bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of OsbZIP23 as a Key Player of the Basic Leucine Zipper Transcription Factor Family for Conferring Abscisic Acid Sensitivity and Salinity and Drought Tolerance in Rice
Authors: Xiang Yong , Tang Ning , Du Hao , Ye Haiyan , Xiong Lizhong 
Published: October 2008

AbstractOsbZIP23 is a member of the basic leucine zipper (bZIP) transcription factor family in rice (Oryza sativa). Expression of OsbZIP23 is strongly induced by a wide spectrum of stresses, including drought, salt, abscisic acid (ABA), and polyethylene glycol treatments, while other stress-responsive genes of this family are slightly induced only by one or two of the stresses. Transactivation assay in yeast demonstrated that OsbZIP23 functions as a transcriptional activator, and the sequences at the N terminus (amino acids 1–59) and a region close to the C terminus (amino acids 210–240) are required for the transactivation activity. Transient expression of OsbZIP23-green fluorescent protein in onion (Allium cepa) cells revealed a nuclear localization of the protein. Transgenic rice overexpressing OsbZIP23 showed significantly improved tolerance to drought and high-salinity stresses and sensitivity to ABA. On the other hand, a null mutant of this gene showed significantly decreased sensitivity to a high concentration of ABA and decreased tolerance to high-salinity and drought stress, and this phenotype can be complemented by transforming the OsbZIP23 back into the mutant. GeneChip and real-time polymerase chain reaction analyses revealed that hundreds of genes were up- or down-regulated in the rice plants overexpressing OsbZIP23. More than half of these genes have been annotated or evidenced for their diverse functions in stress response or tolerance. In addition, more than 30 genes that are possible OsbZIP23-specific target genes were identified based on the comparison of the expression profiles in the overexpressor and the mutant of OsbZIP23. Collectively, these results indicate that OsbZIP23 functions as a transcriptional regulator that can regulate the expression of a wide spectrum of stress-related genes in response to abiotic stresses through an ABA-dependent regulation pathway. We propose that OsbZIP23 is a major player of the bZIP family in rice for conferring ABA-dependent drought and salinity tolerance and has high potential usefulness in genetic improvement of stress tolerance.
Novel Proteins, Putative Membrane Transporters, and an Integrated Metabolic Network Are Revealed by Quantitative Proteomic Analysis of Arabidopsis Cell Culture Peroxisomes
Authors: Eubel Holger , Meyer Etienne H. , Taylor Nicolas L. , Bussell John D. , O'Toole Nicholas , Heazlewood Joshua L. , Castleden Ian , Small Ian D. , Smith Steven M. , Millar A. Harvey 
Published: October 2008

AbstractPeroxisomes play key roles in energy metabolism, cell signaling, and plant development. A better understanding of these important functions will be achieved with a more complete definition of the peroxisome proteome. The isolation of peroxisomes and their separation from mitochondria and other major membrane systems have been significant challenges in the Arabidopsis (Arabidopsis thaliana) model system. In this study, we present new data on the Arabidopsis peroxisome proteome obtained using two new technical advances that have not previously been applied to studies of plant peroxisomes. First, we followed density gradient centrifugation with free-flow electrophoresis to improve the separation of peroxisomes from mitochondria. Second, we used quantitative proteomics to identify proteins enriched in the peroxisome fractions relative to mitochondrial fractions. We provide evidence for peroxisomal localization of 89 proteins, 36 of which have not previously been identified in other analyses of Arabidopsis peroxisomes. Chimeric green fluorescent protein constructs of 35 proteins have been used to confirm their localization in peroxisomes or to identify endoplasmic reticulum contaminants. The distribution of many of these peroxisomal proteins between soluble, membrane-associated, and integral membrane locations has also been determined. This core peroxisomal proteome from nonphotosynthetic cultured cells contains a proportion of proteins that cannot be predicted to be peroxisomal due to the lack of recognizable peroxisomal targeting sequence 1 (PTS1) or PTS2 signals. Proteins identified are likely to be components in peroxisome biogenesis, β-oxidation for fatty acid degradation and hormone biosynthesis, photorespiration, and metabolite transport. A considerable number of the proteins found in peroxisomes have no known function, and potential roles of these proteins in peroxisomal metabolism are discussed. This is aided by a metabolic network analysis that reveals a tight integration of functions and highlights specific metabolite nodes that most probably represent entry and exit metabolites that could require transport across the peroxisomal membrane.
A Genome-Wide and Metabolic Analysis Determined the Adaptive Response of Arabidopsis Cells to Folate Depletion Induced by Methotrexate
Authors: Loizeau Karen , De Brouwer Veerle , Gambonnet Bernadette , Yu Agnès , Renou Jean-Pierre , Van Der Straeten Dominique , Lambert Willy E. , Rébeillé Fabrice , Ravanel Stéphane 
Published: October 2008

