bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Digestive-Tract Microbiota of
Hirudo orientalis
, a European Medicinal Leech
Authors: Laufer Alison S. , Siddall Mark E. , Graf Joerg 
Published: August 2008

ABSTRACT

FDA-approved, postoperative use of leeches can lead to bacterial infections. In this study, we used culture-dependent and culture-independent approaches to characterize the digestive-tract microbiota of
Hirudo orientalis
. Surprisingly, two
Aeromonas
species,
A. veronii
and
A. jandaei
, were cultured. Uncultured
Rikenella
-like bacteria were most similar to isolates from
Hirudo verbana
.
Dynamics of Whole and Lysed Bacterial Cells during Parmigiano-Reggiano Cheese Production and Ripening
Authors: Gatti Monica , De Dea Lindner Juliano , De Lorentiis Angela , Bottari Benedetta , Santarelli Marcela , Bernini Valentina , Neviani Erasmo 
Published: August 2008

ABSTRACT
Microbial succession during Parmigiano-Reggiano cheesemaking was monitored by length heterogeneity PCR (LH-PCR), considering the intact and lysed cells at different stages of cheese production and ripening. When starter species underwent autolysis, species coming from milk were able to grow. For the first time, the LH-PCR technique was applied to study a fermented food.
Insertional Inactivation of Branched-Chain α-Keto Acid Dehydrogenase in
Staphylococcus aureus
Leads to Decreased Branched-Chain Membrane Fatty Acid Content and Increased Susceptibility to Certain Stresses
Authors: Singh Vineet K. , Hattangady Dipti S. , Giotis Efstathios S. , Singh Atul K. , Chamberlain Neal R. , Stuart Melissa K. , Wilkinson Brian J. 
Published: August 2008

ABSTRACT

Staphylococcus aureus
is a major community and nosocomial pathogen. Its ability to withstand multiple stress conditions and quickly develop resistance to antibiotics complicates the control of staphylococcal infections. Adaptation to lower temperatures is a key for the survival of bacterial species outside the host. Branched-chain α-keto acid dehydrogenase (BKD) is an enzyme complex that catalyzes the early stages of branched-chain fatty acid (BCFA) production. In this study, BKD was inactivated, resulting in reduced levels of BCFAs in the membrane of
S. aureus
. Growth of the BKD-inactivated mutant was progressively more impaired than that of wild-type
S. aureus
with decreasing temperature, to the point that the mutant could not grow at 12°C. The growth of the mutant was markedly stimulated by the inclusion of 2-methylbutyrate in the growth medium at all temperatures tested. 2-Methylbutyrate is a precursor of odd-numbered anteiso fatty acids and bypasses BKD. Interestingly, growth of wild-type
S. aureus
was also stimulated by including 2-methylbutyrate in the medium, especially at lower temperatures. The anteiso fatty acid content of the BKD-inactivated mutant was restored by the inclusion of 2-methylbutyrate in the medium. Fluorescence polarization measurements indicated that the membrane of the BKD-inactivated mutant was significantly less fluid than that of wild-type
S. aureus
. Consistent with this result, the mutant showed decreased toluene tolerance that could be increased by the inclusion of 2-methylbutyrate in the medium. The BKD-inactivated mutant was more susceptible to alkaline pH and oxidative stress conditions. Inactivation of the BKD enzyme complex in
S. aureus
also led to a reduction in adherence of the mutant to eukaryotic cells and its survival in a mouse host. In addition, the mutant offers a tool to study the role of membrane fluidity in the interaction of
S. aureus
with antimicrobial substances.
Removal of Antibiotic Resistance Gene-Carrying Plasmids from
Lactobacillus reuteri
ATCC 55730 and Characterization of the Resulting Daughter Strain,
L
.
reuteri
DSM 17938
Authors: Rosander Anna , Connolly Eamonn , Roos Stefan 
Published: August 2008

ABSTRACT

The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract.
Lactobacillus reuteri
ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of β-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known β-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of
L
.
reuteri
were sequenced and comparatively analyzed. The β-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying
tet
(W) tetracycline and
lnu
(A) lincosamide resistance genes, respectively. A new daughter strain,
L
.
reuteri
DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.
The Presence of
icaADBC
Is Detrimental to the Colonization of Human Skin by
Staphylococcus epidermidis
Authors: Rogers K. L. , Rupp M. E. , Fey P. D. 
Published: August 2008

