bluuebunny/crossref_metadata_2025_split huggingface dataset:
Presence of Novel, Potentially Homoacetogenic Bacteria in the Rumen as Determined by Analysis of Formyltetrahydrofolate Synthetase Sequences from Ruminants
Authors: Henderson Gemma , Naylor Graham E. , Leahy Sinead C. , Janssen Peter H. 
Published: January 2010

ABSTRACT

Homoacetogens produce acetate from H
2
and CO
2
via the Wood-Ljungdahl pathway. Some homoacetogens have been isolated from the rumen, but these organisms are expected to be only part of the full diversity present. To survey the presence of rumen homoacetogens, we analyzed sequences of formyltetrahydrofolate synthetase (FTHFS), a key enzyme of the Wood-Ljungdahl pathway. A total of 275 partial sequences of genes encoding FTHFS were PCR amplified from rumen contents of a cow, two sheep, and a deer. Phylogenetic trees were constructed using these FTHFS gene sequences and the translated amino acid sequences, together with other sequences from public databases and from novel nonhomoacetogenic bacteria isolated from the rumen. Over 90% of the FTHFS sequences fell into 34 clusters defined with good bootstrap support. Few rumen-derived FTHFS sequences clustered with sequences of known homoacetogens. Conserved residues were identified in the deduced FTHFS amino acid sequences from known homoacetogens, and their presence in the other sequences was used to determine a “homoacetogen similarity” (HS) score. A homoacetogen FTHFS profile hidden Markov model (HoF-HMM) was used to assess the homology of rumen and homoacetogen FTHFS sequences. Many clusters had low HS scores and HoF-HMM matches, raising doubts about whether the sequences originated from homoacetogens. In keeping with these findings, FTHFS sequences from nonhomoacetogenic bacterial isolates grouped in these clusters with low scores. However, sequences that formed 10 clusters containing no known isolates but representing 15% of our FTHFS sequences from rumen samples had high HS scores and HoF-HMM matches and so could represent novel homoacetogens.
Molecular Monitoring and Isolation of Previously Uncultured Bacterial Strains from the Sheep Rumen
Authors: Koike S. , Handa Y. , Goto H. , Sakai K. , Miyagawa E. , Matsui H. , Ito S. , Kobayashi Y. 
Published: January 2010

ABSTRACT

To estimate the contribution of uncultured bacterial groups to fiber degradation, we attempted to retrieve both ecological and functional information on uncultured groups in the rumen. Among previously reported uncultured bacteria, fiber-associated groups U2 and U3, belonging to the low-GC Gram-positive bacterial group, were targeted. PCR primers and fluorescence
in situ
hybridization (FISH) probe targeting 16S rRNA genes or rRNA were designed and used to monitor the distribution of targets. The population size of group U2 in the rumen was as high as 1.87%, while that of group U3 was only 0.03%. Strong fluorescence signals were observed from group U2 cells attached to plant fibers in the rumen. These findings indicate the ecological significance of group U2 in the rumen. We succeeded in enriching group U2 using rumen-incubated rice straw as the inoculum followed by incubation in an appropriate medium with an agent inhibitory for Gram-negative bacteria. Consequently, we successfully isolated two strains, designated B76 and R-25, belonging to group U2. Both strains were Gram-positive short rods or cocci that were 0.5 to 0.8 μm in size. Strain B76 possessed xylanase and α-
l
-arabinofuranosidase activity. In particular, the xylanase activity of strain B76 was higher than that of xylanolytic
Butyrivibrio fibrisolvens
H17c grown on cellobiose. Strain R-25 showed an α-
l
-arabinofuranosidase activity higher than that of strain B76. These results suggest that strains B76 and R-25 contribute to hemicellulose degradation in the rumen.
High Abundance of Ammonia-OxidizingArchaeain Coastal Waters, Determined Using a Modified DNA Extraction Method
Authors: Urakawa Hidetoshi , Martens-Habbena Willm , Stahl David A. 
Published: January 2010

