Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography

Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.

Calponins Are Recruited to Actin-Rich Structures Generated by Pathogenic Escherichia coli, Listeria, and Salmonella

The ingestion of enteropathogenic Escherichia coli (EPEC), Listeria monocytogenes, or Salmonella enterica serovar Typhimurium leads to their colonization of the intestinal lumen, which ultimately causes an array of ailments ranging from diarrhea to bacteremia. Once in the intestines, these microbes generate various actin-rich structures to attach, invade, or move within the host intestinal epithelial cells. Although an assortment of actin-associated proteins has been identified to varying degrees at these structures, the localization of many actin stabilizing proteins have yet to be analyzed. Here, we examined the recruitment of the actin-associated proteins, calponin 1 and 2 at EPEC pedestals, L. monocytogenes actin clouds, comet tails and listeriopods, and S. Typhimurium membrane ruffles. In other systems, calponins are known to bind to and stabilize actin filaments. In EPEC pedestals, calponin 1 was recruited uniformly throughout the structures while calponin 2 was enriched at the apical tip. During L. monocytogenes infections, calponin 1 was found through all the actin-rich structures generated by the bacteria, while calponin 2 was only present within actin-rich structures formed by L. monocytogenes near the host cell membrane. Finally, both calponins were found within S. Typhimurium-generated membrane ruffles. Taken together, we have shown that although calponin 1 is recruited to actin-rich structures formed by the three bacteria, calponin 2 is specifically recruited to only membrane-bound actin-rich structures formed by the bacteria. Thus, our findings suggest that calponin 2 is a novel marker for membrane-bound actin structures formed by pathogenic bacteria. Anat Rec, 301:2103-2111, 2018. © 2018 Wiley Periodicals, Inc.

Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-κB

The closely related type III secretion system zinc metalloprotease effector proteins GtgA, GogA, and PipA are translocated into host cells during Salmonella infection. They then cleave nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) transcription factor subunits, dampening activation of the NF-κB signaling pathway and thereby suppressing host immune responses. We demonstrate here that GtgA, GogA, and PipA cleave a subset of NF-κB subunits, including p65, RelB, and cRel but not NF-κB1 and NF-κB2, whereas the functionally similar type III secretion system effector NleC of enteropathogenic and enterohemorrhagic Escherichia coli cleaved all five NF-κB subunits. Mutational analysis of NF-κB subunits revealed that a single nonconserved residue in NF-κB1 and NF-κB2 that corresponds to the P1' residue Arg-41 in p65 prevents cleavage of these subunits by GtgA, GogA, and PipA, explaining the observed substrate specificity of these enzymes. Crystal structures of GtgA in its apo-form and in complex with the p65 N-terminal domain explained the importance of the P1' residue. Furthermore, the pattern of interactions suggested that GtgA recognizes NF-κB subunits by mimicking the shape and negative charge of the DNA phosphate backbone. Moreover, structure-based mutational analysis of GtgA uncovered amino acids that are required for the interaction of GtgA with p65, as well as those that are required for full activity of GtgA in suppressing NF-κB activation. This study therefore provides detailed and critical insight into the mechanism of substrate recognition by this family of proteins important for bacterial virulence.

Characterization of the two conformations adopted by the T3SS inner-membrane protein PrgK

The pathogenic bacterium Salmonella enterica serovar Typhimurium utilizes two type III secretion systems (T3SS) to inject effector proteins into target cells upon infection. The T3SS secretion apparatus (the injectisome) is a large macromolecular assembly composed of over twenty proteins, many in highly oligomeric states. A sub-structure of the injectisome, termed the basal body, spans both membranes and the periplasmic space of the bacterium. It is primarily composed of three integral membranes proteins, InvG, PrgH, and PrgK, that form ring structures through which components are secreted. In particular, PrgK possesses a periplasmic region consisting of two globular domains joined by a linker polypeptide. We showed previously that in isolation, this region adopts two distinct conformations, of with only one is observed in the assembled basal body complex. Here, using NMR spectroscopy, we further characterize these two conformations. In particular, we demonstrate that the interaction of the linker region with the first globular domain, as found in the intact basal body, is dependent upon the cis conformation of the Leu77-Pro78 peptide. Furthermore, this interaction is pH-dependent due to coupling with hydrogen bond formation between Tyr75 and His42 in its neutral N^δ1 H tautomeric form. This pH-dependent interaction may play a role in the regulation of the secretion apparatus disassembly in the context of bacterial infection.

Regulation of the AcrAB-TolC efflux pump in Enterobacteriaceae

Bacterial multidrug efflux systems are a major mechanism of antimicrobial resistance and are fundamental to the physiology of Gram-negative bacteria. The resistance-nodulation-division (RND) family of efflux pumps is the most clinically significant, as it is associated with multidrug resistance. Expression of efflux systems is subject to multiple levels of regulation, involving local and global transcriptional regulation as well as post-transcriptional and post-translational regulation. The best-characterised RND system is AcrAB-TolC, which is present in Enterobacteriaceae. This review describes the current knowledge and new data about the regulation of the acrAB and tolC genes in Escherichia coli and Salmonella enterica.

Chemical, physical and morphological properties of bacterial biofilms affect survival of encased Campylobacter jejuni F38011 under aerobic stress

Campylobacter jejuni is a microaerophilic pathogen and leading cause of human gastroenteritis. The presence of C. jejuni encased in biofilms found in meat and poultry processing facilities may be the major strategy for its survival and dissemination in aerobic environment. In this study, Staphylococcus aureus, Salmonella enterica, or Pseudomonas aeruginosa was mixed with C. jejuni F38011 as a culture to form dual-species biofilms. After 4days' exposure to aerobic stress, no viable C. jejuni cells could be detected from mono-species C. jejuni biofilm. In contrast, at least 4.7logCFU/cm² of viable C. jejuni cells existed in some dual-species biofilms. To elucidate the mechanism of protection mode, chemical, physical and morphological features of biofilms were characterized. Dual-species biofilms contained a higher level of extracellular polymeric substances with a more diversified chemical composition, especially for polysaccharides and proteins, than mono-species C. jejuni biofilm. Structure of dual-species biofilms was more compact and their surface was >8 times smoother than mono-species C. jejuni biofilm, as indicated by atomic force microscopy. Under desiccation stress, water content of dual-species biofilms decreased slowly and remained at higher levels for a longer time than mono-species C. jejuni biofilm. The surface of all biofilms was hydrophilic, but total surface energy of dual-species biofilms (ranging from 52.5 to 56.2mJ/m²) was lower than that of mono-species C. jejuni biofilm, leading to more resistance to wetting by polar liquids. This knowledge can aid in developing intervention strategies to decrease the survival and dispersal of C. jejuni into foods or environment.

Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase

Aminoglycoside resistance is commonly conferred by enzymatic modification of drugs by aminoglycoside-modifying enzymes such as aminoglycoside nucleotidyltransferases (ANTs). Here, the first crystal structure of an ANT(3'')(9) adenyltransferase, AadA from Salmonella enterica, is presented. AadA catalyses the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. The structure was solved using selenium SAD phasing and refined to 2.5 Å resolution. AadA consists of a nucleotidyltransferase domain and an α-helical bundle domain. AadA crystallizes as a monomer and is a monomer in solution as confirmed by small-angle X-ray scattering, in contrast to structurally similar homodimeric adenylating enzymes such as kanamycin nucleotidyltransferase. Isothermal titration calorimetry experiments show that ATP binding has to occur before binding of the aminoglycoside substrate, and structure analysis suggests that ATP binding repositions the two domains for aminoglycoside binding in the interdomain cleft. Candidate residues for ligand binding and catalysis were subjected to site-directed mutagenesis. In vivo resistance and in vitro binding assays support the role of Glu87 as the catalytic base in adenylation, while Arg192 and Lys205 are shown to be critical for ATP binding.

