bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of
Euglena gracilis
Plastid-Targeted Proteins Reveals Different Classes of Transit Sequences
Authors: Durnford Dion G. , Gray Michael W. 
Published: December 2006

ABSTRACT

The plastid of
Euglena gracilis
was acquired secondarily through an endosymbiotic event with a eukaryotic green alga, and as a result, it is surrounded by a third membrane. This membrane complexity raises the question of how the plastid proteins are targeted to and imported into the organelle. To further explore plastid protein targeting in
Euglena
, we screened a total of 9,461 expressed sequence tag (EST) clusters (derived from 19,013 individual ESTs) for full-length proteins that are plastid localized to characterize their targeting sequences and to infer potential modes of translocation. Of the 117 proteins identified as being potentially plastid localized whose N-terminal targeting sequences could be inferred, 83 were unique and could be classified into two major groups. Class I proteins have tripartite targeting sequences, comprising (in order) an N-terminal signal sequence, a plastid transit peptide domain, and a predicted stop-transfer sequence. Within this class of proteins are the lumen-targeted proteins (class IB), which have an additional hydrophobic domain similar to a signal sequence and required for further targeting across the thylakoid membrane. Class II proteins lack the putative stop-transfer sequence and possess only a signal sequence at the N terminus, followed by what, in amino acid composition, resembles a plastid transit peptide. Unexpectedly, a few unrelated plastid-targeted proteins exhibit highly similar transit sequences, implying either a recent swapping of these domains or a conserved function. This work represents the most comprehensive description to date of transit peptides in
Euglena
and hints at the complex routes of plastid targeting that must exist in this organism.
Binding Specificities and Potential Roles of Isoforms of Eukaryotic Initiation Factor 4E in
Leishmania
Authors: Yoffe Yael , Zuberek Joanna , Lerer Asaf , Lewdorowicz Magdalena , Stepinski Janusz , Altmann Michael , Darzynkiewicz Edward , Shapira Michal 
Published: December 2006

ABSTRACT

The 5′ cap structure of trypanosomatid mRNAs, denoted cap 4, is a complex structure that contains unusual modifications on the first four nucleotides. We examined the four eukaryotic initiation factor 4E (eIF4E) homologues found in the
Leishmania
genome database. These proteins, denoted LeishIF4E-1 to LeishIF4E-4, are located in the cytoplasm. They show only a limited degree of sequence homology with known eIF4E isoforms and among themselves. However, computerized structure prediction suggests that the cap-binding pocket is conserved in each of the homologues, as confirmed by binding assays to m
7
GTP, cap 4, and its intermediates. LeishIF4E-1 and LeishIF4E-4 each bind m
7
GTP and cap 4 comparably well, and only these two proteins could interact with the mammalian eIF4E binding protein 4EBP1, though with different efficiencies. 4EBP1 is a translation repressor that competes with eIF4G for the same residues on eIF4E; thus, LeishIF4E-1 and LeishIF4E-4 are reasonable candidates for serving as translation factors. LeishIF4E-1 is more abundant in amastigotes and also contains a typical 3′ untranslated region element that is found in amastigote-specific genes. LeishIF4E-2 bound mainly to cap 4 and comigrated with polysomal fractions on sucrose gradients. Since the consensus eIF4E is usually found in 48S complexes, LeishIF4E-2 could possibly be associated with the stabilization of trypanosomatid polysomes. LeishIF4E-3 bound mainly m
7
GTP, excluding its involvement in the translation of cap 4-protected mRNAs. It comigrates with 80S complexes which are resistant to micrococcal nuclease, but its function is yet unknown. None of the isoforms can functionally complement the
Saccharomyces cerevisiae
eIF4E, indicating that despite their structural conservation, they are considerably diverged.
The Multifunctional β-Oxidation Enzyme Is Required for Full Symptom Development by the Biotrophic Maize Pathogen
Ustilago maydis
Authors: Klose Jana , Kronstad James W. 
Published: December 2006

