bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosomal Locus for Cadmium Resistance in
Pseudomonas putida
Consisting of a Cadmium-Transporting ATPase and a MerR Family Response Regulator
Authors: Lee Seon-Woo , Glickmann Eric , Cooksey Donald A. 
Published: July 2002

ABSTRACT

Pseudomonads from environmental sources vary widely in their sensitivity to cadmium, but the basis for this resistance is largely uncharactarized. A chromosomal fragment encoding cadmium resistance was cloned from
Pseudomonas putida
06909, a rhizosphere bacterium, and sequence analysis revealed two divergently transcribed genes,
cadA
and
cadR
. CadA was similar to cadmium-transporting ATPases known mostly from gram-positive bacteria, and to ZntA, a lead-, zinc-, and cadmium-transporting ATPase from
Escherichia coli
. CadR was related to the MerR family of response regulators that normally control mercury detoxification in other bacterial systems. A related gene,
zntR
, regulates
zntA
in
E. coli
, but it is not contiguous with
zntA
in the
E. coli
genome as
cadA
and
cadR
were in
P. putida
. In addition, unlike ZntA and other CadA homologs, but similar to the predicted product of gene PA3690 in the
P. aeruginosa
genome, the
P. putida
CadA sequence had a histidine-rich N-terminal extension. CadR and the product of PA3689 of
P. aeruginosa
also had histidine-rich C-terminal extensions not found in other MerR family response regulators. Mutational analysis indicated that
cadA
and
cadR
are fully responsible for cadmium resistance and partially for zinc resistance. However, unlike
zntA
, they did not confer significant levels of lead resistance. The
cadA
promoter was responsive to Cd(II), Pb(II), and Zn(II), while the
cadR
promoter was only induced by Cd(II). CadR apparently represses its own expression at the transcriptional level. However, CadR apparently does not repress
cadA
. Homologs of the cadmium-transporting ATPase were detected in many other
Pseudomonas
species.
Evaluation of Inoculum Addition To Stimulate In Situ Bioremediation of Oily-Sludge-Contaminated Soil
Authors: Mishra Sanjeet , Jyot Jeevan , Kuhad Ramesh C. , Lal Banwari 
Published: July 2002

ABSTRACT

A full-scale study evaluating an inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil was conducted at an oil refinery where the indigenous population of hydrocarbon-degrading bacteria in the soil was very low (10
3
to 10
4
CFU/g of soil). A feasibility study was conducted prior to the full-scale bioremediation study. In this feasibility study, out of six treatments, the application of a bacterial consortium and nutrients resulted in maximum biodegradation of total petroleum hydrocarbon (TPH) in 120 days. Therefore, this treatment was selected for the full-scale study. In the full-scale study, plots A and B were treated with a bacterial consortium and nutrients, which resulted in 92.0 and 89.7% removal of TPH, respectively, in 1 year, compared to 14.0% removal of TPH in the control plot C. In plot A, the alkane fraction of TPH was reduced by 94.2%, the aromatic fraction of TPH was reduced by 91.9%, and NSO (nitrogen-, sulfur-, and oxygen-containing compound) and asphaltene fractions of TPH were reduced by 85.2% in 1 year. Similarly, in plot B the degradation of alkane, aromatic, and NSO plus asphaltene fractions of TPH was 95.1, 94.8, and 63.5%, respectively, in 345 days. However, in plot C, removal of alkane (17.3%), aromatic (12.9%), and NSO plus asphaltene (5.8%) fractions was much less. The population of introduced
Acinetobacter baumannii
strains in plots A and B was stable even after 1 year. Physical and chemical properties of the soil at the bioremediation site improved significantly in 1 year.
Enhanced Acid Sensitivity of Pressure-Damaged
Escherichia coli
O157 Cells
Authors: Pagán Rafael , Jordan Sarah , Benito Amparo , Mackey Bernard 
Published: July 2002

ABSTRACT

Pressure-damaged
Escherichia coli
O157 cells were more acid sensitive than native cells and were impaired in pH homeostasis. However differences in acid sensitivity were not related to differences in cytoplasmic pH (pH
i
). Cellular β-galactosidase was more acid labile in damaged cells. Sensitization to acid may thus involve loss of protective or repair functions.
Toxic Effects of Linear Alkylbenzene Sulfonate on Metabolic Activity, Growth Rate, and Microcolony Formation ofNitrosomonasandNitrosospiraStrains
Authors: Brandt Kristian K. , Hesselso/e Martin , Roslev Peter , Henriksen Kaj , So/rensen Jan 
Published: July 2002

