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The ability to detect and respond to oxidative stress is crucial to the survival of living organisms. In cells, sensing of increased levels of reactive oxygen species (ROS) activates many defensive mechanisms that limit or repair damage to cell components. The ROS-signaling responses necessary for cell survival under oxidative stress conditions remain incompletely understood, especially for the translational machinery. Here, we found that drug treatments or a genetic deficiency in the thioredoxin system that increase levels of endogenous hydrogen peroxide in the yeast Saccharomyces cerevisiae promote site-specific endonucleolytic cleavage in 25S ribosomal RNA (rRNA) adjacent to the c loop of the expansion segment 7 (ES7), a putative regulatory region located on the surface of the 60S ribosomal subunit. Our data also show that ES7c is cleaved at early stages of the gene expression program that enables cells to successfully counteract oxidative stress and is not a prerequisite or consequence of apoptosis. Moreover, the 60S subunits containing ES7c-cleaved rRNA cofractionate with intact subunits in sucrose gradients and repopulate polysomes after a short starvation-induced translational block, indicating their active role in translation. These results demonstrate that ES7c cleavage in rRNA is an early and sensitive marker of increased ROS levels in yeast cells and suggest that changes in ribosomes may be involved in the adaptive response to oxidative stress., (© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.)

Maintenance of telomere length and structure is essential for cell survival. Telomere synthesis is mediated by the ribonucleoprotein telomerase in 90% of cancer cells, and is regulated mainly by transcription of the human telomerase reverse transcriptase subunit, hTERT. However, transcriptome analysis reveals complex splicing patterns and to date, twenty-two alternatively-spliced hTERT mRNAs have been reported, yet their functions have not been fully elucidated. The best characterized hTERT spliced variants encode for inactive proteins that possess specific deletions within the hTERT catalytic domains. We studied two less well characterized hTERT splice variants (termed INS3 and 4) that encode proteins with intact reverse transcriptase motifs, but alternative C-domains due to insertion of intronic sequences. We determined the prevalence of these mRNA variants in primary cells, telomerase-positive cells and in alternative lengthening of telomere (ALT) cells and found the transcripts to be expressed mainly in telomerase-positive cell lines and to be translated into proteins as illustrated by their association with polysomes. These variants were inactive when expressed in vitro or in cells, retained DNA substrate binding in vitro but were impaired in binding the telomerase RNA component when expressed in, and immunoprecipitated from either telomerase-positive or telomerase-negative ALT cells coexpressing the telomerase RNA component. Stable expression of INS3 and INS4 variants in a hepatocarcinoma cell line inhibited telomerase activity, shortened telomeres and slowed cell growth suggesting a potential dominant-negative function., (Copyright © 2014 Elsevier Masson SAS. All rights reserved.)

Rubisco gene expression was examined in detail in rice (Oryza sativa L.) leaves at different positions, i.e. expanding, mature, and senescent leaves. Rubisco small subunit (RBCS) synthesis and RBCS mRNA levels were maximal in expanding leaves and gradually became lower in mature and senescent leaves, with declines in those of the large subunit (RBCL) being relatively slower. The amount of synthesized RBCL per unit level of RBCL mRNA and polysome loading of RBCL mRNA declined in senescent leaves, whereas such phenomena were not observed for RBCS. These results suggested that gene expression of RBCL is downregulated at the level of its translation when a balance between RBCL and RBCS expression is disturbed by leaf senescence. It has been suggested that RBCS protein is a positive regulator for RBCL mRNA level in expanding rice leaves, as judged from their stoichiometric relationship in RBCS transgenic rice plants. However, the ratio of the RBCL mRNA level to the amount of synthesized RBCS in senescent leaves was significantly higher than that in expanding leaves. Therefore, it is suggested that the decline in RBCL mRNA level in senescent leaves is not fully accounted for by that in the amount of synthesized RBCS. Effects of other factors such as the stability of RBCL mRNA may come into play.

Background: In previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA secondary structures during transcription, including transcription initiation and termination. The model accurately reproduces changes of gene transcription level observed in polymerase sigma-subunit knockout and heat shock experiments in plant plastids. The corresponding computer program and a user guide are available at http://lab6.iitp.ru/en/rivals. Here we apply the model to the analysis of transcription and (partially) translation processes in the mitochondria of frog, rat and human. Notably, mitochondria possess only phage-type polymerases. We consider the entire mitochondrial genome so that our model allows RNA polymerases to complete more than one circle on the DNA strand., Results: Our model of RNA polymerase interaction during transcription initiation and elongation accurately reproduces experimental data obtained for plastids. Moreover, it also reproduces evidence on bulk RNA concentrations and RNA half-lives in the mitochondria of frog, human with or without the MELAS mutation, and rat with normal (euthyroid) or hyposecretion of thyroid hormone (hypothyroid). The transcription characteristics predicted by the model include: (i) the fraction of polymerases terminating at a protein-dependent terminator in both directions (the terminator polarization), (ii) the binding intensities of the regulatory protein factor (mTERF) with the termination site and, (iii) the transcription initiation intensities (initiation frequencies) of all promoters in all five conditions (frog, healthy human, human with MELAS syndrome, healthy rat, and hypothyroid rat with aberrant mtDNA methylation). Using the model, absolute levels of all gene transcription can be inferred from an arbitrary array of the three transcription characteristics, whereas, for selected genes only relative RNA concentrations have been experimentally determined. Conversely, these characteristics and absolute transcription levels can be obtained using relative RNA concentrations and RNA half-lives known from various experimental studies. In this case, the "inverse problem" is solved with multi-objective optimization., Conclusions: In this study, we demonstrate that our model accurately reproduces all relevant experimental data available for plant plastids, as well as the mitochondria of chordates. Using experimental data, the model is applied to estimate binding intensities of phage-type RNA polymerases to their promoters as well as predicting terminator characteristics, including polarization. In addition, one can predict characteristics of phage-type RNA polymerases and the transcription process that are difficult to measure directly, e.g., the association between the promoter's nucleotide composition and the intensity of polymerase binding. To illustrate the application of our model in functional predictions, we propose a possible mechanism for MELAS syndrome development in human involving a decrease of Phe-tRNA, Val-tRNA and rRNA concentrations in the cell. In addition, we describe how changes in methylation patterns of the mTERF binding site and three promoters in hypothyroid rat correlate with changes in intensities of the mTERF binding and transcription initiations. Finally, we introduce an auxiliary model to describe the interaction between polysomal mRNA and ribonucleases.

