bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and Genetic Characterization of a Novel Bacteriocin Locus in
Enterococcus avium
Isolates from Infants
Authors: Birri Dagim Jirata , Brede Dag A. , Forberg Torunn , Holo Helge , Nes Ingolf F. 
Published: November 2009

ABSTRACT

Enterococci are among the most common human intestinal lactic acid bacteria, and they are known to produce bacteriocins. In this study, fecal enterococci were isolated from infants and screened for bacteriocin production. Bacteriocin-producing
Enterococcus avium
isolates were obtained, and a new pediocin-like bacteriocin was purified and characterized. This bacteriocin, termed avicin A, was found to be produced by isolates from two healthy infants. It was purified to homogeneity from culture supernatant by ion-exchange and reversed-phase chromatography, and part of its amino acid sequence was obtained. The sequence of a 7-kb DNA fragment of a bacteriocin locus was determined by PCR and DNA sequencing. The bacteriocin locus was organized into four operon-like structures consisting of (i) the structural genes encoding avicin A and its immunity protein, (ii) a divergicin-like bacteriocin (avicin B) gene, (iii) an ABC bacteriocin transporter gene and two regulatory genes (histamine protein kinase- and response regulator-encoding genes), and (iv) induction peptide pheromone- and transport accessory protein-encoding genes. It was shown that the production of avicin A was regulated by the peptide pheromone-inducible regulatory system. Avicin A shows very high levels of similarity to mundticin KS and enterocin CRL35. This bacteriocin showed strong antimicrobial activity against many species of Gram-positive bacteria, including the food-borne pathogen
Listeria monocytogenes
. The avicin A locus is the first bacteriocin locus identified in
E. avium
to be characterized at the molecular level.
Gene Clusters Involved in Isethionate Degradation by Terrestrial and Marine Bacteria
Authors: Weinitschke Sonja , Sharma Pia I. , Stingl Ulrich , Cook Alasdair M. , Smits Theo H. M. 
Published: November 2009

ABSTRACT

Ubiquitous isethionate (2-hydroxyethanesulfonate) is dissimilated by diverse bacteria. Growth of
Cupriavidus necator
H16 with isethionate was observed, as was inducible membrane-bound isethionate dehydrogenase (IseJ) and inducible transcription of the genes predicted to encode IseJ and a transporter (IseU). Biodiversity in isethionate transport genes was observed and investigated by transcription experiments.
Production of Glycolic Acid by Chemolithotrophic Iron- and Sulfur-Oxidizing Bacteria and Its Role in Delineating and Sustaining Acidophilic Sulfide Mineral-Oxidizing Consortia
Authors: Ñancucheo Ivan , Johnson D. Barrie 
Published: November 2009

ABSTRACT

Glycolic acid was detected as an exudate in actively growing cultures of three chemolithotrophic acidophiles that are important in biomining operations,
Leptospirillum ferriphilum
,
Acidithiobacillus
(
At
.)
ferrooxidans
, and
At. caldus
. Although similar concentrations of glycolic acid were found in all cases, the concentrations corresponded to ca. 24% of the total dissolved organic carbon (DOC) in cultures of
L. ferriphilum
but only ca. 5% of the total DOC in cultures of the two
Acidithiobacillus
spp. Rapid acidification (to pH 1.0) of the culture medium of
At. caldus
resulted in a large increase in the level of DOC, although the concentration of glycolic acid did not change in proportion. The archaeon
Ferroplasma acidiphilum
grew in the cell-free spent medium of
At. caldus
; glycolic acid was not metabolized, although other unidentified compounds in the DOC pool were metabolized. Glycolic acid exhibited levels of toxicity with 21 strains of acidophiles screened similar to those of acetic acid. The most sensitive species were chemolithotrophs (
L. ferriphilum
and
At. ferrivorans
), while the most tolerant species were chemoorganotrophs (
Acidocella
,
Acidobacterium
, and
Ferroplasma
species), and the ability to metabolize glycolic acid appeared to be restricted (among acidophiles) to
Firmicutes
(chiefly
Sulfobacillus
spp.). Results of this study help explain why
Sulfobacillus
spp. rather than other acidophiles are the main organic carbon-degrading bacteria in continuously fed stirred tanks used to bioprocess sulfide mineral concentrates and also why temporary cessation of pH control in these systems, resulting in rapid acidification, often results in a plume of the archaeon
Ferroplasma
.
Detection of Infective Poliovirus by a Simple, Rapid, and Sensitive Flow Cytometry Method Based on Fluorescence Resonance Energy Transfer Technology
Authors: Cantera Jason L. , Chen Wilfred , Yates Marylynn V. 
Published: November 2009

