bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of Active Chimeric Pediocin AcH in
Escherichia coli
in the Absence of Processing and Secretion Genes from the
Pediococcus pap
Operon
Authors: Miller Kurt W. , Schamber Robin , Chen Yanling , Ray Bibek 
Published: December 2019

ABSTRACT

Minimum requirements have been determined for synthesis and secretion of the
Pediococcus
antimicrobial peptide, pediocin AcH, in
Escherichia coli
. The functional mature domain of pediocin AcH (Lys
+1
to Cys
+44
) is targeted into the
E. coli sec
machinery and secreted to the periplasm in active form when fused in frame to the COOH terminus of the secretory protein maltose-binding protein (MBP). The PapC-PapD specialized secretion machinery is not required for secretion of the MBP-pediocin AcH chimeric protein, indicating that in
Pediococcus
, PapC and PapD probably are required for recognition and processing of the leader peptide rather than for translocation of the mature pediocin AcH domain across the cytoplasmic membrane. The chimeric protein displays bactericidal activity, suggesting that the NH
2
terminus of pediocin AcH does not span the phospholipid bilayer in the membrane-interactive form of the molecule. However, the conserved Lys
+1
-Tyr-Tyr-Gly-Asn-Gly-Val
+7
-sequence at the NH
2
terminus is important because deletion of this sequence abolishes activity. The secreted chimeric protein is released into the culture medium when expressed in a periplasmic leaky
E. coli
host. The MBP fusion-periplasmic leaky expression system should be generally advantageous for production and screening of the activity of bioactive peptides.
Detection of Verotoxigenic
Escherichia coli
by Magnetic Capture-Hybridization PCR
Authors: Chen Jinru , Johnson Roger , Griffiths Mansel 
Published: December 2019

ABSTRACT

Magnetic capture-hybridization PCR (MCH-PCR) was used for the detection of 36 verotoxigenic (verotoxin [VT]-producing)
Escherichia coli
(VTEC), 5 VTEC reference, and 13 non-VTEC control cultures. The detection system employs biotin-labeled probes to capture the DNA segments that contain specific regions of the genes for VT1 and VT2 by DNA-DNA hybridization. The hybrids formed were isolated by streptavidin-coated magnetic beads which were collected by a magnetic particle separator and, subsequently, amplified directly by conventional PCR. The detection system was found to be specific for VTEC: no amplification was obtained from non-VTEC controls, whereas VTEC isolates tested positive for one or two specific PCR products. With 5, 7, or 10 h of enrichment, the limits of detection were 10
3
, 10
2
, and 10
0
CFU/ml, respectively, by agarose gel electrophoresis. Southern hybridization did not seem to improve the limit of the detection. When applied to food, MCH-PCR was capable of detecting 10
0
CFU of VTEC per g of ground beef with 15 h of nonselective enrichment. The results of MCH-PCR for pure cultures of VT1- and/or VT2-producing
E. coli
cells were in total agreement with toxin production as measured by a VT enzyme-linked immunosorbent assay.
Purification and Characterization of
O
-Methyltransferase I Involved in Conversion of Demethylsterigmatocystin to Sterigmatocystin and of Dihydrodemethylsterigmatocystin to Dihydrosterigmatocystin during Aflatoxin Biosynthesis
Authors: Yabe Kimiko , Matsushima Ken-ichiro , Koyama Takumi , Hamasaki Takashi 
Published: December 2019