The stem cell protein Lin28 functions to inhibit the biogenesis of a group of miRNAs but also stimulates the expression of a subset of mRNAs at the post-transcriptional level, the underlying mechanism of which is not yet understood. Here we report the characterization of the molecular interplay between Lin28 and RNA helicase A (RHA) known to play an important role in remodeling ribonucleoprotein particles during translation. We show that reducing Lin28 expression results in decreased RHA association with polysomes while increasing Lin28 expression leads to elevated RHA association. Further, the carboxyl terminus of Lin28 is necessary for interaction with both the amino and carboxyl termini of RHA. Importantly, a carboxyl terminal deletion mutant of Lin28 that retains RNA-binding activity fails to interact with RHA and exhibits dominant-negative effects on Lin28-dependent stimulation of translation. Taken together, these results lead us to suggest that Lin28 may stimulate translation by actively recruiting RHA to polysomes., (© The Author(s) 2011. Published by Oxford University Press.)

Various widely known GTPases are associated with diverse crucial cellular processes. However, the functional targets of the universally conserved homologous GTPases Drg1 and Drg2, constituting the DRG subfamily in eukaryotes, remain completely unknown despite their pleiotropic cell growth effects. Contrary to expectations of functional redundancy between Drg1 and Drg2 due to their high homology, the different binding proteins Dfrp1 and Dfrp2, respectively, have been previously identified. Here, we report the first systematic characterization of all these proteins in mammals by analyses in physiological conditions. Our findings are: (1) At least one of the components of the Drg1/Dfrp1 and the Drg2/Dfrp2 complexes is specifically and drastically stabilized by each unique complex formation; and (2) the Drg1/Dfrp1 complex cosediments with polysome, while neither Drg2 nor Dfrp2 is found in ribosomal fractions at all. These results suggest that the Drg1/Dfrp1 complex independently modulates a protein synthesis mechanism different from the Drg2/Dfrp2 complex in mammalian cells.

Nat4, also designated NatD, was previously shown to acetylate the N termini of histones H2A and H4, which have SGGKG and SGRGK N termini (O. K. Song, X. Wang, J. H. Waterborg, and R. Sternglanz, J. Biol. Chem. 278:38109-38112, 2003). The analysis of chimeric proteins with various N-terminal segments of histone H4 fused to iso-1-cytochrome c revealed that efficient acetylation by NatD required at least 30 to 50 amino acid residues of the N terminus of histone H4. This requirement for an extended N terminus is in marked contrast with the major N-terminal acetyl transferases (NATs), i.e., NatA, NatB, and NatC, which require as few as two specific residues and usually no more than four or five. However, similar to the other NATs, NatD is associated with ribosomes. The nat4-Delta strain showed several minor phenotypes, including sensitivity to 3-aminotriazole, benomyl, and thiabendazole. Moreover, these nat4-Delta phenotypes were enhanced in the strain containing K5R K8R K12R replacements in the N-tail of histone H4, suggesting that the lack of N-terminal serine acetylation is synergistic to the lack of acetylation of the H4 N-tail lysines. Thus, N-terminal serine acetylation of histone H4 may be a part of an essential charge patch first described for the histone H2A.Z variant in Tetrahymena species.

Stem cell factor (SCF)-induced activation of phosphoinositide-3-kinase (PI3K) is required for transient amplification of the erythroblast compartment. PI3K stimulates the activation of mTOR (target of rapamycin) and subsequent release of the cap-binding translation initiation factor 4E (eIF4E) from the 4E-binding protein 4EBP, which controls the recruitment of structured mRNAs to polysomes. Enhanced expression of eIF4E renders proliferation of erythroblasts independent of PI3K. To investigate which mRNAs are selectively recruited to polysomes, we compared SCF-dependent gene expression between total and polysome-bound mRNA. This identified 111 genes primarily subject to translational regulation. For 8 of 9 genes studied in more detail, the SCF-induced polysome recruitment of transcripts exceeded 5-fold regulation and was PI3K-dependent and eIF4E-sensitive, whereas total mRNA was not affected by signal transduction. One of the targets, Immunoglobulin binding protein 1 (Igbp1), is a regulatory subunit of protein phosphatase 2A (Pp2a) sustaining mTOR signaling. Constitutive expression of Igbp1 impaired erythroid differentiation, maintained 4EBP and p70S6k phosphorylation, and enhanced polysome recruitment of multiple eIF4E-sensitive mRNAs. Thus, PI3K-dependent polysome recruitment of Igbp1 acts as a positive feedback mechanism on translation initiation underscoring the important regulatory role of selective mRNA recruitment to polysomes in the balance between proliferation and maturation of erythroblasts.

The polysomal ribonuclease 1 (PMR1) mRNA endonuclease forms a selective complex with its translating substrate mRNAs where it is activated to initiate mRNA decay. Previous work showed tyrosine phosphorylation is required for PMR1 targeting to this polysome-bound complex, and it identified c-Src as the responsible kinase. c-Src phosphorylation occurs in a distinct complex, and the current study shows that 90-kDa heat shock protein (Hsp90) is also recovered with PMR1 and c-Src. Hsp90 binding to PMR1 is inhibited by geldanamycin, and geldanamycin stabilizes substrate mRNA to PMR1-mediated decay. PMR1 is inherently unstable and geldanamycin causes PMR1 to rapidly disappear in a process that is catalyzed by the 26S proteasome. We present a model where Hsp90 interacts transiently to stabilize PMR1 in a manner similar to its interaction with c-Src, thus facilitating the tyrosine phosphorylation and targeting of PMR1 to polysomes.

