bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Analysis of the Meat Starter Culture BacteriumStaphylococcus carnosusTM300
Authors: Rosenstein Ralf , Nerz Christiane , Biswas Lalitha , Resch Alexandra , Raddatz Guenter , Schuster Stephan C. , Götz Friedrich 
Published: December 2008

ABSTRACTTheStaphylococcus carnosusgenome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart fromS. aureus,S. epidermidis,S. saprophyticus, andS. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and theoriandterregions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While mostS. aureusgenomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, ΦTM300, and one genomic island, νSCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical ofS. aureusas well as genes involved in biofilm formation, underscoring the nonpathogenic status.
Surface Properties of
Toxoplasma gondii
Oocysts and Surrogate Microspheres
Authors: Shapiro Karen , Largier John , Mazet Jonna A. K. , Bernt William , Ell John R. , Melli Ann C. , Conrad Patricia A. 
Published: December 2008

ABSTRACT

The physical properties that govern the waterborne transmission of
Toxoplasma gondii
oocysts from land to sea were evaluated and compared to the properties of carboxylated microspheres, which could serve as surrogates for
T. gondii
oocysts in transport and water treatment studies. The electrophoretic mobilities of
T. gondii
oocysts, lightly carboxylated Dragon Green microspheres, and heavily carboxylated Glacial Blue microspheres were determined in ultrapure water, artificial freshwater with and without dissolved organic carbon, artificial estuarine water, and artificial seawater. The surface wettabilities of oocysts and microspheres were determined using a water contact angle approach.
Toxoplasma gondii
oocysts and microspheres were negatively charged in freshwater solutions, but their charges were neutralized in estuarine water and seawater. Oocysts, Glacial Blue microspheres, and unwashed Dragon Green microspheres had low contact angles, indicating that they were hydrophilic; however, once washed, Dragon Green microspheres became markedly hydrophobic. The hydrophilic nature and negative charge of
T. gondii
oocysts in freshwater could facilitate widespread contamination of waterways. The loss of charge observed in saline waters may lead to flocculation and subsequent accumulation of
T. gondii
oocysts in locations where freshwater and marine water mix, indicating a high risk of exposure for humans and wildlife in estuarine habitats with this zoonotic pathogen. While microspheres did not have surface properties identical to those of
T. gondii
, similar properties shared between each microsphere type and oocysts suggest that their joint application in transport and fate studies could provide a range of transport potentials in which oocysts are likely to behave.
b
-Type Dihydroorotate Dehydrogenase Is Purified as a H
2
O
2
-Forming NADH Oxidase from
Bifidobacterium bifidum
Authors: Kawasaki Shinji , Satoh Takumi , Todoroki Mitsunori , Niimura Youichi 
Published: December 2008

ABSTRACT

Our previous report showed the existence of microaerophilic
Bifidobacterium
species that can grow well under aerobic conditions rather than anoxic conditions in a liquid shaking culture. The difference in the aerobic growth properties between the O
2
-sensitive and microaerophilic species is due to the existence of a system to produce H
2
O
2
in the growth medium. In this study, we purified and characterized the NADH oxidase that is considered to be a key enzyme in the production of H
2
O
2
.
Bifidobacterium bifidum
, an O
2
-sensitive bacterium and the type species of the genus
Bifidobacterium
, possessed one dominant active fraction of NADH oxidase and a minor active fraction of NAD(P)H oxidase activity detected in the first step of column chromatography for purification of the enzyme. The dominant active fraction was further purified and determined from its N-terminal sequence to be a homologue of
b
-type dihydroorotate dehydrogenase (DHOD), composed of PyrK (31 kDa) and PyrDb (34 kDa) subunits. The genes that encode PyrK and PryDb are tandemly located within an operon structure. The purified enzyme was found to be a heterotetramer showing the typical spectrum of a flavoprotein, and flavin mononucleotide and flavin adenine dinucleotide were identified as cofactors. The purified enzyme was characterized as the enzyme that catalyzes the DHOD reaction and also catalyzes a H
2
O
2
-forming NADH oxidase reaction in the presence of O
2
. The kinetic parameters suggested that the enzyme could be involved in H
2
O
2
production in highly aerated environments.
Biotransformations of 2-Methylisoborneol by Camphor-Degrading Bacteria
Authors: Eaton Richard W. , Sandusky Peter 
Published: December 2008

