bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing
Authors: Luo Chunling , Xie Shuguang , Sun Weimin , Li Xiangdong , Cupples Alison M. 
Published: May 2009

ABSTRACT

The dominant bacterium responsible for carbon uptake from toluene in an agricultural soil was identified by stable isotope probing. Samples were amended with unlabeled toluene or labeled [ring-
13
C
6
]toluene, and DNA was extracted over time. Sequencing indicated that the organism involved belongs to the candidate phylum TM7. Microorganisms in this candidate phylum are of particular interest because although they have been found in a variety of habitats, no stable culture of any species exists, so their general metabolic capabilities are largely unknown.
Substrate Specificity of a Mannose-6-Phosphate Isomerase from
Bacillus subtilis
and Its Application in the Production of
l
-Ribose
Authors: Yeom Soo-Jin , Ji Jung-Hwan , Kim Nam-Hee , Park Chang-Su , Oh Deok-Kun 
Published: May 2009

ABSTRACT

The uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from
Bacillus subtilis
was cloned and expressed in
Escherichia coli
. The maximal activity of the recombinant enzyme was observed at pH 7.5 and 40°C in the presence of 0.5 mM Co
2+
. The isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the C-2 and C-3 positions, such as the
d
and
l
forms of ribose, lyxose, talose, mannose, and allose. The enzyme exhibited the highest activity for
l
-ribulose among all pentoses and hexoses. Thus,
l
-ribose, as a potential starting material for many
l
-nucleoside-based pharmaceutical compounds, was produced at 213 g/liter from 300-g/liter
l
-ribulose by mannose-6-phosphate isomerase at 40°C for 3 h, with a conversion yield of 71% and a volumetric productivity of 71 g liter
−1
h
−1
.
Bacterial Associates of Arboreal Ants and Their Putative Functions in an Obligate Ant-Plant Mutualism
Authors: Eilmus Sascha , Heil Martin 
Published: May 2009

ABSTRACT

Bacterial communities are highly diverse and have great ecological importance. In the present study, we used an in silico analysis of terminal restriction fragments (tRF) to characterize the bacterial community of the plant ant
Pseudomyrmex ferrugineus
. This species is an obligate inhabitant of
Acacia
myrmecophytes and feeds exclusively on plant-derived food sources. Ants are the dominant insect group in tropical rain forests. Associations of ants with microbes, which contribute particularly to the ants’ nitrogen nutrition, could allow these insects to live on mostly or entirely plant-based diets and could thus contribute to the explanation of the high abundances that are reached by tropical ants. We found tRF patterns representing at least 30 prokaryotic taxa, of which the
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Planctomycetes
,
Proteobacteria
, and
Spirochaetes
comprised 93%. Because most bacterial taxa were found in all ant-derived samples studied and because the bacteria detected on the ants’ host plant revealed little overlap with this community, we regard our results as reliably representing the bacterial community that is associated with
P. ferrugineus
. Genera with a likely function as ant symbionts were
Burkholderia
,
Pantoea
,
Weissella
, and several members of the
Enterobacteriaceae
. The presence of these and various other groups was confirmed via independent PCR and cultivation approaches. Many of the bacteria that we detected belong to purportedly N-fixing taxa. Bacteria may represent important further partners in ant-plant mutualisms, and their influences on ant nutrition can contribute to the extraordinary abundance and evolutionary success of tropical arboreal ants.
Diversity and Functional Analysis of LuxR-Type Transcriptional Regulators of Cyclic Lipopeptide Biosynthesis in
Pseudomonas fluorescens
Authors: de Bruijn I. , Raaijmakers J. M. 
Published: May 2009