Abstract
Control of folate homeostasis is essential to sustain the demand for one-carbon (C1) units that are necessary for major biological functions, including nucleotide synthesis and methylation reactions. In this study, we analyzed the genome-wide and metabolic adaptive response of Arabidopsis (Arabidopsis thaliana) cells to folate depletion induced by the antifolate methotrexate. Drug treatment induced a response typical to xenobiotic stress and important changes in folate content and composition. This resulted in a reduction of cell division and primary energy metabolism that was likely associated with perturbation of nucleotide homeostasis. Through a modification of serine metabolism, folate depletion also induced O-acetylserine accumulation and mimicked sulfur deficiency response. The major adaptive response to folate limitation concerned the composition of the folate pool rather than the intracellular level of cofactors. Thus, no significant change in the expression of genes involved in cofactor synthesis, degradation, or trafficking was observed. However, changes in the distribution of C1 derivative pools and increased expression levels for transcripts coding enzymes manipulating C1 moieties in plastids suggested a reorientation of C1 units toward the synthesis of purine and thymidylate. Also, no genomic or metabolic adaptation was built up to counterbalance the major impairment of the methyl index, which controls the efficiency of methylation reactions in the cell. Together, these data suggested that the metabolic priority of Arabidopsis cells in response to folate limitation was to shuttle the available folate derivatives to the synthesis of nucleotides at the expense of methylation reactions.
Interaction of the WD40 Domain of a Myoinositol Polyphosphate 5-Phosphatase with SnRK1 Links Inositol, Sugar, and Stress Signaling
Authors: Ananieva Elitsa A. , Gillaspy Glenda E. , Ely Amanda , Burnette Ryan N. , Erickson F. Les 
Published: October 2008

AbstractIn plants, myoinositol signaling pathways have been associated with several stress, developmental, and physiological processes, but the regulation of these pathways is largely unknown. In our efforts to better understand myoinositol signaling pathways in plants, we have found that the WD40 repeat region of a myoinositol polyphosphate 5-phosphatase (5PTase13; At1g05630) interacts with the sucrose nonfermenting-1-related kinase (SnRK1.1) in the yeast two-hybrid system and in vitro. Plant SnRK1 proteins (also known as AKIN10/11) have been described as central integrators of sugar, metabolic, stress, and developmental signals. Using mutants defective in 5PTase13, we show that 5PTase13 can act as a regulator of SnRK1 activity and that regulation differs with different nutrient availability. Specifically, we show that under low-nutrient or -sugar conditions, 5PTase13 acts as a positive regulator of SnRK1 activity. In contrast, under severe starvation conditions, 5PTase13 acts as a negative regulator of SnRK1 activity. To delineate the regulatory interaction that occurs between 5PTase13 and SnRK1.1, we used a cell-free degradation assay and found that 5PTase13 is required to reduce the amount of SnRK1.1 targeted for proteasomal destruction under low-nutrient conditions. This regulation most likely involves a 5PTase13-SnRK1.1 interaction within the nucleus, as a 5PTase13:green fluorescent protein was localized to the nucleus. We also show that a loss of function in 5PTase13 leads to nutrient level-dependent reduction of root growth, along with abscisic acid (ABA) and sugar insensitivity. 5ptase13 mutants accumulate less inositol 1,4,5-trisphosphate in response to sugar stress and have alterations in ABA-regulated gene expression, both of which are consistent with the known role of inositol 1,4,5-trisphosphate in ABA-mediated signaling. We propose that by forming a protein complex with SnRK1.1 protein, 5PTase13 plays a regulatory role linking inositol, sugar, and stress signaling.
F-Actin Organization and Pollen Tube Tip Growth inArabidopsisAre Dependent on the Gametophyte-Specific Armadillo Repeat Protein ARO1
Authors: Gebert Marina , Dresselhaus Thomas , Sprunck Stefanie 
Published: October 2008

