bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vegetation and Soil Environment Influence the Spatial Distribution of Root-Associated Fungi in a Mature Beech-Maple Forest
Authors: Burke David J. , López-Gutiérrez Juan C. , Smemo Kurt A. , Chan Charlotte R. 
Published: October 2009

ABSTRACT
Although the level of diversity of root-associated fungi can be quite high, the effect of plant distribution and soil environment on root-associated fungal communities at fine spatial scales has received little attention. Here, we examine how soil environment and plant distribution affect the occurrence, diversity, and community structure of root-associated fungi at local patch scales within a mature forest. We used terminal restriction fragment length polymorphism and sequence analysis to detect 63 fungal species representing 28 different genera colonizing tree root tips. At least 32 species matched previously identified mycorrhizal fungi, with the remaining fungi including both saprotrophic and parasitic species. Root fungal communities were significantly different between June and September, suggesting a rapid temporal change in root fungal communities. Plant distribution affected root fungal communities, with some root fungi positively correlated with tree diameter and herbaceous-plant coverage. Some aspects of the soil environment were correlated with root fungal community structure, with the abundance of some root fungi positively correlated with soil pH and moisture content in June and with soil phosphorous (P) in September. Fungal distribution and community structure may be governed by plant-soil interactions at fine spatial scales within a mature forest. Soil P may play a role in structuring root fungal communities at certain times of the year.
Resistance of
Saccharomyces cerevisiae
to High Concentrations of Furfural Is Based on NADPH-Dependent Reduction by at Least Two Oxireductases
Authors: Heer Dominik , Heine Daniel , Sauer Uwe 
Published: October 2009

ABSTRACT

Biofuels derived from lignocellulosic biomass hold promises for a sustainable fuel economy, but several problems hamper their economical feasibility. One important problem is the presence of toxic compounds in processed lignocellulosic hydrolysates, with furfural as a key toxin. While
Saccharomyces cerevisiae
has some intrinsic ability to reduce furfural to the less-toxic furfuryl alcohol, higher resistance is necessary for process conditions. By comparing an evolved, furfural-resistant strain and its parent in microaerobic, glucose-limited chemostats at increasing furfural challenge, we elucidate key mechanism and the molecular basis of both natural and high-level furfural resistance. At lower concentrations of furfural, NADH-dependent oxireductases are the main defense mechanism. At furfural concentrations above 15 mM, however,
13
C-flux and global array-based transcript analysis demonstrated that the NADPH-generating flux through the pentose phosphate pathway increases and that NADPH-dependent oxireductases become the major resistance mechanism. The transcript analysis further revealed that iron transmembrane transport is upregulated in response to furfural. While these responses occur in both strains, high-level resistance in the evolved strain was based on strong induction of
ADH7
, the uncharacterized open reading frame (ORF)
YKL071W
, and four further, likely NADPH-dependent, oxireductases. By overexpressing the
ADH7
gene and the ORF
YKL071W
, we inversely engineered significantly increased furfural resistance in the parent strain, thereby demonstrating that these two enzymes are key elements of the resistance phenotype.
Distribution ofIn VitroFermentation Ability of Lacto-N-Biose I, a Major Building Block of Human Milk Oligosaccharides, in Bifidobacterial Strains
Authors: Xiao Jin-zhong , Takahashi Sachiko , Nishimoto Mamoru , Odamaki Toshitaka , Yaeshima Tomoko , Iwatsuki Keiji , Kitaoka Motomitsu 
Published: October 2009

ABSTRACTThis study investigated the potential utilization of lacto-N-biose I (LNB) by individual strains of bifidobacteria. LNB is a building block for the human milk oligosaccharides, which have been suggested to be a factor for selective growth of bifidobacteria. A total of 208 strains comprising 10 species and 4 subspecies were analyzed for the presence of the galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) gene (lnpA) and examined for growth when LNB was used as the sole carbohydrate source. While all strains ofBifidobacterium longumsubsp.longum,B. longumsubsp.infantis,B. breve, andB. bifidumwere able to grow on LNB, none of the strains ofB. adolescentis,B. catenulatum,B. dentium,B. angulatum,B. animalissubsp.lactis, andB. thermophilumshowed any growth. In addition, some strains ofB. pseudocatenulatum,B. animalissubsp.animalis, andB. pseudolongumexhibited the ability to utilize LNB. With the exception forB. pseudocatenulatum, the presence oflnpAcoincided with LNB utilization in almost all strains. These results indicate that bifidobacterial species, which are the predominant species found in infant intestines, are potential utilizers of LNB. These findings support the hypothesis that GLNBP plays a key role in the colonization of bifidobacteria in the infant intestine.
Genome Shuffling in
Clostridium diolis
DSM 15410 for Improved 1,3-Propanediol Production
Authors: Otte Burkhard , Grunwaldt Eike , Mahmoud Osama , Jennewein Stefan 
Published: October 2009

