bluuebunny/crossref_metadata_2025_split huggingface dataset:
A
Saccharomyces cerevisiae
Mutant Unable To Convert Glucose to Glucose-6-Phosphate Accumulates Excessive Glucose in the Endoplasmic Reticulum due to Core Oligosaccharide Trimming
Authors: Miseta Attila , Tökés-Füzesi Margit , Aiello David P. , Bedwell David M. 
Published: June 2003

ABSTRACT

d
-Glucose is the preferred carbon and energy source for most eukaryotic cells. Immediately following its uptake, glucose is rapidly phosphorylated to glucose-6-phosphate (Glc-6-P). The yeast
Saccharomyces cerevisiae
has three enzymes (Hxk1p, Hxk2p, and Glk1p) that convert glucose to Glc-6-P. In the present study, we found that yeast mutants lacking any two of these enzymes retain the ability to efficiently convert glucose to Glc-6-P and thus maintain a low level of cellular glucose. However, a mutant strain lacking all three glucose-phosphorylating enzymes contained up to 225-fold more intracellular glucose than normal. Drugs that inhibit the synthesis or the trimming of the lipid-linked core oligosaccharide Glu
3
Man
9
GlcNac
2
effectively reduced the accumulation of glucose. Similarly, mutations that block the addition of glucose residues to the core oligosaccharide moiety, such as
alg5Δ
or
alg6Δ
, also diminished glucose accumulation. These results indicate that the intracellular glucose accumulation observed in the glucose phosphorylation mutant results primarily from the trimming of glucose residues from core oligosaccharide chains within the endoplasmic reticulum (ER). Consistent with this conclusion, both [
14
C]glucose exchange and subcellular fractionation experiments indicate that much of the accumulated glucose is retained within an intracellular compartment, suggesting that the efficient transport of glucose from the ER to the cytosol in yeast may be coupled to its rephosphorylation to Glc-6-P. The high level of cellular glucose was associated with an increased level of protein glycation and the release of glucose into the culture medium via its transit through the secretory pathway. Finally, we also found that the accumulation of glucose may lead to a subtle alteration in ion homeostasis, particularly Ca
2+
uptake. This suggests that this mutant strain may serve as a useful model to study the consequences of excessive glucose accumulation and protein glycation.
Rapamycin Treatment Results in GATA Factor-Independent Hyperphosphorylation of the Proline Utilization Pathway Activator in
Saccharomyces cerevisiae
Authors: Saxena Deepti , Kannan K. B. , Brandriss Marjorie C. 
Published: June 2003

ABSTRACT

Treatment of
Saccharomyces cerevisiae
cells with the immunosuppressive drug rapamycin results in a variety of cellular changes in response to perceived nutrient deprivation. Among other effects, rapamycin treatment results in the nuclear localization of the global nitrogen activators Gln3p and Nil1p/Gat1p, which leads to expression of nitrogen assimilation genes. The proline utilization (Put) pathway genes were shown to be among the genes induced by rapamycin. Having previously shown that the Put pathway activator Put3p is differentially phosphorylated in response to the quality of the nitrogen source, we examined the phosphorylation status of Put3p after rapamycin treatment. Treatment with rapamycin resulted in the hyperphosphorylation of Put3p, which was independent of Gln3p, Nil1p, and Ure2p. The relative contributions of global nitrogen (Gln3p and Nil1p) and pathway-specific (Put3p) activators to rapamycin-induced expression of the target gene
PUT1
were also examined. We found that Nil1p and Put3p, but not Gln3p, play major roles in rapamycin-induced
PUT1
expression. Our findings show that perceived nitrogen deprivation triggered by rapamycin treatment and steady-state growth in nitrogen-derepressing conditions are associated with hyperphosphorylation of Put3p and increased
PUT1
expression. Rapamycin treatment and nitrogen derepression may share some, but not all, regulatory elements, since Gln3p and Nil1p do not participate identically in both processes and are not required for hyperphosphorylation. A complex relationship exists among the global and pathway-specific regulators, depending on the nature and quality of the nitrogen source.
RBP38, a Novel RNA-Binding Protein from Trypanosomatid Mitochondria, Modulates RNA Stability
Authors: Sbicego Sandro , Alfonzo Juan D. , Estévez Antonio M. , Rubio Mary Anne T. , Kang Xuedong , Turck Christoph W. , Peris Marian , Simpson Larry 
Published: June 2003