ABSTRACT

O
-Methyltransferase I, which catalyzes conversions both of demethylsterigmatocystin (DMST) to sterigmatocystin (ST) and of dihydrodemethylsterigmatocystin (DHDMST) to dihydrosterigmatocystin (DHST) during aflatoxin biosynthesis, was purified to apparent homogeneity from the cytosol fraction of the mycelia of
Aspergillus parasiticus
NIAH-26 through the following chromatography series: phenyl-Sepharose, DEAE-Sepharose, phenyl-Sepharose, Sephacryl S-300, and Matrex gel Green A. The apparent molecular mass was estimated at 150 kDa based on Sephacryl S-300 gel filtration chromatography, and the denaturing molecular mass was 43 kDa based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The pI of the enzyme was 4.4, and the optimal pH for activity was broad, from 6.5 to 9.0. In competition experiments using the purified enzyme, the formation of ST from DMST was suppressed when DHDMST was added to the reaction mixture and DHST was newly formed. These results indicate that DMST and DHDMST commonly serve as substrates for the enzyme. The

K
m

of the enzyme for DMST was 0.94 μM, and that for DHDMST was 2.5 μM. Interestingly, MT-I kinetics deviated substantially from standard Michaelis-Menten kinetics, demonstrating substrate inhibition at a higher substrate concentration.
Microbial Consumption of Atmospheric Isoprene in a Temperate Forest Soil
Authors: Cleveland C. C. , Yavitt J. B. 
Published: December 2019

ABSTRACT

Isoprene (2-methyl-1,3 butadiene) is a low-molecular-weight hydrocarbon emitted in large quantities to the atmosphere by vegetation and plays a large role in regulating atmospheric chemistry. Until now, the atmosphere has been considered the only significant sink for isoprene. However, in this study we performed both in situ and in vitro experiments with soil from a temperate forest near Ithaca, N.Y., that indicate that the soil provides a sink for atmospheric isoprene and that the consumption of isoprene is carried out by microorganisms. Consumption occurred rapidly in field chambers (672.60 ± 30.12 to 2,718.36 ± 86.40 pmol gdw
−1
day
−1
) (gdw is grams [dry weight] of soil; values are means ± standard deviations). Subsequent laboratory experiments confirmed that isoprene loss was due to biological processes: consumption was stopped by autoclaving the soil; consumption rates increased with repeated exposure to isoprene; and consumption showed a temperature response consistent with biological activity (with an optimum temperature of 30°C). Isoprene consumption was diminished under low oxygen conditions (120 ± 7.44 versus 528.36 ± 7.68 pmol gdw
−1
day
−1
under ambient O
2
concentrations) and showed a strong relationship with soil moisture. Isoprene-degrading microorganisms were isolated from the site, and abundance was calculated as 5.8 × 10
5
± 3.2 × 10
5
cells gdw
−1
. Our results indicate that soil may provide a significant biological sink for atmospheric isoprene.
Molecular Basis of a Bacterial Consortium: Interspecies Catabolism of Atrazine
Authors: de Souza Mervyn L. , Newcombe David , Alvey Sam , Crowley David E. , Hay Anthony , Sadowsky Michael J. , Wackett Lawrence P. 
Published: December 2019

ABSTRACTPseudomonassp. strain ADP contains the genes,atzA, -B, and -C, that encode three enzymes which metabolize atrazine to cyanuric acid. Atrazine-catabolizing pure cultures isolated from around the world contain genes homologous toatzA, -B, and -C. The present study was conducted to determine whether the same genes are present in an atrazine-catabolizing bacterial consortium and how the genes and metabolism are subdivided among member species. The consortium contained four or more bacterial species, but two members,Clavibacter michiganeseATZ1 andPseudomonassp. strain CN1, collectively mineralized atrazine.C. michiganeseATZ1 released chloride from atrazine, produced hydroxyatrazine, and contained a homolog to theatzAgene that encoded atrazine chlorohydrolase.C. michiganeseATZ1 stoichiometrically metabolized hydroxyatrazine toN-ethylammelide and contained genes homologous toatzBandatzC, suggesting that either a functional AtzB or -C catalyzedN-isopropylamine release from hydroxyatrazine.C. michiganeseATZ1 grew on isopropylamine as its sole carbon and nitrogen source, explaining the ability of the consortium to use atrazine as the sole carbon and nitrogen source. A second consortium member,Pseudomonassp. strain CN1, metabolized theN-ethylammelide produced byC. michiganeseATZ1 to transiently form cyanuric acid, a reaction catalyzed by AtzC. A gene homologous to theatzCgene ofPseudomonassp. strain ADP was present, as demonstrated by Southern hybridization and PCR.Pseudomonassp. strain CN1, but notC. michiganese, metabolized cyanuric acid. The consortium metabolized atrazine faster than didC. michiganeseindividually. Additionally, the consortium metabolized a much broader set of triazine ring compounds than did previously described pure cultures in which theatzABCgenes had been identified. These data begin to elucidate the genetic and metabolic bases of catabolism by multimember consortia.
Surface Properties of Bifidobacterial Strains of Human Origin
Authors: Pérez Pablo F. , Minnaard Yessica , Disalvo Edgardo A. , De Antoni Graciela L. 
Published: December 2019

