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Mutational change of membrane architecture. Mutants of Escherichia coli K12 missing major proteins of the outer cell envelope membrane.

Mutants of Escherichia coli have been analyzed which miss two of the major proteins of the outer cell envelope membrane. The two proteins I and II, normally are present at high concentrations (about 10(5) copies per cell). In such mutants, as compared with wild type, the phospholipid-to-protein ratio in the outer membrane has increased by a factor of 2.3 causing a considerable difference in density between wild type and mutant membranes. The concentrations of two other major components of the outer membrane, lipopolysaccharide and Braun's lipoprotein, did not change. The protein-deficient mutants do not exhibit gross functional defects in vitro. An increased sensitivity to EDTA and a slight such increase to dodecyl sulfate (but not to deoxycholate or Triton X-100) was observed, loss of so-called periplasmic enzymes was not found, and other differences to wild type are marginal. The mutants can grow with normal morphology. It is not possible, however, to prepare "ghosts" (particles of size and shape of the cell without murein, surrounded by a derivative of the outer membrane, and possessing the major proteins of this membrane) from them. This fact confirms our earlier suggestion that the proteins in question are required for the shape maintenance phenomenon in ghosts, and the mutants reject the speculation that these proteins are involved in the expression of the genetic information specifying cellular shape. Freeze-fracturing showed that in mutant cells, and in sharp contrast to wild type, the far predominant fracture plane is within the outer membrane. The concentration of the well known densely packed particles at the outer, concave leaflet of this fracture plane is greatly reduced. It was not possible, however, to clearly establish that one or the other protein is part of these particles because these ultrastructural differences were not apparent in mutants missing either one of the proteins only. The biochemical and ultrastructural data allow the conclusion that the loss of two major proteins and the concomitant increase of phospholipid concentration has changed the architecture of the outer membrane from a highly oriented structure, with a large fraction of protein-protein interaction, to one predominantly exhibiting planar lipid bilayer characteristics. E. coli thus can assemble rather different outer membranes, a fact excluding that outer membrane formation constitutes a highly ordered or strictly sequential assembly-line process.

Cell Membrane↗

Mouse hepatoma and liver ferritins. Comparative structural studies.

Pure ferritin from male mouse liver produces a single band of monomers (RF = 0.199) with electrophoresis in polyacrylamide gels at pH 9.0. The five sub-bands within this monomeric band appear to represent charge isomers having the same molecular size. Ferritin from BH3 transplantable mouse hepatoma shows two overlapping bands of monomers (RFA = 0.208 and RFB = 0.240); further electrophoretic studies show that these bands represent two subpopulations of molecules differing both in charge and size. Sub-bands are not found in this hepatoma ferritin. The larger tumor ferritin reaches the same end migration position as all liver isoferritins on gradient gels, signifying a very similar or identical molecular size; however, the absence of sub-bands indicates that this hepatoma ferritin differs in charge from the homologous liver proteins. Liver and hepatoma ferritins both produce a single prominent subunit band corresponding to nominal molecular weights of 22 250 and 21 700, with polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and dithiothreitol. With electrophoresis on polyacrylamide gradient slabs containing sodium dodecyl sulfate and dithiothreitol, both liver and hepatoma ferritins now reveal two subunits bands situated at identical positions. The polypeptides of these two closely spaced bands have a nominal molecular weight difference of less than 1000. Neither the hepatoma nor the liver seems to produce the ferritins found in the other tissue. Nevertheless, all these ferritins are composed of the same two types of subunits, albeit in different relative amounts. Observed distinctions in the ferritins from these normal or neoplastic cells must reflect differences in assembly and processing, as well as in the regulated expression of the same ferritin genes.

Animals↗

Spatial and sub-cellular localization of the membrane cytoskeleton-associated protein alpha-adducin in the rat brain.

