Polyadenylate polymerases

Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF)

In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.

RNA polyadenylation and its consequences in prokaryotes

Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.

Poly(A) Polymerase Distribution in Normal and Malignant Lymphoid Cells

The incorporation of ATP on poly(A) primers catalyzed by poly(A) polymerase was investigated in normal and neoplastic lymphoid cells from animal and human sources. High levels of the enzyme were found in mouse thymus, in chicken bursa and thymus, as well as in neoplastic cells from patients affected by lymphoblastic and Burkitt's lymphomas. Low or very low quantities were found in peripheral blood lymphocytes, chronic lymphocytic leukemia cells, normal lymph nodes and solid lymphoid tissues of Hodgkin's disease. In general, the enzymatic content of neoplastic lymphoid cells reflected those of their normal counterpart. No effect of fasting or cortisone treatment on poly(A) polymerase in mouse spleen, thymus or liver was found. No particular relationships with B, T or non-T, non-B lineages were observed, but some relationship with DNA polymerase alpha was found. Therefore, it may be that poly(A) polymerase levels are related to the proliferative activity of the cellular populations.

Interaction of tricationic corroles with single/double helix of homopolymeric nucleic acids and DNA

In this manuscript a multitechnique approach is proposed to characterize the interaction between new tri-N-methylpyridyl corrole (TMPC) and its germanium(IV) derivative (GeTMPC), with single- and double-stranded nucleic acid homopolymers and calf thymus DNA. The specificity of each spectroscopic technique has been exploited to analyze the different aspects of corrole binding. Noteworthy, this approach allows us to distinguish between H aggregation of TMPC in the presence of polyriboadenilic acid (poly(rA)) and J aggregates in the presence of polyribocytidinic acid (poly(rC)) as well as to identify the formation of GeTMPC dimers in the presence of single-stranded poly(rA) and pseudointercalation with single-stranded poly(rC).

Signals for pre-mRNA cleavage and polyadenylation

Pre-mRNA cleavage and polyadenylation is an essential step for 3' end formation of almost all protein-coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis-acting elements in the pre-mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species.

A history of poly A sequences: from formation to factors to function

Biological polyadenylation, first recognized as an enzymatic activity, remained an orphan enzyme until poly A sequences were found on the 3' ends of eukarvotic mRNAs. Their presence in bacteria viruses and later in archeae (ref. 338) established their universality. The lack of compelling evidence for a specific function limited attention to their cellular formation. Eventually the newer techniques of molecular biology and development of accurate nuclear processing extracts showed 3' end formation to be a two-step process. Pre-mRNA was first cleaved endonucleolytically at a specific site that was followed by sequential addition of AMPs from ATP to the 3' hydroxyl group at the end of mRNA. The site of cleavage was specified by a conserved hexanucleotide, AAUAAA, from 10 to 30 nt upstream of this 3' end. Extensive purification of these two activities showed that more than 10 polypeptides were needed for mRNA 3' end formation. Most of these were in complexes involved in the cleavage step. Two of the best characterized are CstF and CPSF, while two other remain partially purified but essential. Oddly, the specific proteins involved in phosphodiester bond hydrolysis have yet to be identified. The polyadenylation step occurs within the complex of poly A polymerase and poly A-binding protein, PABII, that controls poly A length. That the cleavage complex, CPSF, is also required for this step attests to a tight coupling of the two steps of 3' and formation. The reaction reconstituted from these RNA-free purified factors correctly processes pre-mRNAs. Meaningful analysis of the role of poly A in mRNA metabolism or function was possible once quantities of these proteins most often over-expressed from cDNA clones became available. The large number needed for two simple reactions of an endonuclease, a polymerase and a sequence recognition factor, pointed to 3' end formation as a regulated process. Polyadenylation itself had appeared to require regulation in cases where two poly A sites were alternatively processed to produce mRNA coding for two different proteins. The 64-KDa subunit of CstF is now known to be a regulator of poly A site choice between two sites in the immunoglobulin heavy chain of B cells. In resting cells the site used favors the mRNA for a membrane-bound protein. Upon differentiation to plasma cells, an upstream site is used the produce a secreted form of the heavy chain. Poly A site choice in the calcitonin pre-mRNA involves splicing factors at a pseudo splice site in an intron downstream of the active poly site that interacts with cleavage factors for most tissues. The molecular basis for choice of the alternate site in neuronal tissue is unknown. Proteins needed for mRNA 3' end formation also participate in other RNA-processing reactions: cleavage factors bind to the C-terminal domain of RNA polymerase during transcription; splicing of 3' terminal exons is stimulated port of by cleavage factors that bind to splicing factors at 3' splice sites. nuclear ex mRNAs is linked to cleavage factors and requires the poly A II-binding protein. Most striking is the long-sought evidence for a role for poly A in translation in yeast where it provides the surface on which the poly A-binding protein assembles the factors needed for the initiation of translation. This adaptability of eukaryotic cells to use a sequence of low information content extends to bacteria where poly A serves as a site for assembly of an mRNA degradation complex in E. coli. Vaccinia virus creates mRNA poly A tails by a streamlined mechanism independent of cleavage that requires only two proteins that recognize unique poly A signals. Thus, in spite of 40 years of study of poly A sequences, this growing multiplicity of uses and even mechanisms of formation seem destined to continue.

