bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influx of Enterococci and Associated Antibiotic Resistance and Virulence Genes from Ready-To-Eat Food to the Human Digestive Tract
Authors: Macovei Lilia , Zurek Ludek 
Published: September 2007

ABSTRACT

The influx of enterococcal antibiotic resistance (AR) and virulence genes from ready-to-eat food (RTEF) to the human digestive tract was assessed. Three RTEFs (chicken salad, chicken burger, and carrot cake) were sampled from five fast-food restaurants five times in summer (SU) and winter (WI). The prevalence of enterococci was significantly higher in SU (92.0% of salad samples and 64.0% of burger samples) than in WI (64.0% of salad samples and 24.0% of burger samples). The overall concentrations of enterococci during the two seasons were similar (∼10
3
CFU/g); the most prevalent were
Enterococcus casseliflavus
(41.5% of isolates) and
Enterococcus hirae
(41.5%) in WI and
Enterococcus faecium
(36.8%),
E. casseliflavus
(27.6%), and
Enterococcus faecalis
(22.4%) in SU. Resistance in WI was detected primarily to tetracycline (50.8%), ciprofloxacin (13.8%), and erythromycin (4.6%). SU isolates were resistant mainly to tetracycline (22.8%), erythromycin (22.1%), and kanamycin (13.0%). The most common
tet
gene was
tet
(M) (35.4% of WI isolates and 11.9% of SU isolates). The prevalence of virulence genes (
gelE
,
asa1
,
cylA
, and
esp
) and marker genes for clinical isolates (EF_0573, EF_0592, EF_0605, EF_1420, EF_2144, and pathogenicity island EF_0050) was low (≤12.3%). Genotyping of
E. faecalis
and
E. faecium
using pulsed-field gel electrophoresis revealed that the food contamination likely originated from various sources and that it was not clonal. Our conservative estimate (single AR gene copy per cell) for the influx of
tet
genes alone to the human digestive tract is 3.8 × 10
5
per meal (chicken salad). This AR gene influx is frequent because RTEFs are commonly consumed and that may play a role in the acquisition of AR determinants in the human digestive tract.
Impact of Plant Functional Group, Plant Species, and Sampling Time on the Composition of
nirK
-Type Denitrifier Communities in Soil
Authors: Bremer Christina , Braker Gesche , Matthies Diethart , Reuter Andreas , Engels Christof , Conrad Ralf 
Published: September 2007

ABSTRACT

We studied the influence of eight nonleguminous grassland plant species belonging to two functional groups (grasses and forbs) on the composition of soil denitrifier communities in experimental microcosms over two consecutive years. Denitrifier community composition was analyzed by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified
nirK
gene fragments coding for the copper-containing nitrite reductase. The impact of experimental factors (plant functional group, plant species, sampling time, and interactions between them) on the structure of soil denitrifier communities (i.e., T-RFLP patterns) was analyzed by canonical correspondence analysis. While the functional group of a plant did not affect
nirK
-type denitrifier communities, plant species identity did influence their composition. This effect changed with sampling time, indicating community changes due to seasonal conditions and a development of the plants in the microcosms. Differences in total soil nitrogen and carbon, soil pH, and root biomass were observed at the end of the experiment. However, statistical analysis revealed that the plants affected the
nirK
-type denitrifier community composition directly, e.g., through root exudates. Assignment of abundant T-RFs to cloned
nirK
sequences from the soil and subsequent phylogenetic analysis indicated a dominance of yet-unknown
nirK
genotypes and of genes related to
nirK
from denitrifiers of the order
Rhizobiales
. In conclusion, individual species of nonleguminous plants directly influenced the composition of denitrifier communities in soil, but environmental conditions had additional significant effects.
Kinesin-13 Regulates Flagellar, Interphase, and Mitotic Microtubule Dynamics in
Giardia intestinalis
Authors: Dawson Scott C. , Sagolla Meredith S. , Mancuso Joel J. , Woessner David J. , House Susan A. , Fritz-Laylin Lillian , Cande W. Zacheus 
Published: September 2007

