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1.  Construction of Nontoxigenic Mutants of Nonproteolytic Clostridium botulinum NCTC 11219 by Insertional Mutagenesis and Gene Replacement 
Applied and Environmental Microbiology  2016;82(10):3100-3108.
ABSTRACT
Group II nonproteolytic Clostridium botulinum (gIICb) strains are an important concern for the safety of minimally processed ready-to-eat foods, because they can grow and produce botulinum neurotoxin during refrigerated storage. The principles of control of gIICb by conventional food processing and preservation methods have been well investigated and translated into guidelines for the food industry; in contrast, the effectiveness of emerging processing and preservation techniques has been poorly documented. The reason is that experimental studies with C. botulinum are cumbersome because of biosafety and biosecurity concerns. In the present work, we report the construction of two nontoxigenic derivatives of the type E gIICb strain NCTC 11219. In the first strain, the botulinum toxin gene (bont/E) was insertionally inactivated with a retargeted intron using the ClosTron system. In the second strain, bont/E was exchanged for an erythromycin resistance gene using a new gene replacement strategy that makes use of pyrE as a bidirectional selection marker. Growth under optimal and stressed conditions, sporulation efficiency, and spore heat resistance of the mutants were unaltered, except for small differences in spore heat resistance at 70°C and in growth at 2.3% NaCl. The mutants described in this work provide a safe alternative for basic research as well as for food challenge and process validation studies with gIICb. In addition, this work expands the clostridial genetic toolbox with a new gene replacement method that can be applied to replace any gene in gIICb and other clostridia.
IMPORTANCE The nontoxigenic mutants described in this work provide a safe alternative for basic research as well as for food challenge and process validation studies with psychrotrophic Clostridium botulinum. In addition, this work expands the clostridial genetic toolbox with a new gene replacement method that can be applied to replace any gene in clostridia.
doi:10.1128/AEM.03703-15
PMCID: PMC4959081  PMID: 26994073
2.  Identification of Genes Required for Growth of Escherichia coli MG1655 at Moderately Low pH 
The survival of some pathotypes of Escherichia coli in very low pH environments like highly acidic foods and the stomach has been well documented and contributes to their success as foodborne pathogens. In contrast, the ability of E. coli to grow at moderately low pH has received less attention, although this property can be anticipated to be also very important for the safety of mildly acidic foods. Therefore, the objective of this study was to identify cellular functions required for growth of the non-pathogenic strain E. coli MG1655 at low pH. First, the role of the four E. coli amino acid decarboxylase systems, which are the major cellular mechanisms allowing extreme acid survival, was investigated using mutants defective in each of the systems. Only the lysine decarboxylase (CadA) was required for low pH growth. Secondly, a screening of 8544 random transposon insertion mutants resulted in the identification of six genes affecting growth in LB broth acidified to pH 4.50 with HCl. Two of the genes, encoding the transcriptional regulator LeuO and the elongation factor P-β-lysine ligase EpmA, can be linked to CadA production. Two other genes, encoding the diadenosine tetraphosphatase ApaH and the tRNA modification GTPase MnmE, have been previously implicated in the bacterial response to stresses other than low pH. A fifth gene encodes the LPS heptosyltransferase WaaC, and its mutant has a deep rough colony phenotype, which has been linked to reduced acid tolerance in earlier work. Finally, tatC encodes a secA-independent protein translocase that exports a few dozen proteins and thus is likely to have a pleiotropic phenotype. For mnmE, apaH, epmA, and waaC, de novo in frame deletion and genetic complementation confirmed their role in low pH growth, and these deletion mutants were also affected in growth in apple juice and tomato juice. However, the mutants were not affected in survival in gastric simulation medium at pH 2.5, indicating that growth at moderately low pH and survival of extremely low pH depend mostly on different cellular functions.