ABSTRACT

The adherence of
Bifidobacterium
strains isolated from infant feces and commercial fermented dairy products to enterocyte-like cells was correlated with the autoagglutination and hemagglutination properties of these organisms. These results allowed us to define two groups: (i) cell-adherent bacteria showing hemagglutination and autoagglutination and (ii) non-cell-adherent, nonhemagglutinating, nonautoagglutinating bacteria. Glass adherence was shown to be nonspecific and was discarded as a criterion for selection of adherent cells. Hydrophobicity appeared to be necessary for adhesion to enterocyte-like cells and autoagglutination. Adhesive strains were highly hydrophobic, and the degree of adherence was slightly dependent on the surface potential. Cells autoagglutinated more when the electrostatic negative charges on the cell surface were shielded by a decrease in the pH from 7 to 2. However, in some strains negative charges at the cell surface were adjuvant to adhesion, thus suggesting that specific chemical interactions occurred. The present results provide a method for preliminary selection of bacteria potentially adherent to epithelial cells by means of autoagglutination.
PCR Detection of Cyclic Lipodepsinonapeptide-Producing
Pseudomonas syringae
pv. syringae and Similarity of Strains
Authors: Sorensen Kevin N. , Kim Kwang-Hee , Takemoto Jon Y. 
Published: December 2019

ABSTRACT

Many strains of
Pseudomonas syringae
pv. syringae produce one of four classes of small cyclic lipodepsinonapeptides: syringomycins, syringostatins, syringotoxins, or pseudomycins. These metabolites are phytotoxic and growth inhibitory against a broad spectrum of fungi. Their production is dependent upon the expression of conserved biosynthesis and export genes
syrB
and
syrD
, respectively. PCR and oligonucleotide primers specific for a 752-bp fragment of
syrB
were used to identify cyclic lipodepsinonapeptide-producing strains of
P. syringae
pv. syringae. In contrast, PCR amplification with primers based on
syrD
did not always correlate with possession of the
syrD
gene, as indicated by Southern blot analysis, or with cyclic lipodepsinonapeptide production. Sequence comparisons of 400 nucleotides from the
syrB
PCR-amplified fragments showed 94% plot similarity among 27 strains. In a sequence phenogram, syringostatin and syringotoxin producers were grouped apart from syringomycin-producing strain B301D, with sequences that differed by eight and nine conserved base substitutions, respectively. PCR amplification of the 752-bp
syrB
fragment offers rapid and accurate detection of cyclic lipodepsinonapeptide-producing strains, and its sequence provides some predictive capabilities for identifying syringotoxin and syringostatin producers.
Nisin Resistance inListeria monocytogenesATCC 700302 Is a Complex Phenotype
Authors: Crandall Allison D. , Montville Thomas J. 
Published: December 2019