ABSTRACTStrong inhibitory effects of the anionic surfactant linear alkylbenzene sulfonate (LAS) on four strains of autotrophic ammonia-oxidizing bacteria (AOB) are reported. TwoNitrosospirastrains were considerably more sensitive to LAS than twoNitrosomonasstrains were. Interestingly, the twoNitrosospirastrains showed a weak capacity to remove LAS from the medium. This could not be attributed to adsorption or any other known physical or chemical process, suggesting that biodegradation of LAS took place. In each strain, the metabolic activity (50% effective concentration [EC50], 6 to 38 mg liter−1) was affected much less by LAS than the growth rate and viability (EC50, 3 to 14 mg liter−1) were. However, at LAS levels that inhibited growth, metabolic activity took place only for 1 to 5 days, after which metabolic activity also ceased. The potential for adaptation to LAS exposure was investigated withNitrosomonas europaeagrown at a sublethal LAS level (10 mg liter−1); compared to control cells, preexposed cells showed severely affected cell functions (cessation of growth, loss of viability, and reduced NH4+oxidation activity), demonstrating that long-term incubation at sublethal LAS levels was also detrimental. Our data strongly suggest that AOB are more sensitive to LAS than most heterotrophic bacteria are, and we hypothesize that thermodynamic constraints make AOB more susceptible to surfactant-induced stress than heterotrophic bacteria are. We further suggest that AOB may comprise a sensitive indicator group which can be used to determine the impact of LAS on microbial communities.
Detection of Differential Gene Expression in Biofilm-Forming versus Planktonic Populations of
Staphylococcus aureus
Using Micro-Representational-Difference Analysis
Authors: Becker Petra , Hufnagle Wendy , Peters Georg , Herrmann Mathias 
Published: July 2002

ABSTRACT

Microbial proliferation and biofilm formation on biologic or inert substrates are characteristics of invasive
Staphylococcus aureus
infections and is associated with phenotypic alterations such as reduced antimicrobial susceptibility. To identify genes which are typically expressed in biofilms, a micro-representational-difference analysis (micro-RDA) was adapted for gram-positive bacteria and used with cDNA derived from populations of
S. aureus
DSM 20231 growing in a biofilm or plankonically. In comparison to previously described cDNA RDA protocols, micro-RDA has the advantages that only minimal quantities of total RNA are needed and, most importantly, that total RNA can be used since the large amount of rRNA in total RNA does not interfere with the micro-RDA procedure. Using a series of spiked controls with various amounts of MS2 RNA in a background of total RNA from
S. aureus,
the equivalent of five copies of MS2 per cell were detectable after three rounds of subtractive enrichment. Five genes were identified as being differentially expressed in biofilm versus planktonic cultures. These genes revealed homology to a threonyl-tRNA synthetase, a phosphoglycerate mutase, a triosephosphate isomerase, an alcohol dehydrogenase I, and a ClpC ATPase. Differential levels of expression were subsequently confirmed by standard Northern blotting. In conclusion, micro-RDA is a sensitive and specific method to detect transcripts differentially expressed as a function of different
S. aureus
growth conditions.
Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods
Authors: Eder Wolfgang , Jahnke Linda L. , Schmidt Mark , Huber Robert 
Published: July 2002

ABSTRACT

The brine-seawater interface of the Kebrit Deep, northern Red Sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. Under strictly anaerobic culture conditions, novel halophiles were isolated. The new rod-shaped isolates belong to the halophilic genus
Halanaerobium
and are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. Within the genus
Halanaerobium
, they represent new species which grow chemoorganotrophically at NaCl concentrations ranging from 5 to 34%. The cellular fatty acid compositions are consistent with those of other
Halanaerobium
representatives, showing unusually large amounts of Δ7 and Δ11 16:1 fatty acids. Phylogenetic analysis of the brine-seawater interface sample revealed the presence of various bacterial 16S rRNA gene sequences dominated by cultivated members of the bacterial domain, with the majority affiliated with the genus
Halanaerobium
. The new
Halanaerobium
16S rRNA clone sequences showed the highest similarity (99.9%) to the sequence of isolate KT-8-13 from the Kebrit Deep brine. In this initial survey, our polyphasic approach demonstrates that novel halophiles thrive in the anaerobic, deep-sea brine pool of the Kebrit Deep, Red Sea. They may contribute significantly to the anaerobic degradation of organic matter enriched at the brine-seawater interface.
Nuclear Magnetic Resonance Analysis of [1-
13
C]Dimethylsulfoniopropionate (DMSP) and [1-
13
C]Acrylate Metabolism by a DMSP Lyase-Producing Marine Isolate of the α-Subclass of
Proteobacteria
Authors: Ansede John H. , Pellechia Perry J. , Yoch Duane C. 
Published: July 2002