AbstractThe signal-mediated and spatially controlled assembly and dynamics of actin are crucial for maintaining shape, motility, and tip growth of eukaryotic cells. We report that a novel Armadillo repeat protein in Arabidopsis thaliana, ARMADILLO REPEAT ONLY1 (ARO1), is of fundamental importance for polar growth and F-actin organization in tip-growing pollen tubes. ARO1 is specifically expressed in the vegetative cell of pollen as well as in the egg cell. ARO1-GFP (for green fluorescent protein) fusion proteins accumulate most notably in pollen tube tips and partially colocalize with F-actin in the shank of pollen tubes. ARO1 knockout results in a highly disorganized actin cytoskeleton, growth depolarization, and ultimately tube growth arrest. Tip-localized ARO1-GFP is spatially shifted toward the future site of tip growth, indicating a role of ARO1 in the signaling network controlling tip growth and regulating actin organization. After the pollen tube discharges its contents into the receptive synergid, ARO1-GFP colocalizes with emerging F-actin structures near the site of sperm cell fusion, suggesting additional participation in the mechanism of sperm cell tracking toward the female gametes. The variable localization of ARO1 in the cytoplasm, the nucleus, and at the plasma membrane, however, indicates a multifunctional role like that of β-catenin/Armadillo and the p120 catenins.
Effect of Permeate Drag Force on the Development of a Biofouling Layer in a Pressure-Driven Membrane Separation System
Authors: Eshed L. , Yaron S. , Dosoretz C. G. 
Published: October 2008

ABSTRACT

The effect of permeate flux on the development of a biofouling layer on cross-flow separation membranes was studied by using a bench-scale system consisting of two replicate 100-molecular-weight-cutoff tubular ultrafiltration membrane modules, one that allowed flow of permeate and one that did not (control). The system was inoculated with
Pseudomonas putida
S-12 tagged with a red fluorescent protein and was operated using a laminar flow regimen under sterile conditions with a constant feed of diluted (1:75) Luria-Bertani medium. Biofilm development was studied by using field emission scanning electron microscopy and confocal scanning laser microscopy and was subsequently quantified by image analysis, as well as by determining live counts and by permeate flux monitoring. Biofilm development was highly enhanced in the presence of permeate flow, which resulted in the buildup of complex three-dimensional structures on the membrane. Bacterial transport toward the membrane by permeate drag was found to be a mechanism by which cross-flow filtration contributes to the buildup of a biofouling layer that was more dominant than transport of nutrients. Cellular viability was found to be not essential for transport and adhesion under cross-flow conditions, since the permeate drag overcame the effect of bacterial motility.
Random Mutagenesis Identifies Novel Genes Involved in the Secretion of Antimicrobial, Cell Wall-Lytic Enzymes by
Lactococcus lactis
Authors: Tan Yu Pei , Giffard Philip M. , Barry Daniel G. , Huston Wilhelmina M. , Turner Mark S. 
Published: October 2008

ABSTRACT

Lactococcus lactis
is a gram-positive bacterium that is widely used in the food industry and is therefore desirable as a candidate for the production and secretion of recombinant proteins. Previously, we generated a
L. lactis
strain that expressed and secreted the antimicrobial cell wall-lytic enzyme lysostaphin. To identify lactococcal gene products that affect the production of lysostaphin, we isolated and characterized mutants generated by random transposon mutagenesis that had altered lysostaphin activity. Out of 35,000 mutants screened, only one with no lysostaphin activity was identified, and it was found to contain an insertion in the lysostaphin expression cassette. Ten mutants with higher lysostaphin activity contained insertions in only four different genes, which encode an uncharacterized putative transmembrane protein (llmg_0609) (three mutants), an enzyme catalyzing the first step in peptidoglycan biosynthesis (
murA2
) (five mutants), a putative regulator of peptidoglycan modification (
trmA
) (one mutant), and an uncharacterized enzyme possibly involved in ubiquinone biosynthesis (llmg_2148) (one mutant). These mutants were found to secrete larger amounts of lysostaphin than the control strain (MG1363[
lss
]), and the greatest increase in secretion was 9.8- to 16.1-fold, for the llmg_0609 mutants. The lysostaphin-oversecreting llmg_0609,
murA2
, and
trmA
mutants were also found to secrete larger amounts of another cell wall-lytic enzyme (the
Listeria monocytogenes
bacteriophage endolysin Ply511) than the control strain, indicating that the phenotype is not limited to lysostaphin.
Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and
fla
Short Variable Region Typing of Clonal Complexes of
Campylobacter jejuni
Strains of Human, Bovine, and Poultry Origins in Luxembourg
Authors: Ragimbeau Catherine , Schneider François , Losch Serge , Even Jos , Mossong Joël 
Published: October 2008

