Conformation transitions of eukaryotic polyribosomes during multi-round translation

Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20–30 translation rounds during 6–8 h in wheat germ extract at 25°C). Three distinct types of the conformations were observed: (i) circular polyribosomes, varying from ring-shaped forms to circles collapsed into double rows, (ii) linear polyribosomes, tending to acquire planar zigzag-like forms and (iii) densely packed 3D helices. At the start, during the first two rounds of translation mostly the circular (ring-shaped and double-row) polyribosomes and the linear (free-shaped and zigzag-like) polyribosomes were formed (‘juvenile phase’). The progressive loading of the polyribosomes with translating ribosomes induced the opening of the circular polyribosomes and the transformation of a major part of the linear polyribosomes into the dense 3D helices (‘transitional phase’). After 2 h from the beginning (about 8–10 rounds of translation) this compact form of polyribosomes became predominant, whereas the circular and linear polyribosome fractions together contained less than half of polysomal ribosomes (‘steady-state phase’). The latter proportions did not change for several hours. Functional tests showed a reduced translational activity in the fraction of the 3D helical polyribosomes.     

Inhibition of protein synthesis and induction of helical polysomes in rat liver by N-hydroxy-2-fluorenylacetamide

After a single intraperitoneal injection of the hepatocarcinogen N-hydroxy-2-fluorenylacetamide (OH-FAA), numerous helical polysomes were found in the hepatocytic cytoplasm at 2 and 6 but not 24 h after treatment. Electron microscopy also demonstrated nucleolar segregation, disarray of endoplasmic reticuium (ER), and disaggregation of polyribosomes at the times when helical polysomes were present. Polyribosome disaggregation was confirmed and quantified by determining size distribution of polyribosomes at 2 h after OH-FAA treatment. Protein synthesis was inhibited at the time of helical polysome induction but the degree of inhibition did not noticeably alter the number of helical polysomes found electron microscopically.     

Separate ribosomal pools in sea urchin embryos: ammonia activates a movement between pools

Monoribosomes from unfertilized eggs of Strongylocentrotus purpuratus were shown to translate mRNA less efficiently than ribosomes derived from polyribosomes of embryos, as measured by globin synthesis in a ribosome-dependent rabbit reticulocyte lysate [Danilchik, M. V., & Hille, M. B. (1981) Dev. Biol. 84, 291-298]. Data presented in this paper show that monoribosomes from 16-cell and blastula embryos resemble monoribosomes from unfertilized eggs in translational capacity and are less active than the ribosomes associated with polyribosomes. Thus, we find two distinct populations of ribosomes in embryos. We define the less active monoribosome population as "naive" ribosomes and the more active, functioning polysome-derived ribosomes as "experienced" ribosomes. Naive and experienced ribosomes have the same elongation rates. The relationship between ionic triggers and the conversion of monoribosomes to experienced ribosomes was studied with the Ca2+ ionophore A23187, which releases intracellular Ca2+ stores, and NH4Cl, which alkalinizes the cytoplasm. We found that ribosomes in the monoribosome populations from A23187-activated eggs or from NH4Cl-activated eggs resembled naive monoribosomes from unfertilized eggs in their translational activity. In contrast, ribosomes derived from the polysomes of NH4Cl-treated eggs were as active as the experienced polysome-derived ribosomes from normal embryos. Eggs activated with A23187 did not produce polyribosomes. The presence of significant amounts of experienced ribosomes in NH4Cl-treated eggs implicates alkalinization of the cytoplasm as a stimulus for ribosome activation, which occurs slowly during initial development.     