ABSTRACTNisin resistance inListeria monocytogenesATCC 700302 is a complex phenotype involving alterations in both the cytoplasmic membrane and the cell wall and a requirement for divalent cations. In addition to a lower ratio of C15to C17fatty acids than in the wild-type strain (A. S. Mazzotta and T. J. Montville, J. Appl. Microbiol. 82:32–38, 1997), this nisin-resistant (Nisr) strain contained significantly more zwitterionic phosphatidylethanolamine and less anionic phosphatidylglycerol and cardiolipin. The extraction of cardiolipin was enhanced by a penicillin-lysozyme step to disrupt the cell wall. This study is the first to quantify the phosphatidylethanolamine component of theL. monocytogenescytoplasmic membrane. While these cytoplasmic membrane changes were induced by nisin, the Nisrstrain also showed altered sensitivities to cell wall-acting compounds, even when grown in the absence of nisin, suggesting a constitutive alteration in the strain’s cell wall. A model which integrates the roles of the cell membrane, cell wall, and divalent cations is presented. Finally, nisin resistance inL. monocytogenesATCC 700302 conferred cross-resistance to the class IIa bacteriocin pediocin PA-1 and the class IV leuconocin S.
Effects of Ammonium and Non-Ammonium Salt Additions on Methane Oxidation by
Methylosinus trichosporium
OB3b and Maine Forest Soils
Authors: King G. M. , Schnell S. 
Published: December 2019

ABSTRACT

Additions of ammonium and non-ammonium salts inhibit atmospheric methane consumption by soil at salt concentrations that do not significantly affect the soil water potential. The response of soils to non-ammonium salts has previously raised questions about the mechanism of ammonium inhibition. Results presented here show that inhibition of methane consumption by non-ammonium salts can be explained in part by ion-exchange reactions: cations desorb ammonium, with the level of desorption varying as a function of both the cation and anion added; differential desorption results in differential inhibition levels. Differences in the extent of inhibition among ammonium salts can also be explained in part by the effects of anions on ammonium exchange. In contrast, only minimal effects of cations and anions are observed in liquid cultures of
Methylosinus trichosporium
OB3b. The comparable level of inhibition by equinormal concentrations of NH
4
Cl and (NH
4
)
2
SO
4
and the insensitivity of salt inhibition to increasing methane concentrations (from 10 to 100 ppm) are of particular interest, since both of these patterns are in contrast to results for soils. The greater inhibition of methane consumption for NH
4
Cl than (NH
4
)
2
SO
4
in soils can be attributed to increased ammonium adsorption by sulfate; increasing inhibition by non-ammonium salts with increasing methane concentrations can be attributed to desorbed ammonium and a physiological mechanism proposed previously for pure cultures.
Nitrospira
-Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria
Authors: Hovanec Timothy A. , Taylor Lance T. , Blakis Andrew , Delong Edward F. 
Published: December 2019

ABSTRACT

Oxidation of nitrite to nitrate in aquaria is typically attributed to bacteria belonging to the genus
Nitrobacter
which are members of the α subdivision of the class
Proteobacteria
. In order to identify bacteria responsible for nitrite oxidation in aquaria, clone libraries of rRNA genes were developed from biofilms of several freshwater aquaria. Analysis of the rDNA libraries, along with results from denaturing gradient gel electrophoresis (DGGE) on frequently sampled biofilms, indicated the presence of putative nitrite-oxidizing bacteria closely related to other members of the genus
Nitrospira
. Nucleic acid hybridization experiments with rRNA from biofilms of freshwater aquaria demonstrated that
Nitrospira
-like rRNA comprised nearly 5% of the rRNA extracted from the biofilms during the establishment of nitrification. Nitrite-oxidizing bacteria belonging to the α subdivision of the class
Proteobacteria
(e.g.,
Nitrobacter
spp.) were not detected in these samples. Aquaria which received a commercial preparation containing
Nitrobacter
species did not show evidence of
Nitrobacter
growth and development but did develop substantial populations of
Nitrospira
-like species. Time series analysis of rDNA phylotypes on aquaria biofilms by DGGE, combined with nitrite and nitrate analysis, showed a correspondence between the appearance of
Nitrospira
-like bacterial ribosomal DNA and the initiation of nitrite oxidation. In total, the data suggest that
Nitrobacter winogradskyi
and close relatives were not the dominant nitrite-oxidizing bacteria in freshwater aquaria. Instead, nitrite oxidation in freshwater aquaria appeared to be mediated by bacteria closely related to
Nitrospira moscoviensis
and
Nitrospira marina.
Choline Derivatives Involved in Osmotolerance of
Penicillium fellutanum
Authors: Park Yong-Il , Gander John E. 
Published: December 2019