ABSTRACT

The rapid and effective detection of virus infection is critical for clinical management and prevention of disease spread during an outbreak. Several methods have been developed for this purpose, of which classical serological and viral nucleic acid detection are the most common. We describe an alternative approach that utilizes engineered cells expressing fluorescent proteins undergoing fluorescence resonance energy transfer (FRET) upon cleavage by the viral 2A protease (2A
pro
) as an indication of infection. Quantification of the infectious-virus titers was resolved by using flow cytometry, and utility was demonstrated for the detection of poliovirus 1 (PV1) infection. Engineered buffalo green monkey kidney (BGMK) cells expressing the cyan fluorescent protein (CFP)-yellow fluorescent protein (YFP) substrate linked by a cleavage recognition site for PV1 2A
pro
were infected with different titers of PV1. After incubation at various time points, cells were harvested, washed, and subjected to flow cytometry analysis. The number of infected cells was determined by counting the number of cells with an increased CFP-to-YFP ratio. As early as 5 h postinfection, a significant number of infected cells (3%) was detected by flow cytometry, and cells infected with only 1 PFU were detected after 12 h postinfection. When applied to an environmental water sample spiked with PV1, the flow cytometry-based assay provided a level of sensitivity similar to that of the plaque assay for detecting and quantifying infectious virus particles. This approach, therefore, is more rapid than plaque assays and can be used to detect other viruses that frequently do not form clear plaques on cell cultures.
Spinacia oleracea
L. Leaf Stomata Harboring
Cryptosporidium parvum
Oocysts: a Potential Threat to Food Safety
Authors: Macarisin Dumitru , Bauchan Gary , Fayer Ronald 
Published: November 2009

ABSTRACT

Cryptosporidium parvum
is a cosmopolitan microscopic protozoan parasite that causes severe diarrheal disease (cryptosporidiosis) in mammals, including humans and livestock. There is growing evidence of
Cryptosporidium
persistence in fresh produce that may result in food-borne infection, including sporadic cases as well as outbreaks. However, drinking and recreational waters are still considered the major sources of
Cryptosporidium
infection in humans, which has resulted in prioritization of studies of parasite etiology in aquatic environments, while the mechanisms of transmission and parasite persistence on edible plants remain poorly understood. Using laser scanning confocal microscopy together with fluorescein-labeled monoclonal antibodies,
C. parvum
oocysts were found to strongly adhere to spinach plants after contact with contaminated water, to infiltrate through the stomatal openings in spinach leaves, and to persist at the mesophyll level. These findings and the fact that this pathogenic parasite resists washing and disinfection raise concerns regarding food safety.
The Major Catalase Gene (
katA
) of
Pseudomonas aeruginosa
PA14 Is under both Positive and Negative Control of the Global Transactivator OxyR in Response to Hydrogen Peroxide
Authors: Heo Yun-Jeong , Chung In-Young , Cho Wan-Je , Lee Bo-Young , Kim Jung-Hoon , Choi Kyoung-Hee , Lee Jin-Won , Hassett Daniel J. , Cho You-Hee 
Published: November 2009