Long-term stress leads to the induction of tyrosine hydroxylase (TH) protein and enzymatic activity in the adrenal medulla. This adaptive response is necessary to maintain the catecholamine biosynthetic capacity of adrenal chromaffin cells during periods of sustained catecholamine secretion. In this report we demonstrate that when rats are subjected to short-term stress, TH mRNA is induced for at least 24 h, but TH protein and TH activity (assayed under Vmax conditions) are not increased. In contrast, adrenal TH mRNA, TH protein and TH activity are induced in rats subjected to long-term stress. Using sucrose gradient fractionation, we show that the lack of induction of TH protein after one type of short-term stressor, a single 2-h immobilization stress is associated with a decrease in the percentage of TH mRNA molecules associated with polysomes. In contrast, after repeated immobilizations the polysome profile of TH mRNA is identical to that observed in control animals, even though TH mRNA is induced 2- to 3-fold. These results are consistent with the hypothesis that even though TH mRNA is induced by short-term stressors, mechanisms that control TH mRNA translation must also be appropriately regulated for TH protein to be induced.

The generalized process of mRNA decay involves deadenylation followed by release from translating polysomes, decapping, and exonuclease decay of the mRNA body. In contrast the mRNA endonuclease PMR1 forms a selective complex with its translating substrate mRNA, where it initiates decay by cleaving within the mRNA body. In stressed cells the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 causes translating mRNAs to accumulate with stalled 48S subunits in large subcellular structures termed stress granules (SGs), wherein mRNAs undergo sorting for reinitiation, storage, or decay. Given the unique relationship between translation and PMR1-mediated mRNA decay, we examined the impact of stress-induced dissociation of polysomes on this process. Arsenite stress disrupts the polysome binding of PMR1 and its substrate mRNA but has no impact on the critical tyrosine phosphorylation of PMR1, its association with substrate mRNA, or its association with the functional approximately 680-kDa mRNP complex in which it normally resides on polysomes. We show that arsenite stress drives PMR1 into an RNase-resistant complex with TIA-1, and we identify a distinct domain in the N terminus of PMR1 that facilitates its interaction with TIA-1. Finally, we show that arsenite promotes the delayed association of PMR1 with SGs under conditions which cause tristetraprolin and butyrate response factor 1, proteins that facilitate exonucleolytic mRNA, to exit SGs.

Arsenic is a naturally occurring, worldwide contaminant implicated in numerous pathological conditions in humans, including cancer and several forms of liver disease. One of the contributing factors to these disorders may be the alteration of cytochrome P450 (CYP) levels by arsenic. In rat and human hepatocyte cultures, arsenic, in the form of arsenite, decreases the induction of several CYPs. The present study investigated whether arsenite utilizes transcriptional or post-transcriptional mechanisms to decrease CYP3A23 in primary cultures of rat hepatocytes. In these cultures, a 6-h treatment with 5 microM arsenite abolished dexamethasone (DEX)-mediated induction of CYP3A23 protein and activity, but did not inhibit general protein synthesis. However, arsenite treatment only reduced DEX-induced levels of CYP3A23 mRNA by 30%. The effects of arsenite on CYP3A23 transcription were examined using a luciferase reporter construct containing 1.4 kb of the CYP3A23 promoter. Arsenite caused a 30% decrease in DEX-induced luciferase expression of this reporter. Since arsenite abolished induction of CYP3A23 protein, but caused only a small decrease in CYP3A23 mRNA, the effects of arsenite on translation of CYP3A23 mRNA were investigated. Polysomal distribution analysis showed that arsenite decreased translation by decreasing the DEX-mediated increase in CYP3A23 mRNA association with polyribosomes. Arsenite did not decrease intracellular glutathione or increase lipid peroxidation, suggesting that the effect of arsenite on CYP3A23 does not involve oxidative stress. Overall, the results suggest that low-level arsenite decreases both transcription and translation of CYP3A23 in primary rat hepatocyte cultures.

PMR1 is a polysome-associated mRNA endonuclease that initiates the destabilization of albumin mRNA. The current study examined whether endonuclease-mediated mRNA decay involved the selective binding of PMR1 to substrate mRNA on polysomes. PMR1 is uniformly distributed throughout the cytoplasm on polysomes and in lighter complexes and does not colocalize in cytoplasmic foci with Dcp1. Deletion mutagenesis identified polysome-targeting domains in the N and C termini of PMR1, either of which could target GFP to polysomes. Selectivity in targeting to polysome-bound substrate mRNP was determined by testing the ability of full-length PMR1 or protein lacking targeting domains to recover albumin and luciferase mRNA from dissociated polysomes. Only PMR1 bearing intact polysome-targeting domains selectively recovered albumin mRNA, and polysome targeting of both protein and substrate was required for the efficient degradation of albumin mRNA. Thus, endonuclease-mediated mRNA decay occurs on a polysome-bound complex containing PMR1 and its substrate mRNA.

Estrogen induces a global change in the translation profile of Xenopus hepatocytes, replacing serum protein synthesis with production of the yolk protein precursor vitellogenin. This is accomplished by the coordinate destabilization of serum protein mRNAs and the transcriptional induction and subsequent stabilization of vitellogenin mRNA. Previous work identified an endonuclease activity whose appearance on polysomes correlated with the disappearance of serum protein mRNAs. This enzyme, polysomal ribonuclease 1 (PMR1), is a novel member of the peroxidase gene family. The current study examined the association of PMR1 with its mRNA targets on polysomes and mRNPs. The highest amount of polysome-bound PMR1 was observed prior to estrogen induction of mRNA decay. Its distribution on sucrose density gradients matched the absorbance profile of polysome-bound mRNA, suggesting that PMR1 forms a latent complex with mRNA. Following dissociation with EDTA the 62 kDa PMR1 sedimented with a larger complex of >670 kDa. Estrogen induces a 22-fold increase in unit enzymatic activity of polysome-bound PMR1, and a time-dependent loss of PMR1 from polysomes in a manner that mirrors the disappearance of albumin mRNA. These data suggest that the key step in the extensive estrogen-induced change in mRNA decay in Xenopus liver is activation of a latent mRNA endonuclease associated with its target mRNA.

The presence of specific mRNAs in dendrites and at synapses is well established, but a direct and reliable demonstration that they are associated with polysomes is still missing. To address this point we analyzed the polysomal association of the mRNAs for the alpha-subunit of Ca(2+)/calmodulin-dependent protein kinase II (alpha-CaMKII), for type 1 inositol 1,4,5-trisphosphate receptor (InsP3R1) and for the activity-regulated cytoskeleton-associated protein (Arc) in a synaptosomal preparation devoid of contaminating material from neuronal and glial perikarya. We show that a fraction of alpha-CaMKII, InsP3R1, and Arc mRNAs present in synaptosomes is indeed associated with polysomes. Moreover, we show that polysomal association of alpha-CaMKII mRNA, but not InsP3R1 and Arc mRNAs, increases with depolarization of the synaptosomal membrane. Finally, we show that the synthesis of alpha-CaMKII protein increases with stimulation. Dendritic mRNA recruitment onto polysomes in response to synaptic stimulation might represent one of the mechanisms underlying the processes of learning and memory.

