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The presence of Class II hydrophobins produced by fungi on barley results in primary gushing of beer. Gushing is the spontaneous overfoaming of carbonated beverages by opening of bottles. Solving gushing problems caused by brewing raw materials has received much scientific attention. Lipophilic extract of hops are introduced to brewers as foam suppressor in fermenters. We studied the effects of hop extract on gushing and found that lipophilic hop extract could reduce gushing. The effects are different when hop extract is added before mashing than when it is added after mashing. Hop extract contains fats and waxes and the effects on gushing are explained by a change in the physical state of its components during mashing which are due to temperature effects. Especially the effect of saturated fatty acids and waxes becomes apparent which are known as gushing inducers. This indicates that with respect to gushing potential of the hop extract's components, it is better to be added to cold wort (after mashing and filtration). Our study also showed an important effect of the filtration step on the amount of gushing.

Bacterial cell wall hydrolases (BCWHs) display a remarkable structural and functional diversity that offers perspectives for novel food applications, reaching beyond those of the archetype BCWH and established biopreservative hen egg white lysozyme. Insights in BCWHs from bacteriophages to animals have provided concepts for tailoring BCWHs to target specific pathogens or spoilage bacteria, or, conversely, to expand their working range to Gram-negative bacteria. Genetically modified foods expressing BCWHs in situ showed successful, but face regulatory and ethical concerns. An interesting spin-off development is the use of cell wall binding domains of bacteriophage BCWHs for detection and removal of foodborne pathogens. Besides for improving food safety or stability, BCWHs may also find use as functional food ingredients with specific health effects.

The ability of many bacteria to adhere to surfaces and to form biofilms has major implications in a variety of industries including the food industry, where biofilms create a persistent source of contamination. The formation of a biofilm is determined not only by the nature of the attachment surface, but also by the characteristics of the bacterial cell and by environmental factors. This review focuses on the features of the bacterial cell surface such as flagella, surface appendages and polysaccharides that play a role in this process, in particular for bacteria linked to food-processing environments. In addition, some aspects of the attachment surface, biofilm control and eradication will be highlighted.

Lysozymes (EC 3.2.1.17) are hydrolytic enzymes, characterized by their ability to cleave the beta-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan, the major bacterial cell wall polymer. In the animal kingdom, three major distinct lysozyme types have been identified--the c-type (chicken or conventional type), the g-type (goose-type) and the i-type (invertebrate type) lysozyme. Examination of the phylogenetic distribution of these lysozymes reveals that c-type lysozymes are predominantly present in the phylum of the Chordata and in different classes of the Arthropoda. Moreover, g-type lysozymes (or at least their corresponding genes) are found in members of the Chordata, as well as in some bivalve mollusks belonging to the invertebrates. In general, the latter animals are known to produce i-type lysozymes. Although the homology in primary structure for representatives of these three lysozyme types is limited, their three-dimensional structures show striking similarities. Nevertheless, some variation exists in their catalytic mechanisms and the genomic organization of their genes. Regarding their biological role, the widely recognized function of lysozymes is their contribution to antibacterial defence but, additionally, some lysozymes (belonging to different types) are known to function as digestive enzymes.

The Mrr protein of Escherichia coli K12 is a cryptic Type IV restriction endonuclease whose activity appears to be triggered by high pressure stress. In this report we used high pressure to isolate and analyze several Mrr mutants, and generated a new structural model of the Mrr protein. The activity of a number of spontaneous and strategically constructed Mrr mutants is discussed in the light of this model, providing a first insight into the structure–function relationships of the Mrr enzyme.

BACKGROUND: Arabinoxylan (AX)-derived preparations have raised particular interest by the suggestion that they exert prebiotic properties. Therefore an in vivo experiment was conducted to study the effects of xylooligosaccharides (XOS), arabinoxylooligosaccharides (AXOS) and soluble AX (S-AX) on several groups of gut bacteria of chickens. Chickens were fed a control diet or the same diet supplemented with 2.5 g kg−1 of XOS (average degree of polymerisation (avDP) of 3, average degree of arabinose substitution (avDS) of 0.09), wheat bran-derived AXOS (avDP 9, avDS 0.34) or wheat endosperm alkali-solubilised AX (S-AX, avDP > 6000, avDS 0.5). RESULTS: All treatment groups showed an increase in the number of caecal bifidobacteria after 2 weeks of feeding (P < 0.05), while the treatments did not impact numbers of Enterobacteriaceae and aerobic lactobacilli in the caeca relative to the control. XOS led to a tremendous increase in caecal bifidobacteria counts (108 g−1 for the XOS treatment versus 103 g−1 for the control treatment) after only 1 week of supplementation, while AXOS and S-AX led to similar strong increases in bifidobacteria counts after 2 weeks of supplementation. Addition of S-AX to the diet, but not of AXOS or XOS, led to a significantly decreased (P < 0.05) body weight gain after 2 weeks of feeding relative to animals on the control diet, consistent with its known viscosity-related antinutritive effects in chickens. CONCLUSION: Similar to XOS, AXOS selectively stimulate the presence of bifidobacteria in the caeca of chickens, establishing their bifidogenic effect as a first indicator for prebiotic potential. Copyright © 2008 Society of Chemical Industry

The Mrr protein of Escherichia coli K12 is a cryptic type IV restriction endonuclease with specificity for methylated DNA. Recently it was discovered that endogenous activation of E. coli Mrr could be triggered by high pressure stress, resulting in the generation of double strand breaks in the host chromosome and concomitant induction of the SOS response. In this report we focused on Mrr activity of Salmonella Typhimurium LT2, and although we surprisingly found no evidence of high pressure induced activation, a large number of constitutively activated Mrr mutants could be isolated when the mrr gene was routinely cloned in an expression vector. Analysis of several spontaneous mutants revealed different single mutations that rendered the Mrr protein constitutively active. Moreover, a spontaneous S. Typhimurium mutant could be isolated that displayed an increased basal SOS induction because of a point mutation in the chromosomal mrr gene. Based on these findings the physiological role of Mrr in the cell is discussed.