ABSTRACT

We describe here the isolation and characterization of a novel RNA-binding protein, RBP38, from
Leishmania tarentolae
mitochondria. This protein does not contain any known RNA-binding motifs and is highly conserved among the trypanosomatids, but no homologues were found in other organisms. Recombinant LtRBP38 binds single and double-stranded (ds) RNA substrates with dissociation constants in the 100 nM range, as determined by fluorescence polarization analysis. Downregulation of expression of the homologous gene, TbRBP38, in procyclic
Trypanosoma brucei
by using conditional dsRNA interference resulted in 80% reduction of steady-state levels of RNAs transcribed from both maxicircle and minicircle DNA. In organello pulse-chase labeling experiments were used to determine the stability of RNAs in mitochondria that were depleted of TbRBP38. The half-life of metabolically labeled RNA decreased from ∼160 to ∼60 min after depletion. In contrast, there was no change in transcriptional activity. These observations suggest a role of RBP38 in stabilizing mitochondrial RNA.
Dyskinetoplastic
Trypanosoma brucei
Contains Functional Editing Complexes
Authors: Domingo Gonzalo J. , Palazzo Setareh S. , Wang Bingbing , Pannicucci Brian , Salavati Reza , Stuart Kenneth D. 
Published: June 2003

ABSTRACT

Mitochondrial pre-mRNAs undergo posttranscriptional RNA editing as directed by small guide RNAs (gRNAs) to produce functional mRNAs in kinetoplastid protozoa. The pre-mRNAs and gRNAs are encoded in the maxicircle and minicircle components, respectively, of the kinetoplastid mitochondrial DNA (kDNA), and editing is catalyzed by a multienzyme protein complex.
Trypanosoma evansi
AnTat3/3, which lacks maxicircles but retains a single class of minicircles, and a dyskinetoplastic mutant of
Trypanosoma brucei
EATRO164, which is devoid of kDNA, were both shown to retain genes and proteins for the editing complex. The proteins are present in complexes that immunoprecipitate and sediment indistinguishably from wild-type complexes. The complexes catalyze precleaved insertion and deletion editing as well as full-round deletion editing in vitro. Thus, mutants which lack the natural substrates for RNA editing and all or most gRNAs retain editing complexes that contain the four primary catalytic activities of editing and function in editing, at least in vitro. Therefore neither pre-mRNA nor gRNA is required to form functional RNA-editing complexes.
TbMP44 Is Essential for RNA Editing and Structural Integrity of the Editosome inTrypanosoma brucei
Authors: Wang Bingbing , Ernst Nancy Lewis , Palazzo Setareh S. , Panigrahi Aswini K. , Salavati Reza , Stuart Kenneth 
Published: June 2003

ABSTRACTRNA editing produces mature mitochondrial mRNAs in trypanosomatids by the insertion and deletion of uridylates. It is catalyzed by a multiprotein complex, the editosome. We identified TbMP44 among the components of enriched editosomes by a combination of mass spectrometry and DNA sequence database analysis. Inactivation of an ectopic TbMP44 allele in cells in which the endogenous alleles were disrupted abolished RNA editing, inhibited cell growth, and was eventually lethal to bloodstream form trypanosomes. Loss of TbMP44 mRNA was followed initially by a reduction in the editosome sedimentation coefficient and then by the absence of other editosome proteins despite the presence of the mRNA. Reactivation ofTbMP44gene expression resulted in the resumption of cell growth and the reappearance of editosomes. These data indicate that TbMP44 is a component of the editosome that is essential for editing and critical for the structural integrity of the editosome.
Guanyl Nucleotide Exchange Factor Sql2 and Ras2 Regulate Filamentous Growth in
Ustilago maydis
Authors: Müller Philip , Katzenberger Jörg D. , Loubradou Gabriel , Kahmann Regine 
Published: June 2003

