Transcription mRNA Processing Research Articles

Abstract 3226: PRMT1 is a critical dependency in clear cell renal cell carcinoma with roles in post- transcriptional regulation and DNA damage response

Abstract The majority of sporadic renal cell carcinoma (RCC) cases present as the clear cell subtype (ccRCC) and are associated with the biallelic inactivation of the von Hippel-Lindau (VHL) gene, leading to constitutive activation of the cellular hypoxia response and deleterious alterations to gene expression, metabolism, and growth. Despite the near ubiquity of VHL loss, evidence suggests that it alone is insufficient to drive tumor establishment. Additional loss of function (LOF) mutations in epigenetic regulatory proteins including PBRM1, SETD2 and BAP1 have been identified as tumor drivers. The frequency and penetrance of these mutations in epigenetic regulators implicates a vulnerability in ccRCC that may be exploited to develop new therapies. To explore this vulnerability, the Ailles lab completed a screen of the Structural Genomics Consortium’s (SGC) epiprobe library - a panel of inhibitors targeting an array of epigenetic regulators in patient derived ccRCC models. Among the several promising targets identified, a particularly favorable inhibition profile was noted for MS023, an inhibitor of the type I protein arginine methyltransferase family (PRMT1/3/4/6 and 8). PRMTs transfer methyl groups to nuclear histones and cytoplasmic targets, influencing gene expression, mRNA processing and viability. This growth inhibition was corroborated using an additional type I PRMT compound, GSK3368715. CRISPR-mediated deletion of type I PRMT targets indicated that PRMT1 is the main enzyme responsible for growth inhibition in our ccRCC models. Furthermore, genetic depletion of PRMT1 via shRNA phenocopied pharmacological inhibition and proliferative growth was restored in the presence of MS023 by overexpressing PRMT1. Finally, MS023 treatment of mice bearing ccRCC cell line and patient derived xenografts led to significant inhibition of tumor growth in vivo. Transcriptomic profiling of chemical treatment and PRMT1 genetic depletion demonstrated that PRMT1 inhibition triggers a significant down regulation of genes related to cell cycle progression and DNA damage. ccRCC cells treated with MS023 accumulated significant levels of DNA damage before undergoing cell death, with several DDR-related proteins being down-regulated. Proximity ligation and proteomic analysis (Bio-ID) revealed that PRMT1’s interactors skew heavily towards RNA metabolism regulators and widespread alterations in mRNA processing were noted with MS023 treatment. Evidence continues to mount that PRMT1 is implicated in the biology of cancer, but to our knowledge, no thorough investigations have been performed in the context of ccRCC. Our data suggests that inhibition of PRMT1 inhibits processing of mRNA transcripts, compromises DDR mechanisms, leading to an accumulation of double stranded breaks, cytostasis and cell death. Thus PRMT1 represents a viable therapeutic target in ccRCC. Citation Format: Joseph Walton, Karen Arevalo, Angel SN Ng, Jalna Meens, Christina Karamboulas, Panagiotis Prinos, Brian Raught, Eric Chen, Cheryl Arrowsmith, Laurie Ailles. PRMT1 is a critical dependency in clear cell renal cell carcinoma with roles in post- transcriptional regulation and DNA damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3226.

Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α.

Endoplasmic reticulum (ER) to nucleus homeostatic signaling, known as the unfolded protein response (UPR), relies on the non-canonical splicing of XBP1 mRNA. The molecular switch that initiates splicing is the oligomerization of the ER stress sensor and UPR endonuclease IRE1α (inositol-requiring enzyme 1 alpha). While IRE1α can form large clusters that have been proposed to function as XBP1 processing centers on the ER, the actual oligomeric state of active IRE1α complexes as well as the targeting mechanism that recruits XBP1 to IRE1α oligomers remains unknown. Here, we have developed a single-molecule imaging approach to monitor the recruitment of individual XBP1 transcripts to the ER surface. Using this methodology, we confirmed that stable ER association of unspliced XBP1 mRNA is established through HR2 (hydrophobic region 2)-dependent targeting and relies on active translation. In addition, we show that IRE1α-catalyzed splicing mobilizes XBP1 mRNA from the ER membrane in response to ER stress. Surprisingly, we find that XBP1 transcripts are not recruited into large IRE1α clusters, which are only observed upon overexpression of fluorescently tagged IRE1α during ER stress. Our findings support a model where ribosome-engaged, immobilized XBP1 mRNA is processed by small IRE1α assemblies that could be dynamically recruited for processing of mRNA transcripts on the ER.

