bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shiga Toxin-Producing Escherichia coli O104:H4: a New Challenge for Microbiology
Authors: Muniesa Maite , Hammerl Jens A. , Hertwig Stefan , Appel Bernd , Brüssow Harald 
Published: April 2012

ABSTRACT

In 2011, Germany experienced the largest outbreak with a Shiga toxin-producing
Escherichia coli
(STEC) strain ever recorded. A series of environmental and trace-back and trace-forward investigations linked sprout consumption with the disease, but fecal-oral transmission was also documented. The genome sequences of the pathogen revealed a clonal outbreak with enteroaggregative
E. coli
(EAEC). Some EAEC virulence factors are carried on the virulence plasmid pAA. From an unknown source, the epidemic strains acquired a lambdoid prophage carrying the gene for the Shiga toxin. The resulting strains therefore possess two different mobile elements, a phage and a plasmid, contributing essential virulence genes. Shiga toxin is released by decaying bacteria in the gut, migrates through the intestinal barrier, and is transported via the blood to target organs, like the kidney. In a mouse model, probiotic bifidobacteria interfered with transport of the toxin through the gut mucosa. Researchers explored bacteriophages, bacteriocins, and low-molecular-weight inhibitors against STEC. Randomized controlled clinical trials of enterohemorrhagic
E. coli
(EHEC)-associated hemolytic uremic syndrome (HUS) patients found none of the interventions superior to supportive therapy alone. Antibodies against one subtype of Shiga toxin protected pigs against fatal neurological infection, while treatment with a toxin receptor decoy showed no effect in a clinical trial. Likewise, a monoclonal antibody directed against a complement protein led to mixed results. Plasma exchange and IgG immunoadsoprtion ameliorated the condition in small uncontrolled trials. The epidemic O104:H4 strains were resistant to all penicillins and cephalosporins but susceptible to carbapenems, which were recommended for treatment.
Bactericidal Antibiotics Do Not Appear To Cause Oxidative Stress in Listeria monocytogenes
Authors: Feld Louise , Knudsen Gitte M. , Gram Lone 
Published: April 2012

ABSTRACT

Oxidative stress can be an important contributor to the lethal effect of bactericidal antibiotics in some bacteria, such as
Escherichia coli
and
Staphylococcus aureus
. Thus, despite the different target-specific actions of bactericidal antibiotics, they have a common mechanism leading to bacterial self-destruction by internal production of hydroxyl radicals. The purpose of the present study was to determine if a similar mechanism is involved in antibiotic killing of the infectious human pathogen,
Listeria monocytogenes
. We treated wild-type
L. monocytogenes
and oxidative stress mutants (Δ
sod
and Δ
fri
) with three different bactericidal antibiotics and found no difference in killing kinetics. In contrast, wild-type
E. coli
and an oxidative stress mutant (Δ
sodA
Δ
sodB
) differed significantly in their sensitivity to bactericidal antibiotics. We conclude that bactericidal antibiotics did not appear to cause oxidative stress in
L. monocytogenes
and propose that this is caused by its noncyclic tricarboxylic acid (TCA) pathway. Hence, in this noncyclic metabolism, there is a decoupling between the antibiotic-mediated cellular requirement for NADH and the induction of TCA enzyme activity, which is believed to mediate the oxidative stress reaction.
In VitroFunctional and Immunomodulatory Properties of the Lactobacillus helveticus MIMLh5-Streptococcus salivarius ST3 Association That Are Relevant to the Development of a Pharyngeal Probiotic Product
Authors: Taverniti Valentina , Minuzzo Mario , Arioli Stefania , Junttila Ilkka , Hämäläinen Sanna , Turpeinen Hannu , Mora Diego , Karp Matti , Pesu Marko , Guglielmetti Simone 
Published: April 2012

