Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes

Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting Staphylococcus aureus Cas9 (SauCas9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13-AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13-AcrIIA15 as unique bifunctional inhibitors of SauCas9.

The first confirmed detection of Staphylococcus argenteus in the Czech Republic

Staphylococcus argenteus (S. argenteus) is a novel species of coagulase-positive staphylococci described in 2015. This species is phenotypically highly similar and genetically closely related to Staphylococcus aureus (S. aureus). Until recently, differentiation was only possible by molecular genetic methods, multilocus sequence typing and whole-genome sequencing, which are not generally used in routine laboratories due to time-consumingness and expensiveness. A major improvement in the identification of S. argenteus is the application of MALDI-TOF MS, if the available updated mass spectrum reference database is used. In the short report, we would like to present the first confirmed S. argenteus strain isolated from a patient in the Czech Republic and probably the first published S. argenteus strain in Central and Eastern Europe.

Identification and structural characterization of a novel myeloperoxidase inhibitor from Staphylococcus delphini

Staphylococcus aureus and related species are highly adapted to their hosts and have evolved numerous strategies to evade the immune system. S. aureus shows resistance to killing following uptake into the phagosome, which suggests that the bacterium evades intracellular killing mechanisms used by neutrophils. We recently discovered an S. aureus protein (SPIN for Staphylococcal Peroxidase INhibitor) that binds to and inhibits myeloperoxidase (MPO), a major player in the oxidative defense of neutrophils. To allow for comparative studies between multiple SPIN sequences, we identified a panel of homologs from species closely related to S. aureus. Characterization of these proteins revealed that SPIN molecules from S. agnetis, S. delphini, S. schleiferi, and S. intermedius all bind human MPO with nanomolar affinities, and that those from S. delphini, S. schleiferi, and S. intermedius inhibit human MPO in a dose-dependent manner. A 2.4 Å resolution co-crystal structure of SPIN-delphini bound to recombinant human MPO allowed us to identify conserved structural features of SPIN proteins, and to propose sequence-dependent physical explanations for why SPIN-aureus binds human MPO with higher affinity than SPIN-delphini. Together, these studies expand our understanding of MPO binding and inhibition by a recently identified component of the staphylococcal innate immune evasion arsenal.

Kinetics of volatile marker compounds during ripening of cured loins inoculated with Staphylococcus carnosus

BACKGROUND

The current study was designed to investigate the influence of ripening time (12 weeks, 15 °C) on the volatile compounds and sensory acceptance for North European cured loins inoculated with a proteolytic Staphylococcus carnosus starter culture.

RESULTS

The results demonstrated that the trend of volatile compounds, sensory acceptance and proteolytic activity increased during a ripening of 7 to 9 weeks. A further ripening led to a plateau phase for sensory attributes and aroma-relevant volatile compounds such as benzaldehyde, nonanone and acetophenone. The inoculation of the proteolytic S. carnosus LTH 3838 significantly increased aroma-relevant volatile compounds (3-methylbutanal, benzaldehyde, acetophenone, 1-octen-3-ol) and sensory acceptance up to a score 3.5 and 3.6 for the overall odour and taste by week 9. In addition, compounds such as nonanal, hexanal, 2-pentanone and nonanone, which originate from lipid oxidation, were significantly limited by S. carnosus LTH 3838.

CONCLUSION

A ripening time of 7 to 9 weeks seems to be an optimal period for the production of aroma intensive smoked North European cured loins. © 2016 Society of Chemical Industry.

Natural selenium particles from Staphylococcus carnosus: Hazards or particles with particular promise?

Various bacteria, including diverse Staphylococci, reduce selenite to yield red selenium particles with diameters in the high nanometer to low micrometer range. Formation and accumulation of such particles in bacteria often results in cell death, triggered by a loss of thiols and formation of disruptive deposits inside the cell. Hence certain pathogenic bacteria are rather sensitive to the presence of selenite, whilst other organisms, such as small nematodes, do not employ this kind of nanotechnology, yet become affected by micromolar concentrations of such naturally generated materials. Selenium particles extracted from cultures of Staphylococcus carnosus and apparently stabilized by their natural protein coating, for instance, show considerable activity against the nematode Steinernema feltiae, Escherichia coli and Saccaromyces cerevisiae. Such natural nano- and micro-particles are also more active than mechanically generated selenium particles and may be applied as antimicrobial materials in Medicine and Agriculture.

Role of Ionic Strength in Staphylococcal Cell Aggregation

Cell aggregation plays a key role in biofilm formation and pathogenesis of Staphylococcus species. Although the molecular basis of aggregation in Staphylococci has already been extensively investigated, the influence of environmental factors, such as ionic strength, remains poorly understood. In this paper, we report a new type of cellular aggregation of Staphylococci that depends solely on ionic strength. Seven strains out of 14, all belonging to staphylococcal species, formed large cell clusters within minutes in buffers of ionic strength ranging from 1.5 to 50 mM, whereas isolates belonging to other Gram-positive species did not display this phenotype. Atomic force microscopy (AFM) with chemically functionalized tips provided direct evidence that ionic strength modulates cell surface adhesive properties through changes in cell surface charge. The optimal ionic strength for aggregation was found to be strain dependent, but in all cases, bacterial aggregates formed at an ionic strength of 1.5-50 mM were rapidly dispersed in a solution of higher ionic strength, indicating a reversibility of the cell aggregation process. These findings suggest that some staphylococcal isolates can respond to ionic strength as an external stimulus to trigger rapid cell aggregation in a way that has not yet been reported.

Data-collection strategy for challenging native SAD phasing

Recent improvements in data-collection strategies have pushed the limits of native SAD (single-wavelength anomalous diffraction) phasing, a method that uses the weak anomalous signal of light elements naturally present in macromolecules. These involve the merging of multiple data sets from either multiple crystals or from a single crystal collected in multiple orientations at a low X-ray dose. Both approaches yield data of high multiplicity while minimizing radiation damage and systematic error, thus ensuring accurate measurements of the anomalous differences. Here, the combined use of these two strategies is described to solve cases of native SAD phasing that were particular challenges: the integral membrane diacylglycerol kinase (DgkA) with a low Bijvoet ratio of 1% and the large 200 kDa complex of the CRISPR-associated endonuclease (Cas9) bound to guide RNA and target DNA crystallized in the low-symmetry space group C2. The optimal native SAD data-collection strategy based on systematic measurements performed on the 266 kDa multiprotein/multiligand tubulin complex is discussed.