'Candidatus Liberibacter asiaticus' Multimeric LotP Mediates Citrus sinensis Defense Response Activation.

‘Candidatus Liberibacter asiaticus’ is known as the most pathogenic organism associated with citrus greening disease. Since its publicized emergence in Florida in 2005, ‘Ca. L. asiaticus’ remains unculturable. Currently, a limited number of potential disease effectors have been identified through in silico analysis. Therefore, these potential effectors remain poorly characterized and do not fully explain the complexity of symptoms observed in citrus trees infected with ‘Ca. L. asiaticus.’ LotP has been identified as a potential effector and have been partially characterized. This protein retains structural homology to the substrate binding domain of the Lon protease. LotP interacts with chaperones like GroEL, Hsp40, DnaJ, and ClpX and may exercise its biological role through interactions with different proteins involved in proteostasis networks. Here, we evaluate the interactome of LotP—revealing a new protein–protein interaction target (Lon-serine protease) and its effect on citrus plant tissue integrity. We found that via protein–protein interactions, LotP can enhance Lon protease activity, increasing the degradation rate of its specific targets. Infiltration of purified LotP strained citrus plant tissue causing photoinhibition and chlorosis after several days. Proteomics analysis of LotP tissues recovering after the infiltration revealed a large abundance of plant proteins associated with the stabilization and processing of mRNA transcripts, a subset of important transcription factors; and pathways associated with innate plant defense were highly expressed. Furthermore, interactions and substrate binding module of LotP suggest potential interactions with plant proteins, most likely proteases.

RNA helicase–regulated processing of the Synechocystis rimO–crhR operon results in differential cistron expression and accumulation of two sRNAs

The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp-Glu-Ala-Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO-crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.

Generating Stable Knockout Zebrafish Lines by Deleting Large Chromosomal Fragments Using Multiple gRNAs.

The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR associated protein 9) system has been successfully adopted as a versatile genetic tool for functional manipulations, due to its convenience and effectiveness. Genetics lesions induced by single guide RNA (gRNA) are usually small indel (insertion-deletion) DNA mutations. The impact of this type of CRISPR-induced DNA mutation on the coded mRNA transcription processing and protein translation can be complex. Unexpected or unknown transcripts, generated through alternative splicing, may impede the generation of successful loss-of-function mutants. To create null or null-like loss-of-function mutant zebrafish, we employed simultaneous multiple gRNA injection into single-cell stage embryos. We demonstrated that DNA composed of multiple exons, up to 78kb in length, can be deleted in the smarca2 gene locus. Additionally, two different genes (rnf185 and rnf215) were successfully mutated in F1 fish with multiple exon deletions using this multiplex gRNA injection strategy. We expect this approach will be useful for knock-out studies in zebrafish and other vertebrate organisms, especially when the phenotype of a single gRNA-induced mutant is not clear.

African horse sickness virus NS4 is a nucleocytoplasmic protein that localizes to PML nuclear bodies.

African horse sickness virus (AHSV) is the causative agent of the often fatal disease African horse sickness in equids. The non-structural protein NS4 is the only AHSV protein that localizes to the nucleus. Here we report that all AHSV reference and representative field strains express one of the two forms of NS4, i.e. NS4-I or NS4-II. Both forms of NS4 are nucleocytoplasmic proteins, but NS4-I has a stronger nuclear presence whilst NS4-II has a proportionally higher cytoplasmic distribution. A subtype of NS4-II containing a nuclear localization signal (NLS), named NLS-NS4-II, displays distinct punctate foci in the nucleus. We showed that NS4 likely enters the nucleus via passive diffusion as a result of its small size. Colocalization analysis with nuclear compartments revealed that NS4 colocalizes with promyelocytic leukaemia nuclear bodies (PML-NBs), suggesting a role in the antiviral response or interferon signalling. Interestingly, we showed that two other AHSV proteins also interact with nuclear components. A small fraction of the NS1 tubules were present in the nucleus and associated with PML-NBs; this was more pronounced for a virus strain lacking NS4. A component of nuclear speckles, serine and arginine rich splicing factor 2 (SRSF2) was recruited to viral inclusion bodies (VIBs) in the cytoplasm of AHSV-infected cells and colocalized with NS2. Nuclear speckles are important sites for cellular mRNA transcript processing and maturation. Collectively, these results provide data on three AHSV non-structural proteins interacting with host cell nuclear components that could contribute to overcoming antiviral responses and creating conditions that will favour viral replication.

