bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalase Activity as a Biomarker for Mild-Stress-Induced Robustness in Bacillus weihenstephanensis
Authors: den Besten Heidy M. W. , Effraimidou Styliani , Abee Tjakko 
Published: October 2012

ABSTRACT

Microorganisms are able to survive and grow in changing environments by activating stress adaptation mechanisms which may enhance bacterial robustness. Stress-induced enhanced robustness complicates the predictability of microbial inactivation. Using psychrotolerant
Bacillus weihenstephanensis
strain KBAB4 as a model, we investigated the impact of the culturing temperature on mild-oxidative-stress-induced (cross-)protection toward multiple stresses, including severe oxidative, heat, and acid stresses. Culturing at a refrigeration temperature (7°C) compared to the optimal growth temperature (30°C) affected both the robustness level of
B. weihenstephanensis
and the oxidative stress adaptive response. Scavengers of reactive oxygen species have a crucial role in adaptation to oxidative stresses, and this points to a possible predictive role in mild-oxidative-stress-induced robustness. Therefore, the catalase activity was determined upon mild oxidative stress treatment and was demonstrated to be significantly correlated with the robustness level of mild-stress-treated cells toward severe oxidative and heat stresses but not toward severe acid stress for cells grown at both refrigeration and optimal temperatures. The quantified correlations supported the predictive quality of catalase activity as a biomarker and also underlined that the predictive quality is stress specific. Biomarkers that are able to predict stress-induced enhanced robustness can be used to better understand stress adaptation mechanisms and might allow the design of effective combinations of hurdles to control microbial behavior.
Community and Proteomic Analysis of Methanogenic Consortia Degrading Terephthalate
Authors: Wu Jer-Horng , Wu Feng-Yau , Chuang Hui-Ping , Chen Wei-Yu , Huang Hung-Jen , Chen Shu-Hui , Liu Wen-Tso 
Published: October 2012

ABSTRACT

Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122–130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that
Pelotomaculum
,
Methanosaeta
, and
Methanolinea
were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed
in situ
. The results confirmed that TA was degraded by
Pelotomaculum
spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H
2
/CO
2
, and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.
Isotope-Assisted Screening for Iron-Containing Metabolites Reveals a High Degree of Diversity among Known and Unknown Siderophores Produced by Trichoderma spp
Authors: Lehner Sylvia M. , Atanasova Lea , Neumann Nora K. N. , Krska Rudolf , Lemmens Marc , Druzhinina Irina S. , Schuhmacher Rainer 
Published: October 2012

ABSTRACT

Due to low iron availability under environmental conditions, many microorganisms excrete iron-chelating agents (siderophores) to cover their iron demands. A novel screening approach for the detection of siderophores using liquid chromatography coupled to high-resolution tandem mass spectrometry was developed to study the production of extracellular siderophores of 10 wild-type
Trichoderma
strains. For annotation of siderophores, an in-house library comprising 422 known microbial siderophores was established. After 96 h of cultivation, 18 different iron chelators were detected. Four of those (dimerum acid, fusigen, coprogen, and ferricrocin) were identified by measuring authentic standards.
cis
-Fusarinine, fusarinine A and B, and des-diserylglycylferrirhodin were annotated based on high-accuracy mass spectral analysis. In total, at least 10 novel iron-containing metabolites of the hydroxamate type were found. On average
Trichoderma
spp. produced 12 to 14 siderophores, with 6 common to all species tested. The highest number (15) of siderophores was detected for the most common environmental opportunistic and strongly fungicidic species,
Trichoderma harzianum
, which, however, did not have any unique compounds. The tropical species
T. reesei
had the most distinctive pattern, producing one unique siderophore (
cis
-fusarinine) and three others that were present only in
T. harzianum
and not in other species. The diversity of siderophores did not directly correlate with the antifungal potential of the species tested. Our data suggest that the high diversity of siderophores produced by
Trichoderma
spp. might be the result of further modifications of the nonribosomal peptide synthetase (NRPS) products and not due to diverse NRPS-encoding genes.
Investigation of the Amycolatopsis sp. Strain ATCC 39116 Vanillin Dehydrogenase and Its Impact on the Biotechnical Production of Vanillin
Authors: Fleige Christian , Hansen Gunda , Kroll Jens , Steinbüchel Alexander 
Published: October 2012