ABSTRACT

The cyclic AMP (cAMP)-signaling pathway regulates cell morphology and plays a crucial role during pathogenic development of the plant-pathogenic fungus
Ustilago maydis
. Strains lacking components of this signaling pathway, such as the Gα-subunit Gpa3 or the adenylyl cyclase Uac1, are nonpathogenic and grow filamentously. On the other hand, strains exhibiting an activated cAMP pathway due to a dominant-active allele of
gpa3
display a glossy colony phenotype and are unable to proliferate in plant tumors. Here we present the identification of
sql2
as a suppressor of the glossy colony phenotype of a

gpa3
Q206L

strain.
sql2
encodes a protein with similarity to CDC25-like guanine nucleotide exchange factors, which are known to act on Ras proteins. Overexpression of
sql2
leads to filamentous growth that cannot be suppressed by exogenous cAMP, suggesting that Sql2 does not act upstream of Uac1. To gain more insight in signaling processes regulated by Sql2, we isolated two genes encoding Ras proteins. Expression of dominant active alleles of
ras1
and
ras2
showed that Ras2 induces filamentous growth while Ras1 does not affect cell morphology but elevates pheromone gene expression. These results indicate that Ras1 and Ras2 fulfill different functions in
U. maydis
. Moreover, observed similarities between the filaments induced by
sql2
and
ras2
suggest that Sql2 is an activator of Ras2. Interestingly,
sql2
deletion mutants are affected in pathogenic development but not in mating, indicating a specific function of
sql2
during pathogenesis.
Genetic Interactions of the E3 Ubiquitin Ligase Component FbxA with Cyclic AMP Metabolism and a Histidine Kinase Signaling Pathway during
Dictyostelium discoideum
Development
Authors: Tekinay Turgay , Ennis Herbert L. , Wu Mary Y. , Nelson Margaret , Kessin Richard H. , Ratner David I. 
Published: June 2003

ABSTRACT

Dictyostelium discoideum
amoebae with an altered
fbxA
gene, which is thought to encode a component of an SCF E3 ubiquitin ligase, have defective regulation of cell type proportionality. In chimeras with wild-type cells, the mutant amoebae form mainly spores, leaving the construction of stalks to wild-type cells. To examine the role of
fbxA
and regulated proteolysis, we have recovered the promoter of
fbxA
and shown that it is expressed in a pattern resembling that of a prestalk-specific gene until late in development, when it is also expressed in developing spore cells. Because
fbxA
cells are developmentally deficient in pure culture, we were able to select suppressor mutations that promote sporulation of the original mutant. One suppressor mutation resides within the gene
regA
, which encodes a cyclic AMP (cAMP) phosphodiesterase linked to an activating response regulator domain. In another suppressor, there has been a disruption of
dhkA
, a gene encoding a two-component histidine kinase known to influence
Dictyostelium
development. RegA appears precociously and in greater amounts in the
fbxA
mutant than in the wild type, but in an
fbx
A/
dhk
A double mutant, RegA is restored to wild-type levels. Because the basis of
regA
suppression might involve alterations in cAMP levels during development, the concentrations of cAMP in all strains were determined. The levels of cAMP are relatively constant during multicellular development in all strains except the
dhkA
mutant, in which it is reduced at least sixfold. The level of cAMP in the double mutant
dhkA/fbxA
is relatively normal. The levels of cAMP in the various mutants do not correlate with spore formation, as would be expected on the basis of our present understanding of the signaling pathway leading to the induction of spores. Altered amounts of RegA and cAMP early in the development of the mutants suggest that both
fbxA
and
dhkA
genes act earlier than previously thought.
Changing Patterns of Gene Expression in
Dictyostelium
Prestalk Cell Subtypes Recognized by In Situ Hybridization with Genes from Microarray Analyses
Authors: Maeda Mineko , Sakamoto Haruyo , Iranfar Negin , Fuller Danny , Maruo Toshinari , Ogihara Satoshi , Morio Takahiro , Urushihara Hideko , Tanaka Yoshimasa , Loomis William F. 
Published: June 2003

