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Eukaryotes
Kinds of Eukaryotes Selected AbstractsECOLOGICAL GENOMICS OF MODEL EUKARYOTES,EVOLUTION, Issue 12 2008John K. McKay First page of article [source] Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and EukaryaGEOBIOLOGY, Issue 1 2003Christopher H. House ABSTRACT We constructed genomic trees based on the presence and absence of families of protein-encoding genes observed in 55 prokaryotic and five eukaryotic genomes. There are features of the genomic trees that are not congruent with typical rRNA phylogenetic trees. In the bacteria, for example, Deinococcus radiodurans associates with the Gram-positive bacteria, a result that is also seen in some other phylogenetic studies using whole genome data. In the Archaea, the methanogens plus Archaeoglobus form a united clade and the Euryarchaeota are divided with the two Thermoplasma genomes and Halobacterium sp. falling below the Crenarchaeota. While the former appears to be an accurate representation of methanogen-relatedness, the misplacement of Halobacterium may be an artefact of parsimony. These results imply the last common ancestor of the Archaea was not a methanogen, leaving sulphur reduction as the most geochemically plausible metabolism for the base of the archaeal crown group. It also suggests that methanogens were not a component of the Earth's earliest biosphere and that their origin occurred sometime during the Archean. In the Eukarya, the parsimony analysis of five Eukaryotes using the Crenarchaeota as an outgroup seems to counter the Ecdysozoa hypothesis, placing Caenorhabditis elegans (Nematoda) below the common ancestor of Drosophila melanogaster (Arthropoda) and Homo sapiens (Chordata) even when efforts are made to counter the possible effects of a faster rate of sequence evolution for the C. elegans genome. Further analysis, however, suggests that the gene loss of ,animal' genes is highest in C. elegans and is obscuring the relationships of these organisms. [source] Exploring prokaryotic diversity: there are other molecular worldsMOLECULAR MICROBIOLOGY, Issue 1 2005Luis Angel Fernández Summary Prokaryotes are the major source of biological diversity on earth. This is not simply because of the large number of species present, or because of their diverse growth conditions and environmental niches populated by them, but because of the wealth of genes, metabolic pathways and molecular processes that are only found in prokaryotic cells. Therefore, Bacteria and Archaea (and their phages) cannot be considered any longer as miniaturized models of Eukaryotes, but as a genuine source of unique biological processes that are mediated by unique sets of genes and molecular devices. A true understanding of complex biological phenomena will require a deeper knowledge of this vast prokaryotic world. The second European Molecular Biology Organization (EMBO) conference on Molecular Microbiology entitled ,Exploring Prokaryotic Diversity' explored many aspects of this newly emerging interest in the prokaryotic world. [source] A bioinformatic tool for analysis of EST transcript abundance during infection-related development by Magnaporthe griseaMOLECULAR PLANT PATHOLOGY, Issue 5 2005DARREN M. SOANES SUMMARY Information regarding the levels of mRNA transcript abundance under different conditions, or in specific tissue types, can be obtained by analysis of the frequency of EST sequences in randomly sequenced cDNA libraries. Here we report a bioinformatics tool, which provides a means of identifying genes that are differentially expressed during pathogenesis-related development by the rice blast fungus Magnaporthe grisea. A total of 31 534 M. grisea ESTs were obtained from dbEST at NCBI, clustered into 8821 unique sequences (unisequences) and manually annotated. Transcript profiles were then calculated for 958 unigenes identified from eight different cDNA libraries. The data were integrated into the Consortium for Functional Genomics of Microbial Eukaryotes (COGEME) database (http://cogeme.ex.ac.uk/) and a web-based front end was designed to allow users to access and interrogate the generated datasets. [source] Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in EukaryotesNEW PHYTOLOGIST, Issue 1 2010Gurvan Michel Summary ,Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate d -fructose 6-phosphate is not used to produce sucrose but is converted into d -mannitol. These