bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogenicity Island Markers, Virulence Determinants
malX
and
usp
, and the Capacity of
Escherichia coli
To Persist in Infants' Commensal Microbiotas
Authors: Östblom Anna , Adlerberth Ingegerd , Wold Agnes E. , Nowrouzian Forough L. 
Published: February 2011

ABSTRACT

Virulence-associated genes in bacteria are often located on chromosomal regions, termed pathogenicity islands (PAIs). Several PAIs are found in
Escherichia coli
strains that cause extraintestinal infections, but their role in commensal bowel colonization is unknown. Resident strains are enriched in adhesins (P fimbriae and type 1 fimbriae), capsular antigens (K1 and K5), hemolysin, and aerobactin and mostly belong to phylogenetic group B2. Here, we investigated whether six pathogenicity islands and the virulence determinants
malX
and
usp
are associated with fitness of
E. coli
in the infant bowel microbiota.
E. coli
strains isolated from stools of 130 Swedish infants during the first year of life were examined for their carriage of PAI markers,
malX
, and
usp
by PCR. Carriage was related to strain persistence: long-term colonizers (≥12 months) carried significantly more of PAI II from strain CFT703 (II
CFT703
), IV
536,
and II
J96
and
malX
and
usp
than intermediate colonizers (1 to 11 months) and transient strains (<3 weeks). The accumulation of PAI markers in each individual strain correlated positively with its time of persistence in the colon. Phylogenetic group B2 accounted for 69% of long-term colonizers, 46% of intermediate colonizers and 14% of transient strains. These results support the hypothesis that some bacterial traits contributing to extraintestinal infections have in fact evolved primarily because they increase the fitness of
E. coli
in its natural niche, the colon; accordingly, they may be regarded as fitness islands in the gut.
Distribution and Diversity of
Gallionella
-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh
Authors: Wang Juanjuan , Vollrath Susann , Behrends Thilo , Bodelier Paul L. E. , Muyzer Gerard , Meima-Franke Marion , Den Oudsten Frank , Van Cappellen Philippe , Laanbroek Hendrikus J. 
Published: February 2011

ABSTRACT

Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting
Gallionella-
related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay.
Gallionella
-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of
Gallionella
-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
Inhibitory Spectra and Modes of Antimicrobial Action of Gallotannins from Mango Kernels (Mangifera indicaL.)
Authors: Engels Christina , Schieber Andreas , Gänzle Michael G. 
Published: February 2011

ABSTRACTThis study investigated the antimicrobial activities and modes of action of penta-, hexa-, hepta-, octa-, nona-, and deca-O-galloylglucose (gallotannins) isolated from mango kernels. The MICs and minimum bactericidal concentrations (MBCs) against food-borne bacteria and fungi were determined using a critical dilution assay. Gram-positive bacteria were generally more susceptible to gallotannins than were Gram-negative bacteria. The MICs of gallotannins againstBacillus subtilis,Bacillus cereus,Clostridium botulinum,Campylobacter jejuni,Listeria monocytogenes, andStaphylococcus aureuswere 0.2 g liter−1or less; enterotoxigenicEscherichia coliandSalmonella entericawere inhibited by 0.5 to 1 g liter−1, and lactic acid bacteria were resistant. The use of lipopolysaccharide mutants ofS. entericaindicated that the outer membrane confers resistance toward gallotannins. Supplementation of LB medium with iron eliminated the inhibitory activity of gallotannins againstStaphylococcus aureus, and siderophore-deficient mutants ofS. entericawere less resistant toward gallotannins than was the wild-type strain. Hepta-O-galloylglucose sensitizedLactobacillus plantarumTMW1.460 to hop extract, indicating inactivation of hop resistance mechanisms, e.g., the multidrug resistance (MDR) transporter HorA. Carbohydrate metabolism ofLactococcus lactisMG1363, a conditionally respiring organism, was influenced by hepta-O-galloylglucose when grown under aerobic conditions and in the presence of heme but not under anaerobic conditions, indicating that gallotannins influence the respiratory chain. In conclusion, the inhibitory activities of gallotannins are attributable to their strong affinity for iron and likely additionally relate to the inactivation of membrane-bound proteins.
Inhibition of Predation by
Bdellovibrio bacteriovorus
and
Micavibrio aeruginosavorus
via Host Cell Metabolic Activity in the Presence of Carbohydrates
Authors: Dashiff Aliza , Keeling Thomas G. , Kadouri Daniel E. 
Published: February 2011

