bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional regulation of the one‐carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p
Authors: Subramanian Mohan , Qiao Wen‐ben , Khanam Nurussaba , Wilkins Olivia , Der Sandy D. , Lalich Jonathan D. , Bognar Andrew L. 
Published: June 2005

SummaryThe mechanisms mediating responses to glycine withdrawal in budding yeast were studied using a genome‐wide profiling approach. A striking pattern of repressed expression of genes with an enrichment for those involved in one‐carbon metabolism and AMP biosynthesis was revealed. Sequence analysis of the promoters for the most severely repressed genes identified a conserved sequence, TGACTC, a known binding site for the transcription factors Gcn4p and Bas1p. Loss of BAS1 abolished or significantly reduced the repression of these genes in response to glycine removal but this phenotype was much less apparent in the absence of BAS2 or GCN4. Addition of a Bas1p‐LexA fusion protein to a strain with a LexAop‐LacZ fusion showed a strong glycine effect both in a BAS2 and a bas2 background. A Bas1p‐VP16 fusion protein activated expression in a bas1bas2 strain but no glycine effect was observed while a Bas1p‐Bas2p fusion protein activated expression to a lesser extent with a slight stimulation by glycine. These results suggest that glycine affects Bas1p activation of transcription rather than DNA binding and that Bas2p is not required for this affect. Glycine withdrawal repressed many of the same genes as addition of adenine, a process known to be dependent on Bas1p. However, the glycine response is independent of adenine repression, because glycine regulation occurs normally in ade strains. We did not see any difference in the degree of stimulation by glycine in the presence or absence of adenine even in Ade+ strains. Glycine regulation was also found to be dependent on an intact SHM2 gene, which encodes cytoplasmic serine hydroxymethyltransferase. A reporter plasmid containing a DNA sequence from the GCV2 promoter which confers glycine regulation on heterologous genes was introduced into the yeast deletion set to screen for genes required for glycine regulation. A number of genes, including BAS1 were required for activation by glycine but only the SHM2 gene was required for repression in the absence of glycine. We also showed that regulation of the SHM2 promoter by glycine requires Bas1p but not Bas2p or Gcn4p using a β‐galactosidase reporter. The response of the promoter to glycine required an intact SHM2 gene but was restored in a shm2 strain by addition of formate to the medium.
Novel relationships among DNA methylation, histone modifications and gene expression in Ascobolus
Authors: Barra José L. , Holmes Allyson M. , Grégoire Annie , Rossignol Jean‐Luc , Faugeron Godeleine 
Published: June 2005

SummaryBy studying Ascobolus strains methylated in various portions of the native met2 gene or of the hph transgene, we generalized our previous observation that methylation of the downstream portion of a gene promotes its stable silencing and triggers the production of truncated transcripts which rarely extend through the methylated region. In contrast, methylation of the promoter region does not promote efficient gene silencing. The chromatin state of met2 methylated strains was investigated after partial micrococcal nuclease (MNase) digestion. We show that MNase sensitive sites present along the unmethylated regions are no longer observed along the methylated ones. These chromatin changes are not resulting from the absence of transcription. They are associated, in both met2 and hph, with modifications of core histones corresponding, on the N terminus of histone H3, to an increase of dimethylation of lysine 9 and a decrease of dimethylation of lysine 4. Contrary to other organisms, these changes are independent of the transcriptional state of the genes, and furthermore, no decrease in acetylation of histone H4 is observed in silenced genes.
Salmonella entericaserotype Typhimurium MisL is an intestinal colonization factor that binds fibronectin
Authors: Dorsey Caleb W. , Laarakker Marijke C. , Humphries Andrea D. , Weening Eric H. , Bäumler Andreas J. 
Published: June 2005

