Pneumococcal Predictive Proteins Selected by Microbial Genomic Approach Are Serotype Cross-Reactive and Bind to Host Extracellular Matrix Proteins

Streptococcus pneumoniae is a colonizer of the human nasopharynx, which accounts for most of the community-acquired pneumonia cases and can cause non-invasive and invasive diseases. Current available vaccines are serotype-specific and the use of recombinant proteins associated with virulence is an alternative to compose vaccines and to overcome these problems. In a previous work, we describe the identification of proteins in S. pneumoniae by reverse vaccinology and the genetic diversity of these proteins in clinical isolates. It was possible to purify a half of 20 selected proteins in soluble form. The expression of these proteins on the pneumococcal cells surface was confirmed by flow cytometry. We demonstrated that some of these proteins were able to bind to extracellular matrix proteins and were recognized by sera from patients with pneumococcal meningitis infection caused by several pneumococcal serotypes. In this context, our results suggest that these proteins may play a role in pneumococcal pathogenesis and might be considered as potential vaccine candidates.     

Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression

Streptococcus pneumoniae is a major cause of mortality in children under five years old. In recent years, the emergence of antibiotic-resistant strains of S. pneumoniae increases the threat level of this pathogen. For that reason, the exploration of S. pneumoniae protein virulence factors should be considered in developing new drugs or vaccines, for instance by the analysis of host-pathogen protein-protein interactions (HP-PPIs). In this research, prediction of protein-protein interactions was performed with a logistic regression model with the number of protein domain occurrences as features. By utilizing HP-PPIs of three different pathogens as training data, the model achieved 57–77 % precision, 64–75 % recall, and 96–98 % specificity. Prediction of human-S. pneumoniae protein-protein interactions using the model yielded 5823 interactions involving thirty S. pneumoniae proteins and 324 human proteins. Pathway enrichment analysis showed that most of the pathways involved in the predicted interactions are immune system pathways. Network topology analysis revealed β-galactosidase (BgaA) as the most central among the S. pneumoniae proteins in the predicted HP-PPI networks, with a degree centrality of 1.0 and a betweenness centrality of 0.451853. Further experimental studies are required to validate the predicted interactions and examine their roles in S. pneumoniae infection.     

Development of amperometric magnetogenosensors coupled to asymmetric PCR for the specific detection of <Emphasis Type="Italic">Streptococcus pneumoniae</Emphasis>

A disposable magnetogenosensor for the rapid, specific and sensitive detection of Streptococcus pneumoniae is reported. The developed procedure involves the use of streptavidin-modified magnetic beads, a specific biotinylated capture probe that hybridizes with a specific region of lytA, the gene encoding the pneumococcal major autolysin, and appropriate primers for asymmetric polymerase chain reaction (PCR) amplification. Capture probes and amplicons specific for S. pneumoniae were selected by a careful analysis of all lytA alleles available. The selected primers amplify a 235-bp fragment of pneumococcal lytA. A detection limit (LOD) of 5.1 nM was obtained for a 20-mer synthetic target DNA without any amplification protocol, while the LOD for the asymmetric PCR amplicon was 1.1 nM. A RSD value of 6.9% was obtained for measurements carried out with seven different genosensors for 1.1-nM aPCR product. The strict specificity of the designed primers was demonstrated by aPCR amplification of genomic DNA prepared from different bacteria, including some closely related streptococci. Direct asymmetric PCR (daPCR), using cells directly from broth cultures of S. pneumoniae, showed that daPCR products could be prepared with as few as 2 colony-forming units (CFU). Furthermore, this methodology did not show any cross-reaction with closely related streptococci such as Streptococcus mitis (or Streptococcus pseudopneumoniae) even when present in the culture at concentrations up to 10⁵ times higher than that of S. pneumoniae. Preliminary data for rapid detection of pneumococcus directly in clinical samples has shown that it is possible to discriminate between non-inoculated blood and urine samples and samples inoculated with only 10³ CFU mL⁻¹  S. pneumoniae.     

Phenotypic and genetic diversity of Bacillus thuringiensis strains isolated in India active against Spodoptera litura

