bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas
Authors: Glaubitz Sabine , Kießlich Katrin , Meeske Christian , Labrenz Matthias , Jürgens Klaus 
Published: February 2013

ABSTRACT

Gammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, the
in situ
abundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescence
in situ
hybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (
cbbM
) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. The
cbbM
transcripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.
Occurrence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Turkey and Broiler Barns and Contamination of Air and Soil Surfaces in Their Vicinity
Authors: Friese A. , Schulz J. , Zimmermann K. , Tenhagen B.-A. , Fetsch A. , Hartung J. , Rösler U. 
Published: February 2013

ABSTRACT

The emission of microorganisms, especially resistant bacteria such as methicillin-resistant
Staphylococcus aureus
(MRSA), from poultry farms is of public interest, and its occurrence and relevance are controversially discussed. So far, there are limited data on this issue. In this study, we investigated the occurrence of livestock-associated (LA)-MRSA inside and outside previously tested MRSA-positive poultry barns in Germany. In total, five turkey and two broiler fattening farms were investigated four and three times, respectively. In a longitudinal study during one fattening period, samples were collected from animals, the animals' environment inside the barn, including the air, and the barns' surroundings, such as ambient air and boot swabs of ground surfaces at different distances from the barn. Moreover, a cross-sectional study was carried out once inside the barns on five turkey and four broiler farms during the last third of the fatting period. In the cross-sectional study, LA-MRSA was detected in the air of most barns (7 of 9, 77.8%), as well as in many samples originating from animals, with detections levels of 50 to 54% in broiler and 62 to 77% in turkey farms. In the longitudinal study, LA-MRSA was found in the ambient air outside two turkey barns and on the ground surface on the downwind side of many (44.4%) turkey and broiler farms. The same
spa
types of isolates were observed inside and outside the barns. Transmission of MRSA within poultry farms, as well as emission via the airborne route, seems to be possible.
Nitrogen Removal by a Nitritation-Anammox Bioreactor at Low Temperature
Authors: Hu Ziye , Lotti Tommaso , de Kreuk Merle , Kleerebezem Robbert , van Loosdrecht Mark , Kruit Jans , Jetten Mike S. M. , Kartal Boran 
Published: February 2013

ABSTRACT

Currently, nitritation-anammox (anaerobic ammonium oxidation) bioreactors are designed to treat wastewaters with high ammonium concentrations at mesophilic temperatures (25 to 40°C). The implementation of this technology at ambient temperatures for nitrogen removal from municipal wastewater following carbon removal may lead to more-sustainable technology with energy and cost savings. However, the application of nitritation-anammox bioreactors at low temperatures (characteristic of municipal wastewaters except in tropical and subtropical regions) has not yet been explored. To this end, a laboratory-scale (5-liter) nitritation-anammox sequencing batch reactor was adapted to 12°C in 10 days and operated for more than 300 days to investigate the feasibility of nitrogen removal from synthetic pretreated municipal wastewater by the combination of aerobic ammonium-oxidizing bacteria (AOB) and anammox. The activities of both anammox and AOB were high enough to remove more than 90% of the supplied nitrogen. Multiple aspects, including the presence and activity of anammox, AOB, and aerobic nitrite oxidizers (NOB) and nitrous oxide (N
2
O) emission, were monitored to evaluate the stability of the bioreactor at 12°C. There was no nitrite accumulation throughout the operational period, indicating that anammox bacteria were active at 12°C and that AOB and anammox bacteria outcompeted NOB. Moreover, our results showed that sludge from wastewater treatment plants designed for treating high-ammonium-load wastewaters can be used as seeding sludge for wastewater treatment plants aimed at treating municipal wastewater that has a low temperature and low ammonium concentrations.
Transcriptome Profiling of Botrytis cinerea Conidial Germination Reveals Upregulation of Infection-Related Genes during the Prepenetration Stage
Authors: Leroch Michaela , Kleber Astrid , Silva Evelyn , Coenen Tina , Koppenhöfer Dieter , Shmaryahu Amir , Valenzuela Pablo D. T. , Hahn Matthias 
Published: February 2013