SummaryMisL is an autotransporter protein encoded bySalmonellapathogenicity island 3 (SPI3). To investigate the role of MisL inSalmonella entericaserotype Typhimurium (S.Typhimurium) pathogenesis, we characterized its function during infection of mice and identified a host receptor for this adhesin. In a mouse model ofS.Typhimurium intestinal persistence, amisLmutant was shed with the faeces in significantly lower numbers than the wild type and was impaired in its ability to colonize the cecum. Previous studies have implicated binding of extracellular matrix proteins as a possible mechanism forS.Typhimurium intestinal persistence. A gluthathione‐S‐transferase (GST) fusion protein to the MisL passenger domain (GST–MisL29‐281) was constructed to investigate binding to extracellular matrix proteins. In a solid‐phase binding assay the purified GST–MisL29‐281fusion protein bound to fibronectin and collagen IV, but not to collagen I. MisL expression was not detected by Western blot inS.Typhimurium grown under standard laboratory conditions. However, when expression of the clonedmisLgene was driven by theEscherichia coliarabinose promoter, MisL could be detected in theS.Typhimurium outer membrane by Western blot and on the bacterial cell surface by flow cytometry. Expression of MisL enabledS.Typhimurium to bind fibronectin to its cell surface, resulting in attachment to fibronectin‐coated glass slides and in increased invasiveness for human epithelial cells derived from colonic carcinoma (T84 cells). These data identify MisL as an extracellular matrix adhesin involved in intestinal colonization.
The PhoP/PhoQ system controls the intramacrophage type three secretion system of Salmonella enterica
Authors: Bijlsma Jetta J. E. , Groisman Eduardo A. 
Published: June 2005

SummarySpi/Ssa is a unique type three secretion system that functions exclusively when Salmonella enterica is inside eukaryotic cells. Expression of the Spi/Ssa system and its secreted effectors is dependent on SsrB/SpiR, a two‐component regulatory system encoded in the SPI‐2 pathogenicity island that also harbours the spi/ssa genes. Here we determine that the PhoP/PhoQ two‐component system controls the intramacrophage expression of spi/ssa genes by regulating the SsrB/SpiR system. We establish that PhoP regulates transcription of the response regulator SsrB and demonstrate binding of the PhoP protein to the ssrB promoter both in vivo using chromatin immunoprecipitation in Salmonella‐infected macrophages, and in vitro using purified PhoP protein. We show that PhoP controls the SpiR sensor post‐transcriptionally and identify a region in the 5′ untranslated region of the spiR message that is required for this effect. The demonstration that the PhoP/PhoQ system is directly involved in the regulation of the SPI‐2 pathogenicity island highlights PhoP/PhoQ's central role in Salmonella virulence. We suggest that different regulatory systems convey distinct signals over time to produce the SsrB/SpiR system, which then modulates expression of the Spi/Ssa apparatus and secreted effectors.
Structural basis for segmental gene conversion in generation of Anaplasma marginale outer membrane protein variants
Authors: Futse James E. , Brayton Kelly A. , Knowles Donald P. , Palmer Guy H. 
Published: June 2005

SummaryBacterial pathogens in the genus Anaplasma generate surface coat variants by gene conversion of chromosomal pseudogenes into single‐expression sites. These pseudogenes encode unique surface‐exposed hypervariable regions flanked by conserved domains, which are identical to the expression site flanking domains. In addition, Anaplasma marginale generates variants by recombination of oligonucleotide segments derived from the pseudogenes into the existing expression site copy, resulting in a combinatorial increase in variant diversity. Using the A. marginale genome sequence to track the origin of sequences recombined into the msp2 expression site, we demonstrated that the complexity of the expressed msp2 increases during infection, reflecting a shift from recombination of the complete hypervariable region of a given pseudogene to complex mosaics with segments derived from hypervariable regions of different pseudogenes. Examination of the complete set of 1183 variants with segmental changes revealed that 99% could be explained by one of the recombination sites occurring in the conserved flanking domains and the other within the hypervariable region. Consequently, we propose an ‘anchoring’ model for segmental gene conversion whereby the conserved flanking sequences tightly align and anchor the expression site sequence to the pseudogene. Associated with the recombination sites were deletions, insertions and substitutions; however, these are a relatively minor contribution to variant generation as these occurred in less than 2% of the variants. Importantly, the anchoring model, which can account for more variants than a strict segmental sequence identity mechanism, is consistent with the number of msp2 variants predicted and empirically identified during persistent infection.
The ClpX chaperone modulates assembly of the tubulin‐like protein FtsZ
Authors: Weart Richard B. , Nakano Shunji , Lane Brooke E. , Zuber Peter , Levin Petra Anne 
Published: June 2005

