bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular Expression of a Functional Recombinant
Ganoderma lucidium
Immunomodulatory Protein by
Bacillus subtilis
and
Lactococcus lactis
Authors: Yeh Chuan M. , Yeh Chun K. , Hsu Xun Y. , Luo Qiu M. , Lin Ming Y. 
Published: December 2007

ABSTRACT

Bacillus subtilis
and
Lactococcus lactis
are ideal hosts for the production of extracellular heterologous proteins of major commercial importance. A recombinant gene for the novel
Ganoderma lucidium
immunomodulatory protein LZ-8, recombinant
LZ-8
, was designed encoding the same amino acid sequence but using the preferred codons for both strains and was synthesized by overlapping extension PCR. Using the signal peptide (SP) from subtilisin YaB (SP
YaB
), recombinant LZ-8 was expressed extracellularly in
Bacillus subtilis
and
Lactococcus lactis
. In the absence of SP
YaB
, recombinant LZ-8 was expressed extracellularly in
B. subtilis
, but not in
L. lactis
. The three expressed recombinant LZ-8s showed different capacities for modulating the production of Th1 and Th2 cytokines by peripheral blood mononuclear cells and of tumor necrosis factor alpha by a macrophage cell line.
Characterization of a Novel Angular Dioxygenase from Fluorene-Degrading
Sphingomonas
sp. Strain LB126
Authors: Schuler Luc , Ní Chadhain Sinéad M. , Jouanneau Yves , Meyer Christine , Zylstra Gerben J. , Hols Pascal , Agathos Spiros N. 
Published: December 2007

ABSTRACT

In this study, the genes involved in the initial attack on fluorene by
Sphingomonas
sp. strain LB126 were investigated. The α and β subunits of a dioxygenase complex (FlnA1-FlnA2), showing 63 and 51% sequence identity, respectively, to the subunits of an angular dioxygenase from the gram-positive dibenzofuran degrader
Terrabacter
sp. strain DBF63, were identified. When overexpressed in
Escherichia coli
, FlnA1-FlnA2 was responsible for the angular oxidation of fluorene, 9-hydroxyfluorene, 9-fluorenone, dibenzofuran, and dibenzo-
p
-dioxin. Moreover, FlnA1-FlnA2 was able to oxidize polycyclic aromatic hydrocarbons and heteroaromatics, some of which were not oxidized by the dioxygenase from
Terrabacter
sp. strain DBF63. The quantification of resulting oxidation products showed that fluorene and phenanthrene were the preferred substrates of FlnA1-FlnA2.
Intergeneric Coaggregation among Drinking Water Bacteria: Evidence of a Role for
Acinetobacter calcoaceticus
as a Bridging Bacterium
Authors: Simões Lúcia Chaves , Simões Manuel , Vieira Maria João 
Published: December 2007

ABSTRACT

Intergeneric coaggregation of drinking water bacteria was tested.
Acinetobacter calcoaceticus
was found not only to autoaggregate but also to coaggregate with four of the five other isolates (
Burkholderia cepacia
,
Methylobacterium
sp.,
Mycobacterium mucogenicum
,
Sphingomonas capsulata
, and
Staphylococcus
sp.). In its absence, no coaggregation was found. Interactions were lectin-saccharide mediated. The putative bridging function of
A. calcoaceticus
was evidenced by multispecies biofilm studies, through a strain exclusion process.
Predictive Model for Inactivation of Feline Calicivirus, a Norovirus Surrogate, by Heat and High Hydrostatic Pressure
Authors: Buckow Roman , Isbarn Sonja , Knorr Dietrich , Heinz Volker , Lehmacher Anselm 
Published: December 2007