ABSTRACT

Several microorganisms are known for their efficient anaerobic conversion of glycerol to 1,3-propanediol, with
Clostridium diolis
DSM 15410 as one of the better performers in terms of molar yield and volumetric productivity. However, this performance is still insufficient to compete with established chemical processes. Previous studies have shown that high concentrations of 1,3-propanediol, glycerol, and fermentation side products can limit the productivity of
C. diolis
DSM 15410. Here, we describe the use of genome shuffling for improved 1,3-propanediol fermentation by the strict anaerobe
C. diolis
DSM 15410. By using chemical mutagenesis, strains with superior substrate and product tolerance levels were isolated and higher product yields were obtained. These superior strains were then used for genome shuffling and selection for 1,3-propanediol and organic acid tolerance. After four rounds of genome shuffling and selection, significant improvements were observed, with one strain attaining a 1,3-propanediol volumetric yield of 85 g/liter. This result represents an 80% improvement compared to the yield from the parental wild-type strain.
Bradyrhizobia Nodulating the
Acacia mangium
×
A. auriculiformis
Interspecific Hybrid Are Specific and Differ from Those Associated with Both Parental Species
Authors: Le Roux Christine , Tentchev Diana , Prin Yves , Goh Doreen , Japarudin Yani , Perrineau Marie-Mathilde , Duponnois Robin , Domergue Odile , de Lajudie Philippe , Galiana Antoine 
Published: October 2009

ABSTRACT

In the context of an increasing utilization of the interspecific hybrid
Acacia mangium
×
A. auriculiformis
as a plantation tree in the tropical humid zone, its symbiotic characterization was carried out in comparison with that of its two parental species. Rhizobium strains of diverse geographical origins were isolated from root nodules of the hybrid and its parents. Almost all
Acacia
hybrid isolates were fast growing on yeast extract-mannitol medium, in contrast to those isolated from both parental species, which were mostly slow growing. The rhizobium strains were characterized through partial sequencing of the rRNA operon. In the phylogenetic tree, almost all strains isolated from the hybrid were grouped together in a clade close to
Bradyrhizobium japonicum
, while all strains isolated from both parental species were close to
Bradyrhizobium elkanii
. Inoculation experiments performed under in vitro or greenhouse conditions showed that all strains were infective with their original hosts but exhibited very variable degrees of effectivity according to the host plant tested. Thus, homologous strain-host associations were more effective than heterologous ones. This shows that there is still a high potential for isolating and testing new strains from hybrids to be used as inoculants in the context of large-scale afforestation programs.
Development of a Fluorescent In Situ Method for Visualization of Enteric Viruses
Authors: Rawsthorne Helen , Phister Trevor G. , Jaykus Lee-Ann 
Published: October 2009

ABSTRACT
Studying the interactions between enteric pathogens and their environment is important to improving our understanding of their persistence and transmission. However, this remains challenging in large part because of difficulties associated with tracking pathogens in their natural environment(s). In this study, we report a fluorescent labeling strategy which was applied to murine norovirus (MNV-1), a human norovirus surrogate, and hepatitis A virus (HAV). Specifically, streptavidin-labeled Quantum dots (Q-Dots) were bound to biotinylated capsids of MNV-1 and HAV (bio-MNV-1 and bio-HAV); the process was confirmed by using a sandwich-type approach in which streptavidin-bound plates were reacted with biotinylated virus followed by a secondary binding to Q-Dots with an emission range of 635 to 675 nm (Q-Dots 655). The assay demonstrated a relative fluorescence of 528 ± 48.1 and 112 ± 8.6 for bio-MNV-1 and control MNV-1, respectively. The biotinylation process did not impact virus infectivity, nor did it interfere with the interactions between the virus and host cells or model produce items. Using fluorescent microscopy, it was possible to visualize both bio-HAV and bio-MNV-1 attached to the surfaces of permissive mammalian cells and green onion tissue. The method provides a powerful tool for the labeling and detection of enteric viruses (and their surrogates) which can be used to track virus behavior in situ.
Functional Characterization of Lpt3 and Lpt6, the Inner-Core Lipooligosaccharide Phosphoethanolamine Transferases from
Neisseria meningitidis
Authors: Wenzel Cory Q. , St. Michael Frank , Stupak Jacek , Li Jianjun , Cox Andrew D. , Richards James C. 
Published: October 2009