ABSTRACTThe use of proper bacterial strains as probiotics for the pharyngeal mucosa is a potential prophylactic strategy for upper respiratory tract infections. In this context, we characterizedin vitrothe functional and immunomodulatory properties of the strainsLactobacillus helveticusMIMLh5 andStreptococcus salivariusST3 that were selected during previous investigations as promising pharyngeal probiotics. In this study, we demonstratedin vitrothat strains MIMLh5 and ST3, alone and in combination, can efficiently adhere to pharyngeal epithelial cells, antagonizeStreptococcus pyogenes, and modulate host innate immunity by inducing potentially protective effects. In particular, we found that the strains MIMLh5 and ST3 activate U937 human macrophages by significantly inducing the expression of the proinflammatory cytokine tumor necrosis factor alpha (TNF-α). Nonetheless, the induction of the anti-inflammatory interleukin-10 (IL-10) by MIMLh5 or ST3 was never lower than that of TNF-α, suggesting that these bacteria can potentially exert a regulatory rather than a proinflammatory effect. We also found that the strains MIMLh5 and ST3 induce cyclooxygenase 2 (COX-2) expression and demonstrated that toll-like receptor 2 (TLR-2) participates in the recognition of the strains MIMLh5 and ST3 by U937 cells. Finally, we observed that these microorganisms grow efficiently when cocultured in milk, suggesting that the preparation of a milk-based fermented product containing both MIMLh5 and ST3 can be a practical solution for the administration of these bacteria. In conclusion, we propose the combined use ofL. helveticusMIMLh5 andS. salivariusST3 for the preparation of novel products that display probiotic properties for the pharyngeal mucosa.
Lactobacillus equigenerosi Strain Le1 Invades Equine Epithelial Cells
Authors: Botha Marlie , Botes Marelize , Loos Ben , Smith Carine , Dicks Leon M. T. 
Published: April 2012

ABSTRACT

Lactobacillus equigenerosi
strain Le1, a natural inhabitant of the equine gastrointestinal tract, survived pH 3.0 and incubation in the presence of 1.5% (wt/vol) bile salts for at least 2 h. Strain Le1 showed 8% cell surface hydrophobicity, 60% auto-aggregation, and 47% coaggregation with
Clostridium difficile
C6. Only 1% of the cells adhered to viable buccal epithelial cells and invaded the cells within 20 min after contact. Preincubation of strain Le1 in a buffer containing pronase prevented adhesion to viable epithelial cells. Preincubation in a pepsin buffer delayed invasion from 20 min to 1 h. Strain Le1 did not adhere to nonviable epithelial cells. Administration of
L. equigenerosi
Le1 (1 × 10
9
CFU per 50 kg body weight) to healthy horses did not increase white blood cell numbers. Differential white blood cell counts and aspartate aminotransferase levels remained constant. Glucose, lactate, cholesterol, and urea levels remained constant during administration with
L. equigenerosi
Le1 but decreased during the week after administration.
Isolation of Lactococcus lactis Mutants Simultaneously Resistant to the Cell Wall-Active Bacteriocin Lcn972, Lysozyme, Nisin, and Bacteriophage c2
Authors: Roces Clara , Courtin Pascal , Kulakauskas Saulius , Rodríguez Ana , Chapot-Chartier Marie-Pierre , Martínez Beatriz 
Published: April 2012

ABSTRACT

Lactococcin 972 (Lcn972) is a nonlantibiotic bacteriocin that inhibits cell wall biosynthesis by binding to lipid II. In this work, two mutants resistant to Lcn972,
Lactococcus lactis
D1 and D1-20, with high (>320 arbitrary units [AU]/ml) and low (80 AU/ml) susceptibilities, respectively, have been isolated. Resistance to Lcn972 did not impose a burden to growth under laboratory conditions, nor did it substantially alter the physicochemical properties of the cell surface. However, the peptidoglycan of the mutants featured a higher content of muropeptides with tripeptide side chains than the wild-type strain, linking for the first time peptidoglycan remodelling to bacteriocin resistance. Moreover,
L. lactis
lacking a functional
d,d
-carboxypeptidase DacA (i.e., with a high content of pentapeptide side chain muropeptides) was shown to be more susceptible to Lcn972. Cross-resistance to lysozyme and nisin and enhanced susceptibility to penicillin G and bacitracin was also observed. Intriguingly, the Lcn972-resistant mutants were not infected by the lytic phage c2 and less efficiently infected by phage sk1. Lack of c2 infectivity was linked to a 22.6-kbp chromosomal deletion encompassing the phage receptor protein gene
pip
. The deletion also included maltose metabolic genes and the two-component system (TCS) F. However, a clear correlation between these genes and resistance to Lcn972 could not be clearly established, pointing to the presence of as-yet-unidentified mutations that account for Lcn972 resistance.
Determination of Wolbachia Diversity in Butterflies from Western Ghats, India, by a Multigene Approach
Authors: Salunke Bipinchandra K. , Salunkhe Rahul C. , Dhotre Dhiraj P. , Walujkar Sandeep A. , Khandagale Avinash B. , Chaudhari Rahul , Chandode Rakesh K. , Ghate Hemant V. , Patole Milind S. , Werren John H. , Shouche Yogesh S. 
Published: April 2012