ABSTRACT

The transition from yeast-like to filamentous growth in the biotrophic fungal phytopathogen
Ustilago maydis
is a crucial event for pathogenesis. Previously, we showed that fatty acids induce filamentation in
U. maydis
and that the resulting hyphal cells resemble the infectious filaments observed in planta. To explore the potential metabolic role of lipids in the morphological transition and in pathogenic development in host tissue, we deleted the
mfe2
gene encoding the multifunctional enzyme that catalyzes the second and third reactions in β-oxidation of fatty acids in peroxisomes. The growth of the strains defective in
mfe2
was attenuated on long-chain fatty acids and abolished on very-long-chain fatty acids. The
mfe2
gene was not generally required for the production of filaments during mating in vitro, but loss of the gene blocked extensive proliferation of fungal filaments in planta. Consistent with this observation,
mfe2
mutants exhibited significantly reduced virulence in that only 27% of infected seedlings produced tumors compared to 88% tumor production upon infection by wild-type strains. Similarly, a defect in virulence was observed in developing ears upon infection of mature maize plants. Specifically, the absence of the
mfe2
gene delayed the development of teliospores within mature tumor tissue. Overall, these results indicate that the ability to utilize host lipids contributes to the pathogenic development of
U. maydis
.
VIB-1 Is Required for Expression of Genes Necessary for Programmed Cell Death in
Neurospora crassa
Authors: Dementhon Karine , Iyer Gopal , Glass N. Louise 
Published: December 2006

ABSTRACT

Nonself recognition during somatic growth is an essential and ubiquitous phenomenon in both prokaryotic and eukaryotic species. In filamentous fungi, nonself recognition is also important during vegetative growth. Hyphal fusion between genetically dissimilar individuals results in rejection of heterokaryon formation and in programmed cell death of the fusion compartment. In filamentous fungi, such as
Neurospora crassa
, nonself recognition and heterokaryon incompatibility (HI) are regulated by genetic differences at
het
loci. In
N. crassa
, mutations at the
vib-1
locus suppress nonself recognition and HI mediated by genetic differences at
het-c/pin-c
,
mat
, and
un-24/het-6. vib-1
is a homolog of
Saccharomyces cerevisiae NDT80
, which is a transcriptional activator of genes during meiosis. For this study, we determined that
vib-1
encodes a nuclear protein and showed that VIB-1 localization varies during asexual reproduction and during HI.
vib-1
is required for the expression of genes involved in nonself recognition and HI, including
pin-c
,
tol
, and
het-6
; all of these genes encode proteins containing a HET domain.
vib-1
is also required for the production of downstream effectors associated with HI, including the production of extracellular proteases upon carbon and nitrogen starvation. Our data support a model in which mechanisms associated with starvation and nonself recognition/HI are interconnected. VIB-1 is a major regulator of responses to nitrogen and carbon starvation and is essential for the expression of genes involved in nonself recognition and death in
N. crassa
.
Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote
Monocercomonoides
Authors: Liapounova Natalia A. , Hampl Vladimir , Gordon Paul M. K. , Sensen Christoph W. , Gedamu Lashitew , Dacks Joel B. 
Published: December 2006

ABSTRACT

All eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. Anaerobic eukaryotes face the challenge of fewer molecules of ATP extracted per molecule of glucose due to their lack of a complete tricarboxylic acid cycle. This may have pressured anaerobic eukaryotes to acquire the more ATP-efficient alternative glycolytic enzymes, such as pyrophosphate-fructose 6-phosphate phosphotransferase and pyruvate orthophosphate dikinase, through lateral gene transfers from bacteria and other eukaryotes. Most studies of these enzymes in eukaryotes involve pathogenic anaerobes;
Monocercomonoides
, an oxymonad belonging to the eukaryotic supergroup Excavata, is a nonpathogenic anaerobe representing an evolutionarily and ecologically distinct sampling of an anaerobic glycolytic pathway. We sequenced cDNA encoding glycolytic enzymes from a previously established cDNA library of
Monocercomonoides
and analyzed the relationships of these enzymes to those from other organisms spanning the major groups of
Eukaryota
,
Bacteria
, and
Archaea
. We established that, firstly,
Monocercomonoides
possesses alternative versions of glycolytic enzymes: fructose-6-phosphate phosphotransferase, both pyruvate kinase and pyruvate orthophosphate dikinase, cofactor-independent phosphoglycerate mutase, and fructose-bisphosphate aldolase (class II, type B). Secondly, we found evidence for the monophyly of oxymonads, kinetoplastids, diplomonads, and parabasalids, the major representatives of the Excavata. We also found several prokaryote-to-eukaryote as well as eukaryote-to-eukaryote lateral gene transfers involving glycolytic enzymes from anaerobic eukaryotes, further suggesting that lateral gene transfer was an important factor in the evolution of this pathway for denizens of this environment.
Pheromone-Induced Degradation of Ste12 Contributes to Signal Attenuation and the Specificity of Developmental Fate
Authors: Esch R. Keith , Wang Yuqi , Errede Beverly 
Published: December 2006