ABSTRACT

Campylobacter jejuni
is the most common cause of bacterial gastroenteritis in Luxembourg, with a marked seasonal peak during summer. The majority of these infections are thought to be sporadic, and the relative contribution of potential sources and reservoirs is still poorly understood. We monitored human cases from June to September 2006 (
n
= 124) by molecular characterization of isolates with the aim of rapidly detecting temporally related cases. In addition, isolates from poultry meat (
n
= 36) and cattle cecal contents (
n
= 48) were genotyped for comparison and identification of common clusters between veterinary and human
C. jejuni
populations. A total of 208 isolates were typed by sequencing the
fla
short variable region, macrorestriction analysis resolved by pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). We observed a high diversity of human strains during a given summer season. Poultry and human isolates had a higher diversity of sequence types than isolates of bovine origin, for which clonal complexes CC21 (41.6%) and CC61 (18.7%) were predominant. CC21 was also the most common complex found among human isolates (21.8%). The substantial concordance between PFGE and MLST results for this last group of strains suggests that they are clonally related. Our study indicates that while poultry remains an important source, cattle could be an underestimated reservoir of human
C. jejuni
cases. Transmission mechanisms of cattle-specific strains warrant further investigation.
Metabolic Function of
Corynebacterium glutamicum
Aminotransferases AlaT and AvtA and Impact on
l
-Valine Production
Authors: Marienhagen Jan , Eggeling Lothar 
Published: October 2008

ABSTRACT

Aminotransferases (ATs) interacting with
l
-alanine are the least studied bacterial ATs. Whereas AlaT converts pyruvate to
l
-alanine in a glutamate-dependent reaction, AvtA is able to convert pyruvate to
l
-alanine in an
l
-valine-dependent manner. We show here that the wild type of
Corynebacterium glutamicum
with a deletion of either of the corresponding genes does not exhibit an explicit growth deficiency. However, a double mutant was auxotrophic for
l
-alanine, showing that both ATs can provide
l
-alanine and that they are the only ATs involved. Kinetic studies with isolated enzymes demonstrate that the catalytic efficiency,
k
cat
/
K

m

, of AlaT is higher than 1 order of magnitude in the direction of
l
-alanine formation (3.5 × 10
4
M
−1
s
−1
), but no preference was apparent for AvtA, suggesting that AlaT is the principal
l
-alanine-supplying enzyme. This is in line with the cytosolic
l
-alanine concentration, which is reduced in the exponential growth phase from 95 mM to 18 mM by a deletion of
alaT
, whereas
avtA
deletion decreases the
l
-alanine concentration only to 76 mM. The combined data show that the presence of both ATs has subtle but obvious consequences on balancing intracellular amino acid pools in the wild type. The consequences are more obvious in an
l
-valine production strain where a high intracellular drain-off of the
l
-alanine precursor pyruvate prevails. We therefore used deletion of
alaT
to successfully reduce the contaminating
l
-alanine in extracellular accumulated
l
-valine by 80%.
Genetic Diversity and Abundance of Flavobacterial Proteorhodopsin in China Seas
Authors: Zhao Meiru , Chen Feng , Jiao Nianzhi 
Published: October 2008

ABSTRACTProteorhodopsin (PR) genes related toFlavobacteriawere found to be highly diverse in the East and South China seas and displayed a distinct geographic pattern, which appeared to reflect cold versus warm adaptation when Global Oceanic Sampling database metagenomic data were included. Flavobacterial PR genes were more abundant offshore than nearshore, implying that inheritance of the PR gene could be important forFlavobacterialiving in the oligotrophic environment.
Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of
Listeria monocytogenes
Isolates
Authors: Ward Todd J. , Ducey Thomas F. , Usgaard Thomas , Dunn Katherine A. , Bielawski Joseph P. 
Published: October 2008