ABSTRACT

Members of the genus
Wolbachia
are intracellular bacteria that are widespread in arthropods and establish diverse symbiotic associations with their hosts, ranging from mutualism to parasitism. Here we present the first detailed analyses of
Wolbachia
in butterflies from India with screening of 56 species. Twenty-nine species (52%) representing five families were positive for
Wolbachia
. This is the first report of
Wolbachia
infection in 27 of the 29 species; the other two were reported previously. This study also provides the first evidence of infection in the family Papilionidae. A striking diversity was observed among
Wolbachia
strains in butterfly hosts based on five multilocus sequence typing (MLST) genes, with 15 different sequence types (STs). Thirteen STs are new to the MLST database, whereas ST41 and ST125 were reported earlier. Some of the same host species from this study carried distinctly different
Wolbachia
strains, whereas the same or different butterfly hosts also harbored closely related
Wolbachia
strains. Butterfly-associated STs in the Indian sample originated by recombination and point mutation, further supporting the role of both processes in generating
Wolbachia
diversity. Recombination was detected only among the STs in this study and not in those from the MLST database. Most of the strains were remarkably similar in their
wsp
genotype, despite divergence in MLST. Only two
wsp
alleles were found among 25 individuals with complete hypervariable region (HVR) peptide profiles. Although both
wsp
and MLST show variability, MLST gives better separation between the strains. Completely different STs were characterized for the individuals sharing the same
wsp
alleles.
Characterization of the Biosynthetic Operon for the Antibacterial Peptide Herbicolin in Pantoea vagans Biocontrol Strain C9-1 and Incidence in Pantoea Species
Authors: Kamber Tim , Lansdell Theresa A. , Stockwell Virginia O. , Ishimaru Carol A. , Smits Theo H. M. , Duffy Brion 
Published: April 2012

ABSTRACT

Pantoea vagans
C9-1 is a biocontrol strain that produces at least two antibiotics inhibiting the growth of
Erwinia amylovora
, the causal agent of fire blight disease of pear and apple. One antibiotic, herbicolin I, was purified from culture filtrates of
P. vagans
C9-1 and determined to be 2-amino-3-(oxirane-2,3-dicarboxamido)-propanoyl-valine, also known as
N
ß
-epoxysuccinamoyl-DAP-valine. A plasposon library was screened for mutants that had lost the ability to produce herbicolin I. It was shown that mutants had reduced biocontrol efficacy in immature pear assays. The biosynthetic gene cluster in
P. vagans
C9-1 was identified by sequencing the flanking regions of the plasposon insertion sites. The herbicolin I biosynthetic gene cluster consists of 10 coding sequences (CDS) and is located on the 166-kb plasmid pPag2. Sequence comparisons identified orthologous gene clusters in
Pantoea agglomerans
CU0119 and
Serratia proteamaculans
568. A low incidence of detection of the biosynthetic cluster in a collection of 45
Pantoea
spp. from biocontrol, environmental, and clinical origins showed that this is a rare trait among the tested strains.
Characterization and Identification of Productivity-Associated Rhizobacteria in Wheat
Authors: Anderson Michael , Habiger Joshua 
Published: April 2012

ABSTRACT

The rhizosphere is populated by a numerous and diverse array of rhizobacteria, and many impact productivity in largely unknown ways. Here we characterize the rhizobacterial community in a wheat variety categorized according to shoot biomass using 16S rRNA pyrosequencing abundance data. Plants were grown in homogenized field soil under greenhouse conditions, and DNA was extracted and pyrosequenced, resulting in 29,007 quality sequences. Operational taxonomic units (OTUs) that were significantly associated with biomass productivity were identified using an exact test adjusted for the false-discovery rate. The productivity deviation expressed as a percentage of the total mean square for regression (PMSR) was determined for each OTU. Out of 719 OTUs, 42 showed significant positive associations and 39 showed significant negative associations (
q
value, ≤0.05). OTUs with the greatest net positive associations, by genus, were as follows:
Duganella
, OTU 43 and OTU 3;
Janthinobacterium
, OTU 278;
Pseudomonas
, OTU 588; and
Cellvibrio
, OTU 1847. Those with negative associations were as follows:
Bacteria
, OTU 273;
Chryseobacterium
, OTU 508;
Proteobacteria
, OTU 249; and
Enterobacter
, OTU 357. Shoot biomass productivity was strongly correlated with the balance between the overall abundances of positive- and negative-productivity-associated OTUs. High-productivity rhizospheres contained 9.2 significant positives for every negatively associated rhizobacterium, while low-productivity rhizospheres showed 2.3 significant negatives for every positively associated rhizobacterium. Overall rhizobacterial community diversity as measured by the Chao1, Shannon, and Simpson indexes was nonlinearly related to productivity, closely fitting a wavelike cubic equation. We conclude that shoot biomass productivity is strongly related to the ratio of positive- to negative-productivity-associated rhizobacteria in the rhizosphere. This study identifies significant OTUs composing the productive and unproductive rhizobacterial communities.
Substrate-Induced Change in the Quaternary Structure of Type 2 Isopentenyl Diphosphate Isomerase from Sulfolobus shibatae
Authors: Nakatani Hitomi , Goda Shuichiro , Unno Hideaki , Nagai Takuya , Yoshimura Tohru , Hemmi Hisashi 
Published: April 2012