Summary Pseudomonas aeruginosa bacteriophage endolysins KZ144 (phage φKZ) and EL188 (phage EL) are highly lytic peptidoglycan hydrolases (210 000 and 390 000 units mg−1), active on a broad range of outer membrane-permeabilized Gram-negative species. Site-directed mutagenesis indicates E115 (KZ144) and E155 (EL188) as their respective essential catalytic residues. Remarkably, both endolysins have a modular structure consisting of an N-terminal substrate-binding domain and a predicted C-terminal catalytic module, a property previously only demonstrated in endolysins originating from phages infecting Gram-positives and only in an inverse arrangement. Both binding domains contain conserved repeat sequences, consistent with those of some peptidoglycan hydrolases of Gram-positive bacteria. Fusions of these domains with green fluorescent protein immediately label all outer membrane-permeabilized Gram-negative bacteria tested, isolated P. aeruginosa peptidoglycan and N-acetylated Bacillus subtilis peptidoglycan, demonstrating the broad range of peptidoglycan-binding capacity by these domains. Specifically, A1 chemotype peptidoglycan and fully N-acetylated glucosamine units are essential for binding. Both KZ144 and EL188 appear to be a natural chimeric enzyme, originating from a recombination of a cell wall-binding domain encoded by a Bacillus or Clostridium species and a catalytic domain of an unknown ancestor.

Many bacteria use cell-cell communication to monitor their population density, synchronize their behaviour and socially interact. This communication results in a coordinated gene regulation and is generally called quorum sensing. In gram-negative bacteria, the most common quorum signal molecules are acylated homoserine lactones (AHLs), although other low-molecular-mass signalling molecules have been described such as Autoinducer-2 (AI-2). The phenotypes that are regulated in Serratia species by means of AHLs are remarkably diverse and of profound biological and ecological significance, and often interconnected with other global regulators. Furthermore, AHL- and AI-2-mediated systems (less profoundly studied) are continuously being discovered and explored in Serratia spp., many having interesting twists on the basic theme. Therefore, this review will highlight the current known quorum sensing systems in Serratia spp., including the important nosocomial pathogen Serratia marcescens.

Pressure is an important environmental parameter that varies greatly throughout the biosphere. In surface-adapted bacteria, such as Escherichia coli, high-pressure (HP) shock greatly perturbs cellular homeostasis. Nevertheless, the cellular impact of HP stress and the actual damage it provokes remain poorly characterized. One approach to address this lack of insight is to probe the cell’s genetic response to HP shock. This survey highlights the recent advancements in the characterization of the HP shock response, which seems to encompass parts of the heat shock, cold shock, and SOS response.

We have previously characterized the N -acyl- l -homoserine lactone-based quorum-sensing system of the biofilm isolate Serratia plymuthica RVH1. Here we investigated the role of quorum sensing and of quorum-sensing-dependent production of an antimicrobial compound (AC) on biofilm formation by RVH1 and on the cocultivation of RVH1 and Escherichia coli in planktonic cultures or in biofilms. Biofilm formation of S. plymuthica was not affected by the knockout of splI or splR , the S. plymuthica homologs of the luxI or luxR quorum-sensing gene, respectively, or by the knockout of AC production. E. coli grew well in mixed broth culture with RVH1 until the latter reached 8.5 to 9.5 log CFU/ml, after which the E. coli colony counts steeply declined. In comparison, only a very small decline occurred in cocultures with the S. plymuthica AC-deficient and splI mutants. Complementation with exogenous N -hexanoyl- l -homoserine lactone rescued the wild-type phenotype of the splI mutant. The splR knockout mutant also induced a steep decline of E. coli , consistent with its proposed function as a repressor of quorum-sensing-regulated genes. The numbers of E. coli in 3-day-old mixed biofilms followed a similar pattern, being higher with S. plymuthica deficient in SplI or AC production than with wild-type S. plymuthica , the splR mutant, or the splI mutant in the presence of N -hexanoyl- l -homoserine lactone. Confocal laser scanning microscopic analysis of mixed biofilms established with strains producing different fluorescent proteins showed that E. coli microcolonies were less developed in the presence of RVH1 than in the presence of the AC-deficient mutant.

The effect of hen egg white lysozyme (HEWL) and bacteriophage lambda lysozyme (LaL) in combination with high pressure (HP) treatment on the inactivation of four gram-negative bacteria ( Escherichia coli O157:H7, Shigella flexneri , Yersinia enterocolitica and Salmonella typhimurium ), was studied in skim milk (pH 6.8; a w 0.997) and in banana juice (pH 3.8; a w 0.971). In the absence of lysozymes, S. flexneri was more sensitive to HP in milk than in banana juice, while the opposite was observed for the other three bacteria. In combination with HP treatment, LaL was more effective than HEWL on all bacteria in both milk and banana juice. Depending on the bacteria, inactivation levels in banana juice were increased from 0.4–2.7 log units by HP treatment alone to 3.6–6.5 log units in the presence of 224 U/ml LaL. Bacterial inactivation in milk was also enhanced by LaL but only by 0.5–2.1 log units. Under the experimental conditions used, LaL was more effective in banana juice than in milk, while the effectiveness of HEWL under the same conditions was not significantly affected by the food matrix. This effect could be ascribed to the low pH of the banana juice since LaL was also more effective on E. coli in buffer at pH 3.8 than at pH 6.8. Since neither LaL nor HEWL are enzymatically active at pH 3.8, we analysed bacterial lysis after HP treatment in the presence of these enzymes, and found that inactivation proceeds through a non-lytic mechanism at pH 3.8 and a lytic mechanism at pH 6.8. Based on these results, LaL may offer interesting perspectives for use as an extra hurdle in high pressure food preservation.

