Cytoplasmic polyadenylate processing events accompany the transfer of mRNA from the free mRNP particles to the polysomes in Physarum

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

Design of novel DNA probes to inhibit specific repair pathways is important for basic science applications and for use as therapeutic agents. As shown previously, single pyrophosphate (PP) and O-ethyl-substituted pyrophosphate (SPP) modifications can inhibit the DNA glycosylase activities on damaged DNA. To understand the structural basis of this inhibition, the influence of the PP and SPP internucleotide groups on the helical parameters and geometry of a double-stranded DNA was studied by using molecular modeling tools including molecular dynamics and quantum mechanical-molecular mechanical (QM/MM) approaches. Native and locally modified PP- and SPP-containing DNA duplexes of dodecanucleotide d(C1G2C3G4A5A6T7T8C9G10C11G12) were simulated in aqueous solution. The energies and forces were computed by using the PBE0/6-31+G** approach in the QM part and the AMBER force-field parameters in the MM part. Analysis of the local base-pair helical parameters, internucleotide distances, and overall global structure at the located stationary points revealed a close similarity of the initial and modified duplexes, with only torsion angles of the main chain being altered in the vicinity of introduced chemical modification. Results show that the PP and SPP groups are built into a helix structure without elongation of the internucleotide distance due to flipping-out of phosphate group from the sugar-phosphate backbone. The mechanism of such embedding has only a minor impact on the base pairs stacking and Watson-Crick interactions. Biochemical studies revealed that the PP and SPP groups immediately 5', but not 3', to the 8-oxoguanosine (8oxodG) inhibit translesion synthesis by a DNA polymerase in vitro. These results suggest that subtle perturbations of the DNA backbone conformation influence processing of base lesions.

Importance of polysomal mRNA-associated polypeptides for protein synthesis initiation in yeast

The polysomal mRNA from the cell-free system of the yeast Saccharomyces cerevisiae, in the absence of exogenous energy, binds to the 40S ribosomal subunit thus forming a 48S preinitiation complex which, with energy added, is converted into 80S initiation complex. By using ribosomes with a high affinity to polysomal mRNA (pmRNA) from an edeine-resistant mutant of S. cerevisiae in place of wild-type ribosomes, increased quantities of the 48S preinitiation complex are obtained. The pmRNA is found associated with several polypeptides having molecular masses of 115-98 kDa, 72 kDa, 60 kDa and 51 kDa. These polypeptides, labelled with 125I, interact with 40S and 80S ribosomes and are essential for the formation of the 48S and 80S initiation complexes inasmuch as deproteinized pmRNA alone cannot initiate the process. In addition, other polypeptides present in the cytosol are required to carry out the above-mentioned steps of protein synthesis.

Isolation and characterization of cytoplasmic poly(A) polymerase from cryptobiotic gastrulae of Artemia salina

Poly(A) polymerase has been purified to near homogeneity from the cytoplasm of Artemia salina cryptobiotic gastrulae by ion-exchange chromatography on DEAE-cellulose, DEAE-Sepharose CL-6B and phosphocellulose P11, gel filtration on CL-Sepharose 6B, affinity chromatography on poly(A)-Sepharose 4B and ATP-agarose. The enzyme is fully dependent on exogeneous oligo(riboadenylic acid) and is free of any nuclease or other enzyme activities. In standard assay conditions the enzyme preparation has a specific activity of 5.6 mumol AMP . h-1 . (mg protein)-1. Sodium dodecyl sulphate/polyacrylamide gel electrophoresis reveals the presence of only two proteins with Mr 94 000 and 70 000. The Mr-70 000 protein has been identified as poly(A) polymerase. The enzyme is exclusively activated by Mn2+. Addition of Ca2+, Mg2+, Zn2+, NH4+, K+ or Na+ inhibits the enzymatic reaction. The activity is specific for ATP and competitive inhibition is observed in the presence of other ribonucleoside 5'-triphosphates. AMP incorporation is time-dependent and is increased non-linearly with protein and primer concentration.