SummaryAssembly of the tubulin‐like cytoskeletal protein FtsZ into a ring structure establishes the location of the nascent division site in prokaryotes. Factors that modulate FtsZ assembly are essential for ensuring the precise spatial and temporal regulation of cytokinesis. We have identified ClpX, the substrate recognition subunit of the ClpXP protease, as an inhibitor of FtsZ assembly in Bacillus subtilis. Genetic data indicate that ClpX but not ClpP inhibits FtsZ‐ring formation in vivo. In vitro, ClpX inhibits FtsZ assembly in a ClpP‐independent manner through a mechanism that does not require ATP hydrolysis. Together our data support a model in which ClpX helps maintain the cytoplasmic pool of unassembled FtsZ that is required for the dynamic nature of the cytokinetic ring. ClpX is conserved throughout bacteria and has been shown to interact directly with FtsZ in Escherichia coli. Thus, we speculate that ClpX functions as a general regulator of FtsZ assembly and cell division in a wide variety of bacteria.
RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double‐strand breaks
Authors: Meddows Tom R. , Savory Andrew P. , Grove Jane I. , Moore Timothy , Lloyd Robert G. 
Published: June 2005

SummaryIn rapidly dividing bacterial cells, the machinery for repair of DNA double‐strand breaks has to contend not only with the forces driving replication and transmission of the DNA but also its transcription. By exploiting I‐SceI homing endonuclease to break the Escherichia coli chromosome at one or more defined locations, we have been able to investigate how these processes are co‐ordinated and repair is accomplished. When breaks are induced at a single site, the SOS‐inducible RecN protein and the transcription factor DksA combine to promote efficient repair. When induced at two or more, distantly located sites, RecN becomes almost indispensable. Many cells that do survive have extensive deletions of sequences flanking the break, with end points often coinciding with imperfect repeat elements. These findings herald a much greater complexity for chromosome repair than suggested by current mechanistic models and reveal a role for RecN in protecting the chromosome from break‐induced chromosome rearrangements.
Multiple Rieske genes in prokaryotes: exchangeable Rieske subunits in the cytochrome bc1‐complex of Rubrivivax gelatinosus
Authors: Ouchane Soufian , Nitschke Wolfgang , Bianco Pierre , Vermeglio André , Astier Chantal 
Published: June 2005

SummaryBacterial cytochrome bc1‐complex encoded by the petABC operon consists of three subunits, the Rieske iron‐sulphur protein, the b‐type cytochrome, and the c1‐type cytochrome. Disruption of the petA gene of Rubrivivax gelatinosus is not lethal under photosynthetic growth conditions. However, deletion of both petA and petB results in a photosynthesis‐deficient strain, suggesting the presence of a second gene encoding a Rieske protein and rescuing a functional cytochrome bc1‐complex in the PETA1 mutant. The corresponding petA2 gene was identified and the PETA2 mutant could also grow under photosynthetic conditions. The double mutant PETA12, however, was unable to grow photosynthetically. The presence of a photo‐induced cyclic electron transfer was tested by monitoring the kinetics of cytochrome photo‐oxidation on intact cells; the data confirm the capacity of petA2 to replace petA1 in the bc1‐complex to support photosynthesis. Soluble forms of both PetA1 and PetA2 Rieske proteins were purified from Escherichia coli and found to contain correctly inserted [2Fe‐2S] clusters. Electron paramagnetic resonance (EPR) spectroscopy and midpoint potential measurements showed typical [2Fe‐2S] signals and Em values of +275 mV for both Rieske proteins. The high amino acid sequence similarity and the obtained midpoint potential values argue for a functional role of these proteins in the cytochrome bc1‐complex. The presence of duplicated Rieske genes is not restricted to R. gelatinosus. Phylogenetic trees of Rieske genes from Rubrivivax and other proteobacteria as well as from cyanobacteria were reconstructed. On the basis of the phylogenetic analyses, differing evolutionary origins of duplicated Rieske genes in proteo‐ and cyanobacteria are proposed.
Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor‐independent hydroxylation of xanthine via α‐ketoglutarate‐dependent dioxygenases
Authors: Cultrone Antonietta , Scazzocchio Claudio , Rochet Michel , Montero‐Morán Gabriela , Drevet Christine , Fernández‐Martín Rafael 
Published: June 2005