ABSTRACT

The prominence of the α-subclass of
Proteobacteria
in the marine bacterioplankton community and their role in dimethylsulfide (DMS) production has prompted a detailed examination of dimethylsulfoniopropionate (DMSP) metabolism in a representative isolate of this phylotype, strain LFR. [1-
13
C]DMSP was synthesized, and its metabolism and that of its cleavage product, [1-
13
C]acrylate, were studied using nuclear magnetic resonance (NMR) spectroscopy. [1-
13
C]DMSP additions resulted in the intracellular accumulation and then disappearance of both [1-
13
C]DMSP and [1-
13
C]β-hydroxypropionate ([1-
13
C]β-HP), a degradation product. Acrylate, the immediate product of DMSP cleavage, apparently did not accumulate to high enough levels to be detected, suggesting that it was rapidly β-hydroxylated upon formation. When [1-
13
C]acrylate was added to cell suspensions of strain LFR it was metabolized to [1-
13
C]β-HP extracellularly, where it first accumulated and was then taken up in the cytosol where it subsequently disappeared, indicating that it was directly decarboxylated. These results were interpreted to mean that DMSP was taken up and metabolized by an intracellular DMSP lyase and acrylase, while added acrylate was β-hydroxylated on (or near) the cell surface to β-HP, which accumulated briefly and was then taken up by cells. Growth on acrylate (versus that on glucose) stimulated the rate of acrylate metabolism eightfold, indicating that it acted as an inducer of acrylase activity. DMSP, acrylate, and β-HP all induced DMSP lyase activity. A putative model is presented that best fits the experimental data regarding the pathway of DMSP and acrylate metabolism in the α-proteobacterium, strain LFR.
Development of a Genetic System for
Geobacter sulfurreducens
Authors: Coppi Maddalena V. , Leang Ching , Sandler Steven J. , Lovley Derek R. 
Published: July 2002

ABSTRACT

Members of the genus
Geobacter
are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these organisms, a genetic system was developed for
Geobacter sulfurreducens
. The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established. A protocol for the introduction of foreign DNA into
G. sulfurreducens
by electroporation was also developed. Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in
G. sulfurreducens.
In particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism. When the information and novel methods described above were utilized, the
nifD
gene of
G. sulfurreducens
was disrupted by the single-step gene replacement method. Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of
G. sulfurreducens
to grow in medium lacking a source of fixed nitrogen. Expression of the
nifD
gene in
trans
complemented this phenotype. This paper constitutes the first report of genetic manipulation of a member of the
Geobacter
genus.
Effects of Cell-Bound Microcystins on Survival and Feeding of
Daphnia
spp
Authors: Rohrlack Thomas , Dittmann Elke , Börner Thomas , Christoffersen Kirsten 
Published: July 2002

ABSTRACT

The influence of cell-bound microcystins on the survival time and feeding rates of six
Daphnia
clones belonging to five common species was studied. To do this, the effects of the microcystin-producing
Microcystis
strain PCC7806 and its mutant, which has been genetically engineered to knock out microcystin synthesis, were compared. Additionally, the relationship between microcystin ingestion rate by the
Daphnia
clones and
Daphnia
survival time was analyzed. Microcystins ingested with
Microcystis
cells were poisonous to all
Daphnia
clones tested. The median survival time of the animals was closely correlated to their microcystin ingestion rate. It was therefore suggested that differences in survival among
Daphnia
clones were due to variations in microcystin intake rather than due to differences in susceptibility to the toxins. The correlation between median survival time and microcystin ingestion rate could be described by a reciprocal power function. Feeding experiments showed that, independent of the occurrence of microcystins, cells of wild-type PCC7806 and its mutant are able to inhibit the feeding activity of
Daphnia
. Both variants of PCC7806 were thus ingested at low rates. In summary, our findings strongly suggest that (i) sensitivity to the toxic effect of cell-bound microcystins is typical for
Daphnia
spp., (ii)
Daphnia
spp. and clones may have a comparable sensitivity to microcystins ingested with food particles, (iii)
Daphnia
spp. may be unable to distinguish between microcystin-producing and -lacking cells, and (iv) the strength of the toxic effect can be predicted from the microcystin ingestion rate of the animals.
Cosecretion of Chaperones and Low-Molecular-Size Medium Additives Increases the Yield of Recombinant Disulfide-Bridged Proteins
Authors: Schäffner Jörg , Winter Jeannette , Rudolph Rainer , Schwarz Elisabeth 
Published: July 2002

