Differential utilization of pyrene as the sole source of carbon by Bacillus subtilis and Pseudomonas aeruginosa strains: role of biosurfactants in enhancing bioavailability

AIMS: Our goal is to compare the efficiency of utilization of pyrene as the sole source of carbon for growth and energy by two nonactinomycetous groups of bacteria viz., Bacillus subtilis DM-04 and Pseudomonas aeruginosa mucoid (M) and nonmucoid (NM) strains, isolated from a petroleum-contaminated soil sample of north-east India. METHODS AND RESULTS: Bacillus subtilis DM-04 and P. aeruginosa M and NM bacterial strains were capable of secreting biosurfactant in the culture medium while growing on pyrene and their pyrene utilizing efficiency was demonstrated by correlating the bacterial growth in the presence of pyrene as the sole source of carbon along with a concomitant decrease in pyrene content from the culture medium with respect to time. The biosurfactant secreted by the respective bacterial strains enhanced the apparent solubility of pyrene by factors of 5-7 and influenced the bacterial cell surface hydrophobicity resulting in higher uptake and utilization of pyrene by bacteria. The growth of B. subtilis DM-04 and P. aeruginosa M and NM strains at the expense of pyrene after 96 h showed an assimilation of about 48.0 +/- 1.1% (mean +/- SD) and 32.0 +/- 0.6% (mean +/- SD) of pyrene carbon, respectively, showing differences in metabolism of pyrene by these bacterial strains. CONCLUSIONS: Bacillus subtilis DM-04 strain exhibited higher utilization and cellular assimilation of pyrene compared with P. aeruginosa M and NM strains. Further, the biosurfactants produced by the bacteria under study are capable of enhancing the solubility of pyrene in aqueous media and can influence the cell surface hydrophobicity of the biosurfactant-producing strains that results in a higher uptake of pyrene. SIGNIFICANCE AND IMPACT OF THE STUDY: It may be suggested that the bacteria used in this study are suitable candidates for practical field application for effective in situ bioremediation of pyrene-contaminated sites.     

Bacterial γ-glutamyltranspeptidases: Comparison of Escherichia coli and Pseudomonasγ-glutamyltranspeptidase

Serpulina (Treponema) hyodysenteriae strain A-1 partially purified rRNA, labelled with photobiotin, was used as a non-radioactive probe to identify the rRNA gene restriction patterns of S. hyodysenteriae strains and other spirochetes. Sau3A restriction enzyme digests resulted in similar rRNA gene restriction patterns in S. hyodysenteriae strains from five different countries. Some S. hyodysenteriae strains could be differentiated by variations in their rRNA gene restriction patterns after cleavage of DNA by restriction enzymes SspI or BglII. S. innocens and Treponema succinifaciens, non-pathogenic pig intestinal spirochetes, had rRNA gene restriction patterns that differed markedly from the S. hyodysenteriae patterns, and from each other.     

Applicability of Chromatographic Co‐Elution for Antibiotic Target Identification

Identification of the molecular target is a crucial step in evaluating novel antibiotics. To support target identification, a label‐free method based on chromatographic co‐elution has previously been developed. Target identification by chromatographic coelution (TICC) exploits the alteration of the elution profile of target‐bound drug versus free drug in ion exchange (IEX) chromatography to identify potential target proteins from elution fractions. The applicability of TICC for antibiotic research is investigated by evaluating which proteins, that is, putative targets, can be monitored in Bacillus subtilis. Coelution of components of known protein complexes provides a read‐out for how well the native state of proteins is conserved during chromatography. Rifampicin, which targets RNA polymerase, is used in a proof‐of‐concept study.     

