bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcium signalling in bacteria
Authors: Dominguez Delfina C. 
Published: October 2004

SummaryWhereas the importance of calcium as a cell regulator is well established in eukaryotes, the role of calcium in prokaryotes is still elusive. Over the past few years, there has been an increased interest in the role of calcium in bacteria. It has been demonstrated that as in eukaryotic organisms, the intracellular calcium concentration in prokaryotes is tightly regulated ranging from 100 to 300 nM. It has been found that calcium ions are involved in the maintenance of cell structure, motility, transport and cell differentiation processes such as sporulation, heterocyst formation and fruiting body development. In addition, a number of calcium‐binding proteins have been isolated in several prokaryotic organisms. The characterization of these proteins and the identification of other factors suggest the possibility that calcium signal transduction exists in bacteria. This review presents recent developments of calcium in bacteria as it relates to signal transduction.
Analysis of the N‐terminal DNA binding domain of the IS30 transposase
Authors: Nagy Zita , Szabó Mónika , Chandler Michael , Olasz Ferenc 
Published: October 2004

SummaryIS30 is the founding member of a large family of widely spread bacterial insertion sequences with closely related transposases. The N‐terminal end of the IS30 transposase had been shown to retain sequence‐specific DNA binding activity and to protect the IS30 terminal inverted repeats. Structural predictions revealed the presence of a helix–helix–turn–helix motif (H–HTH2) which, in the case of IS30, is preceded by an additional helix–turn–helix motif (HTH1). Analysis of deletion and point mutants in this region revealed that both motifs are important for IS30 transposition. IS30 exhibits two types of insertion specificity preferring either a 24 bp palindromic hot‐spot (GOHS) or sequences resembling its ends [left and right terminal inverted repeat (IRL and IRR)]. Results are presented suggesting that the HTH1 region is required for GOHS targeting and interferes with the inverted repeat (IR) targeting. On the other hand, H–HTH2 appears to be required for both. The binding activities of the mutant proteins to the terminal IS30 IRs as measured by gel retardation correlated well with these results. Furthermore, close inspection of the H–HTH2 region revealed significant amino acid identity with a similar predicted secondary structure carried by the transcriptional regulator FixJ of Sinorhizobium meliloti and involved in FixJ binding to its target sequence. This suggests that FixJ and IS30 transposase share similar sequence‐specific DNA binding mechanisms.
Communication between Eσ54, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF σ54‐dependent activator during transcription activation
Authors: Bordes Patricia , Wigneshweraraj Siva R. , Chaney Matthew , Dago Angel E. , Morett Enrique , Buck Martin 
Published: October 2004

SummaryConversion of Eσ54 closed promoter complexes to open promoter complexes requires specialized activators which are members of the AAA (ATPases Associated with various cellular Activities) protein family. The ATP binding and hydrolysis activity of Eσ54 activators is used in an energy coupling reaction to remodel the Eσ54 closed promoter complex and to overcome the σ54‐imposed block on open complex formation. The remodelling target for the AAA activator within the Eσ54 closed complex includes a complex interface contributed to by Region I of σ54, core RNA polymerase and a promoter DNA fork junction structure, comprising the Eσ54 regulatory centre. One σ54 binding surface on Eσ54 activators is a conserved sequence known as the GAFTGA motif. Here, we present a detailed characterization of the interaction between Region I of σ54 and the Escherichia coli AAA σ54 activator Phage shock protein F. Using Eσ54 promoter complexes that mimic different conformations adopted by the DNA during open complex formation, we investigated the contribution of the conserved threonine residue in the GAFTGA motif to transcription activation. Our results suggest that the organization of the Eσ54 regulatory centre, and in particular the conformation adopted by the σ54 Region I and the DNA fork junction structure during open complex formation, is communicated to the AAA activator via the conserved T residue of the GAFTGA motif.
Candida albicans lacking the frataxin homologue: a relevant yeast model for studying the role of frataxin
Authors: Santos Renata , Buisson Nicole , Knight Simon A. B. , Dancis Andrew , Camadro Jean‐Michel , Lesuisse Emmanuel 
Published: October 2004