Protein composition and functional activity of various polysome subpopulations isolated from Vicia faba L. leaves and Triticum aestivum L. and Hordeum vulgare L. seedlings were studied. Membrane- and cytoskeleton-bound polysomes were more active in the wheat germ cell-free translational system than free polysomes. Several non-ribosomal proteins were detected in the polysome preparations by gel electrophoresis and Western blot analysis: (1) a canonical actin of mol wt 42 kDa; (2) a 40 kDa protein, demonstrating affinity for ribosomes, sharing some determinants with actin, and present predominantly in the subpopulations of bound polysomes; and (3) an acidic ribosome-associated p40 evenly distributed between free and bound polysomes. The possibility of involvement of these proteins in interactions between polysomes and the actin cytoskeleton is discussed., (Copyright 2000 Academic Press.)

Intracellular and extracellular sources of bicarbonate are essential for sperm motility, sperm binding to the zona pellucida and the acrosome reaction. Carbonic anhydrase II, catalysing the synthesis of bicarbonate within spermatozoa, must play a significant role in these mechanisms. We report here the expression of carbonic anhydrase II during mouse spermatogenesis and the primary structure of testicular transcripts coding for carbonic anhydrase II isolated from adult mouse and human testes. The mouse carbonic anhydrase II (Car2) mRNA displays a 5' untranslated region (UTR) larger than the corresponding somatic sequence. The additional 5' sequence contains the 'TATA box' used in somatic tissues and other promoter sequences, suggesting the use of testis-specific promoters further upstream with read-through of downstream promoters. The 3'UTR of the Car2 mRNA is shorter in mature testicular cells than in somatic cells. Polysomal gradient analysis of carbonic anhydrase II transcripts isolated from adult mouse testis and kidney revealed different translation potential: most of the testicular transcripts were present in the non-polysomal fractions, whereas a considerable fraction of kidney transcripts were polysome-associated. These results suggest that specific transcriptional and post-transcriptional mechanisms regulate the expression of carbonic anhydrase II during mammalian spermatogenesis.

Cardiac muscle expresses sarcoplasmic/endoplasmic-reticulum Ca2+ pump isoform SERCA2a; stomach smooth muscle expresses SERCA2b. In 2-day-old rabbits, cardiac muscle contained levels of SERCA2 protein that were 100-200-fold those in the stomach smooth muscle. In nuclear run-on assays, the rate of SERCA2 gene transcription in heart nuclei was not significantly higher than in the stomach smooth-muscle nuclei. However, the SERCA2 mRNA levels (mean+/-S.E.M.) were (29+/-4)-fold higher in the heart. In both tissues the SERCA2 mRNA was associated with polyribosomes. In a sucrose-density-gradient sedimentation velocity experiment on polyribosomes, there was no difference in the sedimentation pattern of SERCA2 mRNA between the two tissues, suggesting that the translation efficiency of SERCA2 RNA in the two tissues is quite similar. Thus the main difference in the control of SERCA2 expression in the two tissues is post-transcriptional and pretranslational.

Endonucleases are key effectors of mRNA degradation, particularly for mRNAs whose turnover rates are regulated by extracellular stimuli. The rapid clearance of mRNA degradation products in vivo and the need to selectively identify mRNA endonucleases in the presence of many other cellular ribonucleases make the study of these enzymes particularly challenging. We have successfully purified and cloned one such enzyme, termed polysomal RNase 1, or PMR-1. Presented here are protocols either developed in our laboratory or adapted from the work of others that we have used successfully in characterizing PMR-1. We first describe methods to determine whether a particular mRNA is degraded in vivo through an endonuclease-initiated mechanism, and then present approaches for developing an in vitro mRNA degradation system. Next we describe experiments one should perform to optimize reaction conditions, determine cofactor requirements for an endonuclease, map in vitro cleavage sites, and characterize endonucleolytic cleavage products. Finally we describe kinetic parameters one should evaluate in characterizing the enzymology of mRNA endonucleases, with particular concern focused on the relative selectivity of these enzymes for cleavage at preferred sites within target mRNAs., (Copyright 1999 Academic Press.)

Ribonucleases play essential roles in cell growth, differentiation, and the response to stress. This article deals with exoribonucleases, enzymes that degrade RNAs beginning at either the 5' or 3' end and proceed down the length of the RNA. The preparation of a crude extract of a mammalian 3'-to-5' exonuclease is described. Assay conditions for both 5'-to-3' and 3'-to-5' exonucleases are given. One of these is a yeast enzyme that is known to be involved in mRNA decay. Others are vertebrate exonucleases that are presumed to have a role in mRNA stability but have not yet been proven to do so., (Copyright 1999 Academic Press.)

An important mechanism in the up-regulation of cytochrome P-450 2A5 (CYP2A5, coumarin hydroxylase, Coh) is the stabilization of the corresponding mRNA; some evidence suggests that proteins binding to CYP2A5 mRNA may be involved in this stabilization. Here we report that pyrazole, a well known inducer of CYP2A5 and stabilizer of its message, enhances the binding of a set of proteins to 32P-labelled 3'-untranslated region (3'UTR) of CYP2A5 to give 32P-labelled bands of apparent molecular mass 37/39, 45/48 and 70/72 kDa after UV cross-linking/RNase cleavage; in addition, we found different proteins binding to other parts of CYP2A5 mRNA. The 70/72 kDa bands are also formed with the 3'UTR of c-jun. The inducible proteins are found in different cellular subfractions at different concentrations, with a maximum of five-fold induction of binding activity in microsomes. When a gel-mobility-shift assay was combined with UV cross-linking to resolve different pyrazole-inducible RNA-protein complexes into single RNA-binding protein bands, the smallest complex contained a double band of 37/39 kDa, 45/48 kDa bands, 70/72 kDa bands, and additional weaker bands at higher molecular masses (around 120 kDa). This composition was found also for all other complexes detected by gel-mobility-shift assay; occasionally, bands at higher molecular masses were also observed. The proteins of the smallest complex might therefore represent a core with which other proteins interact to build up larger complexes. Binding of proteins 37/39 kDa and 70/72 kDa was located to a 20-base loop and adjacent sequences in a 70 nt AU-rich region of the 3'UTR of the CYP2A5. Based on our previous evidence, this 70-nt sequence may play an important role in the stabilization and processing of the message.