ABSTRACT

Noroviruses, which are members of the
Caliciviridae
family, represent the leading cause of nonbacterial gastroenteritis in developed countries; such norovirus infections result in high economic costs for health protection. Person-to-person contact, contaminated water, and foods, especially raw shellfish, vegetables, and fruits, can transmit noroviruses. We inactivated feline calicivirus, a surrogate for the nonculturable norovirus, in cell culture medium and mineral water by heat and high hydrostatic pressure. Incubation at ambient pressure and 75°C for 2 min as well as treatment at 450 MPa and 15°C for 1 min inactivated more than 7 log
10
PFU of calicivirus per ml in cell culture medium or mineral water. The heat and pressure time-inactivation curves obtained with the calicivirus showed tailing in the logarithmic scale. Modeling by
n
th-order kinetics of the virus inactivation was successful in predicting the inactivation of the infective virus particles. The developed model enables the prediction of the calicivirus reduction in response to pressures up to 500 MPa, temperatures ranging from 5 to 75°C, and various treatment times. We suggest high pressure for processing of foods to reduce the health threat posed by noroviruses.
Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon
Pyrococcus furiosus
Authors: Comfort Donald A. , Chou Chung-Jung , Conners Shannon B. , VanFossen Amy L. , Kelly Robert M. 
Published: December 2007

ABSTRACT

Bioinformatics analysis and transcriptional response information for
Pyrococcus furiosus
grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.
Contribution of Copper Ion Resistance to Survival of
Escherichia coli
on Metallic Copper Surfaces
Authors: Santo Christophe Espírito , Taudte Nadine , Nies Dietrich H. , Grass Gregor 
Published: December 2007

ABSTRACT

Bacterial contamination of touch surfaces poses a serious threat for public health. The use of bactericidal surface materials, such as copper and its alloys, might constitute a way to aid the use of antibiotics and disinfectants, thus minimizing the risk of emergence and spread of multiresistant germs. The survival of
Escherichia coli
on metallic copper surfaces has been studied previously; however, the mechanisms underlying bacterial inactivation on copper surfaces have not been elucidated. Data presented in this study suggest that bacteria are killed rapidly on dry copper surfaces. Several factors, such as copper ion toxicity, copper chelators, cold, osmotic stress, and reactive oxygen species, but not anaerobiosis, influenced killing rates. Strains deleted in copper detoxification systems were slightly more sensitive than was the wild type. Preadaptation to copper enhanced survival rates upon copper surface exposure. This study constitutes a first step toward understanding the reasons for metallic copper surface-mediated killing of bacteria.
Genetic Diversity of Hydrogen-Producing Bacteria in an Acidophilic Ethanol-H2-Coproducing System, Analyzed Using the [Fe]-Hydrogenase Gene
Authors: Xing Defeng , Ren Nanqi , Rittmann Bruce E. 
Published: December 2007

ABSTRACTHydrogen gas (H2) produced by bacterial fermentation of biomass can be a sustainable energy source. The ability to produce H2gas during anaerobic fermentation was previously thought to be restricted to a few species within the generaClostridiumandEnterobacter. This work reports genomic evidence for the presence of novel H2-producing bacteria (HPB) in acidophilic ethanol-H2-coproducing communities that were enriched using molasses wastewater. The majority of the enriched dominant populations in the acidophilic ethanol-H2-coproducing system were affiliated with low-G+C-content gram-positive bacteria,Bacteroidetes, andActinobacteria, based on the 16S rRNA gene. However, PCR primers designed to specifically target bacterialhydAyielded 17 uniquehydAsequences whose amino acid sequences differed from those of known HPB. The putative ethanol-H2-coproducing bacteria comprised 11 novel phylotypes closely related toEthanoligenens harbinense,Clostridium thermocellum, andClostridium saccharoperbutylacetonicum. Furthermore, analysis of the alcohol dehydrogenase isoenzyme also pointed to anE. harbinense-like organism, which is known to have a high conversion rate of carbohydrate to H2and ethanol. We also found six novel HPB that were associated with lactate-, propionate-, and butyrate-oxidizing bacteria in the acidophilic H2-producing sludge. Thus, the microbial ecology of mesophilic and acidophilic H2fermentation involves many other bacteria in addition toClostridiumandEnterobacter.
Adherence of
Helicobacter pylori
to Abiotic Surfaces Is Influenced by Serum
Authors: Williams John C. , McInnis Karla A. , Testerman Traci L. 
Published: December 2007