SummaryWe cloned the CaYFH1 gene that encodes the yeast frataxin homologue in Candida albicans. CaYFH1 was expressed in Δyfh1 Saccharomyces cerevisiae cells, where it compensated for all the phenotypes tested except for the lack of cytochromes. Double ΔCayfh1/ΔCayfh1 mutant had severe defective growth, accumulated iron in their mitochondria, lacked aconitase and succinate dehydrogenase activity and had defective respiration. The reductive, siderophore and haem uptake systems were constitutively induced and the cells excreted flavins, thus behaving like iron‐deprived wild‐type cells. Mutant cells accumulated reactive oxygen species and were hypersensitive to oxidative stress, but not to iron. Cytochromes were less abundant in mutants than in wild‐type cells, but this did not result from defective haem synthesis. The low cytochrome concentration in mutant cells was comparable to that of iron‐deprived wild‐type cells. Mitochondrial iron was still available for haem synthesis in ΔCayfh1/ΔCayfh1 cells, in contrast to S. cerevisaeΔyfh1 cells. CaYFH1 transcription was strongly induced by iron, which is consistent with a role of CaYfh1 in iron storage. Iron also regulated transcription of CaHEM14 (encoding protoporphyrinogen oxidase) but not that of CaHEM15 (encoding ferrochelatase). There are thus profound differences between S. cerevisiae and C. albicans in terms of haem synthesis, cytochrome turnover and the role of frataxin in these processes.
An in vivo inducible gene of Pseudomonas aeruginosa encodes an anti‐ExsA to suppress the type III secretion system
Authors: Ha Un‐Hwan , Kim Jaewha , Badrane Hassan , Jia Jinghua , Baker Henry V. , Wu Donghai , Jin Shouguang 
Published: October 2004

SummaryWe have previously reported on the isolation of in vivo inducible genes of Pseudomonas aeruginosa using IVET system. One of such genes isolated from burn mouse infection model encodes a short open reading frame with unknown function. In this study, we demonstrate that this gene product specifically suppresses the expression of type III secretion genes in P. aeruginosa, thus named PtrA (Pseudomonas type III repressor A). A direct interaction between the PtrA and type III transcriptional activator ExsA was demonstrated, suggesting that its repressor function is probably realized through inhibition of the ExsA protein function. Indeed, an elevated expression of the exsA compensates the repressor effect of the PtrA. Interestingly, expression of the ptrA is highly and specifically induced by copper cation. A copper‐ responsive two‐component regulatory system, copR‐copS, has also been identified and shown to be essential for the copper resistance in P. aeruginosa as well as the activation of ptrA in response to the copper signal. Elevated expression of the ptrA during the infection of mouse burn wound suggests that P. aeruginosa has evolved tight regulatory systems to shut down energy‐expensive type III secretion apparatus in response to specific environmental signals, such as copper stress.
Enterococcus faecalis pheromone‐responsive protein PrgX: genetic separation of positive autoregulatory functions from those involved in negative regulation of conjugative plasmid transfer
Authors: Kozlowicz Briana K. , Bae Taeok , Dunny Gary M. 
Published: October 2004

SummaryThe pCF10 plasmid in Enterococcus faecalis transfers from donor cells to recipients upon induction via peptide pheromone. Two plasmid‐encoded negative regulators produced from the same transcript, PrgX protein and Qa RNA, repress conjugation genes in uninduced donor cells. PrgX positively autoregulates production of both itself and mature Qa RNA, and is believed to repress the prgQ promoter in a pheromone‐sensitive fashion. Previous analysis of PrgX was complicated because mutations in prgX affecting regulation of conjugation also disrupted PrgX autoregulation, suggesting the two functions might be inseparable. In this study, we isolated 14 single amino acid substitutions in PrgX that reduced or eliminated repression of prgQ, without affecting autoregulation or DNA binding. PrgX was shown to bind to its cognate pheromone, cCF10, and most of the mutations lowered the affinity of PrgX for cCF10. Dimerization was affected by five of the mutations and the data indicate that it is required, but insufficient for pheromone induction. We propose a new model for the mechanism used by PrgX for regulation of the prgQ promoter, PrgX autoregulation, and Qa RNA processing.
A regulation cascade controls expression of Porphyromonas gingivalis fimbriae via the FimR response regulator
Authors: Nishikawa Kiyoshi , Yoshimura Fuminobu , Duncan Margaret J. 
Published: October 2004