ABSTRACT

The adaptive response to hydrogen peroxide (H
2
O
2
) in
Pseudomonas aeruginosa
involves the major catalase, KatA, and OxyR. However, neither the molecular basis nor the relationship between the aforementioned proteins has been established. Here, we demonstrate that the transcriptional activation of the
katA
promoter (
katAp
) in response to H
2
O
2
was abrogated in the
P. aeruginosa
PA14
oxyR
null mutant. Promoter deletion analyses revealed that H
2
O
2
-mediated induction was dependent on a region of DNA −76 to −36 upstream of the H
2
O
2
-responsive transcriptional start site. This region harbored the potential operator sites (OxyR-responsive element [ORE]) of the
Escherichia coli
OxyR binding consensus. Deletion of the entire ORE not only abolished H
2
O
2
-mediated induction but also elevated the basal transcription, suggesting the involvement of OxyR and the ORE in both transcriptional activation and repression. OxyR bound to the ORE both
in vivo
and
in vitro
, demonstrating that OxyR directly regulates the
katAp
. Three distinct mobility species of oxidized OxyR were observed in response to 1 mM H
2
O
2
, as assessed by free thiol trapping using 4-acetamido-4′-maleimidylstilbene-2,2′-disulfonic acid. These oxidized species were not observed for the double mutants with mutations in the conserved cysteine (Cys) residues (C199 and C208). The uninduced transcription of
katAp
was elevated in an
oxyR
mutant with a mutation of Cys to serine at 199 (C199S) and even higher in the
oxyR
mutant with a mutation of Cys to alanine at 199 (C199A) but not in
oxyR
mutants with mutations in C208 (C208S and C208A). In both the C199S and the C208S mutant, however,
katAp
transcription was still induced by H
2
O
2
treatment, unlike in the
oxyR
null mutant and the C199A mutant. The double mutants with mutations in both Cys residues (C199S C208S and C199A C208S) did not differ from the C199A mutant. Taken together, our results suggest that
P. aeruginosa
OxyR is a bona fide transcriptional regulator of the
katA
gene, sensing H
2
O
2
based on the conserved Cys residues, involving more than one oxidation as well as activation state
in vivo
.
Evidence that Ubiquinone Is a Required Intermediate for Rhodoquinone Biosynthesis in
Rhodospirillum rubrum
Authors: Brajcich Brian C. , Iarocci Andrew L. , Johnstone Lindsey A. G. , Morgan Rory K. , Lonjers Zachary T. , Hotchko Matthew J. , Muhs Jordan D. , Kieffer Amanda , Reynolds Bree J. , Mandel Sarah M. , Marbois Beth N. , Clarke Catherine F. , Shepherd Jennifer N. 
Published: November 2009

ABSTRACT

Rhodoquinone (RQ) is an important cofactor used in the anaerobic energy metabolism of
Rhodospirillum rubrum
. RQ is structurally similar to ubiquinone (coenzyme Q or Q), a polyprenylated benzoquinone used in the aerobic respiratory chain. RQ is also found in several eukaryotic species that utilize a fumarate reductase pathway for anaerobic respiration, an important example being the parasitic helminths. RQ is not found in humans or other mammals, and therefore inhibition of its biosynthesis may provide a parasite-specific drug target. In this report, we describe several
in vivo
feeding experiments with
R. rubrum
used for the identification of RQ biosynthetic intermediates. Cultures of
R. rubrum
were grown in the presence of synthetic analogs of ubiquinone and the known Q biosynthetic precursors demethylubiquinone, demethoxyubiquinone, and demethyldemethoxyubiquinone, and assays were monitored for the formation of RQ
3
. Data from time course experiments and
S
-adenosyl-
l
-methionine-dependent
O
-methyltransferase inhibition studies are discussed. Based on the results presented, we have demonstrated that Q is a required intermediate for the biosynthesis of RQ in
R. rubrum
.
The Gene CBO0515 from
Clostridium botulinum
Strain Hall A Encodes the Rare Enzyme
N
5
-(Carboxyethyl) Ornithine Synthase, EC 1.5.1.24
Authors: Thompson John , Hill Karen K. , Smith Theresa J. , Pikis Andreas 
Published: November 2009