ABSTRACT

The Ste12 transcription factor of
Saccharomyces cerevisiae
regulates transcription programs controlling two different developmental fates. One is differentiation into a mating-competent form that occurs in response to mating pheromone. The other is the transition to a filamentous-growth form that occurs in response to nutrient deprivation. These two distinct roles for Ste12 make it a focus for studies into regulatory mechanisms that impart biological specificity. The transient signal characteristic of mating differentiation led us to test the hypothesis that regulation of Ste12 turnover might contribute to attenuation of the mating-specific transcription program and restrict activation of the filamentation program. We show that prolonged pheromone induction leads to ubiquitin-mediated destabilization and decreased amounts of Ste12. This depletion in pheromone-stimulated cultures is dependent on the mating-pathway-dedicated mitogen-activated protein kinase Fus3 and its target Cdc28 inhibitor, Far1. Attenuation of pheromone-induced mating-specific gene transcription (
FUS1
) temporally correlates with Ste12 depletion. This attenuation is abrogated in the deletion backgrounds (
fus3Δ
or
far1Δ
) where Ste12 is found to persist. Additionally, pheromone induces haploid invasion and filamentous-like growth instead of mating differentiation when Ste12 levels remain high. These observations indicate that loss of Ste12 reinforces the adaptive response to pheromone and contributes to the curtailing of a filamentation response.
Reciprocal Nuclear Shuttling of Two Antagonizing Zn Finger Proteins Modulates Tup Family Corepressor Function To Repress Chromatin Remodeling
Authors: Hirota Kouji , Hoffman Charles S. , Ohta Kunihiro 
Published: December 2006

ABSTRACT

The
Schizosaccharomyces pombe
global corepressors Tup11 and Tup12, which are orthologs of
Saccharomyces cerevisiae
Tup1, are involved in glucose-dependent transcriptional repression and chromatin alteration of the
fbp1
+
gene. The
fbp1
+
promoter contains two regulatory elements, UAS1 and UAS2, one of which (UAS2) serves as a binding site for two antagonizing C
2
H
2
Zn finger transcription factors, the Rst2 activator and the Scr1 repressor. In this study, we analyzed the role of Tup proteins and Scr1 in chromatin remodeling at
fbp1
+
during glucose repression. We found that Scr1, cooperating with Tup11 and Tup12, functions to maintain the chromatin of the
fbp1
+
promoter in a transcriptionally inactive state under glucose-rich conditions. Consistent with this notion, Scr1 is quickly exported from the nucleus to the cytoplasm at the initial stage of derepression, immediately after glucose starvation, at which time Rst2 is known to be imported into the nucleus. In addition, chromatin immunoprecipitation assays revealed a switching of Scr1 to Rst2 bound at UAS2 during glucose derepression. On the other hand, Tup11 and Tup12 persist in the nucleus and bind to the
fbp1
+
promoter under both derepressed and repressed conditions. These observations suggest that Tup1-like proteins recruited to the
fbp1
+
promoter are controlled by either of two antagonizing C
2
H
2
Zn finger proteins. We propose that the actions of Tup11 and Tup12 are regulated by reciprocal nuclear shuttling of the two antagonizing Zn finger proteins in response to the extracellular glucose concentration. This notion provides new insights into the molecular mechanisms of the Tup family corepressors in gene regulation.
Genetic Evidence that the Acyl Coenzyme A Binding Protein AcbA and the Serine Protease/ABC Transporter TagA Function Together in
Dictyostelium discoideum
Cell Differentiation
Authors: Cabral Matthew , Anjard Christophe , Loomis William F. , Kuspa Adam 
Published: December 2006