The giant adhesin SiiE of Salmonella enterica

Salmonella enterica is a Gram-negative, food-borne pathogen, which colonizes the intestinal tract and invades enterocytes. Invasion of polarized cells depends on the SPI1-encoded type III secretion system (T3SS) and the SPI4-encoded type I secretion system (T1SS). The substrate of this T1SS is the non-fimbrial giant adhesin SiiE. With a size of 595 kDa, SiiE is the largest protein of the Salmonella proteome and consists of 53 repetitive bacterial immunoglobulin (BIg) domains, each containing several conserved residues. As known for other T1SS substrates, such as E. coli HlyA, Ca²⁺ ions bound by conserved D residues within the BIg domains stabilize the protein and facilitate secretion. The adhesin SiiE mediates the first contact to the host cell and thereby positions the SPI1-T3SS to initiate the translocation of a cocktail of effector proteins. This leads to actin remodeling, membrane ruffle formation and bacterial internalization. SiiE binds to host cell apical membranes in a lectin-like manner. GlcNAc and α2–3 linked sialic acid-containing structures are ligands of SiiE. Since SiiE shows repetitive domain architecture, we propose a zipper-like binding mediated by each individual BIg domain. In this review, we discuss the characteristics of the SPI4-T1SS and the giant adhesin SiiE.

[Mutagenesis of cysteine residues in dptC from Salmonella enteric serovar Cerro 87 and its effects on DNA phosphorothioate modification]

OBJECTIVE

DNA phosphorothioate modification (DNA sulfur modification, a non-bridging oxygen swapped with a sulfur) exists in diverse bacteria. Salmonella enterica serovar Cerro 87 is one of the bacteria that harbor the DNA sulfur modification. The modification is carried out by the products of a four-membered gene cluster, dptBCDE. Transformation of Escherichia coli DH10B with the dptBCDE gene cluster endows the strain with DNA sulfur modification capability. Deletion of dptC abolished the modification. Here, we studied the function of dptC in DNA sulfur modification.

METHODS

Six cysteine residues in dptC were mutated individually within the dptBCDE gene cluster. Mutants were then tested for DNA sulfur modification.

RESULTS

Among the 6 cysteine mutations (C39, C146, C262, C273, C280, and C283), 5 abolished DNA modification except for C39, suggesting that C146, C262, C273, C280, and C283 are essential for DNA sulfur modification. Sequence alignment shows that these five cysteine residues are conserved among different strains.

CONCLUSION

Mutation at anyone of C146, C262, C273, C280 and C283 of dptC abolished DNA modification. Our results shed light on further study of DNA sulfur modification biochemical pathway.

Polythiophene synthesis coupled to quartz crystal microbalance and Raman spectroscopy for detecting bacteria

A simple electrochemical procedure was used for the synthesis of a polythiophene containing para-benzenesulfonyl chloride groups. The obtained polymer was shown to be very reactive and directly able to covalently bind nucleophile biomolecules. Protein A and a specific antibody were then successively immobilized on the conductive polymer through a covalent bonding of Protein A with the as-prepared linker for bacteria trapping purpose. All reactions were controlled in situ by cyclic voltammetry, quartz crystal microbalance and Raman spectroscopy. The results were compared to those previously obtained on gold surface modified with the same chemical linker. The conductive polymer led to a very high rate of antibody recognition compared to the gold surface and to literature, probably due to a large available surface obtained after polymerization. One example of pathogenic bacteria "Salmonella enterica paratyphi" detection was successfully tested on the substrates. The presented results are promising for the future design of simple and inexpensive immunocapture-based sensors.

The PduQ enzyme is an alcohol dehydrogenase used to recycle NAD+ internally within the Pdu microcompartment of Salmonella enterica

Salmonella enterica uses a bacterial microcompartment (MCP) for coenzyme B(12)-dependent 1,2-propanediol (1,2-PD) utilization (Pdu). The Pdu MCP consists of a protein shell that encapsulates enzymes and cofactors required for metabolizing 1,2-PD as a carbon and energy source. Here we show that the PduQ protein of S. enterica is an iron-dependent alcohol dehydrogenase used for 1,2-PD catabolism. PduQ is also demonstrated to be a new component of the Pdu MCP. In addition, a series of in vivo and in vitro studies show that a primary function of PduQ is to recycle NADH to NAD(+) internally within the Pdu MCP in order to supply propionaldehyde dehydrogenase (PduP) with its required cofactor (NAD(+)). Genetic tests determined that a pduQ deletion mutant grew slower than wild-type Salmonella on 1,2-PD and that this phenotype was not complemented by a non-MCP associated Adh2 from Zymomonas that catalyzes the same reaction. This suggests that PduQ has a MCP-specific function. We also found that a pduQ deletion mutant had no growth defect in a genetic background having a second mutation that prevents MCP formation which further supports a MCP-specific role for PduQ. Moreover, studies with purified Pdu MCPs demonstrated that the PduQ enzyme can convert NADH to NAD(+) to supply the PduP reaction in vitro. Cumulatively, these studies show that the PduQ enzyme is used to recycle NADH to NAD(+) internally within the Pdu MCP. To our knowledge, this is the first report of internal recycling as a mechanism for cofactor homeostasis within a bacterial MCP.

Receptor-independent interaction of bacterial lipopolysaccharide with lipid and lymphocyte membranes; the role of cholesterol

Lipopolysaccharide (LPS) is a major constituent of bacterial outer membranes where it makes up the bulk of the outer leaflet and plays a key role as determinant of bacterial interactions with the host. Membrane-free LPS is known to activate T-lymphocytes through interactions with Toll-like receptor 4 via multiprotein complexes. In the present study, we investigate the role of cholesterol and membrane heterogeneities as facilitators of receptor-independent LPS binding and insertion, which underpin bacterial interactions with the host in symbiosis, pathogenesis and cell invasion. We use fluorescence spectroscopy to investigate the interactions of membrane-free LPS from intestinal Gram-negative organisms with cholesterol-containing model membranes and with T-lymphocytes. LPS preparations from Klebsiella pneumoniae and Salmonella enterica were found to bind preferentially to mixed lipid membranes by comparison to pure PC bilayers. The same was observed for LPS from the symbiote Escherichia coli but with an order of magnitude higher dissociation constant. Insertion of LPS into model membranes confirmed the preference for sphimgomyelin/cholesterol-containing systems. LPS insertion into Jurkat T-lymphocyte membranes reveals that they have a significantly greater LPS-binding capacity by comparison to methyl-β-cyclodextrin cholesterol-depleted lymphocyte membranes, albeit at slightly lower binding rates.

Microelectrode array biosensor for studying carbohydrate-mediated interactions

Carbohydrate-mediated host-pathogen interactions are essential to bacterial and viral pathogenesis, and represent an attractive target for the development of antiadhesives to prevent infection. We present a versatile microelectrode array-based platform to investigate carbohydrate-mediated protein and bacterial binding, with the objective of developing a generalizable method for screening inhibitors of host-microbe interactions. Microelectrode arrays are well suited for interrogating biological binding events, including proteins and whole-cells, and are amenable to electrochemical derivitization, facilitating rapid deposition of biomolecules. In this study, we achieve microelectrode functionalization with carbohydrates via controlled polymerization of pyrrole to individual microelectrodes, followed by physisorption of neoglycoconjugates to the polypyrrole-coated electrodes. Bioactivity of the immobilized carbohydrates was confirmed with carbohydrate-binding proteins (lectins) detected by both fluorescent and electrochemical means. The platform's ability to analyze whole-cell binding was demonstrated using strains of Escherichia coli and Salmonella enterica, and the dose-dependent inhibition of S. enterica by a soluble carbohydrate antiadhesive.