ABSTRACT

Microtubule depolymerization dynamics in the spindle are regulated by kinesin-13, a nonprocessive kinesin motor protein that depolymerizes microtubules at the plus and minus ends. Here we show that a single kinesin-13 homolog regulates flagellar length dynamics, as well as other interphase and mitotic dynamics in
Giardia intestinalis
, a widespread parasitic diplomonad protist. Both green fluorescent protein-tagged kinesin-13 and EB1 (a plus-end tracking protein) localize to the plus ends of mitotic and interphase microtubules, including a novel localization to the eight flagellar tips, cytoplasmic anterior axonemes, and the median body. The ectopic expression of a kinesin-13 (S280N) rigor mutant construct caused significant elongation of the eight flagella with significant decreases in the median body volume and resulted in mitotic defects. Notably, drugs that disrupt normal interphase and mitotic microtubule dynamics also affected flagellar length in
Giardia
. Our study extends recent work on interphase and mitotic kinesin-13 functioning in metazoans to include a role in regulating flagellar length dynamics. We suggest that kinesin-13 universally regulates both mitotic and interphase microtubule dynamics in diverse microbial eukaryotes and propose that axonemal microtubules are subject to the same regulation of microtubule dynamics as other dynamic microtubule arrays. Finally, the present study represents the first use of a dominant-negative strategy to disrupt normal protein function in
Giardia
and provides important insights into giardial microtubule dynamics with relevance to the development of antigiardial compounds that target critical functions of kinesins in the giardial life cycle.
Candida albicans
Sfl1 Suppresses Flocculation and Filamentation
Authors: Bauer Janine , Wendland Jürgen 
Published: September 2007

ABSTRACT

Hyphal morphogenesis in
Candida albicans
is regulated by multiple pathways which act by either inducing or repressing filamentation. Most notably, Tup1, Nrg1, and Rfg1 are transcriptional repressors, while Efg1, Flo8, Cph1, and Czf1 can induce filamentation. Here, we present the functional analysis of Ca
SFL1
, which encodes the
C. albicans
homolog of the
Saccharomyces cerevisiae SFL1
(suppressor of flocculation) gene. Deletion of Ca
SFL1
results in flocculation (i.e., the formation of clumps) of yeast cells, which is most pronounced in minimal medium. The flocs contained hyphae already under noninducing conditions, and filamentation could be enhanced with hypha-inducing cues at 37°C. Expression of
SFL1
in a heterozygous mutant under the control of the Ca
MET3
promoter was shown to complement these defects and allowed switching between wild-type and mutant phenotypes. Interestingly, increased expression of
SFL1
using a
MET3prom-SFL1
construct prior to the induction of filamentation completely blocked germ tube formation. To localize Sfl1 in vivo, we generated a
SFL1-GFP
fusion. Sfl1-green fluorescent protein was found in the nucleus in both yeast cells and, to a lesser extent, hyphal cells. Using reverse transcription-PCR, we find an increased expression of
ALS1, ALS3, HWP1, ECE1
, and also
FLO8
. Our results suggest that Sfl1 functions in the repression of flocculation and filamentation and thus represents a novel negative regulator of
C. albicans
morphogenesis.
Transcriptional Gene Silencing Reveals Two Distinct Groups of
Entamoeba histolytica
Gal/GalNAc-Lectin Light Subunits
Authors: Bracha Rivka , Nuchamowitz Yael , Wender Nomy , Mirelman David 
Published: September 2007

ABSTRACT

The
Entamoeba histolytica
cell surface Gal/GalNAc-inhibitable lectin is a heterodimer between a heavy (170 kDa) subunit linked via a disulfide bond to a light (31 to 35 kDa) subunit. Five light subunit genes with high homology have been identified (Eh
lgl1
to -
5
). We have previously shown that silencing of the expression of Eh
lgl1
, in the G3 trophozoites which had already been silenced in the amoebapore gene (Eh
ap-a
), also suppressed the transcription of Eh
lgl2
and -
3
(strain RBV). The total absence of the lgl1 to -3 subunits in the RBV trophozoites affected their ability to cap the surface Gal-lectin molecules to the uroid region. We have now found that in the RBV trophozoites, the lgl4 and -5 subunits (31 kDa) are overexpressed and appear to compensate for the missing lgl1 to -3 in the heterodimer complex. Transcriptional silencing of Eh
lgl5
was achieved by transfection of G3 trophozoites with a plasmid containing the open reading frame of Eh
lgl5
ligated to the 5′ promoter region of the Eh
ap-a
gene. The transfected trophozoites (strain L5) were silenced in Eh
lgl5
and the closely related Eh
lgl4
, while the expression of the larger lgl1 to -3 subunits was upregulated. L5 trophozoites retained their ability to cap the Gal-lectin molecules. Attempts to simultaneously silence all of the Eh
lgl
genes have failed so far, possibly due to their crucial importance to the Gal-lectin functions. Our ability to silence part of the genes belonging to the same family can serve as a tool to study the relationships and functions of the members of other gene families.
Hydrogen Production by Termite Gut Protists: Characterization of Iron Hydrogenases of Parabasalian Symbionts of the Termite
Coptotermes formosanus
Authors: Inoue Jun-Ichi , Saita Kanako , Kudo Toshiaki , Ui Sadaharu , Ohkuma Moriya 
Published: September 2007