SummaryLittle is known about how Porphyromonas gingivalis, a Gram‐negative oral anaerobe, senses environmental changes, and how such information is transmitted to the cell. The production of P. gingivalis surface fimbriae is regulated by FimS–FimR, a two component signal transduction system. Expression of fimA, encoding the fimbrilin protein subunit of fimbriae, is positively regulated by the FimR response regulator. In this study we investigated the molecular mechanisms of FimR regulation of fimA expression. Comparative transcription profiling of fimR wild‐type and mutant strains shows that FimR controls the expression of several genes including five clustered around the fimA locus. Chromatin immunoprecipitation assays and electrophoretic mobility shift assays identify and confirm that FimR binds to the promoter region of the first gene in the fimA cluster. Gene expression analyses of mutant strains reveal a transcriptional cascade involving multiple steps, with FimR activating expression of the first gene of the cluster that encodes a key regulatory protein.
Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system
Authors: Hubber Andree , Vergunst Annette C. , Sullivan John T. , Hooykaas Paul J. J. , Ronson Clive W. 
Published: October 2004

SummaryThe symbiosis island of Mesorhizobium loti strain R7A contains genes with strong similarity to the structural vir genes (virB1‐11; virD4) of Agrobacterium tumefaciens that encode the type IV secretion system (T4SS) required for T‐DNA transfer to plants. In contrast, M. loti strain MAFF303099 lacks these genes but contains genes not present in strain R7A that encode a type III secretion system (T3SS). Here we show by hybridization analysis that most M. loti strains contain the VirB/D4 T4SS and not the T3SS. Strikingly, strain R7A vir gene mutants formed large nodules containing bacteroids on Leucaena leucocephala in contrast to the wild‐type strain that formed only uninfected tumour‐like structures. A rhcJ T3SS mutant of strain MAFF303099 also nodulated L. leucocephala, unlike the wild type. On Lotus corniculatus, the vir mutants were delayed in nodulation and were less competitive compared with the wild type. Two strain R7A genes, msi059 and msi061, were identified through their mutant phenotypes as possibly encoding translocated effector proteins. Both Msi059 and Msi061 were translocated through the A. tumefaciens VirB/D4 system into Saccharomyces cerevisiae and Arabidopsis thaliana, as shown using the Cre recombinase Reporter Assay for Translocation (CRAfT). Taken together, these results suggest that the VirB/D4 T4SS of M. loti R7A plays an analogous symbiotic role to that of T3SS found in other rhizobia. The heterologous translocation of rhizobial proteins by the Agrobacterium VirB/D4 T4SS is the first demonstration that rhizobial effector proteins are translocated into plant cells and confirms functional conservation between the M. loti and A. tumefaciens T4SS.
The PAK family kinase Cla4 is required for budding and morphogenesis in Ustilago maydis
Authors: Leveleki Leonora , Mahlert Michael , Sandrock Björn , Bölker Michael 
Published: October 2004

SummaryThe phytopathogenic basidiomycete Ustilago maydis displays a dimorphic switch between budding growth of haploid cells and filamentous growth of the dikaryon. In a screen for mutants affected in morphogenesis and cytokinesis, we identified the serine/threonine protein kinase Cla4, a member of the family of p21‐activated kinases (PAKs). Cells, in which cla4 has been deleted, are viable but they are unable to bud properly. Instead, cla4 mutant cells grow as branched septate hyphae and divide by contraction and fission at septal cross walls. Delocalized deposition of chitinous cell wall material along the cell surface is observed in cla4 mutant cells. Deletion of the Cdc42/Rac1 interaction domain (CRIB) results in a constitutive active Cla4 kinase, whose expression is lethal for the cell. cla4 mutant cells are unable to induce pathogenic development in plants and to display filamentous growth in a mating reaction, although they are still able to secrete pheromone and to undergo cell fusion with wild‐type cells. We propose that Cla4 is involved in the regulation of cell polarity during budding and filamentation.
Differential regulation of ACC synthase genes in cold‐dependent and ‐independent ripening in pear fruit
Authors: EL‐SHARKAWY I. , JONES B. , GENTZBITTEL L. , LELIÈVRE J.‐M. , PECH J. C. , LATCHÉ A. 
Published: October 2004

