bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
Authors: Gladden John M. , Allgaier Martin , Miller Christopher S. , Hazen Terry C. , VanderGheynst Jean S. , Hugenholtz Philip , Simmons Blake A. , Singer Steven W. 
Published: July 2011

ABSTRACT

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli,
Rhodothermus marinus
, and
Thermus thermophilus
. At lower abundance, thermophilic
Chloroflexi
and an uncultivated lineage of the
Gemmatimonadetes
phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
Effect of Soil Clay Content on RNA Isolation and on Detection and Quantification of Bacterial Gene Transcripts in Soil by Quantitative Reverse Transcription-PCR
Authors: Novinscak A. , Filion M. 
Published: July 2011

ABSTRACT
In this study, we evaluated the effect of soil clay content on RNA isolation and on quantitative reverse transcription-PCR (qRT-PCR) quantification of microbial gene transcripts. The amount of clay significantly altered RNA isolation yields and qRT-PCR analyses. Recommendations are made for quantifying microbial gene transcripts in soil samples varying in clay content.
Microbial Utilization and Selectivity of Pectin Fractions with Various Structures
Authors: Onumpai Chatchaya , Kolida Sofia , Bonnin Estelle , Rastall Robert A. 
Published: July 2011

ABSTRACTTo evaluate the fermentation properties of oligosaccharides derived from pectins and their parent polysaccharides, a 5-ml-working-volume, pH- and temperature-controlled fermentor was tested. Six pectic oligosaccharides representing specific substructures found within pectins were prepared. These consisted of oligogalacturonides (average degrees of polymerization [DP] of 5 and 9), methylated oligogalacturonides (average DP of 5), oligorhamnogalacturonides (average DP of 10 as a disaccharide unit of galacturonic acid and rhamnose), oligogalactosides (average DP of 5), and oligoarabinosides (average DP of 6). The influence of these carbohydrates on the human fecal microbiota was evaluated. Use of neutral sugar fractions resulted in an increase inBifidobacteriumpopulations and gave higher organic acid yields. TheBacteroides-Prevotellagroup significantly increased on all oligosaccharides except oligogalacturonides with an average DP of 5. The most selective substrates for bifidobacteria were arabinan, galactan, oligoarabinosides, and oligogalactosides.
Purification and Characterization of the [NiFe]-Hydrogenase of Shewanella oneidensis MR-1
Authors: Shi Liang , Belchik Sara M. , Plymale Andrew E. , Heald Steve , Dohnalkova Alice C. , Sybirna Kateryna , Bottin Hervé , Squier Thomas C. , Zachara John M. , Fredrickson James K. 
Published: July 2011

ABSTRACTShewanella oneidensisMR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant withouthyaBandhydAgenes. Expression of recombinant MR-1 [NiFe]-H2ase intransrestored the mutant's ability to produce H2at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2oxidation to reduction of Tc(VII)O4−and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated reduction of Tc(VII)O4−but not methyl viologen. Under the conditions tested, all Tc(VII)O4−used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O4−was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2·nH2O, which was also the product of Tc(VII)O4−reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H2ase catalyzes Tc(VII)O4−reduction directly by coupling to H2oxidation.
Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Food and Food Products of Poultry Origin in Germany
Authors: Feßler Andrea T. , Kadlec Kristina , Hassel Melanie , Hauschild Tomasz , Eidam Christopher , Ehricht Ralf , Monecke Stefan , Schwarz Stefan 
Published: July 2011