Previous work from this laboratory [Dompenciel,R.E., Garnepudi,V.R. and Schoenberg,D.R. (1995)J. Biol. Chem.270, 6108-6118] described the purification and properties of an estrogen-regulated endonuclease isolated from Xenopus liver polysomes that is involved in the destabilization of albumin mRNA. The present study mapped cleavages made by this enzyme onto the secondary structure of the portion of albumin mRNA bearing the major cleavage sites. The predominant cleavages occur in the overlapping APyrUGA sequence AUUGACUGA present in a single-stranded loop region, and in AUUGA located within a bulged AU-rich stem. A structural mutation which converted the major loop cleavage site to a hairpin bearing one APyrUGA element eliminated cleavage at the intact site. This confirms that the polysomal RNase is specific for single-stranded RNA. Additional point mutations in the major loop characterized the nucleoside sequence requirements for cleavage. Finally, snake venom exonuclease was used to demonstrate the polysomal RNase generates products with a 3' hydroxyl. Binding of an estrogen-induced protein to a portion of the 3'UTR of vitellogenin mRNA may be involved in its stabilization by estrogen [Dodson,R.E. and Shapiro,D.J. (1994)Mol. Cell. Biol.14, 3130-3138]. The core binding site for this protein bears the sequence APyrUGA, suggesting that stabilization may be accomplished by occlusion of a cleavage site for the polysomal RNase.

Endoribonuclease RNase E appears to control the rate-limiting step that mediates the degradation of many mRNA species in bacteria. In this work, an RNase E-like activity in Archaea is described. An endoribonucleolytic activity from the extreme halophile Haloarcula marismortui showed the same RNA substrate specificity as the Escherichia coli RNase E and cross-reacted with a monoclonal antibody raised against E. coli RNase E. The archaeal RNase E activity was partially purified from the extreme halophilic cells and shown, contrary to the E. coli enzyme, to require a high salt concentration for cleavage specificity and stability. These data indicate that a halophilic RNA processing enzyme can specifically recognize and cleave mRNA from E. coli in an extremely salty environment (3 M KCI). Having recently been shown in mammalian cells (A. Wennborg, B. Sohlberg, D. Angerer, G. Klein, and A. von Gabain, Proc. Natl. Acad. Sci. USA 92:7322-7326, 1995), RNase E-like activity has now been identified in all three evolutionary domains: Archaea, Bacteria, and Eukarya. This strongly suggests that mRNA decay mechanisms are highly conserved despite quite different environmental conditions.

We have examined in mouse testis the steady-state levels of mRNAs encoding glutathione peroxidase (GSHPx), catalase (CAT), and superoxide dismutase 2 (SOD-2), three enzymes essential for the antioxidant protection of cells. In RNA preparations derived from prepuberal and adult testes and from isolated populations of meiotic and post-meiotic germ cells, one major GSHPx mRNA of about 0.8 kilobases (kb) and one major CAT mRNA of about 2.4 kb were detected. Three SOD-2 mRNAs of about 2.2, 1.2, and 1.0 kb were found in testis. In contrast to GSHPx and CAT, the mRNA levels of SOD-2 were higher in testis than in liver. SOD-2 mRNA levels are developmentally and translationally regulated with maximal levels of expression in early post-meiotic germ cells, whereas the levels of GSHPx and CAT mRNAs are relatively constant in both prepuberal and adult testes. These data suggest that translational regulation plays a more prominent role for SOD-2 expression than for GSHPx or CAT expression in the mammalian testis.

A 34 kDa, poly(U) and poly(C)-specific ribonuclease, is shown to be tightly bound on purified polysomes from six-day-old larvae of the insect Ceratitis capitata. High salt treatment (400 mM KCl) is necessary to release it completely from the polysomes. Removal of the RNase does not disrupt the structure of the ribosomes, as shown by centrifugation on sucrose gradients and poly U directed polyphenylalanine synthesis.

We reported previously that 3-hydroxy-3-methylglutaryl coenzyme A reductase synthesis is regulated at the translational level by mevalonate. To determine at what stage mevalonate affects reductase synthesis, we examined the distribution of reductase mRNA in polysomes from cells treated with lovastatin alone; lovastatin and 25-hydroxycholesterol; or lovastatin, 25-hydroxycholesterol, and mevalonate. In lovastatin-treated cells, reductase mRNA was primarily associated with heavy polysome fractions. When 25-hydroxycholesterol was added to lovastatin-treated cells, reductase mRNA levels were reduced approximately fourfold in all polysome fractions, with no accompanying redistribution of reductase mRNA into lighter polysome fractions. However, addition of both 25-hydroxycholesterol and mevalonate to lovastatin-treated cells shifted reductase mRNA from heavier to lighter polysome fractions. No change in the distribution of control beta-actin or ribosomal protein S17 mRNA occurred with any of the treatments. These results suggest that mevalonate suppresses reductase synthesis at the level of initiation. When the translation inhibitor cycloheximide was added to all three regimens, reductase mRNA shifted into heavy polysome fractions. Treatment with either lovastatin alone or lovastatin plus 25-hydroxycholesterol resulted in a 50% greater loss of reductase mRNA from the heavy polysome fractions compared to the same fractions from noncycloheximide-treated cells. No loss of reductase mRNA occurred when cycloheximide was added to cells treated with both 25-hydroxycholesterol and mevalonate. beta-Actin mRNA levels and polysome distribution were not significantly changed by cycloheximide under any of these conditions. Translationally mediated suppression of reductase mRNA did not occur when protein synthesis was inhibited with puromycin. Our results indicate that regulation of reductase mRNA levels is translation-dependent and is linked to the rate of elongation.