We have investigated the specificity of six different lysozymes for peptidoglycan substrates obtained by extraction of a number of gram-negative bacteria and Micrococcus lysodeikticus with chloroform/Tris-HCl buffer (chloroform/buffer). The lysozymes included two that are commercially available (hen egg white lysozyme or HEWL, and mutanolysin from Streptomyces globisporus or M1L), and four that were chromatographically purified (bacteriophage lambda lysozyme or LaL, bacteriophage T4 lysozyme or T4L, goose egg white lysozyme or GEWL, and cauliflower lysozyme or CFL). HEWL was much more effective on M. lysodeikticus than on any of the gram-negative cell walls, while the opposite was found for LaL. Also the gram-negative cell walls showed remarkable differences in susceptibility to the different lysozymes, even for closely related species like Escherichia coli and Salmonella Typhimurium. These differences could not be due to the presence of lysozyme inhibitors such as Ivy from E. coli in the cell wall substrates because we showed that chloroform extraction effectively removed this inhibitor. Interestingly, we found strong inhibitory activity to HEWL in the chloroform/buffer extracts of Salmonella Typhimurium, and to LaL in the extracts of Pseudomonas aeruginosa, suggesting that other lysozyme inhibitors than Ivy exist and are probably widespread in gram-negative bacteria.

The bacterial SOS response is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations. Despite the extensive depiction of the SOS regulon itself, its activation by stresses different from typical DNA damaging treatments remains poorly characterized. Recently, we reported the RecA- and LexA-dependent induction of the SOS response in Escherichia coli MG1655 after exposure to high hydrostatic pressure (HP, approximately 100 MPa), a physical stress of which the cellular effects are not well known. We now found this HP mediated SOS response to depend on RecB and not on RecF, which is a strong indication for the involvement of double strand breaks. As the pressures used in this work are thermodynamically unable to break covalent bonds in DNA, we hypothesized the involvement of a cellular function or pathway in the formation of this lesion. A specialized screening allowed us to identify the cryptic type IV restriction endonuclease Mrr as the final effector of this pathway. The HP SOS response and its corresponding phenotypes could be entirely attributed to the HP triggered activation of Mrr restriction activity. Several spontaneously occurring alleles of mrr, incapable of triggering the HP-induced SOS response, were isolated and characterized. These results provide evidence for a specific pathway that transmits the perception of HP stress to induction of the SOS response and support a role for Mrr in bacterial stress physiology.

A highly efficient method was developed for the isolation and purification of the periplasmic Escherichia coli lysozyme inhibitor protein Ivy. After isolation by osmotic shock from an E. coli overexpression strain, Ivy was purified to >95% purity using a single affinity chromatography step with hen egg white lysozyme as a ligand. Further, the specificity of Ivy against various types of lysozymes (hen egg white lysozyme, c-type; mutanolysine, ch-type; cauliflower lysozyme, not further classified; goose egg white lysozyme, g-type; lambda lysozyme, λ-type and T4 lysozyme, v-type) was investigated. Most strongly inhibited was hen egg white lysozyme, followed by goose egg white lysozyme and finally T4 lysozyme, while no inhibition was observed for the other lysozymes. These results clearly indicate that Ivy is a relatively specific inhibitor of vertebrate lysozymes belonging to the c- and g-type and that its inhibition profile corresponds to the structural and evolutionary relatedness of the lysozymes. The availability of pure Ivy and the elucidation of its inhibition profile will contribute to the further identification of its biological function in bacteria.

The inactivation of Escherichia coli MG1655 by high-pressure homogenisation (HPH) at pressures ranging from 100 to 300 MPa was studied in buffered suspensions adjusted to different relative viscosities (1.0, 1.3, 1.7, 2.7 and 4.9) with polyethylene glycol 6000 (PEG 6000). The water activity of these suspensions was not significantly affected by this high molecular weight solute. Bacterial inactivation was found to decrease with increasing viscosity of the suspensions, an effect that was more pronounced at higher pressures. To study the effect of water activity, series of E. coli suspensions having a different water activity (0.953-1.000) but the same relative viscosity (1.3, 1.7, 2.7 and 4.9) were made using PEG of different molecular weights (400, 600, 1000 and 6000), and subjected to HPH treatment. The results indicated that water activity does not influence inactivation. Finally, inactivation of E. coli MG1655 by HPH in skim milk, soy milk and strawberry-raspberry milk drink was found to be the same as in PEG containing buffer of the corresponding viscosity. These results identify fluid viscosity as a major environmental parameter affecting bacterial inactivation by HPH, as opposed to water activity and product composition, and should contribute to the development of HPH applications for the purpose of bacterial inactivation.

Various cell surface molecules and structures have been implicated in biofilm formation in Escherichia coli. This review presents an overview of the occurrence, production and interaction of these components, their influence at one or more developmental stages of biofilm formation, and their potential role as virulence factors in pathogenic E. coli strains.

Shiga toxins (Stxs), also termed Vero toxins, are cytotoxic ribosome inactivating proteins that are produced by a number of gastrointestinal pathogens and that contribute to the severity of the associated diseases. In this work, we constructed and validated a transcriptional fusion of the stx1AB promoter to the gfp reporter gene. The cloned promoter region encompasses both the proximal and the distal promoter regions of stx1AB, mediating control by the host's iron-responsive Fur repressor and the Stx prophage's Q antiterminator protein, respectively. The probe was validated by demonstrating its responsiveness towards mitomycin C and EDTA, and the contribution of host and phage encoded factors could be separated by studying stx1 expression in either wild-type or isogenic lysogenic cells. Moreover, stx1AB expressing populations could be visualized by flow cytometry. The potential use of such a probe for non-destructive online detection of stx1AB expression and visualization of stx1AB expressing populations is further discussed.