ABSTRACT

During a survey of fresh chicken and turkey meat as well as chicken and turkey meat products for the presence of methicillin-resistant
Staphylococcus aureus
(MRSA) isolates in Germany, 32 (37.2%) of 86 samples were MRSA positive. Twenty-eight of these MRSA isolates belonged to clonal complex 398 (CC398), which is widespread among food-producing animals. These CC398 isolates carried SCC
mec
elements of type IV or V and exhibited
spa
type t011, t034, t899, t2346 or t6574 and either the known
dru
types dt2b, dt6j, dt10a, dt10q, dt11a, dt11v, and dt11ab or the novel
dru
types dt6m, dt10as, and dt10at. In addition, two MRSA sequence type 9 (ST9) isolates with a type IV SCC
mec
cassette,
spa
type t1430, and
dru
type dt10a as well as single MRSA ST5 and ST1791 isolates with a type III SCC
mec
cassette,
spa
type t002, and
dru
type dt9v were identified. All but two isolates were classified as multiresistant. A wide variety of resistance phenotypes and genotypes were detected. All isolates were negative for the major virulence factors, such as Panton-Valentine leukocidin, toxic shock syndrome toxin 1, or exfoliative toxins. In contrast to the MRSA CC398 isolates, the four ST9, ST5, or ST1791 isolates harbored the
egc
gene cluster for enterotoxin G, I, M, N, O, and U genes. Although the relevance of contamination of fresh poultry meat or poultry products with MRSA is currently unclear, the presence of multiresistant and, in part, enterotoxigenic MRSA emphasizes the need for further studies to elucidate possible health hazards for consumers.
Genomic and Metabolic Profiling of Nonulosonic Acids in Vibrionaceae Reveal Biochemical Phenotypes of Allelic Divergence in Vibrio vulnificus
Authors: Lewis Amanda L. , Lubin Jean-Bernard , Argade Shilpa , Naidu Natasha , Choudhury Biswa , Boyd E. Fidelma 
Published: July 2011

ABSTRACT

Nonulosonic acids (NulOs) encompass a large group of structurally diverse nine-carbon backbone α-keto sugars widely distributed among the three domains of life. Mammals express a specialized version of NulOs called sialic acids, which are displayed in prominent terminal positions of cell surface and secreted glycoconjugates. Within bacteria, the ability to synthesize NulOs has been demonstrated in a number of human pathogens and is phylogenetically widespread. Here we examine the distribution, diversity, evolution, and function of NulO biosynthesis pathways in members of the family
Vibrionaceae
. Among 27 species of
Vibrionaceae
examined at the genomic level, 12 species contained
nab
gene clusters. We document examples of duplication, divergence, horizontal transfer, and recombination of
nab
gene clusters in different
Vibrionaceae
lineages. Biochemical analyses, including mass spectrometry, confirmed that many species do, in fact, produce di-N-acetylated NulOs. A library of clinical and environmental isolates of
Vibrio vulnificus
served as a model for further investigation of
nab
allele genotypes and levels of NulO expression. The data show that lineage I isolates produce about 20-fold higher levels of NulOs than lineage II isolates. Moreover,
nab
gene alleles found in a subset of
V. vulnificus
clinical isolates express 40-fold higher levels of NulOs than
nab
alleles associated with environmental isolates. Taken together, the data implicate the family
Vibrionaceae
as a “hot spot” of NulO evolution and suggest that these molecules may have diverse roles in environmental persistence and/or animal virulence.
Semicontinuous Culture of Magnetospirillum gryphiswaldense MSR-1 Cells in an Autofermentor by Nutrient-Balanced and Isosmotic Feeding Strategies
Authors: Zhang Yang , Zhang Xiaojuan , Jiang Wei , Li Ying , Li Jilun 
Published: July 2011

ABSTRACT

An improved strategy was developed for the high-density culture of
Magnetospirillum gryphiswaldense
strain MSR-1 and large-scale magnetosome production in both 7.5- and 42-liter autofermentors. By using a nutrient-balanced feeding strategy and the replacement of carbon and nitrogen sources to reduce accumulation of Na
+
and Cl
−
ions, we reduced the factors that tend to inhibit cell growth, particularly the increase of osmotic potential. Semicontinuous culture was thereby achieved in the autofermentor for the first time. When the cells were harvested at 36 and 73 h, magnetosome yields (dry weight) as high as 168.3 and 83.5 mg/liter/day, respectively, were achieved. These values were, respectively, approximately 10 and 5 times higher than the yields achieved in previous studies and represent a significant improvement in magnetosome production efficiency.
Calcineurin Colocalizes with P-Bodies and Stress Granules during Thermal Stress in Cryptococcus neoformans
Authors: Kozubowski Lukasz , Aboobakar Eanas F. , Cardenas Maria E. , Heitman Joseph 
Published: July 2011