ABSTRACT

Type 2 isopentenyl diphosphate isomerase catalyzes the interconversion between two active units for isoprenoid biosynthesis, i.e., isopentenyl diphosphate and dimethylallyl diphosphate, in almost all archaea and in some bacteria, including human pathogens. The enzyme is a good target for discovery of antibiotics because it is essential for the organisms that use only the mevalonate pathway to produce the active isoprene units and because humans possess a nonhomologous isozyme, type 1 isopentenyl diphosphate isomerase. However, type 2 enzymes were reportedly inhibited by mechanism-based drugs for the type 1 enzyme due to their surprisingly similar reaction mechanisms. Thus, a different approach is now required to develop new inhibitors specific to the type 2 enzyme. X-ray crystallography and gel filtration chromatography revealed that the enzyme from a thermoacidophilic archaeon,
Sulfolobus shibatae
, is in the octameric state at a high concentration. Interestingly, a part of the regions that are involved in the substrate binding in the previously reported tetrameric structures is integral to the formation of the tetramer-tetramer interface in the substrate-free octameric structure. Site-directed mutagenesis at such regions resulted in stabilization of the tetramer. Small-angle X-ray scattering, tryptophan fluorescence, and dynamic light scattering analyses showed that substrate binding causes the dissociation of an octamer into tetramers. This property, i.e., incompatibility between octamer formation and substrate binding, might provide clues to develop new specific inhibitors of the archaeal enzyme.
HmuP Is a Coactivator of Irr-Dependent Expression of Heme Utilization Genes in Bradyrhizobium japonicum
Authors: Escamilla-Hernandez Rosalba , O'Brian Mark R. 
Published: April 2012

ABSTRACT

Utilization of heme as an iron source by
Bradyrhizobium japonicum
involves induction of the outer membrane heme receptor gene
hmuR
and other genes within the heme utilization locus. Here, we discovered the
hmuP
gene located upstream of
hmuR
and transcribed divergently from it along with
hmuTUV
.
hmuP
encodes a small protein that accumulated under iron limitation and is transcriptionally controlled by the global iron-responsive regulator Irr, as were all genes within the heme utilization locus. Cross-linking and immunoprecipitation experiments showed that Irr occupies the
hmuR
-
hmuP
promoter
in vivo
. An
hmuP
mutant did not grow on heme as an iron source, but retained the ability to use ferric chloride. Correspondingly, induction of
hmuR
mRNA under iron limitation was severely diminished in an
hmuP
strain, but other genes within the Irr regulon were unaffected. HmuP occupied the
hmuR
-
hmuP
promoter, and thus it plays a direct regulatory role in gene expression. HmuP was not required for Irr occupancy, nor was ectopic expression of
hmuP
from an Irr-independent promoter sufficient to induce the
hmuR
gene. Thus, both HmuP and Irr occupancy are necessary for
hmuR
induction. We suggest that HmuP is a coactivator of Irr-dependent expression of
hmuR
.
Identification of ZapD as a Cell Division Factor That Promotes the Assembly of FtsZ in Escherichia coli
Authors: Durand-Heredia Jorge , Rivkin Eugene , Fan Guoxiang , Morales Jorge , Janakiraman Anuradha 
Published: April 2012

