bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xyr1 (Xylanase Regulator 1) Regulates both the Hydrolytic Enzyme System and
d
-Xylose Metabolism in
Hypocrea jecorina
Authors: Stricker Astrid R. , Grosstessner-Hain Karin , Würleitner Elisabeth , Mach Robert L. 
Published: December 2006

ABSTRACT

Xyr1 (xylanase regulator 1) of the ascomycete
Hypocrea jecorina
(anamorph
Trichoderma reesei
) was recently demonstrated to play an essential role in the transcriptional regulation of the
xyn1
(xylanase 1-encoding) gene expression. Consequently, this study reports on the deletion of the
xyr1
gene from the
H. jecorina
genome. Comparative studies of the growth behavior of the different mutant strains (deleted and retransformed
xyr1
) grown on various carbon sources pointed to the strongly reduced ability of the
xyr1
deletion strain to utilize
d
-xylose and xylan. Transcriptional analysis of the
xyl1
(
d
-xylose reductase 1-encoding) gene as well as measurements of corresponding enzymatic activities gave evidence that Xyr1 takes part in the control of the fungal
d
-xylose pathway, in particular in the regulation of
d
-xylose reductase. It could be demonstrated that the uptake of
d
-xylose into the fungal cell is uninfluenced in the Δ
xyr1
strain. Furthermore, transcriptional regulation of the major hydrolytic enzyme-encoding genes
xyn1
and
xyn2
(xylanases 1 and 2),
cbh1
and
cbh2
(cellobiohydrolases 1 and 2), and
egl1
(endoglucanase 1) is strictly dependent on Xyr1. Regulation of the respective genes via Xyr1 is not affected by the substances mediating induction (xylose, xylobiose, and sophorose) and is indispensable for all modes of gene expression (basal, derepressed, and induced). Moreover, Xyr1, it was revealed, activated transcriptional regulation of inducer-providing enzymes such as β-xylosidase BXLI and β-glucosidase BGLI but was not shown to be involved in the regulation of BGLII.
Transcriptional Regulation of
MDR1
, Encoding a Drug Efflux Determinant, in Fluconazole-Resistant
Candida albicans
Strains through an Mcm1p Binding Site
Authors: Riggle Perry J. , Kumamoto Carol A. 
Published: December 2006

ABSTRACT

Constitutive, high-level transcription of the gene encoding the drug efflux facilitator Mdr1p is commonly observed in laboratory and clinical strains of
Candida albicans
that are resistant to the antifungal drug fluconazole (FLC). In five independently isolated FLC
R
laboratory strains, introduction of a wild-type
MDR1
promoter fragment fused to the yeast enhanced green fluorescent protein (
yEGFP
) reporter gene resulted in high-level expression of GFP, demonstrating that overexpression of
MDR1
is dependent on a
trans-
acting factor. This study identified a 35-bp
MDR1
promoter element, termed the MDRE, that mediates high-level
MDR1
transcription. When inserted into a heterologous promoter, the MDRE was sufficient to mediate high-level expression of the
yEGFP
reporter gene specifically in
MDR1 trans
-activation strains. The MDRE promoted transcription in an orientation-independent and dosage-dependent manner. Deletion of the MDRE in the full-length promoter did not abolish
MDR1 trans-
activation, indicating that elements upstream of the MDRE also contribute to transcription of
MDR1
in these overexpression strains. Analysis of the MDRE sequence indicated that it contains an Mcm1p binding site very similar in organization to the site seen upstream of the
Saccharomyces cerevisiae MFA1
and
STE2
genes. Electrophoretic mobility shift analysis demonstrated that both wild-type, FLC-sensitive and
MDR1 trans
-activated, FLC-resistant strains contain a factor that binds the MDRE. Depletion of Mcm1p, by use of a strain in which
MCM1
expression is under the control of a regulated promoter (44), resulted in a loss of MDRE binding activity. Thus, the general transcription factor Mcm1p participates in the regulation of
MDR1
expression.
Identification and Biochemical Characterization of Serine Hydroxymethyl Transferase in the Hydrogenosome of
Trichomonas vaginalis
Authors: Mukherjee Mandira , Sievers Stuart A. , Brown Mark T. , Johnson Patricia J. 
Published: December 2006