In cells and cell-free extracts, the early steps in histone mRNA decay occur at the 3' terminus and appear to be catalyzed by a polysome-associated 3' to 5' exoribonuclease. We describe the purification of a polysomal 3' to 5' exoribonuclease that is magnesium-dependent, active at pH 7-8 in salt concentrations below 200 mM, and resistant to the inhibitor of the RNase A family of RNases. The purified enzyme is inactive with 3'-phosphorylated RNA substrates and with DNA but can degrade duplex RNA in the absence of added ATP. The enzyme migrates at approximately 37 kDa by native state gel filtration and at 33 kDa in a SDS-polyacrylamide gel. It degrades poly(A) but not a complex of poly(A) with poly(A) binding protein, and it accelerates histone mRNA decay in high salt-washed (enzyme-depleted) polysomes. Similarities between the purified exoribonuclease and the activity that degrades histone mRNA in vitro suggest that the enzyme might be a mammalian messenger ribonuclease.

The mRNA encoding S-adenosylmethionine decarboxylase (AdoMetDC) has an unusual distribution in polysomes from cells of T lymphocyte origin. It associates predominantly with monosomes and small polysomes with none located in the preribosomal or ribonucleoprotein pool. In sharp contrast, it associates broadly with larger polysomes in several nonlymphoid cell lines, including fibroblasts and the adrenal carcinoma line, Y1. The AdoMetDC 5'-transcript leader (5'-TL) is highly conserved between human and bovine mRNAs. It has a length of about 330 nucleotides and contains a 21-nucleotide upstream open reading frame (uORF) approximately 14 nucleotides downstream of the cap site. The AdoMetDC 5'-TL, when used to replace the 5'-TL of the human growth hormone gene in a chimeric expression construct, causes a suppressed polysomal distribution of the chimeric mRNA identical to that of the endogenous AdoMetDC mRNA in the T cell line, Jurkat. In contrast, mRNA encoded by the same chimeric construct, when expressed in Y1 cells, mimics the broad polysomal distribution of the endogenous AdoMetDC mRNA. Mutations that remove the uORF, or prevent its initiation, abolish the translational suppression in T cells, establishing that the uORF is a negative element that modulates the cell-specific polysomal distribution of AdoMetDC mRNA.

The human p68 kinase is an interferon-regulated enzyme that inhibits protein synthesis when activated by double-stranded RNA. We show here that when expressed in Saccharomyces cerevisiae, the p68 kinase produced a growth suppressing phenotype resulting from an inhibition of polypeptide chain initiation consistent with functional protein kinase activity. This slow growth phenotype was reverted in yeast by two different mechanisms: expression of the p68 kinase N-terminus, shown to bind double-stranded RNA in vitro and expression of a mutant form of the alpha-subunit of yeast initiation factor 2, altered at a single phosphorylatable site. These results provide the first direct in vivo evidence that the p68 kinase interacts with the alpha-subunit of eukaryotic initiation factor 2. Sequence similarity with a yeast translational regulator, GCN2, further suggests that this enzyme may be a functional homolog in higher eukaryotes, where its normal function is to regulate protein synthesis through initiation factor 2 phosphorylation.

The substrate specificity of polysome rat liver N alpha-acetyltransferase (NAT) has been examined by utilizing a series of synthetic and natural substrates that has been systematically altered with respect to N-terminal sequence and length. Families of peptides of the structure S-Y-S-G-G-L-L-L were generated by successively replacing the N-terminal serine, the penultimate tyrosine, and the antepenultimate serine with all 19 commonly occurring amino acids, which were then assessed for their reactivity with the rat liver enzyme. Only peptides with N-terminal serine, alanine, methionine, leucine, and phenylalanine were modified. Glycine, lysine, arginine, valine, isoleucine, and tryptophan in the second position are (with N-terminal serine) strongly inhibitory, and proline completely blocks modification. Third-position substitutions have less of an effect on NAT activity with glycine, aspartic acid, glutamic acid, and tryptophan being most inhibiting (with N-terminal Ser-Tyr). These observations are generally in agreement with in situ modifications although there are some significant differences particularly with respect to the amino-terminal residues. Optimal chain length was determined to be 10-11 residues with either synthetic peptides of the structure S-Y-S-(G)n-L-L-L or adrenocorticotropin (ACTH) sequences ranging from 8 to 39 residues. The ACTH peptides were generally found to be severalfold better substrates than the corresponding synthetic ones. Activity was not affected by increased chain length beyond approximately 17 residues. These data support the view that polysome-catalyzed N alpha-acetylation occurs as a cotranslational event on nascent chains of about 20-40 amino acids in length.

Rat liver polysome N alpha-acetyltransferase has been purified to homogeneity by a four-step procedure that utilizes ammonium sulfate precipitation, gel filtration, hydroxylapatite chromatography, and Mono Q ion exchange chromatography. The enzyme is greatly stabilized by the inclusion of EDTA and 0.01% deoxycholate in the isolation buffers. The purified enzyme has a native molecular weight of 190,000 and a subunit molecular weight of 95,000, suggesting that it is a homodimer. The enzyme shows a pH optimum of 8.0 and is strongly inhibited by Cl-, I-, SCN-, and ClO4- and to a lesser degree by sulfate and acetate. It is unaffected by phosphate, citrate, and F- and by Na+ and K+; NH4+ is partially inhibitory. The enzyme is also sensitive to iodoacetic acid. It is generally more similar to yeast N alpha-acetyltransferase [Lee, F.-J. S., Lin, L.-W., & Smith, J. A. (1988) J. Biol. Chem. 263, 14948-14955] than to the hen oviduct enzyme, which contains a 7S RNA subunit [Kamitani, K., & Sakiyama, F. (1989) J. Biol. Chem. 264, 13194-13198], although the amino acid compositions are quite different.

Earlier studies reported that the administration of L-tryptophan increased polyribosomal aggregation, protein synthesis and levels of cytoplasmic poly(A) mRNA in rat liver. This study was concerned with the effects of an L-tryptophan analog, D,L-beta-(1-naphthyl)alanine, in comparison with those of L-tryptophan. Both D,L-beta-(1-naphthyl)alanine and L-tryptophan bound to the L-tryptophan receptor protein and increased poly(A)polymerase and nucleoside triphosphatase activities of hepatic nuclei. However, only L-tryptophan was associated with increases in the release of labeled nuclear RNA (in vitro), in protein synthesis, in polyribosomal aggregation and in glycosylation ([14C]glucosamine incorporation into proteins) of rat liver. These results indicate that although D,L-beta-(1-naphthyl)alanine affected hepatic nuclei (binding and enzyme levels), it did not stimulate nucleocytoplasmic translocation of mRNA and concomitant protein synthesis, as did L-tryptophan.