Characterization of Staphylococcus caprae Clinical Isolates Involved in Human Bone and Joint Infections, Compared with Goat Mastitis Isolates

Staphylococcus caprae is an emerging microorganism in human bone and joint infections (BJI). The aim of this study is to describe the features of S. caprae isolates involved in BJI (H for human) compared with those of isolates recovered in goat mastitis (A for animal). Fourteen isolates of each origin were included. Identifications were performed using a Vitek 2 GP ID card, tuf gene sequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Vitek MS. Molecular typing was carried out using pulsed-field gel electrophoresis (PFGE) and DiversiLab technology. The crystal violet method was used to determine biofilm-forming ability. Virulence factors were searched by PCR. Vitek MS technology provides an accurate identification for the two types of isolates compared to that of gold-standard sequencing (sensitivity, 96.4%), whereas the Vitek 2 GP ID card was more effective for H isolates. Molecular typing methods revealed two distinct lineages corresponding to the origin despite few overlaps: H and A. In our experimental conditions, no significant difference was observed in biofilm production ability between H and A isolates. Nine isolates (5 H isolates and 4 A isolates) behaved as weak producers while one A isolate was a strong producer. Concerning virulence factors, the autolysin atlC and the serine aspartate adhesin (sdrZ) genes were detected in 24 isolates (86%), whereas the lipase gene was always detected, except in one H isolate (96%). The ica operon was present in 23 isolates (82%). Fibrinogen-binding (fbe) or collagen-binding (cna) genes were not detected by using primers designed for Staphylococcus aureus or Staphylococcus epidermidis, even in low stringency conditions. Although S. caprae probably remains underestimated in human infections, further studies are needed to better understand the evolution and the adaptation of this species to its host.

Contribution of Adsorbed Protein Films to Nanoscopic Vibrations Exhibited by Bacteria Adhering through Ligand-Receptor Bonds

Bacteria adhering to surfaces exhibit nanoscopic vibrations that depend on the viscoelasticity of the bond. The quantification of the nanoscopic vibrations of bacteria adhering to surfaces provides new opportunities to better understand the properties of the bond through which bacteria adhere and the mechanisms by which they resist detachment. Often, however, bacteria do not adhere to bare surfaces but to adsorbed protein films, on which adhesion involves highly specific ligand-receptor binding next to nonspecific DLVO interaction forces. Here we determine the contribution of adsorbed salivary protein and fibronectin films to vibrations exhibited by adhering streptococci and staphylococci, respectively. The streptococcal strain used has the ability to adhere to adsorbed salivary proteins films through antigen I/II ligand-receptor binding, while the staphylococcal strain used adheres to adsorbed fibronectin films through a proteinaceous ligand-receptor bond. In the absence of ligand-receptor binding, electrostatic interactions had a large impact on vibration amplitudes of adhering bacteria on glass. On an adsorbed salivary protein film, vibration amplitudes of adhering streptococci depended on the film softness as determined by QCM-D and were reduced after film fixation using glutaraldehyde. On a relatively stiff fibronectin film, cross-linking the film in glutaraldehyde hardly reduced its softness, and accordingly fibronectin film softness did not contribute to vibration amplitudes of adhering staphylococci. However, fixation of the staphylococcus-fibronectin bond further decreased vibration amplitudes, while fixation of the streptococcus bond hardly impacted vibration amplitudes. Summarizing, this study shows that both the softness of adsorbed protein films and the properties of the bond between an adhering bacterium and an adsorbed protein film play an important role in bacterial vibration amplitudes. These nanoscopic vibrations reflect the viscoelasticity of the bacterial bond with a substratum and play important roles in bacterial adhesion, detachment and susceptibility to antimicrobials.

Visualizing the indefinable: three-dimensional complexity of 'infectious diseases'

Background

The words ‘infection’ and ‘inflammation’ lack specific definitions. Here, such words are not defined. Instead, the ability to visualize host-microbial interactions was explored.

Methods

Leukocyte differential counts and four bacterial species (Staphylococcus aureus, Streptococcus dysgalactiae, Staphylococcus chromogenes, and Escherichia coli) were determined or isolated in a cross-sectional and randomized study conducted with 611 bovine milk samples. Two paradigms were evaluated: (i) the classic one, which measures non-structured (count or percent) data; and (ii) a method that, using complex data structures, detects and differentiates three-dimensional (3D) interactions among lymphocytes (L), macrophages (M), and neutrophils (N).

Results

Classic analyses failed to differentiate bacterial-positive (B+) from –negative (B−) observations: B− and B+ data overlapped, even when statistical significance was achieved. In contrast, the alternative approach showed distinct patterns, such as perpendicular data inflections, which discriminated microbial-negative/mononuclear cell-predominating (MCP) from microbial-positive/phagocyte-predominating (PP) subsets. Two PP subcategories were distinguished, as well as PP/culture-negative (false-negative) and MCP/culture-positive (false-positive) observations. In 3D space, MCP and PP subsets were perpendicular to one another, displaying ≥91% specificity or sensitivity. Findings supported five inferences: (i) disease is not always ruled out by negative bacterial tests; (ii) low total cell counts can coexist with high phagocyte percents; (iii) neither positive bacterial isolation nor high cell counts always coincide with PP profiles; (iv) statistical significance is not synonymous with discrimination; and (v) hidden relationships cannot be detected when simple (non-structured) data formats are used and statistical analyses are performed before data subsets are identified, but can be uncovered when complexity is investigated.

Conclusions

Pattern recognition-based assessments can detect host-microbial interactions usually unobserved. Such cutoff-free, confidence interval-free, gold standard-free approaches provide interpretable information on complex entities, such as ‘infection’ and ‘inflammation’, even without definitions. To investigate disease dynamics, combinations of observational and experimental longitudinal studies, on human and non-human infections, are recommended.

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

The CRISPR/Cas9 system is a robust genome editing technology that works in human cells, animals and plants based on the RNA-programmed DNA cleaving activity of the Cas9 enzyme. Building on previous work (Jinek et al., 2013), we show here that new genetic information can be introduced site-specifically and with high efficiency by homology-directed repair (HDR) of Cas9-induced site-specific double-strand DNA breaks using timed delivery of Cas9-guide RNA ribonucleoprotein (RNP) complexes. Cas9 RNP-mediated HDR in HEK293T, human primary neonatal fibroblast and human embryonic stem cells was increased dramatically relative to experiments in unsynchronized cells, with rates of HDR up to 38% observed in HEK293T cells. Sequencing of on- and potential off-target sites showed that editing occurred with high fidelity, while cell mortality was minimized. This approach provides a simple and highly effective strategy for enhancing site-specific genome engineering in both transformed and primary human cells.