seaweeds also store C as ,-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use ,-1,4-glucans (glycogen or starch). ,Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins. ,Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. ,The synthesis of ,-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the ,Chromalveolate hypothesis'. [source] Photosynthetic Eukaryotes of Freshwater Wetland Biofilms: Adaptations and Structural Characteristics of the Extracellular Matrix in the Green Alga, Cosmarium reniforme (Zygnematophyceae, Streptophyta)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2009DAVID S. DOMOZYCH ABSTRACT. Cosmarium reniforme (Zygnematophyceae, Streptophyta) is a green alga that is commonly found in biofilms of wetlands of the Adirondack region, NY (USA). Two distinctive characteristics that are critical to this alga's survival in a benthic biofilm are its elaborate cell morphology and extracellular matrix (ECM). In this study, ultrastructural, immunocytochemical, and experimental methodologies were employed in order to elucidate the cellular characteristics that are critical for survival in a biofilm. The ECM consists of a thick, outwardly lobed cell wall (CW), which contains a patterned network of structurally complex pores. Each pore consists of a narrow channel, terminating internally at a bulb that invaginates localized regions of the plasma membrane. The outer region of the pore contains arabinogalactan protein-like and extensin epitopes that are likely involved in adhesion mechanisms of the cell. External to the CW is the extracellular polymeric substance that is employed in ensheathment of the cell to the substrate and in gliding motility. The architectural design/biochemical make-up of the CW and a secretory system that encompasses the coordinated activities of the endomembrane and cytomotile/cytoskeletal systems provide the organism with effective mechanisms to support life within the biofilm complex. [source] A Hierarchical View of Convergent Evolution in Microbial Eukaryotes,THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2008BRIAN S. LEANDER ABSTRACT. Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence,"parallel", "proximate" and "ultimate",that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life. [source] A Java Applet for Exploring the New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of ProtistsTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 5 2006MATTHIAS WOLF ABSTRACT. We have converted the hierarchically organized new higher level classification of eukaryotes with emphasis on the taxonomy of protists proposed by Adl et al. into an interactive and dynamic Java applet. The current version of the applet can be accessed via http://phylogenetics.bioapps.biozentrum.uni-wuerzburg.de/etv. We use the layout from a Degree-of-Interest tree (DOITree) that effectively displays all the taxonomic information as well as the phylogenetic relationships described in the original article by Adl et al. The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students. [source] The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of ProtistsTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 5 2005SINA M. ADL Abstract. This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles. [source] Decisive factors: a transcription activator can overcome heterochromatin silencingBIOESSAYS, Issue 9 2001Joel C. Eissenberg Eukaryotes organize certain chromosomal intervals into domains capable of si lencing most genes. Examples of silencing domains include the HML/HMR loci and subtelomeric chromatin in yeast, the Barr body X chromosome in mammals, and the pericentric heterochromatin of Drosophila. Silencing chromatin is often correlated with more regularized nucleosomal array than that found in active chromatin, and transcriptional activators appear to be missing from their target sites in silent chromatin. In Drosophila, gene silencing by heterochromatin is often variegated, indicating that a gene may escape silencing in some cells. In a recent study, Ahmad and Henikoff(1) show that a yeast activator can compete successfully with Drosophila heterochromatic silencing factors for target sites in DNA. This competition, together with developmental change in the stability of heterochromatin itself, decides the transcriptional state for a gene subject to heterochromatin repression. BioEssays 23:767,771, 2001. © 2001 John Wiley & Sons, Inc. [source] Genomic Analyses and the Origin of the EukaryotesCHEMISTRY & BIODIVERSITY, Issue 11 2007Maria Abstract The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the ,tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or ,ring' rather than a ,tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes. [source] The roles of actin cytoskeleton and microtubules for membrane recycling of a food vacuole in Tetrahymena thermophilaCYTOSKELETON, Issue 7 2009Maki Sugita Abstract Phagocytosis is a fundamental cellular event for the uptake of nutrients from the environment in several kinds of eukaryote. Most ciliates egest waste and undigested materials in food vacuoles (FVs) through a cytoproct, which is a specific organelle for defecation. It is considered that FV egestion is initiated by fusion between the FV membrane and plasma membrane in a cytoproct and completed with retrieval of the membrane into a cytoplasmic space. In addition, electron microscopy indicated that microfilaments might be involved in the recycling process of the FV membrane in ciliates over 30 years ago; however, there is no conclusive evidence. Here we demonstrated actin organization on FV near a cytoproct in Tetrahymena thermophila by using a marker for a cytoproct. Moreover, it was revealed that cells treated with actin cytoskeletal inhibitor, Latrunculin B, might be suppressed for membrane retrieval in a cytoproct following FV egestion. On the other hand, the actin structures, likely to be the site of membrane retrieval, were frequently observed in the cells treated with cytoplasmic microtubules inhibitor, Nocodazole. We concluded that actin filaments were probably required for recycling of the FV membrane in a cytoproct although the role was not essential for FV egestion. In addition, it was possible that microtubules might be involved in transportation of recycling vesicles of FV coated with F-actin. Cell Motil. Cytoskeleton 2009. © 2009 Wiley-Liss, Inc. [source] A polyploid population of Saccharomyces cerevisiae with separate sexes (dioecy)FEMS YEAST RESEARCH, Issue 6 2010Rim Al Safadi Abstract Saccharomyces cerevisiae has proved to be an interesting model for studies of evolution, with whole-genome duplication shown to have played an important role in the evolution of this species. This phenomenon depends on the formation of a transient stable polyploid state. Previous studies have reported polyploidy to be an unstable state in yeast, but here, we describe a polyploid population of S. cerevisiae. The evolution of higher eukaryotes has also involved the development of different systems of sexual reproduction, the choice between self-fertilization and out-crossing becoming a key issue. Saccharomyces cerevisiae is a hermaphrodite eukaryote, despite the theoretical genetic disadvantages of this strategy, in which self-fertilization occurs. We describe, for the first time, a near-dioecious (with separate sexes) population in this species. Mating type and the MAT locus display complex segregations. Essentially, each strain produces, by meiosis, spores of only one mating type: mata or mat,. Moreover, strains are heterothallic, and diploid nonmating clones generated from a single spore do not sporulate. These three properties limit self-fertilization and strongly favour out-crossing. We suggest that the shift in sexual strategy, from hermaphroditism to dioecy, is specific to the brewing process, which overcomes the sexual isolation probably found in natural biotopes. [source] Liver carcinogen aflatoxin B1 as an inducer of mitotic recombination in a human cell lineMOLECULAR CARCINOGENESIS, Issue 3 2001Peter Markus Stettler Abstract The mycotoxin aflatoxin B1 (AFB1) is one of the most potent rodent and human liver carcinogens. Upon cytochrome P450,specific metabolism, it induces mutations as well as mitotic recombination events in in vitro systems. We have found that in the lower eukaryote yeast, the recombinagenic activity of AFB1 surpasses its mutagenic activity, and we speculated on possible consequences in terms of the mechanism of liver carcinogenesis. In this study we investigated whether the recombinagenic activity of AFB1 also would be identified in human cells. To address this question, we followed the fate of a heterozygous thymidine kinase (tk) allele in the human lymphoblastoid cell line TK6 upon exposure to AFB1. Individual mutants that had lost tk activity were subjected to loss of heterozygosity