Properties of rabbit liver tissue aminoacyl-tRNA synthetases, associated with polyribosomes, were studied under conditions of normal state and within 12 hrs after simulation of myocardium infarction. Under conditions of myocardium infarction the activity of some forms of aminoacyl-tRNA synthetase was decreased in polyribosomes and protein fractions, liberated from polyribosomes by means of washing with buffer containing 0.5 M KCl. Polyribosomes stimulated the synthetases and protected them from heat inactivation. Deterioration of the synthetases interaction with polyribosomes appears to be among the factors responsible for impairment of protein biosynthesis under conditions of myocardium infarction.

We previously found an age-dependent impairment of induction of lipogenic enzymes in rat liver [Iritani et al. (1981) Biochim. Biophys. Acta 665, 636-639]. Further, we have found that after refeeding a fat-free diet to fasted rats, increases in transcriptional rate, mRNA concentration and enzyme induction of hepatic malic enzyme and glucose-6-phosphate dehydrogenase were always lower in 18-month-old rats than in 1.5-month-old rats. In the young rats, the transcriptional rates reached the maximum level in 4 h and the mRNA reached maximum levels in 16 h. The peaks tended to delay in the older rats. The half-lives of the mRNAs were not significantly longer in the old than in the young animals. The incorporation of [3H]leucine into the enzyme proteins was also decreased roughly in proportion to the enzyme induction. The mRNA concentrations in the liver polysomes were roughly proportional to the total mRNA. Thus, no effects of ageing on mRNA stability or on the translational activity of the enzymes could be found. It is suggested that the age-dependent decreases of malic enzyme and glucose-6-phosphate dehydrogenase induction can be mainly ascribed to the transcriptional steps. Moreover, the transcriptional rate, mRNA concentration and induction of malic enzyme were increased by triiodothyronine treatment at a similar rate in both the young and old rats, but the absolute increments were lower in the old animals. The triiodothyronine response to malic enzyme induction also appeared to be primarily decreased at the transcription level.

The effects of various metabolic conditions inducing an overproduction of ketone bodies in the rat were studied at different levels of D-beta-hydroxybutyrate dehydrogenase expression, i.e., enzymatic activity and protein content in purified mitochondria, and translational activity of isolated free cytosolic polysomes. The strongest variations were obtained in diabetes mellitus where the D-beta-hydroxybutyrate dehydrogenase expression is largely decreased. Insulin can reverse this strong effect. Modulation of liver enzyme activity and of enzyme content was observed under the other conditions tested, i.e., a decrease and an increase in starvation and hyperlipidemic conditions, respectively. A comparative study was carried out on the enzyme of extrahepatic tissues, i.e., heart, kidney and brain. The results indicate that the D-beta-hydroxybutyrate dehydrogenase function appears to be controlled, at least at the translational, post-translational and catalytic levels.

1. We present evidence suggesting a sudden switch from translational control to transcriptional control of protein synthesis in mid-exponential growth of bacterial batch cultures. At a critical cell density a switch from large to small polysomes occurs during a short period of exponential growth. The profile of specific polysomes engaged in synthesis of a constitutive enzyme, ribitol dehydrogenase, changes at the same point but in an opposite way: a linear profile peaking at monosomes changes to a dome-shaped profile peaking at about 15 ribosomes/mRNA, which persists into late exponential phase despite a gradual reduction in the total polysome population. The switch in the pattern of protein synthesis is exhibited dramatically by changes in the specific activity or ribitol dehydrogenase in cell extracts at different stages of batch culture. In early exponential phase the specific activity of the enzyme is constant, but it begins to rise suddenly, at the same point at which the polysome profiles change, and continues to increase up to the end of exponential phase. This effect is exhibited by the strains of Klebsiella aerogenes that are inducible for (in the presence of the inducer), consitutive for, or superproducers of ribitol dehydrogenase, and it appears to be unrelated to catabolite repression. 2. The above results depend on improved techniques for production of large amounts of bacterial polysomes and the ability to label nascent peptides attached to polysomes very specifically with radioactive antibody to ribitol dehydrogenase. Our success was due to the observation that sodium heparin completely abolishes non-specific interactions of the antibody with the polysomes.

A simple and rapid procedure is described for purification of carbamyl phosphate synthetase from the matrix fraction of rat liver mitochondria. Antibodies to the enzyme were raised in sheep and purified from antiserum by affinity chromatography on enzyme-bound Sepharose columns. When membrane-free polyribosomes, isolated from a cytosolic fraction of rat liver, were incubated in a messenger-dependent rabbit reticulocyte protein-synthesizing system in the presence of [35S]methionine, the purified antibody precipitated a product of translation representing 0.2% of total trichloroacetic acid-insoluble radioactivity. It demonstrated mobility characteristics in sodium dodecyl sulfate-polyacrylamide gels expected for a polypeptide of molecular mass approximately 5500 daltons larger than the mature mitochondrial form of the enzyme (160,000 daltons). Proteolysis of both the mature and presumptive in vitro precursor forms of the enzyme yielded respective sets of peptide fragments which gave similar patterns upon gel electrophoresis. Excess mitochondrial enzyme effectively competed with the in vitro product for interaction with anti-carbamyl phosphate synthetase antibody.

Effect of cAMP on the activity of polynucleotide phosphorylase (PNPase) was studied in polyribosome fraction of rat liver tissue. Intraperitonel administration of cAMP or of theophilline into rats distinctly decreased the PNPase activity in the polyribosome fraction. The cAMP (1-10(-4) M) inhibited the enzymatic activity only by 8% in polyribosome fraction in vitro, as it was estimated by the reaction of phosphorolysis of endogenous RNA and polyA added. Any attempts were proved to be uncucessful to reveal cAMP, ATP-dependent proteinkinase in rat liver, responsible for the decrease in the PNPase activity in the polyribosome fraction. The cAMP inhibited the increase in the PNPase activity, coupled with protein biosynthesis in polyribosomes. Moreover, cAMP caused a decrease in the PNPase activity in reaction of polyA phosphorolysis and did not affect the rate of endogenous RNA phosphorolysis in polyribosome fraction, isolated from postmitochondrial fraction after incubation for 15 min at 30 degrees. The 3',5'-cyclo AMP (2-10(-6)-2-10(-4) M) stimulated incorporation of 14C-leucine into acid-insoluble material, when postmitochondrial fraction was incubated under the same conditions. The data obtained suggest that cAMP either inhibits specifically the PNPase synthesis or represses the coupled with protein biosynthesis formation of active "heavy" type of PNPase from less active "light" type.