ABSTRACT

Serine hydroxymethyl transferase (SHMT) is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and methylenetetrahydrofolate. We have identified a single gene encoding SHMT in the genome of
Trichomonas vaginalis
, an amitochondriate, deep-branching unicellular protist. The protein possesses a putative N-terminal hydrogenosomal presequence and was shown to localize to hydrogensomes by immunofluorescence analysis, providing evidence of amino acid metabolism in this unusual organelle. In contrast to the tetrameric SHMT that exists in the mammalian host, we found that the
T. vaginalis
SHMT is a homodimer, as found in prokaryotes. All examined SHMT contain an 8-amino-acid conserved sequence, VTTTTHKT, containing the active-site lysyl residue (Lys 251 in TvSHMT) that forms an internal aldimine with PLP. We mutated this Lys residue to Arg and Gln and examined structural and catalytic properties of the wild-type and mutant enzymes in comparison to that reported for the mammalian protein. The oligomeric structure of the mutant K251R and K251Q TvSHMT was not affected, in contrast to that observed for comparable mutations in the mammalian enzyme. Likewise, contrary to that observed for mammalian SHMT, the catalytic activity of K251R TvSHMT was unaffected in the presence of PLP. The K251Q TvSHMT, however, was found to be inactive. These studies indicate that the active site of the parasite enzyme is distinct from its prokaryotic and eukaryotic counterparts and identify TvSHMT as a potential drug target.
Regulation of the Nucleocytoplasmic Distribution of Snf1-Gal83 Protein Kinase
Authors: Hedbacker Kristina , Carlson Marian 
Published: December 2006

ABSTRACT

Snf1 protein kinase containing the β subunit Gal83 is localized in the cytoplasm during growth of
Saccharomyces cerevisiae
cells in abundant glucose and accumulates in the nucleus in response to glucose limitation. Nuclear localization of Snf1-Gal83 requires activation of the Snf1 catalytic subunit and depends on Gal83, but in the
snf1Δ
mutant, Gal83 exhibits glucose-regulated nuclear accumulation. We show here that the N terminus of Gal83, which is divergent from those of the other β subunits, is necessary and sufficient for Snf1-independent, glucose-regulated localization. We identify a leucine-rich nuclear export signal in the N terminus and show that export depends on the Crm1 export receptor. We present evidence that catalytically inactive Snf1 promotes the cytoplasmic retention of Gal83 in glucose-grown cells through its interaction with the C terminus of Gal83; cytoplasmic localization of inactive Snf1-Gal83 maintains accessibility to the Snf1-activating kinases. Finally, we characterize the effects of glucose phosphorylation on localization. These studies define roles for Snf1 and Gal83 in determining the nucleocytoplasmic distribution of Snf1-Gal83 protein kinase.
Genetic Architecture of Hsp90-Dependent Drug Resistance
Authors: Cowen Leah E. , Carpenter Anne E. , Matangkasombut Oranart , Fink Gerald R. , Lindquist Susan 
Published: December 2006

ABSTRACT

Hsp90 potentiates the evolution of azole resistance in the model yeast
Saccharomyces cerevisiae
and the opportunistic pathogen
Candida albicans
via calcineurin. Here, we explored effectors downstream of calcineurin regulating this Hsp90-dependent trait. Using
S. cerevisiae erg3
mutants as a model, we determined that both Crz1 and Hph1 modulate azole resistance.
Nucleocytoplasmic Shuttling of the Rpb4p and Rpb7p Subunits ofSaccharomyces cerevisiaeRNA Polymerase II by Two Pathways
Authors: Selitrennik Michael , Duek Lea , Lotan Rona , Choder Mordechai 
Published: December 2006

ABSTRACTRpb4p and Rpb7p are subunits of the RNA polymerase II ofSaccharomyces cerevisiaethat form a dissociable heterodimeric complex. Whereas the only reported function of Rpb7p is related to transcription, Rpb4p has been found to also act in mRNA export and in the major mRNA decay pathway that operates in the cytoplasm, thus raising the possibility that Rpb4p links between the nuclear and cytoplasmic processes. Here we show that both Rpb4p and Rpb7p shuttle between the nucleus and the cytoplasm. Shuttling kinetics of the two proteins are similar as long as their interaction is possible, suggesting that they shuttle as a heterodimer. Under normal conditions, shuttling of Rpb4p and Rpb7p depends on ongoing transcription. However, during severe stresses of heat shock, ethanol, and starvation, the two proteins shuttle via a transcription-independent pathway. Thus, Rpb4p and Rpb7p shuttle via two pathways, depending on environmental conditions.
Skp1p Regulates Soi3p/Rav1p Association with Endosomal Membranes but Is Not Required for Vacuolar ATPase Assembly
Authors: Brace E. J. , Parkinson Leah P. , Fuller Robert S. 
Published: December 2006