ABSTRACTMolecular characterizations of environmental microbial populations based on recovery and analysis of DNA generally assume efficient or unbiased extraction of DNA from different sample matrices and microbial groups. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition ofNitrosopumilus maritimuscells to track the recovery of DNA from marineArchaea. After the comparison, a simplified phenol-chloroform extraction method was developed and shown to be significantly superior, in terms of both the recovery and the purity of DNA, to other protocols now generally applied to environmental studies. The simplified and optimized method was used to quantify ammonia-oxidizingArchaeaat different depth intervals in a fjord (Hood Canal) by quantitative PCR. The numbers ofArchaeaincreased with depth, often constituting as much as 20% of the total bacterial community.
Inactivation of
Vibrio anguillarum
by Attached and Planktonic
Roseobacter
Cells
Authors: D'Alvise Paul W. , Melchiorsen Jette , Porsby Cisse H. , Nielsen Kristian F. , Gram Lone 
Published: January 2010

ABSTRACT

The purpose of the present study was to investigate the inhibition of
Vibrio
by
Roseobacter
in a combined liquid-surface system. Exposure of
Vibrio anguillarum
to surface-attached roseobacters (10
7
CFU/cm
2
) resulted in significant reduction or complete killing of the pathogen inoculated at 10
2
to 10
4
CFU/ml. The effect was likely associated with the production of tropodithietic acid (TDA), as a TDA-negative mutant did not affect survival or growth of
V. anguillarum
.
Hitherto Unknown [Fe-Fe]-Hydrogenase Gene Diversity in Anaerobes and Anoxic Enrichments from a Moderately Acidic Fen
Authors: Schmidt Oliver , Drake Harold L. , Horn Marcus A. 
Published: January 2010

ABSTRACT

Newly designed primers for [Fe-Fe]-hydrogenases indicated that (i) fermenters, acetogens, and undefined species in a fen harbor hitherto unknown hydrogenases and (ii)
Clostridium
- and
Thermosinus
-related primary fermenters, as well as secondary fermenters related to sulfate or iron reducers might be responsible for hydrogen production in the fen. Comparative analysis of [Fe-Fe]-hydrogenase and 16S rRNA gene-based phylogenies indicated the presence of homologous multiple hydrogenases per organism and inconsistencies between 16S rRNA gene- and [Fe-Fe]-hydrogenase-based phylogenies, necessitating appropriate qualification of [Fe-Fe]-hydrogenase gene data for diversity analyses.
Requirement of the
galU
Gene for Polysaccharide Production by and Pathogenicity and Growth
In Planta
of
Xanthomonas citri
subsp.
citri
Authors: Guo Yinping , Sagaram Uma Shankar , Kim Jeong-soon , Wang Nian 
Published: January 2010

ABSTRACT

Xanthomonas citri
subsp.
citri
is the causal agent of citrus canker, which has a significant impact on citrus production. In this study, we characterized the
galU
gene of
X. citri
subsp.
citri
. Two
galU
mutants (F6 and D12) were identified in an
X. citri
subsp.
citri
EZ-Tn5 <R6Kγori/KAN-2> Tnp transposon library. Rescue cloning, sequence analysis, and Southern blot analysis indicated that both of these mutants had a single copy of the EZ-Tn5 transposon inserted in
galU
in the chromosome. Further study showed that
galU
was required for biosynthesis of extracellular polysaccharides (EPS; xanthan gum) and capsular polysaccharide (CPS) and biofilm formation. Mutation of
galU
resulted in a loss of pathogenicity for grapefruit. The loss of pathogenicity of a
galU
mutant resulted from its inability to grow
in planta
rather than from the effect on virulence genes. Quantitative reverse transcription-PCR assays indicated that mutation of
galU
did not impair the expression of key virulence genes, such as
pthA
of
X. citri
subsp.
citri
. Although D12 had a growth rate similar to that of the wild-type strain in nutrient broth, no D12 population became established in the intercellular spaces of citrus leaves. Coinoculation of a
galU
mutant with the wild-type strain did not promote growth of the
galU
mutant
in planta
. Defects in EPS and CPS production, pathogenicity, and growth
in planta
of the
galU
mutant were complemented to the wild-type level using plasmid pCGU2.1 containing an intact
galU
gene. These data indicate that the
galU
gene contributes to
X. citri
subsp.
citri
growth in intercellular spaces and is involved in EPS and CPS synthesis and biofilm formation.
The RFX Protein RfxA Is an Essential Regulator of Growth and Morphogenesis in Penicillium marneffei
Authors: Bugeja Hayley E. , Hynes Michael J. , Andrianopoulos Alex 
Published: January 2010