Modification of the BAX Salmonella test kit to include a hot start functionality (modification of AOAC Official Method 2003.09)

In 2010, the BAX System PCR assay for Salmonella was modified to include a hot start functionality designed to keep the reaction enzyme inactive until PCR begins. To validate the assay's Official Methods of Analysis status to include this procedure modification, an evaluation was conducted on four food types that were simultaneously analyzed with the BAX System and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual or the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook reference method for detecting Salmonella. Identical performance between the BAX System method and the reference methods was observed. Additionally, lysates were analyzed using both the BAX System Classic and BAX System Q7 instruments with identical results using both platforms for all samples tested. Of the 100 samples analyzed, 34 samples were positive for both the BAX System and reference methods, and 66 samples were negative by both the BAX System and reference methods, demonstrating 100% correlation. No instrument platform variation was observed. Additional inclusivity and exclusivity testing using the modified test kit demonstrated the test kit to be 100% accurate in evaluation of test panels of 352 Salmonella strains and 46 non-Salmonella strains.

A new rapid and micro-scale hydrolysis, using triethylamine citrate, for lipopolysaccharide characterization by mass spectrometry

Endotoxin (lipopolysaccharide, LPS) is, in general, composed of two moieties: a hydrophilic polysaccharide linked to a hydrophobic lipid A terminal unit and forms a major surface component of gram-negative bacteria. The structural features of LPS moieties play a role in pathogenesis and also involve immunogenicity and diagnostic serology. The major toxic factor of LPS resides in the lipid A moiety, anchored in the outer layer of the bacterium, and its relative biological activity is critically related to fine structural features within the molecule. In establishing relationships between structural features and biological activities of LPS it is of the utmost importance to develop new analytical methods that can be applied to the complete unambiguous characterization of a specific LPS molecule. Herein is presented a practical rapid and sensitive analytical procedure for the mass spectral screening of LPS using triethylamine citrate as an agent for both disaggregation and mild hydrolysis of LPS. It provides improved matrix-assisted laser desorption/ionization (MALDI) mass spectra and, in particular, affords the identification of fragments retaining labile substituents present in the native macromolecular LPS structures. The methods were developed and applied using purified LPS of Escherichia coli and Salmonella enterica, as well as more complex LPS of Actnobacillus pleuropneumoniae.

Structural insight into the rotational switching mechanism of the bacterial flagellar motor

Structural analysis of a clockwise-biased rotation mutant of the bacterial flagellar rotor protein FliG provides a new model for the arrangement of FliG subunits in the motor, and novel insights into rotation switching.

The bacterial flagellar motor can rotate either clockwise (CW) or counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are required for rapid switching between the CW and CCW directions. Switching is achieved by a conformational change in FliG induced by the binding of a chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of three domains, FliG_N, FliG_M, and FliG_C, and forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body. Crystal structures have been reported for the FliG_MC domains of Thermotoga maritima, which consist of the FliG_M and FliG_C domains and a helix E that connects these two domains, and full-length FliG of Aquifex aeolicus. However, the basis for the switching mechanism is based only on previously obtained genetic data and is hence rather indirect. We characterized a CW-biased mutant (fliG(ΔPAA)) of Salmonella enterica by direct observation of rotation of a single motor at high temporal and spatial resolution. We also determined the crystal structure of the FliG_MC domains of an equivalent deletion mutant variant of T. maritima (fliG(ΔPEV)). The FliG(ΔPAA) motor produced torque at wild-type levels under a wide range of external load conditions. The wild-type motors rotated exclusively in the CCW direction under our experimental conditions, whereas the mutant motors rotated only in the CW direction. This result suggests that wild-type FliG is more stable in the CCW state than in the CW state, whereas FliG(ΔPAA) is more stable in the CW state than in the CCW state. The structure of the TM-FliG_MC(ΔPEV) revealed that extremely CW-biased rotation was caused by a conformational change in helix E. Although the arrangement of FliG_C relative to FliG_M in a single molecule was different among the three crystals, a conserved FliG_M-FliG_C unit was observed in all three of them. We suggest that the conserved FliG_M-FliG_C unit is the basic functional element in the rotor ring and that the PAA deletion induces a conformational change in a hinge-loop between FliG_M and helix E to achieve the CW state of the FliG ring. We also propose a novel model for the arrangement of FliG subunits within the motor. The model is in agreement with the previous mutational and cross-linking experiments and explains the cooperative switching mechanism of the flagellar motor.

The bacterial flagellum is a rotating organelle that governs cell motility. At the base of each flagellum is a motor powered by the electrochemical potential difference of specific ions across the cytoplasmic membrane. In response to environmental stimuli, rotation of the motor switches between counterclockwise and clockwise, with a corresponding effect on the swimming direction of the cell. Switching is triggered by the binding of the signaling protein phospho-CheY to FliM and FliN, and achieved by conformational changes in the rotor protein FliG. The actual switching mechanism, however, remains unclear. In this study, we characterized a fliG mutant of Salmonella that shows an extreme clockwise-biased rotation, and determined the structure of a fragment of FliG (FliG_MC) of the equivalent mutant variant of Thermotoga maritima. FliG_MC is composed of two domains and covers the regions essential for torque generation and FliM binding. We showed that the mutant structure has a conformational change in the helix connecting the two domains, leading to a domain orientation distinct from that of the wild-type FliG. On the basis of this structure, we propose a new model for the arrangement of FliG subunits in the rotor that is consistent with the previous mutational studies and explains how cooperative switching occurs in the motor.

Two efficient methods for the conjugation of smooth-form lipopolysaccharides with probes bearing hydrazine or amino groups. I. LPS activation with cyanogen bromide

This chapter presents a conjugation method for coupling probes bearing hydrazine or primary amino groups to a smooth(S)-form lipopolysaccharide (LPS). LPS is modified by the activation of the hydroxyl groups present in its O-antigen moiety with cyanogen bromide in aqueous acetone. The method yields conjugates with good labeling ratios, preserving the endotoxic activity of the lipid A moiety. Conjugation of smooth-form LPS from Salmonella enterica sv. Minnesota with dansyl hydrazine and horseradish -peroxidase yields labeling ratios above 300 nmol dansyl per mg LPS, with nearly no loss of the original endotoxin activity. In the case of horseradish peroxidase, introducing a spacer, a ratio of 28 nmol HRP per mg LPS is obtained, preserving 65% of the original endotoxic activity.

Two efficient methods for the conjugation of smooth-form lipopolysaccharides with probes bearing hydrazine or amino groups. II. LPS activation with a cyanopyridinium agent

This chapter presents a conjugation method for coupling probes bearing hydrazine or primary amino groups to a lipopolysaccharide (LPS). LPS is modified by the activation of the hydroxyl groups present in its O-antigen moiety with 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP). The method yields conjugates with good labeling ratios, preserving the endotoxic activity of the lipid A moiety. Conjugation of smooth-form LPS from Salmonella enterica sv. Minnesota with dansyl hydrazine and horseradish peroxidase yields labeling ratios above 110 nmol dansyl/mg LPS, with nearly no loss of the original endotoxic activity. In the case of horseradish peroxidase, introducing a spacer, a ratio of 29 nmol HRP/mg LPS was obtained, preserving 65% of the original endotoxic activity and an enzymatic activity of 120 U/mg.