ABSTRACT

The lipooligosaccharide (LOS) of
Neisseria meningitidis
contains heptose (Hep) residues that are modified with phosphoethanolamine (PEtn) at the 3 (3-PEtn) and/or 6 (6-PEtn) position. The
lpt3
(NMB2010) and
lpt6
(NMA0408) genes of
N. meningitidis
, which are proposed to encode the required HepII 3- and 6-PEtn transferases, respectively, were cloned and overexpressed as C-terminally polyhistidine-tagged fusion proteins in
Escherichia coli
and found to localize to the inner membrane, based on sucrose density gradient centrifugation. Lpt3-His
6
and Lpt6-His
6
were purified from Triton X-100-solubilized membranes by nickel chelation chromatography, and dot blot analysis of enzymatic reactions with 3-PEtn- and 6-PEtn-specific monoclonal antibodies demonstrated conclusively that Lpt3 and Lpt6 are phosphatidylethanolamine-dependent LOS HepII 3- and 6-PEtn transferases, respectively, and that both enzymes are capable of transferring PEtn to both fully acylated LOS and de-O-acylated (de-O-Ac) LOS. Further enzymatic studies using capillary electrophoresis-mass spectrometry (MS) demonstrated that both Lpt3 and Lpt6 are capable of transferring PEtn to de-O-Ac LOS molecules already containing PEtn at the 6 and 3 positions of HepII, respectively, demonstrating that there is no obligate order of PEtn addition in the generation of 3,6-di-PEtn LOS moieties in vitro.
Transcriptional and Functional Analysis of the
Neisseria gonorrhoeae
Fur Regulon
Authors: Jackson Lydgia A. , Ducey Thomas F. , Day Michael W. , Zaitshik Jeremy B. , Orvis Joshua , Dyer David W. 
Published: October 2009

ABSTRACT

To ensure survival in the host, bacteria have evolved strategies to acquire the essential element iron. In
Neisseria gonorrhoeae
, the ferric uptake regulator Fur regulates metabolism through transcriptional control of iron-responsive genes by binding conserved Fur box (FB) sequences in promoters during iron-replete growth. Our previous studies showed that Fur also controls the transcription of secondary regulators that may, in turn, control pathways important to pathogenesis, indicating an indirect role for Fur in controlling these downstream genes. To better define the iron-regulated cascade of transcriptional control, we combined three global strategies—temporal transcriptome analysis, genomewide in silico FB prediction, and Fur titration assays (FURTA)—to detect genomic regions able to bind Fur in vivo. The majority of the 300 iron-repressed genes were predicted to be of unknown function, followed by genes involved in iron metabolism, cell communication, and intermediary metabolism. The 107 iron-induced genes encoded hypothetical proteins or energy metabolism functions. We found 28 predicted FBs in FURTA-positive clones in the promoters and within the open reading frames of iron-repressed genes. We found lower levels of conservation at critical thymidine residues involved in Fur binding in the FB sequence logos of FURTA-positive clones with intragenic FBs than in the sequence logos generated from FURTA-positive promoter regions. In electrophoretic mobility shift assay studies, intragenic FBs bound Fur with a lower affinity than intergenic FBs. Our findings further indicate that transcription under iron stress is indirectly controlled by Fur through 12 potential secondary regulators.
Molecular Basis for the Role of
Staphylococcus aureus
Penicillin Binding Protein 4 in Antimicrobial Resistance
Authors: Navratna Vikas , Nadig Savitha , Sood Varun , Prasad K. , Arakere Gayathri , Gopal B. 
Published: October 2009