Large-sized polysomes in Chironomus tentans salivary glands and their relation to Balbiani ring 75S RNA

Polysomes from the salivary glands of Chironomus tentans were investigated to determine whether Balbiani ring 75S RNA is incorporated into polysomal structures, and thus probably acts as messenger RNA. A new extraction technique for obtaining ribonucleoproteins was applied that gives a high yield of polysomes with only moderate degradation of the cytoplasmic, high molecular weight RNA. The polysomes sedimented in a broad region (200-2,000S) with a peak value of about 700S, which suggested that they were partly of very large sizes. This was confirmed by visualization of the polysomes in the electron microscope: 400S polysomes contained mainly 11-16 ribosomes, and 1,500S polysomes about 60 ribosomes per polysome. However, polysomes containing 100 or more ribosomes were also observed. It was further established that most of the cytoplasmic 75S RNA was located in polysomes, preferentially in the most rapidly sedimenting ones. From the available information on Balbiani ring RNA in cytoplasm and the present demonstration of 75S RNA molecules in polysomes, it was concluded that at least some Balbiani ring RNA, generated as 75S RNA within the Balbiani rings, eventually enters polysomes without being measurably changed in size. The present information on the potential amino acid coding sequences in 75S RNA is discussed in relation to the large size of the polysomes observed.     

Topology of mRNA chain in isolated eukaryotic double-row polyribosomes

In the process of protein synthesis, the translating ribosomes of eukaryotic cells form polyribosomes that are found to be multiplex functional complexes possessing elements of ordered spatial organization. As revealed by a number of electron microscopy studies, the predominant visible configurations of the eukaryotic polyribosomes are circles (circular polyribosomes) and two-stranded formations (so-called double-row polyribosomes). The “long” (i.e. heavy loaded) polyribosomes are usually represented by double-row structures, which can be interpreted as either topologically circular (“col-lapsed rings”), or topologically linear (zigzags or helices). In the present work we have analyzed the mRNA path within the eukaryotic polyribosomes, isolated from a wheat germ cell-free translation system, by integrating two approaches: the visualization of mRNA ends in polyribosomes by marking them with gold nanoparticles (3′-end) and initiating 40S subunits (5′-end), as well as by the cryoelectron tomography. Examination of the location of the mRNA markers in polyribosomes and mutual orientation of ribosomes in them has shown that the double-row polyribosomes of the same sample can have both circular and linear arrangements of their mRNA.     

Partial characterisation of and the effect of insect growth hormones on the ribosomes and polyribosomes of the nematode, Panagrellus redivivus

An investigation of some of the properties of the ribosomes and polyribosomes of Panagrellus redivivus revealed that: the polyribosomal RNA was resolvable into eight species, four of which possessed typical S-values and M.W.s and closely resembled those of Aphelenchus avenae; the estimated S-value of the ribosomes was 92; the polyribosomes were mainly free and not membrane-bound: and, the polyribosomes showed a low level of activity in in vitro amino-acid incorporation. The polysomes (double-labelled or unlabelled) revealed no effect of synthetic juvenile hormone or ß-ecdysone (1 × 10^?5M) on their polyribosomal profile, at intervals up to and including 19 h of incubation.     

ISOLATION OF TWO DISTINCT CLASSES OF POLYSOMES FROM A NUCLEAR FRACTION OF RAT LIVER

Isolated rat liver nuclei were washed with Triton-X-100 in the presence of liver cell sap. This treatment liberated a fraction of polysomes which were isolated by differential centrifugation and were designated "outer membrane polysomes." The outer membrane polysomes synthesized protein in vivo. Shortly after injection of orotic acid-¹⁴C, the RNA of outer membrane polysomes had a higher specific activity than that of cytoplasmic polysomes. It was postulated that outer membrane polysomes may be an intermediate in the transfer of newly synthesized RNA from the nucleus to the cytoplasm. In other experiments, Triton-washed rat liver nuclei were lysed in the presence of deoxycholate and deoxyribonuclease. A ribonucleoprotein fraction was isolated from the lysate by differential centrifugation. This fraction contained "intranuclear ribosomes," which sedimented like partially degraded polysomes in sucrose gradients. This degradation could be partially prevented if intranuclear ribosomes were purified by sedimentation through heavy sucrose. The resulting pellets were termed "intranuclear polysomes" because they contained some undergraded polysomes. Intranuclear polysomes were highly radioactive after a brief pulse with orotic acid-¹⁴C, but did not appear to synthesize protein rapidly in vivo. Intranuclear polysomes may represent the initial stage of assembly of polyribosomes in the nucleus.     