ABSTRACT

Calcineurin is a calcium-calmodulin-activated serine/threonine-specific phosphatase that operates during cellular responses to stress and plays a prominent role in transcriptional control, whereas regulatory events beyond transcription are less well characterized. This study reveals a novel transcription-independent role of calcineurin during the temperature stress response in the human fungal pathogen
Cryptococcus neoformans.
The diffusely cytoplasmic calcineurin catalytic subunit Cna1 relocates to endoplasmic reticulum (ER)-associated puncta and the mother-bud neck when cells are subjected to 37°C. More than 50% of Cna1 puncta contain the P-body constituent decapping enzyme Dcp1 and the stress granule constituent poly(A)-binding protein Pub1. These results support a model in which calcineurin orchestrates thermal stress responses by associating with sites of mRNA processing.
Bile Salts Induce Resistance to Polymyxin in Enterohemorrhagic Escherichia coliO157:H7
Authors: Kus Julianne V. , Gebremedhin Ahferom , Dang Vica , Tran Seav-Ly , Serbanescu Anca , Foster Debora Barnett 
Published: July 2011

ABSTRACT

Many enteric bacteria use bile as an environmental cue to signal resistance and virulence gene expression. Microarray analysis of enterohemorrhagic
Escherichia coli
O157:H7 (EHEC) treated with bile salts revealed upregulation of genes for an efflux system (
acrAB
), a two-component signal transduction system (
basRS
/
pmrAB
), and lipid A modification (
arnBCADTEF
and
ugd
). Bile salt treatment of EHEC produced a
basS
- and
arnT
-dependent resistance to polymyxin.
A Novel Toxin Regulator, the CPE1446-CPE1447 Protein Heteromeric Complex, Controls Toxin Genes in Clostridium perfringens
Authors: Obana Nozomu , Nakamura Kouji 
Published: July 2011

ABSTRACT

Clostridium perfringens
is a Gram-positive anaerobic spore-forming bacterium that is widespread in environmental soil and sewage, as well as in animal intestines. It is also a causative agent of diseases in humans and other animals, and it produces numerous extracellular enzymes and toxins. Although these toxins have been characterized in detail, regulators of toxin genes are less well understood. The present study identified CPE1447 and CPE1446 as novel regulators of toxin gene expression. CPE1447 and CPE1446 are cotranscribed as an operon, and the encoded proteins have a helix-turn-helix (HTH) motif at the N termini of their amino acid sequences, suggesting that CPE1447 and CPE1446 control the target genes as transcriptional regulators. The expression of several genes encoding toxins was changed in both a CPE1446 mutant and a CPE1447-CPE1446 deletion mutant. Complementation of CPE1446 and CPE1447 revealed that CPE1447 and CPE1446 coordinately regulate their target genes. CPE1447 protein was coprecipitated with His-tagged CPE1446 protein, indicating that the CPE1447 and CPE1446 proteins form a stable complex in
C. perfringens
under their native conditions. Although the small RNA that regulates several genes under the VirR/VirS two-component system (VR-RNA) positively affected CPE1447-CPE1446 mRNA expression, it did not control expression of the CPE1447-CPE1446 regulon, demonstrating that CPE1447 and CPE1446 regulate a different set of toxin genes from the VirR/VirS–VR-RNA cascade.
CT406 Encodes a Chlamydial Ortholog of NrdR, a Repressor of Ribonucleotide Reductase
Authors: Case Elizabeth Di Russo , Akers Johnny C. , Tan Ming 
Published: July 2011