doi:10.3389/fmicb.2016.01672
PMCID: PMC5078493  PMID: 27826291
Escherichia coli; acid stress; stress tolerance genes; genetic analysis; acidic foods
3.  Severely Heat Injured Survivors of E. coli O157:H7 ATCC 43888 Display Variable and Heterogeneous Stress Resistance Behavior 
Although minimal food processing strategies aim to eliminate foodborne pathogens and spoilage microorganisms through a combination of mild preservation techniques, little is actually known on the resistance behavior of the small fraction of microorganisms surviving an inimical treatment. In this study, the conduct of severely heat stressed survivors of E. coli O157:H7 ATCC 43888, as an indicator for the low infectious dose foodborne enterohemorrhagic strains, was examined throughout their resuscitation and outgrowth. Despite the fact that these survivors were initially sublethally injured, they were only marginally more sensitive to a subsequent heat treatment and actually much more resistant to a subsequent high hydrostatic pressure (HHP) shock in comparison with unstressed control cells. Throughout further resuscitation, however, their initial HHP resistance rapidly faded out, while their heat resistance increased and surpassed the initial heat resistance of unstressed control cells. Results also indicated that the population eventually emerging from the severely heat stressed survivors heterogeneously consisted of both growing and non-growing cells. Together, these observations provide deeper insights into the particular behavior and heterogeneity of stressed foodborne pathogens in the context of food preservation.
doi:10.3389/fmicb.2016.01845
PMCID: PMC5114269  PMID: 27917163
E. coli O157:H7; sublethal injury; resuscitation; heat resistance; high hydrostatic pressure resistance
4.  A Protein Interaction Map of the Kalimantacin Biosynthesis Assembly Line 
The antimicrobial secondary metabolite kalimantacin (also called batumin) is produced by a hybrid polyketide/non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein–protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites. This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.
doi:10.3389/fmicb.2016.01726
PMCID: PMC5089993  PMID: 27853452
kalimantacin; yeast two-hybrid; protein interactions; secondary metabolite; antibiotics biosynthesis; batumin
5.  Acetoin Synthesis Acquisition Favors Escherichia coli Growth at Low pH 
Applied and Environmental Microbiology  2014;80(19):6054-6061.
Some members of the family Enterobacteriaceae ferment sugars via the mixed-acid fermentation pathway. This yields large amounts of acids, causing strong and sometimes even lethal acidification of the environment. Other family members employ the 2,3-butanediol fermentation pathway, which generates comparatively less acidic and more neutral end products, such as acetoin and 2,3-butanediol. In this work, we equipped Escherichia coli MG1655 with the budAB operon, encoding the acetoin pathway, from Serratia plymuthica RVH1 and investigated how this affected the ability of E. coli to cope with acid stress during growth. Acetoin fermentation prevented lethal medium acidification by E. coli in lysogeny broth (LB) supplemented with glucose. It also supported growth and higher stationary-phase cell densities in acidified LB broth with glucose (pH 4.10 to 4.50) and in tomato juice (pH 4.40 to 5.00) and reduced the minimal pH at which growth could be initiated. On the other hand, the acetoin-producing strain was outcompeted by the nonproducer in a mixed-culture experiment at low pH, suggesting a fitness cost associated with acetoin production. Finally, we showed that acetoin production profoundly changes the appearance of E. coli on several diagnostic culture media. Natural E. coli strains that have laterally acquired budAB genes may therefore have escaped detection thus far. This study demonstrates the potential importance of acetoin fermentation in the ecology of E. coli in the food chain and contributes to a better understanding of the microbiological stability and safety of acidic foods.
doi:10.1128/AEM.01711-14
PMCID: PMC4178668  PMID: 25063653
6.  Two Complete and One Draft Genome Sequence of Nonproteolytic Clostridium botulinum Type E Strains NCTC 8266, NCTC 8550, and NCTC 11219 
Genome Announcements  2015;3(2):e00083-15.