ABSTRACT

The actinomycete
Amycolatopsis
sp. strain ATCC 39116 is capable of synthesizing large amounts of vanillin from ferulic acid, which is a natural cell wall component of higher plants. The desired intermediate vanillin is subject to undesired catabolism caused by the metabolic activity of a hitherto unknown vanillin dehydrogenase (VDH
ATCC 39116
). In order to prevent the oxidation of vanillin to vanillic acid and thereby to obtain higher yields and concentrations of vanillin, the responsible vanillin dehydrogenase in
Amycolatopsis
sp. ATCC 39116 was investigated for the first time by using data from our genome sequence analysis and further bioinformatic approaches. The
vdh
gene was heterologously expressed in
Escherichia coli
, and the encoded vanillin dehydrogenase was characterized in detail. VDH
ATCC 39116
was purified to apparent electrophoretic homogeneity and exhibited NAD
+
-dependent activity toward vanillin, coniferylaldehyde, cinnamaldehyde, and benzaldehyde. The enzyme showed its highest level of activity toward vanillin at pH 8.0 and at a temperature of 44°C. In a next step, a precise
vdh
deletion mutant of
Amycolatopsis
sp. ATCC 39116 was generated. The mutant lost its ability to grow on vanillin and did not show vanillin dehydrogenase activity. A 2.3-times-higher vanillin concentration and a substantially reduced amount of vanillic acid occurred with the
Amycolatopsis
sp. ATCC 39116 Δ
vdh
::Km
r
mutant when ferulic acid was provided for biotransformation in a cultivation experiment on a 2-liter-bioreactor scale. Based on these results and taking further metabolic engineering into account, the
Amycolatopsis
sp. ATCC 39116 Δ
vdh
::Km
r
mutant represents an optimized and industrially applicable platform for the biotechnological production of natural vanillin.
Evaluation of Two Approaches for Assessing the Genetic Similarity of Virioplankton Populations as Defined by Genome Size
Authors: Jamindar Sanchita , Polson Shawn W. , Srinivasiah Sharath , Waidner Lisa , Wommack K. Eric 
Published: October 2012

ABSTRACT
Viral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches—T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting—to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.
The Noncommensal Bacterium Methylococcus capsulatus (Bath) Ameliorates Dextran Sulfate (Sodium Salt)-Induced Ulcerative Colitis by Influencing Mechanisms Essential for Maintenance of the Colonic Barrier Function
Authors: Kleiveland Charlotte R. , Hult Lene T. Olsen , Spetalen Signe , Kaldhusdal Magne , Christofferesen Trine Eker , Bengtsson Oskar , Romarheim Odd Helge , Jacobsen Morten , Lea Tor 
Published: October 2012