ABSTRACT

Chlamydia trachomatis
is an obligate intracellular bacterium that is dependent on its host cell for nucleotides.
Chlamydia
imports ribonucleotide triphosphates (NTPs) but not deoxyribonucleotide triphosphates (dNTPs) and instead uses ribonucleotide reductase to convert imported ribonucleotides into deoxyribonucleotides for DNA synthesis. The genes encoding ribonucleotide reductase have been recently shown to be negatively controlled by a conserved regulator called NrdR. In this study, we provide direct evidence that
Escherichia coli
NrdR is a transcriptional repressor and that
C. trachomatis
CT406 encodes its chlamydial ortholog. We showed that CT406 binds specifically to two NrdR boxes upstream of the
nrdAB
operon in
C. trachomatis
. Using an
in vitro
transcription assay, we confirmed that these NrdR boxes function as an operator since they were necessary and sufficient for CT406-mediated repression. We validated our
in vitro
findings with reporter studies in
E. coli
showing that both
E. coli
NrdR and CT406 repressed transcription from the
E. coli
nrdH
and
C. trachomatis
nrdAB
promoters
in vivo
. This
in vivo
repression was reversed by hydroxyurea treatment. Since hydroxyurea inhibits ribonucleotide reductase and reduces intracellular deoxyribonucleotide levels, these results suggest that NrdR activity is modulated by a deoxyribonucleotide corepressor.
UvrD2 Is Essential in Mycobacterium tuberculosis, but Its Helicase Activity Is Not Required
Authors: Williams Alan , Güthlein Carolin , Beresford Nicola , Böttger Erik C. , Springer Burkhard , Davis Elaine O. 
Published: July 2011

ABSTRACT

UvrD is an SF1 family helicase involved in DNA repair that is widely conserved in bacteria.
Mycobacterium tuberculosis
has two annotated UvrD homologues; here we investigate the role of UvrD2. The
uvrD2
gene at its native locus could be knocked out only in the presence of a second copy of the gene, demonstrating that
uvrD2
is essential. Analysis of the putative protein domain structure of UvrD2 shows a distinctive domain architecture, with an extended C terminus containing an HRDC domain normally found in SF2 family helicases and a linking domain carrying a tetracysteine motif. Truncated constructs lacking the C-terminal domains of UvrD2 were able to compensate for the loss of the chromosomal copy, showing that these C-terminal domains are not essential. Although UvrD2 is a functional helicase, a mutant form of the protein lacking helicase activity was able to permit deletion of
uvrD2
at its native locus. However, a mutant protein unable to hydrolyze ATP or translocate along DNA was not able to compensate for lack of the wild-type protein. Therefore, we concluded that the essential role played by UvrD2 is unlikely to involve its DNA unwinding activity and is more likely to involve DNA translocation and, possibly, protein displacement.
A Novel Testosterone Catabolic Pathway in Bacteria
Authors: Leu Yann-Lii , Wang Po-Hsiang , Shiao Ming-Shi , Ismail Wael , Chiang Yin-Ru 
Published: July 2011

ABSTRACT

Forty years ago, Coulter and Talalay (A. W. Coulter and P. Talalay, J. Biol. Chem. 243:3238–3247, 1968) established the oxygenase-dependent pathway for the degradation of testosterone by aerobes. The oxic testosterone catabolic pathway involves several oxygen-dependent reactions and is not available for anaerobes. Since then, a variety of anaerobic bacteria have been described for the ability to degrade testosterone in the absence of oxygen. Here, a novel, oxygenase-independent testosterone catabolic pathway in such organisms is described.
Steroidobacter denitrificans
DSMZ18526 was shown to be capable of degrading testosterone in the absence of oxygen and was selected as the model organism in this study. In a previous investigation, we identified the initial intermediates involved in an anoxic testosterone catabolic pathway, most of which are identical to those of the oxic pathway demonstrated in
Comamonas testosteroni
. In this study, five additional intermediates of the anoxic pathway were identified. We demonstrated that subsequent steps of the anoxic pathway greatly differ from those of the established oxic pathway, which suggests that a novel pathway for testosterone catabolism is present. In the proposed anoxic pathway, a reduction reaction occurs at C-4 and C-5 of androsta-1,4-diene-3,17-dione, the last common intermediate of both the oxic and anoxic pathways. After that, a novel hydration reaction occurs and a hydroxyl group is thus introduced to the C-1α position of C
19
steroid substrates. To our knowledge, an enzymatic hydration reaction occurring at the A ring of steroid compounds has not been reported before.
A Specialized Aspartokinase Enhances the Biosynthesis of the Osmoprotectants Ectoine and Hydroxyectoine in Pseudomonas stutzeriA1501
Authors: Stöveken Nadine , Pittelkow Marco , Sinner Tatjana , Jensen Roy A. , Heider Johann , Bremer Erhard 
Published: July 2011

