Interactions between the Translation Machinery and Microtubules

Microtubules are components of eukaryotic cytoskeleton that are involved in the transport of various components from the nucleus to the cell periphery and back. They also act as a platform for assembly of complex molecular ensembles. Ribonucleoprotein (RNP) complexes, such as ribosomes and mRNPs, are transported over significant distances (e.g. to neuronal processes) along microtubules. The association of RNPs with microtubules and their transport along these structures are essential for compartmentalization of protein biosynthesis in cells. Microtubules greatly facilitate assembly of stress RNP granules formed by accumulation of translation machinery components during cell stress response. Microtubules are necessary for the cytoplasm-to-nucleus transport of proteins, including ribosomal proteins. At the same time, ribosomal proteins and RNA-binding proteins can influence cell mobility and cytoplasm organization by regulating microtubule dynamics. The molecular mechanisms underlying the association between the translation machinery components and microtubules have not been studied systematically; the results of such studies are mostly fragmentary. In this review, we attempt to fill this gap by summarizing and discussing the data on protein and RNA components of the translation machinery that directly interact with microtubules or microtubule motor proteins.

The Institute of Protein Research of the Russian Academy of Sciences Is 50 Years Old

Here I introduce collection of review articles written by members of the Institute of Protein Research of the Russian Academy of Sciences. This collection commemorates the 50th anniversary of the Institute. The review articles cover a broad range of problems concerning the spatial structure of protein molecules, including the state of the molten globule, protein-RNA interactions, polysome and ribosome structure, the molecular colony method, and the original methods for studying the structure of proteins. Several of the reviews consider the practical use of knowledge about the structure of proteins and protein polymers. They reflect both the long experience of the authors and contemporary scientific data.

Logistics in the cell: cargoes and transportation

Eukaryotic cells are large and thus require a vesicular transport system. The system involves the formation of membrane transport containers, their short- and long-distance movements, recognition of destination points, and fusion with other membranes. Understanding the molecular mechanisms of these processes is of theoretical and practical significance. This special issue of Biochemistry (Moscow) collects surveys and experimental articles describing various aspects of vesicular transport.

[Stress granules in the cells with intact and discrupted microtubules: analysis with new algorithm of image processing]

Stress granules--temporary RNP structures that are formed in cells under stress. They are studied mainly by means of fluorescence microscopy with the quantitative analysis of cell images. We have developed a new algorithm for automatic detection of stress granules in the cytoplasm of cultured animal cells having non-uniform cytoplasmic background. Using this approach, we have found that visible stress granules are formed in cells as "all or nothing", and their number in cells is rather constant. We also show that disruption of cellular microtubules lead to a decrease in the average size of stress granules and an increase in their number in the cell.

[Protein kinase LOSK regulates the network of microtubules and cell locomotion]

It has been found that the inhibition of the activity of protein kinase LOSK reduces the ability of cells to the directed movement over the substrate and changes the parameters of the interaction of cells with the substrate. It is suggested that the chaotization of microtubules leads to the stabilization of cell contacts with the substrate and, consequently, to a slowing down of locomotion.

[Is the microtubule disruption-induced alteration of peroxide concentration a factor inhibiting the assembly of ribonucleoprotein stress granules?]

It has been examined whether the destruction of cell microtubules affects the increase in the intracellular hydrogen peroxide concentration caused by sodium arsenite, which induces the formation of stress ribonucleoprotein granules. As expected, sodium arsenite caused a 50% increase in hydrogen peroxide concentration in HeLa cells; on the other hand, another stress granule inducer tert-buthylhydroquinone did not affect the peroxide concentration. The disruption of microtubules by nocodazole or vinblastine also resulted in some increase in the intracellular peroxide concentration,y taxol did not affect it. The combined treatment of cells with and the microtubule stabilization by taxol did not affect it. The combined treatment of cells with arsenite and antimicrotubule drugs caused an additive effect, and the peroxide concentration increased twice or more. Thus, the inhibition of stress granule formation after microtubule disruption cannot be explained by a decrease in peroxide concentration as compared with the affect of arsenite.