ABSTRACT

Helicobacter pylori
bacteria cultured in a chemically defined medium without serum readily adhere to a variety of abiotic surfaces. Growth produces microcolonies that spread to cover the entire surface, along with a planktonic subpopulation. Serum inhibits adherence. Initial attachment is protein mediated, but other molecules are responsible for more permanent attachment.
System Using Tandem Repeats of the cA Peptidoglycan-Binding Domain from
Lactococcus lactis
for Display of both N- and C-Terminal Fusions on Cell Surfaces of Lactic Acid Bacteria
Authors: Okano Kenji , Zhang Qiao , Kimura Sakurako , Narita Junya , Tanaka Tsutomu , Fukuda Hideki , Kondo Akihiko 
Published: December 2007

ABSTRACT

Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from
Lactococcus lactis
). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and α-amylase from
Streptococcus bovis
148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of
L. lactis
cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of α-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of
Lactobacillus plantarum
and
Lactobacillus casei
.
Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by
Shewanella
spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction
Authors: Pinchuk Grigoriy E. , Ammons Christine , Culley David E. , Li Shu-Mei W. , McLean Jeff S. , Romine Margaret F. , Nealson Kenneth H. , Fredrickson Jim K. , Beliaev Alexander S. 
Published: December 2007

ABSTRACT

The solubility of orthophosphate (PO
4
3−
) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. Here we demonstrate that dissolved extracellular DNA can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus
Shewanella. Shewanella oneidensis
MR-1,
Shewanella putrefaciens
CN32, and
Shewanella
sp. strain W3-18-1 all grew with DNA but displayed different growth rates. W3-18-1 exhibited the highest growth rate with DNA. While strain W3-18-1 displayed Ca
2+
-independent DNA utilization, both CN32 and MR-1 required millimolar concentrations of Ca
2+
for growth with DNA. For
S. oneidensis
MR-1, the utilization of DNA as a sole source of phosphorus is linked to the activities of extracellular phosphatase(s) and a Ca
2+
-dependent nuclease(s), which are regulated by phosphorus availability. Mass spectrometry analysis of the extracellular proteome of MR-1 identified one putative endonuclease (SO1844), a predicted UshA (bifunctional UDP-sugar hydrolase/5′ nucleotidase), a predicted PhoX (calcium-activated alkaline phosphatase), and a predicted CpdB (bifunctional 2′,3′ cyclic nucleotide 2′ phosphodiesterase/3′ nucleotidase), all of which could play important roles in the extracellular degradation of DNA under phosphorus-limiting conditions. Overall, the results of this study suggest that the ability to use exogenous DNA as the sole source of phosphorus is widespread among the shewanellae, and perhaps among all prokaryotes, and may be especially important for nutrient cycling in metal-reducing environments.
The Inhibitory Spectrum of Thermophilin 9 from
Streptococcus thermophilus
LMD-9 Depends on the Production of Multiple Peptides and the Activity of BlpG
St
, a Thiol-Disulfide Oxidase
Authors: Fontaine Laetitia , Hols Pascal 
Published: December 2007

ABSTRACT

The
blp
St
cluster of
Streptococcus thermophilus
LMD-9 was recently shown to contain all the genetic information required for the production of bacteriocins active against other
S. thermophilus
strains. In this study, we further investigated the antimicrobial activity of
S. thermophilus
LMD-9 by testing the susceptibility of 31 bacterial species (87 strains). We showed that LMD-9 displays an inhibitory spectrum targeted toward related gram-positive bacteria, including pathogens such as
Listeria monocytogenes
. Using deletion mutants, we investigated the contribution of the three putative bacteriocin-encoding operons
blpD
St
-
orf2
,
blpU
St
-
orf3
, and
blpE
St
-
blpF
St
(
bac
St
operons) and of the
blpG
St
gene, which encodes a putative modification protein, to the inhibitory spectrum and immunity of strain LMD-9. Our results present evidence that the
blp
St
locus encodes a multipeptide bacteriocin system called thermophilin 9. Among the four class II bacteriocin-like peptides encoded within the
bac
St
operons, BlpD
St
alone was sufficient to inhibit the growth of most thermophilin 9-sensitive species. The
blpD
St
gene forms an operon with its associated immunity gene(s), and this functional bacteriocin/immunity module could easily be transferred to
Lactococcus lactis
. The remaining three Bac
St
peptides, BlpU
St
, BlpE
St
, and BlpF
St
, confer poor antimicrobial activity but act as enhancers of the antagonistic activity of thermophilin 9 by an unknown mechanism. The
blpG
St
gene was also shown to be specifically required for the antilisteria activity of thermophilin 9, since its deletion abolished the sensitivities of most
Listeria
species. By complementation of the motility deficiency of
Escherichia coli dsbA
, we showed that
blpG
St
encodes a functional thiol-disulfide oxidase, suggesting an important role for disulfide bridges within thermophilin 9.
Changes in Bacterial Communities of the Marine Sponge
Mycale laxissima
on Transfer into Aquaculture
Authors: Mohamed Naglaa M. , Enticknap Julie J. , Lohr Jayme E. , McIntosh Scott M. , Hill Russell T. 
Published: December 2007

