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Eukaryotic Organisms (eukaryotic + organism)
Selected AbstractsHistone modifications and chromatin dynamics: a focus on filamentous fungiFEMS MICROBIOLOGY REVIEWS, Issue 3 2008Gerald Brosch Abstract The readout of the genetic information of eukaryotic organisms is significantly regulated by modifications of DNA and chromatin proteins. Chromatin alterations induce genome-wide and local changes in gene expression and affect a variety of processes in response to internal and external signals during growth, differentiation, development, in metabolic processes, diseases, and abiotic and biotic stresses. This review aims at summarizing the roles of histone H1 and the acetylation and methylation of histones in filamentous fungi and links this knowledge to the huge body of data from other systems. Filamentous fungi show a wide range of morphologies and have developed a complex network of genes that enables them to use a great variety of substrates. This fact, together with the possibility of simple and quick genetic manipulation, highlights these organisms as model systems for the investigation of gene regulation. However, little is still known about regulation at the chromatin level in filamentous fungi. Understanding the role of chromatin in transcriptional regulation would be of utmost importance with respect to the impact of filamentous fungi in human diseases and agriculture. The synthesis of compounds (antibiotics, immunosuppressants, toxins, and compounds with adverse effects) is also likely to be regulated at the chromatin level. [source] VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like mannerGENES TO CELLS, Issue 7 2003Tomoyuki Fukuda Background: Inteins and group I introns found in prokaryotic and eukaryotic organisms occasionally behave as mobile genetic elements. During meiosis of the yeast Saccharomyces cerevisiae, the site-specific endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand break (DSB) at an inteinless allele, leading to VMA1 intein homing. Besides the accumulating information on the in vitro activity of VDE, very little has been known about the molecular mechanism of intein homing in yeast nucleus. Results: We developed an assay to detect the product of VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and Tid1p, and found that they all play critical roles in intein inheritance. The absence of DSB end processing proteins, Sae2p and those in the Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing efficiency. As with meiotic recombination, crossover events are frequently observed during intein homing. We also observed that the absence of premeiotic DNA replication caused by hydroxyurea (HU) or clb5, clb6, mutation reduces VDE-mediated DSBs. Conclusion: The repairing system working in intein homing shares molecular machinery with meiotic recombination induced by Spo11p. Moreover, like Spo11p-induced DNA cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced DSB. VMA1 intein thus utilizes several host factors involved in meiotic and recombinational processes to spread its genetic information and guarantee its progeny through establishment of a parasitic relationship with the organism. [source] RNA interference in ticks: a study using histamine binding protein dsRNA in the female tick Amblyomma americanumINSECT MOLECULAR BIOLOGY, Issue 3 2003M. N. Aljamali Abstract RNA interference (RNAi), a gene silencing process, has been recently exploited to determine gene function by degrading specific mRNAs in several eukaryotic organisms. We constructed a double stranded RNA (dsRNA) from a previously cloned putative Amblyomma americanum histamine binding protein (HBP) to test the significance of using this methodology in the assessment of the function and importance of gene products in ectoparasitic ticks. The female salivary glands incubated in vitro with HBP dsRNA had a significantly lower histamine binding ability. In addition, the injection of HBP dsRNA into the unfed females led both to a reduced histamine binding ability in the isolated salivary glands and to an aberrant tick feeding pattern or host response. Molecular data demonstrated less expression of the HBP mRNA in the RNAi group. Taken together, these results suggest that RNAi might be an important tool for assessing the significance of tick salivary gland secreted proteins modulating responses at the tick,host interface. [source] Evolutionary analysis of fructose 2,6-bisphosphate metabolismIUBMB LIFE, Issue 3 2006Paul A. M. Michels Abstract Fructose 2,6-bisphosphate is a potent metabolic regulator in eukaryotic organisms; it affects the activity of key enzymes of the glycolytic and gluconeogenic pathways. The enzymes responsible for its synthesis and hydrolysis, 6-phosphofructo-2-kinase (PFK-2) and fructose-2,6-bisphosphatase (FBPase-2) are present in representatives of all major eukaryotic taxa. Results from a bioinformatics analysis of genome databases suggest that very early in evolution, in a common ancestor of all extant eukaryotes, distinct genes encoding PFK-2 and FBPase-2, or related enzymes with broader substrate specificity, fused resulting in a bifunctional enzyme both domains of which had, or later acquired, specificity for fructose 2,6-bisphosphate. Subsequently, in different phylogenetic lineages duplications of the gene of the bifunctional enzyme occurred, allowing the development of distinct isoenzymes for expression in different tissues, at specific developmental stages or under different nutritional conditions. Independently in different lineages