ABSTRACT

Cyclic lipopeptides (CLPs) are produced by many
Pseudomonas
species and have several biological functions, including a role in surface motility, biofilm formation, virulence, and antimicrobial activity. This study focused on the diversity and role of LuxR-type transcriptional regulators in CLP biosynthesis in
Pseudomonas
species and, specifically, viscosin production by
Pseudomonas fluorescens
strain SBW25. Phylogenetic analyses showed that CLP biosynthesis genes in
Pseudomonas
strains are flanked by LuxR-type regulators that contain a DNA-binding helix-turn-helix domain but lack
N
-acylhomoserine lactone-binding or response regulator domains. For SBW25, site-directed mutagenesis of the genes coding for either of the two identified LuxR-type regulators, designated ViscAR and ViscBCR, strongly reduced transcript levels of the
viscABC
biosynthesis genes and resulted in a loss of viscosin production. Expression analyses further showed that a mutation in either
viscAR
or
viscBCR
did not substantially (change of <2.5-fold) affect transcription of the other regulator. Transformation of the Δ
viscAR
mutant of SBW25 with a LuxR-type regulatory gene from
P. fluorescens
strain SS101 that produces massetolide, a CLP structurally related to viscosin, restored transcription of the
viscABC
genes and viscosin production. The results further showed that a functional
viscAR
gene was required for heterologous expression of the massetolide biosynthesis genes of strain SS101 in strain SBW25, leading to the production of both viscosin and massetolide. Collectively, these results indicate that the regulators flanking the CLP biosynthesis genes in
Pseudomonas
species represent a unique LuxR subfamily of proteins and that viscosin biosynthesis in
P. fluorescens
SBW25 is controlled by two LuxR-type transcriptional regulators.
Antibiotic Overproduction by
rpsL
and
rsmG
Mutants of Various Actinomycetes
Authors: Tanaka Yukinori , Komatsu Mamoru , Okamoto Susumu , Tokuyama Shinji , Kaji Akira , Ikeda Haruo , Ochi Kozo 
Published: May 2009

ABSTRACT

Certain streptomycin resistance mutations (i.e.,
rpsL
and
rsmG
) result in the overproduction of antibiotics in various actinomycetes. Moreover,
rpsL rsmG
double-mutant strains show a further increase in antibiotic production.
rpsL
but not
rsmG
mutations result in a marked enhancement of oligomycin production in
Streptomyces avermitilis
and erythromycin production in
Saccharopolyspora erythraea
, accompanied by increased transcription of a key developmental regulator gene,
bldD
, in the latter organism.
Effects of
Bacillus thuringiensis
δ-Endotoxins on the Pea Aphid (
Acyrthosiphon pisum
)
Authors: Porcar Manuel , Grenier Anne-Marie , Federici Brian , Rahbé Yvan 
Published: May 2009

ABSTRACT

Four
Bacillus thuringiensis
δ-endotoxins, Cry3A, Cry4Aa, Cry11Aa, and Cyt1Aa, were found to exhibit low to moderate toxicity on the pea aphid,
Acyrthosiphon pisum
, in terms both of mortality and growth rate. Cry1Ab was essentially nontoxic except at high rates. To demonstrate these effects, we had to use exhaustive buffer-based controls.
Metabolic Versatility and Indigenous Origin of the Archaeon
Thermococcus sibiricus
, Isolated from a Siberian Oil Reservoir, as Revealed by Genome Analysis
Authors: Mardanov Andrey V. , Ravin Nikolai V. , Svetlitchnyi Vitali A. , Beletsky Alexey V. , Miroshnichenko Margarita L. , Bonch-Osmolovskaya Elizaveta A. , Skryabin Konstantin G. 
Published: May 2009