ABSTRACT

Sequencing of the genome of
Clostridium botulinum
strain Hall A revealed a gene (CBO0515), whose putative amino acid sequence was suggestive of the rare enzyme
N
5
-(1-carboxyethyl) ornithine synthase. To test this hypothesis, CBO0515 has been cloned, and the encoded polypeptide was purified and characterized. This unusual gene appears to be confined to proteolytic strains assigned to group 1 of
C. botulinum
.
Localization of Proteins to Different Layers and Regions ofBacillus subtilisSpore Coats
Authors: Imamura Daisuke , Kuwana Ritsuko , Takamatsu Hiromu , Watabe Kazuhito 
Published: November 2009

ABSTRACTBacterial spores are encased in a multilayered proteinaceous shell known as the coat. InBacillus subtilis, over 50 proteins are involved in spore coat assembly but the locations of these proteins in the spore coat are poorly understood. Here, we describe methods to estimate the positions of protein fusions to fluorescent proteins in the spore coat by using fluorescence microscopy. Our investigation suggested that CotD, CotF, CotT, GerQ, YaaH, YeeK, YmaG, YsnD, and YxeE are present in the inner coat and that CotA, CotB, CotC, and YtxO reside in the outer coat. In addition, CotZ and CgeA appeared in the outermost layer of the spore coat and were more abundant at the mother cell proximal pole of the forespore, whereas CotA and CotC were more abundant at the mother cell distal pole of the forespore. These polar localizations were observed both in sporangia prior to the release of the forespore from the mother cell and in mature spores after release. Moreover, CotB was observed at the middle of the spore as a ring- or spiral-like structure. Formation of this structure requiredcotGexpression. Thus, we conclude not only that the spore coat is a multilayered assembly but also that it exhibits uneven spatial distribution of particular proteins.
Characterization of the CtsR Stress Response Regulon in
Lactobacillus plantarum
Authors: Fiocco Daniela , Capozzi Vittorio , Collins Michael , Gallone Anna , Hols Pascal , Guzzo Jean , Weidmann Stephanie , Rieu Aurélie , Msadek Tarek , Spano Giuseppe 
Published: November 2009

ABSTRACT

Lactobacillus plantarum ctsR
was characterized.
ctsR
was found to be cotranscribed with
clpC
and induced in response to various abiotic stresses.
ctsR
deletion conferred a heat-sensitive phenotype with peculiar cell morphological features. The transcriptional pattern of putative CtsR regulon genes was examined in the Δ
ctsR
mutant. Direct CtsR-dependent regulation was demonstrated by DNA-binding assays using recombinant CtsR and the promoters of the
ctsR
-
clpC
operon and
hsp1
.
The ArcBA Two-Component System of
Escherichia coli
Is Regulated by the Redox State of both the Ubiquinone and the Menaquinone Pool
Authors: Bekker Martijn , Alexeeva Svetlana , Laan Wouter , Sawers Gary , Teixeira de Mattos Joost , Hellingwerf Klaas 
Published: November 2009