of many unicellular eukaryotes one of the domains of the different PFK-2/FBPase-2 isoforms has undergone substitutions of critical catalytic residues, or deletions rendering some enzymes monofunctional. In a considerable number of other unicellular eukaryotes, mainly parasitic organisms, the enzyme seems to have been lost altogether. Besides the catalytic core, the PFK-2/FBPase-2 has often N- and C-terminal extensions which show little sequence conservation. The N-terminal extension in particular can vary considerably in length, and seems to have acquired motifs which, in a lineage-specific manner, may be responsible for regulation of catalytic activities, by phosphorylation or ligand binding, or for mediating protein-protein interactions. IUBMB Life, 58: 133 - 141, 2006 [source] Casein Kinase I: From Obscurity to Center StageIUBMB LIFE, Issue 2 2001Erica Vielhaber Abstract The casein kinase I (CKI) family of protein kinases is a group of highly related, ubiquitously expressed serine/threonine kinases found in all eukaryotic organisms from protozoa to man. Recent advances in diverse fields, including developmental biology and chronobiology, have elucidated roles for CKI in regulating critical processes such as Wnt signaling, circadian rhythm, nuclear import, and Alzheimer's disease progression. [source] Internal amplification controls have not been employed in fungal PCR hence potential false negative resultsJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2007R.R.M. Paterson Abstract Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage. [source] Melanophores: A model system for neuronal transport and exocytosis?JOURNAL OF NEUROSCIENCE RESEARCH, Issue 12 2007Sara Aspengren Abstract Black pigment cells, melanophores, from lower vertebrates are specialized in bidirectional and coordinated translocation of pigment granules, melanosomes, in the cytoplasm. Melanophores develop from the neuronal crest and are most abundant in the dermal and epidermal layers of the skin, where the intracellular distribution of the pigment significantly influences the color of the animal. The transport of pigment is dependent on an intact cytoskeleton and motor proteins associated with cytoskeletal components. The easily cultured melanophores have proved to be excellent models for organelle transport because the intracellular movements of pigment can be visualized via light microscopy, and the granules move in response to defined chemical signals. The ease of achieving a combination of morphological and functional transport studies is the advantage of the melanophore system, and studies on pigment cells have revealed new components of the transport machinery, including molecular motors, their adapters, and transfer of vesicles to other cells. Many cellular components are transported with a combination of the actin- and microtubule-based transport systems, and, since all eukaryotic organisms rely on functional intracellular transport and an intact cytoskeleton, studies on melanophores are important for many aspects of cell biology, including axonal transport. In this review, we present an overview of the research on the pigment transport system and the potential use of pigment cells as a model system. © 2006 Wiley-Liss, Inc. [source] Calcium signalling in bacteriaMOLECULAR MICROBIOLOGY, Issue 2 2004Delfina C. Dominguez Summary Whereas 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. [source] NarE: a novel ADP-ribosyltransferase from Neisseria meningitidisMOLECULAR MICROBIOLOGY, Issue 3 2003Vega Masignani Summary Mono ADP-ribosyltransferases (ADPRTs) are a class of functionally conserved enzymes present in prokaryotic and eukaryotic organisms. In bacteria, these enzymes often act as potent toxins and play an important role in pathogenesis. Here we report a profile-based computational approach that, assisted by secondary structure predictions, has allowed the identification of a previously undiscovered ADP-ribosyltransferase in Neisseria meningitidis (NarE). NarE shows structural homologies with E. coli heat-labile enterotoxin (LT) and cholera toxin (CT) and possesses ADP-ribosylating and NAD-glycohydrolase activities. As in the case of LT and CT, NarE catalyses the transfer of the ADP-ribose moiety to arginine residues. Despite the absence of a signal peptide, the protein is efficiently exported into the periplasm of Neisseria. The narE gene is present in 25 out of 43 strains analysed, is always present in ET-5 and Lineage 3 but absent in ET-37 and Cluster A4 hypervirulent lineages. When present, the gene is 100% conserved in sequence and is inserted upstream of and co-transcribed with the lipoamide dehydrogenase E3 gene. Possible roles in the pathogenesis of N. meningitidis are discussed. [source] Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segmentPROTEIN SCIENCE, Issue 5 2009Wojciech Strzalka Abstract The proliferating cell nuclear antigen (PCNA) is well recognized as one of the essential cellular components of the DNA replication machinery in all eukaryotic organisms. Despite their prominent importance, very little biochemical and structural information about plant PCNAs is available, in comparison with that obtained from other eukaryotic organisms. We have determined the atomic resolution crystal structures of the two distinct Arabidopsis thaliana PCNAs (AtPCNA), both complexed with the C-terminal segment of human p21. Both AtPCNAs form homotrimeric ring structures, which are essentially identical to each other, including the major contacts with the p21 peptide. The structure of the amino-terminal half of the