ABSTRACT

Listeria monocytogenes
is responsible for serious invasive illness associated with consumption of contaminated food and places a significant burden on public health and the agricultural economy. We recently developed a multilocus genotyping (MLGT) assay for high-throughput subtype determination of
L. monocytogenes
lineage I isolates based on interrogation of single nucleotide polymorphisms (SNPs) via multiplexed primer extension reactions. Here we report the development and validation of two additional MLGT assays that address the need for comprehensive DNA sequence-based subtyping of
L. monocytogenes
. The first of these novel MLGT assays targeted variation segregating within lineage II, while the second assay combined probes for lineage III strains with probes for strains representing a recently characterized fourth evolutionary lineage (IV) of
L. monocytogenes
. These assays were based on nucleotide variation identified in >3.8 Mb of comparative DNA sequence and consisted of 115 total probes that differentiated 93% of the 100 haplotypes defined by the multilocus sequence data. MLGT reproducibly typed the 173 isolates used in SNP discovery, and the 10,448 genotypes derived from MLGT analysis of these isolates were consistent with DNA sequence data. Application of the MLGT assays to assess subtype prevalence among isolates from ready-to-eat foods and food-processing facilities indicated a low frequency (6.3%) of epidemic clone subtypes and a substantial population of isolates (>30%) harboring mutations in
inlA
associated with attenuated virulence in cell culture and animal models. These mutations were restricted to serogroup 1/2 isolates, which may explain the overrepresentation of serotype 4b isolates in human listeriosis cases.
Modulation of Chaperone Gene Expression in Mutagenized
Saccharomyces cerevisiae
Strains Developed for Recombinant Human Albumin Production Results in Increased Production of Multiple Heterologous Proteins
Authors: Payne T. , Finnis C. , Evans L. R. , Mead D. J. , Avery S. V. , Archer D. B. , Sleep D. 
Published: October 2008

ABSTRACT

The yeast
Saccharomyces cerevisiae
has been successfully established as a commercially viable system for the production of recombinant proteins. Manipulation of chaperone gene expression has been utilized extensively to increase recombinant protein production from
S. cerevisiae
, focusing predominantly on the products of the protein disulfide isomerase gene
PDI1
and the hsp70 gene
KAR2
. Here we show that the expression of the genes
SIL1, LHS1, JEM1
, and
SCJ1
, all of which are involved in regulating the ATPase cycle of Kar2p, is increased in a proprietary yeast strain, developed by several rounds of random mutagenesis and screening for increased production of recombinant human albumin (rHA). To establish whether this expression contributes to the enhanced-production phenotype, these genes were overexpressed both individually and in combination. The resultant strains showed significantly increased shake-flask production levels of rHA, granulocyte-macrophage colony-stimulating factor, and recombinant human transferrin.
Specific Binding of
Bacillus thuringiensis
Cry2A Insecticidal Proteins to a Common Site in the Midgut of
Helicoverpa
Species
Authors: Hernández-Rodríguez Carmen Sara , Van Vliet Adri , Bautsoens Nadine , Van Rie Jeroen , Ferré Juan 
Published: October 2008

ABSTRACT

For a long time, it has been assumed that the mode of action of Cry2A toxins was unique and different from that of other three-domain Cry toxins due to their apparent nonspecific and unsaturable binding to an unlimited number of receptors. However, based on the homology of the tertiary structure among three-domain Cry toxins, similar modes of action for all of them are expected. To confirm this hypothesis, binding assays were carried out with
125
I-labeled Cry2Ab. Saturation assays showed that Cry2Ab binds in a specific and saturable manner to brush border membrane vesicles (BBMVs) of
Helicoverpa armigera
. Homologous-competition assays with
125
I-Cry2Ab demonstrated that this toxin binds with high affinity to binding sites in
H. armigera
and
Helicoverpa zea
midgut. Heterologous-competition assays showed a common binding site for three toxins belonging to the Cry2A family (Cry2Aa, Cry2Ab, and Cry2Ae), which is not shared by Cry1Ac. Estimation of
K

d

(dissociation constant) values revealed that Cry2Ab had around 35-fold less affinity than Cry1Ac for BBMV binding sites in both insect species. Only minor differences were found regarding
R

t

(concentration of binding sites) values. This study questions previous interpretations from other authors performing binding assays with Cry2A toxins and establishes the basis for the mode of action of Cry2A toxins.