ABSTRACT

ArcBA is a two-component regulatory system of
Escherichia coli
involved in sensing oxygen availability and the concomitant transcriptional regulation of oxidative and fermentative catabolism. Based on
in vitro
data, it has been postulated that the redox state of the ubiquinone pool is the determinant for ArcB kinase activity. Here we report on the
in vivo
regulation of ArcB activation, as determined using a
lacZ
reporter specifically responsive to phosphorylated ArcA. Our results indicate that upon deletion of a ubiquinone biosynthetic enzyme, regulation of ArcB in the anaerobic-aerobic transition is not affected. In contrast, interference with menaquinone biosynthesis leads to inactivation of ArcB during anaerobic growth; this phenotype is fully rescued by addition of a menaquinone precursor. This clearly demonstrates that the menaquinones play a major role in ArcB activation. ArcB shows a complex pattern of regulation when
E. coli
is titrated through the entire aerobiosis range; ArcB is activated under anaerobic and subaerobic conditions and is much less active under fully aerobic and microaerobic conditions. Furthermore, there is no correlation between ArcB activation and the redox state of the ubiquinone pool, but there is a restricted correlation between the total cellular ubiquinone content and ArcB activity due to the considerable increase in the size of the ubiquinone pool with increasing degrees of aerobiosis. These results lead to the working hypothesis that the
in
vivo activity of ArcB in
E. coli
is modulated by the redox state of the menaquinone pool and that the ubiquinone/ubiquinol ratio
in vivo
surely is not the only determinant of ArcB activity.
SleC Is Essential for Germination of
Clostridium difficile
Spores in Nutrient-Rich Medium Supplemented with the Bile Salt Taurocholate
Authors: Burns David A. , Heap John T. , Minton Nigel P. 
Published: November 2009

ABSTRACT

Clostridium difficile
is the major cause of infectious diarrhea and a major burden to health care services. The ability of this organism to form endospores plays a pivotal role in infection and disease transmission. Spores are highly resistant to many forms of disinfection and thus are able to persist on hospital surfaces and disseminate infection. In order to cause disease, the spores must germinate and the organism must grow vegetatively. Spore germination in
Bacillus
is well understood, and genes important for this process have recently been identified in
Clostridium perfringens
; however, little is known about
C. difficile
. Apparent homologues of the spore cortex lytic enzyme genes
cwlJ
and
sleB
(
Bacillus subtilis
) and
sleC
(
C. perfringens
) are present in the
C. difficile
genome, and we describe inactivation of these homologues in
C. difficile
630Δ
erm
and a B1/NAP1/027 clinical isolate. Spores of a
sleC
mutant were unable to form colonies when germination was induced with taurocholate, although decoated
sleC
spores formed the same number of heat-resistant colonies as the parental control, even in the absence of germinants. This suggests that
sleC
is absolutely required for conversion of spores to vegetative cells, in contrast to CD3563 (a
cwlJ
/
sleB
homologue), inactivation of which had no effect on germination and outgrowth of
C. difficile
spores under the same conditions. The B1/NAP1/027 strain R20291 was found to sporulate more slowly and produce fewer spores than 630Δ
erm
. Furthermore, fewer R20291 spores germinated, indicating that there are differences in both sporulation and germination between these epidemic and nonepidemic
C. difficile
isolates.
Differential Target Gene Activation by the
Staphylococcus aureus
Two-Component System
saeRS
Authors: Mainiero Markus , Goerke Christiane , Geiger Tobias , Gonser Christoph , Herbert Silvia , Wolz Christiane 
Published: November 2009

ABSTRACT

The
saePQRS
system of
Staphylococcus aureus
controls the expression of major virulence factors and encodes a histidine kinase (SaeS), a response regulator (SaeR), a membrane protein (SaeQ), and a lipoprotein (SaeP). The widely used strain Newman is characterized by a single amino acid change in the sensory domain of SaeS (Pro18 in strain Newman [SaeS
P
], compared with Leu18 in other strains [SaeS
L
]). SaeS
P
determines activation of the class I
sae
target genes (
coa
,
fnbA
,
eap
,
sib
,
efb
,
fib
,
sae
), which are highly expressed in strain Newman. In contrast, class II target genes (
hla
,
hlb
,
cap
) are not sensitive to the SaeS polymorphism. The SaeS
L
allele (