[MAST2-like protein kinase from grape vine Vitis vinifera: cloning of catalytic domain cDNA]

The aim of our work is the identification of protein kinases phosphorylating microtubule proteins in plant cells. Using bioinformatic approach, we found genes of putative homologues of microtubule-associated mammalian protein kinase MAST2 in higher plant genomes. The gene of closest MAST2 homologue, putative protein, named GMLK (Grape MAST2-Like Kinase, A7NTE9_VITVI), was found in grape Vitis vinifera. We report here the cloning of cDNA of GMLK (A7NTE9) from Pinot Noir grape vine leaves.

[Bioinformatic search for plant homologs of Ste20-like serine/threonine protein kinases]

Eleven plant homologs of animal and yeast Ste20-like protein kinases were identified. It was shown that the nearest plant homologs of the Ste20-like protein kinases are the unknown proteins A9RVK0 from Physcomitrella patens ssp. patens and A7P2E2 from Vitis vinifera. Cladistic analysis showed a protein kinase dstl from Dictyostelium discoideum as the closest protein to the newly found plant homologs. A predicted spatial structure of the A9RVK0 from P. patens ssp. patens catalytic domain is presented.

[Bioinformatic search of plant protein kinases, participating in microtubule protein phosphorylation and cell division regulation]

Bioinformatic search of plant homologues of human protein kinases SLK, PAK6, PAK7, MARK1, MAST2, TTBK1, TTBK2, AURKA, PLK1, PLK2 and PASK participating in microtubular protein phosphorylation and cell division regulation is carried out. The homologues of protein kinases SLK, MAST2 and AURKA were identified. It is found that closest homologue of human AURKA protein kinase is a protein with unknown function A7PY12_VITVI (STALK--Serine-Threonine Aurora-Like Kinase) from grape (Vitis vinifera). Reconstruction and analysis of three-dimensional structure of STALK protein confirmed its relation to the group of AURKA-like protein kinases.

[Disturbance of the radial system of interphase microtubules in the presence of excess serum in cell culture medium]

The role of the orderliness of microtubules in the cell has been studied. For this purpose, a population of Vero cells with chaotically arranged microtubules was used, which was obtained after the addition of excess serum to cell culture medium. An increase in the total area and a slight dispersion of the Golgi apparatus were found; however, the rate of culture growth as a whole remained normal. Thus, the radial arrangement of microtubules is not vital even for cells where it is usually well pronounced.

Microtubules' interaction with cell cortex is required for their radial organization, but not for centrosome positioning

Microtubules in interphase mammalian cells usually form a radial array with minus-ends concentrated in the central region and plus-ends placed at the periphery. This is accepted as correct, that two factors determinate the radial organization of microtubules - the centrosome, which nucleate and anchor the microtubules minus-ends, and the interaction of microtubules with cortical dynein, which positions centrosome in the cell center. However, it looks as if there are additional factors, affecting the radial structure of microtubule system. We show here that in aged Vero cytoplasts (17 h after enucleation) microtubule system lost radial organization and became chaotic. To clear up the reasons of that, we studied centrosome activity, its position in the cytoplasts and microtubule dynamics. We found that centrosome in aged cytoplasts was still active and placed in the central region of the cytoplasm, while after total disruption of the microtubules it was displaced from the center. Microtubules in aged cytoplasts were not stabilized, but they lost their ability to stop to grow near cell cortex and continued to grow reaching it. Aged cytoplast lamellae was partially depleted with dynactin though Golgi remained compact indicating dynein activity. We conclude that microtubule stoppage at cell cortex is mediated by some (protein) factors, and these factors influence radial structure of microtubule system. It seems that the key role in centrosome positioning is played by dynein complexes anchored everywhere in the cytoplasm rather than anchored in cell cortex.