ABSTRACTMany camphor-degrading bacteria that are able to transform 2-methylisoborneol (2-MIB) have been identified. Three of these strains have been examined in detail.Rhodococcus ruberT1 metabolizes camphor through 6-hydroxycamphor but converts 2-MIB to 3-hydroxy-2-MIB.Pseudomonas putidaG1, which metabolizes camphor through 5-hydroxycamphor, converts MIB primarily to 6-hydroxy-2-MIB.Rhodococcus wratislaviensisDLC-cam converts 2-MIB through 5-hydroxy-2-MIB to 5-keto-2-MIB. Together, these three strains produce metabolites resulting from hydroxylation at all of the three available secondary carbons on the six-member ring of 2-MIB.
Bioproduction of
p
-Hydroxystyrene from Glucose by the Solvent-Tolerant Bacterium
Pseudomonas putida
S12 in a Two-Phase Water-Decanol Fermentation
Authors: Verhoef Suzanne , Wierckx Nick , Westerhof R. G. Maaike , de Winde Johannes H. , Ruijssenaars Harald J. 
Published: December 2008

ABSTRACT

Two solvent-tolerant
Pseudomonas putida
S12 strains, originally designed for phenol and
p
-coumarate production, were engineered for efficient production of
p
-hydroxystyrene from glucose. This was established by introduction of the genes
pal
and
pdc
encoding
l
-phenylalanine/
l
-tyrosine ammonia lyase and
p
-coumaric acid decarboxylase, respectively. These enzymes allow the conversion of the central metabolite
l
-tyrosine into
p
-hydroxystyrene, via
p
-coumarate. Degradation of the
p
-coumarate intermediate was prevented by inactivating the
fcs
gene encoding feruloyl-coenzyme A synthetase. The best-performing strain was selected and cultivated in the fed-batch mode, resulting in the formation of 4.5 mM
p
-hydroxystyrene at a yield of 6.7% (C-mol of
p
-hydroxystyrene per C-mol of glucose) and a maximum volumetric productivity of 0.4 mM h
−1
. At this concentration, growth and production were completely halted due to the toxicity of
p
-hydroxystyrene. Product toxicity was overcome by the application of a second phase of 1-decanol to extract
p
-hydroxystyrene during fed-batch cultivation. This resulted in a twofold increase of the maximum volumetric productivity (0.75 mM h
−1
) and a final total
p
-hydroxystyrene concentration of 21 mM, which is a fourfold improvement compared to the single-phase fed-batch cultivation. The final concentration of
p
-hydroxystyrene in the water phase was 1.2 mM, while a concentration of 147 mM (17.6 g liter
−1
) was obtained in the 1-decanol phase. Thus, a
P. putida
S12 strain producing the low-value compound phenol was successfully altered for the production of the toxic value-added compound
p
-hydroxystyrene.
Energy Metabolism Response to Low-Temperature and Frozen Conditions in
Psychrobacter cryohalolentis
Authors: Amato Pierre , Christner Brent C. 
Published: December 2008