ABSTRACT

Bdellovibrio bacteriovorus
and
Micavibrio aeruginosavorus
are highly motile Gram-negative predatory bacteria with the potential of being used as biocontrol agents or living antibiotics. It was suggested previously that sugar-binding proteins play a role in
M. aeruginosavorus
and
B. bacteriovorus
host specificity and predator-prey interactions. The effect of carbohydrates on predation was reexamined in this study. It was demonstrated that the presence of carbohydrates could indeed block predation. However, further investigation demonstrated that inhibition of predation was due to medium acidification by the metabolic activity of the host and not to a blocking of a putative sugar-binding protein. The data presented here might be of value when storing, growing, and cultivating predatory bacteria, as well as when considering environmental conditions that might influence predation in the field.
Proof of Concept for Recombinant Cellular Controls in Quantitative Molecular Pathogen Detection
Authors: Rossmanith Peter , Mester Patrick , Frühwirth Karin , Fuchs Sabine , Wagner Martin 
Published: February 2011

ABSTRACT

In this study, we present the concept of internal sample process controls (ISPCs) to monitor the efficiency of an analytical chain using sample preparation and quantitative PCR (qPCR). A recombinant
Listeria monocytogenes
Δ
prfA
(targeted deletion) strain containing a competitive artificial single-copy genomic target was applied to naturally contaminated samples to demonstrate its analytical suitability as an ISPC.
Contribution of Rapid Evolution of theluxR-luxIIntergenic Region to the Diverse Bioluminescence Outputs ofVibrio fischeriStrains Isolated from Different Environments
Authors: Bose Jeffrey L. , Wollenberg Michael S. , Colton Deanna M. , Mandel Mark J. , Septer Alecia N. , Dunn Anne K. , Stabb Eric V. 
Published: February 2011

ABSTRACTVibrio fischeriserves as a valuable model of bacterial bioluminescence, its regulation, and its functional significance. Light output varies more than 10,000-fold in wild-type isolates from different environments, yet dim and bright strains have similar organization of the light-producingluxgenes, with the activator-encodingluxRdivergently transcribed fromluxICDABEG. By comparing the genomes of bright strain MJ11 and the dimmer ES114, we found that theluxregion has diverged more than most shared orthologs, including those flankinglux. Divergence was particularly high in the intergenic sequence betweenluxRandluxI. Analysis of the intergenicluxregion from 18V. fischeristrains revealed that, with one exception, sequence divergence essentially mirrored strain phylogeny but with relatively high substitution rates. The bases conserved among intergenicluxR-luxIsequences included binding sites for known regulators, such as LuxR and ArcA, and bases of unknown significance, including a striking palindromic repeat. By using this collection of diverseluxR-luxIregions, we found that expression of PluxI-lacZbut not PluxR-lacZtranscriptional reporters correlated with the luminescence output of the strains from which the promoters originated. We also found that exchange of a small stretch of theluxI-luxRintergenic region between two strains largely reversed their relative brightness. Our results show that theluxR-luxIintergenic region contributes significantly to the variable luminescence output amongV. fischeristrains isolated from different environments, although other elements of strain backgrounds also contribute. Moreover, theluxsystem appears to have evolved relatively rapidly, suggesting unknown environment-specific selective pressures.
Synechococcus
sp. Strain PCC 7002
nifJ
Mutant Lacking Pyruvate:Ferredoxin Oxidoreductase
Authors: McNeely Kelsey , Xu Yu , Ananyev Gennady , Bennette Nicholas , Bryant Donald A. , Dismukes G. Charles 
Published: February 2011