Real-time reverse-transcriptase polymerase chain reaction for the rapid detection of Salmonella using invA primers

Recent outbreaks of Salmonella linked to fresh produce emphasize the need for rapid detection methods to help control the spread of disease. Reverse-transcriptase polymerase chain reaction (RT-PCR) can detect the presence of mRNA (shorter half-life than DNA) with greater potential for detecting viable pathogens. The chromosomally located invA gene required for host invasion by Salmonella is widely used for detection of this pathogen by PCR. Detection of Salmonella was undertaken by real-time RT-PCR (rt-RT-PCR) using newly designed invA gene primers to develop a sensitive and specific assay. Salmonella serovars Typhimurium and Enteritidis were grown (7.68 log(10) CFU/mL) in Luria-Bertani broth overnight at 37 degrees C, and RNA was extracted, followed by rt-RT-PCR with and without SYBR green I and agarose gel electrophoresis. All experiments were replicated at least thrice. Detection for both serovars using traditional RT-PCR was lower ( approximately 10(5) CFU/mL) than rt-RT-PCR (10(3) CFU/mL) by gel electrophoresis. Melt curve analysis showed melt temperatures at 87.5 degrees C with Ct values from 12 to 15 for up to 10(3) CFU/mL and improved to 10(2) CFU/mL after further optimization. Further, addition of RNA internal amplification control constructed using in vitro transcription with a T7 RNA polymerase promoter, to the RT-PCR assay also gave detection limits of 10(2) CFU/mL. Cross-reactivity was not observed against a panel of 21 non-Salmonella bacteria. Heat-inactivated (autoclaved) Salmonella showed faint or no detection by rt-RT-PCR or gel electrophoresis. This method has potential to be applied for the detection of Salmonella serovars in fresh produce and the simultaneous detection of foodborne viral (RNA viruses) and bacterial pathogens in a multiplex format.

TRANSIA PLATE Salmonella Gold. Performance Tested Method 010602

A study was conducted to determine the efficacy of detecting low contamination levels of Salmonella in peanut butter using TRANSIA PLATE Salmonella Gold (TPSG). This study was conducted under the AOAC Emergency Response Validation program. A set of samples was each analyzed by the TPSG method and the U.S. Food and Drug Administration's Bacteriological Analytical Manual reference method. Among the 45 total samples and controls, 26 were positive by the TPSG and 24 were positive by the reference method. Statistical analyses of these unpaired samples indicated that for all levels analyzed, the difference between the TPSG and reference method results were not statistically different at the 5% level.

Singlepath Salmonella. Performance Tested Method 060401

Singlepath Salmonella is an immunochromatographic (lateral flow) assay for the presumptive qualitative detection of Salmonella spp. in food. A previous AOAC Performance Tested Method study evaluated Singlepath Salmonella as an effective method for the detection of Salmonella spp. in the following selected foods: dried skimmed milk, black pepper, dried pet food, desiccated coconut, cooked peeled frozen prawns, raw ground beef, and raw ground turkey. In this Emergency Response Validation extension, creamy peanut butter was inoculated with S. enterica. ser. Typhimurium. For low contamination level (1.08 CFU/25 g), a Chi-square value of 0.5 indicated that there was no significant difference between Singlepath Salmonella and the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) reference method. For high-level and uninoculated control there was 100% agreement between the methods.

Foodproof Salmonella Detection Kit. Performance Tested Method 120301

The foodproof Salmonella Detection Kit was previously validated in the Performance Tested Methods program for the detection of Salmonella species in a variety of foods, including milk powder, egg powder, coconut, cocoa powder, chicken breast, minced meat, sliced sausage, sausage, smoked fish, pasta, white pepper, cumin, dough, wet pet food, dry pet food, ice cream, watermelon, sliced cabbage, food dye, and milk chocolate. The method was shown to be equivalent to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) and the U.S. Department of Agriculture, Food Safety and Inspection Service's Microbiology Laboratory Guidebook reference culture procedures. In the first Emergency Response Validation (ERV) extension study, peanut butter was inoculated with S. enterica. ser Typhimurium. For the low inoculation level (1.08 CFU/25 g), a Chi-square value of 2.25 indicated that there was no significant performance difference between the foodproof Salmonella Detection Kit and the FDA-BAM reference method. For high-level inoculation (11.5 CFU/25 g) and uninoculated control, there was 100% agreement between the methods. In the second ERV extension study, peanut butter was inoculated with S. enterica. ser Typhimurium. For both inoculation levels (0.1 and 0.5 CFU/25 g by most probable number), Chi-square values of 0 indicated that there was no significant performance difference between foodproof Salmonella Detection Kit and the FDA-BAM reference method.

iQ-Check Salmonella II: real-time polymerase chain reaction test kit. Performance Tested Method 010803

iQ-Check Salmonella II is a real-time PCR kit for detection of Salmonella in foods. Specific oligonucleotide probes are used to detect target DNA during the amplification, by hybridizing to the amplicons. These probes are linked to a fluorophore, which fluoresces only when hybridized to the target sequence. As part of an Emergency Response Validation due to a massive outbreak and subsequent recall, peanut butter was tested to compare the performance of iQ-Check Salmonella II to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) reference method for detection of Salmonella. A single enrichment in buffered peptone water was used for a reduced enrichment time of 21 +/- 1 h over the 48 h reference method. There was no significant difference in the performance of the iQ-Check kit when compared to the FDA-BAM method, as determined by Chi-square analysis. All samples identified as positive by iQ-Check were confirmed by reference method protocol.

1-2 Test

A study was conducted to determine the efficacy of detecting low contamination levels of Salmonella in peanut butter using the 1-2 Test. This study was conducted under the AOAC Research Institute Emergency Response Validation program. A set of samples was analyzed by the 1-2 Test and the U.S. Food and Drug Administration's Bacteriological Analytical Manual reference method. Among the 90 total samples and controls, 32 samples were positive by the 1-2 Test and the reference method. Statistical analyses of these paired samples indicated that for all levels analyzed, the difference between the 1-2 Test and reference method results were not statistically different at the 5% level.

RAPID'Salmonella chromogenic medium. Performance Tested Method 050701

RAPID'Salmonella is a chromogenic medium for isolation and detection of Salmonella spp. in food, based on two enzymatic activities. All presumptive Salmonella-positive colonies are magenta, including lactose-positive Salmonella. S. Typhi, and S. Paratyphi serotypes, due to detection of C8 esterase activity. In order to differentiate Salmonella from other Enterobacteriaceae, the medium includes a second chromogenic substrate. As part of an Emergency Response Validation due to a massive outbreak and subsequent recall, peanut butter was tested to compare the performance of RAPID'Salmonella to the U.S. Food and Drug Administration's Bacteriological Analytical Manual reference method for detection of Salmonella. Sensitivity and specificity for RAPID'Salmonella were 100%.