A cytoskeletal structure with associated polyribosomes obtained from HeLa cells

A method is described by which HeLa cells can be fractionated to reveal a skeletal-like structure in the cytoplasm. This cytoskeleton has many of the cell's ultrastructural features, such as 100Å filaments, microfilaments, centrioles, and microspikes, although most of the cellular protein, membranes, and microtubules have been extracted. Associated with the cytoskeleton are most of the polysomal, but not the monomeric, ribosomes. These polysomes are distributed throughout the cytoskeleton except in the region of the 100Å filaments, which resembles the distribution in intact cells. Degradation of mRNA with low levels of ribonuclease releases most ribosomes from the cytoskeleton. Prior disaggregation of polyribosomes in vivo releases ribosomes but not mRNA. Cytochalasin B administered in vivo releases the mRNA from the cytoskeleton. These results suggest an attachment of polyribosomes to the cytoskeleton via mRNA.     

Visualizing Compaction of Polysomes in Bacteria

During protein synthesis, many translating ribosomes are bound together with an mRNA molecule to form polysomes (or polyribosomes). While the spatial organization of bacterial polysomes has been well studied in vitro, little is known about how they cluster when cellular conditions are highly constrained. To better understand this, we used electron tomography, template matching, and three-dimensional modeling to analyze the supramolecular network of ribosomes after induction of translational pauses. In Escherichia coli, we overexpressed an mRNA carrying a polyproline motif known to induce pausing during translation. When working with a strain lacking transfer-messenger RNA, the principle actor in the “trans-translation” rescuing system, the cells survived the hijacking of the translation machinery but this resulted in a sharp modification of the ribosomal network. The results of our experiments demonstrate that single ribosomes are replaced with large amounts of compacted polysomes. These polysomes are highly organized, principally forming hairpins and dimers of hairpins that stack together. We propose that these spatial arrangements help maintain translation efficiency when the rescue systems are absent or overwhelmed.     

POLYRIBOSOMES AND CISTERNAL ACCUMULATIONS IN ROOT CELLS OF RADISH

The zone of root hair formation of seedling radish roots, Raphanus sativus L., was studied by phase-contrast and electron microscopy. Localized dilations of the endoplasmic reticulum, which contained a moderately dense proteinaceous material, were found to be a common component of the cytoplasm in cells of the epidermis and cortex. The surfaces of these dilations were covered with polyribosomes in discrete coils commonly composed of 15 to 17 ribosomes. The function of these structures and the fate of the material accumulated in them are unknown. Their similarity to structures described in some types of animal cells is discussed.     

Plant desiccation and protein synthesis: an in vitro system from dry and hydrated mosses using endogenous and synthetic messenger ribonucleic Acid

The conditions and requirements for an in vitro protein synthesizing system from the moss Tortula ruralis are outlined. Using this system the effects of desiccation, achieved quickly or slowly, were studied. Slowly dried moss retained fewer polyribosomes on desiccation but more active ribosomes than rapidly dried moss. Even in the completely desiccated moss the polyribosomes and/or free ribosomes present have retained their synthetic capacities. On rehydration, the slowly dried moss resumed protein synthesis more quickly than moss previously desiccated rapidly. Moss ribosomes are cycloheximide sensitive and chloramphenicol insensitive and thus the major protein synthesis occurs within the cytoplasm on rehydration. Extracted polyribosomes per se can withstand desiccation to a significant extent, suggesting that protection by the cytoplasm might not be necessary. The aquatic moss Hygrohypnum luridum can retain polyribosomal and ribosomal activity during desiccation, but this decreases greatly on rehydration.     

THE RESPONSE OF VENTRAL HORN NEURONS TO AXONAL TRANSECTION

The morphological changes induced in the frog ventral horn neurons by axonal transection have been studied with the electron microscope. During the first 2 wk after axotomy the neuronal nucleus becomes more translucent and the nucleolus becomes enlarged and less compact. The cisternae of the granular endoplasmic reticulum vesiculate and ribosomes dissociate from membranes. Free ribosomes and polysomes are dispersed in the cytoplasmic matrix. Neurofilaments and neurotubules are increased in number. These structures appear to be important in the regeneration of the axon. It is proposed that neurotubules, neurofilaments, and axoplasmic matrix are synthesized by the free polyribosomes in the chromatolytic neuron. By the fourth postoperative week, the neurons show evidence of recovery. The cytoplasm is filled with profiles of granular endoplasmic reticulum and many intercisternal polysomes. The substances being manufactured by the newly formed granular endoplasmic reticulum are not clearly defined, but probably include elements essential to electrical and chemical conduction of impulses. The significance of these observations in respect to recent studies of axoplasmic flow is discussed.     