ABSTRACTDietary inclusion of a bacterial meal has recently been shown to efficiently abolish soybean meal-induced enteritis in Atlantic salmon. The objective of this study was to investigate whether inclusion of this bacterial meal in the diet could abrogate disease development in a murine model of epithelial injury and colitis and thus possibly have therapeutic potential in human inflammatory bowel disease. C57BL/6N mice were fedad libituma control diet or an experimental diet containing 254 g/kg of body weight BioProtein, a bacterial meal consisting ofMethylococcus capsulatus(Bath), together with the heterogenic bacteriaRalstoniasp.,Brevibacillus agri, andAneurinibacillussp. At day 8, colitis was induced by 3.5% dextran sulfate sodium (DSS)ad libitumin the drinking water for 6 days. Symptoms of DSS treatment were less profound after prophylactic treatment with the diet containing the BioProtein. Colitis-associated parameters such as reduced body weight, colon shortening, and epithelial damage also showed significant improvement. Levels of acute-phase reactants, proteins whose plasma concentrations increase in response to inflammation, and neutrophil infiltration were reduced. On the other, increased epithelial cell proliferation and enhanced mucin 2 (Muc2) transcription indicated improved integrity of the colonic epithelial layer. BioProtein mainly consists ofMethylococcus capsulatus(Bath) (88%). The results that we obtained when using a bacterial meal consisting ofM. capsulatus(Bath) were similar to those obtained when using BioProtein in the DSS model. Our results show that a bacterial meal of the noncommensal bacteriumM. capsulatus(Bath) has the potential to attenuate DSS-induced colitis in mice by enhancing colonic barrier function, as judged by increased epithelial proliferation and increased Muc2 transcription.
Exploration of the Genomic Diversity and Core Genome of the Bifidobacterium adolescentis Phylogenetic Group by Means of a Polyphasic Approach
Authors: Duranti Sabrina , Turroni Francesca , Milani Christian , Foroni Elena , Bottacini Francesca , Dal Bello Fabio , Ferrarini Alberto , Delledonne Massimo , van Sinderen Douwe , Ventura Marco 
Published: October 2012

ABSTRACT

In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e.,
Bifidobacterium adolescentis
,
Bifidobacterium catenulatum
, and
Bifidobacterium pseudocatenulatum
, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.
Promoter Swapping Unveils the Role of the Citrobacter rodentium CTS1 Type VI Secretion System in Interbacterial Competition
Authors: Gueguen Erwan , Cascales Eric 
Published: October 2012

ABSTRACT

The type VI secretion system (T6SS) is a versatile secretion machine dedicated to various functions in Gram-negative bacteria, including virulence toward eukaryotic cells and antibacterial activity. Activity of T6SS might be followed
in vitro
by the release of two proteins, Hcp and VgrG, in the culture supernatant.
Citrobacter rodentium
, a rodent pathogen, harbors two T6SS gene clusters,
cts1
and
cts2
. Reporter fusion and Hcp release assays suggested that the CTS1 T6SS was not produced or not active. The
cts1
locus is composed of two divergent operons. We therefore developed a new vector allowing us to swap the two divergent endogenous promoters by

P
tac

and

P
BAD

using the λ red recombination technology. Artificial induction of both promoters demonstrated that the CTS1 T6SS is functional as shown by the Hcp release assay and confers on
C. rodentium
a growth advantage in antibacterial competition experiments with
Escherichia coli
.
Identification and Characterization of a Bile Salt Hydrolase from Lactobacillus salivarius for Development of Novel Alternatives to Antibiotic Growth Promoters
Authors: Wang Zhong , Zeng Ximin , Mo Yiming , Smith Katie , Guo Yuming , Lin Jun 
Published: October 2012

ABSTRACT

Antibiotic growth promoters (AGPs) have been used as feed additives to improve average body weight gain and feed efficiency in food animals for more than 5 decades. However, there is a worldwide trend to limit AGP use to protect food safety and public health, which raises an urgent need to discover effective alternatives to AGPs. The growth-promoting effect of AGPs has been shown to be highly correlated with the decreased activity of intestinal bile salt hydrolase (BSH), an enzyme that is produced by various gut microflora and involved in host lipid metabolism. Thus, BSH inhibitors are likely promising feed additives to AGPs to improve animal growth performance. In this study, the genome of
Lactobacillus salivarius
NRRL B-30514, a BSH-producing strain isolated from chicken, was sequenced by a 454 GS FLX sequencer. A BSH gene identified by genome analysis was cloned and expressed in an
Escherichia coli
expression system for enzymatic analyses. The BSH displayed efficient hydrolysis activity for both glycoconjugated and tauroconjugated bile salts, with slightly higher catalytic efficiencies (
k
cat
/