ABSTRACT

The changes in bacterial communities associated with the marine sponge
Mycale laxissima
on transfer to aquaculture were studied using culture-based and molecular techniques.
M. laxissima
was maintained alive in flowthrough and closed recirculating aquaculture systems for 2 years and 1 year, respectively. The bacterial communities associated with wild and aquacultured sponges, as well as the surrounding water, were assessed using 16S rRNA gene clone library analysis and denaturing gradient gel electrophoresis (DGGE). Bacterial richness and diversity were measured using DOTUR computer software, and clone libraries were compared using S-LIBSHUFF. DGGE analysis revealed that the diversity of the bacterial community of
M. laxissima
increased when sponges were maintained in aquaculture and that bacterial communities associated with wild and aquacultured
M. laxissima
were markedly different than those of the corresponding surrounding water. Clone libraries of bacterial 16S rRNA from sponges confirmed that the bacterial communities changed during aquaculture. These communities were significantly different than those of seawater and aquarium water. The diversity of bacterial communities associated with
M. laxissima
increased significantly in aquaculture. Our work shows that it is important to monitor changes in bacterial communities when examining the feasibility of growing sponges in aquaculture systems because these communities may change. This could have implications for the health of sponges or for the production of bioactive compounds by sponges in cases where these compounds are produced by symbiotic bacteria rather than by the sponges themselves.
Fermentative Utilization of Glycerol by
Escherichia coli
and Its Implications for the Production of Fuels and Chemicals
Authors: Murarka Abhishek , Dharmadi Yandi , Yazdani Syed Shams , Gonzalez Ramon 
Published: December 2007

ABSTRACT

Availability, low prices, and a high degree of reduction make glycerol an ideal feedstock to produce reduced chemicals and fuels via anaerobic fermentation. Although glycerol metabolism in
Escherichia coli
had been thought to be restricted to respiratory conditions, we report here the utilization of this carbon source in the absence of electron acceptors. Cells grew fermentatively on glycerol and exhibited exponential growth at a maximum specific growth rate of 0.040 ± 0.003 h
−1
. The fermentative nature of glycerol metabolism was demonstrated through studies in which cell growth and glycerol utilization were observed despite blocking several respiratory processes. The incorporation of glycerol in cellular biomass was also investigated via nuclear magnetic resonance analysis of cultures in which either 50% U-
13
C-labeled or 100% unlabeled glycerol was used. These studies demonstrated that about 20% of the carbon incorporated into the protein fraction of biomass originated from glycerol. The use of U-
13
C-labeled glycerol also allowed the unambiguous identification of ethanol and succinic, acetic, and formic acids as the products of glycerol fermentation. The synthesis of ethanol was identified as a metabolic determinant of glycerol fermentation; this pathway fulfills energy requirements by generating, in a redox-balanced manner, 1 mol of ATP per mol of glycerol converted to ethanol. A fermentation balance analysis revealed an excellent closure of both carbon (∼95%) and redox (∼96%) balances. On the other hand, cultivation conditions that prevent H
2
accumulation were shown to be an environmental determinant of glycerol fermentation. The negative effect of H
2
is related to its metabolic recycling, which in turn generates an unfavorable internal redox state. The implications of our findings for the production of reduced chemicals and fuels were illustrated by coproducing ethanol plus formic acid and ethanol plus hydrogen from glycerol at yields approaching their theoretical maximum.
Improvement of the Thermostability and Activity of a Pectate Lyase by Single Amino Acid Substitutions, Using a Strategy Based on Melting-Temperature-Guided Sequence Alignment
Authors: Xiao Zhizhuang , Bergeron Hélène , Grosse Stephan , Beauchemin Manon , Garron Marie-Line , Shaya David , Sulea Traian , Cygler Miroslaw , Lau Peter C. K. 
Published: December 2007