[Stress granules: RNP-containing cytoplasmic bodies springing up under stress. The structure and mechanism of organization]

In this review recent data describing stress granules are summarized. Stress granules are specific RNA-containing structures in the cytoplasm of living cells which arise under stress conditions (e. g. heat shock, UV irradiation, energy depletion and oxidative stress). It became evident that stress granules accumulate non-canonical 48S initiation complexes and contain mRNA with associated proteins, small ribosomal subunits and some initiation factors. Stress granules are depleted with ternary complex and large ribosomal subunit. It's proposed that eIF2alpha phosphorylation and ternary complex decrease can be a trigger for stress granule formation. Shuttling nuclear and cytoplasmic RNA-binding protein TIA-1 plays a crucial role in this process. It's proposed that TIA-1 forms prion-like aggregates, and these aggregates are scaffolds for other components of stress granules. Cytoskeletal structures facilitate the accumulation of stress granule components in local cytoplasmic sites. Investigation of process of stress granule formation is important for understanding of cell reaction to stress and translation regulation mechanisms.

[Stochastic computer model of cellular microtubule dynamics]

A computer model of the system of microtubules has been developed to study the mechanisms of action of various factors on this system. The model describes the process of polymerization/depolymerization of microtubules as a set of chemical reactions with certain rate constants using a stochastic approach. Microtubules are visualized in the program field, which makes the model visual. The program imitates the dynamics and structure of the system of cellular microtubules with great, reliability. The parameters generated by the model correlate with the corresponding parameters of microtubules in living cells. We are going to develop this approach to modeling microtubules and similar structures to bring them into a better accord with living systems and to study the influence of various factors on these systems.

[Dynein and dynactin as organizers of the system of cell microtubules]

A review of the role of the microtubule motor dynein and its cofactor dynactin in the formation of a radial system of microtubules in the interphase cells and of mitotic spindle. Deciphering of the structure, functions, and regulation of activity of dynein and dynactin promoted the understanding of mechanisms of cell and tissue morphogenesis, since it turned out that these cells help the cell in finding its center and organize microtubule-determined anisotropy of intracellular space. The structure of dynein and dynactin molecules has been considered, as well as possible pathways of regulation of the dynein activity and the role of dynein in transport of cell components along the microtubules. Attention has also been paid to the functions of dynein and dynactin not related directly to transport: their involvement in the formation of an interphase radial system of microtubules. This system can be formed by self-organization of microtubules and dynein-containing organelles or via organization of microtubules by the centrosome, whose functioning requires dynein. In addition, dynein and dynactin are responsible for cell polarization during its movement, as well as for the position of nucleus, centrosomes, and mitotic spindle in the cell.

[Large subunit of translation initiation factor--3 p170 contains potentially functional nuclear localization signals]

Eukaryotic translation factors and their subunits can have independent cellular functions, including regulation of nuclear events. We analyzed primary structure of p170 large subunit of human translation initiation factor eIF3 and found four potential bipartite nuclear localization signals (NLS). Then we studied whether these NLS were functional, that is were able to direct protein to cell nucleus. Complementary DNA of p170 fragments were expressed in cultured CV-1 and Cos-1 green monkey cells, and localization of fused with GFP proteins was determined by fluorescent microscopy. We established that p170 molecule possessed at least two functional NLS which determined nuclear localization of p170 fragments. At the same time more long p170 fragments containing the same functional NLS could be retained in cytoplasm. We speculate that either using specific factors or after limited proteolysis p170 can enter cell nucleus and participate in genome expression regulation. Also we do not exclude the possibility that functioning of p170 in cytoplasm can be regulated by reversible binding of importins to its NLS.