ABSTRACT

Previous studies have demonstrated that
Staphylococcus epidermidis
isolates colonizing the skin of healthy humans do not typically encode
icaADBC
, the genes responsible for the production of polysaccharide intercellular adhesin or biofilms. It was therefore hypothesized that the presence of
icaADBC
was deleterious to the successful colonization of human skin by
S. epidermidis
. Using a human skin competition model, it was determined that the strong biofilm-producing
S. epidermidis
strain 1457 was outcompeted at 1, 3, and 10 days by an isogenic
icaADBC
mutant (1457
ica
::
dhfr
), suggesting a fitness cost for carriage of
icaADBC
.
Characterization of ApuB, an Extracellular Type II Amylopullulanase from
Bifidobacterium breve
UCC2003
Authors: O'Connell Motherway Mary , Fitzgerald Gerald F. , Neirynck Sabine , Ryan Sinead , Steidler Lothar , van Sinderen Douwe 
Published: August 2008

ABSTRACT

The
apuB
gene of
Bifidobacterium breve
UCC2003 was shown to encode an extracellular amylopullulanase. ApuB is composed of a distinct N-terminally located α-amylase-containing domain which hydrolyzes α-1,4-glucosidic linkages in starch and related polysaccharides and a C-terminally located pullulanase-containing domain which hydrolyzes α-1,6 linkages in pullulan, allowing the classification of this enzyme as a bifunctional class II pullulanase. A knockout mutation of the
apuB
gene in
B. breve
UCC2003 rendered the resulting mutant incapable of growth in medium containing starch, amylopectin, glycogen, or pullulan as the sole carbon and energy source, confirming the crucial physiological role of this gene in starch metabolism.
Asexual Cephalosporin C Producer
Acremonium chrysogenum
Carries a Functional Mating Type Locus
Authors: Pöggeler Stefanie , Hoff Birgit , Kück Ulrich 
Published: August 2008

ABSTRACT

Acremonium chrysogenum
, the fungal producer of the pharmaceutically relevant β-lactam antibiotic cephalosporin C, is classified as asexual because no direct observation of mating or meiosis has yet been reported. To assess the potential of
A. chrysogenum
for sexual reproduction, we screened an expressed sequence tag library from
A. chrysogenum
for the expression of mating type (
MAT
) genes, which are the key regulators of sexual reproduction. We identified two putative mating type genes that are homologues of the α-box domain gene,
MAT1-1-1
and
MAT1-1-2
, encoding an HPG domain protein defined by the presence of the three invariant amino acids histidine, proline, and glycine. In addition, cDNAs encoding a putative pheromone receptor and pheromone-processing enzymes, as well as components of a pheromone response pathway, were found. Moreover, the entire
A. chrysogenum MAT1-1
(Ac
MAT1-1
) gene and regions flanking the
MAT
region were obtained from a genomic cosmid library, and sequence analysis revealed that in addition to Ac
MAT1-1-1
and Ac
MAT1-1-2
, the Ac
MAT1-1
locus comprises a third mating type gene, Ac
MAT1-1-3
, encoding a high-mobility-group domain protein. The α-box domain sequence of Ac
MAT1-1-1
was used to determine the phylogenetic relationships of
A. chrysogenum
to other ascomycetes. To determine the functionality of the Ac
MAT1-1
locus, the entire
MAT
locus was transferred into a
MAT
deletion strain of the heterothallic ascomycete
Podospora anserina
(the PaΔMAT strain). After fertilization with a
P. anserina
MAT1-2 (MAT
+
) strain, the corresponding transformants developed fruiting bodies with mature ascospores. Thus, the results of our functional analysis of the Ac
MAT1-1
locus provide strong evidence to hypothesize a sexual cycle in
A. chrysogenum
.
Protozoal Digestion of Coat-Defective
Bacillus subtilis
Spores Produces “Rinds” Composed of Insoluble Coat Protein
Authors: Carroll Alicia Monroe , Plomp Marco , Malkin Alexander J. , Setlow Peter 
Published: August 2008

ABSTRACT

The
Bacillus subtilis
spore coat is a multilayer, proteinaceous structure that consists of more than 50 proteins. Located on the surface of the spore, the coat provides resistance to potentially toxic molecules as well as to predation by the protozoan
Tetrahymena thermophila
. When coat-defective spores are fed to
Tetrahymena
, the spores are readily digested. However, a residue termed a “rind” that looks like coat material remains. As observed with a phase-contrast microscope, the rinds are spherical or hemispherical structures that appear to be devoid of internal contents. Atomic force microscopy and chemical analyses showed that (i) the rinds are composed of insoluble protein largely derived from both outer and inner spore coat layers, (ii) the amorphous layer of the outer coat is largely responsible for providing spore resistance to protozoal digestion, and (iii) the rinds and intact spores do not contain significant levels of silicon.
Binding Sequences for RdgB, a DNA Damage-Responsive Transcriptional Activator, and Temperature-Dependent Expression of Bacteriocin and Pectin Lyase Genes in
Pectobacterium carotovorum
subsp.
carotovorum
Authors: Yamada Kazuteru , Kaneko Jun , Kamio Yoshiyuki , Itoh Yoshifumi 
Published: August 2008

