Quantitative variation and the ecological role of vulpinic acid and atranorin in thallus of Letharia vulpina

High pressure liquid chromatography was used to determine concentrations of vulpinic acid and atranorin in the thaullus of Letharia vulpina. Vulpinic acid concentration is lowest in the old basal branches of the thallus and increases toward the young branch tips, whereas the reverse is true for atranorin. The suggested role of vulpinic acid as an anti-herbivore defense compound is supported by both this distribution of the compound and our observations that vulpinic acid acts as a feeding deterrent to certain invertebrates. No significant difference in the content of atranorin or vulpinic acid was found in lichens from microhabitats of different sunlight intensities.     

A chemical–genetic interaction map of small molecules using high‐throughput imaging in cancer cells

Small molecules often affect multiple targets, elicit off‐target effects, and induce genotype‐specific responses. Chemical genetics, the mapping of the genotype dependence of a small molecule's effects across a broad spectrum of phenotypes can identify novel mechanisms of action. It can also reveal unanticipated effects and could thereby reduce high attrition rates of small molecule development pipelines. Here, we used high‐content screening and image analysis to measure effects of 1,280 pharmacologically active compounds on complex phenotypes in isogenic cancer cell lines which harbor activating or inactivating mutations in key oncogenic signaling pathways. Using multiparametric chemical–genetic interaction analysis, we observed phenotypic gene–drug interactions for more than 193 compounds, with many affecting phenotypes other than cell growth. We created a resource termed the Pharmacogenetic Phenome Compendium (PGPC), which enables exploration of drug mode of action, detection of potential off‐target effects, and the generation of hypotheses on drug combinations and synergism. For example, we demonstrate that MEK inhibitors amplify the viability effect of the clinically used anti‐alcoholism drug disulfiram and show that the EGFR inhibitor tyrphostin AG555 has off‐target activity on the proteasome. Taken together, this study demonstrates how combining multiparametric phenotyping in different genetic backgrounds can be used to predict additional mechanisms of action and to reposition clinically used drugs.     

Antimicrobial activity of the indolicidin‐derived novel synthetic peptide In‐58

Natural peptides with antimicrobial activity are extremely diverse, and peptide synthesis technologies make it possible to significantly improve their properties for specific tasks. Here, we investigate the biological properties of the natural peptide indolicidin and the indolicidin‐derived novel synthetic peptide In‐58. In‐58 was generated by replacing all tryptophan residues on phenylalanine in D‐configuration; the α‐amino group in the main chain also was modified by unsaturated fatty acid. Compared with indolicidin, In‐58 is more bactericidal, more resistant to proteinase K, and less toxic to mammalian cells. Using molecular physics approaches, we characterized the action of In‐58 on bacterial cells at the cellular level. Also, we have found that studied peptides damage bacterial membranes. Using the Escherichia coli luminescent biosensor strain MG1655 (pcolD’::lux), we investigated the action of indolicidin and In‐58 at the subcellular level. At subinhibitory concentrations, indolicidin and In‐58 induced an SOS response. Our data suggest that indolicidin damages the DNA, but bacterial membrane perturbation is its principal mode of action. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Antimicrobial activities and membrane‐active mechanism of CPF‐C1 against multidrug‐resistant bacteria,a novel antimicrobial peptide derived from skin secretions of the tetraploid frog Xenopus clivii