[Virions and membrane proteins of the potato X virus interact with microtubules and enables tubulin polymerization in vitro]

A study was made of the in vitro interactions of virions and the coat protein (CP) of the potato virus X (PVX) with microtubules (MT). Both virions and CP cosedimented with taxol-stabilized MT. In the presence of PVX CP, tubulin polymerized to produce structures resistant to chilling. Electron microscopy revealed the aberrant character of the resulting tubulin polymers (protofilaments and their sheets), which differed from MT assembled in the presence of cell MAP2. In contrast, PVX virions induced the assembly of morphologically normal MT sensitive to chilling. Virions were shown to compete with MAP2 for MT binding, suggesting an overlap for the MT sites interacting with MAP2 and with PVX virions. It was assumed that PVX virions interact with MT in vivo and that, consequently, cytoskeleton elements participate in intracellular compartmentalization of the PVX genome.

Enzymatic activity of protein kinase LOSK: possible regulatory role of the structural domain

LOSK (LOng Ste20-like Kinase) protein kinases of mammals belong to a recently identified family of GCK kinases which are involved in the induction of apoptosis. LOSK have an N-terminal acidic catalytic domain and a long C-terminal basic structural domain which is cleaved off in cells by caspases during apoptosis. To study the LOSK enzymatic activity and its dependence on the structural domain, two preparations of this protein kinase were prepared: a natural full-length protein immunoprecipitated from CHO-K1 cultured cells and a recombinant N-terminal catalytic fragment synthesized in E. coli. Both preparations displayed the ability for autophosphorylation and the ability for phosphorylation of MBP and of H1 histone, and their activities were comparable. H1 histone was a better substrate for LOSK than casein and ATP was a better substrate than other nucleotides. The pH dependence of the activity of the immunoprecipitated protein was more pronounced than the pH dependence of its recombinant fragment deprived of the C-terminal domain. The catalytic and the structural domains of LOSK can interact through electrostatic forces; therefore, effects were studied of various polyions at the concentration of 0.1 mg/ml on the activity. Heparin, protamine sulfate, and poly(L-Lys) decreased tenfold the ability of the full-length kinase to phosphorylate H1 histone. Heparin did not affect the activity of the recombinant fragment, whereas protamine sulfate and poly(L-Lys) had a slight effect. Moreover, protamine increased fourfold the autophosphorylation of the immunoprecipitated protein kinase. These data suggest that the structural C-terminal domain of LOSK should be involved in the regulation of its protein kinase activity: the LOSK protein kinase with C-terminal domain cleaved off could significantly less depend on conditions in the cell than the full-size enzyme.

Transcription factors NF-kappaB and AP-1/c-fos in cell response to nocodazole

The effects of nocodazole (an agent causing degradation of microtubules in vitro) on the content of transcription factors NF-kappaB and AP-1/c-fos in the nuclei of cultured cells CHO-K1 and HeLa, as well as on the activity of these factors in the nuclei of T-cell hybridoma 2B4 were studied. Immunoblotting, immunofluorescence, and gel retardation techniques revealed that in all cell lines studied nocodazole induced rapid and considerable activation (an increased content in the nuclei) of transcription factor AP-1/c-fos. In 2B4 cells, nocodazole had no effect on the activity of NF-kappaB, but in CHO-K1 and HeLa cells it caused a transient decrease, sometimes followed by an increase in the content of subunit p50. Besides, nocodazole inhibited proteolytic degradation of NF-kappaB in CHO-K1 and HeLa cells and caused a short-term decrease in the content of subunit p65 in CHO-K1 cells. The results suggest that nocodazole may interfere with the genome expression, and these alterations should be taken into consideration, whatever experimental studies this substance is used in.