ABSTRACT

The tubulin homolog FtsZ forms a polymeric membrane-associated ring structure (Z ring) at midcell that establishes the site of division and provides an essential framework for the localization of a multiprotein molecular machine that promotes division in
Escherichia coli
. A number of regulatory proteins interact with FtsZ and modulate FtsZ assembly/disassembly processes, ensuring the spatiotemporal integrity of cytokinesis. The Z-associated proteins (ZapA, ZapB, and ZapC) belong to a group of FtsZ-regulatory proteins that exhibit functionally redundant roles in stabilizing FtsZ-ring assembly by binding and bundling polymeric FtsZ at midcell. In this study, we report the identification of ZapD (YacF) as a member of the
E. coli
midcell division machinery. Genetics and cell biological evidence indicate that ZapD requires FtsZ but not other downstream division proteins for localizing to midcell, where it promotes FtsZ-ring assembly via molecular mechanisms that overlap with ZapA. Biochemical evidence indicates that ZapD directly interacts with FtsZ and promotes bundling of FtsZ protofilaments. Similarly to ZapA, ZapB, and ZapC, ZapD is dispensable for division and therefore belongs to the growing group of FtsZ-associated proteins in
E. coli
that aid in the overall fitness of the division process.
Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia
Authors: Trost Eva , Blom Jochen , de Castro Soares Siomar , Huang I-Hsiu , Al-Dilaimi Arwa , Schröder Jasmin , Jaenicke Sebastian , Dorella Fernanda A. , Rocha Flavia S. , Miyoshi Anderson , Azevedo Vasco , Schneider Maria P. , Silva Artur , Camello Thereza C. , Sabbadini Priscila S. , Santos Cíntia S. , Santos Louisy S. , Hirata Raphael , Mattos-Guaraldi Ana L. , Efstratiou Androulla , Schmitt Michael P. , Ton-That Hung , Tauch Andreas 
Published: April 2012

ABSTRACT

Corynebacterium diphtheriae
is one of the most prominent human pathogens and the causative agent of the communicable disease diphtheria. The genomes of 12 strains isolated from patients with classical diphtheria, endocarditis, and pneumonia were completely sequenced and annotated. Including the genome of
C. diphtheriae
NCTC 13129, we herewith present a comprehensive comparative analysis of 13 strains and the first characterization of the pangenome of the species
C. diphtheriae
. Comparative genomics showed extensive synteny and revealed a core genome consisting of 1,632 conserved genes. The pangenome currently comprises 4,786 protein-coding regions and increases at an average of 65 unique genes per newly sequenced strain. Analysis of prophages carrying the diphtheria toxin gene
tox
revealed that the toxoid vaccine producer
C. diphtheriae
Park-Williams no. 8 has been lysogenized by two copies of the ω

tox

+
phage, whereas
C. diphtheriae
31A harbors a hitherto-unknown
tox
+
corynephage. DNA binding sites of the
tox
-controlling regulator DtxR were detected by genome-wide motif searches. Comparative content analysis showed that the DtxR regulons exhibit marked differences due to gene gain, gene loss, partial gene deletion, and DtxR binding site depletion. Most predicted pathogenicity islands of
C. diphtheriae
revealed characteristics of horizontal gene transfer. The majority of these islands encode subunits of adhesive pili, which can play important roles in adhesion of
C. diphtheriae
to different host tissues. All sequenced isolates contain at least two pilus gene clusters. It appears that variation in the distributed genome is a common strategy of
C. diphtheriae
to establish differences in host-pathogen interactions.
Genetic Analysis of 15 Protein Folding Factors and Proteases of the Escherichia coli Cell Envelope
Authors: Weski Juliane , Ehrmann Michael 
Published: April 2012

ABSTRACTEach cell hosts thousands of proteins that vary greatly in abundance, structure, and chemical properties. To ensure that all proteins are biologically active and properly localized, efficient quality control systems have evolved. While the structure, function, and regulation of some individual protein folding factors and proteases were resolved up to atomic resolution, others remain poorly characterized. In addition, little is known about which factors are required for viability under specific stress conditions. We therefore determined the physiological implications of 15 factors of theE. colicell envelope by an integrated genetic approach comprising phenotypic analyses. Our data indicate thatsurAandtspnull mutations are a lethal combination in rich medium, thatsurA dsbAandsurA dsbCdouble mutants are temperature sensitive, and thatsurA ptrA,surA yfgC,dsbA fkpA,degP tsp,degP ppiD,tsp ppiD, anddegP dsbAdouble mutants are temperature sensitive in rich medium containing 0.5 M NaCl, whiledegP dsbA,degP yfgC,tsp ydgD, anddegP tspdouble mutants do not grow in the presence of SDS/EDTA. Furthermore, we show that indegP dsbA,degP tsp, anddegP yfgCdouble mutants a subpopulation of LamB exists as unfolded monomers. In addition,dsbAnull mutants expressed lower levels of the outer membrane proteins LptD, LamB, FhuA, and OmpW while FhuA levels were reduced insurAsingle anddegP ppiDdouble mutants. Lower FhuA levels indegP ppiDstrains depend on Tsp, since in atsp degP ppiDtriple mutant FhuA levels are restored.