analysis of the tk locus and its flanking markers. Fluorescence in situ hybridization analysis on chromosome 17 also was performed. In parallel, a similar analysis was performed on TK6 cells exposed to the alkylating agent N -nitrosomethylurea, a well-known classic point mutagen. Our analysis showed a difference in the molecular mechanism leading to inactivation of the tk allele upon exposure to these two mutagens. In AFB1 -exposed cells the fraction of recombination-derived mutants predominated, whereas in N -nitrosomethylurea,exposed cells the fraction of point mutants was higher. Thus, the recombinagenic activity of AFB1 previously identified in a lower eukaryote also was found in the human cell line TK6. Our data support the hypothesis that mitotic recombination represents a central mechanism of action in AFB1 -induced liver carcinogenesis. © 2001 Wiley-Liss, Inc. [source] Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestansMOLECULAR MICROBIOLOGY, Issue 2 2003Audrey M. V. Ah Fong Summary Cdc14 proteins are important regulators of mitosis and the cell cycle. These phosphatases have been studied previously only in yeasts and metazoans, which grow by fission or budding. Here we describe a homologue (piCdc14) from the oomycete Phytophthora infestans, a primitive eukaryote lacking a classical cell cycle. PiCdc14 complements a cdc14ts mutant of Saccharomyces cerevisiae and may function like other Cdc14 proteins, but displays a strikingly different pattern of expression. Whereas previously studied Cdc14 genes are constitutively transcribed, piCdc14 is not expressed during normal growth but instead only during asexual sporulation. In transformants of P. infestans expressing a fusion between the piCdc14 promoter and the ,-glucuronidase reporter, expression was first detected in sporangiophore initials, persisted in sporangiophores bearing immature sporangia, and later became restricted to mature sporangia. After germination, expression ended a few hours before the resumption of mitosis in hyphae emerged from the spores. Homology-dependent silencing experiments supported an essential role of piCdc14 in sporulation. It is proposed that the function of piCdc14 may be to synchronise nuclear behaviour during sporulation and maintain dormancy in spores until germination. These results help illuminate the process of sporulation in oomycetes and the evolution of the cell cycle in eukaryotes. [source] The secreted proteome profile of developing Dictyostelium discoideum cellsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2010Deenadayalan Bakthavatsalam Abstract Dictyostelium discoideum is a unicellular eukaryote that, when starved, aggregates to form multicellular structures. In this report, we identified the proteins secreted by developing Dictyostelium cells using MS-based proteomics. A total of 349 different secreted proteins were identified, indicating that at least 2.6% of the 13,600 predicted proteins in the Dictyostelium genome are secreted. Gene ontology analysis suggests that many of the secreted proteins are involved in protein and carbohydrate metabolism, and proteolysis. [source] Proteome analysis of Schizosaccharomyces pombe by two-dimensional gel electrophoresis and mass spectrometryPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2006Kyung-Hoon Hwang Abstract The fission yeast Schizosaccharomyces pombe (S. pombe) is a unicellular eukaryote and contains many genes and regulatory mechanisms that are close to those of mammals. In this study, we performed a global proteomic analysis of the fission yeast S. pombe wild type h,S L 972 proteome. More than 1500 protein spots were visualized on silver stained 2-D gels in the 3,10 pI range with a high resolution and high reproducibility. Protein identification was carried out by MALDI-TOF-MS and/or nanoLC-MS/MS. Advantage of the complementarity of these two MS approaches was used to enhance the identification quality. So far, 364 proteins (representing 157 different proteins) have been identified. We report here the identification of 117 new proteins on our 2-D reference map of this yeast compared to the first reference map. Of these identified proteins, 40.1% were involved in metabolism. The present work provides a very useful tool for all studies relying on S. pombe as a model organism and is a considerable complement to the first reference map of S. pombe published recently by Sun and coworkers (Sun, N., Jang, J., Lee, S., Kim, S. et al.., Proteomics 2005, 5, 1574,1579). [source] Folate synthesis in plants: the last step of the p -aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyaseTHE PLANT JOURNAL, Issue 4 2004Gilles J.C. Basset Summary In plants, the last step in the synthesis of p -aminobenzoate (PABA) moiety of folate remains to be elucidated. In Escherichia coli, this step is catalyzed by the PabC protein, a , -lyase that converts 4-amino-4-deoxychorismate (ADC) , the reaction product of the PabA and PabB enzymes , to PABA and pyruvate. So far, the only known plant enzyme involved in PABA synthesis is ADC synthase, which has fused domains homologous to E. coli PabA and PabB and is located in plastids. ADC synthase has no lyase activity, implying that plants have a separate ADC lyase. No such lyase is known in any eukaryote. Genomic and phylogenetic approaches identified Arabidopsis and tomato cDNAs encoding PabC homologs with putative chloroplast-targeting peptides. These cDNAs were shown to encode functional enzymes by complementation of an E. coli pabC mutant, and by demonstrating that the partially purified recombinant proteins convert ADC to PABA. Plant ADC lyase is active as dimer and is not feedback inhibited by physiologic concentrations of PABA, its glucose ester, or folates. The full-length Arabidopsis ADC lyase polypeptide was translocated into isolated pea chloroplasts and, when fused to green fluorescent protein, directed the passenger protein to Arabidopsis chloroplasts in transient expression experiments. These data indicate that ADC lyase, like ADC synthase, is present in plastids. As shown previously for the ADC synthase transcript, the level of ADC lyase mRNA in the pericarp of tomato fruit falls sharply as ripening advances, suggesting that the expression of these two enzymes is coregulated. [source] Dinoflagellate mitochondrial genomes: stretching the rules of molecular biologyBIOESSAYS, Issue 2 2009Ross F. Waller Abstract Mitochondrial genomes represent relict bacterial genomes derived from a progenitor ,-proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene-impoverished of any free-living eukaryote, encoding only two to three proteins. The organization and expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans-splicing is required to assemble full-length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether. [source] Structure of TTHA1623, a novel metallo-,-lactamase superfamily protein from Thermus thermophilus HB8ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Akihiro Yamamura TTHA1623 is a metallo-,-lactamase superfamily protein from the extremely thermophilic bacterium Thermus thermophilus HB8. Homologues of TTHA1623 exist in a wide range of bacteria and archaea and one eukaryote, Giardia lamblia, but their function remains unknown. To analyze the structural properties of TTHA1623, the crystal structures of its iron-bound and zinc-bound forms have been determined to 2.8 and 2.2,Ĺ resolution, respectively. TTHA1623 possesses an ,,,,-fold similar to that of other metallo-,-lactamase superfamily proteins with glyoxalase II-type metal coordination. However, TTHA1623 exhibits a putative substrate-binding pocket with a unique shape. [source] Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapyACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2006Maria Ehn Cytidine triphosphate synthetase (CTPS) is a key enzyme in nucleic acid and phospholipid biosynthesis and its activity is increased in certain human cancers, making it a promising drug target. The crystal structure of the synthetase domain of human CTPS, which represents the first structure of a CTPS from an eukaryote, has been determined. The structure is homotetrameric and each active site is formed by three different subunits. Sulfate ions bound to the active sites indicate the positions of phosphate-binding sites for the substrates ATP and UTP and the feedback inhibitor CTP. Together with earlier structures of bacterial CTPS, the human CTPS structure provides an extended understanding of the structure,function relationship of CTPS-family members. The structure also serves as a basis for structure-based design of anti-proliferative inhibitors. [source] AMP-activated protein kinase and cancerACTA PHYSIOLOGICA, Issue 1 2009W. Wang Abstract AMP-activated protein kinase (AMPK) is a cellular energy sensor that is conserved in eukaryotes. Elevated AMP/ATP ratio activates