ABSTRACT

Penicillin binding proteins (PBPs) are membrane-associated proteins that catalyze the final step of murein biosynthesis. These proteins function as either transpeptidases or carboxypeptidases and in a few cases demonstrate transglycosylase activity. Both transpeptidase and carboxypeptidase activities of PBPs occur at the
d
-Ala-
d
-Ala terminus of a murein precursor containing a disaccharide pentapeptide comprising
N
-acetylglucosamine and
N
-acetyl-muramic acid-
l
-Ala-
d
-Glu-
l
-Lys-
d
-Ala-
d
-Ala. β-Lactam antibiotics inhibit these enzymes by competing with the pentapeptide precursor for binding to the active site of the enzyme. Here we describe the crystal structure, biochemical characteristics, and expression profile of PBP4, a low-molecular-mass PBP from
Staphylococcus aureus
strain COL. The crystal structures of PBP4-antibiotic complexes reported here were determined by molecular replacement, using the atomic coordinates deposited by the New York Structural Genomics Consortium. While the
pbp4
gene is not essential for the viability of
S. aureus
, the knockout phenotype of this gene is characterized by a marked reduction in cross-linked muropeptide and increased vancomycin resistance. Unlike other PBPs, we note that expression of PBP4 was not substantially altered under different experimental conditions, nor did it change across representative hospital- or community-associated strains of
S. aureus
that were examined.
In vitro
data on purified recombinant
S. aureus
PBP4 suggest that it is a β-lactamase and is not trapped as an acyl intermediate with β-lactam antibiotics. Put together, the expression analysis and biochemical features of PBP4 provide a framework for understanding the function of this protein in
S. aureus
and its role in antimicrobial resistance.
The AraC/XylS Family Activator RhaS Negatively Autoregulates
rhaSR
Expression by Preventing Cyclic AMP Receptor Protein Activation
Authors: Wickstrum Jason R. , Skredenske Jeff M. , Balasubramaniam Vinitha , Jones Kyle , Egan Susan M. 
Published: October 2009

ABSTRACT

The
Escherichia coli
RhaR protein activates expression of the
rhaSR
operon in the presence of its effector,
l
-rhamnose. The resulting RhaS protein (plus
l
-rhamnose) activates expression of the
l
-rhamnose catabolic and transport operons,
rhaBAD
and
rhaT
, respectively. Here, we further investigated our previous finding that
rhaS
deletion resulted in a threefold increase in
rhaSR
promoter activity, suggesting RhaS negative autoregulation of
rhaSR
. We found that RhaS autoregulation required the cyclic AMP receptor protein (CRP) binding site at
rhaSR
and that RhaS was able to bind to the RhaR binding site at
rhaSR
. In contrast to the expected repression, we found that in the absence of both RhaR and the CRP binding site at the
rhaSR
promoter, RhaS activated expression to a level comparable with RhaR activation of the same promoter. However, when the promoter included the RhaR and CRP binding sites, the level of activation by RhaS and CRP was much lower than that by RhaR and CRP, suggesting that CRP could not fully coactivate with RhaS. Taken together, our results indicate that RhaS negative autoregulation involves RhaS competition with RhaR for binding to the RhaR binding site at
rhaSR
. Although RhaS and RhaR activate
rhaSR
transcription to similar levels, CRP cannot effectively coactivate with RhaS. Therefore, once RhaS reaches a relatively high protein concentration, presumably sufficient to saturate the RhaS-activated promoters, there will be a decrease in
rhaSR
transcription. We propose a model in which differential DNA bending by RhaS and RhaR may be the basis for the difference in CRP coactivation.
Three-Dimensional Structure of Different Functional Forms of the
Vibrio cholerae
Hemolysin Oligomer: a Cryo-Electron Microscopic Study
Authors: Dutta Somnath , Mazumdar Budhaditya , Banerjee Kalyan K. , Ghosh Amar N. 
Published: October 2009