ABSTRACT

Studies of cold-active enzymes have provided basic information on the molecular and biochemical properties of psychrophiles; however, the physiological strategies that compensate for low-temperature metabolism remain poorly understood. We investigated the cellular pools of ATP and ADP in
Psychrobacter cryohalolentis
K5 incubated at eight temperatures between 22°C and −80°C. Cellular ATP and ADP concentrations increased with decreasing temperature, and the most significant increases were observed in cells that were incubated as frozen suspensions (<−5°C). Respiratory uncoupling significantly decreased this temperature-dependent response, indicating that the proton motive force was required for energy adaptation to frozen conditions. Since ATP and ADP are key substrates in metabolic and energy conservation reactions, increasing their concentrations may provide a strategy for offsetting the kinetic temperature effect, thereby maintaining reaction rates at low temperature. The adenylate levels increased significantly <1 h after freezing and also when the cells were osmotically shocked to simulate the elevated solute concentrations encountered in the liquid fraction of the ice. Together, these data demonstrate that a substantial change in cellular energy metabolism is required for the cell to adapt to the low temperature and water activity conditions encountered during freezing. This physiological response may represent a critical biochemical compensation mechanism at low temperature, have relevance to cellular survival during freezing, and be important for the persistence of microorganisms in icy environments.
Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees
Authors: Taghavi Safiyh , Garafola Craig , Monchy Sébastien , Newman Lee , Hoffman Adam , Weyens Nele , Barac Tanja , Vangronsveld Jaco , van der Lelie Daniel 
Published: December 2008

ABSTRACT

The association of endophytic bacteria with their plant hosts has a beneficial effect for many different plant species. Our goal is to identify endophytic bacteria that improve the biomass production and the carbon sequestration potential of poplar trees (
Populus
spp.) when grown in marginal soil and to gain an insight in the mechanisms underlying plant growth promotion. Members of the
Gammaproteobacteria
dominated a collection of 78 bacterial endophytes isolated from poplar and willow trees. As representatives for the dominant genera of endophytic gammaproteobacteria, we selected
Enterobacter
sp. strain 638,
Stenotrophomonas maltophilia
R551-3,
Pseudomonas putida
W619, and
Serratia proteamaculans
568 for genome sequencing and analysis of their plant growth-promoting effects, including root development. Derivatives of these endophytes, labeled with
gfp
, were also used to study the colonization of their poplar hosts. In greenhouse studies, poplar cuttings (
Populus deltoides
×
Populus nigra
DN-34) inoculated with
Enterobacter
sp. strain 638 repeatedly showed the highest increase in biomass production compared to cuttings of noninoculated control plants. Sequence data combined with the analysis of their metabolic properties resulted in the identification of many putative mechanisms, including carbon source utilization, that help these endophytes to thrive within a plant environment and to potentially affect the growth and development of their plant hosts. Understanding the interactions between endophytic bacteria and their host plants should ultimately result in the design of strategies for improved poplar biomass production on marginal soils as a feedstock for biofuels.
Novel Nicotine Oxidoreductase-Encoding Gene Involved in Nicotine Degradation by
Pseudomonas putida
Strain S16
Authors: Tang Hongzhi , Wang Lijuan , Meng Xiangzhou , Ma Lanying , Wang Shuning , He Xiaofei , Wu Geng , Xu Ping 
Published: December 2008

ABSTRACT

There are quite a few ongoing biochemical investigations of nicotine degradation in different organisms. In this work, we identified and sequenced a gene (designated
nicA
) involved in nicotine degradation by
Pseudomonas putida
strain S16. The gene product, NicA, was heterologously expressed and characterized as a nicotine oxidoreductase catalyzing the initial steps of nicotine metabolism. Biochemical analyses using resting cells and the purified enzyme suggested that
nicA
encodes an oxidoreductase, which converts nicotine to 3-succinoylpyridine through pseudooxynicotine. Based on enzymatic reactions and direct evidence obtained using H
2
18
O labeling, the process may consist of enzyme-catalyzed dehydrogenation, followed by spontaneous hydrolysis and then repetition of the dehydrogenation and hydrolysis steps. Sequence comparisons revealed that the gene showed 40% similarity to genes encoding NADH dehydrogenase subunit I and cytochrome
c
oxidase subunit I in eukaryotes. Our findings demonstrate that the molecular mechanism for nicotine degradation in strain S16 involves the pyrrolidine pathway and is similar to the mechanism in mammals, in which pseudooxynicotine, the direct precursor of a potent tobacco-specific lung carcinogen, is produced.
Tritium Suicide Selection Identifies Proteins Involved in the Uptake and Intracellular Transport of Sterols in
Saccharomyces cerevisiae
Authors: Sullivan David P. , Georgiev Alexander , Menon Anant K. 
Published: December 2008