Ultrastructural changes in rat colorectal epithelium and tumors after treatment with N-methyl-N'-nitro-N-nitrosoguanidine and secondary bile acids.

Transmission electron microscopy (TEM) was used to study ultrastructural changes that accompanied the tumorous transformation of the descending rat colon epithelial cells, following short treatment with a direct carcinogen, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), with subsequent prolonged treatment with secondary bile acids, lithocholic (LCA) and deoxycholic (DCA), which enhanced tumor formation. Colon epithelial cells after long treatment with bile acids alone were characterized by the presence of an irregular nuclear membrane, ring-shaped rough endoplasmic reticulum (RER), collagen-like tonofilaments and membrane-bound mucous vacuoles. Tumor cells which developed following treatment with MNNG alone were characterized by the irregular shape of the nuclear membrane and, sometimes, by polynuclei, accumulation of large amounts of mitochondria, loss of cell-cell contacts and by endocytosis of the cell membrane. After combined treatment with MNNG and LCA, many mitochondria lost their membranous envelope; in the cytoplasm many collagen-like tonofilaments, ring-shaped RER and many free ribosomes were present. After treatment with MNNG and DCA, many polysomes were found in the cytoplasm. It was apparent that treatment with MNNG alone caused the development of adenocarcinoma-like tumors, while additional treatment with secondary bile acids significantly enhanced these changes, which were accompanied by the development of atypia and anaplasia of epithelial cells, with many irregularities in intracellular organization.     

Histone synthesis in Rhynchosciara salivary glands. I. Site and timing of synthesis.

The site of histone synthesis was studied in polytene cells of the salivary glands of the Rhynchosciara americana (Diptera). It was found that, as is the case in non-polytene systems, these proteins are synthesized in the cytoplasm in a class of light polysomes which contain 3-4 ribosomes. This class of polyribosomes is most active at about 5 days before pupation when the nuclei are most active in DNA synthesis and the chromosomes of the gland show many open 'DNA puffs'.     

Comparative study of the ultrastructure of immune and normal phytohemagglutinin-treated lymphocytes]

Immune lymphocytes sorbed on the surface of the target cells were characterized during the period of the first three hours of combined incubation by the presence of the electron-dense matrix, abundance of mitochondria and lipids; small lymphocytes had disseminated ribosome organized into polysomes in the medium lymphocytes forming individual cysterns of the granular endoplasmic reticulum in the large lymphocytes, this indicating active protein synthesis by these cells. There were also revealed cells of plasmatic type. Cells incubated with the PHA for one hour represented a homogenous population of small lymphocytes of the same size as the clear cytoplasm containing free ribosomes and individual mitochondria. The proportion of the medium lymphocytes and the blasts increased with increase of the incubation period. These are cells with the clear cytoplasm freely disseminated polyribosomes in which no developed granular endoplasmic reticulum was sometimes revealed. The presence of two types of cells whose ultrastructure reflected their functional characteristics is discussed.     

Red-Far Red Reversible Effect on Polysome Formation in the Embryos of Pinus thunbergii Seeds

Polysome formation in the embryos of Pinus thunbergii seeds was studied. Free ribosomes were dissociated to smaller subunits in a high salt buffer, but the complex ribosomes were not. The free ribosomes could be distinguished from monomer ribosomes derived from polysomes after RNase treatment. The monomer ribosomes present in the embryos of the dark-imbibed seeds were predominantly free ribosomes; very small quantities of polysomes could be detected in the embryos from dark-imbibed seeds. Such polysomes remained at a very low level during dark imbibition at least for a month. The level of polysomes increased 4 hours after a brief exposure to red light. The effect of red light on polysome formation was partially reversed when followed by far red light irradiation.     