Group II (gII) nonproteolytic Clostridium botulinum strains are a major cause of foodborne botulism outbreaks. Here, we report two complete genome sequences of gII type E strains NCTC 8266 and NCTC 8550 and one draft genome sequence of type E NCTC 11219.
doi:10.1128/genomeA.00083-15
PMCID: PMC4357750  PMID: 25767228
7.  Formate hydrogen lyase mediates stationary-phase deacidification and increases survival during sugar fermentation in acetoin-producing enterobacteria 
Two fermentation types exist in the Enterobacteriaceae family. Mixed-acid fermenters produce substantial amounts of lactate, formate, acetate, and succinate, resulting in lethal medium acidification. On the other hand, 2,3-butanediol fermenters switch to the production of the neutral compounds acetoin and 2,3-butanediol and even deacidify the environment after an initial acidification phase, thereby avoiding cell death. We equipped three mixed-acid fermenters (Salmonella Typhimurium, S. Enteritidis and Shigella flexneri) with the acetoin pathway from Serratia plymuthica to investigate the mechanisms of deacidification. Acetoin production caused attenuated acidification during exponential growth in all three bacteria, but stationary-phase deacidification was only observed in Escherichia coli and Salmonella, suggesting that it was not due to the consumption of protons accompanying acetoin production. To identify the mechanism, 34 transposon mutants of acetoin-producing E. coli that no longer deacidified the culture medium were isolated. The mutations mapped to 16 genes, all involved in formate metabolism. Formate is an end product of mixed-acid fermentation that can be converted to H2 and CO2 by the formate hydrogen lyase (FHL) complex, a reaction that consumes protons and thus can explain medium deacidification. When hycE, encoding the large subunit of hydrogenase 3 that is part of the FHL complex, was deleted in acetoin-producing E. coli, deacidification capacity was lost. Metabolite analysis in E. coli showed that introduction of the acetoin pathway reduced lactate and acetate production, but increased glucose consumption and formate and ethanol production. Analysis of a hycE mutant in S. plymuthica confirmed that medium deacidification in this organism is also mediated by FHL. These findings improve our understanding of the physiology and function of fermentation pathways in Enterobacteriaceae.
doi:10.3389/fmicb.2015.00150
PMCID: PMC4340222  PMID: 25762991
mixed-acid fermentation; 2; 3-butanediol fermentation; acid stress; hydrogenase 3; formate hydrogen lyase
8.  Genome Sequence of Serratia plymuthica RVH1, Isolated from a Raw Vegetable-Processing Line 
Genome Announcements  2014;2(1):e00021-14.
We announce the genome sequence of Serratia plymuthica strain RVH1, a psychroloterant strain that was isolated from a raw vegetable-processing line and that regulates the production of primary metabolites (acetoin and butanediol), antibiotics, and extracellular enzymes through quorum sensing.
doi:10.1128/genomeA.00021-14
PMCID: PMC3916479  PMID: 24503985
9.  The Zeamine Antibiotics Affect the Integrity of Bacterial Membranes 
The zeamines (zeamine, zeamine I, and zeamine II) constitute an unusual class of cationic polyamine-polyketide-nonribosomal peptide antibiotics produced by Serratia plymuthica RVH1. They exhibit potent bactericidal activity, killing a broad range of Gram-negative and Gram-positive bacteria, including multidrug-resistant pathogens. Examination of their specific mode of action and molecular target revealed that the zeamines affect the integrity of cell membranes. The zeamines provoke rapid release of carboxyfluorescein from unilamellar vesicles with different phospholipid compositions, demonstrating that they can interact directly with the lipid bilayer in the absence of a specific target. DNA, RNA, fatty acid, and protein biosynthetic processes ceased simultaneously at subinhibitory levels of the antibiotics, presumably as a direct consequence of membrane disruption. The zeamine antibiotics also facilitated the uptake of small molecules, such as 1-N-phenylnaphtylamine, indicating their ability to permeabilize the Gram-negative outer membrane (OM). The valine-linked polyketide moiety present in zeamine and zeamine I was found to increase the efficiency of this process. In contrast, translocation of the large hydrophilic fluorescent peptidoglycan binding protein PBDKZ-GFP was not facilitated, suggesting that the zeamines cause subtle perturbation of the OM rather than drastic alterations or defined pore formation. At zeamine concentrations above those required for growth inhibition, membrane lysis occurred as indicated by time-lapse microscopy. Together, these findings show that the bactericidal activity of the zeamines derives from generalized membrane permeabilization, which likely is initiated by electrostatic interactions with negatively charged membrane components.
doi:10.1128/AEM.03146-14
PMCID: PMC4292508  PMID: 25452285
10.  Isolation and Validation of an Endogenous Fluorescent Nucleoid Reporter in Salmonella Typhimurium 
PLoS ONE  2014;9(4):e93785.