Bacillus thuringiensis strains isolated from different agroclimatic regions of India were found to harbor cry1 family genes. Of 831 strains 18 that were found to produce 130- and 68-kDa mol wt proteins in sodium dodecyl sulfate polyacrylamide gel electrophoresis were subjected to bioassay against second instar larvae of Spodoptera litura. According to the time response curve, while the highest toxic activity against S. litura was observed in PBT-782 with an LT₅₀ of 25.46 h, strains PBT-372, PBT-574, PBT-801, and PBT-716 in descending order of merit had LT₅₀ values of 36.81, 48.18, 50.35, and 73.53 h. The results of the field experiment testing the efficacy of different B. thuringiensis strains in controlling S. litura larvae infecting peanut plants showed that the chemical insecticide chlorpyriphos was the most effective in controlling S. litura throughout the study period. However, among B. thuringiensis strains, PBT-372 was superior. All the B. thuringiensis strains except PBT-689 were found to contain cry1Ac1-type gene. However, only nine strains contained cry1Aa1 gene. While cry1Ab1 was present only in PBT-372 and PBT-689, cry1Ca1 was present in PBT-574, PBT-688, PBT-689, and PBT-695. cry1Da1 was detected only in PBT-688 and PBT-692. None of the strains contained cry1Ba1 and cry1Ea1 genes. When polymerase chain reaction analysis using cry1Ca1 primer was performed, PBT-695 produced an unexpected 739-bp product, which showed 33% homology with cry1Ca1 gene between nucleotides 1819 and 2107. Our results indicated that among the field-collected B. thuringiensis strains, PBT-372 harbors multiple cry-type genes and could be employed for biological control of insects.     

A Chimeric Siderophore Halts Swarming Vibrio

Some bacteria swarm under some circumstances; they move rapidly and collectively over a surface. In an effort to understand the molecular signals controlling swarming, we isolated two bacterial strains from the same red seaweed, Vibrio alginolyticus B522, a vigorous swarmer, and Shewanella algae B516, which inhibits V. alginolyticus swarming in its vicinity. Plate assays combined with NMR, MS, and X‐ray diffraction analyses identified a small molecule, which was named avaroferrin, as a potent swarming inhibitor. Avaroferrin, a previously unreported cyclic dihydroxamate siderophore, is a chimera of two well‐known siderophores: putrebactin and bisucaberin. The sequenced genome of S. algae revealed avaroferrin’s biosynthetic gene cluster to be a mashup of putrebactin and bisucaberin biosynthetic genes. Avaroferrin blocks swarming through its ability to bind iron in a form that cannot be pirated by V. alginolyticus, thereby securing this essential resource for its producer.     

Characterization of heterologous and native enzyme activity profiles in metabolically engineered Zymomonas mobilis strains during batch fermentation of glucose and xylose mixtures

Zymomonas mobilis has been metabolically engineered to broaden its substrate utilization range to include d-xylose and l-arabinose. Both genomically integrated and plasmid-bearing Z. mobilis strains that are capable of fermenting the pentose d-xylose have been created by incorporating four genes: two genes encoding xylose utilization metabolic enzymes (xylA/xylB) and two genes encoding pentose phosphate pathway enzymes (talB/tktA). We have characterized the activities of the four newly introduced enzymes for xylose metabolism, along with those of three native glycolytic enzymes, in two different xylose-fermenting Z. mobilis strains. These strains were grown on glucose-xylose mixtures in computer-controlled fermentors. Samples were collected and analyzed to determine extracellular metabolite concentrations as well as the activities of several intracellular enzymes in the xylose and glucose uptake and catabolism pathways. These measurements provide new insights on the possible bottlenecks in the engineered metabolic pathways and suggest methods for further improving the efficiency of xylose fermentation.     

A secretome-based methodology may provide a better characterization of the virulence of Listeria monocytogenes: preliminary results

Four strains of Listeria monocytogenes with different levels of virulence were studied. Two strains were consistently evaluated as virulent (strain 3077) and of low virulence (strain 3993), whereas the other two strains (3006 and 3049) originated conflicting results in what the evaluation tests were concerned: both were shown to exhibit low virulence when evaluated by in vitro assays, but virulent when the analyses were performed under in vivo conditions.To clarify the virulence potential of the selected strains, a proteomic approach was used after incubating L. monocytogenes cultures under conditions favoring the expression of virulence factors (minimal medium, at 37 °C). Bacterial proteins present in the liquid culture media were precipitated from late exponential phase cultures, fractionated by SDS-PAGE and identified by MALDI-TOF-MS.Three virulence factors differentially expressed were detected: protein p60, listeriolysin O (LLO) and internalin C (InlC). Clustering analysis of the four L. monocytogenes strains based on their secretome profiles allowed their categorization in two groups: the virulent group, composed by strains 3077 and 3049, and the low virulence group, containing strains 3993 and 3006. The results presented in this work suggest that the virulent potential of a particular L. monocytogenes strain may be predicted from the levels of both listeriolysin O (LLO) and internalin C (InlC) present in its secretome when the bacterium is grown under conditions favoring the expression of virulence factors. Following validation of this proposal through the analysis of a large array of strains, this methodology exhibits a great potential to be developed into an accurate and rapid method to characterize L. monocytogenes strain virulence.     