Hospital‐acquired infections caused by multidrug‐resistant bacteria pose significant challenges for treatment, which necessitate the development of new antibiotics. Antimicrobial peptides are considered potential alternatives to conventional antibiotics. The skin of Anurans (frogs and toads) amphibians is an extraordinarily rich source of antimicrobial peptides. CPF‐C1 is a typical cationic antimicrobial peptide that was originally isolated from the tetraploid frog Xenopus clivii. Our results showed that CPF‐C1 has potent antimicrobial activity against both sensitive and multidrug‐resistant bacteria. It disrupted the outer and inner membranes of bacterial cells. CPF‐C1 induced both propidium iodide uptake into the bacterial cell and the leakage of calcein from large liposome vesicles, which suggests a mode of action that involves membrane disturbance. Scanning electron microscopy and transmission electron microscopy verified the morphologic changes of CPF‐C1‐treated bacterial cells and large liposome vesicles. The membrane‐dependent mode of action signifies that the CPF‐C1 peptide functions freely and without regard to conventional resistant mechanisms. Additionally, it is difficult for bacteria to develop resistance against CPF‐C1 under this action mode. Other studies indicated that CPF‐C1 had low cytotoxicity against mammalian cell. In conclusion, considering the increase in multidrug‐resistant bacterial infections, CPF‐C1 may offer a new strategy that can be considered a potential therapeutic agent for the treatment of diseases caused by multidrug‐resistant bacteria. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

The chitin‐binding capability of Cy‐AMP1 from cycad is essential to antifungal activity

Antimicrobial peptides are important components of the host innate immune responses by exerting broad‐spectrum microbicidal activity against pathogenic microbes. Cy‐AMP1 found in the cycad (Cycas revoluta) seeds has chitin‐binding ability, and the chitin‐binding domain was conserved in knottin‐type and hevein‐type antimicrobial peptides. The recombinant Cy‐AMP1 was expressed in Escherichia coli and purified to study the role of chitin‐binding domain. The mutants of Cy‐AMP1 lost chitin‐binding ability completely, and its antifungal activity was markedly decreased in comparison with native Cy‐AMP1. However, the antimicrobial activities of the mutant peptides are nearly identical to that of native one. It was suggested that the chitin‐binding domain plays an essential role in antifungal, but not antimicrobial, activity of Cy‐AMP1. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B‐cell lymphomas

The computational identification of oncogenic lesions is still a key open problem in cancer biology. Although several methods have been proposed, they fail to model how such events are mediated by the network of molecular interactions in the cell. In this paper, we introduce a systems biology approach, based on the analysis of molecular interactions that become dysregulated in specific tumor phenotypes. Such a strategy provides important insights into tumorigenesis, effectively extending and complementing existing methods. Furthermore, we show that the same approach is highly effective in identifying the targets of molecular perturbations in a human cellular context, a task virtually unaddressed by existing computational methods. To identify interactions that are dysregulated in three distinct non‐Hodgkin's lymphomas and in samples perturbed with CD40 ligand, we use the B‐cell interactome (BCI), a genome‐wide compendium of human B‐cell molecular interactions, in combination with a large set of microarray expression profiles. The method consistently ranked the known gene in the top 20 (0.3%), outperforming conventional approaches in 3 of 4 cases.     

The effects of a vegetable‐derived probiotic lactic acid bacterium on the immune response

The objective of this study was to investigate the probiotic properties of the fermented vegetable derived lactic acid bacterium, L. plantarum. L. plantarum 10hk2 showed antibacterial activity against pathogenic bacteria and immunomodulating effects on murine macrophage cell lines. RAW 264.7 cells stimulated with viable cells of this probiotic strain increased the amounts of pro‐inflammatory mediators such as IL‐1β, IL‐6 and TNF‐α, as well as the anti‐inflammatory mediator, IL‐10. ICR mice fed with viable cells of L. plantarum 10hk2 had reduced numbers of enteric Salmonella and Shigella species in comparison to controls from 2 weeks after supplementation, and this effect was observed for up to 4 weeks. The findings of this study suggest that this specific lactic acid bacterial strain, which is derived from vegetable fermentation, holds great promise for use in probiotics and as a food additive since it can reduce the number of some pathogenic bacteria through production of lactic acids.     

Plant defensin MtDef4-derived antifungal peptide with multiple modes of action and potential as a bio-inspired fungicide

Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.     