When challenged with unfavorable conditions, microorganisms can develop a stress response that allows them to adapt to or survive in the new environment. A common feature of the numerous specific stress response pathways that have been described in a wide range of bacteria is that they are energy demanding and therefore often transient. In addition, stress responses may come too late or be insufficient to protect the cell or the population against very sudden or severe stresses. However, it seems that microorganisms can also enhance their chances of survival under stress by increasing the generation of diversity at the population level. This can be achieved either by creating genetic diversity by a variety of mechanisms involving for example constitutive or transient mutators and contingency loci, or by revealing phenotypic diversity that remained dormant due to a mechanism called genetic buffering. This review gives an overview of these emerging diversity-generating mechanisms, which seem to play an important role in the ability of microbial populations to overcome stress challenges.

The product of the Escherichia coli ORFan gene ykfE was recently shown to be a strong inhibitor of C-type lysozyme in vitro. The gene was correspondingly renamed ivy (inhibitor of vertebrate lysozyme), but its biological function in E. coli remains unknown. In this work, we investigated the role of Ivy in the resistance of E. coli to the bactericidal effect of lysozyme in the presence of outer-membrane-permeabilizing treatments. Both in the presence of lactoferrin (3.0 mg/ml) and under high hydrostatic pressure (250 MPa), the lysozyme resistance of E. coli MG1655 was decreased by knock-out of Ivy, and increased by overexpression of Ivy. However, knock-out of Ivy did not increase the lysozyme sensitivity of an E. coli MG1655 mutant previously described to be resistant to lysozyme under high pressure. These results indicate that Ivy is one of several factors that affect lysozyme resistance in E. coli, and suggest a possible function for Ivy as a host interaction factor in commensal and pathogenic E. coli.

Bacterial populations that are exposed to rapidly changing and sometimes hostile environments constantly switch between growth, survival, and death. Understanding bacterial survival and death are therefore cornerstones in a full comprehension of microbial life. During the last few years, new insights have emerged regarding the mechanisms of bacterial inactivation under stressful conditions. Particularly under mildly lethal stress, the ultimate cause of inactivation often seems mediated by the cell itself and is subject to additional regulation that integrates information about the global state of the cell and its environmental and social surrounding. This article explores the thin line between bacterial growth and inactivation and focuses on some emerging bacterial survival strategies, both from an individual cell and from a population perspective.

High pressure can sensitize gram-negative bacteria to antimicrobial peptides or proteins through the permeabilization of their outer membranes; however, the range of compounds to which sensitivity is induced is species and strain dependent. We studied the role of outer-membrane properties in this sensitization by making use of a series of rough and deep rough mutants of Salmonella enterica serovar Typhimurium that show an increased degree of lipopolysaccharide (LPS) truncation, along with Pseudomonas aeruginosa PhoP and PhoQ mutants with altered outer-membrane properties. The outer-membrane properties of P. aernginosa were also modulated through the use of different Mg2- concentrations in the growth medium. Each of these strains was challenged under high pressure (15 min at 270 MPa for Salmonella Typhimurium and 15 min at 100 MPa for P. aerttginosa) in phosphate buffer with lysozyme (100 microg/ml), nisin (100 IU/ml), lactoferricin (20 microg/ml), and HEL96-116 (100 microg/ml), a synthetic lysozyme-derived peptide, and sensitization levels were compared. The results obtained indicated that outer-membrane properties affected high-pressure sensitization differently for different compounds. LPS truncation in Salmonella Typhimurium was correlated with increased sensitization to lysozyme (up to 1.5 log10 units) and nisin (up to 1.2 log10 units) but with decreased sensitization to lactoferricin under pressure. For P. aeruginosa, the pattern of sensitization to lactoferricin and nisin resembled that of polymyxin B at atmospheric pressure, suggesting that pressure induces the self-promoted uptake of both peptides. Sensitization to HEL96-116 was not affected by outer-membrane properties for either organism. Hence, outer-membrane permeabilization by high pressure cannot be explained by a single unifying mechanism and is dependent on the organism, the outer-membrane properties, and the nature of the antimicrobial compound. On the basis of these findings, the use of antimicrobial cocktails targeting different bacteria and fractions of bacterial populations may enhance the efficacy of high pressure as a preservation treatment.

The purpose of this review is to describe the antibacterial properties and mode of action of lysozyme against gram-positive and gram-negative bacteria, and to provide insight in the underlying causes of bacterial resistance or sensitivity to lysozyme. Such insight improves our understanding of the role of this ubiquitous enzyme in antibacterial defense strategies in nature and provides a basis for the development and improvement of applications of this enzyme as an antibacterial agent. The bactericidal properties of lysozyme are primarily ascribed to its N-acetylmuramoylhydrolase enzymic activity, resulting in peptidoglycan hydrolysis and cell lysis. However, an increasing body of evidence supports the existence of a nonenzymic and/or nonlytic mode of action. Because gram-negative bacteria, including some major foodborne pathogens, are normally insensitive to lysozyme by virtue of their outer membrane that acts as a physical barrier preventing access of the enzyme, several strategies have been developed to extend the working spectrum of lysozyme to gram-negative bacteria. These include denaturation of lysozyme, modification of lysozyme by covalent attachment of polysaccharides, fatty acids and other compounds, attachment of C-terminal hydrophobic peptides to lysozyme by genetic modification, and the use of outer membrane permeabilizing agents such as EDTA or polycations or permeabilizing treatments such as high hydrostatic pressure treatment.