Cell-free transcription in Xenopus egg extract

Soluble extracts prepared from Xenopus eggs have been used extensively to study various aspects of cellular and developmental biology. During early egg development, transcription of the zygotic genome is suppressed. As a result, traditional extracts derived from unfertilized and early stage eggs possess little or no intrinsic transcriptional activity. In this study, we show that Xenopus nucleoplasmic extract (NPE) supports robust transcription of a chromatinized plasmid substrate. Although prepared from eggs in a transcriptionally inactive state, the process of making NPE resembles some aspects of egg fertilization and early embryo development that lead to transcriptional activation. With this system, we observed that promoter-dependent recruitment of transcription factors and RNA polymerase II leads to conventional patterns of divergent transcription and pre-mRNA processing, including intron splicing and 3' cleavage and polyadenylation. We also show that histone density controls transcription factor binding and RNA polymerase II activity, validating a mechanism proposed to regulate genome activation during development. Together, these results establish a new cell-free system to study the regulation, initiation, and processing of mRNA transcripts.

Exposure to environmental toxicants reduces global N6-methyladenosine RNA methylation and alters expression of RNA methylation modulator genes

The epitranscriptome comprises more than 100 forms of RNA modifications. Of these, N6-methyladenosine (m6A) is the most abundant form of RNA methylation, with roles in modulating mRNA transcript processing and regulation. The aims of the study were to examine changes in m6A RNA methylation in A549 lung epithelial cells in response to environmental toxicants, and differential gene expression of m6A modulator genes (‘readers’, ‘writers’ and ‘erasers’) in human subjects exposed to particulate matter (PM) and in lung cancer tissue using publicly-available microarray datasets. Global m6A methylation levels were measured in total RNA after exposure to two carcinogens (PM and sodium arsenite) for 24- and 48-h, and to two endocrine disruptors (bisphenol A and vinclozolin) for 24-h. Global m6A methylation level significantly decreased with exposure to >62 μg/ml PM, >1 μM sodium arsenite, >1 μM bisphenol A (BPA), and 0.1 μM vinclozolin. In an analysis of a published dataset derived from a population study, we observed that m6A writers (METTL3 and WTAP), erasers (FTO and ALKBH5) and readers (HNRPC) showed significantly higher expression among participants in the high-PM2.5 exposure group compared to those in the low-exposure control group (all p < 0.05). Further, the m6A writer METTL3 shows reduced expression in lung tumors in comparison to normal lung epithelia (p < 0.0001). Our findings reveal that m6A RNA methylation can be modified by exposure to environmental toxicants, and exposure to particulate matter is associated with differential expression level of m6A RNA methylation modification machinery.

KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing

Onset of the lytic phase in the KSHV life cycle is accompanied by the rapid, global degradation of host (and viral) mRNA transcripts in a process termed host shutoff. Key to this destruction is the virally encoded alkaline exonuclease SOX. While SOX has been shown to possess an intrinsic RNase activity and a potential consensus sequence for endonucleolytic cleavage identified, the structures of the RNA substrates targeted remained unclear. Based on an analysis of three reported target transcripts, we were able to identify common structures and confirm that these are indeed degraded by SOX in vitro as well as predict the presence of such elements in the KSHV pre-microRNA transcript K12-2. From these studies, we were able to determine the crystal structure of SOX productively bound to a 31 nucleotide K12-2 fragment. This complex not only reveals the structural determinants required for RNA recognition and degradation but, together with biochemical and biophysical studies, reveals distinct roles for residues implicated in host shutoff. Our results further confirm that SOX and the host exoribonuclease Xrn1 act in concert to elicit the rapid degradation of mRNA substrates observed in vivo, and that the activities of the two ribonucleases are co-ordinated.