ABSTRACT

We used microarrays carrying most of the genes that are developmentally regulated in
Dictyostelium
to discover those that are preferentially expressed in prestalk cells. Prestalk cells are localized at the front of slugs and play crucial roles in morphogenesis and slug migration. Using whole-mount in situ hybridization, we were able to verify 104 prestalk genes. Three of these were found to be expressed only in cells at the very front of slugs, the PstA cell type. Another 10 genes were found to be expressed in the small number of cells that form a central core at the anterior, the PstAB cell type. The rest of the prestalk-specific genes are expressed in PstO cells, which are found immediately posterior to PstA cells but anterior to 80% of the slug that consists of prespore cells. Half of these are also expressed in PstA cells. At later stages of development, the patterns of expression of a considerable number of these prestalk genes changes significantly, allowing us to further subdivide them. Some are expressed at much higher levels during culmination, while others are repressed. These results demonstrate the extremely dynamic nature of cell-type-specific expression in
Dictyostelium
and further define the changing physiology of the cell types. One of the signals that affect gene expression in PstO cells is the hexaphenone DIF-1. We found that expression of about half of the PstO-specific genes were affected in a mutant that is unable to synthesize DIF-1, while the rest appeared to be DIF independent. These results indicate that differentiation of some aspects of PstO cells can occur in the absence of DIF-1.
MFE1, a Member of the Peroxisomal Hydroxyacyl Coenzyme A Dehydrogenase Family, Affects Fatty Acid Metabolism Necessary for Morphogenesis in
Dictyostelium
spp
Authors: Matsuoka Satomi , Saito Tamao , Kuwayama Hidekazu , Morita Naoki , Ochiai Hiroshi , Maeda Mineko 
Published: June 2003

ABSTRACT

β-Oxidation of long-chain fatty acids and branched-chain fatty acids is carried out in mammalian peroxisomes by a multifunctional enzyme (MFE) or
d
-bifunctional protein, with separate domains for hydroxyacyl coenzyme A (CoA) dehydrogenase, enoyl-CoA hydratase, and steroid carrier protein SCP2. We have found that
Dictyostelium
has a gene,
mfeA
, encoding MFE1 with homology to the hydroxyacyl-CoA dehydrogenase and SCP2 domains. A separate gene,
mfeB
, encodes MFE2 with homology to the enoyl-CoA hydratase domain. When grown on a diet of bacteria,
Dictyostelium
cells in which
mfeA
is disrupted accumulate excess cyclopropane fatty acids and are unable to develop beyond early aggregation. Axenically grown mutant cells, however, developed into normal fruiting bodies composed of spores and stalk cells. Comparative analysis of whole-cell lipid compositions revealed that bacterially grown mutant cells accumulated cyclopropane fatty acids that remained throughout the developmental stages. Such a persistent accumulation was not detected in wild-type cells or axenically grown mutant cells. Bacterial phosphatidylethanolamine that contains abundant cyclopropane fatty acids inhibited the development of even axenically grown mutant cells, while dipalmitoyl phosphatidylethanolamine did not. These results suggest that MFE1 protects the cells from the increase of the harmful xenobiotic fatty acids incorporated from their diets and optimizes cellular lipid composition for proper development. Hence, we propose that this enzyme plays an irreplaceable role in the survival strategy of
Dictyostelium
cells to form spores for their efficient dispersal in nature.
Evidence that Synthesis of the
Saccharomyces cerevisiae
Mitochondrially Encoded Ribosomal Protein Var1p May Be Membrane Localized
Authors: Fiori Alessandro , Mason Thomas L. , Fox Thomas D. 
Published: June 2003

ABSTRACT

The 5′-untranslated leaders of mitochondrial mRNAs appear to localize translation within the organelle.
VAR1
is the only yeast mitochondrial gene encoding a major soluble protein. A chimeric mRNA bearing the
VAR1
untranslated regions and the coding sequence for pre-Cox2p appears to be translated at the inner membrane surface. We propose that translation of the ribosomal protein Var1p is also likely to occur in close proximity to the inner membrane.
Modified mandated choice for organ procurement
Authors: Chouhan P , Draper H 
Published: June 2003

Presumed consent to organ donation looks increasingly unlikely to be a palatable option for increasing organ procurement in the UK following the publication of the report into events at Alder Hey and elsewhere. Yet, given that the alternative to increasing the number of cadaveric organs available is either to accept a greater number of live donations, or accept that people will continue to die for the want of an organ, public policy makers remain obliged to consider other means of increasing the procurement rate.In this paper, we meet the main objections to mandated choice (namely that it undermines autonomy and that mandated donation is preferable). We have modified the traditional approach to mandated choice to take into account the force of the objection that mandated donation is preferable, by accepting that people can and do make bad decisions about organ donation and proposing that all accompanying public education and information about cadaveric donation should be directed in favour of donation.
ECOLOGY, ECONOMY AND REDEMPTION AS DYNAMIC: THE CONTRIBUTIONS OF JANE JACOBS AND BERNARD LONERGAN
Authors: Byrne Patrick 
Published: June 2003