Optimization of a direct spectrophotometric method to investigate the kinetics and inhibition of sialidases

Backgrounds

Streptococcus pneumoniae expresses three distinct sialidases, NanA, NanB, and NanC, that are believed to be key virulence factors and thus, potential important drug targets. We previously reported that the three enzymes release different products from sialosides, but could share a common catalytic mechanism before the final step of product formation. However, the kinetic investigations of the three sialidases have not been systematically done thus far, due to the lack of an easy and steady measurement of sialidase reaction rate.

Results

In this work, we present further kinetic characterization of pneumococcal sialidases by using a direct spectrophotometric method with the chromogenic substrate p-nitrophenyl-N-acetylneuraminic acid (p-NP-Neu5Ac). Using our assay, the measured kinetic parameters of the three purified pneumococcal sialidase, NanA, NanB and NanC, were obtained and were in perfect agreement with the previously published data. The major advantage of this alternative method resides in the direct measurement of the released product, allowing to readily determine of initial reaction rates and record complete hydrolysis time courses.

Conclusion

We developed an accurate, fast and sensitive spectrophotometric method to investigate the kinetics of sialidase-catalyzed reactions. This fast, sensitive, inexpensive and accurate method could benefit the study of the kinetics and inhibition of sialidases in general.     

Genome-wide computational analyses of microRNAs and their targets from Canis familiaris

By computational analyses, we identified 357 miRNA candidates from Canis familiaris genome, among which 300 are homology of characterized human miRNAs, the remains are not reported in any other animal. Of the 357 miRNA genes, 142 are organized into 53 clusters, and two clusters locate in the paternally imprinted region. These dog miRNAs may regulate more than 800 possible targets, which are involved in a wide range of cellular processes. Remarkably, miR-186 resides in the eighth intron of its target gene in the same orientation, suggesting a feedback regulation of miRNA on its host gene.     

Multiplex identification of drug‐resistant Gram‐positive pathogens using stuffer‐free MLPA system

Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture‐based methods require relatively longer time to identify drug‐resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug‐resistant Gram‐positive pathogens, we developed a method by using stuffer‐free multiplex ligation‐dependent probe amplification (MLPA) coupled with high‐resolution CE single‐strand conformation polymorphisms (CE‐SSCP) system. We designed three probe sets for genes specific to Gram‐positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram‐positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain‐specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target‐specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug‐resistant Gram‐positive pathogens from sepsis patients’ blood.     

Microbial products. II. Granaticinic acid,a new antibiotic from a thermophilic streptomycete

Streptomyces sp. XT-11989 produces a mixture of two antibiotics with litmus-like indicator properties. One of them was shown to be identical with granaticin, the other was identified as [1S,3S,4S,7R,9R,10S,13R]-4,7,9,10-tetrahydro-5,12-dioxo-4, 6,10,11,13-pentahydroxy-1,9-dimethyl-(1H,3H)-7,10-ethanonaphtho[2,3-c: 6,7-c]dipyran-3-acetic acid and termed granaticinic acid. Microbial production and nuclear magnetic resonance data of these antibiotics are discussed and the antibacterial properties of the antibiotics are compared.

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Mikrobielle produkte. II. Granaticinsäure, ein neues Antibiotikum von einem thermophilen Streptomyceten

Zusammenfassung Der Streptomycetenstamm XT-11989 produziert eine Mischung von zwei Antibiotika mit Lakmus-ähnlichen Indikatoreigenschaften. Eines dieser Antibiotika erwies sich als Granaticin, das andere wurde als [1S,3S,4S,7R,9R,10S,13R]-4,7,9,10-tetrahydro-5,12-dioxo-4,6,10,11,13-pentahydroxy-1,9-dimethyl-(1H,3H)-7,10-ethanonaphto[2,3-c: 6,7-c]dipyran-3-essigsäure identifiziert und Granaticinsäure benannt. Mikrobiologische Produktion und Kernresonanzdaten dieser antibiotika werden besprochen und ihre antibakteriellen Eigenschaften verglichen.

     

Transition metal complexes of a novel quinoxaline‐based tridentate ONO donor ligand: synthesis,spectral characterization,thermal, in vitro pharmacological and molecular modeling studies