Studies on the identification and characterization of constituents of rat brain synaptic junctions have lead to the isolation of cDNA clones encoding segments of alpha-adducin. These and other studies suggest that adducin, a protein involved in promoting the assembly of actin and spectrin filaments at the plasma membrane, may play a role in dynamic assembly-disassembly processes underlying synaptic plasticity. In order to verify that brain alpha-adducin is indeed a constituent of synaptic structures, we have generated monoclonal antibodies against epitopes in the C-terminal region of alpha-adducin and have determined its spatial and sub-cellular distribution in postnatal day-30 rat brain. Alpha-adducin is found to be highly enriched in regions with high synapse densities of the hippocampus, corpus striatum, cerebral cortex and cerebellum. Immuno-electron microscopic analysis of peroxidase stained sections of the hippocampus and the cerebellum revealed that alpha-adducin is localized at distinct sub-cellular structures. In the CA1 and CA3 regions of the hippocampus alpha-adducin immunoreactivity is found in a distinct subset of dendrites and dendritic spines. In the molecular layer of the cerebellum, a distinct fraction of pre-synaptic terminals of parallel fiber terminals is labeled. In both cases the majority of synaptic structures does not contain adducin. Significant immunoreactivity is also detected in processes of glial cells both in the hippocampus and the cerebellum.

Animals↗

Immunofluorescence studies on cartilage matrix synthesis. The synthesis of link protein, chondroitin sulfate proteoglycan monomer and type II collagen.

A comparison of the synthesis and deposition of fibrous type II collagen and the constituents of chondroitin sulfate proteoglycan (CSPG) aggregates, CSPG monomer and link protein, was made for chicken sternal chondrocytes in culture, using simultaneous double immunofluorescence and lectin localization. Chondrocytes deposited only CSPG constituents--and not type II collagen--into the extracellular matrix (ECM). Intracellular precursors of CSPG monomer were localized primarily in perinuclear regions, but were observed in other cytoplasmic vesicles as well. Link protein antibodies stained the same intracellular structures, but stained the perinuclear cytoplasm less intensely. In contrast, type II procollagen was distributed in vesicles throughout the cytoplasm and was clearly absent from the distinctive, CSPG precursor-containing vesicles. Fluorescence-labelled lectins were used to further identify intracellular membrane compartments. Wheat germ agglutinin (WGA) and Ricinus lectins (which recognize carbohydrates added in the Golgi) stained the perinuclear cytoplasm, while concanavalin A (conA) (which recognizes mannose-rich oligosaccharides added co-translationally) stained vesicles throughout the rest of the cytoplasm and not the perinuclear cytoplasm. The distinctive CSPG-containing vesicles were not stained with WGA or Ricinus agglutinins. Data presented elsewhere demonstrate that the vesicles do not react with monoclonal antibodies which recognize chondroitin sulfate (CS) or keratan sulfate (KS) determinants. Thus, we conclude that the vesicles accumulate CSPG precursors which have not been modified by Golgi-mediated processes. The data indicate that matrix molecules may be segregated selectively prior to transit through the Golgi complex. The co-distribution of link protein and CSPG monomer precursors in vesicles prior to further, Golgi-mediated modification may reflect an as yet undetermined function of these vesicles in the processing or assembly of CSPG.

Animals↗

Use of alpha- and beta-tubulin mutants for the study of spontaneous and induced chromosomal mis-distribution in Aspergillus nidulans.

The effect of two different mutations, one involving an alpha-tubulin (tubA) and the other a beta-tubulin (benA33) gene, on somatic segregation has been investigated in diploid strains of A. nidulans. Both mutations, particularly benA33, increase the level of spontaneous chromosomal mis-distribution (CMD) phenomena, without affecting the frequency of crossing-over. The employment of homozygous strains for each of the two mutations in sensitivity tests toward various chemicals, allowed the clear identification of those interfering with microtubule assembly-disassembly processes (i.e. chloral hydrate, diamide, aminocarb, N-ethyl-maleimide, p-chlormercuribenzoate). Such compounds turned out to be very efficient and specific inducers of CMD in a somatic segregation assay performed using the wild-type strain P1. The same assay, when carried out with some of these compounds but employing a tubA/tubA strain, revealed a marked proneness toward CMD to be associated with such mutation, which is known to confer microtubule hypostability.

Aspergillus↗

Effect of proteoglycans on type I collagen fibre formation.