Initiation with methionine of the synthesis of rat liver catalase [EC 1.11.1.6] has been investigated. Analysis of the N-terminal residue of nascent catalase peptides labeled in vivo with injected radioactive amino acids, including [3H]methionine, indicated a remarkably high content of methionine. By fractionating [3H]methionine-labeled nascent catalase according to chain length, it was found that peptides of shorter chain length contained more N-terminal methionine relative to total methionine incorporated. In addition, only a small amount of [3H]methionine was detected as the N-terminal amino acid when newly completed catalase was examined by Edman degradation. These results indicate that the synthesis of liver catalase is initiated with methionine, and suggest the presence of a mechanism for its subsequent removal from the N-terminal position. Catalase was also synthesized in a cell-free system directed by the catalase mRNA, using [3H]Met-tRNAf or [3H]Met-tRNAm. The results obtained in such in vitro experiments were in good agreement with those from in vivo studies, and further showed that the N-terminal methionine was provided by a specific initiator tRNA, i.e. tRNA Met f.

cDNA clones, containing the entire coding region of rat L-type pyruvate kinase, were isolated and their nucleotide sequences were determined by the dideoxy-chain-termination method. The predicted coding region, which spans 543 amino acids, established the complete amino acid sequence of the L-type isozyme of pyruvate kinase for the first time. The deduced amino acid sequence of the L type has one phosphorylation site in its amino terminus and shows about 68% and 48% homologies with M1-type pyruvate kinase of chicken and yeast pyruvate kinase respectively. Domain A exhibits higher homology than domains B and C. The residues in the active site of the L-type enzyme of rats, lying between domains B and A2, are rather different from those of the M1-type enzyme of chickens, but other residues constituting the active site are identical with those of the chicken M1 type except for one amino acid substitution.

In cell-free systems from Escherichia coli, hygromycin A inhibits polypeptide synthesis directed by either poly(U) or phage R 17 RNA, and the reaction of puromycin with either natural peptidyl-tRNA, or AcPhe-tRNA, or the 3'-terminal fragment of AcLeu-tRNA (C-A-C-C-A-LeuAc). In contrast, the antibiotic does no inhibit the enzymatic binding of Phe-tRNA to ribosomes or the translocation of AcPhe-tRNA. It is concluded that hygromycin A is a specific inhibitor of the peptide bond formation step of protein synthesis. The action of hygromycin A on peptidyl transfer is similar to that of chloramphenicol, an antibiotic that shares some common structural features with hygromycin A. Both antibiotics inhibit the binding of C-A-C-C-A-Leu to the acceptor site of peptidyl transferase and stimulate that of C-A-C-C-A-LeuAc to the donor site of the enzyme. Moreover, hygromycin A blocks the binding of chloramphenicol to ribosomes, indicating that the binding sites of the antibiotics may be closely related. Hygromycin A is a more potent agent than chloramphenicol and binds quite strongly to ribosomes.

The sites of synthesis of microsomal membrane proteins, NADPH-cytochrome c reductase and cytochrome b5, were investigated by three methods; the in vitro synthesis of these proteins by isolated rough microsomes, the immunoprecipitation of polyribosomes carrying their nascent peptides, and the immunoprecipitation of in vivo-labeled nascent peptides. The in vitro incorporation experiment confirmed that the synthesis of these microsomal proteins was carried out by the bound polyribosomes of rough microsomes. When free and bound polyribosomes were separately examined by the other two methods, we found that NADPH-cytochrome c reductase was synthesized by both classes of polyribosomes whereas cytochrome b5 was synthesized only by bound polyribosomes.

Messenger RNA of rat 3-oxoacyl-CoA thiolase (acetyl-CoA acyltransferase), a mitochondrial matrix enzyme involved in fatty acid beta-oxidation, was enriched by immunoprecipitation of rat liver free polysomes and recombinant plasmids were prepared from the enriched mRNA by a modification of the vector-primer method of Okayama and Berg. The transformants were initially screened for 3-oxoacyl-CoA thiolase cDNA sequences by differential colony hybridization with [32P]cDNAs, synthesized from the immunopurified and unpurified mRNAs. The cDNA clones for 3-oxoacyl-CoA thiolase were identified by hybrid-arrested translation and hybrid-selected translation. One of the clones, designated pT1-1, contained a 700-base insert and hybridized to a mRNA species of 1.6 X 10(3) bases in rat liver. The transformants were rescreened using the cDNA insert of pT1-1 as a hybridization probe and a clone (pT1-19) with a 1.5 X 10(3)-base insert was obtained. Activity and concentration of 3-oxoacyl-CoA thiolase mRNA were quantified by in vitro translation and dot-blot analysis using the cDNA insert as a hybridization probe. The level of translatable and hybridizable mRNA in rat liver was increased about 5.1-fold and 4.6-fold, respectively, after administration of di-(2-ethylhexyl)phthalate, a potent inducer of the enzyme. The 3-oxoacyl-CoA thiolase mRNA levels thus determined correlated closely with levels of the activity and amount of this enzyme.

Rat liver polysomes washed with 0.5-1.5 M KCl at 37 degrees C keep a constant protein kinase activity revealed only by auto-phosphorylation of ribosomal proteins. The enzyme catalyzes the transfer of the gamma-phosphate group from ATP to serine (75%) but also to threonine residues (25%). It is released when polysomes are dissociated into subunits using centrifugation through a sucrose gradient containing a high K+/Mg++ ratio. Its properties have been compared with those of the two other enzymatic activities which are, in contrast, washed out during salt treatment of polysomes. After release upon polysome dissociation, this third activity is able to phosphorylate histone II A. Protection of the enzyme in the polysome structure against salt treatment, suggests that it is located at the junction of the two subunits.