Evidence of two forms of poly(A) polymerase in germinated wheat embryos and their regulation by a novel protein kinase

Two forms of poly(A) polymerase (PAPI and PAPII) from germinated wheat embryos have been resolved on DEAE-cellulose ion-exchange chromatography by a linear gradient of 0-500 mM (NH(4))(2)SO(4). Further purification shows that both forms are monomeric in nature with an identical molecular weight, approximately 65 kDa. The phosphoprotein nature of PAPI and PAPII has been established by in vivo labelling with (32)P-orthophosphate. Acid hydrolysis of both (32)P-labelled purified PAPI and PAPII has revealed that phosphorylations generally take place in serine and threonine residues. PAPI and PAPII have also been characterised with respect to V(max) and K(m) for poly(A). The V(max) and K(m) values of PAPI are 28.57 and 11.37 microg, respectively, whereas 34.48 and 7.04 microg of PAPII. In vitro dephosphorylation of the purified enzyme by alkaline phosphatase leads to a significant loss of the enzyme activity, which is regained upon phosphorylation by a 65 kDa protein kinase (PK) purified from wheat embryos. The extent of phosphorylation by protein kinase shows that PK has similar affinity towards both PAPI and PAPII, whereas the phosphate incorporation in PAPII is twofold higher than PAPI suggesting their distinct chemical nature.

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.

Interaction of water-soluble porphyrins with single- and double-stranded polyribonucleotides

CD and uv-visible absorption studies with several tetracationic water-soluble porphyrin derivatives show that some of these species can serve as probes to discriminate between A- and B-conformational forms of single-stranded polynucleotides. It is also observed that these porphyrins can participate in the formation of double helices by forming transient intermediate complexes en-route to duplex formation.

High-performance ion-exchange chromatography of oligoribonucleotides using linear and hyperbolic salt gradients

A method for separation and chain length determination of oligo- and polynucleotides by high-performance anion-exchange chromatography was developed, which allows resolution of individual fragments according to their chain length n, up to n approximately 10 by linear gradient of sodium chloride and up to n approximately 30 by an hyperbolic gradient of this salt. The hyperbolic relationship between n and the salt concentration at which elution of the fragment occurs allows determination of the degree of polymerization of oligo- and polynucleotides with unknown n. The method proposed can be used for estimation of the effective charge of nucleic acids with complex structure.