p21 peptide, containing the typical PIP box sequence, is remarkably similar to those observed in the previously reported crystal structures of the human and archaeal PCNA-PIP box complexes. Meanwhile, the carboxy-terminal halves of the p21 peptide in the plant PCNA complexes are bound to the protein in a unique manner, most probably because of crystal packing effects. A surface plasmon resonance analysis revealed high affinity between each AtPCNA and the C-terminal fragment of human p21. This result strongly suggests that the interaction is functionally significant, although no plant homologs of p21 have been identified yet. We also discovered that AtPCNA1 and AtPCNA2 form heterotrimers, implying that hetero-PCNA rings may play critical roles in cellular signal transduction, particularly in DNA repair. [source] Prediction of partial membrane protein topologies using a consensus approachPROTEIN SCIENCE, Issue 12 2002Johan Nilsson PCT, partial consensus topology; TMH, transmembrane helix Abstract We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole-genome analysis reveals that a reliable partial consensus topology can be predicted for ,70% of all membrane proteins in a typical bacterial genome and for ,55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology. [source] Insights into yeast adaptive response to the agricultural fungicide mancozeb: A toxicoproteomics approachPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009Pedro M. Santos Abstract Toxicogenomics has the potential to elucidate gene,environment interactions to identify genes that are affected by a particular chemical at the early stages of the toxicological response and to establish parallelisms between different organisms. The fungicide mancozeb, widely used in agriculture, is an ethylene-bis-dithiocarbamate complex with manganese and zinc. Exposure to this pesticide has been linked to the development of idiopathic Parkinson's disease and cancer. Given that many signalling pathways and their molecular components are substantially conserved among eukaryotic organisms, we used Saccharomyces cerevisiae to get insights into the molecular mechanisms of mancozeb toxicity and adaptation based on expression proteomics. The early global response to mancozeb was analysed by quantitative proteomics using 2-DE. The target genes (e.g. TSA1, TSA2, SOD1, SOD2, AHP1, GRE2, GRX1, CYS3, PRE3, PRE6, PRE8, PRE9, EFT1, RPS5, TIF11, HSP31, HSP26, HSP104, HSP60, HSP70 -family) and the putative main transcription activators (e.g. Yap1, Msn2/Msn4, Met4, Hsf1, Aft1, Pdr1, Skn7, Rpn4p, Gcn4) of the complex mancozeb-induced expression changes are related with yeast response to stress, in particular to oxidative stress, protein translation initiation and protein folding, disassembling of protein aggregates and degradation of damaged proteins. Our results also suggest that this study provided powerful indications that may be useful to expand the knowledge obtained in yeast not only to the global response to mancozeb toxicity in phytopathogenic fungi but also to humans. [source] The response of protist and metazoan communities in permeable pavement structures to high oil loadingsTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005S. J. COUPE Permeable pavement structures (PPS) have been demonstrated to provide an efficient and sustainable method of controlling urban derived hydrocarbon contamination. Until recently, laboratory PPS mesocosm models have used crushed granite as the load bearing sub-base material. However, the use of virgin stone may not be the optimal choice of substrate, as this is not necessarily sustainable or cost effective in the long term when compared to the use of recycled materials. However, recycled materials such as waste concrete may change the environmental conditions in PPS mesocosms, and the characteristics of the eukaryotic community may become different from those which have been previously described. In the current experiment, granite and recycled concrete sub-base materials were compared for their ability to retain 900 g/m2 of clean mineral oil applied to the mesocosm surface. It was observed that, even at this very high oil loading, 99.95% of the applied oil was retained within granite and concrete-based structures, but the effluent was two pH units more alkaline in concrete mesocosms than granite. The eukaryotic microfauna in the effluent from both mesocosm types showed a ten-fold increase in protist abundance, and a doubling in the number of protist genera, compared with earlier work using only 18 g/m2 of applied oil. Five genera of testate amoebae not previously recorded in PPS were identified, these included Arcella, Assulina, Cryptodifflugia, Cyclopyxis and Difflugia in addition to the three genera observed previously using the lower oil application. Metazoan abundances increased from 1.5 × 101 organisms per ml using the lower oil loadings to 2.0 × 103/ml in the current experiment. Rotifers and nematodes were the most numerous, but tardigrades were also observed in both concrete and granite-based mesocosms. Despite the differences in effluent pH, it was apparent that there were only marginal differences in the eukaryotic microbiology of the two mesocosm types. This was thought to be due to the layered structural arrangement of the pavement and the location of the highly oil-retentive polypropylene geotextile and extensive biofilm layer positioned above the concrete sub-base. Work is now underway to find oil loadings that will adversely affect the abundance and diversity of eukaryotic organisms in PPS mesocosms. [source] Reversal