ABSTRACT

Fungi are small eukaryotes capable of undergoing multiple complex developmental programs. The opportunistic human pathogen
Penicillium marneffei
is a dimorphic fungus, displaying vegetative (proliferative) multicellular hyphal growth at 25°C and unicellular yeast growth at 37°C.
P. marneffei
also undergoes asexual development into differentiated multicellular conidiophores bearing uninucleate spores. These morphogenetic processes require regulated changes in cell polarity establishment, cell cycle dynamics, and nuclear migration. The RFX (regulatory factor X) proteins are a family of transcriptional regulators in eukaryotes. We sought to determine how the sole
P. marneffei
RFX protein, RfxA, contributes to the regulation of morphogenesis. Attempts to generate a haploid
rfxA
deletion strain were unsuccessful, but we did isolate an
rfxA
+
/
rfxA
Δ heterozygous diploid strain. The role of RfxA was assessed using conditional overexpression, RNA interference (RNAi), and the production of dominant interfering alleles. Reduced RfxA function resulted in defective mitoses during growth at 25°C and 37°C. This was also observed for the heterozygous diploid strain during growth at 37°C. In contrast, overexpression of
rfxA
caused growth arrest during conidial germination. The data show that
rfxA
must be precisely regulated for appropriate nuclear division and to maintain genome integrity. Perturbations in
rfxA
expression also caused defects in cellular proliferation and differentiation. The data suggest a role for RfxA in linking cellular division with morphogenesis, particularly during conidiation and yeast growth, where the uninucleate state of these cell types necessitates coupling of nuclear and cellular division tighter than that observed during multinucleate hyphal growth.
The TEA Transcription Factor Tec1 Confers Promoter-Specific Gene Regulation by Ste12-Dependent and -Independent Mechanisms
Authors: Heise Barbara , van der Felden Julia , Kern Sandra , Malcher Mario , Brückner Stefan , Mösch Hans-Ulrich 
Published: January 2010

ABSTRACT

In
Saccharomyces cerevisiae
, the TEA transcription factor Tec1 is known to regulate target genes together with a second transcription factor, Ste12. Tec1-Ste12 complexes can activate transcription through Tec1 binding sites (TCSs), which can be further combined with Ste12 binding sites (PREs) for cooperative DNA binding. However, previous studies have hinted that Tec1 might regulate transcription also without Ste12. Here, we show that
in vivo
, physiological amounts of Tec1 are sufficient to stimulate TCS-mediated gene expression and transcription of the
FLO11
gene in the absence of Ste12.
In vitro
, Tec1 is able to bind TCS elements with high affinity and specificity without Ste12. Furthermore, Tec1 contains a C-terminal transcriptional activation domain that confers Ste12-independent activation of TCS-regulated gene expression. On a genome-wide scale, we identified 302 Tec1 target genes that constitute two distinct classes. A first class of 254 genes is regulated by Tec1 in a Ste12-dependent manner and is enriched for genes that are bound by Tec1 and Ste12
in vivo
. In contrast, a second class of 48 genes can be regulated by Tec1 independently of Ste12 and is enriched for genes that are bound by the stress transcription factors Yap6, Nrg1, Cin5, Skn7, Hsf1, and Msn4. Finally, we find that combinatorial control by Tec1-Ste12 complexes stabilizes Tec1 against degradation. Our study suggests that Tec1 is able to regulate TCS-mediated gene expression by Ste12-dependent and Ste12-independent mechanisms that enable promoter-specific transcriptional control.
Farnesol Induces Hydrogen Peroxide Resistance in Candida albicans Yeast by Inhibiting the Ras-Cyclic AMP Signaling Pathway
Authors: Deveau Aurélie , Piispanen Amy E. , Jackson Angelyca A. , Hogan Deborah A. 
Published: January 2010