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

The CRISPR/Cas9 system is a robust genome editing technology that works in human cells, animals and plants based on the RNA-programmed DNA cleaving activity of the Cas9 enzyme. Building on previous work (Jinek et al., 2013), we show here that new genetic information can be introduced site-specifically and with high efficiency by homology-directed repair (HDR) of Cas9-induced site-specific double-strand DNA breaks using timed delivery of Cas9-guide RNA ribonucleoprotein (RNP) complexes. Cas9 RNP-mediated HDR in HEK293T, human primary neonatal fibroblast and human embryonic stem cells was increased dramatically relative to experiments in unsynchronized cells, with rates of HDR up to 38% observed in HEK293T cells. Sequencing of on- and potential off-target sites showed that editing occurred with high fidelity, while cell mortality was minimized. This approach provides a simple and highly effective strategy for enhancing site-specific genome engineering in both transformed and primary human cells.

Screening, detection, and serotyping methods for toxin genes and enterotoxins in Staphylococcus strains

Staphylococcus aureus continues to play a significant role in foodborne outbreak investigations, with numerous individuals sickened each year after ingesting assorted foods contaminated with staphylococcal enterotoxins. The purpose of this study was to evaluate the use of several methods for the screening, detection, and enterotoxin serotyping of staphylococcal bacterial strains for classical staphylococcal enterotoxins (SEs; SEA, SEB, SEC, SED, and SEE) and the newly described SE and SE-like enterotoxin genes (seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq, ser, ses, set, and seu). Inclusivity and exclusivity panels of staphylococcal strains were tested using a multiplex PCR method in addition to three polyvalent commercially prepared ELISA systems for the detection of SEA-SEE and one monovalent assay for the identification of classical SE serotypes. The results indicate an overall agreement between serological detection methods with a few exceptions, and molecular characterization identified an abundance of SE and SE-like enterotoxin genes including several potentially enterotoxigenic isolates that would have otherwise been missed by ELISA-based methods. These findings demonstrate the significance of PCR for future screening purposes and the use of ELISA systems for the detection and enterotoxin serotyping of staphylococcal bacterial strains.

Improvement in Staphylococcus and Bacillus strain differentiation by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling by using microwave-assisted enzymatic digestion

RATIONALE

Distinguishing between individual bacterial strains below the species level is a challenge to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial profiling. We propose a quick method for improving strain differentiation of two Staphylococcus and one Bacillus species.

METHODS

An alternative procedure to the extraction protocol recommended by Bruker Daltonics was developed. Ethanol-sterilized cells of six S. aureus and six S. haemolyticus strains were digested by trypsin using 2-min microwave irradiation and were then analyzed. Twenty-eight strains belonging to two ecotypes of B. subtilis were subjected to the same procedure to extend the scope of the method.

RESULTS

S. aureus and S. haemolyticus strains, only partially distinguishable by the standard sample preparation procedure, were subjected to microwave-assisted tryptic digestion. The repeatability of the procedure was checked in three experiments accomplished at weekly intervals. Clear distinction of the strains was achieved by cluster analysis. The differentiation of B. subtilis ecotypes was also improved significantly by the digestion method. The discriminatory power of the novel method was supported by an increase in the number of strain-specific peaks, as compared to the standard method.

CONCLUSIONS

The method modulates the discriminatory power of MALDI-TOF MS profiling. The differentiation of a set of S. aureus, S. haemolyticus and B. subtilis strains was improved significantly after microwave-accelerated tryptic digestion of the cellular material.

Photodynamic oxidation of Staphylococcus warneri membrane phospholipids: new insights based on lipidomics

RATIONALE

The photodynamic process involves the combined use of light and a photosensitizer, which, in the presence of oxygen, originates cytotoxic species capable of oxidizing biological molecules, such as lipids. However, the effect of the photodynamic process in the bacterial phospholipid profile by a photosensitizer has never been reported. A lipidomic approach was used to study the photodynamic oxidation of membrane phospholipids of Staphylococcus warneri by a tricationic porphyrin [5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin triiodide, Tri-Py(+)-Me-PF].

METHODS

S. warneri (10(8) colony forming units mL(-1)) was irradiated with white light (4 mW cm(-2), 21.6 J cm(-2)) in the presence of Tri-Py(+)-Me-PF (5.0 μM). Non-photosensitized bacteria were used as control (irradiated without porphyrin). After irradiation, total lipids were extracted and separated by thin-layer chromatography (TLC). Isolated fractions of lipid classes were quantified by phosphorus assay and analyzed by mass spectrometry (MS): off-line TLC/ESI-MS, hydrophilic interaction (HILIC)-LC/MS and MS/MS.

RESULTS

The most representative classes of S. warneri phospholipids were identified as phosphatidylglycerols (PGs) and cardiolipins (CLs). Lysyl-phosphatidylglycerols (LPGs), phosphatidylethanolamines (PEs), phosphatidylcholines (PCs) and phosphatidic acids (PAs) were also identified. After photodynamic treatment, an overall increase in the relative abundance of PGs was observed as well as the appearance of new oxidized species from CLs, including hydroxy and hydroperoxy derivatives. Formation of high amounts of lipid hydroperoxides was confirmed by FOX2 assay. Photodynamic oxidation of phospholipid standards revealed the formation of hydroperoxy and dihydroperoxy derivatives, confirming the observed CL oxidized species in S. warneri.

CONCLUSIONS

Membrane phospholipids of S. warneri are molecular targets of the photoinactivation process induced by Tri-Py(+) -Me-PF. The overall modification in the relative amount of phospholipids and the formation of lipid hydroxides and hydroperoxides indicate the lethal damage caused to photosensitized bacterial cells.

Optimization of marine waste based-growth media for microbial lipase production using mixture design methodology

Lipase production by Staphylococcus xylosus and Rhizopus oryzae was investigated using a culture medium based on a mixture of synthetic medium and supernatants generated from tuna by-products and Ulva rigida biomass. The proportion of the three medium components was optimized using the simplex-centroid mixture design method (SCMD). Results indicated that the experimental data were in good agreement with predicted values, indicating that SCMD was a reliable method for determining the optimum mixture proportion of the growth medium. Maximal lipase activities of 12.5 and 23.5 IU/mL were obtained with a 50:50 (v:v) mixture of synthetic medium and tuna by-product supernatant for Staphylococcus xylosus and Rhizopus oryzae, respectively. The predicted responses from these mixture proportions were also validated experimentally.

In situ-monitoring of biofilm formation by using surface-enhanced Raman scattering

A biofilm is a complex biochemical structure composed of microorganisms and extracellular polymeric substances used by microorganisms to adhere to each other and to surfaces. The monitoring of molecular changes during biofilm formation in situ can provide valuable insights in medicine, microbiology, and industrial processes. In this study, we investigated the characterization of biofilm produced by two model bacteria by using surface-enhanced Raman scattering (SERS) with the use of core silver (AgNPs)-shell chitosan nanoparticles (c-AgNPs), which are prepared by coating citrate-reduced AgNPs with a thin layer of chitosan averaging 10 nm. The chitosan thin film acts as porous layer and prevents the excess interactions of biological media secreted by bacteria. The two model bacteria, Escherichia coli and Staphylococcus cohnii, gram positive and gram negative, respectively, were chosen for the study. The SERS spectra were acquired directly from the growth culture by simply placing c-AgNPs substrate on the biofilm formed during the growth of the bacteria for in situ monitoring. It was found that c-AgNPs are effective SERS substrates to monitor molecular changes in the biofilm during the biofilm formation.