ABSTRACT

The
nifJ
gene codes for pyruvate:ferredoxin oxidoreductase (PFOR), which reduces ferredoxin during fermentative catabolism of pyruvate to acetyl-coenzyme A (acetyl-CoA). A
nifJ
knockout mutant was constructed that lacks one of two pathways for the oxidation of pyruvate in the cyanobacterium
Synechococcus
sp. strain PCC 7002. Remarkably, the photoautotrophic growth rate of this mutant increased by 20% relative to the wild-type (WT) rate under conditions of light-dark cycling. This result is attributed to an increase in the quantum yield of photosystem II (PSII) charge separation as measured by photosynthetic electron turnover efficiency determined using fast-repetition-rate fluorometry (

F
v

/

F
m

). During autofermentation, the excretion of acetate and lactate products by
nifJ
mutant cells decreased 2-fold and 1.2-fold, respectively. Although
nifJ
cells displayed higher
in vitro
hydrogenase activity than WT cells, H
2
production
in vivo
was 1.3-fold lower than the WT level. Inhibition of acetate-CoA ligase and pyruvate dehydrogenase complex by glycerol eliminated acetate production, with a resulting loss of reductant and a 3-fold decrease in H
2
production by
nifJ
cells compared to WT cells. Continuous electrochemical detection of dissolved H
2
revealed two temporally resolved phases of H
2
production during autofermentation, a minor first phase and a major second phase. The first phase was attributed to reduction of ferredoxin, because its level decreased 2-fold in
nifJ
cells. The second phase was attributed to glycolytic NADH production and decreased 20% in
nifJ
cells. Measurement of the intracellular NADH/NAD
+
ratio revealed that the reductant generated by PFOR contributing to the first phase of H
2
production was not in equilibrium with bulk NADH/NAD
+
and that the second phase corresponded to the equilibrium NADH-mediated process.
Molecular Characterization of a Novel
N
-Acetylneuraminate Lyase from
Lactobacillus plantarum
WCFS1
Authors: Sánchez-Carrón Guiomar , García-García María Inmaculada , López-Rodríguez Ana Belén , Jiménez-García Sofía , Sola-Carvajal Agustín , García-Carmona Francisco , Sánchez-Ferrer Álvaro 
Published: February 2011

ABSTRACT

N
-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of
N
-acetylneuraminic acid (Neu5Ac) to form pyruvate and
N
-acetyl-
d
-mannosamine (ManNAc). In nature,
N
-acetylneuraminate lyase occurs mainly in pathogens. However, this paper describes how an
N
-acetylneuraminate lyase was cloned from the human gut commensal
Lactobacillus plantarum
WCFS1 (LpNAL), overexpressed, purified, and characterized for the first time. This novel enzyme, which reaches a high expression level (215 mg liter
−1
culture), shows similar catalytic efficiency to the best NALs previously described. This homotetrameric enzyme (132 kDa) also shows high stability and activity at alkaline pH (pH > 9) and good temperature stability (60 to 70°C), this last feature being further improved by the presence of stabilizing additives. These characteristics make LpNAL a promising biocatalyst. When its sequence was compared with that of other, related (real and putative) NALs described in the databases, it was seen that NAL enzymes could be divided into four structural groups and three subgroups. The relation of these subgroups with human and other mammalian NALs is also discussed.
Mitosis in the Human Malaria Parasite Plasmodium falciparum
Authors: Gerald Noel , Mahajan Babita , Kumar Sanjai 
Published: February 2011

ABSTRACT

Malaria is caused by intraerythrocytic protozoan parasites belonging to
Plasmodium
spp. (phylum
Apicomplexa
) that produce significant morbidity and mortality, mostly in developing countries.
Plasmodium
parasites have a complex life cycle that includes multiple stages in anopheline mosquito vectors and vertebrate hosts. During the life cycle, the parasites undergo several cycles of extreme population growth within a brief span, and this is critical for their continued transmission and a contributing factor for their pathogenesis in the host. As with other eukaryotes, successful mitosis is an essential requirement for
Plasmodium
reproduction; however, some aspects of
Plasmodium
mitosis are quite distinct and not fully understood. In this review, we will discuss the current understanding of the architecture and key events of mitosis in
Plasmodium falciparum
and related parasites and compare them with the traditional mitotic events described for other eukaryotes.
Plasmodium falciparum var Gene Silencing Is Determined bycisDNA Elements That Form Stable and Heritable Interactions
Authors: Swamy Lakshmi , Amulic Borko , Deitsch Kirk W. 
Published: February 2011