ABSTRACTLate pear cultivars such as Passe‐Crassane (PC) require a long chilling treatment before they are capable of ripening. Early cultivars such as Old‐Home (OH) have no cold prerequisite. The regulation of 1‐aminocyclopropane‐1‐carboxylic acid synthase (ACS) genes was studied in OH, PC and in OH × PC hybrids in order to determine the role of this gene family in the cold requirement. Of the seven Pc‐ACS cDNAs isolated, four (Pc‐ACS1a/b and Pc‐ACS2a/b) showed differential expression associated with the cold requirement. Pc‐ACS1a transcripts accumulated throughout the cold treatment and, with Pc‐ACS2a, during ripening of cold‐dependent cultivars. Pc‐ACS1b and Pc‐ACS2b were detected only during ripening of cold‐independent genotypes. Furthermore, Pc‐ACS2a transcript accumulation was negatively regulated by ethylene, whereas Pc‐ACS2b was positively regulated by the hormone. Pc‐ACS3, 4 and 5 transcript accumulation was similar in all genotypes. Genetic analyses of OH, PC, and 22 OH × PC progenies demonstrated that late, cold‐dependent cultivars were homozygous for Pc‐ACS1a and 2a whereas early, cold‐independent cultivars were heterozygous for Pc‐ACS1(a/b) and homozygous for Pc‐ACS2b. A model is presented in which differences in Pc‐ACS alleles and gene expression between cold‐ and non‐cold‐requiring pears are critical in determining the ripening behaviour of the cultivars.
Does oxygen limit nitrogenase activity in soybean exposed to elevated CO2?
Authors: CEN Y.‐P. , LAYZELL D. B. 
Published: October 2004

ABSTRACTSoybean (Glycine max L. Merr) plants grown under control (360 µmol mol−1) or elevated CO2 concentration (800 µmol mol−1) from 33 to 42 d after sowing were assayed for various components of in vivo nitrogenase activity to test the hypothesis that increasing carbohydrate supply to nodules would increase the potential (i.e. O2 saturated) nitrogenase activity and impose a more severe O2 limitation on both nodule metabolism and total nitrogenase activity. Within 51 h of elevated CO2 treatment, significant increases relative to control plants were seen in total nitrogenase activity expressed per plant. After 6 d of elevated CO2, the total nitrogenase activity per plant was 18% higher than that in control. This was attributed to an initial increase in nodule size, and a subsequent increase in nodule number following plant exposure to elevated CO2. However, after 9 d of elevated CO2, the potential and total nitrogenase activities per gram nodule dry weight were lower, not higher than corresponding values in plants in the control treatment. These results did not support the hypothesis. It was concluded that the metabolic capacity of the control nodules were not limited by carbohydrate supply, at least at the assay temperatures employed here.
Acclimation of a terrestrial plant to submergence facilitates gas exchange under water
Authors: MOMMER L. , PEDERSEN O. , VISSER E. J. W. 
Published: October 2004

ABSTRACTFlooding imposes stress upon terrestrial plants since it severely hampers gas exchange rates between the shoot and the environment. The resulting oxygen deficiency is considered to be the major problem for submerged plants. Oxygen microelectrode studies have, however, shown that aquatic plants maintain relatively high internal oxygen pressures under water, and even may release oxygen via the roots into the sediment, also in dark. Based on these results, we challenge the dogma that oxygen pressures in submerged terrestrial plants immediately drop to levels at which aerobic respiration is impaired. The present study demonstrates that the internal oxygen pressure in the petioles of Rumex palustris plants under water is indeed well above the critical oxygen pressure for aerobic respiration, provided that the air‐saturated water is not completely stagnant. The beneficial effect of shoot acclimation of this terrestrial plant species to submergence for gas exchange capacity is also shown. Shoot acclimation to submergence involved a reduction of the diffusion resistance to gases, which was not only functional by increasing diffusion of oxygen into the plant, but also by increasing influx of CO2, which enhances underwater photosynthesis.
Differential expression of dehydrin genes in wild barley, Hordeum spontaneum, associated with resistance to water deficit
Authors: SUPRUNOVA T. , KRUGMAN T. , FAHIMA T. , Chen G. , SHAMS I. , KOROL A. , NEVO E. 
Published: October 2004