ABSTRACT

Attempts were made to engineer the periplasm of
Escherichia coli
to an expression compartment of heterologous proteins in their native conformation. As a first approach the low-molecular-size additive
l
-arginine and the redox compound glutathione (GSH) were added to the culture medium. Addition of 0.4 M
l
-arginine and 5 mM reduced GSH increased the yield of a native tissue-type plasminogen activator variant (rPA), consisting of the kringle-2 and the protease domain, and a single-chain antibody fragment (scFv) up to 10- and 37-fold, respectively. A variety of other medium additives also had positive effects on the yield of rPA. In a second set of experiments, the effects of cosecreted ATP-independent molecular chaperones on the yields of native therapeutic proteins were investigated. At optimized conditions, cosecretion of
E. coli
DnaJ or murine Hsp25 increased the yield of native rPA by a factor of 170 and 125, respectively. Cosecretion of DnaJ also dramatically increased the amount of a second model protein, native proinsulin, in the periplasm. The results of this study are anticipated to initiate a series of new approaches to increase the yields of native, disulfide-bridged, recombinant proteins in the periplasm of
E. coli
.
gly
Gene Cloning and Expression and Purification of Glycinecin A, a Bacteriocin Produced by
Xanthomonas campestris
pv. glycines 8ra
Authors: Heu Sunggi , Oh Jonghee , Kang Youngsung , Ryu Sangryeol , Cho Somi K. , Cho Youngsup , Cho Moonjae 
Published: July 2002

ABSTRACT

Glycinecin A, a bacteriocin produced by
Xanthomonas campestris
pv. glycines, inhibits the growth of
X. campestris
pv. vesicatoria. We have cloned and expressed the genes encoding glycinecin A in
Escherichia coli
. Recombinant glycinecin A was purified from cell extracts by ammonium sulfate precipitation followed by chromatography on Q-Sepharose, Mono Q (ion exchange), and size exclusion columns. Purified glycinecin A is composed of two polypeptides, is active over a wide pH range (6 to 9), and is stable at temperatures up to 60°C. Glycinecin A is a heterodimer consisting of 39- and 14-kDa subunits, as revealed through size exclusion chromatography and cross-linking analysis. Two genes,
glyA
and
glyB
, encoding the 39- and 14-kDa subunits, respectively, were identified based on the N-terminal sequences of the subunits. From the nucleotide sequences of
glyA
and
glyB
, we conclude that both genes are translated as bacteriocin precursors that include N-terminal leader sequences. When expressed in
E. coli
, recombinant glycinecin A was found primarily in cell extracts. In contrast, most glycinecin A from
Xanthomonas
was found in the culture media.
E. coli
transformed with either
glyA
or
glyB
separately did not show the bacteriocin activity.
Dehalogenation of Chlorinated Hydroxybiphenyls by Fungal Laccase
Authors: Schultz Asgard , Jonas Ulrike , Hammer Elke , Schauer Frieder 
Published: July 2002

ABSTRACT

We have investigated the transformation of chlorinated hydroxybiphenyls by laccase produced by
Pycnoporus cinnabarinus
. The compounds used were transformed to sparingly water-soluble colored precipitates which were identified by gas chromatography-mass spectrometry as oligomerization products of the chlorinated hydroxybiphenyls. During oligomerization of 2-hydroxy-5-chlorobiphenyl and 3-chloro-4-hydroxybiphenyl, dechlorinated C—C-linked dimers were formed, demonstrating the dehalogenation ability of laccase. In addition to these nonhalogenated dimers, both monohalogenated and dihalogenated dimers were identified.
Occurrence of Beauvericin and Enniatins in Wheat Affected by
Fusarium avenaceum
Head Blight
Authors: Logrieco A. , Rizzo A. , Ferracane R. , Ritieni A. 
Published: July 2002