ABSTRACT

Pectobacterium carotovorum
subsp.
carotovorum
strain Er simultaneously produces the phage tail-like bacteriocin carotovoricin (Ctv) and pectin lyase (Pnl) in response to DNA-damaging agents. The regulatory protein RdgB of the Mor/C family of proteins activates transcription of
pnl
through binding to the promoter. However, the optimal temperature for the synthesis of Ctv (23°C) differs from that for synthesis of Pnl (30°C), raising the question of whether RdgB directly activates
ctv
transcription. Here we report that RdgB directly regulates Ctv synthesis. Gel mobility shift assays demonstrated RdgB binding to the P
0
, P
1
, and P
2
promoters of the
ctv
operons, and DNase I footprinting determined RdgB-binding sequences (RdgB boxes) on these and on the
pnl
promoters. The RdgB box of the
pnl
promoter included a perfect 7-bp inverted repeat with high binding affinity to the regulator (
K

d

[dissociation constant] = 150 nM). In contrast, RdgB boxes of the
ctv
promoters contained an imperfect inverted repeat with two or three mismatches that consequently reduced binding affinity (
K

d

= 250 to 350 nM). Transcription of the
rdgB
and
ctv
genes was about doubled at 23°C compared with that at 30°C. In contrast, the amount of
pnl
transcription tripled at 30°C. Thus, the inverse synthesis of Ctv and Pnl as a function of temperature is apparently controlled at the transcriptional level, and reduced
rdgB
expression at 30°C obviously affected transcription from the
ctv
promoters with low-affinity RdgB boxes. Pathogenicity toward potato tubers was reduced in an
rdgB
knockout mutant, suggesting that the RdgAB system contributes to the pathogenicity of this bacterium, probably by activating
pnl
expression.
Bioaccumulation of Palladium by
Desulfovibrio fructosivorans
Wild-Type and Hydrogenase-Deficient Strains
Authors: Mikheenko I. P. , Rousset M. , Dementin S. , Macaskie L. E. 
Published: August 2008

ABSTRACT

Wild-type
Desulfovibrio fructosivorans
and three hydrogenase-negative mutants reduced Pd(II) to Pd(0). The location of Pd(0) nanoparticles on the cytoplasmic membrane of the mutant retaining only cytoplasmic membrane-bound hydrogenase was strong evidence for the role of hydrogenases in Pd(0) deposition. Hydrogenase activity was retained at acidic pH, shown previously to favor Pd(0) deposition.
Cross-Species Hybridization with
Fusarium verticillioides
Microarrays Reveals New Insights into
Fusarium fujikuroi
Nitrogen Regulation and the Role of AreA and NMR
Authors: Schönig Birgit , Brown Daren W. , Oeser Birgitt , Tudzynski Bettina 
Published: August 2008

ABSTRACT

In filamentous fungi, the GATA-type transcription factor AreA plays a major role in the transcriptional activation of genes needed to utilize poor nitrogen sources. In
Fusarium fujikuroi
, AreA also controls genes involved in the biosynthesis of gibberellins, a family of diterpenoid plant hormones. To identify more genes responding to nitrogen limitation or sufficiency in an AreA-dependent or -independent manner, we examined changes in gene expression of
F. fujikuroi
wild-type and Δ
areA
strains by use of a
Fusarium verticillioides
microarray representing ∼9,300 genes. Analysis of the array data revealed sets of genes significantly down- and upregulated in the
areA
mutant under both N starvation and N-sufficient conditions. Among the downregulated genes are those involved in nitrogen metabolism, e.g., those encoding glutamine synthetase and nitrogen permeases, but also those involved in secondary metabolism. Besides AreA-dependent genes, we found an even larger set of genes responding to N starvation and N-sufficient conditions in an AreA-independent manner. To study the impact of NMR on AreA activity, we examined the expression of several AreA target genes in the wild type and in
areA
and
nmr
deletion and overexpression mutants. We show that NMR interacts with AreA as expected but affects gene expression only in early growth stages. This is the first report on genome-wide expression studies examining the influence of AreA on nitrogen-responsive gene expression in a genome-wide manner in filamentous fungi.
PKC1
Is Essential for Protection against both Oxidative and Nitrosative Stresses, Cell Integrity, and Normal Manifestation of Virulence Factors in the Pathogenic Fungus
Cryptococcus neoformans
Authors: Gerik Kimberly J. , Bhimireddy Sujit R. , Ryerse Jan S. , Specht Charles A. , Lodge Jennifer K. 
Published: August 2008