Circular polysomes predominate on the rough endoplasmic reticulum of somatotropes and mammotropes in the rat anterior pituitary

We have studied the shape and size distribution of membrane-bound polysomes in somatotropes and mammotropes, which are the sources, respectively, of growth hormone and of prolactin in the rat pituitary. The observations were made in conventional electron micrographs of these cells in situ, where occasional surface or en face views of the rough endoplasmic reticulum allow the polysomes to be seen as rows of ribosomes arranged in distinctive patterns on the membranes. It is possible by this means to characterize the shape and number of ribosomes for the total population of bound polysomes in the respective cell types. The great majority of membrane-bound polysomes in these two cell types (81% in somatotropes, 78% in mammotropes) have an approximately circular shape and contain an average of 6.8 (somatotropes) or 6.5 (mammotropes) ribosomes, which is an appropriate size for translation of the polypeptide hormones produced by these cells. About 17% of the membrane-bound polysomes in somatotropes and 20% in mammotropes have a spiral shape, resembling somewhat the letter "G," and contain about eight to nine ribosomes in both cell types. The preponderance of circular polysomes on the rough endoplasmic reticulum of somatotropes and mammotropes suggests the possibility that ribosomes (or the 40S ribosomal subunit) may recycle on the polysome after the translation of growth hormone or of prolactin.     

Requirements for extraction of polyribosomes from lyophilised peel tissue of climacteric pear

Profiles of polyribosomes have been obtained from lyophilised peel tissue of climacteric pear (Pyrus communis cv Passe-Crassane) isolated in various buffers. Messenger RNA chains bearing up to 7 ribosomes (heptamers) were resolved and exhibited the highest absorption peak. High vacuolar concentrations of phenolics and acids, which are major obstacles in extracting fruit polyribosomes, were circumvented with the use of polyethylene glycol, insoluble polyvinylpyrrolidone (Polyclar AT), extraction at low temperature and high ionic strength buffer. Addition of Ca²⁺ to the extracting medium precipitated polysomes but ethyleneglycol bis(2-aminoethylether) tetra-acetic acid (EGTA), a divalent cation chelator with a high affinity for Ca²⁺, increases the proportion of polyribosomes.     

Hydrophobic binding of ribosomes and polysomes to agarose gels

Rat liver ribosomes and polyribosomes could be immobilized in agarose gels at 4°C and pH 7.6, using KCl or NaCl molarities of 0.25 or higher. The binding could be effected in the presence of excess protein and/or detergents. Polysomes attached to endoplasmic membrane fragments did not bind to agarose even at 0.5m KCl; tRNAs were also not bound. The larger (60 S) subunit of liver ribosomes was also completely immobilized at 0.3m KCl, while the immobilization of the smaller (40 S) subunit was poor even at 1m KCl. The ribosomal subunits could be essentially quantitatively desorbed at 4°C by a low ionic strength elution, while the recovery of gel-bound polysomes was of the order of 80 to 85% under these conditions. The polysomes that recovered from agarose at low ionic strength were active inin vitro incorporation of amino acids into polypeptides.     

Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study

The polyribosomes newly formed on recombinant GFP-encoding mRNAs in a wheat germ cell-free translation system were analyzed using cryo-electron tomography, with sub-tomogram averaging of polysomal ribosomes and reconstruction of 3D structures of individual polyribosomes. The achieved level of resolution in the reconstructed polyribosomes allowed deducing the mRNA path by connecting adjacent exit and entry sites at the ribosomes inside each polyribosome. In this way, the circularity of a significant fraction (about 50%) of translating polyribosomes was proved in the case of the capped poly(A)-tailed mRNA, in agreement with the existing paradigm of the circularization via interaction of cap-bound initiation factor eIF4F with poly(A)-binding protein. However, translation of the capped mRNA construct without poly(A) tail, but with unspecific 3′-UTR derived from non-coding plasmid sequence, also led to the formation of circular polyribosomes in similar proportion (40%). Moreover, the polyribosomes formed on the uncapped non-polyadenylated mRNA with non-synergistic 5′- and 3′-UTRs proved to be circular as well, and appeared in the same proportion as in the previous cases. Thus, the formation of circular polyribosomes was found to be virtually independent of the presence of cap structure and poly(A) tail in mRNA, in contrast to the longstanding paradigm in the field.