Multiple factors are required for poly(A) addition to a mRNA 3' end

Polyadenylation of pre-mRNAs in the nucleus involves a specific endonucleolytic cleavage, followed by the addition of approximately 200 adenylic acid residues. We have assayed HeLa nuclear extracts for the activity that catalyzes the poly(A) addition reaction. The authenticity of the in vitro assay was indicated by the observation that the poly(A) tract added in vitro is approximately 200 nucleotides in length. We have fractionated nuclear extracts in order to define components involved in specific poly(A) addition. No single fraction from DEAE-Sephacel chromatography of a HeLa nuclear extract possessed the specific poly(A) addition activity. However, if the various fractions were recombined, activity was restored, indicating the presence of multiple components. Further fractionation revealed the presence of at least two factors necessary for the poly(A) addition reaction. The reconstituted system retains the characteristics and specificity seen in the crude extract. Additional purification of one of the factors strongly suggests it to be a previously characterized poly(A) polymerase which, when assayed in the absence of the other factor, can add AMP to an RNA terminus but without specificity. Thus, the other component of the reaction may provide specificity to the process. In contrast to the 3' cleavage reaction, the poly(A) addition machinery does not possess an essential RNA component, as assayed by micrococcal nuclease digestion, nor do anti-Sm sera inhibit the reaction. Thus, the total process of formation of a polyadenylated mRNA 3' end is complex and requires the concerted action of distinct nuclear components.

A 64 kd nuclear protein binds to RNA segments that include the AAUAAA polyadenylation motif

A 64 kd protein was shown to bind to RNAs that contain functional polyadenylation signals by a UV cross-linking procedure in which label was transferred from RNA substrate to protein in cell-free polyadenylation extracts. The 64 kd nuclear protein bound specifically to three different substrates (adenovirus type 5 L3, SV40 early, and SV40 late polyadenylation domains), as determined by competition experiments and partial protease analysis. Deleted derivatives of the SV40 late substrate that retained the sequence 5'-CUGCAAUAAACAAGUU-3' were able to bind the 64 kd polypeptide. This sequence contains the canonical AAUAAA element that has been shown to be indispensable for polyadenylation. A single nucleotide change, converting AAUAAA to AAGAAA, prevented binding of the 64 kd moiety. The 64 kd protein was shown to be distinct from poly(A) polymerase by biochemical fractionation.

An RNA polymerase mutant with reduced accuracy of chain elongation

A new Escherichia coli RNA polymerase mutant was isolated which exhibited reduced accuracy of chain elongation in vivo and in vitro. The novel isolation procedure consisted of simultaneous selection for rifampicin resistance and screening for increased leakiness of an early, strongly polar nonsense mutation of lacZ, one of a special class of mutations whose leakiness reflects mainly transcriptional rather than translational errors. The spontaneous mutant thus isolated displayed a 3-4-fold increase in the leakiness of two different lacZ mutations of this class. Transduction analysis indicated that a single mutation, mapping in or very near the rpoB gene for the beta subunit of RNA polymerase, conferred both rifampicin resistance and increased nonsense leakiness. In an in vitro fidelity assay, homogeneous RNA polymerases from the mutant and parent strains exhibited error rates of 1/0.90 X 10(5) and 1/2.0 X 10(5), respectively, for the poly[d(A-T)] X poly[d(A-T)]-directed misincorporation of noncomplementary GMP. These error rates were verified by product analyses which further revealed that GMP was misincorporated in place of AMP in the synthesis of poly[r(A-U)]. The error rate of wild-type K12 RNA polymerase from a different source was 1/2.0 X 10(5), while that of a hybrid RNA polymerase, containing mutant core enzyme and wild-type sigma subunit, was 1/0.64 X 10(5). These error rates confirmed the selection of a transcriptional accuracy mutant. The error frequencies observed are much lower than those reported in other in vitro assays. The safeguards used to avoid artifactually enhanced misincorporation, and to thereby quantitate lower error rates, are discussed.

RNA sequence containing hexanucleotide AAUAAA directs efficient mRNA polyadenylation in vitro

To determine whether a specific nucleotide sequence is required to direct polyadenylation of a simian virus 40 early pre-mRNA in a soluble HeLa whole-cell lysate, we constructed a series of rearranged and deleted DNA templates, transcribed them in vitro, and determined whether the resultant RNAs could be polyadenylated when incubated in whole-cell lysate. When a 237-base-pair DNA fragment encoding the 3' end of the simian virus 40 early pre-mRNA was transferred to recombinant plasmids encoding RNAs that were not substrates for polyadenylation, the resultant RNAs could now be polyadenylated efficiently. In one case, the chimeric RNA was polyadenylated even more efficiently than was the original simian virus 40 early transcript. Analysis of the RNAs produced from the deletion mutant templates revealed that only RNAs containing at least one copy of the AAUAAA sequence situated near the 3' end and implicated in 3'-end formation and polyadenylation in vivo could be polyadenylated in vitro. Surprisingly, this sequence directed polyadenylation of pre-mRNAs not only when near the RNA 3' end, i.e., 50 nucleotides or less away, but also when the 3' end was situated over 400 nucleotides downstream. Thus, our results show that a polyadenylic acid polymerase activity in HeLa lysates can recognize a specific nucleotide sequence in pre-mRNA and then, in the absence of the nucleolytic cleavage that presumably occurs in vivo, locate the RNA 3' end and use it as a primer for polyadenylic acid 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.

