bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning, Nucleotide Sequencing, and Functional Analysis of a Novel, Mobile Cluster of Biodegradation Genes from
Pseudomonas aeruginosa
Strain JB2
Authors: Hickey W. J. , Sabat G. , Yuroff A. S. , Arment A. R. , Pérez-Lesher J. 
Published: July 2002

ABSTRACT

We have identified in
Pseudomonas aeruginosa
strain JB2 a novel cluster of mobile genes encoding degradation of hydroxy- and halo-aromatic compounds. Nineteen open reading frames were located and, based on sequence similarities, were putatively identified as encoding a ring hydroxylating oxygenase (
hybABCD
), an ATP-binding cassette-type transporter, an extradiol ring-cleavage dioxygenase, transcriptional regulatory proteins, enzymes mediating chlorocatechol degradation, and transposition functions. Expression of
hybABCD
in
Escherichia coli
cells effected stoichiometric transformation of 2-hydroxybenzoate (salicylate) to 2,5-dihydroxybenzoate (gentisate). This activity was predicted from sequence similarity to functionally characterized genes,
nagAaGHAb
from
Ralstonia
sp. strain U2 (S. L. Fuenmayor, M. Wild, A. L. Boyes, and P. A. Williams, J. Bacteriol. 180:2522–2530, 1998), and is the second confirmed example of salicylate 5-hydroxylase activity effected by an oxygenase outside the flavoprotein group. Growth of strain JB2 or
Pseudomonas huttiensis
strain D1 (an organism that had acquired the 2-chlorobenzoate degradation phenotype from strain JB2) on benzoate yielded mutants that were unable to grow on salicylate or 2-chlorobenzoate and that had a deletion encompassing
hybABCD
and the region cloned downstream. The mutants' inability to grow on 2-chlorobenzoate suggested the loss of additional genes outside of, but contiguous with, the characterized region. Pulsed-field gel electrophoresis revealed a plasmid of >300 kb in strain D1, but no plasmids were detected in strain JB2. Hybridization analyses confirmed that the entire 26-kb region characterized here was acquired by strain D1 from strain JB2 and was located in the chromosome of both organisms. Further studies to delineate the element's boundaries and functional characteristics could provide new insights into the mechanisms underlying evolution of bacterial genomes in general and of catabolic pathways for anthropogenic pollutants in particular.
Physiological Ecology of
Clostridium glycolicum
RD-1, an Aerotolerant Acetogen Isolated from Sea Grass Roots
Authors: Küsel Kirsten , Karnholz Arno , Trinkwalter Tanja , Devereux Richard , Acker Georg , Drake Harold L. 
Published: July 2002

ABSTRACT

An anaerobic, H
2
-utilizing bacterium, strain RD-1, was isolated from the highest growth-positive dilution series of a root homogenate prepared from the sea grass
Halodule wrightii
. Cells of RD-1 were gram-positive, spore-forming, motile rods that were linked by connecting filaments. Acetate was produced in stoichiometries indicative of an acetyl coenzyme A (acetyl-CoA) pathway-dependent metabolism when RD-1 utilized H
2
-CO
2
, formate, lactate, or pyruvate. Growth on sugars or ethylene glycol yielded acetate and ethanol as end products. RD-1 grew at the expense of glucose in the presence of low initial concentrations (up to 6% [vol/vol]) of O
2
in the headspace of static, horizontally incubated culture tubes; the concentration of O
2
decreased during growth in such cultures. Peroxidase, NADH oxidase, and superoxide dismutase activities were detected in the cytoplasmic fraction of cells grown in the presence of O
2
. In comparison to cultures incubated under strictly anoxic conditions, acetate production decreased, higher amounts of ethanol were produced, and lactate and H
2
became significant end products when RD-1 was grown on glucose in the presence of O
2
. Similarly, when RD-1 was grown on fructose in the presence of elevated salt concentrations, lower amounts of acetate and higher amounts of ethanol and H
2
were produced. When the concentration of O
2
in the headspace exceeded 1% (vol/vol), supplemental H
2
was not utilized. The 16S rRNA gene of RD-1 had a 99.7% sequence similarity to that of
Clostridium glycolicum
DSM 1288
T
, an organism characterized as a fermentative anaerobe. Comparative experiments with
C
.
glycolicum
DSM 1288
T
demonstrated that it had negligible H
2
- and formate-utilizing capacities. However, carbon monoxide dehydrogenase was detected in both RD-1 and
C
.
glycolicum
DSM 1288
T
. A 91.4% DNA-DNA hybridization between the genomic DNA of RD-1 and that of
C
.
glycolicum
DSM 1288
T
confirmed that RD-1 was a strain of
C
.
glycolicum
. These results indicate that (i) RD-1 metabolizes certain substrates via the acetyl-CoA pathway, (ii) RD-1 can tolerate and consume limited amounts of O
2
, (iii) oxic conditions favor the production of ethanol, lactate, and H
2
by RD-1, and (iv) the ability of RD-1 to cope with limited amounts of O
2
might contribute to its survival in a habitat subject to daily gradients of photosynthesis-derived O
2
.
An Altered
Pseudomonas
Diversity Is Recovered from Soil by Using Nutrient-Poor
Pseudomonas
-Selective Soil Extract Media
Authors: Aagot Nina , Nybroe Ole , Nielsen Preben , Johnsen Kaare 
Published: July 2002