Collagen fibrillogenesis is a multistep process involving assembly of molecules into fibrils and bundles of fibrils. The exact role of proteoglycans in collagen fibrillogenesis is unclear. The purpose of these studies is to study the effect of proteoglycans on collagen fibrillogenesis in vitro. Results of these studies suggest that the proteoglycans dermatan sulphate and chondroitin sulphate do not change the final turbidity and hence the diameter of fibrils formed during the early stages of fibrillogenesis. This suggests that proteoglycans may not influence the early phases of collagen assembly, such as nucleation. However, proteoglycans added during the final stages of collagen fibre formation in vitro cause changes in ultimate tensile strength. In the presence of the high-molecular-weight proteoglycan, the ultimate tensile strength is increased by a factor of 1.5 above that of the control, whilst in the presence of low-molecular weight chondroitin sulphate proteoglycan the tensile strength is significantly decreased. It is concluded that proteoglycans influence the later stages of fibre formation. The presence of high-molecular-weight chondroitin sulphate proteoglycan leads to efficient stress transfer between collagen fibrils, altering the ultimate tensile strength. The results of these studies will be useful in optimizing the design of collagen tendon-ligament prostheses.

Animals↗

Mechanism of effector cell blockade--IV. Induction by monoclonal anti-mu or anti-idiotypic antibody, role of secreted IgM and mechanism of decreased secretion.

Effector cell blockade (ECB), the inhibition of antibody synthesis by antigen or antigen-antibody complexes, was shown to be induced by monoclonal anti-mu or anti-idiotypic antibodies. An initial event in the induction of blockade was demonstrated to be the build up on the cell surface of a complex of membrane Ig, and either antigen or anti-mu or anti-Id antibody, together with secreted IgM. Trapping of secreted IgM in this complex was not, however, sufficient to account for the overall reduction in antibody secretion. This reduction was not due to reduced translation of mu mRNA, but rather to blockade of the normal process of assembly of the IgM molecule which was followed by increased intracellular degradation of intermediate precursor molecules. These findings have shown ECB to be a rapidly induced negative feedback control of IgM secretion which, at least initially, could be reversed. ECB may act in vivo as a flexible first-line mechanism for prevention of overproduction of IgM antibodies.

Animals↗

Production of functionally active murine and murine::human chimeric F(ab')2 fragments in COS-1 cells.

We report here the synthesis, in nonlymphoid cells, of two functionally active recombinant F(ab')2 fragments directed against the tumor marker, human placental alkaline phosphatase (hPLAP). The truncated heavy chain (HC) sequences, E6Hf2 and E6Hy3f2, of the murine F(ab')2 fragment, E6F2, and of the murine::human chimeric F(ab')2 fragment, E6(Hy3,kappa)F2, respectively, were engineered by introducing an in-phase stop codon within the second constant domain of the corresponding parental HC sequence. The antibody-encoding genes were placed under control of the simian virus 40 late promoter and each HC sequence, together with the light chain (LC) sequence, was transiently expressed in COS-1 cells. The truncated HCs were correctly synthesized, processed and assembled with the murine LC and subsequently secreted into the culture medium as functionally active entities with stable hinge region interactions. These results indicate that, under the conditions used, the hinge region was sufficient for the formation of divalent molecules. However, Western blotting revealed the presence of hPLAP-binding half-molecules of E6F2, which was not the case for E6(Hy3,kappa)F2. Since E6F2 and E6(Hy3,kappa)F2 mainly differ by the length of their hinge region (22 and 62 aa residues, respectively) and the number of inter-HC disulfide bridges (four and eleven, respectively), it may be concluded that F(ab')2 fragments with an extended hinge region and several inter-HC disulfide bridges are formed more efficiently.

Alkaline Phosphatase↗

Pathways for the nuclear transport of proteins and RNAs.

The nuclear pore complex catalyses the import and export of both proteins and RNAs. The molecular mechanisms of RNA and protein translocation through the nuclear pore are likely to be similar; however, their signals and targeting apparatus may differ. Recent insights into RNA transport have come from studies of kinetic control mechanisms and the preconditions for translocation that include processing, RNP assembly, and a targeting function for 5' caps.

Journal Article↗

The plant Golgi apparatus: a factory for complex polysaccharides and glycoproteins.

The Golgi apparatus of plant cells serves two major functions: it assembles and processes the oligosaccharide side chains of glycoproteins, and it synthesizes the complex polysaccharides of the cell wall matrix, the hemicelluloses and pectins. The first function is common to plant and animal cells while the second is unique to plants. The recent introduction of novel biochemical and electron microscopical techniques, as well as the production and the application of highly specific anti-glycan antibody probes have led to major advances in understanding the structural and functional organization of plant Golgi stacks.