ABSTRACT

Vibrio cholerae
hemolysin (HlyA) is a 65-kDa water-soluble pore-forming toxin that causes lysis of eukaryotic cells by destroying selective permeability of the plasma membrane bilayer. The HlyA monomer self-assembles on the target cell surface to the more stable β-barrel amphipathic heptamer, which inserts into the membrane bilayer to form a diffusion channel. Deletion of the 15-kDa β-prism lectin domain at the C terminus generates a 50-kDa hemolysin variant (HlyA50) with an ∼1,000-fold decrease in hemolytic activity. Because functional differences are eventually dictated by structural differences, we determined three-dimensional structures of 65- and 50-kDa HlyA oligomers, using cryo-electron microscopy and single-particle methods. Our study clearly shows that the HlyA oligomer has sevenfold symmetry but that the HlyA50 oligomer is an asymmetric molecule. The HlyA oligomer has bowl-like, arm-like, and ring-like domains. The bowl-like domain is coupled with the ring-like domain, and seven side openings are present just beneath the ring-like domain. Although a central channel is present in both HlyA and HlyA50 oligomers, they differ in pore size as well as in shape of the molecules and channel. These structural differences may be relevant to the striking difference in efficiencies of functional channel formation by the two toxin forms.
Crystal Structures of the Lumazine Protein fromPhotobacterium kishitaniiin Complexes with the Authentic Chromophore, 6,7-Dimethyl- 8-(1′-d-Ribityl) Lumazine, and Its Analogues, Riboflavin and Flavin Mononucleotide, at High Resolution
Authors: Sato Yuichi , Shimizu Satoshi , Ohtaki Akashi , Noguchi Keiichi , Miyatake Hideyuki , Dohmae Naoshi , Sasaki Satoshi , Odaka Masafumi , Yohda Masafumi 
Published: October 2009

ABSTRACTLumazine protein (LumP) is a fluorescent accessory protein having 6,7-dimethyl-8-(1′-d-ribityl) lumazine (DMRL) as its authentic chromophore. It modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength. To obtain structural information on the native structure as well as the interaction with bacterial luciferase, we have determined the crystal structures of LumP fromPhotobacterium kishitaniiin complexes with DMRL and its analogues, riboflavin (RBF) and flavin mononucleotide (FMN), at resolutions of 2.00, 1.42, and 2.00 Å. LumP consists of two β barrels that have nearly identical folds, the N-terminal and C-terminal barrels. The structures of LumP in complex with all of the chromophores studied are all essentially identical, except around the chromophores. In all of the structures, the chromophore is tethered to the narrow cavity via many hydrogen bonds in the N-terminal domain. These are absent in the C-terminal domain. Hydrogen bonding in LumP-FMN is decreased in comparison with that in LumP-RBF because the phosphate moiety of FMN protrudes out of the narrow cavity. In LumP-DMRL, the side chain of Gln65 is close to the ring system, and a new water molecule that stabilizes the ligand is observed near Ser48. Therefore, DMRL packs more tightly in the ligand-binding site than RBF or FMN. A docking simulation of bacterial luciferase and LumP suggests that the chromophore is located close enough for direct energy transfer to occur. Moreover, the surface potentials around the ligand-binding sites of LumP and bacterial luciferase exhibit complementary charge distributions, which would have a significant effect on the interaction between LumP and luciferase.
Pantothenate Kinase from the Thermoacidophilic Archaeon
Picrophilus torridus
Authors: Takagi Masakazu , Tamaki Hideyuki , Miyamoto Yukiko , Leonardi Roberta , Hanada Satoshi , Jackowski Suzanne , Chohnan Shigeru 
Published: October 2009

ABSTRACT

Pantothenate kinase (CoaA) catalyzes the first step of the coenzyme A (CoA) biosynthetic pathway and controls the intracellular concentrations of CoA through feedback inhibition in bacteria. An alternative enzyme found in archaea, pantoate kinase, is missing in the order
Thermoplasmatales
. The PTO0232 gene from
Picrophilus torridus
, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type I CoaA. The cloned gene clearly complements the poor growth of the temperature-sensitive
Escherichia coli
CoaA mutant strain ts9, and the recombinant protein expressed in
E. coli
cells transfers phosphate to pantothenate at pH 5 and 55°C. In contrast to
E. coli
CoaA, the
P. torridus
enzyme is refractory to feedback regulation by CoA, indicating that in
P. torridus
cells the CoA levels are not regulated by the CoaA step. These data suggest the existence of two subtypes within the class of prokaryotic type I CoaAs.