Co(II), Ni(II), Cu(II) and Zn(II) complexes of a novel tridentate heterocyclic ligand, 3‐{[(2‐benzoyl‐4‐chlorophenyl)imino]methyl}quinoxalin‐2(1H)‐one, have been synthesized. The ligand and the metal complexes were characterized using elemental analysis, molar conductance and magnetic susceptibility measurements, and UV–visible, Fourier transform infrared, ¹H NMR, ¹³C NMR, electron spin resonance and DART mass spectral data. The ligand behaves as a tridentate one, coordinating through two oxygen atoms from two keto groups and through the azomethine nitrogen atom. The thermal properties of the newly synthesized compounds were determined using thermogravimetric analysis. The ligand and its metal complexes were subjected to powder X‐ray diffraction analysis by which average crystallite size and unit cell parameters were calculated. The electrochemical behaviour of the compounds was studied using cyclic voltammetry. The ligand and the metal complexes were screened for their in vitro antimicrobial activities against the bacterial strains E. coli, K. pneumoniae, S. pneumoniae and S. aureus and the fungal species A. niger, A. flavus, P. chrysogenum and R. stolonifer. DNA binding, DNA cleavage and antioxidant activities of the compounds were also evaluated. The compounds bind with DNA through groove binding. The Cu(II) and Zn(II) complexes exhibit higher superoxide anion and hydrogen peroxide scavenging activities, respectively. The Cu(II) complex exhibits better anticancer activity against the MCF7 cell line. The compounds were subjected to molecular docking study against B‐DNA dodecamer d(CGCGAATTCGCG)₂ and vascular endothelial growth factor receptor kinase to justify the experimental DNA binding and MTT assay. Density functional theory studies were used to optimize the geometry of the compounds and to calculate the nonlinear optical properties. Copyright © 2016 John Wiley & Sons, Ltd.     

What to Learn from a Comparative Genomic Sequence Analysis of <Emphasis Type="Italic">L</Emphasis>-Carnitine Dehydrogenase

Summary. In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

Construction of recombinant Bacillus subtilis for production of polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are polyesters of hydroxyalkanoates synthesized by numerous bacteria as intracellular carbon and energy storage compounds and accumulated as granules in the cytoplasm of cells. In this work, we constructed two recombinant plasmids, pBE2C1, and pBE2C1AB, containing one or two PHA synthse, genes, respectively. The two plasmids were inserted into Bacillus subtilis DB104 to generate modified strains, B. subtilis/pBE2C1 and B. subtilis/pBE2C1AB. The two recombinants strains were subjected to fermentation and showed PHA accumulation, the first reported example of mcl-PHA production in B. subtilis. Gas Chromatography analysis identified the compound produced by B. subtilis/pBE2C1 to be a hydroxydecanoate-co-hydroxydodecanoate (HD-co-HDD) polymer whereas that produced by B. subtilis/pBE2C1AB was a hydroxybutyrate-co-hydroxyde-canoate-co-hydroxydodecanoate (HB-HD-HDD) polymer.     

Synthesis of Novel Fused Thiazolo[3,2‐a]pyrimidin‐3‐ols and Evaluation for their Antibacterial Activity

A series of novel fused thiazolo[3,2‐a]pyrimidin‐3‐ol derivatives have been synthesized by reaction of fused pyrimidine‐thiones with 4‐substituted phenacyl bromide/3(2‐bromoacetyl)coumarin in refluxing acetic acid with good yields. All the synthesized compounds were confirmed by spectral studies and screened for their in vitro antibacterial activity against Staphylococcus aureus, Bacillus thuringiensis (Gram positive), Escherichia coli, and Klebsiella pneumoniae (Gram negative) bacterial strains. Activity results revealed that all the compounds were weak to good active against the tested bacterial strains on comparing with the standard drug gentamicin.     

Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates**

Two Burkholderia gladioli strains isolated from the lungs of cystic fibrosis patients were found to produce unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of about 45 % of B. gladioli isolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S assay indicated that these metabolites bind ferric iron, which suppresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes, suggesting that these metabolites may function as siderophores in B. gladioli.     

Selective Photoreceptor Gene Knock‐out Reveals a Regulatory Role for the Growth Behavior of Pseudomonas syringae

The plant pathogen Pseudomonas syringae (Ps) is a well‐established model organism for bacterial infection of plants. The genome sequences of two pathovars, pv. syringae and pv. tomato, revealed one gene encoding a blue and two genes encoding red/far red light‐sensing photoreceptors. Continuing former molecular characterization of the photoreceptor proteins, we here report selective photoreceptor gene disruption for pv. tomato aiming at identification of potentially regulatory functions of these photoreceptors. Transformation of Ps cells with linear DNA constructs yielded interposon mutations of the corresponding genes. Cell growth studies of the generated photoreceptor knock‐out mutants revealed their role in light‐dependent regulation of cell growth and motility. Disruption of the blue‐light (BL) receptor gene caused a growth deregulation, in line with an observed increased virulence of this mutant (Moriconi et al., Plant J., 2013, 76, 322). Bacterial phytochrome‐1 (BphP1) deletion mutant caused unaltered cell growth, but a stronger swarming capacity. Inactivation of its ortholog, BphP2, however, caused reduced growth and remarkably altered dendritic swarming behavior. Combined knock‐out of both bacteriophytochromes reproduced the swarming pattern observed for the BphP2 mutant alone. A triple knock‐out mutant showed a growth rate between that of the BL (deregulation) and the phytochrome‐2 mutant (growth reduction).