Bacterial quorum‐sensing signal IQS induces host cell apoptosis by targeting POT1–p53 signalling pathway

Pseudomonas aeruginosa, an opportunistic life‐threatening human bacterial pathogen, employs quorum‐sensing (QS) signal molecules to modulate virulence gene expression. 2‐(2‐hydroxyphenyl)‐thiazole‐4‐carbaldehyde (IQS) is a recently identified QS signal that integrates the canonical lasR‐type QS of P. aeruginosa and host phosphate stress response to fine‐tune its virulence production for a successful infection. To address the role of IQS in pathogen–host interaction, we here present that IQS inhibits host cell growth and stimulates apoptosis in a dosage‐dependent manner. By downregulating the telomere‐protecting protein POT1 in host cells, IQS activates CHK1, CHK2, and p53 in an Ataxia telangiectasia mutated (ATM)/ATM and RAD3‐related (ATR)‐dependent manner and induces DNA damage response. Overexpression of POT1 in host cells presents a resistance to IQS treatment. These results suggest a pivotal role of IQS in host apoptosis, highlighting the complexity of pathogenesis mechanisms developed by P. aeruginosa during infection.     

Microbial consortium-mediated reprogramming of defence network in pea to enhance tolerance against Sclerotinia sclerotiorum

Aims: To evaluate the potentiality of three rhizosphere microorganisms in suppression of Sclerotinia rot in pea in consortia mode and their impact on host defence responses. Methods and Results: Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 from rhizospheric soils were selected based on compatibility, antagonistic and plant growth promotion activities. The microbes were used as consortia to assess their ability to trigger the phenylpropanoid and antioxidant activities and accumulation of proline, total phenol and pathogenesis‐related (PR) proteins in pea under the challenge of the soft‐rot pathogen Sclerotinia sclerotiorum. The triple‐microbe consortium and single‐microbe treatments showed 1·4–2·3 and 1·1–1·7‐fold increment in defence parameters, respectively, when compared to untreated challenged control. Activation of the phenylpropanoid pathway and accumulation of total phenolics were highest at 48 h, whereas accumulation of proline and PR proteins along with activities of the antioxidant enzymes was highest at 72 h. Conclusions: The compatible microbial consortia triggered defence responses in an enhanced level in pea than the microbes alone and provided better protection against Sclerotinia rot. Significance and Impact of the Study: Rhizosphere microbes in consortium can enhance protection in pea against the soft‐rot pathogen through augmented elicitation of host defence responses.     

Evaluation of critical nutritional parameters and their significance in the production of rhamnolipid biosurfactants from Pseudomonas aeruginosa BS‐161R

Eleven biosurfactant producing bacteria were isolated from different petroleum‐contaminated soil and sludge samples. Among these 11 isolates, two were identified as promising, as they reduced the surface tension of culture medium to values below 27 mN m^?1. Besides biosurfactant production property, they exhibited good flocculating activity. Microbacterium sp. was identified as a new addition to the list of biosurfactant and bioflocculant‐producers. Optimization of various conditions for rhamnolipid production was carried out for one of the promising isolate, Pseudomonas aeruginosa BS‐161R. Bioglycerol (2.5%), as a cheap renewable carbon source, attained better rhamnolipid yield, while sodium nitrate appeared to be the preferable nitrogen source. The optimum carbon to nitrogen (C/N) and carbon to iron (C/Fe) ratios achieved were 15 and 28,350, respectively, which favored rhamnolipid production. Physical parameters like pH, temperature, and agitation speed also affected the production of rhamnolipids. Results from shake flask optimization indicated that the concentration of bioglycerol, sodium nitrate, and iron were the most significant factors affecting rhamnolipid production, which was supported by the results of central composite rotatable design. After optimization of the culture conditions, the production of rhamnolipids increased by ninefold from 0.369 to 3.312 g L^?1. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

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.     