ABSTRACT

We designed five
Pseudomonas
-selective soil extract NAA media containing the selective properties of trimethoprim and sodium lauroyl sarcosine and 0 to 100% of the amount of Casamino Acids used in the classical
Pseudomonas
-selective Gould's S1 medium. All of the isolates were confirmed to be
Pseudomonas
by a
Pseudomonas
-specific OprF antibody and a
Pseudomonas
-specific PCR targeting 16S ribosomal DNA. The
Pseudomonas
isolates were characterized by classical physiological tests, repetitive extragenic palindromic-PCR, Fourier transform infrared spectroscopy, and carbon source utilization patterns. Several of these analyses showed that the amount of Casamino Acids significantly influenced the diversity of the recovered
Pseudomonas
isolates. Furthermore, the data suggested that specific
Pseudomonas
subpopulations were represented on the nutrient-poor media. The NAA 1:100 medium, containing ca. 15 mg of organic carbon per liter, consistently gave significantly higher
Pseudomonas
CFU counts than Gould's S1 when tested on four Danish soils. NAA 1:100 may, therefore, be a better medium than Gould's S1 for enumeration and isolation of
Pseudomonas
from the low-nutrient soil environment.
Surface Expression of the Conserved C Repeat Region of Streptococcal M6 Protein within the Pip Bacteriophage Receptor ofLactococcus lactis
Authors: Geller Bruce L. , Wade Nadine , Gilberts Thomas D. , Hruby Dennis E. , Johanson Ryan , Topisirovic Ljubisa 
Published: July 2002

ABSTRACTThe C repeat region of the M6 protein (M6c) fromStreptococcus pyogeneswas expressed within the Pip bacteriophage receptor on the surface ofLactococcus lactis.M6c was also detected in the culture medium. Thepip-emm6callele was integrated into the chromosome and stably expressed without antibiotic selection. The level of cell-associated surface expression of PipM6c was 0.015% of total cellular protein. The amount of PipM6c on the cell surface was increased about 17-fold by expressingpip-emm6cfrom a high-copy-number plasmid. Replacing the nativepippromoter with stronger promoters isolated previously fromLactobacillus acidophilusincreased surface expression of PipM6c from the high-copy-number plasmid up to 27-fold. Concomitantly, the amount of PipM6c in the medium increased 113-fold. The amount of PipM6c did not vary greatly between exponential- and stationary-phase cultures. Western blots indicated that the full-length PipM6c protein and most of the numerous proteolytic products were found only on the cell surface, whereas only one proteolytic fragment was found in the culture medium.
16S Ribosomal DNA Terminal Restriction Fragment Pattern Analysis of Bacterial Communities in Feces of Rats Fed
Lactobacillus acidophilus
NCFM
Authors: Kaplan Christopher W. , Astaire Johanna C. , Sanders Mary Ellen , Reddy Bandaru S. , Kitts Christopher L. 
Published: July 2002