ABSTRACT

We evaluated
Fusarium
contamination and the levels of hexadepsipeptide mycotoxins in 13 wheat samples affected by head blight in Finland.
Fusarium avenaceum
was the dominant species (91%) isolated from all samples, but isolates of
F. culmorum
(4%),
F. tricinctum
(3%), and
F. poae
(2%) also were recovered. Beauvericin (0.64 to 3.5 μg/g) was detected in all 13 samples. Enniatin B (trace to 4.8 μg/g) was detected in 12 samples, enniatin B
1
(trace to 1.9 μg/g) was detected in 8 samples, and enniatin A
1
(trace to 6.9 μg/g) was detected in 10 samples. Ten of 13 strains of
F. avenaceum
and 2 strains of
F. poae
and
F. tricinctum
produced beauvericin in culture on rice (trace to 70, 9.4, and 33 μg/g, respectively). All strains also produced enniatins (trace to 2,700 μg/g). This is the first report on the natural cooccurence of beauvericin and enniatins in wheat infected predominantly by
F. avenaceum
.
Molecular Method To Assess the Diversity of
Burkholderia
Species in Environmental Samples
Authors: Salles Joana Falcão , De Souza Francisco Adriano , van Elsas Jan Dirk 
Published: July 2002

ABSTRACT

In spite of the importance of many members of the genus
Burkholderia
in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the
Burkholderia
diversity in soil samples. Primers specific for the genus
Burkholderia
were developed based on the 16S rRNA gene sequence and were evaluated in PCRs performed with genomic DNAs from
Burkholderia
and non-
Burkholderia
species as the templates. The primer system used exhibited good specificity and sensitivity for the majority of established species of the genus
Burkholderia
. DGGE analyses of the PCR products obtained showed that there were sufficient differences in migration behavior to distinguish the majority of the 14
Burkholderia
species tested. Sequence analysis of amplicons generated with soil DNA exclusively revealed sequences affiliated with sequences of
Burkholderia
species, demonstrating that the PCR-DGGE method is suitable for studying the diversity of this genus in natural settings. A PCR-DGGE analysis of the
Burkholderia
communities in two grassland plots revealed differences in diversity mainly between bulk and rhizosphere soil samples; the communities in the latter samples produced more complex patterns.
Bacterial Cell Surface Display of Organophosphorus Hydrolase for Selective Screening of Improved Hydrolysis of Organophosphate Nerve Agents
Authors: Cho Catherine Mee-Hie , Mulchandani Ashok , Chen Wilfred 
Published: July 2002

ABSTRACTOrganophosphorus hydrolase (OPH) is a bacterial enzyme that has been shown to degrade a wide range of neurotoxic organophosphate nerve agents. However, the effectiveness of degradation varies dramatically, ranging from highly efficient with paraoxon to relatively slow with methyl parathion. Sequential cycles of DNA shuffling and screening were used to fine-tune and enhance the activity of OPH towards poorly degraded substrates. Because of the inaccessibility of these pesticides across the cell membrane, OPH variants were displayed on the surface ofEscherichia coliusing the truncated ice nucleation protein in order to isolate novel enzymes with truly improved substrate specificities. A solid-phase top agar method based on the detection of the yellow productp-nitrophenol was developed for the rapid prescreening of potential variants with improved hydrolysis of methyl parathion. Two rounds of DNA shuffling and screening were carried out, and several improved variants were isolated. One variant in particular, 22A11, hydrolyzes methyl parathion 25-fold faster than does the wild type. Because of the success that we achieved with directed evolution of OPH for improved hydrolysis of methyl parathion, we believe that we can easily extend this method in creating other OPH variants with improved activity against poorly degraded pesticides such as diazinon and chlorpyrifos and nerve agents such as sarin and soman.
Melanin Production and Use as a Soluble Electron Shuttle for Fe(III) Oxide Reduction and as a Terminal Electron Acceptor byShewanella algaeBrY
Authors: Turick Charles E. , Tisa Louis S. , Caccavo, Frank 
Published: July 2002

ABSTRACTDissimilatory metal-reducing bacteria (DMRB) utilize numerous compounds as terminal electron acceptors, including insoluble iron oxides. The mechanism(s) of insoluble-mineral reduction by DMRB is not well understood. Here we report that extracellular melanin is produced byShewanella algaeBrY. The extracted melanin served as the sole terminal electron acceptor. Upon reduction the reduced, soluble melanin reduced insoluble hydrous ferric oxide in the absence of bacteria, thus demonstrating that melanin produced byS. algaeBrY is a soluble Fe(III)-reducing compound. In the presence of bacteria, melanin acted as an electron conduit to Fe(III) minerals and increased Fe(III) mineral reduction rates. Growth ofS. algaeBrY occurred in anaerobic minimal medium supplemented with melanin extracted from previously grown aerobic cultures ofS. algaeBrY. Melanin produced byS. algaeBrY imparts increased versatility to this organism as a soluble Fe(III) reductant, an electron conduit for iron mineral reduction, and a sole terminal electron acceptor that supports growth.