[Translation initiation factor eIF3 is able to bind with microtubules in mammalian cells]

Association of the translation apparatus with the cytoskeleton is essential for its transportation within the cell and probably also for translation regulation. Very little is known about the involvement of particular proteins of this association. A polypeptide homologous with the heavy chain of translation initiation factor eIF3 p170 was found earlier in a microtubule preparation from adrenal cells. Antibody A167 directed against the recombinant fragment of p170 has been generated to study eIF3 interaction with microtubules in mammalian cells. This antibody was shown to recognize a single 170 kDa polypeptide in eIF3 preparations as well as in homogenates of various cell types. A167 allowed detection of the 170 kDa polypeptide in microtubule preparation from bovine brain and confirmation of its presence in microtubule preparations from adrenal cells. As shown by immunofluorescence microscopy using A167, the 170 kDa polypeptide is mainly located in the endoplasm within numerous small and some large granules. Cell treatment with cycloheximide resulted in growth and clustering of the large granules, and partial antigen redistribution along cellular microtubules. These new experimental data indicate that mammalian translation factor eIF3 may bind with microtubules.

[Spermatozoa of the loach Misgurnus fossilis as a test system for identification of new centromere proteins]

We studied the possibility of using the spermatozoa of the loach Misgurnus fossilis L. for identification of centrosome proteins. It has been shown that the centrosome of the loach spermatozoa consists of a pair of centrioles of the standard structure and contains the marker protein gamma-tubulin, cytoplasmic microtubules branch out from it, and it does not contain any additional structures characteristic of the centrosomes of spermatozoa of many other fishes. A preparation enriched with intact centrosomes has been obtained from the loach spermatozoa. These centrosomes contained gamma-tubulin although they lost their ability to induce polymerization of microtubules. The preparation of loach centrosomes was successfully used to obtain a set of monoclonal antibodies against the mammalian centrosome. A new protein kinase LOSTEK was identified with the help of one of these monoclonal antibodies, SN2-3D2, which was localized in the centrosome and on then microtubules in both loach spermatozoa and cultured mammalian cells. Hence, the loach spermatozoa are a promising object for identification of new proteins of the mammalian centrosome.

Exclusively juvenile centrioles in Xenopus laevis oocytes injected with preparations of mature centrioles

Activated oocytes of Xenopus laevis were injected with centriole preparations isolated either from spermatozoa of loach fish Misgurnus fossilis or from rat liver. These injections induced the development of cytasters in the ooplasm and egg cleavage. Electron microscopic study of cytasters was made at the stage that corresponded to interphase between first and second cleavage divisions. This study revealed in cytasters singleton centrioles surrounded by pericentriolar material and numerous microtubules. Surprisingly, the ultrastructure of centrioles in cytasters corresponded to that of juvenile, newly formed vertebrate centrioles, whereas the injected preparations contained only adult mature centrioles. We suggested that xenogenic centrioles injected to Xenopus laevis oocytes could dissolve after formation of centrioles made from molecules of oocyte origin. A special mechanism that eliminates male centrioles after egg fertilization is speculated.

Antibodies against EMC virus RNA-VPg recognize Tyr-(5'P-->O)-pU and immunostain infected cells

Covalent complexes of nucleic acids and proteins are widespread among viruses. Covalent complexes of RNA and proteins are proposed to exist in eukaryotic cells. The goal of this work was to obtain specific antibodies to the covalent linkage unit (CLU) between virus RNA and protein to search cellular RNA-protein complexes. Antibodies were generated by direct immunization of a rabbit with the BSA-coupled EMC virus RNA-VPg complex. By a dot-blot immunoassay and immunofluorescent microscopy it was found that the antibodies specifically recognize both EMC virus RNA-VPg and synthetic CLU-containing compounds. Thus, a fraction of the antibodies was directed to CLU.

A major 170 kDa protein associated with bovine adrenal medulla microtubules: a member of the centrosomin family?

Microtubules isolated from bovine adrenal medulla cells contain a major 170 kDa protein (p170). p170 is heat-labile and is associated with microtubules in an ATP-insensitive manner. This protein was purified to near homogeneity using FPLC. A preparation containing purified p170 caused bundling of microtubules. By microsequencing of p170, two polypeptides were identified which appeared to be identical to a recently sequenced p167 centrosomin-related protein. Polyclonal affinity-purified anti-p170 antibody was found to immunostain microtubules and to recognize the 170 kDa polypeptide in culture cells. We suggest that p170 is a new member of a centrosomin family and is a new structural protein associated with microtubules in some cell types.