ABSTRACTAntigenic variation in the human malaria parasitePlasmodium falciparumdepends on the transcriptional regulation of thevargene family. In each individual parasite, mRNA is expressed exclusively from 1vargene out of ∼60, while the rest of the genes are transcriptionally silenced. Both modifications to chromatin structure and DNA regulatory elements associated with eachvargene have been implicated in the organization and maintenance of the silent state. Whether silencing is established at the level of entire chromosomal regions via heterochromatin spreading or at the level of individualvarpromoters through the action of a silencing element within eachvarintron has been debated. Here, we consider both possibilities, using clonal parasite lines carrying chromosomally integrated transgenes. We confirm a previous finding that the loss of an adjacentvarintron results invarpromoter activation and further show that transcriptional activation of avarpromoter within a cluster does not affect the transcriptional activity of neighboringvarpromoters. Our results provide more evidence for the hypothesis thatvargenes are primarily silenced at the level of an individual gene, rather than by heterochromatin spreading. We also tested the intrinsic directionality of an intron's silencing effect on upstream or downstreamvarpromoters. We found that an intron is capable of silencing in either direction and that, once established, avarpromoter-intron pair is stably maintained through many generations, suggesting a possible role in epigenetic memory. This study provides insights into the regulation of endogenousvargene clusters.
An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis
Authors: Madhusoodanan Jyoti , Seo Keun Seok , Remortel Brian , Park Joo Youn , Hwang Sun Young , Fox Lawrence K. , Park Yong Ho , Deobald Claudia F. , Wang Dan , Liu Song , Daugherty Sean C. , Gill Ann Lindley , Bohach Gregory A. , Gill Steven R. 
Published: February 2011

ABSTRACT

Cocolonization of human mucosal surfaces causes frequent encounters between various staphylococcal species, creating opportunities for the horizontal acquisition of mobile genetic elements. The majority of
Staphylococcus aureus
toxins and virulence factors are encoded on
S. aureus
pathogenicity islands (SaPIs). Horizontal movement of SaPIs between
S. aureus
strains plays a role in the evolution of virulent clinical isolates. Although there have been reports of the production of toxic shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by coagulase-negative staphylococci, no associated pathogenicity islands have been found in the genome of
Staphylococcus epidermidis
, a generally less virulent relative of
S. aureus
. We show here the first evidence of a composite

S

.

e

pidermidis
p
athogenicity
i
sland (SePI), the product of multiple insertions in the genome of a clinical isolate. The taxonomic placement of
S. epidermidis
strain FRI909 was confirmed by a number of biochemical tests and multilocus sequence typing. The genome sequence of this strain was analyzed for other unique gene clusters and their locations. This pathogenicity island encodes and expresses staphylococcal enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL), as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblotting. We present here an initial characterization of this novel pathogenicity island, and we establish that it is stable, expresses enterotoxins, and is not obviously transmissible by phage transduction. We also describe the genome sequence, excision, replication, and packaging of a novel bacteriophage in
S. epidermidis
FRI909, as well as attempts to mobilize the SePI element by this phage.
Fatty Acid-Related Phylogeny of Myxobacteria as an Approach to Discover Polyunsaturated Omega-3/6 Fatty Acids
Authors: Garcia Ronald , Pistorius Dominik , Stadler Marc , Müller Rolf 
Published: February 2011