ABSTRACT

In the vast number of random mutagenesis experiments that have targeted protein thermostability, single amino acid substitutions that increase the apparent melting temperature (

T
m

) of the enzyme more than 1 to 2°C are rare and often require the creation of a large library of mutated genes. Here we present a case where a single beneficial mutation (R236F) of a hemp fiber-processing pectate lyase of
Xanthomonas campestris
origin (PL

Xc

) produced a 6°C increase in

T
m

and a 23-fold increase in the half-life at 45°C without compromising the enzyme's catalytic efficiency. This success was based on a variation of sequence alignment strategy where a mesophilic amino acid sequence is matched with the sequences of its thermophilic counterparts that have established

T
m

values. Altogether, two-thirds of the nine targeted single amino acid substitutions were found to have effects either on the thermostability or on the catalytic activity of the enzyme, evidence of a high success rate of mutation without the creation of a large gene library and subsequent screening of clones. Combination of R236F with another beneficial mutation (A31G) resulted in at least a twofold increase in specific activity while preserving the improved

T
m

value. To understand the structural basis for the increased thermal stability or activity, the variant R236F and A31G R236F proteins and wild-type PL

Xc

were purified and crystallized. By structure analysis and computational methods, hydrophobic desolvation was found to be the driving force for the increased stability with R236F.
The Genetically Remote Pathogenic Strain NVH391-98 of the
Bacillus cereus
Group Is Representative of a Cluster of Thermophilic Strains
Authors: Auger Sandrine , Galleron Nathalie , Bidnenko Elena , Ehrlich S. Dusko , Lapidus Alla , Sorokin Alexei 
Published: December 2007

ABSTRACT

Bacteria of the
Bacillus cereus
group are known to cause food poisoning. A rare phylogenetically remote strain, NVH391-98, was recently characterized to encode a particularly efficient cytotoxin K presumably responsible for food poisoning. This pathogenic strain and its close relatives can be phenotypically distinguished from other strains of the
B. cereus
group by the inability to grow at temperatures below 17°C and by the ability to grow at temperatures from 48 to 53°C. A temperate phage, phBC391A2, residing in the genome of NVH391-98 allows us to distinguish the three known members of this thermophilic strain cluster.
Microbiological Quality of Bagged Cut Spinach and Lettuce Mixes
Authors: Valentin-Bon Iris , Jacobson Andrew , Monday Steven R. , Feng Peter C. H. 
Published: December 2007

ABSTRACT

Analysis of 100 bagged lettuce and spinach samples showed mean total bacterial counts of 7.0 log
10
CFU/g and a broad range of <4 to 8.3 log
10
CFU/g. Most probable numbers (MPN) of ≥11,000 /g coliforms were found in 55 samples, and generic
Escherichia coli
bacteria were detected in 16 samples, but no
E. coli
count exceeded 10 MPN/g.
Poly(3-Hydroxybutyrate) (PHB) Depolymerase PhaZa1 Is Involved in Mobilization of Accumulated PHB in
Ralstonia eutropha
H16
Authors: Uchino Keiichi , Saito Terumi , Jendrossek Dieter 
Published: December 2007

ABSTRACT

The recently finished genome sequence of
Ralstonia eutropha
H16 harbors nine genes that are thought to encode functions for intracellular depolymerization (mobilization) of storage poly(3-hydroxybutyrate) (PHB). Based on amino acid similarities, the gene products belong to four classes (PhaZa1 to PhaZa5, PhaZb, PhaZc, and PhaZd1/PhaZd2). However, convincing direct evidence for the in vivo roles of the gene products is poor. In this study, we selected four candidate genes (
phaZa1
,
phaZb
,
phaZc
, and
phaZd1
) representing the four classes and investigated the physiological function of the gene products (i) with recombinant
Escherichia coli
strains and (ii) with
R. eutropha
null mutants. Evidence for weak but significant PHB depolymerase activity was obtained only for PhaZa1. The physiological roles of the other potential PHB depolymerases remain uncertain.