ABSTRACT

Cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (H
2
) that is emitted by the termites; however, little is known about the physiology and biochemistry of H
2
production from cellulose in the gut symbiotic protists due to their formidable unculturability. In order to understand the molecular basis for H
2
production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (Fe hydrogenases) in
Pseudotrichonympha grassii
, a large cellulolytic symbiont in the phylum Parabasalia, in the gut of the termite
Coptotermes formosanus
. The two Fe hydrogenases were phylogenetically distinct and had different N-terminal accessory domains. The long-form protein represented a phylogenetic lineage unique among eukaryotic Fe hydrogenases, whereas the short form was monophyletic with those of other parabasalids. Active recombinant enzyme forms of these two Fe hydrogenases were successfully obtained without the specific auxiliary maturases. Although they differed in their extent of specific activity and optimal pH, both enzymes preferentially catalyzed H
2
evolution rather than H
2
uptake. H
2
evolution, at least that associated with the short-form enzyme, was still active even under high hydrogen partial pressure. H
2
evolution activity was detected in the hydrogenosomal fraction of
P. grassii
cells; however, the vigorous H
2
uptake activity of the endosymbiotic bacteria compensated for the strong H
2
evolution activity of the host protists. The results suggest that termite gut symbionts are a rich reservoir of novel Fe hydrogenases whose properties are adapted to the gut environment and that the potential of H
2
production in termite guts has been largely underestimated.
Fully Codon-Optimized
luciferase
Uncovers Novel Temperature Characteristics of the
Neurospora
Clock
Authors: Gooch Van D. , Mehra Arun , Larrondo Luis F. , Fox Julie , Touroutoutoudis Melissa , Loros Jennifer J. , Dunlap Jay C. 
Published: September 2007

ABSTRACT

We report the complete reconstruction of the firefly
luciferase
gene, fully codon optimized for expression in
Neurospora crassa
. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the
frq
or
eas/ccg-2
promoter is used to drive
luciferase
, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony assay that will facilitate luciferase-based screens. The signals from sorbose-grown colonies of strains in which the
frq
promoter drives
luciferase
exhibit the properties of circadian rhythms and can be tracked for many days to weeks. This reporter now makes it possible to follow the clock in real time, even in strains or under conditions in which the circadian rhythm in conidial banding is not expressed. This property has been used to discover short, ca. 15-h period rhythms at high temperatures, at which banding becomes difficult to observe in race tubes, and to generate a high-resolution temperature phase-response curve.
Motility and Chemotaxis in
Agrobacterium tumefaciens
Surface Attachment and Biofilm Formation
Authors: Merritt Peter M. , Danhorn Thomas , Fuqua Clay 
Published: September 2007

ABSTRACT

Bacterial motility mechanisms, including swimming, swarming, and twitching, are known to have important roles in biofilm formation, including colonization and the subsequent expansion into mature structured surface communities. Directed motility requires chemotaxis functions that are conserved among many bacterial species. The biofilm-forming plant pathogen
Agrobacterium tumefaciens
drives swimming motility by utilizing a small group of flagella localized to a single pole or the subpolar region of the cell. There is no evidence for twitching or swarming motility in
A. tumefaciens.
Site-specific deletion mutations that resulted in either aflagellate, flagellated but nonmotile, or flagellated but nonchemotactic
A. tumefaciens
derivatives were examined for biofilm formation under static and flowing conditions. Nonmotile mutants were significantly deficient in biofilm formation under static conditions. Under flowing conditions, however, the aflagellate mutant rapidly formed aberrantly dense, tall biofilms. In contrast, a nonmotile mutant with unpowered flagella was clearly debilitated for biofilm formation relative to the wild type. A nontumbling chemotaxis mutant was only weakly affected with regard to biofilm formation under nonflowing conditions but was notably compromised in flow, generating less adherent biomass than the wild type, with a more dispersed cellular arrangement. Extragenic suppressor mutants of the chemotaxis-impaired, straight-swimming phenotype were readily isolated from motility agar plates. These mutants regained tumbling at a frequency similar to that of the wild type. Despite this phenotype, biofilm formation by the suppressor mutants in static cultures was significantly deficient. Under flowing conditions, a representative suppressor mutant manifested a phenotype similar to yet distinct from that of its nonchemotactic parent.
Virulence and Prodigiosin Antibiotic Biosynthesis inSerratiaAre Regulated Pleiotropically by the GGDEF/EAL Domain Protein, PigX
Authors: Fineran Peter C. , Williamson Neil R. , Lilley Kathryn S. , Salmond George P. C. 
Published: September 2007