PI3K/Akt/mTOR, a pathway less recognized for staphylococcal superantigen-induced toxicity

Immunostimulating staphylococcal enterotoxin B (SEB) and related superantigenic toxins cause diseases in humans and laboratory animals by activating cells of the immune system. These toxins bind directly to the major histocompatibility complex (MHC) class II molecules on antigen-presenting cells and specific Vβ regions of T-cell receptors (TCR), resulting in hyperactivation of both T lymphocytes and monocytes/macrophages. Activated host cells produce excessive amounts of proinflammatory cytokines and chemokines, especially tumor necrosis factor α, interleukin 1 (IL-1), IL-2, interferon γ (IFNγ), and macrophage chemoattractant protein 1 causing clinical symptoms of fever, hypotension, and shock. The well-explored signal transduction pathways for SEB-induced toxicity downstream from TCR/MHC ligation and interaction of cell surface co-stimulatory molecules include the mitogen-activated protein kinase cascades and cytokine receptor signaling, culminating in NFκB activation. Independently, IL-2, IFNγ, and chemokines from activated T cells signal via the phosphoinositide 3-kinase (PI3K), the serine/threonine kinases, Akt and mammalian target of rapamycin (mTOR) pathways. This article reviews the signaling molecules induced by superantigens in the activation of PI3K/Akt/mTOR pathways leading to staphylococcal superantigen-induced toxicity and updates potential therapeutics against superantigens.

Influence of the subsurface composition of a material on the adhesion of staphylococci

Controlling the interface between bacteria and solid materials has become an important task in biomedical science. For a fundamental and comprehensive understanding of adhesion it is necessary to seek quantitative information about the involved interactions. Most studies concentrate on the modification of the surface (chemical composition, hydrophobicity, or topography) neglecting, however, the influence of the bulk material, which always contributes to the overall interaction via van der Waals forces. In this study, we applied AFM force spectroscopy and flow chamber experiments to probe the adhesion of Staphylococcus carnosus to a set of tailored Si wafers, allowing for a separation of short- and long-range forces. We provide experimental evidence that the subsurface composition of a substrate influences bacterial adhesion. A coarse estimation of the strength of the van der Waals forces via the involved Hamaker constants substantiates the experimental results. The results demonstrate that the uppermost layer is not solely responsible for the strength of adhesion. Rather, for all kinds of adhesion studies, it is equally important to consider the contribution of the subsurface.

Bioenergetics for the growth of Staphylococcus lentus in biocompatible choline salts

Choline-based biocompatible salts were used as "nutrients" for the growth of Staphylococcus lentus bacteria. Increase in the growth rate of bacteria was observed, compared to conventional carbon sources. In the case of the ionic liquid, choline lactate, the increase was pronounced. Bacterial growth was correlated with power-time curve in an investigation monitored online by reaction calorimetry. From the power-time curve, three phases of the growth can be distinctly seen. Heat yield coefficients estimated for the growth of S. lentus were found to match well with those reported hitherto. A comparative study of heat yields (catabolic) between glucose and choline lactate revealed significant information; the heat yield due to choline lactate (Y (Q/S)) consumption and oxygen (Y (Q/O)) were 23.4 kJ/g and 435 kJ/mol and whereas that for glucose with oxygen were 9.6 kJ/g and 427 kJ/mol, respectively, showing clearly the preferential affinity of choline lactate by the bacteria rather than glucose. This study also established that the use of ionic liquids as nutrients can be monitored using bioreaction calorimetry.

Identification of staphylococcal lipoteichoic acid-binding proteins in human serum by high-resolution LTQ-Orbitrap mass spectrometry

Lipoteichoic acid (LTA), a major virulence factor of Gram-positive bacteria, is associated with bacterial adherence to host cells, biofilm formation, and inflammation. LTA-binding proteins (LTA-BPs) play an important role in the host immune response by initially recognizing and responding to LTA during infections. In this study, we screened for LTA-BPs in human serum using LTA-immobilized beads and high-throughput mass spectrometry. Highly pure and structurally intact LTA was prepared from Staphylococcus aureus and immobilized onto N-hydroxysuccinimide-activated Sepharose(®) 4 Fast Flow beads. The immobilization process does not seem to affect the biological activity of LTA since LTA-immobilized beads could stimulate macrophages and activate Toll-like receptor 2. Then, the LTA-immobilized beads were incubated with the human serum to capture LTA-BPs and their molecular identities were determined using high-resolution LTQ-Orbitrap hybrid Fourier transform mass spectrometry. LTA-BPs captured at high frequencies were neutrophil-activating peptide 2, prohibitin-2, alpha-1-anti-trypsin, histidine-rich glycoprotein, apolipoproteins, complements, and coagulation factor, most of which are known to be related with the host immune responses against infections. As high-throughput, efficient, accurate and sensitive, this screening method could be widely applicable to the identification of novel binding proteins to microbial virulence factors with glycolipid structures.

Predicting pKa values with continuous constant pH molecular dynamics

Knowledge of pK(a) values is important for understanding structure and function relationships in proteins. Over the past two decades, theoretical methods for pK(a) calculations have been mainly based on macroscopic models, in which the protein is considered as a low-dielectric cavity embedded in a high-dielectric continuum. In recent years, constant pH molecular dynamics methods have been developed based on a microscopic description of the protein. We describe here the methodology of continuous constant pH molecular dynamics (CPHMD), which has emerged as one of the most robust and accurate tools for predicting protein pK(a)s and for the study of pH-modulated conformational dynamics. We illustrate the utility of CPHMD by the calculation of pK(a)s for surface residues in ribonuclease A, buried residues in staphylococcal nuclease, and titratable groups in the intrinsically flexible protein α-lactalbumin. We will compare the CPHMD results with experimental data as well as calculations from PB-based and empirical methods. These examples demonstrate the accuracy and robustness of the CPHMD method and its ability to capture the correlation between ionization equilibria and conformational dynamics as well as the local dielectric response to structural rearrangement. Finally, we discuss future improvement of the CPHMD method.