Carbohydrate Sequence↗

Association and dissociation of the cell puncturing complex of bacteriophage T4 is controlled by both pH and temperature.

The tail lysozyme, gp5, of bacteriophage T4 is a trimeric protein and all the subunits are nicked between Ser351 and Ala352 during assembly through processing. When subsequently heated, the resulting (gp5*)(3) (gp5C)(3) (the asterisk "*" denotes that the intact pre-gp5 trimer has been nicked) dissociates into three gp5* (three independent N-terminal monomeric peptides, that carry lysozyme moieties at the C-termini of gp5*), and a C-terminal trimeric beta-helical structure (gp5C)(3). The interaction between gp27 and gp5* during infection is sundered by reducing pH. This dissociation would be physiologically relevant because the lysozyme moieties should be free in the periplasm (where the pH is low) and would digest the peptidoglycan layer, thereby enabling the tail tube to contact the inner membrane, and probably help to form a pore for DNA injection.

Bacteriophage T4↗

A mitotic role for BRCA1/BARD1 in tumor suppression?

The tumor-suppressor protein BRCA1 is thought to act by preserving genomic integrity. In this issue of Cell, Joukov et al. demonstrate that the BRCA1/BARD1 heterodimer participates in mitotic spindle assembly, a process conducted by the GTPase Ran. Loss of this mitotic function might contribute to tumorigenesis.

Animals↗

Construction and characterization of a rock-cluster-based EST analysis pipeline.

Open access to vast amount of expression sequence tags (ESTs) data in the public databases has provided a powerful platform for gene identification, gene expression studies and comparative/functional genomic studies. To facilitate management of large-scale EST data, high performance cluster and analysis softwares, especially parallel softwares, are fundamentally essential. We reported herein a convenient approach to construct a high performance computating (HPC) cluster based on popular Rocks and a perl-scripted analysis pipeline for EST pre-processing, clustering, assembling and annotation and any other desired analysis modules through parallel computing. We tested the system using different datasets on increasing nodes. Our present results showed that the cluster and pipeline accelerate the EST analysis without artificial interference.

Cluster Analysis↗

Novel functions for integrins in epithelial morphogenesis.

Dorsal closure during Drosophila embryogenesis provides a valuable model for epithelial morphogenesis and wound healing. Previous studies have focused on two cell populations, the dorsal epidermis and the extraembryonic amnioserosa. Here, we demonstrate that there is an additional player, the large yolk cell. We find that integrins are expressed in the amnioserosa and yolk cell membrane and that they are required for three processes: (1) assembly of an intervening extracellular matrix, (2) attachment between these two cell layers, and (3) contraction of the amnioserosa cells. We also provide evidence for integrin-extracellular matrix interactions occurring between the lateral surfaces of the amnioserosa cell and the leading edge epidermis that effectively mediate cell-cell adhesion. Thus, dorsal closure shares mechanistic similarities with vertebrate epithelial morphogenetic events, including epiboly, that also employ an underlying substrate.

Animals↗

Double-stranded DNA stimulates the fibrillation of alpha-synuclein in vitro and is associated with the mature fibrils: an electron microscopy study.

Filamentous aggregates formed by alpha-synuclein are a prominent and presumably key etiological factor in Parkinson's and other neurodegenerative diseases characterized by motor disorders. Numerous studies have demonstrated that various environmental and intracellular factors affect the fibrillation properties of alpha-synuclein, e.g. by accelerating the process of assembly. Histones, the major component and constituent of chromatin, interact specifically with alpha-synuclein and enhance its fibrillation significantly. Here, we report that another component of chromatin, double-stranded DNA (dsDNA), either linear or supercoiled, also interacts with wild-type alpha-synuclein, leading to a significant stimulation of alpha-synuclein assembly into mature fibrils characterized by a reduced lag phase. In general, the morphology of the fibrils remains unchanged in the presence of linear dsDNA. Electron microscopy reveals that DNA forms various types of complexes upon association with the fibrils at their surface without distortion of the double-helical structure. The existence of these complexes was confirmed by the electrophoresis, which also demonstrated that a fraction of the associated DNA was resistant to digestion by restriction endonucleases. Fibrils assembled from the alpha-synuclein mutants A30P and A53T and the C-terminally truncated variants (encoding amino acid residues 1-108 or 1-124) also form complexes with linear dsDNA. Possible mechanisms and implications of dsDNA-alpha-synuclein interactions are discussed.