ABSTRACT

16S ribosomal DNA terminal restriction fragment patterns from rat fecal samples were analyzed to track the dynamics of
Lactobacillus acidophilus
NCFM and discern bacterial populations that changed during feeding with NCFM.
Lactobacillus johnsonii
and
Ruminococcus flavefaciens
were tentatively identified as such bacterial populations. The presence of
L. johnsonii
was confirmed by isolation from feces.
Deep Desulfurization of Extensively Hydrodesulfurized Middle Distillate Oil by
Rhodococcus
sp. Strain ECRD-1
Authors: Grossman M. J. , Lee M. K. , Prince R. C. , Minak-Bernero V. , George G. N. , Pickering I. J. 
Published: July 2002

ABSTRACT

Dibenzothiophene (DBT), and in particular substituted DBTs, are resistant to hydrodesulfurization (HDS) and can persist in fuels even after aggressive HDS treatment. Treatment by
Rhodococcus
sp. strain ECRD-1 of a middle distillate oil whose sulfur content was virtually all substituted DBTs produced extensive desulfurization and a sulfur level of 56 ppm.
Effects of Alkylphosphates and Nitrous Oxide on Microbial Degradation of Polycyclic Aromatic Hydrocarbons
Authors: Bogan Bill W. , Lahner Lisa M. , Trbovic Vesna , Szajkovics Ann M. , Paterek J. Robert 
Published: July 2002

ABSTRACT

We conducted a series of liquid-culture experiments to begin to evaluate the abilities of gaseous sources of nitrogen and phosphorus to support biodegradation of polycyclic aromatic hydrocarbons (PAHs). Nutrients examined included nitrous oxide, as well as triethylphosphate (TEP) and tributylphosphate (TBP). Cultures were established using the indigenous microbial populations from one manufactured gas plant (MGP) site and one crude oil-contaminated drilling field site. Mineralization of phenanthrene was measured under alternative nutrient regimes and was compared to that seen with ammoniacal nitrogen and PO
4
. Parallel cultures were used to assess removal of a suite of three- to five-ring PAHs. In summary, the abilities of the different communities to degrade PAH when supplemented with N
2
O, TEP, and TBP were highly variable. For example, in the MGP soil, organic P sources, especially TBP, supported a considerably higher degree of removal of low-molecular-weight PAHs than did PO
4
; however, loss of high-molecular-weight compounds was impaired under these conditions. The disappearance of most PAHs was significantly less in the oil field soil when organophosphates were used. These results indicate that the utility of gaseous nutrients for PAH bioremediation in situ may be limited and will very likely have to be assessed on a case-by-case basis.
Cloning of a Phenol Oxidase Gene from
Acremonium murorum
and Its Expression in
Aspergillus awamori
Authors: Gouka Robin J. , van der Heiden Monique , Swarthoff Ton , Verrips C. Theo 
Published: July 2002

ABSTRACT

Fungal multicopper oxidases have many potential industrial applications, since they perform reactions under mild conditions. We isolated a phenol oxidase from the fungus
Acremonium murorum
var.
murorum
that was capable of decolorizing plant chromophores (such as anthocyanins)
.
This enzyme is of interest in laundry-cleaning products because of its broad specificity for chromophores. We expressed an
A.
murorum
cDNA library in
Saccharomyces cerevisiae
and subsequently identified enzyme-producing yeast colonies based on their ability to decolor a plant chromophore. The cDNA sequence contained an open reading frame of 1,806 bp encoding an enzyme of 602 amino acids. The phenol oxidase was overproduced by
Aspergillus awamori
as a fusion protein with glucoamylase, cleaved in vivo
,
and purified from the culture broth by hydrophobic-interaction chromatography. The phenol oxidase is active at alkaline pH (the optimum for syringaldazine is pH 9) and high temperature (optimum, 60°C) and is fully stable for at least 1 h at 60°C under alkaline conditions. These characteristics and the high production level of 0.6 g of phenol oxidase per liter in shake flasks, which is equimolar with the glucoamylase protein levels, make this enzyme suitable for use in processes that occur under alkaline conditions, such as laundry cleaning.
Induction of
bphA
, Encoding Biphenyl Dioxygenase, in Two Polychlorinated Biphenyl-Degrading Bacteria, Psychrotolerant
Pseudomonas
Strain Cam-1 and Mesophilic
Burkholderia
Strain LB400
Authors: Master Emma R. , Mohn William W. 
Published: July 2002