Identification of Staphylococcus intermedius Group by MALDI-TOF MS

The Staphylococcus intermedius Group includes S. intermedius, S. pseudintermedius and S. delphini, coagulase-positive bacteria commonly isolated from animals. The identification of organisms belonging to this group is presently carried out using molecular methods. This study assessed the suitability of MALDI-TOF MS for their identification. 69 strains of different biological and geographic origins, identified by partial hsp60 gene sequencing as S. intermedius (n=15), S. pseudintermedius (n=32) and S. delphini (n=22), were analyzed by MALDI-TOF MS. The estimated sensitivity, specificity and efficiency were calculated. In addition we computed the agreement between the outcome of MALDI-TOF MS identification and partial hsp60 gene sequencing. The sensitivity of MALDI-TOF MS was higher for S. intermedius [0.95 (95% CI: 0.68-0.99)], than for S. pseudintermedius [0.78 (95% CI: 0.60-0.90)] and S. delphini [0.64 (95% CI: 0.41-0.83)], whereas the specificity was 1 for S. intermedius and S. delphini and 0.97 (95% CI: 0.86-0.99) for S. pseudintermedius. The Cohen's kappa coefficient indicated almost perfect agreement between MALDI-TOF MS and hsp60 gene sequencing for the identification of S. intermedius [0.96 (95% CI: 0.87-1.04)], and substantial agreement for S. delphini and S. pseudintermedius [0.70 (95% CI: 0.52-0.89) and 0.76 (95% CI: 0.616-0.92), respectively]. The overall efficiency of the proteomic identification ranged between 0.88 (95% CI: 0.78-0.95) for S. pseudintermedius and S. delphini and 0.99 (95% CI: 0.92-0.99) for S. intermedius. MALDI-TOF MS is thus a valuable and reliable tool for the rapid and accurate identification of bacteria belonging to the S. intermedius Group.

Involvement of cell shape and flagella in the bacterial retention during percolation of contaminated water through soil columns in tropical region

Microorganisms' retention in soil contributes to the natural purification of groundwater. Bacteria found in groundwater are generally of various shapes. The aim of this study was to assess the importance of cell shape and flagella in bacterial retention during polluted water percolation through two soil columns CA and CB, in the equatorial region in Central Africa. Percolation tests were carried out using different water loads samples which were contaminated by Escherichia coli (straight rods, peritrichous flagella), Vibrio parahaemolyticus (rods bacteria, polar flagella), and Staphylococcus saprophyticus (spherical, free-flagellum). It has been noted that showed that through soil column CA, the mean values of cells retention ratios (T(R)) varied with bacteria species considered, and from one applied water load sample to another. E. coli T(R) and that of S. saprophyticus were not significantly different (P> 0.05) for the two soil columns. V. parahaemolyticus T(R) significantly differed from that of E. coli and S. saprophyticus through soil column CA (P< 0.01) when the highest water load was applied, and through soil column CB (P< 0.05) for each of water load applied. A relative hierarchical arrangement of retained cells based on the T(R) showed that V. parahaemolyticus was less retained through the 2 soil columns. S. saprophyticus in most cases was more retained than others. The physical properties of the bacterial cell must be taken into consideration when evaluating the transfer of bacteriological pollutants towards groundwater.

Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Whole-cell fingerprinting by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in combination with a dedicated bioinformatic software tool (MALDI Biotyper 2.0) was used to identify 152 staphylococcal strains corresponding to 22 staphylococcal species. Spectra of the 152 isolates, previously identified at the species level using a sodA gene-based oligonucleotide array, were analyzed against the main spectra of 3,030 microorganisms. A total of 151 strains out of 152 (99.3%) were correctly identified at the species level; only one strain was identified at the genus level. The MALDI-TOF MS method revealed different clonal lineages of Staphylococcus epidermidis that were of either human or environmental origin, which suggests that the MALDI-TOF MS method could be useful in the profiling of staphylococcal strains. The topology of the dendrogram generated by the MALDI Biotyper 2.0 software from the spectra of 120 Staphylococcus reference strains (representing 36 species) was in general agreement with that inferred from the 16S rRNA gene-based analysis. Our findings indicate that the MALDI-TOF MS technology, associated with a broad-spectrum reference database, is an effective tool for the swift and reliable identification of Staphylococci.

[Effect of lantibiotic warnerin on lipid bilayer membranes]

The effect of the lantibiotic warnerin on the ionic permeability of artificial membranes has been studied. Membranes were composed of different lipid fractions, including lipids isolated from warnerin-sensitive cells of Staphylococcus epidermidis. It was shown that warnerin selectively interacts with artificial membranes of different lipid composition, which leads, in some cases, to the formation of ionic channels. A computer model of the spatial structure of warnerin has been coustructed, which supports a high probability of the membranotropic activity of this peptide.

Mass spectrometry-based approaches for the detection of proteins of Staphylococcus species

Mass spectrometry (MS) has become a powerful and popular method to analyze macromolecules from biological systems towards the application of clinical chemistry. Disease markers related to infections can be identified with MS analysis in combination with electrophoresis or chromatographic separations. Further, direct analysis of whole pathogenic bacterial cells (taken directly from a colony) by MS can reveal specific biomarkers that can be used for taxonomy. A brief introduction to the two advanced ionization techniques, electrospray ionization and matrix-assisted laser desorption/ionization, for MS is provided in this review. Sample preparation, separation and MS-related techniques for staphylococcal proteins analysis are summarized. The review is concluded with some current clinical applications of mass spectrometry in the area of biomarker research, vaccine development, diagnosis and strain typing of infectious Staphylococci.

Silver nanorod arrays as a surface-enhanced Raman scattering substrate for foodborne pathogenic bacteria detection

Surface-enhanced Raman scattering (SERS) using novel silver nanorod array substrates has been used for the detection of pathogenic bacteria. The substrate consists of a base layer of 500 nm silver film on a glass slide and a layer of silver nanorod array with a length of approximately 1 microm produced by the oblique angle deposition method at a vapor incident angle of 86 degrees . Spectra from whole cell bacteria, Generic Escherichia coli, E. coli O157:H7, E. coli DH 5alpha, Staphylococcus aureus, S. epidermidis, and Salmonella typhimurium, and bacteria mixtures have been obtained. This SERS active substrate can detect spectral differences between Gram types, different species, their mixture, and strains. Principal component analysis (PCA) has been applied to classify the spectra. Viable and nonviable cells have also been examined, and significantly reduced SERS responses were observed for nonviable cells. SERS detection of bacteria at the single cell level, excited at low incident laser power (12 micro W) and short collection time (10 s), has also been demonstrated. These results indicate that the SERS-active silver nanorod array substrate is a potential analytical sensor for rapid identification of microorganisms with a minimum of sample preparation.