ABSTRACT

The acyl coenzyme A (CoA) binding protein AcbA is cleaved to form a peptide (SDF-2) that coordinates spore encapsulation during the morphogenesis of
Dictyostelium discoideum
fruiting bodies. We present genetic evidence that the misspecification of cell types seen in mutants of the serine protease/ABC transporter TagA results from the loss of normal interactions with AcbA. Developmental phenotypes resulting from aberrant expression of the TagA protease domain, such as the formation of supernumerary tips on aggregates and the production of excess prestalk cells, are suppressed by null mutations in the
acbA
gene. Phenotypes resulting from the deletion of
tagA
, such as overexpression of the prestalk gene
ecmB
and the misexpression of the prespore gene
cotB
in stalk cells, are also observed in
acbA
mutants. Moreover,
tagA
−
mutants fail to produce SDF-2 during fruiting body morphogenesis but are able to do so if they are stimulated with exogenous SDF-2. These results indicate that the developmental program depends on TagA and AcbA working in concert with each other during cell type differentiation and suggest that TagA is required for normal SDF-2 signaling during spore encapsulation.
bla
VIM-2
and
bla
VIM-7
Carbapenemase-Producing
Pseudomonas aeruginosa
Isolates Detected in a Tertiary Care Medical Center in the United States: Report from the MYSTIC Program
Authors: Aboufaycal H. , Sader H. S. , Rolston K. , Deshpande L. M. , Toleman M. , Bodey G. , Raad I. , Jones R. N. 
Published: December 2006

ABSTRACT

Two
Pseudomonas aeruginosa
strains resistant to beta-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and carbapenems and susceptible only to polymyxin B (MIC ≤ 2 μg/ml) were identified as part of the Meropenem Yearly Susceptibility Test Information Collection program. Metallo-β-lactamase screening tests were positive, PCR yielded products with
bla
VIM
primers, and sequence analysis revealed
bla
VIM-7
and
bla
VIM-2
. The isolates had distinct ribotype and pulsed-field gel electorphoresis patterns and appeared independently, remote in time and location, at the same cancer center.
Improved Multilocus Sequence Typing Scheme for
Staphylococcus epidermidis
Authors: Thomas Jonathan C. , Vargas Miguel R. , Miragaia Maria , Peacock Sharon J. , Archer Gordon L. , Enright Mark C. 
Published: December 2006

ABSTRACT

We evaluated three multilocus sequence typing (MLST) schemes for
Staphylococcus epidermidis
and selected the seven most discriminatory loci for the formation of a new, more powerful MLST scheme. This improved scheme gave 31 sequence types (STs) and 5 clonal complexes (CCs), whereas the other schemes delineate 16 to 24 STs and 1 to 3 CCs.
Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases
Authors: Mascher Thorsten , Helmann John D. , Unden Gottfried 
Published: December 2006

SUMMARYTwo-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. They consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. Histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. They can be identified and classified by virtue of their conserved cytoplasmic kinase domains. In contrast, the sensor domains are highly variable, reflecting the plethora of different signals and modes of sensing. In order to gain insight into the mechanisms of stimulus perception by bacterial histidine kinases, we here survey sensor domain architecture and topology within the bacterial membrane, functional aspects related to this topology, and sequence and phylogenetic conservation. Based on these criteria, three groups of histidine kinases can be differentiated. (i) Periplasmic-sensing histidine kinases detect their stimuli (often small solutes) through an extracellular input domain. (ii) Histidine kinases with sensing mechanisms linked to the transmembrane regions detect stimuli (usually membrane-associated stimuli, such as ionic strength, osmolarity, turgor, or functional state of the cell envelope) via their membrane-spanning segments and sometimes via additional short extracellular loops. (iii) Cytoplasmic-sensing histidine kinases (either membrane anchored or soluble) detect cellular or diffusible signals reporting the metabolic or developmental state of the cell. This review provides an overview of mechanisms of stimulus perception for members of all three groups of bacterial signal-transducing histidine kinases.
How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria
Authors: Deutscher Josef , Francke Christof , Postma Pieter W. 
Published: December 2006