ABSTRACT

Cell wall integrity is crucial for fungal growth, survival, and pathogenesis. Responses to environmental stresses are mediated by the highly conserved Pkc1 protein and its downstream components. In this study, we demonstrate that both oxidative and nitrosative stresses activate the PKC1 cell integrity pathway in wild-type cells, as measured by phosphorylation of Mpk1, the terminal protein in the PKC1 phosphorylation cascade. Furthermore, deletion of
PKC1
shows that this gene is essential for defense against both oxidative and nitrosative stresses; however, other genes involved directly in the PKC1 pathway are dispensable for protection against these stresses. This suggests that Pkc1 may have multiple and alternative functions other than activating the mitogen-activated protein kinase cascade from a “top-down” approach. Deletion of
PKC1
also causes osmotic instability, temperature sensitivity, severe sensitivity to cell wall-inhibiting agents, and alterations in capsule and melanin. Furthermore, the vital cell wall components chitin and its deacetylated form chitosan appear to be mislocalized in a
pkc1Δ
strain, although this mutant contains wild-type levels of both of these polymers. These data indicate that loss of Pkc1 has pleiotropic effects because it is central to many functions either dependent on or independent of PKC1 pathway activation. Notably, this is the first time that Pkc1 has been implicated in protection against nitrosative stress in any organism.
The Gluconeogenic Enzyme Fructose-1,6-Bisphosphatase Is Dispensable for Growth of the Yeast
Yarrowia lipolytica
in Gluconeogenic Substrates
Authors: Jardón Raquel , Gancedo Carlos , Flores Carmen-Lisset 
Published: August 2008

ABSTRACT

The genes encoding gluconeogenic enzymes in the nonconventional yeast
Yarrowia lipolytica
were found to be differentially regulated. The expression of
Y. lipolytica FBP1
(Yl
FBP1
) encoding the key enzyme fructose-1,6-bisphosphatase was not repressed by glucose in contrast with the situation in other yeasts; however, this sugar markedly repressed the expression of Yl
PCK1
, encoding phosphoenolpyruvate carboxykinase, and Yl
ICL1
, encoding isocitrate lyase. We constructed
Y. lipolytica
strains with two different disrupted versions of Yl
FBP1
and found that they grew much slower than the wild type in gluconeogenic carbon sources but that growth was not abolished as happens in most microorganisms. We attribute this growth to the existence of an alternative phosphatase with a high

K
m

(2.3 mM) for fructose-1,6-bisphosphate. The gene Yl
FBP1
restored fructose-1,6-bisphosphatase activity and growth in gluconeogenic carbon sources to a
Saccharomyces cerevisiae fbp1
mutant, but the introduction of the
FBP1
gene from
S. cerevisiae
in the Yl
fbp1
mutant did not produce fructose-1,6-bisphosphatase activity or growth complementation. Subcellular fractionation revealed the presence of fructose-1,6-bisphosphatase both in the cytoplasm and in the nucleus.
Role of Acetyl Coenzyme A Synthesis and Breakdown in Alternative Carbon Source Utilization in
Candida albicans
Authors: Carman Aaron J. , Vylkova Slavena , Lorenz Michael C. 
Published: August 2008