of the silencing of tetracycline-controlled genes requires the coordinate action of distinctly acting transcription factorsTHE JOURNAL OF GENE MEDICINE, Issue 1 2005Renata Pankiewicz Abstract Background Regulation of genes transferred to eukaryotic organisms is often limited by the lack of consistent expression levels in all transduced cells, which may result in part from epigenetic gene silencing effects. This reduces the efficacy of ligand-controlled gene switches designed for somatic gene transfers such as gene therapy. Methods A doxycycline-controlled transgene was stably introduced in human cells, and clones were screened for epigenetic silencing of the transgene. Various regulatory proteins were targeted to the silent transgene, to identify those that would mediate regulation by doxycycline. Results A doxycycline-controlled minimal promoter was found to be prone to gene silencing, which prevents activation by a fusion of the bacterial TetR DNA-binding domain with the VP16 activator. DNA modification studies indicated that the silenced transgene adopts a poorly accessible chromatin structure. Several cellular transcriptional activators were found to restore an accessible DNA structure when targeted to the silent transgene, and they cooperated with Tet-VP16 to mediate regulation by doxycycline. Conclusions Reversal of the silencing of a tetracycline-regulated minimal promoter requires a chromatin-remodeling activity for subsequent promoter activation by the Tet-VP16 fusion protein. Thus, distinct regulatory elements may be combined to obtain long-term regulation and persistent expression of exogenous genes in eukaryotic cells. Copyright © 2004 John Wiley & Sons, Ltd. [source] Critical catalytic functional groups in the mechanism of aspartate-,-semialdehyde dehydrogenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Julio Blanco Aspartate-,-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of ,-aspartyl phosphate to l -aspartate-,-semialdehyde in the aspartate biosynthetic pathway. This pathway is not found in humans or other eukaryotic organisms, yet is required for the production of threonine, isoleucine, methionine and lysine in most microorganisms. The mechanism of this enzyme has been examined through the structures of two active-site mutants of ASADH from Haemophilus influenzae. Replacement of the enzyme active-site cysteine with serine (C136S) leads to a dramatic loss of catalytic activity caused by the expected decrease in nucleophilicity, but also by a change in the orientation of the serine hydroxyl group relative to the cysteine thiolate. In contrast, in the H277N active-site mutant the introduced amide is oriented in virtually the same position as that of the histidine imidazole ring. However, a shift in the position of the bound reaction intermediate to accommodate this shorter asparagine side chain, coupled with the inability of this introduced amide to serve as a proton acceptor, results in a 100-fold decrease in the catalytic efficiency of H277N relative to the native enzyme. These mutant enzymes have the same overall fold and high structural identity to native ASADH. However, small perturbations in the positioning of essential catalytic groups or reactive intermediates have dramatic effects on catalytic efficiency. [source] Golgi biogenesis in simple eukaryotesCELLULAR MICROBIOLOGY, Issue 3 2007Cynthia Y. He Summary The accurate duplication of cellular organelles is important to ensure propagation through successive generations. The semi-conserved replication of DNA and DNA-containing organelles has been well studied, but the mechanisms used to duplicate most other organelles remain elusive. These include the centrosomes, which act as microtubule organizing centres during interphase and orient the mitotic spindle poles during mitosis. Centrosomes can also act as basal bodies, nucleating the growth of cilia or flagella. Even less understood are the mechanisms used to duplicate membrane-bound organelles that do not contain DNA. These include organelles involved in the secretory pathway such as the endoplasmic reticulum and the Golgi apparatus. This review will summarize the current knowledge of Golgi biogenesis in simple eukaryotic organisms, in particular, two protozoan parasites, Toxoplasma gondii and Trypanosoma brucei. [source] Biological systems of the host cell involved in Agrobacterium infectionCELLULAR MICROBIOLOGY, Issue 1 2007Vitaly Citovsky Summary Genetic transformation of plants by Agrobacterium, which in nature causes neoplastic growths, represents the only known case of trans -kingdom DNA transfer. Furthermore, under laboratory conditions, Agrobacterium can also transform a wide range of other eukaryotic species, from fungi to sea urchins to human cells. How can the Agrobacterium virulence machinery function in such a variety of evolutionarily distant and diverse species? The answer to this question lies in the ability of Agrobacterium to hijack fundamental cellular processes which are shared by most eukaryotic organisms. Our knowledge of these host cellular functions is critical for understanding the molecular mechanisms that underlie genetic transformation of eukaryotic cells. This review outlines the bacterial virulence machinery and provides a detailed discussion of seven major biological systems of the host cell,cell surface receptor arrays, cellular motors, nuclear import, chromatin targeting, targeted proteolysis, DNA repair, and plant immunity , thought to participate in the Agrobacterium -mediated genetic transformation. [source] | ||||||||||||||||||||||