Translational repression of mRNA for eucaryotic elongation factors in Friend erythroleukemia cells

Poly(A)-containing mRNA was prepared from polyribosomes and postpolyribosomal messenger ribonucleoprotein particles (mRNP) from Friend erythroleukemic cells. Both mRNA types were translated in vitro and the 35S-labeled translation products examined by two-dimensional gel electrophoresis. Among the most abundant untranslated mRNA species was the mRNA coding for eucaryotic elongation factor Tu (eEF-Tu). In addition, the mRNA for eucaryotic elongation factor Ts was also present in Friend cells in untranslated form. Calculations based on translation assays indicate that eEF-Tu represents about 15% of the translation products of RNP mRNA and that approximately 40% of the eEF-Tu synthesized in vitro is encoded by translationally repressed mRNA. This repressed mRNA can be activated by addition of cycloheximide to cell cultures. At the level of 0.1 micrograms/ml, cycloheximide was found to inhibit cellular protein synthesis by about 50% while augmenting the relative rate of eEF-Tu synthesis 1.6-fold. This result suggested that eEF-Tu mRNA might initiate poorly. However, addition of supersaturating levels of mRNA to a reticulocyte lysate augmented eEF-Tu synthesis about twofold, while generally depressing the synthesis of other proteins by about 40%. Thus the storage of large amounts of eEF-Tu mRNA in vivo is unlikely to be due directly to the ineffectiveness of the mRNA in competing for the initiation machinery of the cell. The results presented in this report suggest that the supply of active eEF-Tu in erythroleukemic cells is controlled, at least in part, by a translational mechanism.

Rapid increase of calcitonin-specific mRNA after acute hypercalcemia

The regulation of calcitonin (CT) secretion by calcium was studied by measuring CT mRNA extracted from thyroids of normal rats subjected to acute calcium stimulation in vivo. The 15000-Mr primary translation product of CT mRNA was identified by immunoprecipitation using specific antibodies. While total mRNA and total radioactivity incorporated after translation of total mRNA remained unaffected by the calcium stimulation, a fourfold increase in radioactivity incorporated in CT primary translation product occurred as early as 2 min after calcium administration. This peak coincided with a rise in plasma levels of the hormone and preceded a detectable decrease in tissue stores. These results suggest that calcium ion, either directly or indirectly via its action on intracellular stores of the hormone or its precursors, causes a rapid increase in cell levels of translatable CT mRNA. In view of the extremely short time (2 min) in which this increase occurs, the action is probably at the post-transcriptional level as no increase in CT mRNA levels could be detected by hybridization assay using a specific cDNA probe for human CT mRNA.

Efficient translation and polyribosome binding of 125I-labelled rabbit globin messenger ribonucleoprotein

Rabbit polyribosomal globin messenger ribonucleoprotein (mRNP) was labelled under mild conditions, using 125I and Iodogen, in the protein moiety so that the fate of mRNA-associated proteins could be followed during translation. 125I-mRNP was shown to retain functional activity in the nuclease-treated reticulocyte lysate translation system under optimal labelling conditions. Polyribsome binding of 125I-mRNP and its sensitivity to cycloheximide indicated a functional- and translation-dependent binding of mRNP proteins. The results constitute a successful and direct approach to the study of mRNA-associated proteins in translational control.

Lectin-induced changes among polyadenylated and non-polyadenylated mRNA in lymphocytes. mRNAs for actin, tubulin and calmodulin respond differently

The differentiation of T-cell-enriched concanavalin-A-stimulated bovine lymphocytes was studied in vitro. mRNA was isolated from resting and stimulated cells. The amount of polyadenylated RNA increases from 3.6 X 10(-9) to 12 X 10(-9) micrograms/cell during 40 h concanavalin A stimulation. The estimated maximum length of the 3'-poly(A) tract in this RNA is reduced from 240 to 220 residues in stimulated cells. During translation in the rabbit reticulocyte lysate in vitro mRNA from stimulated cells consistently incorporates about 1.6-3 times more radioactivity/micrograms RNA into proteins than mRNA from resting cells. Three translation products have been identified on two-dimensional gels as actin, tubulin and calmodulin. Large quantitative shifts are seen between proteins translated from mRNAs isolated from resting cells and stimulated cells respectively. Actin and calmodulin are already major products from resting cell mRNA. Actin, however, increases about fivefold after stimulation while calmodulin does not change. Tubulin appears in substantial amounts only among stimulated cell mRNA products. Tubulin and calmodulin, on the other hand, remain mainly in the polyadenylated RNA fraction after stimulation while 50% of the actin together with a group of about six other major products is found among proteins translated from non-polyadenylated RNA. We conclude that in lectin-stimulated lymphocytes, besides a general increase in the amount of mRNA, alterations in post-transcriptional processing reactions are active in determining the fate of individual mRNAs.