A proteomic approach to understand MMP‐3‐driven developmental processes in the postnatal cerebellum: Chaperonin CCT6A and MAP kinase as contributing factors

Matrix metalloproteinase‐3 (MMP‐3) deficiency in mice was previously reported to result in a transiently retarded granule cell migration at postnatal day 8 (P8) and a sustained disturbed arborization of Purkinje cell dendrites from P8 on, concomitant with a delayed synapse formation between granule cells and Purkinje cells and resulting in mild deficits in motor performance in adult animals. However, the molecular mechanisms by which MMP‐3 contributes to proper development of the cerebellar cortex during the first postnatal weeks remains unknown. In this study, we used a functional proteomics approach to investigate alterations in protein expression in postnatal cerebella of wild‐type versus MMP‐3 deficient mice, and to further elucidate MMP‐3‐dependent pathways and downstream targets in vivo. At P8, two‐dimensional difference gel electrophoresis and mass spectrometry identified 20 unique proteins with a different expression between the two genotypes. Subsequent “Ingenuity Pathway Analysis” and Western blotting indicate that the chaperonin containing T‐complex polypeptide 1, subunit 6A and the MAP kinase signaling pathway play a key role in the MMP‐3‐dependent regulation of neurite outgrowth and neuronal migration in the developing brain. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 1033–1048, 2015     

Ex and in vivo characterization of the wavelength‐dependent 3‐photon action cross‐sections of red fluorescent proteins covering the 1700‐nm window

Multiphoton action cross‐sections are the prerequisite for excitation light selection. At the 1700‐nm window suitable for deep‐tissue imaging, wavelength‐dependent 3‐photon action cross‐sections ησ₃ for RFPs are unknown, preventing wavelength selection. Here we demonstrate: (1) ex vivo measurement of wavelength‐dependent ησ₃ for purified RFPs; (2) a multiphoton imaging guided measurement system for in vivo measurement; and (3) in vivo measurement of wavelength‐dependent ησ₃ in RFP labeled cells. These fundamental results will provide guidelines for excitation wavelength selection for 3‐photon fluorescence imaging of RFPs at the 1700‐nm window, and augment the existing database of multiphoton action cross‐sections for fluorophores.      

In vitro antimicrobial activity and mechanism of action of novel carbohydrate fatty acid derivatives against Staphylococcus aureus and MRSA

Aims: This study investigates the antimicrobial activity and mode of action of novel carbohydrate fatty acid (CFA) derivatives against Staphylococcus aureus and methicillin‐resistant Staph. aureus (MRSA). Methods and Results: Minimum inhibitory concentrations (MICs) and the effect of CFA derivatives on lag phase were determined using a broth microdilution method. Lauric acid carbohydrate esters and corresponding ether analogues showed the greatest antimicrobial activity with MIC values between 0·04 and 0·16 mmol l^?1. Leakage studies at 260 nm following exposure to CFA derivatives at 4× MIC showed a significant increase in membrane permeability for all compounds, after c. 15 min exposure except for the lauric beta ether CFA derivative. Further assessment using both BacLight and luminescence ATP assays confirmed that an increase in membrane permeability and reduced metabolic activity was associated with CFA treatment. Conclusions: All strains were significantly inhibited by the novel compounds studied, and efficacy was related to specific structural features. Cell‐membrane permeabilization was associated with CFA treatment and may account for at least a component of the mode of action of these compounds. Significance and Impact of the Study: This study reports the antimicrobial action of CFA compounds against a range of Staph. aureus and MRSA strains, and provides insights into their mode of action.     

Multi‐enzymatic one‐pot reduction of dehydrocholic acid to 12‐keto‐ursodeoxycholic acid with whole‐cell biocatalysts