Characterization of anti-Legionella activity of warnericin RK and delta-lysin I from Staphylococcus warneri

Legionella pneumophila, the causative agent of Legionnaires' disease, is a waterborne bacteria. It can multiply in man-made water systems and infect people who inhale contaminated droplets. We have previously reported a Staphylococcus warneri strain that display an anti-Legionella activity. In this work, we characterized three anti-Legionella peptides that are produced by S. warneri. One peptide, warnericin RK, is original, while the two others are delta-lysin I and delta-lysin II, whose genes were previously described. Due to high sequence similarity of the two delta-lysins, further characterization was performed only on delta-lysin I. Warnericin RK and delta-lysin I displayed the same antibacterial spectrum, which is almost restricted to the Legionella genus. Also, both peptides have a hemolytic activity. These results led to the hypothesis that warnericin RK and delta-lysin I share a similar mode of action, and that Legionella should have a specific feature that may explain the high specificity of these antibacterial peptides.

Convective assembly of bacteria for surface-enhanced Raman scattering

A sample preparation method based on convective assembly for "whole-microorganism" identification using surface-enhanced Raman scattering (SERS) is developed. With this technique, a uniform sample can easily be prepared with silver nanoparticles. During the deposition process, bacteria and nanoparticles are assembled to form a unique well-ordered structure with great reproducibility. The SERS spectra acquired from the samples prepared with this technique have better quality and improved reproducibility for SERS spectra obtained from the same sample and limited variation due to the consistent sample preparation. E. coli, a Gram-negative bacilli, and Staphylococcus cohnii, a Gram-positive coccus, are studied as model bacteria.

Poly-N-acetylglucosamine is not a major component of the extracellular matrix in biofilms formed by icaADBC-positive Staphylococcus lugdunensis isolates

Staphylococcus lugdunensis is a pathogen of heightened virulence that causes infections resembling those caused by Staphylococcus aureus rather than those caused by its coagulase-negative staphylococcal counterparts. Many types of S. lugdunensis infection, including native valve endocarditis, prosthetic joint infection, and intravascular catheter-related infection, are associated with biofilm etiology. Poly-N-acetylglucosamine (PNAG), a polysaccharide synthesized by products of the icaADBC locus, is a common mechanism of intercellular adhesion in staphylococcal biofilms. Here we report the characterization of ica homologues and the in vitro biofilm formation properties of a collection of S. lugdunensis clinical isolates. Isolates formed biofilms in microtiter wells to various degrees. Biofilm formation by most isolates was enhanced with glucose but diminished by sodium chloride or ethanol. icaADBC homologues were found in all S. lugdunensis isolates tested, although the locus organization differed substantially from that of other staphylococcal ica loci. icaR was not detected in S. lugdunensis, but a novel open reading frame with putative glycosyl hydrolase function is located upstream of the ica locus. icaADBC sequence heterogeneity did not explain the variability in biofilm formation among isolates. PNAG was not detected in S. lugdunensis extracts by immunoblotting with an anti-deacetylated PNAG antibody or wheat germ agglutinin. Confocal microscopy with fluorescently labeled wheat germ agglutinin showed a paucity of PNAG in S. lugdunensis biofilms, but abundant extracellular protein was visualized with SYPRO Ruby staining. Biofilms were resistant to detachment by dispersin B and sodium metaperiodate but were susceptible to detachment by proteases. Despite the genetic presence of icaADBC homologues in S. lugdunensis isolates, PNAG is not a major component of the extracellular matrix of in vitro biofilms formed by this species. Our data suggest that the S. lugdunensis biofilm matrix contains proteinaceous factors.

Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens

Five coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human blood cultures in different German and Belgian medical facilities. A novel species, ‘Staphylococcus pettenkoferi’ was proposed recently to accommodate two of these strains (B3117T and A6664), although the name was not validly published. All five strains belonged to the genus Staphylococcus because they were non-motile, Gram-positive, catalase-positive cocci with peptidoglycan type (A3α type l-lys–gly2–4–l-Ser–Gly), menaquinone pattern (MK-7, MK-6 and MK-8) and major cellular fatty acids (ai-C15 : 0, ai-C17 : 0 and i-C15 : 0) that corresponded to those of staphylococci. Phenotypically, the isolates most closely resembled Staphylococcus capitis subsp. capitis and Staphylococcus auricularis, but they could be distinguished from these species by physiological tests and chemotaxonomic investigations. The results of DNA–DNA hybridization, chemotaxonomic investigations and 16S rRNA gene and RNA polymerase B gene (rpoB) sequence analysis enabled strains B3117T, K6999, 229 and 230 to be differentiated genotypically and phenotypically from known Staphylococcus species, indicating that these isolates are representatives of a novel species. The name Staphylococcus pettenkoferi sp. nov. is proposed for this novel species, with strain B3117T (=CIP 107711T=CCUG 51270T) as the type strain. Due to differences in the results of physiological and chemotaxonomic investigations and DNA–DNA hybridization data, strain A6664 was not included in the description of the novel species.

Susceptibility of staphylococcal biofilms to enzymatic treatments depends on their chemical composition

Bacterial infections are serious complications after orthopaedic implant surgery. Staphylococci, with Staphylococcus epidermidis as a leading species, are the prevalent and most important species involved in orthopaedic implant-related infections. The biofilm mode of growth of these bacteria on an implant surface protects the organisms from the host's immune system and from antibiotic therapy. Therapeutic agents that disintegrate the biofilm matrix would release planktonic cells into the environment and therefore allow antibiotics to eliminate the bacteria. An addition of a biofilm-degrading agent to a solution used for washing-draining procedures of infected orthopaedic implants would greatly improve the efficiency of the procedure and thus help to avoid the removal of the implant. We have previously shown that the extracellular staphylococcal matrix consists of a poly-N-acetylglucosamine (PNAG), extracellular teichoic acids (TAs) and protein components. In this study, we accessed the sensitivity of pre-formed biofilms of five clinical staphylococcal strains associated with orthopaedic prosthesis infections and with known compositions of the biofilm matrix to periodate, Pectinex Ultra SP, proteinase K, trypsin, pancreatin and dispersin B, an enzyme with a PNAG-hydrolysing activity. We also tested the effect of these agents on the purified carbohydrate components of staphylococcal biofilms, PNAG and TA. We found that the enzymatic detachment of staphylococcal biofilms depends on the nature of their constituents and varies between the clinical isolates. We suggest that a treatment with dispersin B followed by a protease (proteinase K or trypsin) could be capable to eradicate biofilms of a variety of staphylococcal strains on inert surfaces.