ABSTRACT

Penicillium fellutanum
is osmotolerant and xerotolerant when cultured in a low-phosphate medium containing 3 M NaCl. Glycerol and erythritol accumulated in cultures with NaCl concentrations up to 2 M; glycerol was the only detectable polyol in cultures containing 3 M NaCl. In cultures with 3 M NaCl, the intracellular levels of glycine betaine and choline-
O
-sulfate were 22- and 2.6-fold greater (70 and 46 mM), respectively, than those of cultures without added NaCl. The levels of glycine betaine and glycerol decreased in mycelia transferred from a medium containing 3 M NaCl into a fresh medium without added NaCl. NaCl at 3 M inhibited mycelial mass accumulation; this inhibition was partially corrected by supplementation of cultures with glycine betaine (2 mM) or choline-
O
-sulfate (10 mM). The presence of exogenous choline chloride (2 mM) in plate cultures protected the cells from stress from 3 M NaCl. The data suggest that glycine betaine and choline-
O
-sulfate are secondary osmoprotectants which are effective at the point that the cell is incapable of synthesizing more glycerol.
Production of Respirable Vesicles Containing Live
Legionella pneumophila
Cells by Two
Acanthamoeba
spp
Authors: Berk Sharon G. , Ting Rebecca S. , Turner Glenn W. , Ashburn Rebecca J. 
Published: December 2019

ABSTRACT

Two
Acanthamoeba
species, fed at three temperatures, expelled vesicles containing living
Legionella pneumophila
cells. Vesicles ranged from 2.1 to 6.4 μm in diameter and theoretically could contain several hundred bacteria. Viable
L. pneumophila
cells were observed within vesicles which had been exposed to two cooling tower biocides for 24 h. Clusters of bacteria in vesicles were not dispersed by freeze-thawing and sonication. Such vesicles may be agents for the transmission of legionellosis associated with cooling towers, and the risk may be underestimated by plate count methods.
Phylogenetic Diversity of Ultraplankton Plastid Small-Subunit rRNA Genes Recovered in Environmental Nucleic Acid Samples from the Pacific and Atlantic Coasts of the United States
Authors: Rappé Michael S. , Suzuki Marcelino T. , Vergin Kevin L. , Giovannoni Stephen J. 
Published: December 2019

ABSTRACT

The scope of marine phytoplankton diversity is uncertain in many respects because, like bacteria, these organisms sometimes lack defining morphological characteristics and can be a challenge to grow in culture. Here, we report the recovery of phylogenetically diverse plastid small-subunit (SSU) rRNA gene (rDNA) clones from natural plankton populations collected in the Pacific Ocean off the mouth of Yaquina Bay, Oreg. (OCS clones), and from the eastern continental shelf of the United States off Cape Hatteras, N.C. (OM clones). SSU rRNA gene clone libraries were prepared by amplifying rDNAs from nucleic acids isolated from plankton samples and cloning them into plasmid vectors. The PCR primers used for amplification reactions were designed to be specific for bacterial SSU rRNA genes; however, plastid genes have a common phylogenetic origin with bacteria and were common in both SSU rRNA gene clone libraries. A combination of restriction fragment length polymorphism analyses, nucleic acid sequencing, and taxon-specific oligonucleotide probe hybridizations revealed that 54 of the 116 OCS gene clones were of plastid origin. Collectively, clones from the OCS and OM libraries formed at least eight unique lineages within the plastid radiation, including gene lineages related to the classes
Bacillariophyceae
,
Cryptophyceae
,
Prymnesiophyceae
,
Chrysophyceae
, and
Prasinophyceae
; for a number of unique clones, no close phylogenetic neighbors could be identified with confidence. Only a group of two OCS rRNA gene clones showed close identity to the plastid SSU rRNA gene sequence of a cultured organism [
Emiliania huxleyi
(Lohmann) Hay and Mohler; 99.8% similar]. The remaining clones could not be identified to the genus or species level. Although cryptic species are not as prevalent among phytoplankton as they are among their bacterial counterparts, this genetic survey nonetheless uncovered significant new information about phytoplankton diversity.
Biodegradation of Phosphonomycin by
Rhizobium huakuii
PMY1
Authors: McGrath John W. , Hammerschmidt Friedrich , Quinn John P. 
Published: December 2019