ABSTRACT

Skp1p is an essential component of SCF-type E3 ubiquitin ligase complexes and associates with these through binding to F-box proteins. Skp1p also binds F-box proteins in a number of non-SCF complexes. The Skp1p-associated yeast protein Soi3p/Rav1p (hereafter referred to as Rav1p) is a component of the RAVE complex required for regulated assembly of vacuolar ATPase (V-ATPase). Rav1p is also involved in transport of TGN proteins and endocytic cargo between early and late endosomes. To evaluate the role of Skp1p in the RAVE complex, we made use of the fact that overexpression of Rav1p is toxic because it sequesters Skp1p from essential interactions. We isolated a separation of function allele of
SKP1
,
skp1
(
Asn108Tyr
), that completely abrogated the Rav1p interaction but allowed Skp1p to perform other essential cellular functions. Cells containing the
skp1
(
Asn108Tyr
) allele as the sole source of Skp1p exhibited normal V-ATPase assembly and activity. However, in the
skp1
(
Asn108Tyr
) mutant strain, the membrane-associated pool of Rav1-green fluorescent protein was increased, suggesting that Skp1p is important for the release of Rav1p from endosomal membranes where it functions in V-ATPase assembly. Thus, although part of the RAVE complex, Skp1p does not appear to be involved in V-ATPase assembly but instead in the cycling of the complex off membranes. This work also provides a generalizable approach to defining the roles of interactions of Skp1p with individual F-box proteins through the isolation of special alleles of
SKP1
.
Messing with Bacterial Quorum Sensing
Authors: González Juan E. , Keshavan Neela D. 
Published: December 2006

SUMMARYQuorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. Several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. Interestingly, eukaryotes produce quorum-sensing-interfering (QSI) compounds that have a positive or negative influence on the bacterial signaling network. This eukaryotic interference could result in further fine-tuning of bacterial quorum sensing. Furthermore, recent work involving the synthesis of structural homologs to the various quorum-sensing signal molecules has resulted in the development of additional QSI compounds that could be used to control pathogenic bacteria. The creation of transgenic plants that express bacterial quorum-sensing genes is yet another strategy to interfere with bacterial behavior. Further investigation on the manipulation of quorum-sensing systems could provide us with powerful tools against harmful bacteria.
The Bacterial Actin-Like Cytoskeleton
Authors: Carballido-López Rut 
Published: December 2006

SUMMARYRecent advances have shown conclusively that bacterial cells possess distant but true homologues of actin (MreB, ParM, and the recently uncovered MamK protein). Despite weak amino acid sequence similarity, MreB and ParM exhibit high structural homology to actin. Just like F-actin in eukaryotes, MreB and ParM assemble into highly dynamic filamentous structures in vivo and in vitro. MreB-like proteins are essential for cell viability and have been implicated in major cellular processes, including cell morphogenesis, chromosome segregation, and cell polarity. ParM (a plasmid-encoded actin homologue) is responsible for driving plasmid-DNA partitioning. The dynamic prokaryotic actin-like cytoskeleton is thought to serve as a central organizer for the targeting and accurate positioning of proteins and nucleoprotein complexes, thereby (and by analogy to the eukaryotic cytoskeleton) spatially and temporally controlling macromolecular trafficking in bacterial cells. In this paper, the general properties and known functions of the actin orthologues in bacteria are reviewed.
Impact of Protein Kinase PKR in Cell Biology: from Antiviral to Antiproliferative Action
Authors: García M. A. , Gil J. , Ventoso I. , Guerra S. , Domingo E. , Rivas C. , Esteban M. 
Published: December 2006