The number of bacterial and fungal strains that have developed resistance against the classical antibiotics continues to grow. The intensified search for new antibiotic lead compounds has resulted in the discovery of numerous endogenous peptides with antimicrobial properties in plants, bacteria and animals. Their possible applications as anti-infective agents are often limited by their size, in reference to production costs and susceptibility to proteases. In this article, we report recent isolations of antimicrobial compounds from insects, with molecular masses less than 1 kDa. Experimental approaches are discussed and the first data on the antimicrobial properties of β-alanyl-tyrosine (252 Da), one of such low molecular mass compounds isolated from the fleshfly Neobellieria bullata, are presented. We also offer evidence for the constitutive presence of antimicrobial compounds in insects of different orders, in addition to the previously identified inducible antimicrobial peptides.

Starchy endosperm cell wall degradation by a fungal starter culture [Noots et al ., Journal of Agricultural and Food Chemistry 49 (2001) 975–981] was studied using inoculated non-germinating barley subjected to conditions resembling those of a traditional malting process. The β-glucanase and xylanase production by Rhizopus VII during processing was investigated and cell wall degradation was assessed by Calcofluor modification, friability, and β-glucan content determinations. The level of enzymes produced increased progressively during the process step corresponding to germination in a regular malting process. As the majority of the modified, non-germinating barley kernels showed 90–100% modification, the cell wall degradation by the starter culture activity was rapid and largely homogeneous at the kernel level. No distinct pattern of cell wall degradation was identified in kernel longitudinal cross sections. Several lines of experimental evidence suggest that the invasion of the starter culture through the outer layers of the barley kernel is the rate-limiting step for endosperm cell wall degradation.

Recent microbiological data have revealed that Gram-negative bacteria are able to protect themselves against the lytic action of host lysozymes by secreting proteinaceous inhibitors. Four distinct classes of such inhibitors have been discovered that specifically act against c-type, g-type and i-type lysozymes. Here, the 1.24 Å resolution crystal structure of the periplasmic i-type lysozyme inhibitor from Aeromonas hydrophila (PliI-Ah) in complex with the i-type lysozyme from Meretrix lusoria is reported. The structure is the first to explain the inhibitory mechanism of the PliI family at the atomic level. A distinct `ridge' formed by three exposed PliI loops inserts into the substrate-binding groove of the lysozyme, resulting in a complementary `key-lock' interface. The interface is principally stabilized by the interactions made by the PliI-Ah residues Ser104 and Tyr107 belonging to the conserved SGxY motif, as well as by the other conserved residues Ser46 and Asp76. The functional importance of these residues is confirmed by inhibition assays with the corresponding point mutants of PliI-Ah. The accumulated structural data on lysozyme-inhibitor complexes from several classes indicate that in all cases an extensive interface of either a single or a double `key-lock' type is formed, resulting in highly efficient inhibition. These data provide a basis for the rational development of a new class of antibacterial drugs. journal: Acta Crystallographica Section D: Biological Crystallography content_type: research papers peer_reviewed: Yes review_process: Single blind received: 2 July 2014 accepted: 26 November 2014 published_online: 23 January 2015 supplementary_materials: This article has supporting information copyright: © 2015 International Union of Crystallography ispartof: Acta Crystallographica D vol:71 issue:Pt 2 pages:344-351 ispartof: location:United States status: published

Several yeasts, such as Candida utilis, Dekkera bruxellensis, Hanseniaspora guilliermondii, Kloeckera apiculata, Saccharomyces cerevisiae and Schizosaccharomyces pombe, were found to coaggregate with Escherichia coli, but S. pombe showed much less coflocculation than the other yeasts (Peng et al. 2001)). S. pombe is known to have galactose-rich cell walls and we investigated whether this might be responsible for its different behavior by studying the wild-type TP4-1D, with a mannose to galactose ratio of 1 to 1.2, and the glycosylation mutant gms1delta (Man:Gal=1:0). The wild-type induced very low levels of coflocculation (3%) while gms1delta induced a remarkable amount of coflocculation (48%). Coflocculation of the mutant was inhibited by mannose but not affected by galactose or glucose. The S. cerevisiae mnn2 mutant, with a mannan structure similar to gms1delta, also showed a high degree of coflocculation (40%). However, S. cerevisiae mutant mnn9, with a mature core similar to S. pombe, showed decreased coflocculation (21.3%). Both these S. cerevisae mutants were sensitive to mannose inhibition. Coflocculation of E. coli and gms1delta also could be inhibited by gms1delta mannan and plant lectins, such as HHA, GNA and NPA, specific to either alpha-1-3- or alpha-1-6-linked mannosyl units. From these results we conclude that the E. coli lectins may have specificity for alpha-1-6- and alpha-1-3-linked mannose residues either in the outer chain or in the core of S. pombe, but in wild-type strains these mannose residues are shielded by galactose residues.

Strains of fungi from different origins, including isolates of the natural microflora of barley, were screened for their ability to modify barley starchy endosperm cell walls in situ. In an initial step, fungi were selected that degrade the major component of the cell walls, that is, (1-->3),(1-->4)-beta-D-glucan, in vitro on artificial media. Nongerminating, sterilized barley, obtained by gamma-irradiation, was inoculated with such fungi and subjected to solid state fermentation under conditions resembling those of a traditional malting process. For some strains of fungi, a clear correlation between the production of endo-beta-glucanase and the friability of the treated kernels was found. Image analysis of Calcofluor stained longitudinal sections of barley kernels fermented with the endo-beta-glucanase producing strains showed that starchy endosperm cell walls were modified. As malt quality is inversely related to its (1-->3),(1-->4)-beta-D-glucan content, the selected strains have high potential to be used as starter cultures during malt production, contributing to the processing quality of the final product.