Animals↗

Three-dimensional structure of a double apoptosome formed by the Drosophila Apaf-1 related killer.

The Drosophila Apaf-1 related killer (Dark) forms an apoptosome that activates Dronc, an apical procaspase in the intrinsic cell death pathway. To study this process, we assembled a large Dark complex in the presence of dATP. Remarkably, we found that cytochrome c was not required for assembly and when added, cytochrome c did not bind to the Dark complex. We then determined a 3D structure of the Dark complex at 18.8A resolution using electron cryo-microscopy and single particle methods. In the structure, eight Dark subunits form a wheel-like particle and two of these rings associate face-to-face. In contrast, Apaf-1 forms a single ring that is comprised of seven subunits and each Apaf-1 binds a molecule of cytochrome c. We then used relevant crystal structures to model the Dark complex. This analysis shows that a single Dark ring and the Apaf-1 apoptosome share many key features. When taken together, the data suggest that a single ring in the Dark complex may represent the Drosophila apoptosome. Thus, our analysis provides a domain model of this complex and gives insights into its function.

Animals↗

The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation.

We have investigated the mechanism by which transcription accelerates cleavage and polyadenylation in vitro. By using a coupled transcription-processing system, we show that rapid and efficient 3' end processing occurs in the absence of crowding agents like polyvinyl alcohol. The continuity of the RNA from the poly(A) signal down to the polymerase is critical to this processing. If this tether is cut with DNA oligonucleotides and RNaseH during transcription, the efficiency of processing is drastically reduced. The polymerase is known to be an integral part of the cleavage and polyadenylation apparatus. RNA polymerase II pull-down and immobilized template experiments suggest that the role of the tether is to hold the poly(A) signal close to the polymerase during the early stages of processing complex assembly until the complex is sufficiently mature to remain stably associated with the polymerase on its own.

DNA-Directed RNA Polymerases↗

Toxicogenomics of endoplasmic reticulum stress inducer tunicamycin in the small intestine and liver of Nrf2 knockout and C57BL/6J mice.

This objective of this study was to investigate the toxicogenomics and the spatial regulation of global gene expression profiles elicited by endoplasmic reticulum (ER) stress inducer tunicamycin (TM) in mouse small intestine and liver as well as to identify TM-modulated nuclear factor-E2-related factor 2 (Nrf2)-dependent genes. Gene expression profiles were analyzed using 45,000 Affymetrix mouse genome 430 2.0 array and GeneSpring 7.2 software. Microarray results were validated by quantitative real-time reverse transcription-PCR analyses. Clusters of genes that were either induced or suppressed more than two-fold by TM treatment compared with vehicle in C57BL/6J/Nrf2 (-/-; knockout) and C57BL/6J Nrf2 (+/+; wildtype) mice genotypes were identified. Amongst these, in small intestine and liver, 1291 and 750 genes, respectively, were identified as Nrf2-dependent and upregulated, and 1370 and 943 genes, respectively, as Nrf2-dependent and downregulated. Based on their biological functions, these genes can be categorized into molecular chaperones and heat shock proteins, ubiquitination/proteolysis, apoptosis/cell cycle, electron transport, detoxification, cell growth/differentiation, signaling molecules/interacting partners, kinases and phosphatases, transport, biosynthesis/metabolism, nuclear assembly and processing, and genes related to calcium and glucose homeostasis. Phase II detoxification/antioxidant genes as well as putative interacting partners of Nrf2 such as nuclear corepressors and coactivators, were also identified as Nrf2-dependent genes. The identification of TM-regulated and Nrf2-dependent genes in the unfolded protein response to ER stress not only provides potential novel insights into the gestalt biological effects of TM on the toxicogenomics and spatial regulation of global gene expression profiles in cancer pharmacology and toxicology, but also points to the pivotal role of Nrf2 in these biological processes.

Animals↗