RNA sequence containing hexanucleotide AAUAAA directs efficient mRNA polyadenylation in vitro

To determine whether a specific nucleotide sequence is required to direct polyadenylation of a simian virus 40 early pre-mRNA in a soluble HeLa whole-cell lysate, we constructed a series of rearranged and deleted DNA templates, transcribed them in vitro, and determined whether the resultant RNAs could be polyadenylated when incubated in whole-cell lysate. When a 237-base-pair DNA fragment encoding the 3' end of the simian virus 40 early pre-mRNA was transferred to recombinant plasmids encoding RNAs that were not substrates for polyadenylation, the resultant RNAs could now be polyadenylated efficiently. In one case, the chimeric RNA was polyadenylated even more efficiently than was the original simian virus 40 early transcript. Analysis of the RNAs produced from the deletion mutant templates revealed that only RNAs containing at least one copy of the AAUAAA sequence situated near the 3' end and implicated in 3'-end formation and polyadenylation in vivo could be polyadenylated in vitro. Surprisingly, this sequence directed polyadenylation of pre-mRNAs not only when near the RNA 3' end, i.e., 50 nucleotides or less away, but also when the 3' end was situated over 400 nucleotides downstream. Thus, our results show that a polyadenylic acid polymerase activity in HeLa lysates can recognize a specific nucleotide sequence in pre-mRNA and then, in the absence of the nucleolytic cleavage that presumably occurs in vivo, locate the RNA 3' end and use it as a primer for polyadenylic acid synthesis.

Thyroid hormone regulation of poly(adenylate) polymerase activities in neuronal nuclei of developing rat brain cortex

Neuronal and glial cell-enriched nuclei were prepared from developing rat brain cortex to study the effect of thyroxine on nuclear poly(A) polymerase. Long-term thyroxine treatment stimulated the activity of the chromatin-associated enzyme of neuronal nuclei without significantly affecting that of glial nuclei. The nuclear content of poly(A)-containing RNA in neuronal nuclei was also increased by thyroxine administrations. A single dose of thyroxine enhanced both the chromatin-bound and the free, nucleoplasmic form of neuronal poly(A) polymerase in hypothyroid rats aged 12 days. The results suggest that thyroid hormones may regulate both transcriptional and post-transcriptional events in target cell nuclei.

Base-specific ribonucleases potentially involved in heterogeneous nuclear RNA processing and poly(A) metabolism

Polyadenylation and splicing of heterogeneous nuclear RNA, two crucial steps in mRNA processing, are apparently enzymatically mediated processes. This contribution summarizes the properties and the presumed functions of the known poly(A) catabolic enzymes (endoribonuclease IV and V, 2',3'- exoribonuclease ) as well as those of the pyrimidine-specific endoribonucleases associated with snRNP -hnRNP complexes (endoribonuclease VII, acidic pI 4.1 endoribonuclease and poly(U)-specific U1 snRNP -nuclease).

Androgen regulation of poly(A) polymerase in the ventral prostate of rat

The effect of various hormones on the levels of poly(A) polymerase in the ventral prostate of castrated rats was investigated. It was observed that this enzyme is specifically induced by androgens; progesterone and estradiol-17 beta did not cause stimulation of poly(A) polymerase activity. Dihydrotestosterone-induced poly(A) polymerase was inhibited by cordycepin, actinomycin-D and cycloheximide, which indicates that the genetic transcription leading to the enzyme poly(A) polymerase is regulated by androgens in the ventral prostate.