SUMMARYThe double-stranded RNA-dependent protein kinase PKR is a critical mediator of the antiproliferative and antiviral effects exerted by interferons. Not only is PKR an effector molecule on the cellular response to double-stranded RNA, but it also integrates signals in response to Toll-like receptor activation, growth factors, and diverse cellular stresses. In this review, we provide a detailed picture on how signaling downstream of PKR unfolds and what are the ultimate consequences for the cell fate. PKR activation affects both transcription and translation. PKR phosphorylation of the alpha subunit of eukaryotic initiation factor 2 results in a blockade on translation initiation. However, PKR cannot avoid the translation of some cellular and viral mRNAs bearing special features in their 5′ untranslated regions. In addition, PKR affects diverse transcriptional factors such as interferon regulatory factor 1, STATs, p53, activating transcription factor 3, and NF-κB. In particular, how PKR triggers a cascade of events involving IKK phosphorylation of IκB and NF-κB nuclear translocation has been intensively studied. At the cellular and organism levels PKR exerts antiproliferative effects, and it is a key antiviral agent. A point of convergence in both effects is that PKR activation results in apoptosis induction. The extent and strength of the antiviral action of PKR are clearly understood by the findings that unrelated viral proteins of animal viruses have evolved to inhibit PKR action by using diverse strategies. The case for the pathological consequences of the antiproliferative action of PKR is less understood, but therapeutic strategies aimed at targeting PKR are beginning to offer promising results.
DNA Replication in the Archaea
Authors: Barry Elizabeth R. , Bell Stephen D. 
Published: December 2006

SUMMARY
The archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus. In recent years, considerable advances have been made in understanding the biochemistry of the archaeal replication proteins. Furthermore, a number of structures have now been obtained for individual components and higher-order assemblies of archaeal replication factors, yielding important insights into the mechanisms of DNA replication in both archaea and eukaryotes.
Induction of apoptosis in K562 cells by jolkinolide B
Authors: Luo Huiying , Wang Aiqin 
Published: December 2006

Jolkinolide B, a bioactive diterpene isolated from the roots of Euphorbia fischeriana Steud, has various biological and pharmacological properties. In this study, the cytotoxicity of highly purified jolkinolide B was tested in human chronic myeloid leukemia (K562) and 2 other cell lines (human esophageal carcinoma Eca-109 and human hepatoma HepG2). The results indicate a significant decrease in the proliferation of all the 3 cell lines when treated with jolkinolide B for 24 h; the IC50 value of cytotoxicity was 12.1 μg/mL (for K562 cells), >50.0 μg/mL (for HepG2 cells), and 23.7 μg/mL (for Eca-109 cells). Further study of K562 cells involving fluorescence and transmission electron microscopy revealed characteristic apoptotic features, such as cell shrinkage, membrane blebbing, loss of microvilli, and nuclear condensation. Agarose electrophoresis of genomic DNA showed a typical fragmentation pattern for apoptotic cells. A kinetic cell-cycle analysis demonstrated that the cell cycle was arrested in the G1 phase. All these results suggest that the anti-proliferation effect of jolkinolide B on K562 cells is achieved by arresting the cell cycle in the G1 phase and subsequently inducing apoptosis.
Effect of stress on hepatic 11β-hydroxysteroid dehydrogenase activity and its influence on carbohydrate metabolism
Authors: Altuna María Eugenia , Lelli Sandra Marcela , Martín de Viale Leonor C. San , Damasco María Cristina 
Published: December 2006

Stress activates the synthesis and secretion of catecholamines and adrenal glucocorticoids, increasing their circulating levels. In vivo, hepatic 11β-hydroxysteroid dehydrogenase 1 (HSD1) stimulates the shift of 11-dehydrocorticosterone to corticosterone, enhancing active glucocorticoids at tissue level. We studied the effect of 3 types of stress, 1 induced by bucogastric overload with 200 mmol/L HCl causing metabolic acidosis (HCl), the second induced by bucogastric overload with 0.45% NaCl (NaCl), and the third induced by simulated overload (cannula), on the kinetics of hepatic HSD1 of rats and their influence on the activity of the gluconeogenic enzyme phosphoenolpyruvate carboxykinase, glycemia, and glycogen deposition. Compared with unstressed controls, all types of stress significantly increased HSD1 activity (146% cannula, 130% NaCl, and 253% HCl), phosphoenolpyruvate carboxykinase activity (51% cannula, 48% NaCl, and 86% HCl), and glycemia (29% cannula, 30% NaCl, and 41% HCl), but decreased hepatic glycogen (68% cannula, 68% NaCl, and 78% HCl). Owing to these results, we suggest the following events occur when stress is induced: an increase in hepatic HSD1 activity, augmented active glucocorticoid levels, increased gluconeogenesis, and glycemia. Also involved are the multiple events indirectly related to glucocorticoids, which lead to the depletion of hepatic glycogen deposits, thereby contributing to increased glycemia. This new approach shows that stress increments the activity of hepatic HSD1 and suggests that this enzyme could be involved in the development of the Metabolic Syndrome.
Effects of sympathetic stimulation during cooling on hypothermic as well as posthypothermic hemodynamic function
Authors: Kondratiev T.V. , Tveita T. 
Published: December 2006