SdrI, a serine-aspartate repeat protein identified in Staphylococcus saprophyticus strain 7108, is a collagen-binding protein

A gene encoding a serine-aspartate repeat protein of Staphylococcus saprophyticus, an important cause of urinary tract infections in young women, has been cloned and sequenced. In contrast to other SD repeat proteins, SdrI carries 21 additional N-terminal repeats with a consensus sequence of (P/A)ATKE(K/E)A(A/V)(T/I)(A/T/S)EE and has the longest SD(AD)(1-5) repetitive region (854 amino acids) described so far. This highly repetitive sequence contains only the amino acids serine, asparagine, and a distinctly greater amount of alanine (37%) than all other known SD repeat proteins (2.3 to 4.4%). In addition, it is a collagen-binding protein of S. saprophyticus and the second example in this organism of a surface protein carrying the LPXTG motif. We constructed an isogenic sdrI knockout mutant that showed decreased binding to immobilized collagen compared with wild-type S. saprophyticus strain 7108. Binding could be reconstituted by complementation. Collagen binding is specifically caused by SdrI, and the recently described UafA protein, the only LPXTG-containing protein in the genome sequence of the type strain, is not involved in this trait. Our experiments suggest that, as in other staphylococci, the presence of different LPXTG-anchored cell wall proteins is common in S. saprophyticus and support the notion that the presence of matrix-binding surface proteins is common in staphylococci.

[Physico-chemical properties of staphylococci of different species in resistance to human thrombodefensins]

Testing 54 strains of staphylococci (Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. warneri, S. hominis, S. capitis) revealed that S. aureus in contrast to coagulase-negative staphylococci (CNS) is more resistant to bactoriocidal action of human thrombodefensins (resistance index: 60.3 vs 25.6%), less hydrophilicolipophilic balance-HLB: -0.42 vs -0.64) and less charged (x-potential: -32.4 vs -35.6 mV). In groups of staphylococci (S. aureus and CNS) correlation links of bacterial resistance to human thrombodefensins with their HLB and x-potential (r=-0.32...-0.36). By In vitro experiments, it was shown that 5 passages of staphylococci in meat-peptonic broth with human thrombodefensins (50 mkg protein/ml) lead to adaptation of bacteria followed by the formation of resistance to cationic peptides from thrombocytes, a decrease of hydrophobicity and x-potencial. The role of physico-chemical properties in providing thrombodefensin-resistance of staphylococci as a developmental factor of infectious-and-inflammatory process and persistence of bacteria was confirmed with Salmonella infection.

A pilot study to compare the use of the Excorim staphylococcal protein immunoadsorption system and IVIG in chronic inflammatory demyelinating polyneuropathy

Chronic inflammatory demyelinating polyneuropathy (CIDP) is an immune mediated neuropathy responding to immunomodulation with IVIG or plasma exchange (PE). We tested the efficacy and safety of selective immunoglobulin removal by Excorim immunoadsorption (IA) in a pilot trial in CIDP patients randomized to monthly IA or IVIG treatments for 6 months. Response rates at 2 and 6 months were greater with IA due to longer disease duration and greater disability at baseline in the patients receiving IVIG. IA appears to be a safe and efficacious therapy for patients with CIDP, but an appropriately powered clinical trial with stratification for disease duration is required.

Identification ofStaphylococcus piscifermentans from dog feces

The AD 2 strain isolated from feces of a healthy dog in Slovakia was characterized phenotypically by the conventional tests and commercial identification kits API Staph and ID32 Staph. Results of biochemical tests identified the strain as S. piscifermentans, fully corresponding with the species description. Further characterization by whole-cell protein profile analysis (SDS-PAGE) confirmed the identification based on biochemical tests and showed that the AD 2 strain is S. piscifermentans; lactic acid production, urease activity, bacteriocin production and the antibiotic susceptibility of it were also determined. S. piscifermentans AD 2 isolated first from an animal source was deposited in the Czech Collection of Microorganisms as Staphylococcus piscifermentans CCM 7165.

NMR Spectroscopic Study of Noble Gas Binding into the Engineered Cavity of HPr(I14A) from Staphylococcus carnosus

Xenon binding into preexisting cavities in proteins is a well-known phenomenon. Here we investigate the interaction of helium, neon, and argon with hydrophobic cavities in proteins by NMR spectroscopy. 1H and 15N chemical shifts of the I14A mutant of the histidine-containing phosphocarrier protein (HPr(I14A)) from Staphylococcus carnosus are analyzed by chemical shift mapping. Total noble gas induced chemical shifts, Delta, are calculated and compared with the corresponding values obtained using xenon as a probe atom. This comparison reveals that the same cavity is detected with both argon and xenon. Measurements using the smaller noble gases helium and neon as probe atoms do not result in comparable effects. The dependence of amide proton and nitrogen chemical shifts on the argon concentration is investigated in the range from 10 mM up to 158 mM. The average dissociation constant for argon binding into the engineered cavity is determined to be about 90 mM.

Solution structure of the active-centre mutant I14A of the histidine-containing phosphocarrier protein from Staphylococcus carnosus

High-pressure NMR experiments performed on the histidine-containing phosphocarrier protein (HPr) from Staphylococcus carnosus have shown that residue Ile14, which is located in the active-centre loop, exhibits a peculiarly small pressure response. In contrast, the rest of the loop shows strong pressure effects as is expected for typical protein interaction sites. To elucidate the structural role of this residue, the mutant protein HPr(I14A), in which Ile14 is replaced by Ala, was produced and studied by solution NMR spectroscopy. On the basis of 1406 structural restraints including 20 directly detected hydrogen bonds, 49 1H(N)-15N, and 25 1H(N)-1Halpha residual dipolar couplings, a well resolved three-dimensional structure could be determined. The overall fold of the protein is not influenced by the mutation but characteristic conformational changes are introduced into the active-centre loop. They lead to a displacement of the ring system of His15 and a distortion of the N-terminus of the first helix, which supports the histidine ring. In addition, the C-terminal helix is bent because the side chain of Leu86 located at the end of this helix partly fills the hydrophobic cavity created by the mutation. Xenon, which is known to occupy hydrophobic cavities, causes a partial reversal of the mutation-induced structural effects. The observed structural changes explain the reduced phosphocarrier activity of the mutant and agree well with the earlier suggestion that Ile14 represents an anchoring point stabilizing the active-centre loop in its correct conformation.

Purification and Characterization of Warnericin RB4, Anti-Alicyclobacillus Bacteriocin, Produced by Staphylococcus warneri RB4

In this study we characterized a bacteriocin, warnericin RB4, produced by Staphylococcus warneri RB4. Warnericin RB4 activity was completely inactivated by trypsin and actinase E. The activity was stable at 100 degrees C for 15 min, and had a pH range of 2 to 6. S. warneri RB4 showed antibacterial activity against only Alicyclobacillus acidoterrestris, A. acidocaldarius, and Micrococcus luteus, among 34 bacterial species tested. The amino acid sequence of the purified bacteriocin contained 27 amino acid residues (K-K-K-S-G-V-I-P-X-V-X-H-D-X-H-M-N-X-F-Q-F-V-F-X-X-X-S). The molecular mass of the bacteriocin was estimated to be 2,958.2 Da by ESI-MS. These results show that the Warnericin RB4 exhibiting specific antibacterial activity against thermo-acidophiles, Alicyclobacillus spp., is a Nukacin ISK-1 or closely related bacteriocin, classified with class IA (Lacticin 481 types). This is the first report that Warnericin RB-4 is effective to inhibit the growth of causative microorganisms of spoilage in various acidic drinks. Warnericin RB4 might prove useful in fruit juices and fruit juice-containing drinks.

Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips

Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88-residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on-line cell high-pressure nuclear magnetic resonance technique in the pressure range from 3 MPa to 200 MPa and in the temperature range from 257 K to 313 K. The ring of Tyr6 is buried sandwiched between a beta-sheet and alpha-helices (the water-accessible area is less than 0.26 nm2), its hydroxyl proton being involved in an internal hydrogen bond. The ring flip rates 10(1)-10(5) s(-1) were determined from the line shape analysis of H(delta1, delta2) and H(epsilon1,epsilon2) of Tyr6, giving an activation volume DeltaV++ of 0.044 +/- 0.008 nm3 (27 mL mol(-1)), an activation enthalpy DeltaH++ of 89 +/- 10 kJ mol(-1), and an activation entropy DeltaS++ of 16 +/- 2 JK(-1) mol(-1). The DeltaV++) and DeltaH++ values for HPr found previously for Tyr and Phe ring flips of BPTI and cytochrome c fall within the range of DeltaV(double dagger) of 28 to 51 mL mol(-1) and DeltaH++ of 71 to 155 kJ mol(-1). The fairly common DeltaV++ and DeltaH++ values are considered to represent the extra space or cavity required for the ring flip and the extra energy required to create a cavity, respectively, in the core part of a globular protein. Nearly complete cold denaturation was found to take place at 200 MPa and 257 K independently from the ring reorientation process.

Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations

Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.

Determination of microbial volatile organic compounds from Staphylococcus pasteuri against Tuber borchii using solid-phase microextraction and gas chromatography/ion trap mass spectrometry

The mycelium of Tuber borchii Vittad., a commercial truffle species, is used as a model system for in vitro ectomycorrhizal synthesis, infected seedling production and biotechnological applications. Our fungal cultures were accidentally contaminated with a Staphylococcus pasteuri strain, showing a strong antifungal activity against T. borchii mycelium. In order to identify the antifungal volatile agents produced by S. pasteuri, solid-phase microextraction (SPME) with gas chromatography and mass spectrometry (GC/MS) was used. Using this method 65 microbial volatile organic compounds (MVOCs), synthesized by this bacterium in either single or in fungal-bacterial dual culture, were identified. SPME combined with GC/MS may be a useful method for the determination of MVOCs involved in the antifungal activity. These results showed that bacteria with unusual biological activities could be a major problem during large-scale production of inoculum for truffle-infected seedling.

A fibrinogen-binding protein ofStaphylococcus lugdunensis

A gene called fbl, encoding a Staphylococcus lugdunensis fibrinogen-binding protein, was identified by phage display. The encoded protein, Fbl, is a member of the Sdr-family, a group of staphylococcal cell surface proteins containing a characteristic serine-aspartate repeat region. The fibrinogen-binding domain was mapped to 313 amino acids, and shows 62% identity to the corresponding region in clumping factor (ClfA) from Staphylococcus aureus. Anti-serum against ClfA cross-reacted with Fbl, and blocked S. lugdunensis adherence to fibrinogen. Twelve clinical isolates of S. lugdunensis analysed by Southern blot all had an fbl-like gene.

Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy

RELAX-JT2 is an extension of RELAX, a program for the simulation of 1H 2D NOESY spectra and (15)N or (13)C edited 3D NOESY-HSQC spectra of biological macromolecules. In addition to the already existing NOE-simulation it allows the proper simulation of line shapes by the integrated calculation of T(2) times and multiplet structures caused by J-couplings. Additionally the effects of relaxation mediated by chemical shift anisotropy are taken into account. The new routines have been implemented in the program AUREMOL, which aims at the automated NMR structure determination of proteins in solution. For a manual or automatic assignment of experimental spectra that is based on the comparison with the corresponding simulated spectra, the additional line shape information now available is a valuable aid. The new features have been successfully tested with the histidine-containing phosphocarrier protein HPr from Staphylococcus carnosus.

Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data

Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been extensively studied by NMR and X-ray crystallography, and are often used as model structures in developing de novo or ab initio strategies for predicting protein structure. These small three-helix-bundle structures, reported in free proteins or Ig-bound complexes, have been determined previously using medium- to high-resolution data. Although the location and relative orientation of the three helices in most of these published 3D domain structures are consistent, there are significant differences among the reported structures regarding the tilt angle of the first helix (helix 1). We have applied residual dipolar coupling data, together with nuclear Overhauser enhancement and scalar coupling data, in refining the NMR solution structure of an engineered IgG-binding domain (Z domain) of SpA. Our results demonstrate that the three helices are almost perfectly antiparallel in orientation, with the first helix tilting slightly away from the other two helices. We propose that this high-accuracy structure of the Z domain of SpA is a more suitable target for theoretical predictions of the free domain structure than previously published lower-accuracy structures of protein A domains.

Use of the Phase Diagram Method to Analyze the Protein Unfolding-Refolding Reactions: Fishing Out the “Invisible” Intermediates

Partially folded conformations are important players in protein self-organization, function, and misfolding, thus attracting the intensive and constant attention of researchers. Different conformational states of proteins can be easily discriminated from one another using the multiparametric approach, which usually involves the application of several physicochemical methods sensitive to the various structural levels of a protein molecule. This approach gives the most complete information about the structural changes in protein during its de- and renaturation. However, in many cases researches are interested in a brief and simple test for the appearance of an intermediate state. The binding of the hydrophobic fluorescent probe ANS represents one of the well-established techniques, allowing the retrieval of such information. We are introducing another approach, based on the analysis of the spectroscopic data in a form of spectral diagrams. The essence of this method is to build the Ilambda1, versus Ilambda2 dependence, where Ilambda1 and Ilambda2 are the spectral intensity values (e.g., fluorescence, CD, FTIR, absorbance, etc.) measured on wavelengths lambda1 and lambda2. We are showing that this approach gives the detailed description of the protein unfolding pathway, detects the numerous partially folded species, and even fishes out the hidden intermediates. An application of this method for the analysis of the equilibrium and kinetic unfolding/refolding of several proteins under the variety of conditions is described. Advantages and disadvantages of the technique suggested are also discussed.