The effect of divalent cations on the inactivation of Escherichia coli by high hydrostatic pressure was investigated. The presence of 0.5 mmol l-1 of CaCl2, MgCl2, MnCl2 and FeCl2 reduced pressure inactivation of E. coli MG1655, while 0.5 mmol l-1 of ZnCl2, NiCl2, CuCl2 and CoCl2 increased inactivation. Baroprotection by Ca2+ was found to be dose-dependent up to at least 80 mmol l-1 and was studied in more detail in terms of inactivation kinetics. Logarithmic survivor plots against time deviated from first order kinetics, suggesting that MG1655 cultures were heterogeneous with regard to pressure resistance. All cultures were shown to contain a small proportion of cells that were only slowly inactivated. Addition of Ca2+ increased the proportion of these tolerant cells in the cultures up to 1000-fold at 80 mmol l-1, but did not affect their inactivation rate. The addition of EDTA resulted in the opposite effect, lowering the proportion of pressure-tolerant cells in the cultures. Three pressure-resistant mutants of E. coli MG1655 were found to be more resistant to EDTA under pressure compared with MG1655, and were unaffected by Ca2+ under pressure. In addition, these mutants had a 30-40% lower Ca2+ content than MG1655. Based on these results, it is postulated that pressure killing of E. coli MG1655 is mediated primarily by the destabilization of Ca(2+)-binding components, and that the mutations underlying pressure resistance have resulted in pressure-stable targets with reduced Ca(2+)-binding affinity.

Graphs for survival under high hydrostatic pressure (450 MPa; 25°C; citrate-phosphate buffer, pH 7.0) of stationary-growth-phase cells of eight Staphylococcus aureus strains were found to be nonlinear. The strains could be classified into two groups on the basis of the shoulder length. Some of them showed long shoulders of up to 20 min at 450 MPa, while others had shoulders of

The purpose of the study was to determine the distribution of Mycobacterium avium ssp. paratuberculosis (MAP) across the main milk and colostrum fractions (cream, curd, and whey). Raw milk and colostrum were inoculated with 1 of 2 MAP strains, ATCC 19698 or S-23, yielding initial concentrations of 10 6 to 10 7 cfu/mL. After fractionation, for milk as well as for colostrum, 80 to 90% of the recovered MAP cells were found in the curd fraction and 10 to 20% in the cream fraction. Total MAP colony counts in milk whey were 4 to 5 log 10 units lower than colony counts of inoculated milk. In colostrum, colony counts were 2 to 3 log 10 units lower in whey than in inoculated colostrum. Because of the slow growth of MAP and to proceed more smoothly with set-up and optimization of the method, luminescent MAP strains were used. The high correlation coefficient (r=0.960) between colony counts and luminescence measurements showed that the use of luminescent MAP strains during method development was plausible.

It is generally acknowledged that biofilms are the dominant lifestyle of bacteria, both in the natural environment as on manmade settings such as industrial and medical devices. This attached form of cell growth consists of slime matrix embedded bacteria of either a single, but mostly of multiple microbial species that form an interdependent structured community, capable of coordinated and collective behavior. Although research on multispecies biofilms is still in its infancy, this review will focus on these complex communities where cooperation and antagonism are keys to increase the fitness of the different species and where intercellular interactions and communication are means to achieve this goal.

Tetragenococcus halophilus is known to flourish in extreme salt environments. Recently, this halophilic bacterium also appeared as the dominant microflora during storage of sugar thick juice, an intermediate product of beet sugar production. Although T. halophilus can cause degradation of thick juice, dominance of this bacterium does not always result in degradation. In this study T. halophilus strains from high-salt and high-sugar environments, and in particular from degraded and non-degraded thick juice, were compared in detail. Both physiological and genetic characterization using Biolog, repetitive PCR fingerprinting (rep-PCR) and random amplified polymorphic DNA (RAPD) technology, revealed clear differences between T. halophilus strains isolated from salt- and sugar-rich environments. However, no strain pattern could be specifically and systematically associated with degraded or non-degraded thick juice. Remarkably, halophilic T. halophilus strains were not able to grow in sugar thick juice. Irrespective of the differences between the strains from high-salt or high-sugar environments, DNA-DNA hybridization grouped all strains within the species T. halophilus, except one isolate from sugar thick juice that showed different physiological and genetic characteristics, and that may represent a new species of Tetragenococcus.

The diversity of the bacterial population in sugar thick juice, an intermediate product in the production of beet sugar, which exhibits an extremes osmophilic environment with a water activity value (a(w)) less than 0.86, was assessed with both culture-dependent and -independent 16S ribosomal RNA (rRNA) gene-based analyses. In comparison with previous studies, the number of different thick juice bacterial species increased from 29 to 72. Remarkably, a limited, gram-positive, culturable flora, encompassing species of Bacillus, Staphylococcus and mainly Tetragenococcus dominated thick juice during storage, while a more heterogeneous and unculturable fraction of Acinetobacter, Sporolactobacillus and Thermus species could be detected in freshly produced thick juice. Notably, almost all bacteria detected in the thick juice were also detected in the air, emphasising the importance of further investigation and assessment of strategies to reduce (air) contamination during processing and storage. The discovery of the contamination source may be used for the development of management strategies for thick juice degradation resulting from microbial activity. (c) 2008 Elsevier Ltd. All rights reserved. ispartof: Food Microbiology vol:25 issue:6 pages:831-836 ispartof: location:England status: published

A reverse zymogram method for the detection of bacterial lysozyme inhibitors was developed. This method was validated by using a periplasmic protein extract of Escherichia coli containing a known inhibitor and subsequently led to the detection of a new proteinaceous hen egg white lysozyme inhibitor in Proteus mirabilis .