ABSTRACT

Acetyl coenzyme A (acetyl-CoA) is the central intermediate of the pathways required to metabolize nonfermentable carbon sources. Three such pathways, i.e., gluconeogenesis, the glyoxylate cycle, and β-oxidation, are required for full virulence in the fungal pathogen
Candida albicans
. These processes are compartmentalized in the cytosol, mitochondria, and peroxosomes, necessitating transport of intermediates across intracellular membranes. Acetyl-CoA is trafficked in the form of acetate by the carnitine shuttle, and we hypothesized that the enzymes that convert acetyl-CoA to/from acetate, i.e., acetyl-CoA hydrolase (
ACH1
) and acetyl-CoA synthetase (
ACS1
and
ACS2
), would regulate alternative carbon utilization and virulence. We show that
C. albicans
strains depleted for
ACS2
are unviable in the presence of most carbon sources, including glucose, acetate, and ethanol; these strains metabolize only fatty acids and glycerol, a substantially more severe phenotype than that of
Saccharomyces cerevisiae acs2
mutants. In contrast, deletion of
ACS1
confers no phenotype, though it is highly induced in the presence of fatty acids, perhaps explaining why
acs2
mutants can utilize fatty acids. Strains lacking
ACH1
have a mild growth defect on some carbon sources but are fully virulent in a mouse model of disseminated candidiasis. Both
ACH1
and
ACS2
complement mutations in their
S. cerevisiae
homolog. Together, these results show that acetyl-CoA metabolism and transport are critical for growth of
C. albicans
on a wide variety of nutrients. Furthermore, the phenotypic differences between mutations in these highly conserved genes in
S. cerevisiae
and
C. albicans
support recent findings that significant functional divergence exists even in fundamental metabolic pathways between these related yeasts.
Identification and Characterization of Epp, the Secreted Processing Protease for the
Vibrio anguillarum
EmpA Metalloprotease
Authors: Varina Maureen , Denkin Steven M. , Staroscik Andrew M. , Nelson David R. 
Published: August 2008

ABSTRACT

The zinc metalloprotease EmpA is a virulence factor for the fish pathogen
Vibrio anguillarum
. Previous studies demonstrated that EmpA is secreted as a 46-kDa proenzyme that is activated extracellularly by the removal of an ∼10-kDa propeptide. We hypothesized that a specific protease is responsible for processing secreted pro-EmpA into mature EmpA. To identify the protease responsible for processing pro-EmpA, a minitransposon mutagenesis (using mini-Tn
10
Km) clone bank of
V. anguillarum
was screened for reduced protease activity due to insertions in undescribed genes. One mutant with reduced protease activity was identified. The region containing the mini-Tn
10
Km was cloned, sequenced, and found to contain
epp
, an open reading frame encoding a putative protease. Further characterization of
epp
was done using strain M101, created by single-crossover insertional mutagenesis. Protease activity was absent in M101 cultures even when
empA
protease activity was induced by salmon gastrointestinal mucus. When the
epp
mutation was complemented with a wild-type copy of
epp
(M102), protease activity was restored. Western blot analysis of sterile filtered culture supernatants from wild-type (M93Sm) cells, M101 cells, and M102 cells revealed that only pro-EmpA was present in M101supernatants; both pro-EmpA and mature EmpA were detected in M93Sm and M102 supernatants. When sterile filtered culture supernatants from the
empA
mutant strain (M99) and M101 were mixed, protease activity was restored. Western blot analysis revealed that pro-EmpA in M101 culture supernatant was processed to mature EmpA only after mixing with M99 culture supernatant. These data show that Epp is the EmpA-processing protease.
Whole-Genome Transcriptional Profiling of
Bradyrhizobium japonicum
during Chemoautotrophic Growth
Authors: Franck William L. , Chang Woo-Suk , Qiu Jing , Sugawara Masayuki , Sadowsky Michael J. , Smith Stephanie A. , Stacey Gary 
Published: August 2008

ABSTRACT

Bradyrhizobium japonicum
is a facultative chemoautotroph capable of utilizing hydrogen gas as an electron donor in a respiratory chain terminated by oxygen to provide energy for cellular processes and carbon dioxide assimilation via a reductive pentose phosphate pathway. A transcriptomic analysis of
B. japonicum
cultured chemoautotrophically identified 1,485 transcripts, representing 17.5% of the genome, as differentially expressed when compared to heterotrophic cultures. Genetic determinants required for hydrogen utilization and carbon fixation, including the uptake hydrogenase system and components of the Calvin-Benson-Bassham cycle, were strongly induced in chemoautotrophically cultured cells. A putative isocitrate lyase (
aceA
; blr2455) was among the most strongly upregulated genes, suggesting a role for the glyoxylate cycle during chemoautotrophic growth. Addition of arabinose to chemoautotrophic cultures of
B. japonicum
did not significantly alter transcript profiles. Furthermore, a subset of nitrogen fixation genes was moderately induced during chemoautotrophic growth. In order to specifically address the role of isocitrate lyase and nitrogenase in chemoautotrophic growth, we cultured
aceA
,
nifD
, and
nifH
mutants under chemoautotrophic conditions. Growth of each mutant was similar to that of the wild type, indicating that the glyoxylate bypass and nitrogenase activity are not essential components of chemoautotrophy in
B. japonicum
.