Bacterial larvicides for vector control: mode of action of toxins and implications for resistance

Vector control can be an effective strategy to interrupt disease transmission and biolarvicides based on the entomopathogenic bacteria Bacillus sphaericus, and Bacillus thuringiensis serovar israelensis (Bti) have been successfully used to control species of public health relevance from the genera Aedes, Culex, Anopheles and Simulium. The most important feature of these agents is their ability to produce insecticidal proteins with selective action on the larval midgut. These protoxins are produced as crystals that, once ingested by larvae, are processed into active toxins, interact with receptors in the midgut epithelium and trigger cytopathological effects leading to larval death. B. sphaericus and Bti toxins share the initial steps of the mode of action; however, they interact with different midgut molecules. B. sphaericus presents a single larvicidal factor, the binary (Bin) toxin, whose action relies on the binding to one class of midgut receptors, while Bti crystals contain four protoxins (Cry4Aa, Cry4Ba, Cry11Aa and Cyt1Aa), which display interactions with multiple midgut receptors. The mode of action of B. sphaericus displays a greater potential for resistance selection, compared to Bti, and, to date, there is no record of insect resistance to the latter, contrarily to B. sphaericus. The set of mosquitocidal toxins and their interaction with midgut target sites are described in this review, as well as the implications for the potential to select resistance amongst exposed populations. These biolarvicides have specific mode of action that rely on unique interactions and make them the most selective agents to control Diptera insects actually available.     

RnhP is a plasmid‐borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610

RNA‐DNA hybrids form throughout the chromosome during normal growth and under stress conditions. When left unresolved, RNA‐DNA hybrids can slow replication fork progression, cause DNA breaks, and increase mutagenesis. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion. Here we show that, in addition to chromosomally encoded RNase HII and RNase HIII, Bacillus subtilis NCIB 3610 encodes a previously uncharacterized RNase HI protein, RnhP, on the endogenous plasmid pBS32. Like other RNase HI enzymes, RnhP incises Okazaki fragments, ribopatches, and a complementary RNA‐DNA hybrid. We show that while chromosomally encoded RNase HIII is required for pBS32 hyper‐replication, RnhP compensates for the loss of RNase HIII activity on the chromosome. Consequently, loss of RnhP and RNase HIII impairs bacterial growth. We show that the decreased growth rate can be explained by laggard replication fork progression near the terminus region of the right replichore, resulting in SOS induction and inhibition of cell division. We conclude that all three functional RNase H enzymes are present in B. subtilis NCIB 3610 and that the plasmid‐encoded RNase HI contributes to chromosome stability, while the chromosomally encoded RNase HIII is important for chromosome stability and plasmid hyper‐replication.     

Species‐Specific Barriers to Tree Regeneration in High Elevation Habitats of West Virginia

Herbaceous competition and herbivory have been identified as critical barriers to restoration of native tree species in degraded landscapes around the world; however, the combined effects of competition and herbivory are poorly understood. We experimentally manipulated levels of herbivory and herbaceous competition and analyzed the response of tree seedling performance over three growing seasons as a function of species and habitat in north‐central West Virginia. Four native tree species were planted in old field and forest experimental plots: Castanea dentata (American chestnut), Quercus rubra (red oak), Acer saccharum (sugar maple), and Picea rubens (red spruce). Red spruce demonstrated the highest growth increment and greatest survival (64%) and most consistent results among treatments and habitats. Red spruce survival was not reduced in the presence of Odocoileus virginianus (white‐tailed deer) browse and herbaceous competition; however, growth was improved by suppression of herbaceous competition. We suspect that this deciduous forest landscape would regenerate to a red spruce dominated forest if seed source was available. In contrast, the other three species tested had very low survival when exposed to deer and were more responsive to competing vegetation and habitat type. American chestnut had low survival and growth across all treatments, suggesting basic climate limitations. Vigorous natural regeneration of Prunus serotina (black cherry) occurred in forest plots where both competing herbs and deer were excluded. Our results demonstrated the importance of testing multiple potential recruitment barriers and species at once and the need for species and habitat‐specific restoration treatments.     