Ivy is a lysozyme inhibitor that protects Escherichia coli against lysozyme-mediated cell wall hydrolysis when the outer membrane is permeabilized by mutation or by chemical or physical stress. In the current work, we have investigated whether Ivy is necessary for the survival or growth of E. coli MG1655 and Pseudomonas aeruginosa PAO1 in hen egg white and in human saliva and breast milk, which are naturally rich in lysozyme and in membrane-permeabilizing components. Wild-type E. coli was able to grow in saliva and breast milk but showed partial inactivation in egg white. The knockout of Ivy did not affect growth in breast milk but slightly increased sensitivity to egg white and caused hypersensitivity to saliva, resulting in the complete inactivation of 10 4 CFU ml −1 of bacteria within less than 5 hours. The depletion of lysozyme from saliva completely restored the ability of the ivy mutant to grow like the parental strain. P. aeruginosa , in contrast, showed growth in all three substrates, which was not affected by the knockout of Ivy production. These results indicate that lysozyme inhibitors like Ivy promote bacterial survival or growth in particular lysozyme-rich secretions and suggest that they may promote the bacterial colonization of specific niches in the animal host.

The industrial storage of sugar thick juice was simulated on a laboratory scale. Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis and the application of Clone Libraries in parallel with classical microbiology were used to study the bacterial diversity and all revealed a dominance (>99%) of Tetragenococcus halophilus during storage. The degradation of thick juice correlated with the appearance of L-lactic acid and high concentrations of T. halophilus. In addition, pure cultures of T. halophilus induced degradation of sterile thick juice. A specific PCR was developed to detect T. halophilus and industrial thick juice samples from Belgium, Germany and France all contained T. halophilus, suggesting a consistent association of this organism with thick juice. T. halophilus has been known only as a halophile thus far, and this report is the first to show an association of this organism with a sugar-rich environment. ispartof: Food Microbiology vol:25 issue:2 pages:413-21 ispartof: location:England status: published

The parameters influencing outer membrane permeability of Pseudomonas aeruginosa PAO1 under high hydrostatic pressure were quantified and optimized, using fusion between a specific A1 gamma peptidoglycan-binding domain and green fluorescent protein (PBD-GFP). Based on the obtained data, optimal conditions were defined to assess the synergistic bactericidal action between high hydrostatic pressure and peptidoglycan hydrolysis by bacteriophage-encoded endolysins KZ144 and EL188. Under high hydrostatic pressure, both endolysins show similar inactivation of P. aeruginosa as the commonly used hen egg white lysozyme or slightly higher inactivation in the case of EL188 at 150 and 200 MPa. The partial contribution of pressure to the bacterial inactivation increases with higher pressure, while the partial contribution of the enzymes is maximal at the onset pressure of outer membrane permeabilization for the PBD-GFP protein (175 MPa). This study's results demonstrate the usefulness of this approach to determine optimal synergy for hurdle technology applications. ispartof: FEMS Microbiology Letters vol:280 issue:1 pages:113-119 ispartof: location:England status: published

Aeromonas hydrophila AH-1N shows biphasic growth in glucose containing broth at 30 °C. The first phase is characterized by strong acidification, while the second phase is accompanied by an increase in medium pH. Disruption of AHL production by knockout of ahyI did not affect the first growth phase, but resulted in further acidification which completely blocked the second growth phase and even caused cell death. The block could be relieved by addition of 5 μM (or less) synthetic N-butanoyl- l -homoserine lactone (C4-HSL), the major AHL produced by A. hydrophila AH-1N. Further analysis revealed that, as shown previously for Serratia plymuthica, butanediol fermentation is regulated by AHL-mediated quorum sensing in A. hydrophila AH-1N. These results indicate that A. hydrophila switches to butanediol fermentation to reduce medium acidification under certain conditions and to allow further growth if nutrient resources are not yet exhausted.

Autoinducer-2 (AI-2) is a signalling molecule proposed to act as a 'universal' signal for interspecies communication, regulating niche-specific genes with diverse functions in various bacteria. We have previously reported the production of AI-2 in strains from different Serratia species and recently, the luxS gene of two Serratia strains was isolated and shown to affect distinct phenotypes. In the current work, we have identified the luxS gene of Serratia plymuthica RVH1, and studied its effect on the N-acyl-L-homoserine lactone-regulated 2,3-butanediol fermentation, production of extracellular protease, chitinase, nuclease and antibacterial compound, and on biofilm formation. None of these phenotypes was affected by luxS knockout. However, overexpression of the luxS gene in RVH1, which was accompanied by an increased production of AI-2, resulted in a slower growth. This growth retardation was also observed when RVH1 was grown in spent culture medium from the AI-2-overproducing strain, but not in spent culture medium from the luxS knockout strain. These results suggest that luxS primarily fulfils a metabolic role and may not regulate a coordinated behaviour controlled by cell-to-cell signalling in S. plymuthica RVH1.

Quorum sensing by means of N-acyl-l-homoserine lactones (AHLs) is widespread in Gram-negative bacteria, where diverse AHLs influence a wide variety of functions, even in a single genus such as Serratia. Here we report the identification and characterization of the quorum sensing system of Serratia plymuthica strain RVH1. This strain isolated from a raw vegetable processing line produces at least three AHLs which were identified as N-butanoyl- (C4-HSL), N-hexanoyl- (C6-HSL) and N-(3-oxo-hexanoyl)-homoserine lactone (3-oxo-C6-HSL). The identified LuxI homolog SplI synthesizes 3-oxo-C6-HSL, and influences the production of C4-HSL and C6-HSL, as splI gene inactivation resulted in loss of 3-oxo-C6-HSL production and smaller amounts of C4-HSL and C6-HSL produced. SplI-dependent quorum sensing controls 2,3-butanediol fermentation (previously reported) and the production of an extracellular chitinase, nuclease, protease and antibacterial compound. The identity of the latter is not yet elucidated, but appears to be different from the known antibacterial compounds produced by Serratia strains. SplR, the homolog of the LuxR regulator, appears to act as a repressor of synthesis of extracellular enzymes and antibacterial compound and to autorepress its own expression, probably by binding to a 21bp lux box sequence.