ABSTRACTDehydrin gene (Dhn) expression is associated with plant response to dehydration. The aim of the present study was to investigate the association of differential expression of Dhn genes (Dhn 1, 3, 5, 6, and 9) with drought tolerance found in wild barley (Hordeum spontaneum). Tolerant and sensitive genotypes were identified from Israeli (Tabigha microsite) and Jordanian (Jarash and Waddi Hassa) populations (based on scoring of water loss rate of 390 genotypes). The five Dhn genes were up‐regulated by dehydration in resistant and sensitive wild barley genotypes. Notably, differences between resistant and sensitive genotypes were detected, mainly in the expression of Dhn1 and Dhn6 genes, depending on the duration of dehydration stress. Dhn1 tended to react earlier (after 3 h) and higher (12 h and 24 h) in resistant compared to sensitive genotypes. The level of expression of Dhn6 was significantly higher in the resistant genotypes at the earlier stages after stress. However, after 12 and 24 h Dhn6 expression was relatively higher in sensitive genotypes. The present results may indicate that these genes have some functional role in the dehydration tolerance in wild barley. The authors suggest that the observed differences of Dhn expression in wild barley, originating from different micro‐ and macro ecogeographic locations, may be the result of adaptive edaphic and climatic selective pressures.
Distribution, developmental and stress responses of antioxidant metabolism in Malus
Authors: DAVEY M. W. , FRANCK C. , KEULEMANS J. 
Published: October 2004

ABSTRACTA comprehensive study was carried out to examine the interactions between the two major hydrophilic antioxidants l‐ascorbate (vitamin C, l‐AA), and glutathione (γ‐glutamyl cysteinylglycine, GSH), and other antioxidant pools in tissues of Malus, to identify factors affecting steady‐state cellular concentrations. We show that in Malus, each tissue type has a characteristic and different l‐AA/GSH ratio and that in fruit, exocarp (epidermal) tissue acclimated to high light has higher l‐AA levels but lower GSH levels than shaded (green) areas. Maturing seeds were characterized by the highest concentrations of GSH and a highly oxidized l‐AA pool. It is demonstrated that fruit seeds are capable of l‐AA biosynthesis, but that this occurs exclusively by means of the Smirnoff–Wheeler pathway. By contrast, foliar tissue was also able to synthesize l‐AA using uronic acid substrates. Unlike the fruit of some other plant species however, the remaining fruit tissues are incapable of de novol‐AA biosynthesis. The observed differences in the steady‐state concentrations of l‐AA and GSH and the capacity to withstand stress in fruit, were also independent of the rates of uptake of photosynthate or of l‐AA, but were correlated with the protective effect provided by phenolic compounds in these tissues. During development and maturation, l‐AA and GSH levels in apple fruit declined steadily while foliar levels remained essentially constant throughout. However there was no apparent relationship between the free sugar contents of the fruit and antioxidant concentrations.
Transcriptional Response of
Candida albicans
upon Internalization by Macrophages
Authors: Lorenz Michael C. , Bender Jennifer A. , Fink Gerald R. 
Published: October 2004

ABSTRACT

The opportunistic fungal pathogen
Candida albicans
is both a benign gut commensal and a frequently fatal systemic pathogen. The interaction of
C. albicans
with the host's innate immune system is the primary factor in this balance; defects in innate immunity predispose the patient to disseminated candidiasis. Because of the central importance of phagocytic cells in defense against fungal infections, we have investigated the response of
C. albicans
to phagocytosis by mammalian macrophages using genomic transcript profiling. This analysis reveals a dramatic reprogramming of transcription in
C. albicans
that occurs in two successive steps. In the early phase cells shift to a starvation mode, including gluconeogenic growth, activation of fatty acid degradation, and downregulation of translation. In a later phase, as hyphal growth enables
C. albicans
to escape from the macrophage, cells quickly resume glycolytic growth. In addition, there is a substantial nonmetabolic response imbedded in the early phase, including machinery for DNA damage repair, oxidative stress responses, peptide uptake systems, and arginine biosynthesis. Further, a surprising percentage of the genes that respond specifically to macrophage contact have no known homologs, suggesting that the organism has undergone substantial evolutionary adaptations to the commensal or pathogen lifestyle. This transcriptional reprogramming is almost wholly absent in the related, but nonpathogenic, yeast
Saccharomyces cerevisiae
, suggesting that these large-scale and coordinated changes contribute significantly to the ability of this organism to survive and cause disease in vivo.