saeS
L

) is dominant over the SaeS
P
allele, as shown by single-copy integration of

saePQRS
L

in strain Newman, which results in severe repression of class I target genes. The differential effect on target gene expression is explained by different requirements for SaeR phosphorylation. From an analysis of
saeS
deletion strains and strains with mutated SaeR phosphorylation sites, we concluded that a high level of SaeR phosphorylation is required for activation of class I target genes. However, a low level of SaeR phosphorylation, which can occur independent of SaeS, is sufficient to activate class II target genes. Using inducible
saeRS
constructs, we showed that the expression of both types of target genes is independent of the
saeRS
dosage and that the typical growth phase-dependent gene expression pattern is not driven by SaeRS.
Bypassing Isophthalate Inhibition by Modulating Glutamate Dehydrogenase (GDH): Purification and Kinetic Characterization of NADP-GDHs from Isophthalate-Degrading
Pseudomonas aeruginosa
Strain PP4 and
Acinetobacter lwoffii
Strain ISP4
Authors: Vamsee-Krishna C. , Phale Prashant S. 
Published: November 2009

ABSTRACT

Pseudomonas aeruginosa
strain PP4 and
Acinetobacter lwoffii
strain ISP4 metabolize isophthalate as a sole source of carbon and energy. Isophthalate is known to be a competitive inhibitor of glutamate dehydrogenase (GDH), which is involved in C and N metabolism. Strain PP4 showed carbon source-dependent modulation of NADP-GDH; GDH
I
was produced when cells were grown on isophthalate, while GDH
II
was produced when cells were grown on glucose. Strain ISP4 produced a single form of NADP-GDH, GDH
P
, when it was grown on either isophthalate or rich medium (2YT). All of the forms of GDH were purified to homogeneity and characterized. GDH
I
and GDH
II
were found to be homotetramers, while GDH
P
was found to be a homohexamer. GDH
II
was more sensitive to inhibition by isophthalate (2.5- and 5.5-fold more sensitive for amination and deamination reactions, respectively) than GDH
I
. Differences in the N-terminal sequences and electrophoretic mobilities in an activity-staining gel confirmed the presence of two forms of GDH, GDH
I
and GDH
II
, in strain PP4. In strain ISP4, irrespective of the carbon source, the GDH
P
produced showed similar levels of inhibition with isophthalate. However, the specific activity of GDH
P
from isophthalate-grown cells was 2.5- to 3-fold higher than that of GDH
P
from 2YT-grown cells. Identical N-terminal sequences and electrophoretic mobilities in the activity-staining gel suggested the presence of a single form of GDH
P
in strain ISP4. These results demonstrate the ability of organisms to modulate GDH either by producing an entirely different form or by increasing the level of the enzyme, thus enabling strains to utilize isophthalate more efficiently as a sole source of carbon and energy.
Induction of nitric oxide by erythropoietin is mediated by the β common receptor and requires interaction with VEGF receptor 2
Authors: Sautina Larysa , Sautin Yuri , Beem Elaine , Zhou Zhuo , Schuler Anna , Brennan Jennafer , Zharikov Sergey I. , Diao YanPeng , Bungert Jorg , Segal Mark S. 
Published: November 2009

AbstractVascular endothelial growth factor (VEGF) and erythropoietin (EPO) have profound effects on the endothelium and endothelial progenitor cells (EPCs), which originate from the bone marrow and differentiate into endothelial cells. Both EPO and VEGF have demonstrated an ability to increase the number and performance properties of EPCs. EPC behavior is highly dependent on nitric oxide (NO), and both VEGF and EPO can stimulate intracellular NO. EPO can bind to the homodimeric EPO receptor (EPO-R) and the heterodimeric receptor, EPO-R and the common β receptor (βC-R). Although VEGF has several receptors, VEGF-R2 appears most critical to EPC function. We demonstrate that EPO induction of NO is dependent on the βC-R and VEGF-R2, that VEGF induction of NO is dependent on the expression of the βC-R, and that the βC-R and VEGF-R2 interact. This is the first definitive functional and structural evidence of an interaction between the 2 receptors and has implications for the side effects of EPO.