ABSTRACT

Botrytis cinerea
causes gray mold on a great number of host plants. Infection is initiated by airborne conidia that invade the host tissue, often by penetration of intact epidermal cells. To mimic the surface properties of natural plant surfaces, conidia were incubated on apple wax-coated surfaces, resulting in rapid germination and appressorium formation. Global changes in gene expression were analyzed by microarray hybridization between conidia incubated for 0 h (dormant), 1 h (pregermination), 2.5 h (postgermination), 4 h (appressoria), and 15 h (early mycelium). Considerable changes were observed, in particular between 0 h and 1 h. Genes induced during germination were enriched in those genes encoding secreted proteins, including lytic enzymes. Comparison of wild-type and a nonpathogenic MAP kinase mutant (
bmp1
) revealed marked differences in germination-related gene expression, in particular related to secretory proteins. Using promoter-GFP reporter strains, we detected a strictly germination-specific expression pattern of a putative chitin deacetylase gene (
cda1
). In contrast, a cutinase gene (
cutB
) was found to be expressed only in the presence of plant lipids, in a developmentally less stringent pattern. We also identified a coregulated gene cluster possibly involved in secondary metabolite synthesis which was found to be controlled by a transcription factor also encoded in this cluster. Our data demonstrate that early conidial development in
B. cinerea
is accompanied by rapid shifts in gene expression that prepare the fungus for germ tube outgrowth and host cell invasion.
Nucleosome Assembly Factors CAF-1 and HIR Modulate Epigenetic Switching Frequencies in an H3K56 Acetylation-Associated Manner in Candida albicans
Authors: Stevenson John S. , Liu Haoping 
Published: February 2013

ABSTRACT

CAF-1 and HIR are highly conserved histone chaperone protein complexes that function in the assembly of nucleosomes onto chromatin. CAF-1 is characterized as having replication-coupled nucleosome activity, whereas the HIR complex can assemble nucleosomes independent of replication. Histone H3K56 acetylation, controlled by the acetyltransferase Rtt109 and deacetylase Hst3, also plays a significant role in nucleosome assembly. In this study, we generated a set of deletion mutants to genetically characterize pathway-specific and overlapping functions of CAF-1 and HIR in
C. albicans
. Their roles in epigenetic maintenance of cell type were examined by using the white-opaque switching system in
C. albicans
. We show that CAF-1 and HIR play conserved roles in UV radiation recovery, repression of histone gene expression, correct chromosome segregation, and stress responses. Unique to
C. albicans
, the
cac2Δ/Δ
mutant shows increased sensitivity to the Hst3 inhibitor nicotinamide, while the
rtt109Δ/Δ cac2Δ/Δ
and
hir1Δ/Δ cac2Δ/Δ
mutants are resistant to nicotinamide. CAF-1 plays a major role in maintaining cell types, as the
cac2Δ/Δ
mutant exhibited increased switching frequencies in both directions and switched at a high frequency to opaque in response to nicotinamide. Like the
rtt109Δ/Δ
mutant, the
hir1Δ/Δ cac2Δ/Δ
double mutant is defective in maintaining the opaque cell fate and blocks nicotinamide-induced opaque formation, and the defects are suppressed by ectopic expression of the master white-opaque regulator Wor1. Our data suggest an overlapping function of CAF-1 and HIR in epigenetic regulation of cell fate determination in an H3K56 acetylation-associated manner.
Factors Supporting Cysteine Tolerance and Sulfite Production in Candida albicans
Authors: Hennicke Florian , Grumbt Maria , Lermann Ulrich , Ueberschaar Nico , Palige Katja , Böttcher Bettina , Jacobsen Ilse D. , Staib Claudia , Morschhäuser Joachim , Monod Michel , Hube Bernhard , Hertweck Christian , Staib Peter 
Published: February 2013