Proteins associated with poly(A)+RNA of cockerel liver: effects of estradiol stimulation

The protein population of poly(A)-containing messenger ribonucleoprotein (mRNP) from cockerel liver was analyzed before and after estradiol induction. Polysomal and free mRNP were isolated by thermal elution from oligo(dT)-cellulose. The proteins were separated by two-dimensional electrophoresis (of which the first dimension was a nonequilibrium pH gradient) and were visualized by silver staining. In order to determine similarities and differences between proteins of various mRNP fractions, trace amounts of 125I-labeled protein from one fraction were coelectrophoresed with stainable amounts of protein from another fraction on the same gel. Of 27 proteins analyzed, 15 were common to polysomal and free mRNP, 7 were specific to polysomal mRNP, and 5 were specific to free mRNP. Moreover, estradiol strongly influenced 11 proteins. Six proteins changed either in relative intensity or in distribution between polysomal and free mRNP fractions. Three major proteins appeared in both fractions, and two additional proteins disappeared from the free mRNP fraction after estradiol treatment. The results suggest that the protein population in polysomal mRNP is quite complex and that the profound influence of estradiol on protein synthesis in cockerel liver may be connected to changes in the protein composition of mRNP.

Stored messenger ribonucleoprotein particles in differentiated sclerotia of Physarum polycephalum

Starvation induces vegetative microplasmodia of Physarum polycephalum to differentiate into translationally-dormant sclerotia. The existence and the biochemical nature of stored mRNA in sclerotia is examined in this report. The sclerotia contain about 50% of the poly (A)-containing RNA [poly(A)+RNA] complement of microplasmodia as determined by [3H]-poly(U) hybridization. The sclerotial poly(A)+RNA sequences are associated with proteins in a ribonucleoprotein complex [poly(A)+mRNP] which sediments more slowly than the polysomes. Sclerotial poly(A)+RNP sediments more rapidly than poly(A)+RNP derived from the polysomes of microplasmodia despite the occurrence of poly(A)+RNA molecules of a similar size in both particles suggesting the existence of differences in protein composition. Isolation of poly(A)+RNP by oligo (dT)-cellulose chromatography and the analysis of its associated proteins by polyacrylamide gel electrophoresis show that sclerotial poly(A)+RNP contains at least 14 major polypeptides, 11 of which are different in electrophoretic mobility from the polypeptides found in polysomal poly(A)+RNP. Three of the sclerotial poly(A)+RNP polypeptides are associated with the poly(A) sequence (18, 46, and 52 x 10(3) mol. wt. components), while the remaining eight are presumably bound to non-poly(A) portions of the poly(A)+RNA. Although distinct from polysomal poly(A)+RNP, the sclerotial poly(A)+RNP is similar in sedimentation behavior and protein composition (with two exceptions) to the microplasmodial free cytoplasmic poly(A)+RNP. The results suggest that dormant sclerotia store mRNA sequences in association with a distinct set of proteins and that these proteins are similar to those associated with the free cytoplasmic poly(A)+RNP of vegetative plasmodia.

Cytoplasmic processing events in the polyadenylate region of Physarum messenger RNA

Cytoplasmic processing events in the poly(A) region of mRNA from Physarum polycephalum are reviewed. Two classes of poly-containing RNA [poly(A)+ RNA] exist in the cytoplasm. One contains very short poly(A) sequences, averaging about 15 adenylate residues, while the other contains relatively long poly(A) sequences, averaging about 60 residues. Molecules with short poly(A) sequences are found exclusively in the polysomes while those with long poly(A) sequences are restricted to the free cytoplasmic mRNP. Since proteins are associated with only the long poly(A) sequences the poly(A) . protein complex is also restricted to the free mRNP. The long poly(A) sequences are relatively short-lived. They are degraded by two distinct processes, a shortening process in which 15-20 residues are gradually removed and a turnover process in which long poly(A) tracts are rapidly converted to the short sequences. This process, along with the dissociation of the poly(A) . protein complex, occurs when poly(A)+ RNA molecules located in free mRNP are transferred to the polysomes. Poly(A) . protein complex dissociation appears to precede poly(A) turnover during translational selection. The significance of these processing events in relation to mRNA maturation is discussed.