ABSTRACT

We investigated induction of biphenyl dioxygenase in the psychrotolerant polychlorinated biphenyl (PCB) degrader
Pseudomonas strain
Cam-1 and in the mesophilic PCB degrader
Burkholderia strain
LB400. Using a counterselectable gene replacement vector, we inserted a
lacZ
-Gm
r
fusion cassette between chromosomal genes encoding the large subunit (
bphA
) and small subunit (
bphE
) of biphenyl dioxygenase in Cam-1 and LB400, generating Cam-10 and LB400-1, respectively. Potential inducers of
bphA
were added to cell suspensions of Cam-10 and LB400-1 incubated at 30°C, and then beta-galactosidase activity was measured. Biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately six times greater than the basal level in cells incubated with pyruvate. In contrast, the beta-galactosidase activities in LB400-1 incubated with biphenyl and in LB400-1 incubated with pyruvate were indistinguishable. At a concentration of 1 mM, most of the 40 potential inducers tested were inhibitory to induction by biphenyl of beta-galactosidase activity in Cam-10. The exceptions were naphthalene, salicylate, 2-chlorobiphenyl, and 4-chlorobiphenyl, which induced beta-galactosidase activity in Cam-10, although at levels that were no more than 30% of the levels induced by biphenyl. After incubation for 24 h at 7°C, biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately four times greater than the basal level in cells incubated with pyruvate. The constitutive level of beta-galactosidase activity in LB400-1 grown at 15°C was approximately five times less than the level in LB400-1 grown at 30°C. Thus, there are substantial differences in the effects of physical and chemical environmental conditions on genetic regulation of PCB degradation in different bacteria.
Carbon Limitation Induces ς
S
-Dependent Gene Expression in
Pseudomonas fluorescens
in Soil
Authors: Koch Birgit , Worm Jakob , Jensen Linda E. , Højberg Ole , Nybroe Ole 
Published: July 2002

ABSTRACT

Recent studies employing reporter gene technology indicate that the availabilities of the major nutrients nitrogen, phosphate, and iron to
Pseudomonas
are not severely limited in bulk soil. Indirect evidence has pointed to carbon limitation as a severe nutritional stress in this environment. We show that a plasmid (pGM115)-borne transcriptional fusion between the ς
S
-dependent
Escherichia coli
promoter
P

fic

and
lacZ
functions as a reliable reporter for carbon availability in
Pseudomonas fluorescens.
When
P. fluorescens
strain DF57(pGM115) was introduced into bulk soil, carbon-limiting conditions were indicated by citrate-repressible induction of β-galactosidase activity. To address carbon availability at the single-cell level, we developed an immunofluorescence double-staining procedure for individual DF57 cells expressing β-galactosidase from
P

fic

. Changes in cell size and expression of β-galactosidase were analyzed by flow cytometry. Cells extracted from soil microcosms reduced their size less than carbon-starved cells in pure culture and showed an increased tendency to aggregate. The single-cell analysis revealed that for cells residing in soil, the expression of β-galactosidase became heterogeneous and only a DF57 subpopulation appeared to be carbon limited. In soil amended with barley straw, limited nitrogen availability has been determined by use of the bioluminescent reporter strain
P. fluorescens
DF57-N3. We used strain DF57-N3(pGM115) as a double reporter for carbon and nitrogen limitation that allowed us to study the dynamics of carbon and nitrogen availabilities in more detail. In straw-amended soil β-galactosidase activity remained low, while nitrogen limitation-dependent bioluminescence appeared after a few days. Hence, nitrogen became limited under conditions where carbon resources were not completely exhausted.
Prevalence, Antigenic Specificity, and Bactericidal Activity of Poultry Anti-
Campylobacter
Maternal Antibodies
Authors: Sahin Orhan , Zhang Qijing , Meitzler Jerrel C. , Harr Brian S. , Morishita Teresa Y. , Mohan R. 
Published: July 2002