ABSTRACT

Farnesol, a
Candida albicans
cell-cell signaling molecule that participates in the control of morphology, has an additional role in protection of the fungus against oxidative stress. In this report, we show that although farnesol induces the accumulation of intracellular reactive oxygen species (ROS), ROS generation is not necessary for the induction of catalase (Cat1)-mediated oxidative-stress resistance. Two antioxidants, α-tocopherol and, to a lesser extent, ascorbic acid effectively reduced intracellular ROS generation by farnesol but did not alter farnesol-induced oxidative-stress resistance. Farnesol inhibits the Ras1-adenylate cyclase (Cyr1) signaling pathway to achieve its effects on morphology under hypha-inducing conditions, and we demonstrate that farnesol induces oxidative-stress resistance by a similar mechanism. Strains lacking either Ras1 or Cyr1 no longer exhibited increased protection against hydrogen peroxide upon preincubation with farnesol. While we also observed the previously reported increase in the phosphorylation level of Hog1, a known regulator of oxidative-stress resistance, in the presence of farnesol, the
hog1
/
hog1
mutant did not differ from wild-type strains in terms of farnesol-induced oxidative-stress resistance. Analysis of Hog1 levels and its phosphorylation states in different mutant backgrounds indicated that mutation of the components of the Ras1-adenylate cyclase pathway was sufficient to cause an increase of Hog1 phosphorylation even in the absence of farnesol or other exogenous sources of oxidative stress. This finding indicates the presence of unknown links between these signaling pathways. Our results suggest that farnesol effects on the Ras-adenylate cyclase cascade are responsible for many of the observed activities of this fungal signaling molecule.
Sterol Regulatory Element Binding Proteins in Fungi: Hypoxic Transcription Factors Linked to Pathogenesis
Authors: Bien Clara M. , Espenshade Peter J. 
Published: January 2010

ABSTRACT

Sterol regulatory element binding proteins (SREBPs) are membrane-bound transcription factors whose proteolytic activation is controlled by the cellular sterol concentration. Mammalian SREBPs are activated in cholesterol-depleted cells and serve to regulate cellular lipid homeostasis. Recent work demonstrates that SREBP is functionally conserved in fungi. While the ability to respond to sterols is conserved, fungal SREBPs are hypoxic transcription factors required for adaptation to a low-oxygen environment. In the fission yeast
Schizosaccharomyces pombe
, oxygen regulates the SREBP homolog Sre1 by independently controlling both its proteolytic activation and its degradation. SREBP is also required for adaptation to hypoxia in the human pathogens
Cryptococcus neoformans
and
Aspergillus fumigatus
. In these organisms, SREBP is required for virulence and resistance to antifungal drugs, making the SREBP pathway a potential target for antifungal therapy.
Bug22p, a Conserved Centrosomal/Ciliary Protein Also Present in Higher Plants, Is Required for an Effective Ciliary Stroke in Paramecium
Authors: Laligné C. , Klotz C. , Garreau de Loubresse N. , Lemullois M. , Hori M. , Laurent F. X. , Papon J. F. , Louis B. , Cohen J. , Koll F. 
Published: January 2010

ABSTRACT

Centrioles, cilia, and flagella are ancestral conserved organelles of eukaryotic cells. Among the proteins identified in the proteomics of ciliary proteins in
Paramecium
, we focus here on a protein, Bug22p, previously detected by cilia and basal-body high-throughput studies but never analyzed
per se
. Remarkably, this protein is also present in plants, which lack centrioles and cilia. Bug22p sequence alignments revealed consensus positions that distinguish species with centrioles/cilia from plants. In
Paramecium
, antibody and green fluorescent protein (GFP) fusion labeling localized Bug22p in basal bodies and cilia, and electron microscopy immunolabeling refined the localization to the terminal plate of the basal bodies, the transition zone, and spots along the axoneme, preferentially between the membrane and the microtubules. RNA interference (RNAi) depletion of Bug22p provoked a strong decrease in swimming speed, followed by cell death after a few days. High-speed video microscopy and morphological analysis of Bug22p-depleted cells showed that the protein plays an important role in the efficiency of ciliary movement by participating in the stroke shape and rigidity of cilia. The defects in cell swimming and growth provoked by RNAi can be complemented by expression of human Bug22p. This is the first reported case of complementation by a human gene in a ciliate.
Complete Genome Sequence of the Plant Pathogen
Erwinia amylovora
Strain ATCC 49946
Authors: Sebaihia M. , Bocsanczy A. M. , Biehl B. S. , Quail M. A. , Perna N. T. , Glasner J. D. , DeClerck G. A. , Cartinhour S. , Schneider D. J. , Bentley S. D. , Parkhill J. , Beer S. V. 
Published: January 2010

ABSTRACT

Erwinia amylovora
causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
Alternative Route for Glyoxylate Consumption during Growth on Two-Carbon Compounds by
Methylobacterium extorquens
AM1
Authors: Okubo Yoko , Yang Song , Chistoserdova Ludmila , Lidstrom Mary E. 
Published: January 2010