ABSTRACT

Sterol transport between the plasma membrane (PM) and the endoplasmic reticulum (ER) occurs by a nonvesicular mechanism that is poorly understood. To identify proteins required for this process, we isolated
Saccharomyces cerevisiae
mutants with defects in sterol transport. We used
Upc2-1
cells that have the ability to take up sterols under aerobic conditions and exploited the observation that intracellular accumulation of exogenously supplied [
3
H]cholesterol in the form of [
3
H]cholesteryl ester requires an intact PM-ER sterol transport pathway.
Upc2-1
cells were mutagenized using a transposon library, incubated with [
3
H]cholesterol, and subjected to tritium suicide selection to isolate mutants with a decreased ability to accumulate [
3
H]cholesterol. Many of the mutants had defects in the expression and trafficking of Aus1 and Pdr11, PM-localized ABC transporters that are required for sterol uptake. Through characterization of one of the mutants, a new role was uncovered for the transcription factor Mot3 in controlling expression of Aus1 and Pdr11. A number of mutants had transposon insertions in the uncharacterized Ydr051c gene, which we now refer to as
DET1
(
d
ecreased
e
rgosterol
t
ransport). These mutants expressed Aus1 and Pdr11 normally but were severely defective in the ability to accumulate exogenously supplied cholesterol. The transport of newly synthesized sterols from the ER to the PM was also defective in
det1
Δ cells. These data indicate that the cytoplasmic protein encoded by
DET1
is involved in intracellular sterol transport.
Mutational Analysis of the
Candida albicans
Ammonium Permease Mep2p Reveals Residues Required for Ammonium Transport and Signaling
Authors: Dabas Neelam , Schneider Sabrina , Morschhäuser Joachim 
Published: December 2008

ABSTRACT

The ammonium permease Mep2p mediates ammonium uptake and also induces filamentous growth in the human-pathogenic yeast
Candida albicans
in response to nitrogen limitation. The C-terminal cytoplasmic tail of Mep2p contains a signaling domain that is not required for ammonium transport but is essential for Mep2p-dependent morphogenesis. Progressive C-terminal truncations showed Y433 to be the last amino acid that is essential for the induction of filamentous growth, thereby delimiting the Mep2p signaling domain. To understand in more detail how the signaling activity of Mep2p is regulated by ammonium availability and transport, we mutated conserved amino acid residues that have been implicated in ammonium binding or uptake. Mutation of D180, which has been proposed to mediate initial contact with extracellular ammonium, or the pore-lining residues H188 and H342 abolished Mep2p expression, indicating that these residues are important for protein stability. Mutation of F239, which together with F126 is thought to form an extracytosolic gate to the conductance channel, abolished both ammonium uptake and Mep2p-dependent filament formation, despite proper localization of the protein. On the other hand, mutation of W167, which is assumed to participate with Y122, F126, and S243 in the recruitment and coordination of the ammonium ion at the extracytosolic side of the cell membrane, also abolished filament formation without having a strong impact on ammonium transport, demonstrating that extracellular alterations in Mep2p can affect intracellular signaling. Mutation of Y122 reduced ammonium uptake much more strongly than mutation of W167 but still allowed efficient filament formation, indicating that the signaling activity of Mep2p is not directly correlated with its transport activity. These results provide important insights into ammonium transport and control of morphogenesis by Mep2p in
C. albicans
.
Cloning and Characterization of Uronate Dehydrogenases from Two Pseudomonads andAgrobacterium tumefaciensStrain C58
Authors: Yoon Sang-Hwal , Moon Tae Seok , Iranpour Pooya , Lanza Amanda M. , Prather Kristala Jones 
Published: December 2008