Phosphorylation and immunology of poly(A) polymerase

Phosphorylation of poly(A) polymerase by protein kinase NI (a cyclic nucleotide-independent nuclear kinase closely associated with poly(A) polymerase at early stages of purification) resulted in as much as 7-fold activation of poly(A) polymerase. Phosphorylation causes an increase in the rate rather than the extent of polyadenylation. Antibodies raised in rabbits against purified poly(A) polymerase from Morris hepatoma 3924A reacted specifically with poly(A) polymerase following "Western" transfer of the enzyme onto diazobenzyloxyl methyl paper. Using iodinated enzyme, a competition radioimmunoassay for poly(A) polymerase was developed. Using the radioimmunoassay, it was shown that Morris hepatoma 3924A contains 100 micrograms of poly(A) polymerase/mg DNA or 10(7) molecules of the enzyme/cell nucleus. Nuclear poly(A) polymerase from fetal liver, but not from normal liver, was able to compete well with hepatoma enzyme in the radioimmunoassay. These data suggest that the tumor poly(A) polymerase is probably an oncofetal antigen, resulting from derepression of a gene not normally expressed in adult liver.

Occurrence of short-sized oligo(A) fragments during course of cell cycle and ageing

Affinity chromatography of nucleic acids precipitated by N-cetyl-N,N,N-trimethyl ammonium bromide on poly(U)-Sepharose has proved to be a suitable method for a nearly quantitative isolation of oligo(A) sequences down to a chain length of 4 nucleotide units. Analysis of short oligo(A) fragments in synchronized L5178y mouse lymphoma cells after labeling with [3H]Ado revealed that the percentage of A2-6 sequences on the total radioactivity amounted in S-phase cells to 1.6%, while the value obtained for the stationary L-cell system was 8.0%. The alterations of occurrence and chain length distribution of short oligo(A) fragments during ageing were studied in two age groups of female quails: mature (250-320 days old) and senescent animals (3-3.5 yr old). It was found that the amount of low molecular weight oligo(A) fragments gradually decreases during ageing of the animals; the amount in the mature animal group was significantly higher (6-fold) than in the old animal group. The decreased amounts of oligo(A) during S phase and ageing could in part be due to posttranslational modification of enzymes involved in poly(A) metabolism. It could be demonstrated that both homogeneous poly(A) anabolic poly(A) polymerase and homogeneous poly(A) catabolic endoribonuclease IV are phosphorylated by nuclear protein kinase NI.

Androgen regulation of nuclear poly(A) polymerase activities in rat ventral prostate

The existence of nucleoplasmic and chromatin bound forms of poly(A) polymerase in the rat ventral prostate has been demonstrated. The levels of the prostate chromatin and nucleoplasmic poly(A) polymerase activities appeared to be under the influence of testosterone. Castration reduced both free and bound prostatic poly(A) polymerase activities to 30% of the normal values. Administration of testosterone to castrated rat resulted in increases in both nuclear poly(A) polymerase activities at 2-4 h after androgen replacement. The results suggest that post-transcriptional processing is under androgenic control.

Developmental changes in poly(A) polymerase activity in Artemia

The levels of poly(A) polymerase activity have been determined during Artemia early development. Poly(A) polymerase activity increases steadily during postgastrular embryonic development reaching a maximum shortly after hatching. The rise of poly(A) polymerase is concomitant with an increase in poly(A) content and with a change in the subcellular distribution of the enzyme activity, the major increase corresponding to the nuclear fraction. Only one isoenzyme of poly(A) polymerase has been identified in Artemia embryos and nauplii despite changes in enzyme levels and subcellular changes during early development. Poly(A) polymerase is not associated with the cytoplasmic poly(A)-containing ribonucleoprotein particles stored in Artemia dormant embryos.