SummaryThe xanthine oxidases and dehydrogenases are among the most conserved enzymes in all living kingdoms. They contain the molybdopterin cofactor Moco. We show here that in the fungi, in addition to xanthine dehydrogenase, a completely different enzyme is able to catalyse the oxidation of xanthine to uric acid. In Aspergillus nidulans this enzyme is coded by the xanA gene. We have cloned the xanA gene and determined its sequence. A deletion of the gene has the same phenotype as the previously known xanA1 miss‐sense mutation. Homologues of xanA exist only in the fungal kingdom. We have inactivated the cognate gene of Schizosaccharomyces pombe and this results in strongly impaired xanthine utilization as a nitrogen source. We have shown that the Neurospora crassa homologue is functionally equivalent to xanA. The enzyme coded by xanA is an α‐ketoglutarate‐ and Fe(II)‐dependent dioxygenase which shares a number of properties with other enzymes of this group. This work shows that only in the fungal kingdom, an alternative mechanism of xanthine oxidation, not involving Moco, has evolved using the dioxygenase scaffold.
Mapping of essential replication functions of the linear plasmid lp17 of B. burgdorferi by targeted deletion walking
Authors: Beaurepaire Cécile , Chaconas George 
Published: June 2005

SummaryThe genome of the Lyme disease pathogen Borrelia burgdorferi strain B31 MI includes one linear chromosome, 10 circular and 12 linear plasmids. Members of four paralogous gene families, revealed by genome sequencing, have been suggested as replication/partition functions for both the linear and circular plasmids. Some of these genes have been experimentally shown to be essential for the replication of the B. burgdorferi replicons that encode them. In this study, we located the region essential for replication of lp17, the second smallest linear plasmid in B. burgdorferi. We used a novel in vivo method, targeted deletion walking, to systematically delete DNA from either the left or right end of lp17. We report that the region essential for replication of lp17 is 1.8 kb (bp 7946–9766) and contains only one intact open reading frame (BBD14). Expression of BBD14 is required for the replication, suggesting that it is the replication initiator for lp17. The BBD14 protein is a member of paralogous family (PF) 62 and we present the first experimental evidence for the role of a PF 62 member. Adjacent non‐coding sequences are also required, suggesting that the origin lies at least partially outside the coding region. Surprisingly, deletion of BBD21, the ParA orthologue (PF 32), had little effect upon plasmid stability or incompatibility. Finally, data are presented suggesting that lp17 replication occurs preferentially on a linear rather than a circular DNA molecule.
Swi/SNF‐GCN5‐dependent chromatin remodelling determines induced expression of GDH3, one of the paralogous genes responsible for ammonium assimilation and glutamate biosynthesis in Saccharomyces cerevisiae
Authors: Avendaño Amaranta , Riego Lina , DeLuna Alexander , Aranda Cristina , Romero Guillermo , Ishida Cecilia , Vázquez‐Acevedo Miriam , Rodarte Beatriz , Recillas‐Targa Félix , Valenzuela Lourdes , Zonszein Sergio , González Alicia 
Published: June 2005

SummaryIt is accepted that Saccharomyces cerevisiae genome arose from complete duplication of eight ancestral chromosomes; functionally normal ploidy was recovered because of the massive loss of 90% of duplicated genes. There is evidence that indicates that part of this selective conservation of gene pairs is compelling to yeast facultative metabolism. As an example, the duplicated NADP‐glutamate dehydrogenase pathway has been maintained because of the differential expression of the paralogous GDH1 and GDH3 genes, and the biochemical specialization of the enzymes they encode. The present work has been aimed to the understanding of the regulatory mechanisms that modulate GDH3 transcriptional activation. Our results show that GDH3 expression is repressed in glucose‐grown cultures, as opposed to what has been observed for GDH1, and induced under respiratory conditions, or under stationary phase. Although GDH3 pertains to the nitrogen metabolic network, and its expression is Gln3p‐regulated, complete derepression is ultimately determined by the carbon source through the action of the SAGA and SWI/SNF chromatin remodelling complexes. GDH3 carbon‐mediated regulation is over‐imposed to that exerted by the nitrogen source, highlighting the fact that operation of facultative metabolism requires strict control of enzymes, like Gdh3p, involved in biosynthetic pathways that use tricarboxylic acid cycle intermediates.
An ATP‐binding cassette‐type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein
Authors: Müller Axel , Thomas Gavin H. , Horler Richard , Brannigan James A. , Blagova Elena , Levdikov Vladimir M. , Fogg Mark J. , Wilson Keith S. , Wilkinson Anthony J. 
Published: June 2005