This experimental study was performed to explore hemodynamic effects of a moderate dose epinephrine (Epi) during hypothermia and to test the hypothesis whether sympathetic stimulation during cooling affects myocardial function following rewarming. Two groups of male Wistar rats (each, n = 7) were cooled to 15 °C, maintained at this temperature for 1 h, and then rewarmed. Group 1 received 1 μg/min Epi, i.v., for 1 h during cooling to 28 °C, a dose known to elevate cardiac output (CO) by approximately 25% at 37 °C. Group 2 served a saline solution control. At 37 °C, Epi infusion elevated CO, left ventricular systolic pressure, maximum rate of left ventricle pressure rise, and mean arterial pressure. During cooling to 28 °C, these variables, with the exception of mean arterial pressure, decreased in parallel to those in the saline solution group. In contrast, in the Epi group, mean arterial pressure remained increased and total peripheral resistance was significantly elevated at 28 °C. Compared with corresponding prehypothermic values, most hemodynamic variables were lowered after 1 h at 15 °C in both groups (except for stroke volume). After rewarming, alterations in hemodynamic variables in the Epi-treated group were more prominent than in saline solution controls. Thus, before cooling, continuous Epi infusion predominantly stimulates myocardial mechanical function, materialized as elevation of CO, left ventricular systolic pressure, and maximum rate of left ventricle pressure rise. Cooling, on the other hand, apparently eradicates central hemodynamic effects of Epi and during stable hypothermia, elevation of peripheral vascular vasopressor effects seem to take over. In contrast to temperature-matched, non-Epi stimulated control rats, a significant depression of myocardial mechanical function occurs during rewarming following a moderate sympathetic stimulus during initial cooling.
Contribution of catabolic tissue replacement to the turnover of stable isotopes in Danio rerio
Authors: Tarboush Rania A. , MacAvoy Stephen E. , Macko Stephen A. , Connaughton Victoria 
Published: December 2006

Stable isotopes of carbon, nitrogen, and sulfur in organisms can trace nutrient sources and determine trophic interactions. However, time is required for an organism to reflect the isotopic composition of its diet. The rate at which an organism incorporates the isotopic signature of its food has a growth (k) component and a metabolic tissue replacement (m) component. This study shows that metabolic tissue replacement accounts for between 68% and 80% of the observed changes in isotopic signature in zebra danio ( Danio rerio (Hamilton, 1822)) muscle following a dietary shift, with the remainder owing to growth of new tissue. The half-lives of carbon, nitrogen, and sulfur were ~53, ~147 and ~58 days, respectively. This indicates that a significant period of isotopic disequilibria exists before zebra danio resemble dietary isotopic composition. These results show that catabolic replacement of tissue, as well as growth, must be taken into account when predicting the rate of isotope incorporation in warm-water fish. When using isotopic ratios to decipher food webs and trophic interactions, researchers should be aware that the often held assumption of isotopic equilibrium between diet and consumer may be violated.
Changes in sex ratio over time in the endangered iguana Cyclura cychlura inornata
Authors: Smith Geoffrey R. , Iverson John B. 
Published: December 2006

Changes in sex ratio of a population over time can indicate possible conservation concerns. Using population estimates for males and females, we examined changes in the sex ratio of two populations of the endangered Allen’s Cay Rock Iguana ( Cyclura cychlura inornata Barbour and Noble, 1916) in the Bahamas over nearly 25 years. The sex ratios of both populations changed from strongly male-biased early in the study to nearly 1:1 in recent years. We hypothesize that this shift has occurred because of the recovery of these populations from intense harvesting (particularly of females) over the previous 100 years and, more recently, because of the removal of large males from the islands either by poachers or by tourists.