TaqMan Salmonella enterica Detection Kit. Performance Tested Method 020803

Peanut butter spiked with Salmonella enterica ser. Typhimurium was prepared by an independent laboratory and sent to Applied Biosystems to determine the sensitivity and specificity of the TaqMan Salmonella enterica Detection Kit for detecting Salmonella in peanut butter. The samples were spiked at three levels: five no-spike (0 CFU/25 g); 20 low-spike (0.2 CFU/25 g); and 20 high-spike (2 CFU/25 g). They were coded to create a blind set of 45 samples. The samples were processed based on an unpaired test design that included enrichment in buffered peptone water for the candidate method and lactose broth for the reference method. In the candidate method, a 1 mL aliquot of enriched sample was extracted using PrepMan Ultra Sample Preparation Reagent; the sample was amplified on the Applied Biosystems 7500 real-time PCR system, and analyzed for detection of Salmonella using RapidFinder Version 1.0 software. All samples processed by the candidate method were confirmed by culture according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual procedures. Sensitivity, specificity, and Chi-square analysis were calculated by combining candidate method results with those of the reference method that were collected by the independent laboratory. The TaqMan Salmonella enterica Detection Kit showed 40% sensitivity, 100% specificity, and a Chi-square value equal to 1.52. Chi-square analysis indicated the candidate method and the reference method were comparable. Although the candidate method sensitivity was only 40% when compared with the reference method (unpaired samples), the sensitivity was > 100% when the candidate method results were compared with those of the confirmation method (same sample enrichment).

DuPont Qualicon BAX System polymerase chain reaction assay. Performance Tested Method 100201

A recent outbreak of Salmonella in peanut butter has highlighted the need for validation of rapid detection methods. A multilaboratory study for detecting Salmonella in peanut butter was conducted as part of the AOAC Research Institute Emergency Response Validation program for methods that detect outbreak threats to food safety. Three sites tested spiked samples from the same master mix according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) method and the BAX System method. Salmonella Typhimurium (ATCC 14028) was grown in brain heart infusion for 24 h at 37 degrees C, then diluted to appropriate levels for sample inoculation. Master samples of peanut butter were spiked at high and low target levels, mixed, and allowed to equilibrate at room temperature for 2 weeks. Spike levels were low [1.08 most probable number (MPN)/25 g]; high (11.5 MPN/25 g) and unspiked to serve as negative controls. Each master sample was divided into 25 g portions and coded to blind the samples. Twenty portions of each spiked master sample and five portions of the unspiked sample were tested at each site. At each testing site, samples were blended in 25 g portions with 225 mL prewarmed lactose broth until thoroughly homogenized, then allowed to remain at room temperature for 55-65 min. Samples were adjusted to a pH of 6.8 +/- 0.2, if necessary, and incubated for 22-26 h at 35 degrees C. Across the three reporting laboratories, the BAX System detected Salmonella in 10/60 low-spike samples and 58/60 high-spike samples. The reference FDA-BAM method yielded positive results for 11/60 low-spike and 58/60 high-spike samples. Neither method demonstrated positive results for any of the 15 unspiked samples.

CHROMagar Salmonella Detection Test Kit. Performance Tested Method 020502

BBL CHROMagar Salmonella was evaluated by an external food testing laboratory for the recovery of Salmonella in peanut butter using the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) procedure. The peanut butter was found to be negative for the presence of Salmonella and, therefore, was seeded with heat-stressed Salmonella at target concentrations of 0.2 and 2 CFU/25 g. The Salmonella-seeded samples remained at room temperature for 14 days before analysis to stabilize the Salmonella in the food environment. Twenty 25 g test portions from each seeded level and five 25 g samples of uninoculated control samples were processed using enrichment broths as outlined in the FDA-BAM procedure. BBL CHROMagar Salmonella-prepared plates were evaluated with the FDA reference method media (bismuth sulfite, xylose lysine desoxycholate, and Hektoen enteric agars). Fractionally positive results were obtained from the lower inoculum level of peanut butter samples. Five positive cultures were recovered from both the BBL CHROMagar Salmonella and reference methods. The two methods gave identical results for all cultures resulting in a method agreement of 100%. McNemar's chi2 test, which assesses the evidence for difference in marginal proportions between two methods, could not be evaluated because it requires one or more discrepant cultures. However, because there were no discrepant cultures, the marginal proportions for the two methods were identical; therefore, there is no evidence of a difference between the methods. This study demonstrates that the results from BBL CHROMagar Salmonella are comparable to the three reference method media for the detection of Salmonella in peanut butter using the FDA-BAM procedures.

Intracellular concentrations of enrofloxacin in quinolone-resistant Salmonella enterica subspecies enterica serovar Choleraesuis

The emergence of fluoroquinolone-resistant strains of Salmonella enterica subspecies enterica serovar Choleraesuis is an important concern in several countries, including Japan. We examined the intracellular concentration of enrofloxacin in S. Choleraesuis to determine the existence of a relationship with the emergence of quinolone resistance. The intracellular concentration of enrofloxacin was significantly lower in nalidixic acid-resistant isolates compared with nalidixic acid-susceptible isolates. In the presence of carbonyl cyanide m-chlorophenylhydrazone, the intracellular concentration of enrofloxacin increased in all isolates, with no significant difference in the intracellular concentration between nalidixic acid-susceptible and -resistant isolates. The frequency of emergence of fluoroquinolone-resistant mutants was higher in susceptible isolates with a low intracellular concentration of enrofloxacin. The results presented suggest that a decrease in the intracellular concentration of enrofloxacin is related to active efflux pumps and contributes to the emergence of fluoroquinolone resistance.

Rapid classification and identification of salmonellae at the species and subspecies levels by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry

Variations in the mass spectral profiles of multiple housekeeping proteins of 126 strains representing Salmonella enterica subsp. enterica (subspecies I), S. enterica subsp. salamae (subspecies II), S. enterica subsp. arizonae (subspecies IIIa), S. enterica subsp. diarizonae (subspecies IIIb), S. enterica subsp. houtenae (subspecies IV), and S. enterica subsp. indica (subspecies VI), and Salmonella bongori were analyzed to obtain a phylogenetic classification of salmonellae based on whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometric bacterial typing. Sinapinic acid produced highly informative spectra containing a large number of biomarkers and covering a wide molecular mass range (2,000 to 40,000 Da). Genus-, species-, and subspecies-identifying biomarker ions were assigned on the basis of available genome sequence data for Salmonella, and more than 200 biomarker peaks, which corresponded mainly to abundant and highly basic ribosomal or nucleic acid binding proteins, were selected. A detailed comparative analysis of the biomarker profiles of Salmonella strains revealed sequence variations corresponding to single or multiple amino acid changes in multiple housekeeping proteins. The resulting mass spectrometry-based bacterial classification was very comparable to the results of DNA sequence-based methods. A rapid protocol that allowed identification of Salmonella subspecies in minutes was established.

Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery

The small regulatory protein Crl binds to sigmaS, the RNA polymerase stationary phase sigma factor. Crl facilitates the formation of the sigmaS-associated holoenzyme (EsigmaS) and thereby activates sigmaS-dependent genes. Using a real time surface plasmon resonance biosensor, we characterized in greater detail the specificity and mode of action of Crl. Crl specifically forms a 1:1 complex with sigmaS, which results in an increase of the association rate of sigmaS to core RNA polymerase without any effect on the dissociation rate of EsigmaS. Crl is also able to associate with preformed EsigmaS with a higher affinity than with sigmaS alone. Furthermore, even at saturating sigmaS concentrations, Crl significantly increases EsigmaS association with the katN promoter and the productive isomerization of the EsigmaS-katN complex, supporting a direct role of Crl in transcription initiation. Finally, we show that Crl does not bind to sigma70 itself but is able at high concentrations to form a weak and transient 1:1 complex with both core RNA polymerase and the sigma70-associated holoenzyme, leaving open the possibility that Crl might also exert a side regulatory role in the transcriptional activity of additional non-sigmaS holoenzymes.