ABSTRACT

Thermococcus
species are widely distributed in terrestrial and marine hydrothermal areas, as well as in deep subsurface oil reservoirs.
Thermococcus sibiricus
is a hyperthermophilic anaerobic archaeon isolated from a well of the never flooded oil-bearing Jurassic horizon of a high-temperature oil reservoir. To obtain insight into the genome of an archaeon inhabiting the oil reservoir, we have determined and annotated the complete 1,845,800-base genome of
T
.
sibiricus
. A total of 2,061 protein-coding genes have been identified, 387 of which are absent in other members of the order
Thermococcales
. Physiological features and genomic data reveal numerous hydrolytic enzymes (e.g., cellulolytic enzymes, agarase, laminarinase, and lipases) and metabolic pathways, support the proposal of the indigenous origin of
T
.
sibiricus
in the oil reservoir, and explain its survival over geologic time and its proliferation in this habitat. Indeed, in addition to proteinaceous compounds known previously to be present in oil reservoirs at limiting concentrations, its growth was stimulated by cellulose, agarose, and triacylglycerides, as well as by alkanes. Two polysaccharide degradation loci were probably acquired by
T
.
sibiricus
from thermophilic bacteria following lateral gene transfer events. The first, a “saccharolytic gene island” absent in the genomes of other members of the order
Thermococcales
, contains the complete set of genes responsible for the hydrolysis of cellulose and β-linked polysaccharides. The second harbors genes for maltose and trehalose degradation. Considering that agarose and laminarin are components of algae, the encoded enzymes and the substrate spectrum of
T
.
sibiricus
indicate the ability to metabolize the buried organic matter from the original oceanic sediment.
Identification of a Polyketide Synthase Coding Sequence Specific for Anatoxin-a-Producing
Oscillatoria
Cyanobacteria
Authors: Cadel-Six Sabrina , Iteman Isabelle , Peyraud-Thomas Caroline , Mann Stéphane , Ploux Olivier , Méjean Annick 
Published: May 2009

ABSTRACT

We report the identification of a sequence from the genome of
Oscillatoria
sp. strain PCC 6506 coding for a polyketide synthase. Using 50 axenic cyanobacteria, we found this sequence only in the genomes of
Oscillatoria
strains producing anatoxin-a or homoanatoxin-a, indicating its likely involvement in the biosynthesis of these toxins.
Influence of
Pythium oligandrum
Biocontrol on Fungal and Oomycete Population Dynamics in the Rhizosphere
Authors: Vallance Jessica , Le Floch Gaétan , Déniel Franck , Barbier Georges , Lévesque C. André , Rey Patrice 
Published: May 2009

ABSTRACT

Fungal and oomycete populations and their dynamics were investigated following the introduction of the biocontrol agent
Pythium oligandrum
into the rhizosphere of tomato plants grown in soilless culture. Three strains of
P. oligandrum
were selected on the basis of their ability to form oospores (resting structures) and to produce tryptamine (an auxin-like compound) and oligandrin (a glycoprotein elicitor). Real-time PCR and plate counting demonstrated the persistence of large amounts of the antagonistic oomycete in the rhizosphere throughout the cropping season (April to September). Inter-simple-sequence-repeat analysis of the
P. oligandrum
strains collected from root samples at the end of the cropping season showed that among the three strains used for inoculation, the one producing the smallest amount of oospores was detected at 90%. Single-strand conformational polymorphism analysis revealed increases in the number of members and the complexity of the fungal community over time. There were no significant differences between the microbial ecosystems inoculated with
P. oligandrum
and those that were not treated, except for a reduction of
Pythium dissotocum
(ubiquitous tomato root minor pathogen) populations in inoculated systems during the last 3 months of culture. These findings raise interesting issues concerning the use of
P. oligandrum
strains producing elicitor and auxin molecules for plant protection and the development of biocontrol.
Induction of Immune Responses in Mice after Oral Immunization with RecombinantLactobacillus caseiStrains Expressing EnterotoxigenicEscherichia coliF41 Fimbrial Protein
Authors: Liu Jian-Kui , Hou Xi-Lin , Wei Chun-Hua , Yu Li-Yun , He Xiao-Jie , Wang Gui-Hua , Lee Jong-Soo , Kim Chul-Joong 
Published: May 2009