Characterization of nuclear cap binding complex protein genes (CBP20 and CBP80) from Brassica juncea

Nuclear cap binding complex proteins, CBP20 and CBP80, participate in mRNA transcript processing and also play an important role in abiotic stress tolerance. Brassica juncea is a major oilseed crop, and in this study, we reported the cloning and characterization of CBP20 and CBP80 genes from this species. A full-length BjCBP20 cDNA of 1075bp was cloned containing an open reading frame of 783bp encoding a polypeptide of 260 amino acids. Two genomic sequences of 1792bp and 1712bp were also cloned for BjCBP20, both of these having eight exons and seven introns. Likewise, 2538bp BjCBP80 sequence was cloned which encoded a protein sequence of 845 amino acids. Two genomic sequences of 5672bp and 5190bp consisting of eighteen exons and seventeen introns were cloned. Bioinformatics analysis of deduced proteins revealed the presence of the signature RRM domain in BjCBP20 and MIF4G domain in BjCBP80. Nuclear localization signal was present in BjCBP20. The phylogenetic analysis revealed less conservation in BjCBP80 than BjCBP20 when compared to proteins from other organisms. Expression analysis by qRT-PCR depicted steady levels of both the proteins in developmental stages. BjCBP80 showed highest expression in young leaves while lowest level of expression of BjCBP20 was seen in mature leaves. Under salt and osmotic stress, BjCBP80 level decreased initially and then regained back to normal levels. In osmotic stress, the BjCBP20 levels decreased while no significant change was observed under salt stress.

Post-transcriptional Regulation of Programmed Cell Death 4 (PDCD4) mRNA by the RNA-binding Proteins Human Antigen R (HuR) and T-cell Intracellular Antigen 1 (TIA1)

Post-transcriptional processing of mRNA transcripts plays a critical role in establishing the gene expression profile of a cell. Such processing events are mediated by a host of factors, including RNA-binding proteins and microRNAs. A number of critical cellular pathways are subject to regulation at multiple levels that allow fine-tuning of key biological responses. Programmed cell death 4 (PDCD4) is a tumor suppressor and an important modulator of mRNA translation that is regulated by a number of mechanisms, most notably as a target of the oncomiR, miR-21. Here, we provide evidence for post-transcriptional regulation of PDCD4 by the RNA-binding proteins, HuR and TIA1. Complementary approaches reveal binding of both HuR and TIA1 to the PDCD4 transcript. Consistent with a model where RNA-binding proteins modulate the PDCD4 transcript, knockdown of HuR and/or TIA1 results in a significant decrease in steady-state PDCD4 mRNA and protein levels. However, fractionation experiments suggest that the mode of regulation of the PDCD4 transcript likely differs in the cytoplasm and the nucleus as the pool of PDCD4 mRNA present in the cytoplasm is more stable than the nuclear pool of PDCD4 transcript. We observe a competitive mode of binding between HuR and TIA1 on the PDCD4 transcript in the cytoplasm, suggesting that these two factors dynamically interact with one another as well as the PDCD4 transcript to maintain tight control of PDCD4 levels. Overall, this study reveals an additional set of regulatory interactions that modulate the expression of PDCD4, a key pro-apoptotic factor, and also reveals new insights into how HuR and TIA1 functions are integrated to achieve such regulation.

Hyperstructure interactions influence the virulence of the type 3 secretion system in yersiniae and other bacteria