A group of Escherichia coli and Salmonella enterica O antigens sharing a common backbone structure

The O-antigen moiety of the LPS is one of the most variable cell surface components of the Gram-negative bacterial outer membrane. Variation is due to the presence of different sugars and sugar linkages. Here, it is reported that a group of Escherichia coli O serogroups (O17, O44, O73, O77 and O106), and the Salmonella enterica serogroup O : 6,14 (H), share a common four-sugar backbone O-subunit structure, and possess almost identical O-antigen gene clusters. Whereas the E. coli O77 antigen does not have any substitutions, the other O antigens in this group differ by the addition of one or two glucose side branches at various positions of the backbone. The O-antigen gene clusters for all members of the group encode only the proteins required for biosynthesis of the common four-sugar backbone. The identification of three genes within a putative prophage in the E. coli O44 genome is also reported; these genes are presumably involved in the glucosylation of the basic tetrasaccharide unit. This was confirmed by deletion of one of the genes, which encodes a putative glucosyltransferase. Structural analysis of the O antigen produced by the mutant strain demonstrated the absence of glucosylation. An O-antigen structure shared by five E. coli and one S. enterica serogroups, all of which have a long evolutionary history, suggests that the common backbone may be important for the survival of E. coli strains in the environment, or for their pathogenicity.

Crystal structure of a novel prokaryotic Ser/Thr kinase and its implication in the Cpx stress response pathway

The Cpx signalling system of Escherichia coli and Salmonella enterica senses extracytoplasmic stress and controls expression of factors that allow the bacterium to adapt to these stressors and thereby enhance survival. Many of the Cpx-responsive genes products are of unknown function. We determined the crystal structure of one of these gene products, called YihE in E. coli, which exhibits a eukaryotic kinase fold. Functional assays established that both YihE and the S. enterica YihE homologue, RdoA, undergo autophosphorylation and phosphorylate protein substrates at Ser/Thr residues in vitro, demonstrating that YihE/RdoA is a novel Ser/Thr protein kinase in prokaryotic cells. Phenotypic analysis of yihE/rdoA null strains indicates that this kinase is most abundant in stationary phase, and is important for long-term cell survival and for expression of surface appendages in both a Cpx-independent and -dependent manner. YihE/RdoA is therefore a previously unknown kinase component of a new type of bacterial phosphorelay mechanism, adding kinase activity as another response to the Cpx sensing system that functions to maintain cellular homeostasis.

The role of cellulose and O-antigen capsule in the colonization of plants by Salmonella enterica

Numerous salmonellosis outbreaks have been associated with vegetables, in particular sprouted seed. Thin aggregative fimbriae (Tafi), a component of the extracellular matrix responsible for multicellular behavior, are important for Salmonella enterica attachment and colonization of plants. Here, we demonstrate that the other surface polymers composing the extracellular matrix, cellulose, and O-antigen capsule also play a role in colonization of plants. Mutations in bacterial cellulose synthesis (bcsA) and O-antigen capsule assembly and translocation (yihO) reduced the ability to attach to and colonize alfalfa sprouts. A colanic acid mutant was unaffected in plant attachment or colonization. Tafi, cellulose synthesis, and O-antigen capsule, all of which contribute to attachment and colonization of plants, are regulated by AgfD, suggesting that AgfD is a key regulator for survival outside of hosts of Salmonella spp. The cellulose biosynthesis regulator adrA mutant was not affected in the ability to attach to or colonize plants; however, promoter probe assays revealed expression by cells attached to alfalfa sprouts. Furthermore, quantitative reverse-transcriptase polymerase chain reaction revealed differential expression of agfD and adrA between planktonic and plant-attached cells. In addition, there was no correlation among mutants between biofilm formation in culture and attachment to plants. Outside of animal hosts, S. enterica appears to rely on an arsenal of adhesins to persist on plants, which can act as vectors and perpetuate public health concerns.

Biophysical Characterization of the Interaction of Endotoxins with Hemoglobins

Bacterial endotoxin (lipopolysaccharide, LPS) is the major component of the outer leaflet of the outer membrane in gram-negative bacteria. During severe infections, bacteria may reach the blood circuit of humans, and endotoxins may be released from the bacteria due to cell division or cell death. In particular enterobacterial forms of LPS represent extremely strong activator molecules of the human immune system causing a rapid induction of cytokine production in monocytes and macrophages. Various mammalian blood proteins have been documented to display LPS binding activities mediating normally decreasing effects in the biological activity of LPS. In more recent studies, the essential systemic oxygen transportation protein hemoglobin (Hb) has been shown to amplify LPS-induced cytokine production on immune cells. The mechanism responsible for this effect is poorly understood. Here, we characterize the interaction of hemoglobin with LPS by using biophysical methods. The data presented, revealing the changes of the type and size of supramolecular aggregates of LPS in the presence of Hb, allow a better understanding of the hemoglobin-induced increase in bioactivity of LPS.

Compensatory evolution reveals functional interactions between ribosomal proteins S12, L14 and L19

Certain mutations in S12, a ribosomal protein involved in translation elongation rate and translation accuracy, confer resistance to the aminoglycoside streptomycin. Previously we showed in Salmonella typhimurium that the fitness cost, i.e. reduced growth rate, due to the amino acid substitution K42N in S12 could be compensated by at least 35 different mutations located in the ribosomal proteins S4, S5 and L19. Here, we have characterized in vivo the fitness, translation speed and translation accuracy of four different L19 mutants. When separated from the resistance mutation located in S12, the three different compensatory amino acid substitutions in L19 at position 40 (Q40H, Q40L and Q40R) caused a decrease in fitness while the G104A change had no effect on bacterial growth. The rate of protein synthesis was unaffected or increased by the mutations at position 40 and the level of read-through of a UGA nonsense codon was increased in vivo, indicating a loss of translational accuracy. The mutations in L19 increased sensitivity to aminoglycosides active at the A-site, further indicating a perturbation of the decoding step. These phenotypes are similar to those of the classical S4 and S5 ram (ribosomal ambiguity) mutants. By evolving low-fitness L19 mutants by serial passage, we showed that the fitness cost conferred by the L19 mutations could be compensated by additional mutations in the ribosomal protein L19 itself, in S12 and in L14, a protein located close to L19. Our results reveal a novel functional role for the 50 S ribosomal protein L19 during protein synthesis, supporting published structural data suggesting that the interaction of L14 and L19 with 16 S rRNA could influence function of the 30 S subunit. Moreover, our study demonstrates how compensatory fitness-evolution can be used to discover new molecular functions of ribosomal proteins.

The FliN-FliH interaction mediates localization of flagellar export ATPase FliI to the C ring complex

FliH regulates the flagellar export ATPase FliI, preventing nonproductive ATP hydrolysis. FliH has been shown to stably associate with the C ring protein FliN. Analysis of this complex reveals that FliH is required for FliI localization to the C ring, and thus FliH not only inhibits FliI ATPase activity but also may act to target FliI to the basal body. Quantitative binding studies revealed a KD of 110 nM for FliH binding to FliN. The KD for FliH binding of a FliN variant from a temperature-sensitive nonflagellate fliN point mutant was determined to be 270 nM, suggesting a molecular explanation for its phenotype. Another variant FliN from a temperature-sensitive mutant with a different phenotype displayed binding with an intermediate affinity. Weak export activity in a fliN null mutant was greatly increased by overproduction of FliI, mimicking a previously observed FliH bypass effect and supporting the conclusion that FliN-FliH binding is important for localization of FliI to the C ring and thus the membrane-embedded export apparatus beyond. A model incorporating the present findings is presented.