In this study we adapted a Mud-based delivery system to construct a random yfp reporter gene (encoding the yellow fluorescent protein) insertion library in the genome of Salmonella Typhimurium LT2, and used fluorescence activated cell sorting and fluorescence microscopy to screen for translational fusions that were able to clearly and specifically label the bacterial nucleoid. Two such fusions were obtained, corresponding to a translational yfp insertion in iscR and iolR, respectively. Both fusions were further validated, and the IscR::YFP fluorescent nucleoid reporter together with time-lapse fluorescence microscopy was subsequently used to monitor nucleoid dynamics in response to the filamentation imposed by growth of LT2 at high hydrostatic pressure (40–45 MPa). As such, we were able to reveal that upon decompression the apparently entangled LT2 chromosomes in filamentous cells rapidly and efficiently segregate, after which septation of the filament occurs. In the course of the latter process, however, cells with a “trilobed” nucleoid were regularly observed, indicative for an imbalance between septum formation and chromosome segregation.
doi:10.1371/journal.pone.0093785
PMCID: PMC3973593  PMID: 24695782
12.  Does Virulence Assessment of Vibrio anguillarum Using Sea Bass (Dicentrarchus labrax) Larvae Correspond with Genotypic and Phenotypic Characterization? 
PLoS ONE  2013;8(8):e70477.
Background
Vibriosis is one of the most ubiquitous fish diseases caused by bacteria belonging to the genus Vibrio such as Vibrio (Listonella) anguillarum. Despite a lot of research efforts, the virulence factors and mechanism of V. anguillarum are still insufficiently known, in part because of the lack of standardized virulence assays.
Methodology/Principal Findings
We investigated and compared the virulence of 15 V. anguillarum strains obtained from different hosts or non-host niches using a standardized gnotobiotic bioassay with European sea bass (Dicentrarchus labrax L.) larvae as model hosts. In addition, to assess potential relationships between virulence and genotypic and phenotypic characteristics, the strains were characterized by random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (rep-PCR) analyses, as well as by phenotypic analyses using Biolog’s Phenotype MicroArray™ technology and some virulence factor assays.
Conclusions/Significance
Virulence testing revealed ten virulent and five avirulent strains. While some relation could be established between serotype, genotype and phenotype, no relation was found between virulence and genotypic or phenotypic characteristics, illustrating the complexity of V. anguillarum virulence. Moreover, the standardized gnotobiotic system used in this study has proven its strength as a model to assess and compare the virulence of different V. anguillarum strains in vivo. In this way, the bioassay contributes to the study of mechanisms underlying virulence in V. anguillarum.
doi:10.1371/journal.pone.0070477
PMCID: PMC3735585  PMID: 23936439
13.  Emergence and Stability of High-Pressure Resistance in Different Food-Borne Pathogens 
High hydrostatic pressure (HHP) processing is becoming a valuable nonthermal food pasteurization technique, although there is reasonable concern that bacterial HHP resistance could compromise the safety and stability of HHP-processed foods. While the degree of natural HHP resistance has already been shown to vary greatly among and within bacterial species, a still unresolved question remains as to what extent different food-borne pathogens can actually develop HHP resistance. In this study, we therefore examined and compared the intrinsic potentials for HHP resistance development among strains of Escherichia coli, Shigella flexneri, Salmonella enterica serovars Typhimurium and Enteritidis, Yersinia enterocolitica, Aeromonas hydrophila, Pseudomonas aeruginosa, and Listeria innocua using a selective enrichment approach. Interestingly, of all strains examined, the acquisition of extreme HHP resistance could be detected in only some of the E. coli strains, indicating that a specific genetic predisposition might be required for resistance development. Furthermore, once acquired, HHP resistance proved to be a very stable trait that was maintained for >80 generations in the absence of HHP exposure. Finally, at the mechanistic level, HHP resistance was not necessarily linked to derepression of the heat shock genes and was not related to the phenomenon of persistence.
doi:10.1128/AEM.00030-12
PMCID: PMC3346480  PMID: 22344661
14.  Variation of Intragenic Tandem Repeat Tract of tolA Modulates Escherichia coli Stress Tolerance 
PLoS ONE  2012;7(10):e47766.