ABSTRACTGram-negative bacteria of the genusSerratiaare opportunistic human, plant, and insect pathogens.Serratiasp. strain ATCC 39006 secretes pectinases and cellulases and produces the secondary metabolites carbapenem and prodigiosin. Mutation of a gene (pigX) resulted in an extremely pleiotropic phenotype: prodigiosin antibiotic biosynthesis, plant virulence, and pectinase production were all elevated. PigX controlled secondary metabolism by repressing the transcription of the target prodigiosin biosynthetic operon (pigA-pigO). The transcriptional start site ofpigXwas determined, andpigXexpression occurred in parallel with Pig production. Detailed quantitative intracellular proteome analyses enabled the identification of numerous downstream targets of PigX, including OpgG, mutation of which reduced the production of the plant cell wall-degrading enzymes and virulence. The highly pleiotropic PigX regulator contains GGDEF and EAL domains with noncanonical motifs and is predicted to be membrane associated. Genetic evidence suggests that PigX might function as a cyclic dimeric GMP phosphodiesterase. This is the first characterization of a GGDEF and EAL domain protein inSerratiaand the first example of the regulation of antibiotic production by a GGDEF/EAL domain protein.
Antigen 84, an Effector of Pleiomorphism inMycobacterium smegmatis
Authors: Nguyen Liem , Scherr Nicole , Gatfield John , Walburger Anne , Pieters Jean , Thompson Charles J. 
Published: September 2007

ABSTRACTWhile in most rod-shaped bacteria, morphology is based on MreB-like proteins that form an actin-like cytoskeletal scaffold for cell wall biosynthesis, the factors that determine the more flexible rod-like shape in actinobacteria such asMycobacteriumspecies are unknown. Here we show that aMycobacterium smegmatisprotein homologous to eubacterial DivIVA-like proteins, includingM. tuberculosisantigen 84 (Ag84), localized symmetrically to centers of peptidoglycan biosynthesis at the poles and septa. Controlled gene disruption experiments indicated that the gene encoding Ag84,wag31, was essential; when overexpressed, cells became longer and wider, with Ag84 asymmetrically distributed at one pole. Many became grossly enlarged, bowling-pin-shaped cells having up to 80-fold-increased volume. In these cells, Ag84 accumulated predominantly at a bulbous pole that was apparently generated by uncontrolled cell wall expansion. In some cells, Ag84 was associated with exceptional sites of cell wall expansion (buds) that evolved into branches.M. bovisBCG Ag84 was able to form oligomers in vitro, perhaps reflecting its superstructure in vivo. These data suggested a role for Ag84 in cell division and modulating cell shape in pleiomorphic actinobacteria.
Strain-Ecotype Specificity in
Sinorhizobium meliloti
-
Medicago truncatula
Symbiosis Is Correlated to Succinoglycan Oligosaccharide Structure
Authors: Simsek Senay , Ojanen-Reuhs Tuula , Stephens Samuel B. , Reuhs Bradley L. 
Published: September 2007