ABSTRACT

Methylobacterium extorquens
AM1 is a facultative methylotroph capable of growth on both single-carbon and multicarbon compounds. Mutants defective in a pathway involved in converting acetyl-coenzyme A (CoA) to glyoxylate (the ethylmalonyl-CoA pathway) are unable to grow on both C
1
and C
2
compounds, showing that both modes of growth have this pathway in common. However, growth on C
2
compounds via the ethylmalonyl-CoA pathway should require glyoxylate consumption via malate synthase, but a mutant lacking malyl-CoA/β-methylmalyl-CoA lyase activity (MclA1) that is assumed to be responsible for malate synthase activity still grows on C
2
compounds. Since glyoxylate is toxic to this bacterium, it seemed likely that a system is in place to keep it from accumulating. In this study, we have addressed this question and have shown by microarray analysis, mutant analysis, metabolite measurements, and
13
C-labeling experiments that
M. extorquens
AM1 contains an additional malyl-CoA/β-methylmalyl-CoA lyase (MclA2) that appears to take part in glyoxylate metabolism during growth on C
2
compounds. In addition, an alternative pathway appears to be responsible for consuming part of the glyoxylate, converting it to glycine, methylene-H
4
F, and serine. Mutants lacking either pathway have a partial defect for growth on ethylamine, while mutants lacking both pathways are unable to grow appreciably on ethylamine. Our results suggest that the malate synthase reaction is a bottleneck for growth on C
2
compounds by this bacterium, which is partially alleviated by this alternative route for glyoxylate consumption. This strategy of multiple enzymes/pathways for the consumption of a toxic intermediate reflects the metabolic versatility of this facultative methylotroph and is a model for other metabolic networks involving high flux through toxic intermediates.
A Superfamily 3 DNA Helicase Encoded by Plasmid pSSVi from the Hyperthermophilic ArchaeonSulfolobus solfataricusUnwinds DNA as a Higher-Order Oligomer and Interacts with Host Primase
Authors: Guo Xin , Huang Li 
Published: January 2010

ABSTRACTReplication proteins encoded by nonconjugative plasmids from the hyperthermophilic archaea of the orderSulfolobalesshow great diversity in amino acid sequence. We have biochemically characterized ORF735, a replication protein from pSSVi, an integrative nonconjugative plasmid fromSulfolobus solfataricusP2. We show that ORF735 is a DNA helicase of superfamily 3. It unwound double-stranded DNA (dsDNA) in a 3′-to-5′ direction in the presence of ATP over a wide range of temperatures, from 37°C to 75°C, and possessed DNA-stimulated ATPase activity. ORF735 existed in solution as a salt-stable dimer and was capable of assembling into a salt-sensitive oligomer that was significantly larger than a hexamer in the presence of a divalent cation (Mg2+) and an adenine nucleotide (ATP, dATP, or ADP) or its analog (ATPγS or AMPPNP). Both N-terminal and C-terminal portions of ORF735 (87 and 160 amino acid residues, respectively, in size) were required for protein dimerization but dispensable for the formation of the higher-order oligomer. The protein unwound DNA only as a large oligomer. Yeast two-hybrid and coimmunoprecipitation assays revealed that ORF735 interacted with the noncatalytic subunit of host primase. These findings provide clues to the functional role of ORF735 in pSSVi DNA replication.
Tn502and Tn512AreresSite Hunters That Provide Evidence of Resolvase-Independent Transposition to Random Sites
Authors: Petrovski Steve , Stanisich Vilma A. 
Published: January 2010

ABSTRACTIn this study, we report on the transposition behavior of the mercury(II) resistance transposons Tn502and Tn512, which are members of the Tn5053family. These transposons exhibit targeted and oriented insertion in theparregion of plasmid RP1, sincepar-encoded components, namely, the ParA resolvase and its cognateresregion, are essential for such transposition. Tn502and, under some circumstances, Tn512can transpose whenparis absent, providing evidence for an alternative,par-independent pathway of transposition. We show that the alternative pathway proceeds by a two-step replicative process involving random target selection and orientation of insertion, leading to the formation of cointegrates as the predominant product of the first stage of transposition. Cointegrates remain unresolved because the transposon-encoded (TniR) recombination system is relatively inefficient, as is the host-encoded (RecA) system. In the presence of theres-ParA recombination system, TniR-mediated (and RecA-mediated) cointegrate resolution is highly efficient, enabling resolution both of cointegrates involving functional transposons (Tn502and Tn512) and of defective elements (In0 and In2). These findings implicate the target-encoded accessory functions in the second stage of transposition as well as in the first. We also show that thepar-independent pathway enables the formation of deletions in the target molecule.