Enhancement of the organic solvent‐stability of the LST‐03 lipase by directed evolution

LST‐03 lipase from an organic solvent‐tolerant Pseudomonas aeruginosa LST‐03 has high stability and activity in the presence of various organic solvents. In this research, enhancement of organic solvent‐stability of LST‐03 lipase was attempted by directed evolution. The structural gene of the LST‐03 lipase was amplified by the error prone‐PCR method. Organic solvent‐stability of the mutated lipases was assayed by formation of a clear zone of agar which contained dimethyl sulfoxide (DMSO) and tri‐n‐butyrin and which overlaid a plate medium. And the organic solvent‐stability was also confirmed by measuring the half‐life of activity in the presence of DMSO. Four mutated enzymes were selected on the basis of their high organic solvent‐stability in the presence of DMSO. The organic solvent‐stabilities of mutated LST‐03 lipase in the presence of various organic solvents were measured and their mutated amino acid residues were identified. The half‐lives of the LST‐03‐R65 lipase in the presence of cyclohexane and n‐decane were about 9 to 11‐fold longer than those of the wild‐type lipase, respectively. Some substituted amino acid residues of mutated LST‐03 lipases have been located at the surface of the enzyme molecules, while some other amino acid residues have been changed from neutral to basic residues. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Characterization of Pseudomonas aeruginosa phage KPP21 belonging to family Podoviridae genus N4‐like viruses isolated in Japan

Bacteriophages (phages) belonging to the family Podoviridae genus N4‐like viruses have been used as therapeutic agent in phage therapy against Pseudomonas aeruginosa infections. P. aeruginosa phage KPP21 was isolated in Japan, and phylogenetically investigated the phages belonging to this viral genus. Morphological and genetic analyses confirmed that phage KPP21 belongs to the family Podoviridae genus N4‐like viruses. Moreover, phylogenetic analyses based on putative DNA polymerase and major virion protein showed that P. aeruginosa phages belonging to the genus N4‐like viruses are separated into two lineages and that phage KPP21 is in the same clade as phage LUZ7.     

Label‐Free Quantitative Proteomics Distinguishes General and Site‐Specific Host Responses to Pseudomonas aeruginosa Infection at the Ocular Surface

Mass spectrometry‐based proteomics enables the unbiased and sensitive profiling of cellular proteomes and extracellular environments. Recent technological and bioinformatic advances permit identifying dual biological systems in a single experiment, supporting investigation of infection from both the host and pathogen perspectives. At the ocular surface, Pseudomonas aeruginosa is commonly associated with biofilm formation and inflammation of the ocular tissues, causing damage to the eye. The interaction between P. aeruginosa and the immune system at the site of infection describes limitations in clearance of infection and enhanced pathogenesis. Here, the extracellular environment (eye wash) of murine ocular surfaces infected with a clinical isolate of P. aeruginosa is profiled and neutrophil marker proteins are detected, indicating neutrophil recruitment to the site of infection. The first potential diagnostic markers of P. aeruginosa‐associated keratitis are also identified. In addition, the deepest murine corneal proteome to date is defined and proteins, categories, and networks critical to the host response are detected. Moreover, the first identification of bacterial proteins attached to the ocular surface is reported. The findings are validated through in silico comparisons and enzymatic profiling. Overall, the work provides comprehensive profiling of the host–pathogen interface and uncovers differences between general and site‐specific host responses to infection.     

Antibacterial aryl‐crowned polyketide from Bacillus subtilis associated with seaweed Anthophycus longifolius

Aims

Microbiological, biotechnological and chemical characterization of a previously undescribed aryl‐crowned polyketide from Bacillus subtilis MTCC 10403 isolated from brown seaweed Anthophycus longifolius with activity against opportunistic Gram‐negative food‐borne pathogenic bacterial strains.