A paradigm shift in our thinking about the intricacies of the host-parasite interaction is required that considers bacterial structures and their relationship to bacterial pathogenesis. It has been proposed that interactions between extended macromolecular assemblies, termed hyperstructures (which include multiprotein complexes), determine bacterial phenotypes. In particular, it has been proposed that hyperstructures can alter virulence. Two such hyperstructures have been characterized in both pathogenic and nonpathogenic bacteria. Present within a number of both human and plant Gram-negative pathogens is the type 3 secretion system (T3SS) injectisome which in some bacteria serves to inject toxic effector proteins directly into targeted host cells resulting in their paralysis and eventual death (but which in other bacteria prevents the death of the host). The injectisome itself comprises multiple protein subunits, which are all essential for its function. The degradosome is another multiprotein complex thought to be involved in cooperative RNA decay and processing of mRNA transcripts and has been very well characterized in nonpathogenic Escherichia coli. Recently, experimental evidence has suggested that a degradosome exists in the yersiniae as well and that its interactions within the pathogens modulate their virulence. Here, we explore the possibility that certain interactions between hyperstructures, like the T3SS and the degradosome, can ultimately influence the virulence potential of the pathogen based upon the physical locations of hyperstructures within the cell.

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

Post-transcriptional control of mRNA transcript processing by RNA binding proteins (RBPs) is an important step in the regulation of gene expression and protein production. The post-transcriptional regulatory network is similar in complexity to the transcriptional regulatory network and is thought to be organized in RNA regulons, coherent sets of functionally related mRNAs combinatorially regulated by common RBPs. We integrated genome-wide transcriptional and translational expression data in yeast with large-scale regulatory networks of transcription factor and RBP binding interactions to analyze the functional organization of post-transcriptional regulation and RNA regulons at a system level. We found that post-transcriptional feedback loops and mixed bifan motifs are overrepresented in the integrated regulatory network and control the coordinated translation of RNA regulons, manifested as clusters of functionally related mRNAs which are strongly coexpressed in the translatome data. These translatome clusters are more functionally coherent than transcriptome clusters and are expressed with higher mRNA and protein levels and less noise. Our results show how the post-transcriptional network is intertwined with the transcriptional network to regulate gene expression in a coordinated way and that the integration of heterogeneous genome-wide datasets allows to relate structure to function in regulatory networks at a system level.

New findings on protein expression in copper deficient rat heart using proteomic approaches

Dietary Cu-deficiency not only causes a hypertrophic cardiomyopathy but also increases cancer risk in rodent models. The present studies were undertaken to determine the effect of Cu-deficiency on protein profiles in rat heart tissue. Male Sprague-Dawley rats were fed diets that were either copper adequate (6.0 μg copper/g diet n = 6) or copper deficient (0.3 μg copper/g diet n = 6) for 5 wk. An approach using liquid chromatography mass spectrometry analysis coupled with DNA gel shift and immunodection dot blotting revealed a 132 kDa protein complex in the protein extract from hearts of Cu-deficient, but not Cu-adequate rats. This complex contained a collagen alpha (I) chain precursor as well as a leucine-rich protein 130 (DNA binding protein). These data suggest that Cu-deficiency may have a potential to influence DNA stability and mRNA transcript processing. Another approach to determine the effect of Cu deficiency on protein profiles used the combination of the isotope-coded affinity tag (ICAT) method and Western blotting analysis. ICAT analysis suggested that protein profiles from heart tissue of Cu-deficient rats were different from those of Cu-adequate rats; seven major protein species differed by more than a 100% increase or a 50% decrease. Western blotting analysis confirmed an 85% increase in fibulin-5 (also known DANCE/EVEC) in Cu-deficient rat heart, and suggested a critical biological function of Cu in controlling vascular redox state, scaffolding of cells to elastic fiber, and preventing elastinopathy in the rat heart.

Evolution of the RNA polymerase II C-terminal domain.

In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of RPB1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that the enhanced control over RNA polymerase II transcription conveyed by acquired CTD/protein interactions was an important step in the evolution of intricate patterns of gene expression that are a hallmark of large, developmentally complex eukaryotic organisms.