ABSTRACT

The amino acid cysteine has long been known to be toxic at elevated levels for bacteria, fungi, and humans. However, mechanisms of cysteine tolerance in microbes remain largely obscure. Here we show that the human pathogenic yeast
Candida albicans
excretes sulfite when confronted with increasing cysteine concentrations. Mutant construction and phenotypic analysis revealed that sulfite formation from cysteine in
C. albicans
relies on cysteine dioxygenase Cdg1, an enzyme with similar functions in humans. Environmental cysteine induced not only the expression of the
CDG1
gene in
C. albicans
, but also the expression of
SSU1
, encoding a putative sulfite efflux pump. Accordingly, the deletion of
SSU1
resulted in enhanced sensitivity of the fungal cells to both cysteine and sulfite. To study the regulation of sulfite/cysteine tolerance in more detail, we screened a
C. albicans
library of transcription factor mutants in the presence of sulfite. This approach and subsequent independent mutant analysis identified the zinc cluster transcription factor Zcf2 to govern sulfite/cysteine tolerance, as well as cysteine-inducible
SSU1
and
CDG1
gene expression.
cdg1
Δ and
ssu1
Δ mutants displayed reduced hypha formation in the presence of cysteine, indicating a possible role of the newly proposed mechanisms of cysteine tolerance and sulfite secretion in the pathogenicity of
C. albicans
. Moreover,
cdg1
Δ mutants induced delayed mortality in a mouse model of disseminated infection. Since sulfite is toxic and a potent reducing agent, its production by
C. albicans
suggests diverse roles during host adaptation and pathogenicity.
Draft Genome Sequence of a Clinical Strain of Yersinia enterocolitica (IP10393) of Bioserotype 4/O:3 from France
Authors: Savin Cyril , Frangeul Lionel , Ma Laurence , Bouchier Christiane , Moszer Ivan , Carniel Elisabeth 
Published: February 2013

ABSTRACT

We sequenced the genome of a clinical isolate of
Yersinia enterocolitica
(IP10393) from France. This strain belongs to bioserotype 4/O:3, which is the most common pathogenic subgroup worldwide. The draft genome has a size of 4,463,212 bp and a G+C content of 47.0%, and it is predicted to contain 4,181 coding sequences.
Molecular Kinetics of Reviving Bacterial Spores
Authors: Segev Einat , Rosenberg Alex , Mamou Gideon , Sinai Lior , Ben-Yehuda Sigal 
Published: February 2013

ABSTRACT

Bacterial spores can remain dormant for years, yet they possess a remarkable potential to rapidly resume a vegetative life form. Here, we identified a distinct phase at the onset of spore outgrowth, designated the ripening period. This transition phase is exploited by the germinating spore for molecular reorganization toward elongation and subsequent cell division. We have previously shown that spores of different ages, kept under various temperatures, harbor dissimilar molecular reservoirs (E. Segev, Y. Smith, and S. Ben-Yehuda, Cell
148:
139–149, 2012). Utilizing this phenomenon, we observed that the length of the ripening period can vary according to the spore molecular content. Importantly, the duration of the ripening period was found to correlate with the initial spore rRNA content and the kinetics of rRNA accumulation upon exiting dormancy. Further, the synthesis of the ribosomal protein RplA and the degradation of the spore-specific protein SspA also correlated with the duration of the ripening period. Our data suggest that the spore molecular cargo determines the extent of the ripening period, a potentially crucial phase for a germinating spore in obtaining limited resources during revival.
Growth Inhibition of Sporomusa ovata by Incorporation of Benzimidazole Bases into Cobamides
Authors: Mok Kenny C. , Taga Michiko E. 
Published: February 2013

ABSTRACT

Phenolyl cobamides are unique members of a class of cobalt-containing cofactors that includes vitamin B
12
(cobalamin). Cobamide cofactors facilitate diverse reactions in prokaryotes and eukaryotes. Phenolyl cobamides are structurally and chemically distinct from the more commonly used benzimidazolyl cobamides such as cobalamin, as the lower axial ligand is a phenolic group rather than a benzimidazole. The functional significance of this difference is not well understood. Here we show that in the bacterium
Sporomusa ovata
, the only organism known to synthesize phenolyl cobamides, several cobamide-dependent acetogenic metabolisms have a requirement or preference for phenolyl cobamides. The addition of benzimidazoles to
S. ovata
cultures results in a decrease in growth rate when grown on methanol, 3,4-dimethoxybenzoate, H
2
plus CO
2
, or betaine. Suppression of native
p
-cresolyl cobamide synthesis and production of benzimidazolyl cobamides occur upon the addition of benzimidazoles, indicating that benzimidazolyl cobamides are not functionally equivalent to the phenolyl cobamide cofactors produced by
S. ovata
. We further show that
S. ovata
is capable of incorporating other phenolic compounds into cobamides that function in methanol metabolism. These results demonstrate that
S. ovata
can incorporate a wide range of compounds as cobamide lower ligands, despite its preference for phenolyl cobamides in the metabolism of certain energy substrates. To our knowledge,
S. ovata
is unique among cobamide-dependent organisms in its preferential utilization of phenolyl cobamides.
Characterizing the Hexose-6-Phosphate Transport System of Vibrio cholerae, a Utilization System for Carbon and Phosphate Sources
Authors: Moisi Manuel , Lichtenegger Sabine , Tutz Sarah , Seper Andrea , Schild Stefan , Reidl Joachim 
Published: February 2013