Summary Campylobacter jejuni is a Gram‐negative food‐borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain–Barré syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two‐domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a Kd of ∼10−7 M consistent with a role as a receptor for a high‐affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC‐type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni.
Atypical antipsychotics: newer options for mania and maintenance therapy
Authors: Vieta Eduard , Goikolea Jose M 
Published: June 2005

Atypical antipsychotics have been used to treat patients with schizophrenia for many years, but now there is increasing evidence of their utility in the treatment of bipolar disorder. In the past few years several atypical agents have received regulatory approval for use in bipolar mania. Through a review of randomized controlled trials for five commonly used atypical drugs, olanzapine, risperidone, quetiapine, ziprasidone and aripiprazole, this article evaluates their efficacy in the acute and maintenance phases of bipolar disorder. The evidence shows that atypical antipsychotics are effective in the treatment of manic symptoms, either alone or in combination with traditional mood stabilizers such as lithium and divalproex. Although emerging data indicate that atypical antipsychotics will be a promising addition to those therapies that are currently available for managing patients during the maintenance phase of bipolar illness, their potential in the long‐term management of bipolar disorder remains to be fully explored.Atypical antipsychotics appear to have broadly similar efficacy against manic symptoms of bipolar disorder, but there are important differences in their tolerability profiles, which are likely to be of particular relevance during long‐term treatment. A brief assessment of tolerability issues surrounding the use of atypical agents in bipolar disorder and other aspects of treatment that have impact on the clinical effectiveness of the therapy are considered.
Evaluation of the effectiveness of sildenafil using questionnaire methods versus audio‐visual sexual stimulation
Authors: SUETOMI TAKAHIRO , ENDO FUMIYASU , TAKESHIMA HITOSHI , AKAZA HIDEYUKI 
Published: June 2005

Abstract  Aim:  In the present study, an audio‐visual sexual stimulation (AVSS) test was used to evaluate the effectiveness of sildenafil, and the AVSS test was coevaluated with the international index of erectile function (IIEF) questionnaire.Methods:  Forty‐two patients with erectile dysfunction (ED) were examined (age range, 28–73 years; mean, 51.9 ± 11.4 years). Each patient answered the IIEF questionnaire and underwent laboratory tests and the AVSS test before administration of sildenafil. The IIEF questionnaire and AVSS test (1 h after administration of 25 mg or 50 mg sildenafil) were re‐evaluated in the outpatient clinic 4 weeks later. Questions 3 and 4 of the IIEF test were used to evaluate the effectiveness of sildenafil. Sildenafil was determined to be effective if each score totalled four or five after administration.Results:  The rate of effectiveness of sildenafil was 52.4%, and the mean score of the IIEF 5 improved from 7.2 to 15.4 following treatment with sildenafil. The maximum and mean rigidity of the penile tip improved after the sildenafil treatment (36.1%vs 57.7% and 14.2%vs 35.8%, respectively). The maximum and mean rigidity of the penile base rose (42.4%vs 57.7% and 17.9%vs 36.8, respectively). Similarly, following treatment with sildenafil, the penile tumescence increased from 6.6 cm to 7.6 cm at the penile tip and from 7.5 cm to 8.5 cm at the penile base.Conclusions:  In some ED patients the results of the IIEF questionnaire are not always consistent with those of objective evaluation, including AVSS. In these patients, combined assessment using the IIEF and AVSS might be more useful to evaluate the precise effectiveness of sildenafil, rather than relying on the IIEF results alone.