ABSTRACT

Poultry are considered the major reservoir for
Campylobacter jejuni
, a leading bacterial cause of human food-borne diarrhea. To understand the ecology of
C. jejuni
and develop strategies to control
C. jejuni
infection in the animal reservoir, we initiated studies to examine the potential role of anti-
Campylobacter
maternal antibodies in protecting young broiler chickens from infection by
C. jejuni
. Using an enzyme-linked immunosorbent assay (ELISA), the prevalence of anti-
C. jejuni
antibodies in breeder chickens, egg yolks, and broilers from multiple flocks of different farms were examined. High levels of antibodies to the organism were detected in serum samples of breeder chickens and in egg yolk contents. To determine the dynamics of anti-
Campylobacter
maternal antibody transferred from yolks to hatchlings, serum samples collected from five broiler flocks at weekly intervals from 1 to 28 or 42 days of age were also examined by ELISA. Sera from the 1-day and 7-day-old chicks showed high titers of antibodies to
C. jejuni
. Thereafter, antibody titers decreased substantially and were not detected during the third and fourth weeks of age. The disappearance of anti-
Campylobacter
maternal antibodies during 3 to 4 weeks of age coincides with the appearance of
C. jejuni
infections observed in many broiler chicken flocks. As shown by immunoblotting, the maternally derived antibodies recognized multiple membrane proteins of
C. jejuni
ranging from 19 to 107 kDa. Moreover, in vitro serum bactericidal assays showed that anti-
Campylobacter
maternal antibodies were active in antibody-dependent complement-mediated killing of
C. jejuni
. Together, these results highlight the widespread presence of functional anti-
Campylobacter
antibodies in the poultry production system and provide a strong rationale for further investigation of the potential role of anti-
C. jejuni
maternal antibodies in protecting young chickens from infection by
C. jejuni
.
Cloning, Characterization, and Transcription of Three Laccase Genes from
Gaeumannomyces graminis
var.
tritici
, the Take-All Fungus
Authors: Litvintseva Anastasia P. , Henson Joan M. 
Published: July 2002

ABSTRACT

Gaeumannomyces graminis
var.
tritici
, a filamentous ascomycete, is an important root pathogen of cereals that causes take-all disease and results in severe crop losses worldwide. Previously we identified a polyphenol oxidase (laccase) secreted by the fungus when induced with copper. Here we report cloning and partial characterization of three laccase genes (
LAC1
,
LAC2
, and
LAC3
) from
G. graminis
var.
tritici.
Predicted polypeptides encoded by these genes had 38 to 42% amino acid sequence identity and had conserved copper-binding sites characteristic of laccases. The sequence of the
LAC2
predicted polypeptide matched the N-terminal sequence of the secreted laccase that we purified in earlier studies. We also characterized expression patterns of these genes by reverse transcription-PCR.
LAC1
was transcribed constitutively, and transcription of
LAC2
was Cu inducible. All three genes were transcribed in planta; however, transcription of
LAC3
was observed only in planta or in the presence of host (wheat) plant homogenate.
Saccharomyces cerevisiae URH1
(Encoding Uridine-Cytidine
N
-Ribohydrolase): Functional Complementation by a Nucleoside Hydrolase from a Protozoan Parasite and by a Mammalian Uridine Phosphorylase
Authors: Mitterbauer Rudolf , Karl Thomas , Adam Gerhard 
Published: July 2002