In recent work we discovered that the intragenic tandem repeat (TR) region of the tolA gene is highly variable among different Escherichia coli strains. The aim of this study was therefore to investigate the biological function and dynamics of TR variation in E. coli tolA. The biological impact of TR variation was examined by comparing the ability of a set of synthetic tolA variants with in frame repeat copies varying from 2 to 39 to rescue the altered susceptibility of an E. coli ΔtolA mutant to deoxycholic acid, sodium dodecyl sulfate, hyperosmolarity, and infection with filamentous bacteriophage. Interestingly, although each of the TolA variants was able to at least partly rescue the ΔtolA mutant, the extent was clearly dependent on both the repeat number and the type of stress imposed, indicating the existence of opposing selective forces with regard to the optimal TR copy number. Subsequently, TR dynamics in a clonal population were assayed, and we could demonstrate that TR contractions are RecA dependent and enhanced in a DNA repair deficient uvrD background, and can occur at a frequency of 6.9×10−5.
doi:10.1371/journal.pone.0047766
PMCID: PMC3477136  PMID: 23094082
15.  Role of Lysozyme Inhibitors in the Virulence of Avian Pathogenic Escherichia coli 
PLoS ONE  2012;7(9):e45954.
Lysozymes are key effectors of the animal innate immunity system that kill bacteria by hydrolyzing peptidoglycan, their major cell wall constituent. Recently, specific inhibitors of the three major lysozyme families occuring in the animal kingdom (c-, g- and i-type) have been discovered in Gram-negative bacteria, and it has been proposed that these may help bacteria to evade lysozyme mediated lysis during interaction with an animal host. Escherichia coli produces two inhibitors that are specific for c-type lysozyme (Ivy, Inhibitor of vertebrate lysozyme; MliC, membrane bound lysozyme inhibitor of c-type lysozyme), and one specific for g-type lysozyme (PliG, periplasmic lysozyme inhibitor of g-type lysozyme). Here, we investigated the role of these lysozyme inhibitors in virulence of Avian Pathogenic E. coli (APEC) using a serum resistance test and a subcutaneous chicken infection model. Knock-out of mliC caused a strong reduction in serum resistance and in in vivo virulence that could be fully restored by genetic complementation, whereas ivy and pliG could be knocked out without effect on serum resistance and virulence. This is the first in vivo evidence for the involvement of lysozyme inhibitors in bacterial virulence. Remarkably, the virulence of a ivy mliC double knock-out strain was restored to almost wild-type level, and this strain also had a substantial residual periplasmic lysozyme inhibitory activity that was higher than that of the single knock-out strains. This suggests the existence of an additional periplasmic lysozyme inhibitor in this strain, and indicates a regulatory interaction in the expression of the different inhibitors.
doi:10.1371/journal.pone.0045954
PMCID: PMC3458809  PMID: 23049900
17.  Goose-Type Lysozyme Inhibitor (PliG) Enhances Survival of Escherichia coli in Goose Egg Albumen ▿  
Applied and Environmental Microbiology  2011;77(13):4697-4699.
The goose-type lysozyme inhibitor PliG enhances the survival of Escherichia coli in goose but not in chicken egg white, which contains goose- and chicken-type lysozymes, respectively. These results indicate that both the type of host lysozyme and the type of bacterial lysozyme inhibitor may affect bacterium-host interactions.
doi:10.1128/AEM.00427-11
PMCID: PMC3127702  PMID: 21602367
18.  Biological Approach to Modeling of Staphylococcus aureus High-Hydrostatic-Pressure Inactivation Kinetics▿  
Applied and Environmental Microbiology  2010;76(21):6982-6990.