AMPK, which inhibits energy-consuming processes and activates energy-producing processes to restore the energy homeostasis inside the cell. AMPK activators, metformin and thiazolidinediones, are used for the treatment of type II diabetes. Recently, reports have indicated that AMPK may also be a beneficial target for cancer treatment. Cancer cells have characteristic metabolic changes different from normal cells and, being a key metabolic regulator, AMPK may regulate the switch. AMPK may act to inhibit tumorigenesis through regulation of cell growth, cell proliferation, autophagy, stress responses and cell polarity. [source] LKB1 and AMP-activated protein kinase control of mTOR signalling and growthACTA PHYSIOLOGICA, Issue 1 2009R. J. Shaw Abstract The AMP-activated serine/threonine protein kinase (AMPK) is a sensor of cellular energy status found in all eukaryotes that is activated under conditions of low intracellular ATP following stresses such as nutrient deprivation or hypoxia. In the past 5 years, work from a large number of laboratories has revealed that one of the major downstream signalling pathways regulated by AMPK is the mammalian target-of-rapamycin [mammalian target of rapamycin (mTOR) pathway]. Interestingly, like AMPK, the mTOR serine/threonine kinase plays key roles not only in growth control and cell proliferation but also in metabolism. Recent work has revealed that across eukaryotes mTOR orthologues are found in two biochemically distinct complexes and only one of those complexes (mTORC1 in mammals) is acutely sensitive to rapamycin and regulated by nutrients and AMPK. Many details of the molecular mechanism by which AMPK inhibits mTORC1 signalling have also been decoded in the past 5 years. AMPK directly phosphorylates at least two proteins to induce rapid suppression of mTORC1 activity, the TSC2 tumour suppressor and the critical mTORC1 binding subunit raptor. Here we explore the molecular connections between AMPK and mTOR signalling pathways and examine the physiological processes in which AMPK regulation of mTOR is critical for growth or metabolic control. The functional conservation of AMPK and TOR in all eukaryotes, and the sequence conservation around the AMPK phosphorylation sites in raptor across all eukaryotes examined suggest that this represents a fundamental cell growth module connecting nutrient status to the cell growth machinery. These findings have broad implications for the control of cell growth by nutrients in a number of cellular and organismal contexts. [source] Delayed embryonic development and impaired cell growth and survival in Actg1 null mice,CYTOSKELETON, Issue 9 2010Tina M. Bunnell Abstract Actins are among the most highly expressed proteins in eukaryotes and play a central role in nearly all aspects of cell biology. While the intricate process of development undoubtedly requires a properly regulated actin cytoskeleton, little is known about the contributions of different actin isoforms during embryogenesis. Of the six actin isoforms, only the two cytoplasmic actins, ,cyto - and ,cyto -actin, are ubiquitously expressed. We found that ,cyto -actin null (Actg1,/,) mice were fully viable during embryonic development, but most died within 48 h of birth due to respiratory failure and cannibalization by the parents. While no morphogenetic defects were identified, Actg1,/, mice exhibited stunted growth during embryonic and postnatal development as well as delayed cardiac outflow tract formation that resolved by birth. Using primary mouse embryonic fibroblasts, we confirm that ,cyto -actin is not required for cell migration. The Actg1,/, cells, however, exhibited growth impairment and reduced cell viability, defects which perhaps contribute to the stunted growth and developmental delays observed in Actg1,/, embryos. Since the total amount of actin protein was maintained in Actg1,/, cells, our data suggests a distinct requirement for ,cyto -actin in cell growth and survival. © 2010 Wiley-Liss, Inc. [source] Actin on DNA,An ancient and dynamic relationship,CYTOSKELETON, Issue 8 2010Kari-Pekka Skarp Abstract In the cytoplasm of eukaryotic cells the coordinated assembly of actin filaments drives essential cell biological processes, such as cell migration. The discovery of prokaryotic actin homologues, as well as the appreciation of the existence of nuclear actin, have expanded the scope by which the actin family is utilized in different