SUMMARYThe phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
Uses for JNK: the Many and Varied Substrates of the c-Jun N-Terminal Kinases
Authors: Bogoyevitch Marie A. , Kobe Bostjan 
Published: December 2006

SUMMARYThe c-Jun N-terminal kinases (JNKs) are members of a larger group of serine/threonine (Ser/Thr) protein kinases from the mitogen-activated protein kinase family. JNKs were originally identified as stress-activated protein kinases in the livers of cycloheximide-challenged rats. Their subsequent purification, cloning, and naming as JNKs have emphasized their ability to phosphorylate and activate the transcription factor c-Jun. Studies of c-Jun and related transcription factor substrates have provided clues about both the preferred substrate phosphorylation sequences and additional docking domains recognized by JNK. There are now more than 50 proteins shown to be substrates for JNK. These include a range of nuclear substrates, including transcription factors and nuclear hormone receptors, heterogeneous nuclear ribonucleoprotein K, and the Pol I-specific transcription factor TIF-IA, which regulates ribosome synthesis. Many nonnuclear substrates have also been characterized, and these are involved in protein degradation (e.g., the E3 ligase Itch), signal transduction (e.g., adaptor and scaffold proteins and protein kinases), apoptotic cell death (e.g., mitochondrial Bcl2 family members), and cell movement (e.g., paxillin, DCX, microtubule-associated proteins, the stathmin family member SCG10, and the intermediate filament protein keratin 8). The range of JNK actions in the cell is therefore likely to be complex. Further characterization of the substrates of JNK should provide clearer explanations of the intracellular actions of the JNKs and may allow new avenues for targeting the JNK pathways with therapeutic agents downstream of JNK itself.
Effect of uroguanylin on potassium and bicarbonate transport in rat renal tubules
Authors: Amorim José Benedito Oliveira , Musa-Aziz Raif , Lessa Lucilia M.A. , Malnic Gerhard , Fonteles Manassés Claudino 
Published: December 2006

The effect of uroguanylin (UGN) on K+and H+secretion in the renal tubules of the rat kidney was studied using in vivo stationary microperfusion. For the study of K+secretion, a tubule was punctured to inject a column of FDC-green-colored Ringer's solution with 0.5 mmol KCl/L ± 10−6mol UGN/L, and oil was used to block fluid flow. K+activity and transepithelial potential differences (PD) were measured with double microelectrodes (K+ion-selective resin vs. reference) in the distal tubules of the same nephron. During perfusion, K+activity rose exponentially, from 0.5 mmol/L to stationary concentration, allowing for the calculation of K+secretion (JK). JKincreased from 0.63 ± 0.06 nmol·cm–2·s–1in the control group to 0.85 ± 0.06 in the UGN group (p < 0.01). PD was –51.0 ± 5.3 mV in the control group and –50.3 ± 4.98 mV in the UGN group. In the presence of 10−7mol iberiotoxin/L, the UGN effect was abolished: JKwas 0.37 ± 0.038 nmol·cm–2·s–1in the absence of, and 0.38 ± 0.025 in the presence of, UGN, indicating its action on maxi-K channels. In another series of experiments, renal tubule acidification was studied, using a similar method: proximal and distal tubules were perfused with solutions containing 25 mmol NaHCO3/L. Acidification half-time was increased both in proximal and distal segments and, as a consequence, bicarbonate reabsorption decreased in the presence of UGN (in proximal tubules, from 2.40 ± 0.26 to 1.56 ± 0.21 nmol·cm–2·s–1). When the Na+/H+exchanger was inhibited by 10−4mol hexamethylene amiloride (HMA)/L, the control and UGN groups were not significantly different. In the late distal tubule, after HMA, UGN significantly reduced JHCO3–, indicating an effect of UGN on H+-ATPase. These data show that UGN stimulated JK+by acting on maxi-K channels, and decreased JHCO3–by acting on NHE3 in proximal and H+-ATPase in distal tubules.