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 <3.5 min. All strains showed tails. No significant differences in the inactivation rate were found during the log-linear death phase among the eight strains. The entry into stationary growth phase resulted both in an increase in shoulder length and in a decrease in the inactivation rate. However, whereas shoulder length proved to depend on sigma B factor activity, the inactivation rate did not. Recovery in anaerobiosis decreased the inactivation rate but did not affect the shoulder length. Addition of the minimum noninhibitory concentration of sodium chloride to the recovery medium resulted in a decrease in shoulder length and in an increase in the inactivation rate for stationary-growth-phase cells. In the tail region, up to 90% of the population remained sensitive to sodium chloride.
doi:10.1128/AEM.00900-10
PMCID: PMC2976245  PMID: 20817808
19.  Evidence for an evolutionary antagonism between Mrr and Type III modification systems 
Nucleic Acids Research  2011;39(14):5991-6001.
The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease with specificity for methylated DNA. While Mrr nuclease activity can be elicited by high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes distinct genotoxicity when expressed in Salmonella typhimurium LT2. Genetic screening enabled us to contribute this toxicity entirely to the presence of the endogenous Type III restriction modification system (StyLTI) of S. typhimurium LT2. The StyLTI system consists of the Mod DNA methyltransferase and the Res restriction endonuclease, and we revealed that expression of the LT2 mod gene was sufficient to trigger Mrr activity in E. coli MG1655. Moreover, we could demonstrate that horizontal acquisition of the MG1655 mrr locus can drive the loss of endogenous Mod functionality present in S. typhimurium LT2 and E. coli ED1a, and observed a strong anti-correlation between close homologues of MG1655 mrr and LT2 mod in the genome database. This apparent evolutionary antagonism is further discussed in the light of a possible role for Mrr as defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases.
doi:10.1093/nar/gkr219
PMCID: PMC3152355  PMID: 21504983
20.  Rapid Acquisition of Gigapascal-High-Pressure Resistance by Escherichia coli 
mBio  2011;2(1):e00130-10.
Pressure and temperature are important environmental variables that influence living systems. However, while they vary over a considerable range on Earth and other planets, it has hardly been addressed how straightforwardly and to what extent cellular life can acquire resistance to extremes of these parameters within a defined genomic context and a limited number of generations. Nevertheless, this is a very pertinent question with respect to the penetration of life in allegedly inhospitable environments. In this study, directed evolution was used to reveal the potential of the nonsporulating and mesophilic model bacterium Escherichia coli to develop the ability to survive exposure to high temperature or pressure. While heat resistance could only marginally be increased, our data show that piezoresistance could readily and reproducibly be extended into the GPa range, thereby greatly exceeding the currently recognized maximum for growth or survival.
IMPORTANCE
While extremophilic microorganisms generally serve as the reference for microbial survival capacities in inhospitable environments, we set out to examine how readily a mesophilic model bacterium such as Escherichia coli could build up resistance to extremes of temperature or pressure within a very short evolutionary time scale. Both heat and high pressure constitute ecologically important physical stresses that are able to irrevocably penetrate the entire cell. Our results for the first time establish that cellular life can acquire resistance to pressures extending into the GPa range.
doi:10.1128/mBio.00130-10
PMCID: PMC3025523  PMID: 21264062
21.  The Rcs Two-Component System Regulates Expression of Lysozyme Inhibitors and Is Induced by Exposure to Lysozyme▿  
Journal of Bacteriology  2009;191(6):1979-1981.
The Escherichia coli Rcs regulon is triggered by antibiotic-mediated peptidoglycan stress and encodes two lysozyme inhibitors, Ivy and MliC. We report activation of this pathway by lysozyme and increased lysozyme sensitivity when Rcs induction is genetically blocked. This lysozyme sensitivity could be alleviated by complementation with Ivy and MliC.
doi:10.1128/JB.01549-08
PMCID: PMC2648352  PMID: 19136591
22.  Detection of a Lysozyme Inhibitor in Proteus mirabilis by a New Reverse Zymogram Method▿  
Applied and Environmental Microbiology  2008;74(15):4978-4981.