ABSTRACT

The facultative human pathogen
Vibrio cholerae
transits between the gastrointestinal tract of its host and aquatic reservoirs.
V. cholerae
adapts to different situations by the timely coordinated expression of genes during its life cycle. We recently identified a subclass of genes that are induced at late stages of infection. Initial characterization demonstrated that some of these genes facilitate the transition of
V. cholerae
from host to environmental conditions. Among these genes are uptake systems lacking detailed characterization or correct annotation. In this study, we comprehensively investigated the function of the VCA0682-to-VCA0687 gene cluster, which was previously identified as
in vivo
induced. The results presented here demonstrate that the operon encompassing open reading frames VCA0685 to VCA0687 encodes an ABC transport system for hexose-6-phosphates with

K
m

values ranging from 0.275 to 1.273 μM for glucose-6P and fructose-6P, respectively. Expression of the operon is induced by the presence of hexose-6P controlled by the transcriptional activator VCA0682, representing a UhpA homolog. Finally, we provide evidence that the operon is essential for the utilization of hexose-6P as a C and P source. Thereby, a physiological role can be assigned to hexose-6P uptake, which correlates with increased fitness of
V. cholerae
after a transition from the host into phosphate-limiting environments.
Characterization of a Novel Rieske-Type Alkane Monooxygenase System in Pusillimonas sp. Strain T7-7
Authors: Li Ping , Wang Lei , Feng Lu 
Published: February 2013

ABSTRACT

The cold-tolerant bacterium
Pusillimonas
sp. strain T7-7 is able to utilize diesel oils (C
5
to C
30
alkanes) as a sole carbon and energy source. In the present study, bioinformatics, proteomics, and real-time reverse transcriptase PCR approaches were used to identify the alkane hydroxylation system present in this bacterium. This system is composed of a Rieske-type monooxygenase, a ferredoxin, and an NADH-dependent reductase. The function of the monooxygenase, which consists of one large (46.711 kDa) and one small (15.355 kDa) subunit, was further studied using
in vitro
biochemical analysis and
in vivo
heterologous functional complementation tests. The purified large subunit of the monooxygenase was able to oxidize alkanes ranging from pentane (C
5
) to tetracosane (C
24
) using NADH as a cofactor, with greatest activity on the C
15
substrate. The large subunit also showed activity on several alkane derivatives, including nitromethane and methane sulfonic acid, but it did not act on any aromatic hydrocarbons. The optimal reaction condition of the large subunit is pH 7.5 at 30°C. Fe
2+
can enhance the activity of the enzyme evidently. This is the first time that an alkane monooxygenase system belonging to the Rieske non-heme iron oxygenase family has been identified in a bacterium.
FtsH-Mediated Coordination of Lipopolysaccharide Biosynthesis in Escherichia coli Correlates with the Growth Rate and the Alarmone (p)ppGpp
Authors: Schäkermann Michael , Langklotz Sina , Narberhaus Franz 
Published: February 2013