ABSTRACT

In an analysis of 47 aerobic myxobacterial strains, representing 19 genera in suborders
Cystobacterineae
,
Nannocystineae
,
Sorangiineae
, and a novel isolate, “
Aetherobacter
” SBSr008, an enormously diverse array of fatty acids (FAs) was found. The distribution of straight-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) supports the reported clustering of strains in the phylogenetic tree based on 16S rRNA genes. This finding additionally allows the prediction and assignment of the novel isolate SBSr008 into its corresponding taxon.
Sorangiineae
predominantly contains larger amounts of SCFA (57 to 84%) than BCFA. On the other hand,
Cystobacterineae
exhibit significant BCFA content (53 to 90%), with the exception of the genus
Stigmatella
. In
Nannocystineae
, the ratio of BCFA and SCFA seems dependent on the taxonomic clade. Myxobacteria could also be identified and classified by using their specific and predominant FAs as biomarkers.
Nannocystineae
is remarkably unique among the suborders for its absence of hydroxy FAs. After the identification of arachidonic (AA) FA in
Phaselicystidaceae
, eight additional polyunsaturated fatty acids (PUFAs) belonging to the omega-6 and omega-3 families were discovered. Here we present a comprehensive report of FAs found in aerobic myxobacteria. Gliding bacteria belonging to
Flexibacter
and
Herpetosiphon
were chosen for comparative analysis to determine their FA profiles in relation to the myxobacteria.
Lactococcus lactis ZitR Is a Zinc-Responsive Repressor Active in the Presence of Low, Nontoxic Zinc Concentrations In Vivo
Authors: Llull Daniel , Son Olivier , Blanié Sandrine , Briffotaux Julien , Morello Eric , Rogniaux Hélène , Danot Olivier , Poquet Isabelle 
Published: February 2011

ABSTRACT

In the family
Streptococcaceae
, the genes encoding zinc ABC uptake systems (called
zit
or
adc
) are regulated by a coencoded MarR family member (i.e., ZitR or AdcR), whereas in the great majority of bacteria, these genes are regulated by Zur, the Fur-like zinc-responsive repressor. We studied the
zit
operon from
Lactococcus lactis
and its regulation in response to Zn(II)
in vivo. zit
transcription is repressed by Zn(II) in a wide concentration range starting from nontoxic micromolar levels and is derepressed at nanomolar concentrations. The level of
zit
promoter downregulation by environmental Zn(II) is correlated with the intracellular zinc content. The helix-turn-helix domain of ZitR is required for downregulation.
In vitro
, the purified protein is a dimer that complexes up to two zinc ligands per monomer and specifically binds two intact palindromic operator sites overlapping the −35 and −10 boxes of the
zit
promoter. DNA binding is abolished by the chelator EDTA or TPEN and fully restored by Zn(II) addition, indicating that the active repressor complexes Zn(II) with high affinity. These results suggest that derepression under starvation conditions could be an essential emergency mechanism for preserving Zn(II) homeostasis by uptake; under Zn(II)-replete conditions, the function of ZitR repression could be to help save energy rather than to avoid Zn(II) toxicity. The characterization of a MarR family zinc-responsive repressor in this report gives insight into the way
Streptococcaceae
efficiently adapt to Zn(II) fluctuations in their diverse ecological niches.
The Interplay of ClpXP with the Cell Division Machinery in Escherichia coli
Authors: Camberg Jodi L. , Hoskins Joel R. , Wickner Sue 
Published: February 2011

ABSTRACT

ClpXP is a two-component protease composed of ClpX, an ATP-dependent chaperone that recognizes and unfolds specific substrates, and ClpP, a serine protease. One ClpXP substrate in
Escherichia coli
is FtsZ, which is essential for cell division. FtsZ polymerizes and forms the FtsZ ring at midcell, where division occurs. To investigate the role of ClpXP in cell division, we examined the effects of
clpX
and
clpP
deletions in several strains that are defective for cell division. Together, our results suggested that ClpXP modulates cell division through degradation of FtsZ and possibly other cell division components that function downstream of FtsZ ring assembly. In the
ftsZ84
strain, which is temperature sensitive for filamentation due to a mutation in
ftsZ
, we observed that deletion of
clpX
or
clpP
suppresses filamentation and reduces FtsZ84 degradation. These results are consistent with ClpXP playing a role in cell division by modulating the level of FtsZ through degradation. In another division-defective strain, Δ
minC
, the additional deletion of
clpX
or
clpP
delays cell division and exacerbates filamentation. Our results demonstrate that ClpXP modulates division in cells lacking MinC by a mechanism that requires ATP-dependent degradation. However, antibiotic chase experiments
in vivo
indicate that FtsZ degradation is slower in the Δ
minC
strain than in the wild type, suggesting there may be another cell division component degraded by ClpXP. Taken together these studies suggest that ClpXP may degrade multiple cell division proteins, thereby modulating the precise balance of the components required for division.