cell types. In bacteria, actin has been implicated in DNA movement tasks, while the connection with the RNA polymerase machinery appears to exist in both prokaryotes and eukaryotes. Within the nucleus, actin has further been shown to play a role in chromatin remodeling and RNA processing, possibly acting to link these to transcription, thereby facilitating the gene expression process. The molecular mechanism by which actin exerts these newly discovered functions is still unclear, because while polymer formation seems to be required in bacteria, these species lack conventional actin-binding proteins to regulate the process. Furthermore, although the nucleus contains a plethora of actin-regulating factors, the polymerization status of actin within this compartment still remains unclear. General theme, however, seems to be actin's ability to interact with numerous binding partners. A common feature to the novel modes of actin utilization is the connection between actin and DNA, and here we aim to review the recent literature to explore how this connection is exploited in different contexts. [source] Kinesin-5 is not essential for mitotic spindle elongation in DictyosteliumCYTOSKELETON, Issue 11 2008Irina Tikhonenko Abstract The proper assembly and operation of the mitotic spindle is essential to ensure the accurate segregation of chromosomes and to position the cytokinetic furrow during cell division in eukaryotes. Not only are dynamic microtubules required but also the concerted actions of multiple motor proteins are necessary to effect spindle pole separation, chromosome alignment, chromatid segregation, and spindle elongation. Although a number of motor proteins are known to play a role in mitosis, there remains a limited understanding of their full range of functions and the details by which they interact with other spindle components. The kinesin-5 (BimC/Eg5) family of motors is largely considered essential to drive spindle pole separation during the initial and latter stages of mitosis. We have deleted the gene encoding the kinesin-5 member in Dictyostelium, (kif13), and find that, in sharp contrast with results found in vertebrate, fly, and yeast organisms, kif13, cells continue to grow at rates indistinguishable from wild type. Phenotype analysis reveals a slight increase in spindle elongation rates in the absence of Kif13. More importantly, there is a dramatic, premature separation of spindle halves in kif13, cells, suggesting a novel role of this motor in maintaining spindle integrity at the terminal stages of division. Cell Motil. Cytoskeleton 2008. © 2008 Wiley-Liss, Inc. [source] The ,II isotype of tubulin is present in the cell nuclei of a variety of cancersCYTOSKELETON, Issue 2 2004I-Tien Yeh Abstract Tubulin, the subunit protein of microtubules, has generally been thought to be exclusively a cytoplasmic protein in higher eukaryotes. We have previously shown that cultured rat kidney mesangial cells contain the ,II isotype of tubulin in their nuclei in the form of an ,,II dimer [Walss et al., 1999: Cell Motil. Cytoskeleton 42:274,284, 1999]. More recently, we examined a variety of cancerous and non-cancerous cell lines and found ,II in the nuclei of all of the former and only a few of the latter (Walss-Bass et al., 2002: Cell Tissue Res. 308:215,223]. In order to determine if ,II -tubulin occurs in the nuclei of actual cancers as well as in cancer cell lines, we used the immunoperoxidase method to look for nuclear ,II in a variety of tumors excised from 201 patients. We found that 75% of these tumors contain ,II in their nuclei. Distribution of nuclear ,II was highly dependent on the type of cancer, with 100% of the colon and prostate cancers, but only 19% of the skin tumors, having nuclear ,II. Nuclear ,II was particularly marked in tumors of epithelial origin, of which 83% showed nuclear ,II, in contrast to 54% in tumors of non-epithelial origin. In many cases, ,II staining occurred very strongly in the nuclei and not in the cytoplasm; in other cases, ,II was present in both. In many cases, particularly metastases, otherwise normal cells adjacent to the tumor also showed nuclear ,II, suggesting that cancer cells may influence nearby cells to synthesize ,II and localize it to their nuclei. Our results have implications for the diagnosis, biology, and chemotherapy of cancer. Cell Motil. Cytoskeleton 57:96,106, 2004. © 2004 Wiley-Liss, Inc. [source] Plant profilin