ABSTRACTIn an effort to develop a safe and effective vaccine for the prevention of enterotoxigenicEscherichia coli(ETEC) F41 infections, we have developed a surface antigen display system using poly-γ-glutamate synthetase A (PgsA) as an anchoring matrix. The recombinant fusion proteins comprised of PgsA and fimbrial protein of F41 were stably expressed inLactobacillus casei525. Surface localization of the fusion protein was verified by immunoblotting, immunofluorescence microscopy, and flow cytometry. Oral inoculation of recombinantL. casei525 into specific-pathogen-free BALB/c mice resulted in significant mucosal immunoglobulin A (IgA) titers that remained elevated for >16 weeks. High levels of IgG responses in sera specific for F41 fimbriae were also induced, with prominent IgG1 titers as well as IgG2a and IgG2b titers. The helper T-cell (Th) response was Th2-cell dominant, as evidenced by increased mucosal and systemic interleukin-4-producing T cells and a concomitant elevation of serum IgG1 antibody responses. More than 80% of the mice were protected against challenge with a 2 × 104-fold 50% lethal dose of standard-type F41 (C83919). The induced antibodies were important for eliciting a protective immune response against F41 infection. These results indicated that the use of recombinantL. casei525 could be a valuable strategy for future vaccine development for ETEC.
mcrA
-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities
Authors: Steinberg Lisa M. , Regan John M. 
Published: May 2009

ABSTRACT

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (
mcrA
) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total
mcrA
and
mcrA
levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the
Methanosaetaceae
,
Methanosarcina
,
Methanobacteriaceae
, and
Methanocorpusculaceae
and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus
Methanosarcina
, whereas the sample from the pig manure digester contained detectable levels of only members of the
Methanobacteriaceae
. The acidic peat samples were dominated by both
Methanosarcina
spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.
Behavior of the Meat-Borne Bacterium
Lactobacillus sakei
during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice
Authors: Chiaramonte Fabrizio , Blugeon Sébastien , Chaillou Stéphane , Langella Philippe , Zagorec Monique 
Published: May 2009

ABSTRACT

A
Lactobacillus sakei
strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne
L. sakei
strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three
L. sakei
strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10
9
CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total
L. sakei
population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that
L. sakei
is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of
Escherichia coli
strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.
Retention and Release of
Cryptosporidium parvum
Oocysts by Experimental Biofilms Composed of a Natural Stream Microbial Community
Authors: Wolyniak E. A. , Hargreaves B. R. , Jellison K. L. 
Published: May 2009

ABSTRACT

Cryptosporidium parvum
oocysts accumulate on biofilm surfaces. The percentage of oocysts attached to biofilms remained nearly constant while oocysts were supplied to the system but decreased to a new steady-state level once oocysts were removed from the feed. More oocysts attached to summer biofilm cultures than winter biofilm cultures.
Dispersion of Multidrug-Resistant
Enterococcus faecium
Isolates Belonging to Major Clonal Complexes in Different Portuguese Settings
Authors: Freitas Ana R. , Novais Carla , Ruiz-Garbajosa Patricia , Coque Teresa M. , Peixe Luísa 
Published: May 2009

ABSTRACT

The population structure of 56
Enterococcus faecium
isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections.
Detection, Distribution, and Organohalogen Compound Discovery Implications of the Reduced Flavin Adenine Dinucleotide-Dependent Halogenase Gene in Major Filamentous Actinomycete Taxonomic Groups
Authors: Gao Peng , Huang Ying 
Published: May 2009