Synthesis of polyadenylate-containing RNA in vitro in permeable cells of Escherichia coli B

As a starting point for the study of the biosynthesis of polyadenylated RNA in bacteria, the characteristics of RNA synthesis by cells of Escherichia coli B made permeable to small molecules by treatment with toluene were examined. Such cells mediated the incorporation of radiolabeled ribonucleoside triphosphates into RNA in a reaction that was sensitive to inhibitors of RNA polymerase and required the simultaneous presence of the four ribonucleoside triphosphates. Between 10 to 15% of the RNA synthesized under these conditions was polyadenylated as shown by affinity chromatography on oligo(dT)-cellulose. The presence of orthophosphate or dADP, inhibitors of polynucleotide phosphorylase, had no effect on the reaction and the rate of RNA synthesis was indistinguishable in the polynucleotide phosphorylase-deficient strain PR-7 and in its otherwise isogenic parent strain PR-100. The poly(A) tracts associated with the newly synthesized RNA could be isolated after exhaustive digestion with pancreatic and T1 ribonucleases and accounted for 14% of the poly(A)-RNA. At least 74% of the poly(A) sequences were located at the 3' ends of RNA molecules and their weight-average length was 48 nucleotide residues. The size distribution of total RNA and poly(A)-RNA synthesized in the toluenized cell system was similar to that of the corresponding pulse-labeled fractions derived from growing cultures. The sequence complexity of poly(A)-RNA and unadenylated RNA synthesized in toluenized cells with [alpha-32P]CTP as the labeled substrate was analyzed by hybridization to fragments of Escherichia coli B DNA generated by digestion with EcoRI restriction endonuclease and immobilized on nitrocellulose sheets. Both RNA fractions hybridized with many DNA fractions, the hybridization patterns being similar with poly(A)-RNA and unadenylated RNA. This indicated that many different types of RNA transcripts synthesized in toluenized cells were subject to polyadenylation, but that polyadenylation was incomplete so that each transcript was present in both an adenylated and an unadenylated state.

Accurate and specific polyadenylation of mRNA precursors in a soluble whole-cell lysate

Conditions have been developed which allow for the efficient, accurate, and specific polyadenylation of exogenously added mRNA precursors in a whole-cell lysate derived from HeLa cells. Precursors are prepared by in vitro transcription using linear DNA templates in a HeLa whole-cell lysate, purified, and added to another lysate. Under optimal conditions (which are quite precise with respect to several variables), 70% or more of the precursor molecules become polyadenylated, and the length of the poly(A) segment added is controlled much as it is in vivo, giving rise to 150-300-nucleotide long stretches of poly(A). Under suboptimal conditions, both the fraction of precursor RNA that becomes polyadenylated and also the length of the poly(A) segment added are reduced. The in vitro polyadenylation reaction is also remarkably specific: Only in vitro-synthesized pre-mRNAs that contain a 3' end located at or slightly downstream from the corresponding in vivo mRNA 3' end site can be efficiently polyadenylated in vitro. These results suggest that the poly(A) polymerase requires one or more protein (or RNA) factors in order to bring about accurate and specific polyadenylation in vitro, and that the poly(A) polymerase complex must interact with a specific recognition signal at the 3' end of mRNA precursors in order to catalyze subsequent polyadenylation.

Interaction of polyribosomal components and polyribonucleotides with microtubule proteins

To demonstrate the affinity of RNA-containing polyribosomal components (isolated from L5178y cells) to microtubules, microtubule protein was attached to an insoluble matrix. In contrast to ribosomes, poly(A)(+)mRNA and poly(A)-RNP were found to bind to the matrix. Using synthetic polyribonucleotides, no significant differences in the binding properties of single- and double stranded polymers of different base composition to microtubule protein were observed. However, binding is dependent on the size of the polymer; a minimal chain length of 12 nucleotide units is required.

Age-dependent gene induction in quail oviduct. XV. Alterations of the poly(A)-associated protein pattern and of the poly(A) chain length of mRNA