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.
doi:10.1128/AEM.00219-08
PMCID: PMC2519368  PMID: 18539812
23.  Role of the Lysozyme Inhibitor Ivy in Growth or Survival of Escherichia coli and Pseudomonas aeruginosa Bacteria in Hen Egg White and in Human Saliva and Breast Milk▿  
Applied and Environmental Microbiology  2008;74(14):4434-4439.
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 104 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.
doi:10.1128/AEM.00589-08
PMCID: PMC2493159  PMID: 18515493
24.  A New Family of Lysozyme Inhibitors Contributing to Lysozyme Tolerance in Gram-Negative Bacteria 
PLoS Pathogens  2008;4(3):e1000019.
Lysozymes are ancient and important components of the innate immune system of animals that hydrolyze peptidoglycan, the major bacterial cell wall polymer. Bacteria engaging in commensal or pathogenic interactions with an animal host have evolved various strategies to evade this bactericidal enzyme, one recently proposed strategy being the production of lysozyme inhibitors. We here report the discovery of a novel family of bacterial lysozyme inhibitors with widespread homologs in gram-negative bacteria. First, a lysozyme inhibitor was isolated by affinity chromatography from a periplasmic extract of Salmonella Enteritidis, identified by mass spectrometry and correspondingly designated as PliC (periplasmic lysozyme inhibitor of c-type lysozyme). A pliC knock-out mutant no longer produced lysozyme inhibitory activity and showed increased lysozyme sensitivity in the presence of the outer membrane permeabilizing protein lactoferrin. PliC lacks similarity with the previously described Escherichia coli lysozyme inhibitor Ivy, but is related to a group of proteins with a common conserved COG3895 domain, some of them predicted to be lipoproteins. No function has yet been assigned to these proteins, although they are widely spread among the Proteobacteria. We demonstrate that at least two representatives of this group, MliC (membrane bound lysozyme inhibitor of c-type lysozyme) of E. coli and Pseudomonas aeruginosa, also possess lysozyme inhibitory activity and confer increased lysozyme tolerance upon expression in E. coli. Interestingly, mliC of Salmonella Typhi was picked up earlier in a screen for genes induced during residence in macrophages, and knockout of mliC was shown to reduce macrophage survival of S. Typhi. Based on these observations, we suggest that the COG3895 domain is a common feature of a novel and widespread family of bacterial lysozyme inhibitors in gram-negative bacteria that may function as colonization or virulence factors in bacteria interacting with an animal host.
Author Summary
Lysozyme is an ancient bactericidal enzyme that is part of the antibacterial defense system of vertebrate and invertebrate animals. Bacteria colonizing or infecting an animal host have developed various ways to overcome lysozyme action, a recently proposed mechanism being the production of lysozyme inhibitors. However, the only high affinity bacterial lysozyme inhibitor known thus far is produced only in few bacteria, and this raised questions about their wider relevance in bacteria–host interactions. We here report the discovery of a novel and distinct family of bacterial lysozyme inhibitors that is widely distributed among the Proteobacteria, including several major pathogens. The family comprises periplasmic as well as membrane-bound inhibitors, and both types contribute to lysozyme tolerance of bacterial cells, as we experimentally demonstrate for the periplasmic inhibitor from Salmonella Typhimurium and the membrane-bound inhibitors from Escherichia coli and Pseudomonas aeruginosa. Interestingly, a gene encoding one of the newly identified inhibitors has been previously found to promote macrophage survival of Salmonella Typhi. The widespread occurrence of lysozyme inhibitors in bacteria is likely to reflect their functional importance in a wide range of bacteria–host interactions. As such, they are also attractive novel targets for antibacterial drug development.
doi:10.1371/journal.ppat.1000019
PMCID: PMC2267010  PMID: 18369469
25.  Role of Quorum Sensing and Antimicrobial Component Production by Serratia plymuthica in Formation of Biofilms, Including Mixed Biofilms with Escherichia coli▿  
Applied and Environmental Microbiology  2006;72(11):7294-7300.
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.
doi:10.1128/AEM.01708-06
PMCID: PMC1636202  PMID: 16997989

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