ABSTRACTUronate dehydrogenase has been cloned fromPseudomonas syringaepv. tomato strain DC3000,Pseudomonas putidaKT2440, andAgrobacterium tumefaciensstrain C58. The genes were identified by using a novel complementation assay employing anEscherichia colimutant incapable of consuming glucuronate as the sole carbon source but capable of growth on glucarate. A shotgun library ofP. syringaewas screened in the mutantE. coliby growing transformed cells on minimal medium containing glucuronic acid. Colonies that survived were evaluated for uronate dehydrogenase, which is capable of converting glucuronic acid to glucaric acid. In this manner, a 0.8-kb open reading frame was identified and subsequently verified to beudh. Homologous enzymes inP. putidaandA. tumefacienswere identified based on a similarity search of the sequenced genomes. Recombinant proteins from each of the three organisms expressed inE. coliwere purified and characterized. For all three enzymes, the turnover number (kcat) with glucuronate as a substrate was higher than that with galacturonate; however, the Michaelis constant (Km) for galacturonate was lower than that for glucuronate. TheA. tumefaciensenzyme was found to have the highest rate constant (kcat= 1.9 × 102s−1on glucuronate), which was more than twofold higher than those of both of the pseudomonad enzymes.
Delineation of the Species
Haemophilus influenzae
by Phenotype, Multilocus Sequence Phylogeny, and Detection of Marker Genes
Authors: Nørskov-Lauritsen Niels , Overballe Merete D. , Kilian Mogens 
Published: December 2008

ABSTRACT

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of
Haemophilus influenzae
by comparative analysis of
H. influenzae
reference strains with closely related bacteria including strains assigned to
Haemophilus haemolyticus
, cryptic genospecies biotype IV, and the never formally validated species “
Haemophilus intermedius”
. Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of
H. influenzae
from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of
H. influenzae
strains. The division was corroborated by the differential presence of genes encoding
H. influenzae
adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the
iga
gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains (“
H. intermedius
”) closely related to
H. influenzae
was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g.,
Haemophilus parainfluenzae
. Strains previously assigned to
H. haemolyticus
formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of “
H. intermedius
” and cryptic genospecies biotype IV. Although
H. influenzae
is phenotypically more homogenous than some other
Haemophilus
species, the genetic diversity and multicluster structure of strains traditionally associated with
H. influenzae
make it difficult to define the natural borders of that species.
The Hfq-Dependent Small Noncoding RNA NrrF Directly Mediates Fur-Dependent Positive Regulation of Succinate Dehydrogenase in
Neisseria meningitidis
Authors: Metruccio Matteo M. E. , Fantappiè Laura , Serruto Davide , Muzzi Alessandro , Roncarati Davide , Donati Claudio , Scarlato Vincenzo , Delany Isabel 
Published: December 2008

ABSTRACT

Previous microarray studies have suggested that an indirect mechanism of Fur regulation may be present in meningococcus at the posttranscriptional level through a small regulatory RNA (sRNA) system analogous to that of
Escherichia coli
and
Pseudomonas aeruginosa
. Recently, a Fur-regulated sRNA, NrrF, was identified that is involved in the iron regulation of the
sdhA
and
sdhC
succinate dehydrogenase genes. Here we report a detailed transcriptional analysis of the
nrrF
gene and show that NrrF is a Hfq-dependent sRNA. The Hfq protein mediates
nrrF
downregulation and Fur-dependent upregulation of the
sdhCDAB
operon, the major in vivo NrrF-regulated operon. NrrF forms a duplex in vitro with a region of complementarity overlapping the
sdhDA
mRNA junction. Furthermore, Hfq binds to NrrF in vitro and considerably enhances the efficiency of the interaction of the sRNA with the identified target. Our data suggest that Hfq-meditated binding of NrrF to the in vivo target in the
sdhCDAB
mRNA may cause the rapid degradation of the transcript, resulting in Fur-dependent positive regulation of succinate dehydrogenase. In addition, while the upregulation of
sodB
and
fumB
by Fur is dependent on the Hfq protein, it is unaffected in the
nrrF
knockout, which suggests that there is more than one sRNA regulator involved in iron homeostasis in meningococcus.