Biofilm-associated proteins

Although exopolysaccharides are important and often essential compounds of the biofilm matrix, recent evidences suggest that a group of surface proteins plays a leading role during the development of the microbial communities. The first member of this group of proteins was described in a Staphylococcus aureus bovine mastitis isolate and was named Bap, for biofilm-associated protein. Later on, other surface proteins homologous to Bap and involved in biofilm development have been described in many gram-positive and gram-negative bacteria. In this review, we have summarized our knowledge about three members of this group of proteins: Bap of S. aureus, Esp of Enterococcus faecalis and BapA of Salmonella enterica ser. Enteritidis.

Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted beta strand displacement mechanism

Gram-negative pathogens commonly use the chaperone-usher pathway to assemble adhesive multisubunit fibers on their surface. In the periplasm, subunits are stabilized by a chaperone that donates a beta strand to complement the subunits' truncated immunoglobulin-like fold. Pilus assembly proceeds through a "donor-strand exchange" (DSE) mechanism whereby this complementary beta strand is replaced by the N-terminal extension (Nte) of an incoming pilus subunit. Using X-ray crystallography and real-time electrospray ionization mass spectrometry (ESI-MS), we demonstrate that DSE requires the formation of a transient ternary complex between the chaperone-subunit complex and the Nte of the next subunit to be assembled. The process is crucially dependent on an initiation site (the P5 pocket) needed to recruit the incoming Nte. The data also suggest a capping reaction displacing DSE toward product formation. These results support a zip-in-zip-out mechanism for DSE and a catalytic role for the usher, the molecular platform at which pili are assembled.

Differentiation of outer membrane proteins from Salmonellaenterica serotypes using Fourier transform infrared spectroscopy and chemometrics

AIMS

To differentiate between outer membrane proteins (OMPs) from six Salmonellaenterica serotypes using a Fourier transform infrared (FTIR) spectroscopy method and chemometrics.

METHODS AND RESULTS

The OMPs from Salmonella serotypes (Typhimurium, Enteritidis, Thomasville, Hadar, Seftenberg and Brandenburg) were isolated using a sarcosyl extraction method. OMP profiles on SDS-PAGE exhibited two or three bands between 48 and 54 kDa. Spectra of 10 microl of OMP preparations (5 mg ml(-1)) dried on a gold reflective slide were collected using 128 scans at 4 cm(-1) resolution and units of log (1/R) and analyzed using canonical variate analysis (CVA) and linear discriminant analysis (LDA). The CVA of Salmonella OMP spectra in the 1800-1500 cm(-1) region separated the serotypes and LDA provided a 100% correct classification.

CONCLUSIONS

The use of a FTIR method combined with chemometrics provided better differentiation of Salmonella OMPs than the OMP pattern analysis by SDS-PAGE.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to demonstrate that spectra of OMP extracts from Salmonella serotypes can be used for 100% correct classification of the serotypes studied.

A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites

A comprehensive method of quantifying intracellular metabolite concentrations would be a valuable addition to the arsenal of tools for holistic biochemical studies. Here, we describe a step toward the development of such method: a quantitative assay for 90 nitrogen-containing cellular metabolites. The assay involves reverse-phase high-performance liquid chromatography separation followed by electrospray ionization and detection of the resulting ions using triple-quadrupole mass spectrometry in selected reaction monitoring mode. For 79 of the 90 metabolites, the assay is linear with a limit of detection of 10 ng/mL or less. Using this method, 36 metabolites can be reliably detected in extracts of the bacterium Salmonella enterica, with the identity of each metabolite confirmed by the presence, on growing of the bacteria in (13)C-glucose, of a peak corresponding to the isotope-labeled form of the compound. Quantitation in biological samples is performed by mixing unlabeled test cell extract with (13)C-labeled standard extract, and determining the (12)C/(13)C-ratio for each metabolite. Using this approach, the metabolomes of growing (exponential phase) and carbon-starved (stationary phase) bacteria were compared, revealing 16 metabolites that are significantly down-regulated and five metabolites that are significantly up-regulated, in stationary phase.

Improved cell typing by charge-state deconvolution of matrix-assisted laser desorption/ionization mass spectra

Robust, specific, and rapid identification of toxic strains of bacteria and viruses, to guide the mitigation of their adverse health effects and optimum implementation of other response actions, remains a major analytical challenge. This need has driven the development of methods for classification of microorganisms using mass spectrometry, particularly matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), that allows high-throughput analyses with minimum sample preparation. We describe a novel approach to cell typing based on pattern recognition of MALDI mass spectra, which involves charge-state deconvolution in conjunction with a new correlation analysis procedure. The method is applicable to both prokaryotic and eukaryotic cells. Charge-state deconvolution improves the quantitative reproducibility of spectra because multiply charged ions resulting from the same biomarker attaching a different number of protons are recognized and their abundances are combined. This allows a clearer distinction of bacterial strains or of cancerous and normal liver cells. Improved class distinction provided by charge-state deconvolution was demonstrated by cluster spacing on canonical variate score charts and by correlation analyses. Deconvolution may enhance detection of early disease state or therapy progress markers in various tissues analyzed by MALDI-MS.

Structural and biological characterization of highly purified hepta-acyl lipid A present in the lipopolysaccharide of the Salmonella enterica sv. Minnesota Re deep rough mutant strain R595

One major component of the Salmonella enterica sv. Minnesota Re deep rough mutant (strain R595) lipopolysaccharide is hepta-acyl lipid A (LA(hepta)). In a recent publication [Tanamoto K-I, Azumi S. Salmonella-type heptaacylated lipid A is inactive and acts as an antagonist of lipopolysaccharide action on human line cells. J Immunol 2000; 164: 3149-3156] the corresponding synthetic hepta-acyl lipid A (compound 516) was reported to be agonistically inactive but to rather suppress pro-inflammatory activation by the endotoxic hexa-acyl lipid A (LA(hexa), compound 506) and S-form LPS from Escherichia coli in the human macrophage-like cell lines THP-1 and U937. These results, however, were in contrast to previous findings with human mononuclear cells (hMNC) isolated from peripheral blood, in which compound 516 was found to be an agonist, expressing low, but significant, cytokine-inducing activity as compared to LA(hexa). We have investigated the structure of natural LA(hepta) from the S. enterica sv. Minnesota Re deep rough mutant strain (R595) by TLC immunoblot, MALDI-TOF mass spectrometry and NMR spectroscopy. Using these techniques, the structural identity between LA(hepta) and the synthetic compound 516 was confirmed. In corroboration of previous findings with studies employing compound 516, purified LA(hepta) was found to induce the production of TNF-alpha, IL-1beta and IL-6 in hMNC, thus displaying moderate agonistic activity. Furthermore, we showed that LA(hepta) agonistically activated nuclear translocation of NF-kappaB in THP-1 cells, thus clearly ruling out the possibility that LA(hepta) is an antagonist and that its biological activity is influenced by the type of human myeloid cells used for testing endotoxicity (hMNC versus THP-1 cells).

Chaperone release and unfolding of substrates in type III secretion

Type III protein secretion systems are essential virulence factors of many bacteria pathogenic to humans, animals and plants. These systems mediate the transfer of bacterial virulence proteins directly into the host cell cytoplasm. Proteins are thought to travel this pathway in a largely unfolded manner, and a family of customized cytoplasmic chaperones, which specifically bind cognate secreted proteins, are essential for secretion. Here we show that InvC, an ATPase associated with a Salmonella enterica type III secretion system, has a critical function in substrate recognition. Furthermore, InvC induces chaperone release from and unfolding of the cognate secreted protein in an ATP-dependent manner. Our results show a similarity between the mechanisms of substrate recognition by type III protein secretion systems and AAA + ATPase disassembly machines.