ABSTRACT

Nucleoside hydrolases catalyze the cleavage of N-glycosidic bonds in nucleosides, yielding ribose and the respective bases. While nucleoside hydrolase activity has not been detected in mammalian cells, many protozoan parasites rely on nucleoside hydrolase activity for salvage of purines and/or pyrimidines from their hosts. In contrast, uridine phosphorylase is the key enzyme of pyrimidine salvage in mammalian hosts and many other organisms. We show here that the open reading frame (ORF)
YDR400w
of
Saccharomyces cerevisiae
carries the gene encoding uridine hydrolase (
URH1
). Disruption of this gene in a conditionally pyrimidine-auxotrophic
S. cerevisiae
strain, which is also deficient in uridine kinase (
urk1
), leads to the inability of the mutant to utilize uridine as the sole source of pyrimidines. Protein extracts of strains overexpressing
YDR400w
show increased hydrolase activity only with uridine and cytidine, but no activity with inosine, adenosine, guanosine, and thymidine as substrates, demonstrating that ORF
YDR400w
encodes a uridine-cytidine
N
-ribohydrolase. Expression of a homologous cDNA from a protozoan parasite (
Crithidia fasciculata
) in a
ura3 urk1 urh1
mutant is sufficient to restore growth on uridine. Growth can also be restored by expression of a human uridine phosphorylase cDNA. Yeast strains expressing protozoan
N
-ribohydrolases or host phosphorylases could therefore become useful tools in drug screens for specific inhibitors.
Modeling Growth and Bacteriocin Production by
Lactobacillus amylovorus
DCE 471 in Response to Temperature and pH Values Used for Sourdough Fermentations
Authors: Messens Winy , Neysens Patricia , Vansieleghem Wim , Vanderhoeven Johan , De Vuyst Luc 
Published: July 2002

ABSTRACT

The biokinetics of cell growth of
Lactobacillus amylovorus
DCE 471 and bacteriocin production by this strain were investigated as a function of the temperatures (28 to 44°C) and pH values (pH 4.2 to 6.4) that are characteristic of a sourdough fermentation process. The influence of temperature and pH on microbial behavior is described by using a successfully validated predictive model.
Application of Amplified Fragment Length Polymorphism Fingerprinting for Taxonomy and Identification of the Soft Rot Bacteria
Erwinia carotovora
and
Erwinia chrysanthemi
Authors: Avrova Anna O. , Hyman Lizbeth J. , Toth Rachel L. , Toth Ian K. 
Published: July 2002

ABSTRACT

The soft rot bacteria
Erwinia carotovora
and
Erwinia chrysanthemi
are important pathogens of potato and other crops. However, the taxonomy of these pathogens, particularly at subspecies level, is unclear. An investigation using amplified fragment length polymorphism (AFLP) fingerprinting was undertaken to determine the taxonomic relationships within this group based on their genetic relatedness. Following cluster analysis on the similarity matrices derived from the AFLP gels, four clusters (clusters 1 to 4) resulted. Cluster 1 contained
Erwinia carotovora
subsp.
carotovora
(subclusters 1a and 1b) and
Erwinia carotovora
subsp.
odorifera
(subcluster 1c) strains, while cluster 2 contained
Erwinia carotovora
subsp.
atroseptica
(subcluster 2a) and
Erwinia carotovora
subsp.
betavasculorum
(subcluster 2b) strains. Clusters 3 and 4 contained
Erwinia carotovora
subsp.
wasabiae
and
E. chrysanthemi
strains, respectively. While
E. carotovora
subsp.
carotovora
and
E. chrysanthemi
showed a high level of molecular diversity (23 to 38% mean similarity),
E. carotovora
subsp.
odorifera
,
E. carotovora
subsp.
betavasculorum
,
E. carotovora
subsp.
atroseptica
, and
E. carotovora
subsp.
wasabiae
showed considerably less (56 to 76% mean similarity), which may reflect their limited geographical distributions and/or host ranges. The species- and subspecies-specific banding profiles generated from the AFLPs allowed rapid identification of unknown isolates and the potential for future development of diagnostics. AFLP fingerprinting was also found to be more differentiating than other techniques for typing the soft rot erwinias and was applicable to all strain types, including different serogroups.