ABSTRACT

Molecular signals, including Nod factors and succinoglycan, are necessary for the establishment of nitrogen-fixing nodules (Fix
+
) in
Medicago truncatula
-
Sinorhizobium meliloti
symbiosis. This report shows that
M. truncatula
-
S. meliloti
interactions involve ecotype-strain specificity, as
S. meliloti
Rm41 and NRG247 are Fix
+
(compatible) on
M. truncatula
A20 and Fix
−
(incompatible) on
M. truncatula
A17, the Fix phenotypes are reversed with
S. meliloti
NRG185 and NRG34, and there is a correlation between the host specificity and succinoglycan oligosaccharide structure.
S. meliloti
NRG185 produces oligosaccharides that are almost fully succinylated, with two succinate groups per subunit, whereas the oligosaccharides produced by
S. meliloti
Rm41 include many nonsuccinylated subunits, as well as subunits with a single succinate group and others with malate. The results of this study demonstrated the following: (i) incompatibility is not a consequence of an avirulence factor or lack of Nod factor activity; (ii) the Fix
+
phenotypes are succinoglycan dependent; (iii) there is structural variability in the succinoglycan oligosaccharide populations between
S. meliloti
strains; (iv) the structural nature of the succinoglycan oligosaccharides is correlated to compatibility; most importantly, (v) an
S. meliloti
Rm41 derivative, carrying
exo
genes from an
M. truncatula
A17-compatible strain, produced a modified population of succinoglycan oligosaccharides (similar to the donor strain) and was Fix
+
on A17.
Differential Roles of Individual Domains in Selection of Secretion Route of a
Streptococcus parasanguinis
Serine-Rich Adhesin, Fap1
Authors: Chen Qiang , Sun Baiming , Wu Hui , Peng Zhixiang , Fives-Taylor Paula M. 
Published: September 2007

ABSTRACT

Fimbria-associated protein 1 (Fap1) is a high-molecular-mass glycosylated surface adhesin required for fimbria biogenesis and biofilm formation in
Streptococcus parasanguinis
. The secretion of mature Fap1 is dependent on the presence of SecA2, a protein with some homology to, but with a different role from, SecA. The signals that direct the secretion of Fap1 to the SecA2-dependent secretion pathway rather than the SecA-dependent secretion pathway have not yet been identified. In this study, Fap1 variants containing different domains were expressed in both
secA2
wild-type and mutant backgrounds and were tested for their ability to be secreted by the SecA- or SecA2-dependent pathway. The presence or absence of the cell wall anchor domain (residues 2531 to 2570) at the C terminus did not alter the selection of the Fap1 secretion route. The Fap1 signal peptide (residues 1 to 68) was sufficient to support the secretion of a heterologous protein via the SecA-dependent pathway, suggesting that the signal peptide was sufficient for recognition by the SecA-dependent pathway. The minimal sequences of Fap1 required for the SecA2-dependent pathway included the N-terminal signal peptide, nonrepetitive region I (residues 69 to 102), and part of nonrepetitive region II (residues 169 to 342). The two serine-rich repeat regions (residues 103 to 168 and 505 to 2530) were not required for Fap1 secretion. However, they were both involved in the specific inhibition of Fap1 secretion via the SecA-dependent pathway.
Role of SufI (FtsP) in Cell Division of
Escherichia coli
: Evidence for Its Involvement in Stabilizing the Assembly of the Divisome
Authors: Samaluru Harish , SaiSree L. , Reddy Manjula 
Published: September 2007

ABSTRACT

The function of SufI, a well-studied substrate of the TatABC translocase in
Escherichia coli
, is not known. It was earlier implicated in cell division, based on the finding that multiple copies of
sufI
suppressed the phenotypes of cells with mutations in
ftsI
(
ftsI23
), which encodes a divisomal transpeptidase. Recently,
sufI
was identified as both a multicopy suppressor gene and a synthetic lethal mutant of
ftsEX
, which codes for a division-specific putative ABC transporter. In this study, we show that
sufI
is essential for the viability of
E. coli
cells subjected to various forms of stress, including oxidative stress and DNA damage. The
sufI
mutant also exhibits
sulA
-independent filamentation, indicating a role in cell division. The phenotypes of the
sufI
mutant are suppressed by factors that stabilize FtsZ ring assembly, such as increased expression of cell division proteins FtsQAZ or FtsN or the presence of the gain-of-function
ftsA
* (FtsA R286W) mutation, suggesting that SufI is a divisomal protein required during stress conditions. In support of this, multicopy
sufI
suppressed the divisional defects of mutants carrying the
ftsA12
,
ftsQ1
, or
ftsK44
allele but not those of mutants carrying
ftsZ84
. Most of the division-defective mutants, in particular those carrying a Δ
ftsEX
or
ftsI23
allele, exhibited sensitivity to oxidative stress or DNA damage, and this sensitivity was also abolished by multiple copies of SufI. All of these data suggest that SufI is a division component involved in protecting or stabilizing the divisomal assembly under conditions of stress. Since
sufI
fulfils the requirements to be designated an
fts
gene, we propose that it be renamed
ftsP
.