ABSTRACT

The biodegradation by
Rhizobium huakuii
PMY1 of up to 10 mM phosphonomycin as a carbon, energy, and phosphorus source with accompanying P
i
release is described. This biodegradation represents a further mechanism of resistance to this antibiotic and a novel, phosphate-deregulated route for organophosphonate metabolism by
Rhizobium
spp.
Differentiation of
Campylobacter
Isolates on the Basis of Sensitivity to Boiling in Water as Measured by PCR-Detectable DNA
Authors: Mohran Zaynab S. , Arthur Ray R. , Oyofo Buhari A. , Peruski Leonard F. , Wasfy Momtaz O. , Ismail Tharwat F. , Murphy James R. 
Published: December 2019

ABSTRACT

Differential sensitivity for the release of PCR-detectable genomic DNA upon boiling in water is reported for 45
Campylobacter jejuni
and
Campylobacter coli
strains isolated in Egypt. All of the strains released PCR-detectable DNA when treated with proteinase K and sodium dodecyl sulfate. When DNA was extracted from these strains by boiling in water, nine (20%) of the strains were PCR negative or resistant to boiling, suggesting the presence of boiling-sensitive and boiling-resistant phenotypes.
Improvement of the Immunomagnetic Separation Method Selective for
Escherichia coli
O157 Strains
Authors: Tomoyasu Takahiro 
Published: December 2019

ABSTRACT

Immunomagnetic separation is a useful enrichment method selective for
Escherichia coli
O157 cells against non-O157
E. coli
cells from a preenrichment culture. However,
E. coli
cells are adsorbed onto a solid surface nonspecifically. With the conventional immunomagnetic separation method, this nonspecific adsorption interfered with immunomagnetic separation. It was found that this interference could be reduced with a low-ionic-strength solution. When immunomagnetic separation was carried out with this solution, the proportion of
E. coli
O157 cells to non-O157
E. coli
cells increased from 9.6 to 31.4 times compared to the proportion obtained by the conventional immunomagnetic separation method. The effectiveness of this solution was successfully evaluated by the use of
E. coli
O157-spiked samples.
c
-Type Cytochromes and Manganese Oxidation in
Pseudomonas putida
MnB1
Authors: Caspi Ron , Tebo Bradley M. , Haygood M. G. 
Published: December 2019

ABSTRACT

Pseudomonas putida
MnB1 is an isolate from an Mn oxide-encrusted pipeline that can oxidize Mn(II) to Mn oxides. We used transposon mutagenesis to construct mutants of strain MnB1 that are unable to oxidize manganese, and we characterized some of these mutants. The mutants were divided into three groups: mutants defective in the biogenesis of
c
-type cytochromes, mutants defective in genes that encode key enzymes of the tricarboxylic acid cycle, and mutants defective in the biosynthesis of tryptophan. The mutants in the first two groups were cytochrome
c
oxidase negative and did not contain
c
-type cytochromes. Mn(II) oxidation capability could be recovered in a
c
-type cytochrome biogenesis-defective mutant by complementation of the mutation.