Butanediol fermentation in two Serratia species is shown to be affected by N -acyl- l -homoserine lactone-dependent quorum sensing. Knockout of quorum-sensing signal production caused a shift towards enhanced acid production, resulting in early growth arrest, which was reversible by the addition of synthetic signal molecules.

The bacterial SOS regulon encodes a response to DNA damage that not only functions to relieve the incurred damage but also enhances adaptation through mutagenesis and the lateral spread of virulence factors. Recent papers have demonstrated that certain stimuli can indirectly generate the SOS-inducing signal by activation of endogenous DNA damage mechanisms rather than by direct DNA damage. We suggest that these endogenous triggers have been recruited by bacteria to enable adaptation to various types of stresses. ispartof: Trends in Microbiology vol:14 issue:10 pages:421-423 ispartof: location:England status: published

N-acyl-L-homoserine lactone (AHL) mediated quorum sensing is a widespread communication system in gram-negative bacteria which regulates a wide range of target genes in a cell density-dependent manner. Although Escherichia coli is not capable of synthesizing AHL molecules because it lacks an AHL synthase encoding gene, it does produce a predicted AHL receptor of the LuxR family, named SdiA. In this work, we used a promoter trap library to screen for E. coli MG1655 promoters whose expression was affected by synthetic N-hexanoyl-L-homoserine lactone (C6-HSL), and we identified six upregulated and nine downregulated promoters, which also responded to synthetic 3-oxo-N-hexanoyl-L-homoserine lactone (3-oxo-C6-HSL). The AHL responsiveness of these promoters was eliminated by knock-out of sdiA, and was temperature dependent, since the identified promoters showed a response at 30 degrees C but not, or only very weakly at 37 degrees C. In addition, in line with the observed induction of gadA encoding a glutamate decarboxylase, we could demonstrate an increased acid tolerance of E. coli upon exposure to C6-HSL. In conclusion, our work shows that E. coli has the capacity to alter its pattern of gene expression and its phenotypical properties in response to AHLs by means of the AHL responsive transcriptional regulator SdiA.

The antibacterial working range of six lysozymes was tested under ambient and high pressure, on a panel of five gram-positive (Enterococcus faecalis, Bacillus subtilis, Listeria innocua, Staphylococcus aureus and Micrococcus lysodeikticus) and five gram-negative bacteria (Yersinia enterocolitica, Shigella flexneri, Escherichia coli O157:H7, Pseudomonas aeruginosa and Salmonella typhimurium). The lysozymes included two that are commercially available (hen egg white lysozyme or HEWL, and mutanolysin from Streptomyces globisporus or M1L), and four that were chromatographically purified (bacteriophage lambda lysozyme or LaL, bacteriophage T4 lysozyme or T4L, goose egg white lysozyme or GEWL, and cauliflower lysozyme or CFL). T4L, LaL and GEWL were highly pure as evaluated by silver staining of SDS-PAGE gels and zymogram analysis while CFL was only partially pure. At ambient pressure each gram-positive test organism displayed a specific pattern of sensitivity to the six lysozymes, but none of the gram-negative bacteria was sensitive to any of the lysozymes. High pressure treatment (130-300 MPa, 25 degrees C, 15 min) sensitised several gram-positive and gram-negative bacteria for one or more lysozymes. M. lysodeikticus and P. aeruginosa became sensitive to all lysozymes under high pressure, S. typhimurium remained completely insensitive to all lysozymes, and the other bacteria showed sensitisation to some of the lysozymes. The possible applications of the different lysozymes as biopreservatives, and the possible reasons for the observed differences in bactericidal specificity are discussed.

Recently, we isolated from a raw vegetable processing line a Serratia strain with strong biofilm-forming capacity and which produced N-acyl-l-homoserine lactones (AHLs). Within the Enterobacteriaceae, strains of the genus Serratia are a frequent cause of human nosocomial infections; in addition, biofilm formation is often associated with persistent infections. In the current report, we describe the detailed characterization of the isolate using a variety of genotypic and phenotypic criteria. Although the strain was identified as Serratia plymuthica on the basis of its small subunit ribosomal RNA (16S rRNA) gene sequence, it differed from the S. plymuthica type strain in production of pigment and antibacterial compounds, and in AHL production profile. Nevertheless, the identification as S. plymuthica could be confirmed by gyrB phylogeny and DNA:DNA hybridization.

The inactivation of suspensions of Escherichia coli MG1655 by high-pressure homogenization was studied over a wide range of pressures (100-300 MPa) and initial temperatures of the samples (5-50 degrees C). Bacterial inactivation was positively correlated with the applied pressure and with the initial temperature. When samples were adjusted to different concentrations of poly(ethylene glycol) to have the same viscosity at different temperatures below 45 degrees C and then homogenized at these temperatures, no difference in inactivation was observed. These observations strongly suggest, for the first time, that the influence of temperature on bacterial inactivation by high-pressure homogenization is only through its effect on fluid viscosity. At initial temperatures > or =45 degrees C, corresponding to an outlet sample temperature >65 degrees C, the level of inactivation was higher than what would be predicted on the basis of the reduced viscosity at these temperatures, suggesting that under these conditions heat starts to contribute to cellular inactivation in addition to the mechanical effects that are predominant at lower temperatures. Second-order polynomial models were proposed to describe the impact of a high-pressure homogenization treatment of E. coli MG1655 as a function of pressure and temperature or as a function of pressure and viscosity. The pressure-viscosity inactivation model provided a better quality of fit of the experimental data and furthermore is more comprehensive and versatile than the pressure-temperature model because in addition to viscosity it implicitly incorporates temperature as a variable.