Methods and Results

A culture‐dependent method was used to isolate heterotrophic B. subtilis associated with A. longifolius and assessed for its antimicrobial properties. Minimum inhibitory concentration (MIC) of the title compound against the test pathogens was analysed by microtube dilution coupled with the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide‐based colorimetric endpoint detection. Bacillus subtilis MTCC 10403 was found to be antagonistic against Gram‐negative food‐borne pathogenic Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Salmonella enterica serotype Typhi, Aeromonas hydrophila and Vibrio sp. (diameter of zone of growth inhibition 13–22 mm). Bacillus subtilis was assessed for the presence of secondary metabolite coding polyketide synthase (pks) gene ( KC589397 , 700‐bp gene product) and carboxylate siderophore framework in the aryl‐crowned polyketide designated as 7‐O‐6′‐(2″‐acetylphenyl)‐5′‐hydroxyhexanoate‐macrolactin by exhaustive spectroscopic techniques. The MIC assay showed that the reference antibiotics tetracycline and ampicillin were active at 25 μg ml^?1 against the test pathogens, whereas the newly isolated polyketide displayed anti‐infective properties against E. coli, A. hydrophilla, P. aeruginosa and Vibrio sp. at a lower concentration (MIC <13 μg ml^?1). The MIC of the aryl macrolactin against K. pneumoniae was comparable with that of the referral antibiotics (~25 μg ml^?1). The mode of antimicrobial action of acryl‐crowned macrolactin was found to be iron chelating similar to siderophores. Putative biosynthetic pathway of the pks gene product further validated its molecular attributions.

Conclusions

This study recognized new variant of antimicrobial aryl‐crowned polyketide bearing methyl 6′‐(2″‐acetylphenyl)‐5′‐hydroxyhexanoate moiety at the C‐7 position of the macrolactin system from A. longifolius‐associated bacterium B. subtilis.

Significance and Impact of the Study

This study revealed seaweed‐associated micro‐organisms as promising biological strata to produce new‐generation anti‐infective agents.     

First Chemical Analysis and Characterization of the Male Species‐Specific Cephalic Labial‐Gland Secretions of South American Bumblebees

The evolution of signals and reproductive traits involved in the pre‐mating recognition has been in focus of abundant research in several model species, such as bumblebees (genus Bombus). However, the most‐studied bumblebee reproductive trait, the male cephalic labial gland secretions (CLGS), remains unknown among bumblebee species from South America. In this study, the CLGS of five South American bumblebees of the subgenera Thoracobombus (Bombus excellens and B. atratus) and Cullumanobombus (B. rubicundus, B. hortulanus, and B. melaleucus) were investigated, by comparing the chemical compositions of their secretions to those of closely related European species. The results showed an obvious interspecific differentiation in both subgenera. The interspecific differentiation among the species of the Thoracobombus subgenus involved different compounds present at high contents (main compounds), while those of the Cullumanobombus subgenus shared the same main components. This suggests that among the species of the Cullumanobombus subgenus, the differentiation in minor components could lead to species discrimination.     

Inhibitors of the Pseudomonas aeruginosa quorum‐sensing regulator,QscR

QscR is a quorum‐sensing (QS) signal receptor that controls expression of virulence genes in the prevalent opportunistic pathogen, Pseudomonas aeruginosa. Unlike the previously reported LuxR‐type QS receptor proteins, that is, LasR and TraR, QscR can be obtained as an apo‐protein that can reversibly form an active complex in vitro with its cognate signal molecule, 3‐oxododecanoyl‐homoserine lactone (3OC12‐HSL), and subsequently bind to target promoter DNA sequences. To search for potential QS inhibitors, an in vitro gel retardation assay was developed using the purified QscR. Both the in vitro assay and the in vivo cell‐based assay using QscR‐overproducing recombinant strains were applied in the screening process. Furanones were chosen for testing the activity as QS inhibitors because they have been reported to strongly inhibit expression of QS‐related genes in Agrobacterium tumefaciens. Among more than a hundred furanones tested, three compounds showed strong and dose‐dependent inhibitory effects on QscR in both assays. One compound in particular, designated as F2, could completely inhibit the 3OC12‐HSL‐dependent QscR activity in vitro at a concentration of 50‐fold molar excess over 3OC12‐HSL. However, with the furanones F3 and F4, which are structurally similar to F2 but with a nitro group instead of the amine moiety, significantly decreased activities were observed. These results suggest that (i) the in vitro assay is a sensitive and reliable tool for screening QS inhibitors, and (ii) furanones are potentially important QS inhibitors for many LuxR‐type receptor proteins. Biotechnol. Bioeng. 2010; 106: 119–126. © 2010 Wiley Periodicals, Inc.     

Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics

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