The effect of ageing on polyadenylate [poly(A)] metabolism of mRNA was studied in two age groups of female quails: mature (250-320 days' old) and senescent animals (3-3.5 years' old). In introductory experiments it was shown that poly(A)-associated proteins can not be recovered from cytosol by affinity chromatography. We isolated the poly(A)-associated proteins from polyribosomal poly(A)-ribonucleoprotein complex [poly(A)-RNP] and radioactively labeled them with dansyl chloride. Three main protein species were identified with molecular masses of 48000 (P48), 35000 (P35) and 24000 (P24). During ageing the percentage portion of P48 in poly(A)-RNP from liver (mitotic tissue) and from oviduct or heart (post-mitotic tissue) is reduced at the expense of P35 and P24. Quantitative analyses revealed that the amount of poly(A)-RNP in the different organs decreases significantly with age if the values are based on DNA. The protein content in poly(A)-RNP was found to be reduced especially in post-mitotic tissue. From this finding we assume that the number of poly(A)-associated protein molecules per poly(A) stretch drops from approximately 4.7 molecules (mature oviduct) to 1.9 molecules (senescent oviduct). Control experiments revealed that free, non-polyribosomal poly(A)-RNP accounts only for 10% of total poly(A)-RNP. The size of the poly(A) segment of mRNA decreases with age. After labeling with [3H] dimethylsulfate, the poly(A) stretch from mature oviduct was found to consist mainly of 120-180 AMP units, and those from mature liver and mature heart of 110 and 100, respectively. In organs from senescent animals the percentage of shorter poly(A) stretches is enlarged; on the average, poly(A)-70 chains were detected. These results support the assumption that age-dependent changes occur also on the post-transcriptional level during the maturation steps of poly(A)(-) hnRNA to poly(A)-(+) mRNA.

Simultaneous presence of terminal adenylyl, cytidylyl, guanylyl, and uridylyl transferase in healthy tomato leaf tissue: separation from RNA-dependent RNA polymerase and characterization of the terminal transferases

The presence of terminal nucleotidyl transferase activities catalyzing the addition of AMP, CMP, GMP, and UMP residues to the 3' ends of oligonucleotide primers was detected in healthy tomato plants. These enzyme activities copurify with RNA-dependent RNA polymerase during the initial stages of purification. Their separation from RNA-dependent RNA polymerase is finally achieved by DEAE chromatography: terminal transferase activities are retained on DEAE while RNA-dependent RNA polymerase does not bind in the presence of 20 mM MgCl2. Elution by a linear gradient of 0 to 400 mM NH4Cl releases all four terminal transferase activities from the DEAE column at a concentration of 270 mM NH4Cl, thus suggesting that they may belong to one enzyme molecule; this question, however, needs further clarification. The enzyme activities are completely dependent on the presence of an RNA primer and are strongly influenced by its base composition as well as its chain length. Characterization of the respective reaction products by electrophoresis on 15% polyacrylamide sequencing gels reveals striking differences as to the number of nucleotides added to a given primer. In the case of UMP transfer to U8 or A8 and in the case of GMP transfer to A8 only 1 to 6 nucleoside monophosphates are added to the 3' terminus of the oligonucleotide primer, whereas in the case of AMP transfer to A8 or U8, the CMP transfer to A8, and the GMP transfer to U8, longer chains of minimally 30 nucleotides are added to the respective primer. After gradient elution from DEAE the transferase preparation displays no nucleolytic activity when incubated in the presence of 3H-labelled ribosomal RNA or [3H]poly(A) X poly(U). Only in the case of [3H]poly(A) and [3H]poly(U) or [3H]poly(C) 10 to 15% of the radioactivity is transferred to acid-soluble counts.

Anti-poly(A) polymerase antibodies in sera of tumor-bearing rats and human cancer patients

Poly(A) polymerase (polynucleotide adenylyltransferase; ATP:polynucleotide adenylyltransferase, EC 2.7.7.19) was covalently linked to diazobenzyloxymethyl-filters and used to screen the sera from a number of tumor-bearing rats and human cancer patients for antibodies to poly(A) polymerase. Sera from rats that had been inoculated with any of several Morris hepatomas or a mammary adenocarcinoma contained immunoglobulins capable of complexing with poly(A) polymerase. No antibodies to the enzyme could be detected in sera from control animals or from those bearing tumors for short periods of time. Antibodies to poly(A) polymerase were also observed in sera from human patients with leukemia, polycythemia vera, and Wilms tumor. The antibodies were not evident in sera from normal volunteers or from patients with nonneoplastic diseases. These included lupus erythematosus, a disorder in which antibodies are produced against an array of nuclear proteins. Immunoglobulins from the serum of one of the human patients were capable of inhibiting poly(A) polymerase activity in vitro, whereas those prepared from the serum of a normal volunteer did not affect enzyme activity. As determined by the diazobenzyloxymethyl-filter technique, the relative concentration of antibodies in the sera of an individual with leukemia (in remission) increased severalfold during a relapse. These data suggest that the presence of antibodies to poly(A) polymerase may be characteristic of sera from cancer patients and that the relative concentration of these antibodies may be indicative of the disease state.