Ultrahigh-Throughput Proteomics Using Fast RPLC Separations with ESI-MS/MS

We describe approaches for proteomics analysis using electrospray ionization-tandem mass spectrometry coupled with fast reversed-phase liquid chromatography (RPLC) separations. The RPLC separations used 50-microm-i.d. fused-silica capillaries packed with submicrometer-sized C18-bonded porous silica particles and achieved peak capacities of 130-420 for analytes from proteome tryptic digests. When these separations were combined with linear ion trap tandem mass spectrometry measurements, approximately 1000 proteins could be identified in 50 min from approximately 4000 identified tryptic peptides; approximately 550 proteins in 20 min from approximately 1800 peptides; and approximately 250 proteins in 8 min from approximately 700 peptides for a S. oneidensis tryptic digest. The dynamic range for protein identification with the fast separations was determined to be approximately 3-4 orders of magnitude of relative protein abundance on the basis of known proteins in human blood plasma analyses. We found that 55% of the MS/MS spectra acquired during the entire analysis (and up to 100% of the MS/MS spectra acquired from the most data-rich zone) provided sufficient quality for identifying peptides. The results confirm that such analyses using very fast (minutes) RPLC separations based on columns packed with microsized porous particles are primarily limited by the MS/MS analysis speed.

Rapid phenotypic characterization of Salmonella enterica strains by pyrolysis metastable atom bombardment mass spectrometry with multivariate statistical and artificial neural network pattern recognition

Pyrolysis mass spectrometry was investigated for rapid characterization of bacteria. Spectra of Salmonella were compared to their serovars, pulsed-field gel electrophoresis (PFGE) patterns, antibiotic resistance profiles, and MIC values. Pyrolysis mass spectra generated via metastable atom bombardment were analyzed by multivariate principal component-discriminant analysis and artificial neural networks (ANNs). Spectral patterns developed by discriminant analysis and tested with Leave-One-Out (LOO) cross-validation distinguished Salmonella strains by serovar (97% correct) and by PFGE groups (49%). An ANN model of the same PFGE groups was cross-validated, using the LOO rule, with 92% agreement. Using an ANN, thirty previously unseen spectra were correctly classified by serotype (97%) and at the PFGE level (67%). Attempts by ANN to model spectra grouped by resistance profile-but ignoring PFGE or serotype-failed (10% correct), but ANNs differentiating ten samples of the same serotype/PFGE class were more successful. To assess the information content of PyMS data serendipitously associated with or directly related to resistance character, the ten isolates were grouped into four, three, or two categories. The four categories corresponded to four resistance profiles. The four class and three class ANNs showed much improved but insufficient modeling power. The two-class ANN and a corresponding multivariate model maximized inferential power for a coarse antibiotic-resistance-related distinction. They each cross-validated by LOO at 90%. This is the first direct correlation of pyrolysis metastable atom bombardment mass spectrometry with immunological (e.g. serology) or molecular biology (e.g. PFGE) based techniques.

Structural and genetic characterization of enterohemorrhagic Escherichia coli O145 O antigen and development of an O145 serogroup-specific PCR assay

Enterohemorrhagic Escherichia coli O145 strains are emerging as causes of hemorrhagic colitis and hemolytic uremic syndrome. In this study, we present the structure of the E. coli O145 O antigen and the sequence of its gene cluster. The O145 antigen has repeat units containing three monosaccharide residues: 2-acetamido-2-deoxy-D-glucose (GlcNAc), 2-acetamidoylamino-2,6-dideoxy-L-galactose, and N-acetylneuraminic acid. It is very closely related to Salmonella enterica serovar Touera and S. enterica subsp. arizonae O21 antigen. The E. coli O145 gene cluster is located between the JUMPStart sequence and the gnd gene and consists of 15 open reading frames. Putative genes for the synthesis of the O-antigen constituents, for sugar transferase, and for O-antigen processing were annotated based on sequence similarities and the presence of conserved regions. The putative genes located in the E. coli O145 O-antigen gene cluster accounted for all functions expected for synthesis of the structure. An E. coli O145 serogroup-specific PCR assay based on the genes wzx and wzy was also developed by screening E. coli and Shigella isolates of different serotypes.

Fluorescence measurements of free [Mg2+] by use of mag-fura 2 in Salmonella enterica

The Mg2+ fluorescent dye mag-fura 2, entrapped in cells or organelles, has frequently been used for dual excitation ratio-metric determinations of free ionic Mg2+ concentrations in eukaryotic, mostly mammalian cells. Here we report its successful application to measure free Mg2+ concentrations ([Mg2+]i) in Salmonella enterica cells. When kept in nominally Mg2+ free buffer (resting conditions), the [Mg2+]i of wild-type cells has been determined to be 0.9 mM. An increase in the external Mg2+ concentration ([Mg2+]e) resulted in a rapid increase of [Mg2+]i, saturating within a few seconds at about 1.5 mM with [Mg2+]e of 20 mM. In contrast, cells lacking the Mg2+ transport proteins CorA, MgtA, MgtB failed to show this rapid increase. Instead, their [Mg2+]i increased steadily over extended periods of time and saturated at concentrations below those of wild-type cells. Mg2+ uptake rates increased more than 15-fold when corA was overexpressed in these mutant cells. Uptake of Mg2+ into corA expressing cells was strongly stimulated by nigericin, which increased the membrane potential DeltaPsi at the expense of DeltapH, and drastically reduced by valinomycin, which decreased the membrane potential DeltaPsi. These results reveal mag-fura 2 as a useful indicator to measure steady-state [Mg2+]i values in resting bacterial cells and to determine Mg2+ uptake rates. They confirm the role of CorA as the major Mg2+ transport protein and reveal the membrane potential as driving force for Mg2+ uptake into S. enterica cells.

Mucosal immunization with purified flagellin from Salmonella induces systemic and mucosal immune responses in C3H/HeJ mice

This study investigated the immune response elicited in C3H/HeJ mice after oral, parenteral and nasal immunization with purified flagellin from Salmonella enterica serovar Enteritidis alone or conjugated to starch microparticles as adjuvant or together with the uptake-enhancer recombinant cholera toxin B-subunit (rCTB). Systemic (IgM-IgG, IgA, IgG2a, IgG2b, IgG1) and local (s-IgA) humoral immune responses in the mice were analyzed using enzyme-linked immunosorbent assays (ELISA). Primed splenocytes were also stimulated in vitro with flagellin and the supernatants analyzed for cytokine production. Finally, immunized mice were challenged orally with live Salmonella. A high flagellin-specific IgM-IgG response was seen in all groups, especially in mice immunized nasally with flagellin plus rCTB or subcutaneously, but a strong systemic antibody response was also induced when free antigen was given orally. Intranasal or subcutaneous immunization of mice with flagellin plus rCTB or oral immunization with flagellin plus microparticles resulted in a significantly greater mucosal response (higher s-IgA titers in feces) than seen in the control group (P <0.05). The mucosal IgA responses were significantly correlated with the serum IgA titers. The subclass profile in serum revealed a mixed Th1/Th2-type response, with a predominance of Th1-type, as indicated by the subclass ratio (IgG1/IgG2a + IgG2b). The splenocytes stimulated in vitro produced interferon (IFN)-gamma, at levels, which increased with time. The group immunized with flagellin plus rCTB subcutaneously had a relatively higher IFN-gamma response than the other groups. Interleukin (IL)-2 was also produced, especially in mice immunized nasally or subcutaneously with flagellin conjugated to microparticles. However, neither IL-4 nor IL-5 was produced in any of the groups. After oral challenge with live serovar Enteritidis, the groups immunized orally or nasally with free flagellin had significantly lower degree of infection than the control group (P <0.05).