ABSTRACT

The outer membrane is the first line of defense for Gram-negative bacteria and serves as a major barrier for antibiotics and other harmful substances. The biosynthesis of lipopolysaccharides (LPS), the essential component of the outer membrane, must be tightly controlled as both too much and too little LPS are toxic. In
Escherichia coli
, the cellular level of the key enzyme LpxC, which catalyzes the first committed step in LPS biosynthesis, is adjusted by proteolysis carried out by the essential and membrane-bound protease FtsH. Here, we demonstrate that LpxC is degraded in a growth rate-dependent manner with half-lives between 4 min and >2 h. According to the cellular demand for LPS biosynthesis, LpxC is degraded during slow growth but stabilized when cells grow rapidly. Disturbing the balance between LPS and phospholipid biosynthesis in favor of phospholipid production in an
E. coli
strain encoding a hyperactive FabZ protein abolishes growth rate dependency of LpxC proteolysis. Lack of the alternative sigma factor RpoS or inorganic polyphosphates, which are known to mediate growth rate-dependent gene regulation in
E. coli
, did not affect proteolysis of LpxC. In contrast, absence of RelA and SpoT, which synthesize the alarmone (p)ppGpp, deregulated LpxC degradation resulting in rapid proteolysis in fast-growing cells and stabilization during slow growth. Our data provide new insights into the essential control of LPS biosynthesis in
E. coli
.
A Rex Family Transcriptional Repressor Influences H
2
O
2
Accumulation by Enterococcus faecalis
Authors: Vesić Dušanka , Kristich Christopher J. 
Published: February 2013

ABSTRACT

Rex factors are bacterial transcription factors thought to respond to the cellular NAD
+
/NADH ratio in order to modulate gene expression by differentially binding DNA. To date, Rex factors have been implicated in regulating genes of central metabolism, oxidative stress response, and biofilm formation. The genome of
Enterococcus faecalis
, a low-GC Gram-positive opportunistic pathogen, encodes
EF2638
, a putative Rex factor. To study the role of
E. faecalis
Rex, we purified EF2638 and evaluated its DNA binding activity
in vitro
. EF2638 was able to bind putative promoter segments of several
E. faecalis
genes in an NADH-responsive manner, indicating that it represents an authentic Rex factor. Transcriptome analysis of a Δ
EF2638
mutant revealed that genes likely to be involved in anaerobic metabolism were upregulated during aerobic growth, and the mutant exhibited an altered NAD
+
/NADH ratio. The Δ
EF2638
mutant also exhibited a growth defect when grown with aeration on several carbon sources, suggesting an impaired ability to cope with oxidative stress. Inclusion of catalase in the medium alleviated the growth defect. H
2
O
2
measurements revealed that the mutant accumulates significantly more H
2
O
2
than wild-type
E. faecalis
. In summary, EF2638 represents an authentic Rex factor in
E. faecalis
that influences the production or detoxification of H
2
O
2
in addition to its more familiar role as a regulator of anaerobic gene expression.
High Hydrostatic Pressure Induces Counterclockwise to Clockwise Reversals of the Escherichia coli Flagellar Motor
Authors: Nishiyama Masayoshi , Sowa Yoshiyuki , Kimura Yoshifumi , Homma Michio , Ishijima Akihiko , Terazima Masahide 
Published: February 2013

ABSTRACT

The bacterial flagellar motor is a reversible rotary machine that rotates a left-handed helical filament, allowing bacteria to swim toward a more favorable environment. The direction of rotation reverses from counterclockwise (CCW) to clockwise (CW), and vice versa, in response to input from the chemotaxis signaling circuit. CW rotation is normally caused by binding of the phosphorylated response regulator CheY (CheY-P), and strains lacking CheY are typically locked in CCW rotation. The detailed mechanism of switching remains unresolved because it is technically difficult to regulate the level of CheY-P within the concentration range that produces flagellar reversals. Here, we demonstrate that high hydrostatic pressure can induce CW rotation even in the absence of CheY-P. The rotation of single flagellar motors in
Escherichia coli
cells with the
cheY
gene deleted was monitored at various pressures and temperatures. Application of >120 MPa pressure induced a reversal from CCW to CW at 20°C, although at that temperature, no motor rotated CW at ambient pressure (0.1 MPa). At lower temperatures, pressure-induced changes in direction were observed at pressures of <120 MPa. CW rotation increased with pressure in a sigmoidal fashion, as it does in response to increasing concentrations of CheY-P. Application of pressure generally promotes the formation of clusters of ordered water molecules on the surfaces of proteins. It is possible that hydration of the switch complex at high pressure induces structural changes similar to those caused by the binding of CheY-P.