Ursodeoxycholic acid (UDCA) is a bile acid of industrial interest as it is used as an agent for the treatment of primary sclerosing cholangitis and the medicamentous, non‐surgical dissolution of gallstones. Currently, it is prepared industrially from cholic acid following a seven‐step chemical procedure with an overall yield of <30%. In this study, we investigated the key enzymatic steps in the chemo‐enzymatic preparation of UDCA—the two‐step reduction of dehydrocholic acid (DHCA) to 12‐keto‐ursodeoxycholic acid using a mutant of 7β‐hydroxysteroid dehydrogenase (7β‐HSDH) from Collinsella aerofaciens and 3α‐hydroxysteroid dehydrogenase (3α‐HSDH) from Comamonas testosteroni. Three different one‐pot reaction approaches were investigated using whole‐cell biocatalysts in simple batch processes. We applied one‐biocatalyst systems, where 3α‐HSDH, 7β‐HSDH, and either a mutant of formate dehydrogenase (FDH) from Mycobacterium vaccae N10 or a glucose dehydrogenase (GDH) from Bacillus subtilis were expressed in a Escherichia coli BL21(DE3) based host strain. We also investigated two‐biocatalyst systems, where 3α‐HSDH and 7β‐HSDH were expressed separately together with FDH enzymes for cofactor regeneration in two distinct E. coli hosts that were simultaneously applied in the one‐pot reaction. The best result was achieved by the one‐biocatalyst system with GDH for cofactor regeneration, which was able to completely convert 100 mM DHCA to >99.5 mM 12‐keto‐UDCA within 4.5 h in a simple batch process on a liter scale. Biotechnol. Bioeng. 2013; 110: 68–77. © 2012 Wiley Periodicals, Inc.     

Proteomics approach to understand reduced clearance of mycobacteria and high viral titers during HIV–mycobacteria co‐infection

Environmental mycobacteria, highly prevalent in natural and artificial (including chlorinated municipal water) niches, are emerging as new threat to human health, especially to HIV‐infected population. These seemingly harmless non‐pathogenic mycobacteria, which are otherwise cleared, establish as opportunistic infections adding to HIV‐associated complications. Although immune‐evading strategies of pathogenic mycobacteria are known, the mechanisms underlying the early events by which opportunistic mycobacteria establish infection in macrophages and influencing HIV infection are unclear. Proteomics of phagosome‐enriched fractions from Mycobacterium bovis Bacillus Calmette–Guérin (BCG) mono‐infected and HIV–M. bovis BCG co‐infected THP‐1 cells by LC‐MALDI‐MS/MS revealed differential distribution of 260 proteins. Validation of the proteomics data showed that HIV co‐infection helped the survival of non‐pathogenic mycobacteria by obstructing phagosome maturation, promoting lipid biogenesis and increasing intracellular ATP equivalents. In turn, mycobacterial co‐infection up‐regulated purinergic receptors in macrophages that are known to support HIV entry, explaining increased viral titers during co‐infection. The mutualism was reconfirmed using clinically relevant opportunistic mycobacteria, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium phlei that exhibited increased survival during co‐infection, together with increase in HIV titers. Additionally, the catalogued proteins in the study provide new leads that will significantly add to the understanding of the biology of opportunistic mycobacteria and HIV coalition.     

A comparison of the chitin synthase-inhibitory and antifungal efficacy of nucleoside-peptide antibiotics: structure-activity relationships

Abstract Using Mucor rouxii , the chitin synthase (ChS)-inhibitory and antifungal activity was determined of 6 nucleoside-peptide antibiotics (NPAs) representing pairs of structural analogues, each consisting of a dipeptide (DP) and a corresponding tripeptide (TP). These were the nikkomycins X and I (X, I), the nikkomycins Z and J (Z, J), and the polyoxins D and A (D, A). Although all were very good ChS-inhibitors (X and A being best, with K _i approx. 0.5 μM), only X and Z elicited a strong response in vivo as determined by the degree of inhibition exerted on N -acetylglucosamine (GlcNAc) incorporation into the chitin fraction, the survival rate, and the minimum inhibitory concentration (MIC). The MIC values were about 2 μM (for X and Z) and 100 μM (for I, J, D and A). Certain DPs and TPs reduced the antifungal activity of X, the effect being much more pronounced with DPs. It is suggested that uptake of NPAs involves the transpeptidase reaction of the γ-glutamyl cycle, the observed antagonism thus resulting from competition for a common carrier.