AbstractBernard Lonergan, S.J. and Jane Jacobs have devoted much of their intellectual careers to thinking out the dynamic natural-human environment. Lonergan and Jacobs worked in very different lines of research - systematic theology and urban economics, respectively. Despite predictable differences in their thought, there are also remarkable commonalities in their analyses. Both thinkers have argued that the same dynamic principles that govern the functioning of natural ecologies are also to be found when human social and economic systems function well, but are absent when human systems go wrong. Both have argued that the violation of principles that pertain to natural ecologies is destructive not only of the natural environment, but of communal and economic well-being as well. Jacobs came to prominence with the 1961 publication of her classic, The Death and Life of Great American Cities. She has since gone on to extend her analysis to the unique characteristics of urban economics in several books and articles. In her most recent book The Nature of Economies (2000), Jacobs draws the results of her previous work on urban economic patterns into a synthesis with recent insights into biological systems. She argues that exactly the same principles (or "processes" as she prefers to call them) that sustain vital, evolving natural ecologies also underpin robust and dynamic economies. Where Jacobs's work gives a richly detailed account of the processes shared alike by natural and human systems, Lonergan developed a parallel, integral account of natural processes, human social and economic organization, and the "economy of salvation." In his classic work, Insight, Lonergan argues that the dynamics of human innovations and self-correction correspond in striking ways to the emergence, growth, development, and decline in the natural order. Unlike natural ecologies, however, the possibilities of genuine social and economic development are distorted, Lonergan argues, by the forces of "bias." In his role of theologian, Lonergan goes on to explore how divine grace heals the distorted dynamics of natural and human ecologies.
THE ECOLOGICAL COMMUNITY AND THE NARRATIVE OF CREATION
Authors: Scott Dane 
Published: June 2003

AbstractThe ideal of an ecological community uniting humans to the earth is an important normative ideal in environmental ethics. In this paper I will briefly look at one of the more popular stories that provides the philosophical underpinnings for this ideal. This is the story told by Baird Callicott, through his interpretation of Leopold's land ethic. In the critical portion of this essay, I point to problems with this account. The goal is not to prove this story false, but to indicate its inadequacies. In the constructive portion, I will discuss the philosophical underpinnings for an alternative story for realizing the hoped-for ecological community from the perspective of the Judeo-Christian tradition. This alternative story relies on an account of moral agency found in the narrative ethics of Alasdair MacIntrye. But it also reclaims neglected insights from Josiah Royce. In this account a community narrative is required that formed through a dialogue between the scientifically informed idea of the ecological community and the Judeo-Christian narrative of creation.
CONTROLLING CONSUMPTION: A ROLE FOR CHRISTIANITY?
Authors: Laurendeau Normand 
Published: June 2003

AbstractEconomic globalization suggests that sustainability will be threatened more by consumption than by population. While technology should prove helpful, our major environmental threat appears to be the rising demand for products and services. Hence, in the long run, sustainability requires human actions to prevent systemic harm rather than technical solutions that might merely reduce specific harm to the environment. In general, Christianity has dealt only weakly with the ethics of sustainability, and especially with the continuing consumption of global resources by affluent nations. In this paper, I analyze the potential for a new Christian focus on the satisfaction, satiation, and sublimation of material needs and desires. Important queries considered by the analysis include the following: (1) Does technology create metaphysical desire? (2) Is consumption thus inherently addictive? (3) Can religion help control this addiction? Employing dispositive and operative aspects of responsibility theory, I argue that a convivial future requires that we give prime attention to the demands of both distributive justice and environmental sustainability. On this basis, Christianity ought to place greater emphasis on equity issues associated with conservation, resource reduction, and renewable energy. Unfortunately, responsibility theory is inherently responsive rather than proactive, and thus probably more appropriate for avoiding a worse rather than creating a better future. My suggestion is that an eschatological approach to sustainability may offer new hope for the control of rampant materialism. In particular, Christianity must take seriously the need for an eventual re-integration between technology and religion. This re-integration should focus primarily on respecting physical limits, especially in an uncertain world characterized by a rising rich-poor gap. Such respect defines a new kenotic technology, which leads naturally to an allied kenotic consumption. As a result, Christian responsibility suggests that we can best imitate Christ by moderating profligate life-styles. From this perspective, the Church's prime responsibility in an environmental age is to model much better than it currently does the re-conversion of modern material growth to post-modern spiritual growth.