K
m

) on glycoconjugated bile salts. The optimal pH and temperature for the BSH activity were 5.5 and 41°C, respectively. Examination of a panel of dietary compounds using the purified BSH identified some potent BSH inhibitors, in which copper and zinc have been recently demonstrated to promote feed digestion and body weight gain in different food animals. In sum, this study identified and characterized a BSH with broad substrate specificity from a chicken
L. salivarius
strain and established a solid platform for us to discover novel BSH inhibitors, the promising feed additives to replace AGPs for enhancing the productivity and sustainability of food animals.
Protective Role of Spore Structural Components in Determining Bacillus subtilis Spore Resistance to Simulated Mars Surface Conditions
Authors: Moeller Ralf , Schuerger Andrew C. , Reitz Günther , Nicholson Wayne L. 
Published: October 2012

ABSTRACT

Spores of wild-type and mutant
Bacillus subtilis
strains lacking various structural components were exposed to simulated Martian atmospheric and UV irradiation conditions. Spore survival and mutagenesis were strongly dependent on the functionality of all of the structural components, with small acid-soluble spore proteins, coat layers, and dipicolinic acid as key protectants.
Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System
Authors: Bidart Gonzalo N. , Ruiz Jimena A. , de Almeida Alejandra , Méndez Beatriz S. , Nikel Pablo I. 
Published: October 2012

ABSTRACT

Bioprocesses conducted under conditions with restricted O
2
supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative anaerobe
Escherichia coli
has elaborate sensing and signal transduction mechanisms for redox control in response to the availability of O
2
and other electron acceptors. The ArcBA two-component system consists of ArcB, a membrane-associated sensor kinase, and ArcA, the cognate response regulator. The tripartite hybrid kinase ArcB possesses a transmembrane, a PAS, a primary transmitter (H1), a receiver (D1), and a phosphotransfer (H2) domain. Metabolic fluxes were compared under anoxic conditions in a wild-type
E. coli
strain, its Δ
arcB
derivative, and two partial
arcB
deletion mutants in which ArcB lacked either the H1 domain or the PAS-H1-D1 domains. These analyses revealed that elimination of different segments in ArcB determines a distinctive distribution of
d
-glucose catabolic fluxes, different from that observed in the Δ
arcB
background. Metabolite profiles, enzyme activity levels, and gene expression patterns were also investigated in these strains. Relevant alterations were observed at the P-enol-pyruvate/pyruvate and acetyl coenzyme A metabolic nodes, and the formation of reduced fermentation metabolites, such as succinate,
d
-lactate, and ethanol, was favored in the mutant strains to different extents compared to the wild-type strain. These phenotypic traits were associated with altered levels of the enzymatic activities operating at these nodes, as well as with elevated NADH/NAD
+
ratios. Thus, targeted modification of global regulators to obtain different metabolic flux distributions under anoxic conditions is emerging as an attractive tool for metabolic engineering purposes.
Ethanol Production and Maximum Cell Growth Are Highly Correlated with Membrane Lipid Composition during Fermentation as Determined by Lipidomic Analysis of 22 Saccharomyces cerevisiae Strains
Authors: Henderson Clark M. , Lozada-Contreras Michelle , Jiranek Vladimir , Longo Marjorie L. , Block David E. 
Published: October 2012