ABSTRACTThe compatible solutes ectoine and hydroxyectoine are widely produced by bacteria as protectants against osmotic and temperature stress.l-Aspartate-beta-semialdehyde is used as the precursor molecule for ectoine/hydroxyectoine biosynthesis that is catalyzed by the EctABCD enzymes.l-Aspartate-beta-semialdehyde is a central intermediate in different biosynthetic pathways and is produced froml-aspartate by aspartokinase (Ask) and aspartate-semialdehyde-dehydrogenase (Asd). Ask activity is typically stringently regulated by allosteric control to avoid gratuitous synthesis of aspartylphosphate. Many organisms have evolved multiple forms of aspartokinase, and feedback regulation of these specialized Ask enzymes is often adapted to the cognate biochemical pathways. The ectoine/hydroxyectoine biosynthetic genes (ectABCD) are followed in a considerable number of microorganisms by anaskgene (ask_ect), suggesting that Ask_Ect is a specialized enzyme for this osmoadaptive biosynthetic pathway. However, none of these Ask_Ect enzymes have been functionally characterized.Pseudomonas stutzeriA1501 synthesizes both ectoine and hydroxyectoine in response to increased salinity, and it possesses two Ask enzymes: Ask_Lys and Ask_Ect. We purified both Ask enzymes and found significant differences with regard to their allosteric control: Ask_LysC was inhibited by threonine and in a concerted fashion by threonine and lysine, whereas Ask_Ect showed inhibition only by threonine. TheectABCD_askgenes fromP. stutzeriA1501 were cloned and functionally expressed inEscherichia coli, and this led to osmostress protection. AnE. colistrain carrying the plasmid-basedectABCD_askgene cluster produced significantly more ectoine/hydroxyectoine than a strain expressing theectABCDgene cluster alone. This finding suggests a specialized role for Ask_Ect in ectoine/hydroxyectoine biosynthesis.
Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190
Authors: Sales Christopher M. , Mahendra Shaily , Grostern Ariel , Parales Rebecca E. , Goodwin Lynne A. , Woyke Tanja , Nolan Matt , Lapidus Alla , Chertkov Olga , Ovchinnikova Galina , Sczyrba Alexander , Alvarez-Cohen Lisa 
Published: July 2011

ABSTRACT

Pseudonocardia dioxanivorans
CB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus
Pseudonocardia
for which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants.
Transcriptional Profiling of Nitrogen Fixation in Azotobacter vinelandii
Authors: Hamilton Trinity L. , Ludwig Marcus , Dixon Ray , Boyd Eric S. , Dos Santos Patricia C. , Setubal João C. , Bryant Donald A. , Dean Dennis R. , Peters John W. 
Published: July 2011

ABSTRACT

Most biological nitrogen (N
2
) fixation results from the activity of a molybdenum-dependent nitrogenase, a complex iron-sulfur enzyme found associated with a diversity of bacteria and some methanogenic archaea.
Azotobacter vinelandii
, an obligate aerobe, fixes nitrogen via the oxygen-sensitive Mo nitrogenase but is also able to fix nitrogen through the activities of genetically distinct alternative forms of nitrogenase designated the Vnf and Anf systems when Mo is limiting. The Vnf system appears to replace Mo with V, and the Anf system is thought to contain Fe as the only transition metal within the respective active site metallocofactors. Prior genetic analyses suggest that a number of
nif
-encoded components are involved in the Vnf and Anf systems. Genome-wide transcription profiling of
A. vinelandii
cultured under nitrogen-fixing conditions under various metal amendments (e.g., Mo or V) revealed the discrete complement of genes associated with each nitrogenase system and the extent of cross talk between the systems. In addition, changes in transcript levels of genes not directly involved in N
2
fixation provided insight into the integration of central metabolic processes and the oxygen-sensitive process of N
2
fixation in this obligate aerobe. The results underscored significant differences between Mo-dependent and Mo-independent diazotrophic growth that highlight the significant advantages of diazotrophic growth in the presence of Mo.