Chinese hamster protein homologous to human putative protein kinase KIAA0204 is associated with nuclei, microtubules and centrosomes in CHO-K1 cells

Monoclonal antibody raised against a preparation of loach fish sperm centrosomes was used for screening of cDNA expressing library of Chinese hamster CHO-K1 cells. Two positive clones appeared to encode 628 amino acid protein fragment that was 72% identical to human KIAA0204 protein, i.e. putative protein kinase. Polyclonal antibodies raised against products of cDNA expression in E. coli recognized 210-kDa polypeptide in CHO-K1 cells and immunostained nuclear speckles, centrosomes and microtubules in these cells. The 210-kDa polypeptide (named MAK-L) co-sedimented with exogenous microtubules. Thus, one more protein kinase seems to be associated with the microtubule network in vertebrate cells.

[Centrosomal proteins]

The review summarizes recent data on structure and function of nearly two dozen centrosomal proteins of the animal cells; centrosome is an organelle that organizes cellular microtubules. Most of these data were obtained by molecular biology techniques including screening of phage expression cDNA libraries with centrosome-specific antibodies, bacterial expression of recombinant proteins recognized by these antibodies, analysis of multiple non-allelic gene of cytoskeletal proteins, etc. new classification of centrosomal proteins is suggested based on their possible centrosomal function comprising proteins of microtubule polymerization templates, structural proteins of pericentriolar material, microtubule severing proteins, microtubule-dependent transport-catalyzing motor proteins, regulatory proteins (specific protein kinases, phosphatases, etc), and centriolar proteins.

[Reorganization of the system of intermediate filaments and detection of the organization centers after centrifugation of cells attached to a substrate]

Cultured pig kidney epithelial cells were centrifuged at 20,000 gav so that the centrifugation force was oriented parallel to the substrate, fixed and processed for indirect immunofluorescent staining with tubulin and vimentin antibodies. After a 2 hour centrifugation vimentin filaments aggregated in the centripetal parts of the cells (probably, because of their association with floating lipid vesicles). Microtubule-organizing centers were found near the centripetal poles of the nuclei, which migrated in the direction of the centrifugal force. The distribution of the cytoplasmic microtubules did not change during centrifugation. The staining of the cultures one hour after centrifugation revealed vimentin-containing spots with radiating intermediate filaments in most of the cells. These spots were localized near the cell nuclei; double immunofluorescent staining with tubulin and vimentin antibodies showed that their position was identical to that of the microtubule-organizing centers. Similar foci of vimentin filaments were seen in the cells after a 3-4 hour centrifugation. Probably, these structures participate in organizing the intermediate filament cytoskeleton in cells.

[A cytoskeletal protein with a molecular weight of 100 kD is a component of the endosomes participating in receptor-mediated endocytosis]

Our previous paper (Rodionov et al., 1985) reported production of monoclonal antibodies RN-17 reacting in cultured fibroblasts with a protein having a molecular weight of 100 kD. Immunofluorescence and immunoelectron microscopy showed that this protein was a component of microtubules, intermediate filaments and coated vesicles. We challenged a possibility whether these coated vesicles containing the 100 kD protein may take part in the receptor-mediated endocytosis. alpha 2-Macroglobulin conjugated with fluorescein isothiocyanate or 20 nm colloidal gold particles was used as a marker of the receptor-mediated endocytosis. Mouse embryo fibroblasts or Swiss 3T3 cells were incubated with labeled alpha 2 M, fixed and "stained" with DN-17 antibody, and the distribution of alpha 2 M and 100 kD protein was examined within the same cells. In both cell lines the endocytic vesicles contained 100 kD protein and alpha 2 M. Therefore 100 kD protein is a component of endocytic vesicles. Probably this protein mediates microtubule-dependent transport of endocytic vesicles in the cells.