ABSTRACTOptimizing ethanol yield during fermentation is important for efficient production of fuel alcohol, as well as wine and other alcoholic beverages. However, increasing ethanol concentrations during fermentation can create problems that result in arrested or sluggish sugar-to-ethanol conversion. The fundamental cellular basis for these problem fermentations, however, is not well understood. Small-scale fermentations were performed in a synthetic grape must using 22 industrialSaccharomyces cerevisiaestrains (primarily wine strains) with various degrees of ethanol tolerance to assess the correlation between lipid composition and fermentation kinetic parameters. Lipids were extracted at several fermentation time points representing different growth phases of the yeast to quantitatively analyze phospholipids and ergosterol utilizing atmospheric pressure ionization-mass spectrometry methods. Lipid profiling of individual fermentations indicated that yeast lipid class profiles do not shift dramatically in composition over the course of fermentation. Multivariate statistical analysis of the data was performed using partial least-squares linear regression modeling to correlate lipid composition data with fermentation kinetic data. The results indicate a strong correlation (R2= 0.91) between the overall lipid composition and the final ethanol concentration (wt/wt), an indicator of strain ethanol tolerance. One potential component of ethanol tolerance, the maximum yeast cell concentration, was also found to be a strong function of lipid composition (R2= 0.97). Specifically, strains unable to complete fermentation were associated with high phosphatidylinositol levels early in fermentation. Yeast strains that achieved the highest cell densities and ethanol concentrations were positively correlated with phosphatidylcholine species similar to those known to decrease the perturbing effects of ethanol in model membrane systems.
Increasing the Heme-Dependent Respiratory Efficiency of Lactococcus lactis by Inhibition of Lactate Dehydrogenase
Authors: Arioli Stefania , Zambelli Daniele , Guglielmetti Simone , De Noni Ivano , Pedersen Martin B. , Pedersen Per Dedenroth , Dal Bello Fabio , Mora Diego 
Published: October 2012

ABSTRACT

The discovery of heme-induced respiration in
Lactococcus lactis
has radically improved the industrial processes used for the biomass production of this species. Here, we show that inhibition of the lactate dehydrogenase activity of
L. lactis
during growth under respiration-permissive conditions can stimulate aerobic respiration, thereby increasing not only growth efficiency but also the robustness of this organism.
NeuroBactrus, a Novel, Highly Effective, and Environmentally Friendly Recombinant Baculovirus Insecticide
Authors: Shim Hee Jin , Choi Jae Young , Wang Yong , Tao Xue Ying , Liu Qin , Roh Jong Yul , Kim Jae Su , Kim Woo Jin , Woo Soo Dong , Jin Byung Rae , Je Yeon Ho 
Published: October 2012

ABSTRACT

A novel recombinant baculovirus, NeuroBactrus, was constructed to develop an improved baculovirus insecticide with additional beneficial properties, such as a higher insecticidal activity and improved recovery, compared to wild-type baculovirus. For the construction of NeuroBactrus, the
Bacillus thuringiensis
crystal protein gene (here termed
cry1-5
) was introduced into the
Autographa californica
nucleopolyhedrovirus (AcMNPV) genome by fusion of the polyhedrin–
cry1-5
–polyhedrin genes under the control of the polyhedrin promoter. In the opposite direction, an insect-specific neurotoxin gene,
AaIT
, from
Androctonus australis
was introduced under the control of an early promoter from
Cotesia plutellae
bracovirus by fusion of a partial fragment of
orf603
. The polyhedrin–Cry1-5–polyhedrin fusion protein expressed by the NeuroBactrus was not only occluded into the polyhedra, but it was also activated by treatment with trypsin, resulting in an ∼65-kDa active toxin. In addition, quantitative PCR revealed that the neurotoxin was expressed from the early phase of infection. NeuroBactrus showed a high level of insecticidal activity against
Plutella xylostella
larvae and a significant reduction in the median lethal time against
Spodoptera exigua
larvae compared to those of wild-type AcMNPV. Rerecombinant mutants derived from NeuroBactrus in which
AaIT
and/or
cry1-5
were deleted were generated by serial passages
in vitro
. Expression of the foreign proteins (
B. thuringiensis
toxin and AaIT) was continuously reduced during the serial passage of the NeuroBactrus. Moreover, polyhedra collected from
S. exigua
larvae infected with the serially passaged NeuroBactrus showed insecticidal activity similar to that of wild-type AcMNPV. These results suggested that NeuroBactrus could be recovered to wild-type AcMNPV through serial passaging.