ABSTRACT

Halogenases have been shown to play a significant role in biosynthesis and introducing the bioactivity of many halogenated secondary metabolites. In this study, 54 reduced flavin adenine dinucleotide (FADH
2
)-dependent halogenase gene-positive strains were identified after the PCR screening of a large collection of 228 reference strains encompassing all major families and genera of filamentous actinomycetes. The wide distribution of this gene was observed to extend to some rare lineages with higher occurrences and large sequence diversity. Subsequent phylogenetic analyses revealed that strains containing highly homologous halogenases tended to produce halometabolites with similar structures, and halogenase genes are likely to propagate by horizontal gene transfer as well as vertical inheritance within actinomycetes. Higher percentages of halogenase gene-positive strains than those of halogenase gene-negative ones contained polyketide synthase genes and/or nonribosomal peptide synthetase genes or displayed antimicrobial activities in the tests applied, indicating their genetic and physiological potentials for producing secondary metabolites. The robustness of this halogenase gene screening strategy for the discovery of particular biosynthetic gene clusters in rare actinomycetes besides streptomycetes was further supported by genome-walking analysis. The described distribution and phylogenetic implications of the FADH
2
-dependent halogenase gene present a guide for strain selection in the search for novel organohalogen compounds from actinomycetes.
Novel Toxin-Antitoxin System Composed of Serine Protease and AAA-ATPase Homologues Determines the High Level of Stability and Incompatibility of the Tumor-Inducing Plasmid pTiC58
Authors: Yamamoto Shinji , Kiyokawa Kazuya , Tanaka Katsuyuki , Moriguchi Kazuki , Suzuki Katsunori 
Published: May 2009

ABSTRACT

Stability of plant tumor-inducing (Ti) plasmids differs among strains. A high level of stability prevents basic and applied studies including the development of useful strains. The nopaline type Ti plasmid pTiC58 significantly reduces the transconjugant efficiency for incoming incompatible plasmids relative to the other type, such as octopine-type plasmids. In this study we identified a region that increases the incompatibility and stability of the plasmid. This region was located on a 4.3-kbp segment about 38 kbp downstream of the replication locus,
repABC
. We named two open reading frames in the segment,
ietA
and
ietS
, both of which were essential for the high level of incompatibility and stability. Plasmid stabilization by
ietAS
was accomplished by a toxin-antitoxin (TA) mechanism, where IetS is the toxin and IetA is the antitoxin. A database search revealed that putative IetA and IetS proteins are highly similar to AAA-ATPases and subtilisin-like serine proteases, respectively. Amino acid substitution experiments in each of the highly conserved characteristic residues, in both putative enzymes, suggested that the protease activity is essential and that ATP binding activity is important for the operation of the TA system. The
ietAS
-containing
repABC
plasmids expelled Ti plasmids even in strains which were tolerant to conventional Ti-curing treatments.
Redundant Hydrogen Peroxide Scavengers Contribute to
Salmonella
Virulence and Oxidative Stress Resistance
Authors: Hébrard Magali , Viala Julie P. M. , Méresse Stéphane , Barras Frédéric , Aussel Laurent 
Published: May 2009

ABSTRACT

Salmonella enterica
serovar Typhimurium is an intracellular pathogen that can survive and replicate within macrophages. One of the host defense mechanisms that
Salmonella
encounters during infection is the production of reactive oxygen species by the phagocyte NADPH oxidase. Among them, hydrogen peroxide (H
2
O
2
) can diffuse across bacterial membranes and damage biomolecules. Genome analysis allowed us to identify five genes encoding H
2
O
2
degrading enzymes: three catalases (KatE, KatG, and KatN) and two alkyl hydroperoxide reductases (AhpC and TsaA). Inactivation of the five cognate structural genes yielded the HpxF
−
mutant, which exhibited a high sensitivity to exogenous H
2
O
2
and a severe survival defect within macrophages. When the phagocyte NADPH oxidase was inhibited, its proliferation index increased 3.7-fold. Moreover, the overexpression of
katG
or
tsaA
in the HpxF
−
background was sufficient to confer a proliferation index similar to that of the wild type in macrophages and a resistance to millimolar H
2
O
2
in rich medium. The HpxF
−
mutant also showed an attenuated virulence in a mouse model. These data indicate that
Salmonella
catalases and alkyl hydroperoxide reductases are required to degrade H
2
O
2
and contribute to the virulence. This enzymatic redundancy highlights the evolutionary strategies developed by bacterial pathogens to survive within hostile environments.