Endoplasmic reticulum nuclease. Purification and specificity

An endonuclease, which was originally identified for its RNA polymerase inhibitory activity, was isolated from rat liver endoplasmic reticulum. The enzyme yields on gel chromatography four active fractions of different molecular weights (Mr 5.3 X 10(4), 9 X 10(4), 1.55 X 10(5) and Sephacryl S-200 fraction at V0). Each fraction contains polypeptide chains which give a single band on sodium dodecylsulphate electrophoresis (Mr 5.4 X 10(4). This indicates that the enzyme is an oligomeric protein and each of its subunits exhibits the same or very similar molecular weights. Deoxyribonucleoside and ribonucleoside triphosphates can bind to the endoplasmic reticulum nuclease. Binding is enhanced in the presence of divalent cations particularly Mg2+. The enzyme exhibits mainly RNase activity but can also degrade denatured DNA and DNA . RNA hybrids which contain breaks in one of the two strands. Poly(A) and mainly poly(U) are most susceptible to its nucleolytic activity whereas poly(C) is completely resistant.

Terminal uridylyl transferase of Vigna unguiculata: purification and characterization of an enzyme catalyzing the addition of a single UMP residue to the 3'-end of an RNA primer

An enzyme which catalyzes the addition of a single UMP residue from UTP to the 3'-end of an RNA primer and which is referred to as terminal uridylyl transferase (TUT) has been extensively purified from the membrane fraction of vigna unguiculata leaves. The purification procedure involved (i) solubilization by cation depletion (ii) DEAE-Sepharose CL-6B column chromatography (iii) affinity chromatography of poly(U)-Sepharose 4B and (iv) glycerol gradient centrifugation. The molecular weight of the native enzyme was approximately 50,000 as determined by velocity sedimentation. Under conditions that were optimal for UMP-incorporation (5 mM Mg2+, low salt, 30 degrees C) TUT displayed a marked specificity for UTP as substrate, was unable to incorporate deoxyribonucleoside triphosphates and required a single-stranded oligo- or polyribonucleotide as primer. When oligoA20, tRNAasp of E. coli or alfalfa mosaic virus RNA 4 were used as primers at various substrate to primer ratio's, the vast majority of the product appeared to consist of primer molecules elongated with a single UMP residue as shown by polyacrylamide gelelectrophoresis and nearest neighbour analysis. We believe TUT to be a novel enzyme which has not been reported before and which may be a feasible tool in RNA sequencing as it enables the specific 3'-terminal labeling of RNA molecules.

Age-dependent gene induction in quail oviduct X. Alterations on the post-transcriptional level (enzymic aspect)

In quail oviducts the rate of synthesis of avidin, the biological end-point marker for the molecular events caused by progesterone, decreases with age. The cause of the reduced capacity of avidin induction has been studied on the molecular biological level polyadenylation of RNA which is one step in the process of post-transcriptional modification of heterogeneous nuclear RNA resulting in the formation of functional mRNA molecules. This novel approach was biochemically possible after the discovery of the poly(A) anabolic enzyme (poly(A) polymerase) and the two poly(A) catabolic enzymes (endoribonuclease IV and 5'-exoribonuclease). These enzymes are involved in the synthesis and degradation of the poly(A) segment of mRNA in vitro and most likely also in poly(A) metabolism in intact cell systems. Enzymatically controlled poly(A) metabolism of mRNA is regulated by the following interrelations: poly(A)-associated proteins and endoribonuclease IV; labilizing factor and poly(A)-associated proteins; 5'-exoribonuclease in cooperation with endoribonuclease IV and poly(A) polymerase. A close correlation between high levels of poly(A) catabolic enzymes and low rate of protein synthesis which was established in cell culture systems, seems also to be partially the biochemical cause for the reduced avidin synthesis in aging quail oviduct.