isovariants are distinctly regulated in vegetative and reproductive tissuesCYTOSKELETON, Issue 1 2002Muthugapatti K. Kandasamy Abstract Profilin is a low-molecular weight, actin monomer-binding protein that regulates the organization of actin cytoskeleton in eukaryotes, including higher plants. Unlike the simple human or yeast systems, the model plant Arabidopsis has an ancient and highly divergent multi-gene family encoding five distinct profilin isovariants. Here we compare and characterize the regulation of these profilins in different organs and during microspore development using isovariant-specific monoclonal antibodies. We show that PRF1, PRF2, and PRF3 are constitutive, being strongly expressed in all vegetative tissues at various stages of development. These profilin isovariants are also predominant in ovules and microspores at the early stages of microsporogenesis. In contrast, PRF4 and PRF5 are late pollen-specific and are not detectable in other cell types of the plant body including microspores and root hairs. Immunocytochemical studies at the subcellular level reveal that both the constitutive and pollen-specific profilins are abundant in the cytoplasm. In vegetative cell types, such as root apical cells, profilins showed localization to nuclei in addition to the cytoplasmic staining. The functional diversity of profilin isovariants is discussed in light of their spatio-temporal regulation during vegetative development, pollen maturation, and pollen tube growth. Cell Motil. Cytoskeleton 52:22,32, 2002. © 2002 Wiley-Liss, Inc. [source] Non-core subunit eIF3h of translation initiation factor eIF3 regulates zebrafish embryonic developmentDEVELOPMENTAL DYNAMICS, Issue 6 2010Avik Choudhuri Abstract Eukaryotic translation initiation factor eIF3, which plays a central role in translation initiation, consists of five core subunits that are present in both the budding yeast and higher eukaryotes. However, higher eukaryotic eIF3 contains additional (non-core) subunits that are absent in the budding yeast. We investigated the role of one such non-core eIF3 subunit eIF3h, encoded by two distinct genes,eif3ha and eif3hb, as a regulator of embryonic development in zebrafish. Both eif3h genes are expressed during early embryogenesis, and display overlapping yet distinct and highly dynamic spatial expression patterns. Loss of function analysis using specific morpholino oligomers indicates that each isoform has specific as well as redundant functions during early development. The morphant phenotypes correlate with their spatial expression patterns, indicating that eif3h regulates development of the brain, heart, vasculature, and lateral line. These results indicate that the non-core subunits of eIF3 regulate specific developmental programs during vertebrate embryogenesis. Developmental Dynamics 239:1632,1644, 2010. © 2010 Wiley-Liss, Inc. [source] Molecular evidence for widespread occurrence of Foraminifera in soilsENVIRONMENTAL MICROBIOLOGY, Issue 9 2010Franck Lejzerowicz Summary Environmental SSU rDNA-based surveys are contributing to the dramatic revision of eukaryotic high-level diversity and phylogeny as the number of sequence data increases. This ongoing revolution gives the opportunity to test for the presence of some eukaryotic taxa in environments where they have not been found using classical microscopic observations. Here, we test whether the foraminifera, a group of single-celled eukaryotes, considered generally as typical for the marine ecosystems are present in soil. We performed foraminiferal-specific nested PCR on 20 soil DNA samples collected in contrasted environments. Unexpectedly, we found that the majority of the samples contain foraminiferal SSU rDNA sequences. In total, we obtained 49 sequences from 17 localities. Phylogenetic analysis clusters them in four groups branching among the radiation of early foraminiferal lineages. Three of these groups also include sequences originated from previous freshwater surveys, suggesting that there were up to four independent colonization events of terrestrial and/or freshwater ecosystems by ancestral foraminifera. As shown by our data, foraminifera are a widespread and diverse component of soil microbial communities. Yet, identification of terrestrial foraminiferal species and understanding of their ecological role represent an exciting challenge for future research. [source] | ||||||||||||||||||||||||||||||||||||||||