer, B. M., and Dunn, B. M. (1996) J. Biol. Chem. 271, 15590-15596]. E180Q, Y10F, and D187N exhibit significantly higher kcat/Km values (2-, 3-, and 6-fold, respectively) at pH 3.7 and 4.75 compared to srCatD, indicating that these residues are important in stabilizing the CatD(hi). E5Q exhibits a 2-fold lower kcat/Km compared to srCatD at both pH values, indicating the importance of E5 in stabilizing the CatD(lo). Accordingly, full time-course "pH-jump" (pH 5.5-4.75) studies of substrate hydrolysis indicate that E180Q, D187N, and Y10F have shorter kinetic lag phases that represent the change from CatD(hi) to CatD(lo) compared to srCatD and E5Q. Intrinsic tryptophan fluorescence reveals that the variants have a native-like structure over the pH range of our assays. The results indicate that E180 and D187 participate as an electrostatic switch that initiates the conformational change of CatD(lo) to CatD(hi) and Y10 stabilizes CatD(hi) by hydrogen bonding to the catalytic Asp 33. E5 appears to play a less significant role as an ionic switch that stabilizes CatD(lo).     

Nisin Resistance of Streptococcus bovis

The growth of Streptococcus bovis JB1 was initially inhibited by nisin (1 μM), and nisin caused a more than 3-log decrease in viability. However, some of the cells survived, and these nisin-resistant cells grew as rapidly as untreated ones. To see if the nisin resistance was merely a selection, nisin-sensitive cells were obtained from agar plates lacking nisin. Results indicated that virtually any nisin-sensitive cell could become nisin-resistant if the ratio of nisin to cells was not too high and the incubation period was long enough. Isolates obtained from the rumen were initially nisin sensitive, but they also developed nisin resistance. Nisin-resistant cultures remained nisin resistant even if nisin was not present, but competition studies indicated that nisin-sensitive cells could eventually displace the resistant ones if nisin was not present. Nisin-sensitive, glucose-energized cells lost virtually all of their intracellular potassium if 1 μM nisin was added, but resistant cells retained potassium even after addition of 10 μM nisin. Nisin-resistant cells were less hydrophobic and more lysozyme-resistant than nisin-sensitive cells. Because the nisin-resistant cells bound less cytochrome c, it appeared that nisin was being excluded by a net positive (i.e., less negative) charge. Nisin-resistant cells had more lipoteichoic acid than nisin-sensitive cells, and deesterified lipoteichoic acids from nisin-resistant cells migrated more slowly through a polyacrylamide gel than those from nisin-sensitive cells. These results indicated that lipoteichoic acids could be modified to increase the resistance of S. bovis to nisin. S. bovis JB1 cultures were still sensitive to monensin, tetracycline, vancomycin, and bacitracin, but ampicillin resistance was 1,000-fold greater.