The Identification of the Inhibitory γ-Subunits of the Type 6 Retinal Cyclic Guanosine Monophosphate Phosphodiesterase in Non-retinal Tissues: Differential Processing of mRNA Transcripts

Here, we report that mouse lung expresses γ-subunit (PDEγ) transcripts of the rod and cone photoreceptor cGMP phosphodiesterase genes (Pde6g and Pde6h, respectively). Moreover, a major 14-kDa protein (p14) in lung membranes was immunostained with antibodies that react with both rod and cone PDEγ. We show that p14 is, in fact, a mixture of rod and cone PDEγ, based on three additional lines of evidence. First, p14 was also immunostained with antibodies specific for the cone PDEγ isoform. Second, the expression of p14 immunostained with antibodies recognizing both rod and cone PDEγ was substantially reduced in lung membranes from Pde6g−/− mice. In contrast, the fraction of p14 stained with cone PDEγ-specific antibodies was not altered in the Pde6g−/− mice. Third, the absence of the Pde6g transcript was correlated with reduced levels of p14 in Pde6g−/− mice. We have also found that mouse lung contains a small Pde6h transcript that has a 41-bp deletion resulting in a frame change, derived by differential mRNA processing of exon 3 of Pde6h. BLAST searches also revealed a rat ovary EST that has the same 41-bp deletion causing the same frame change. However, the premature in-frame stop codon seen in the short Pde6h transcript is absent and the regular stop codon is out of frame leading to a predicted ORF extension into the 3′ UTR. These findings show that rod and cone PDEγ isoforms are expressed in lung and seem to have a critical role in regulating p42/p44 mitogen-activated protein kinase signaling.

Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes.

We have examined the distribution of RNA transcription and processing factors in the amphibian oocyte nucleus or germinal vesicle. RNA polymerase I (pol I), pol II, and pol III occur in the Cajal bodies (coiled bodies) along with various components required for transcription and processing of the three classes of nuclear transcripts: mRNA, rRNA, and pol III transcripts. Among these components are transcription factor IIF (TFIIF), TFIIS, splicing factors, the U7 small nuclear ribonucleoprotein particle, the stem-loop binding protein, SR proteins, cleavage and polyadenylation factors, small nucleolar RNAs, nucleolar proteins that are probably involved in pre-rRNA processing, and TFIIIA. Earlier studies and data presented here show that several of these components are first targeted to Cajal bodies when injected into the oocyte and only subsequently appear in the chromosomes or nucleoli, where transcription itself occurs. We suggest that pol I, pol II, and pol III transcription and processing components are preassembled in Cajal bodies before transport to the chromosomes and nucleoli. Most components of the pol II transcription and processing pathway that occur in Cajal bodies are also found in the many hundreds of B-snurposomes in the germinal vesicle. Electron microscopic images show that B-snurposomes consist primarily, if not exclusively, of 20- to 30-nm particles, which closely resemble the interchromatin granules described from sections of somatic nuclei. We suggest the name pol II transcriptosome for these particles to emphasize their content of factors involved in synthesis and processing of mRNA transcripts. We present a model in which pol I, pol II, and pol III transcriptosomes are assembled in the Cajal bodies before export to the nucleolus (pol I), to the B-snurposomes and eventually to the chromosomes (pol II), and directly to the chromosomes (pol III). The key feature of this model is the preassembly of the transcription and processing machinery into unitary particles. An analogy can be made between ribosomes and transcriptosomes, ribosomes being unitary particles involved in translation and transcriptosomes being unitary particles for transcription and processing of RNA.

Messenger ribonucleic acids for alpha- and beta-isoforms of cyclic adenosine 3',5'-monophosphate-dependent protein kinase subunits present in the anterior pituitary: regulation of RII beta and C alpha gene expression by the cyclic nucleotide and phorbol ester.

Expression of the genes encoding the alpha- and beta-isoforms of the catalytic (C) and regulatory type I (RI) and type II (RII) subunits of cAMP-dependent protein kinases (PKA) in the anterior pituitary gland of rats was examined by hybridization of specific 32P-labeled cDNA probes to mRNA. C alpha, C beta, RI alpha, RI beta, RII alpha, and RII beta mRNAs were all present in the anterior pituitary gland and cultured cells, but in different proportions; C alpha was the most abundant, and RII alpha was the least. For C alpha, C beta, RI beta, and RII alpha, Northern blot analysis revealed single mRNAs with sizes of 2.4, 4.5, 2.8, and 6.0 kilobases (kb), respectively. For RI alpha, three distinct mRNAs (1.7, 3.2, and 3.7 kb) were identified, and for RII beta, two were found (1.8 and 3.5 kb). Compared to other tissues and species, including ovine and rat pituitary and testis, differences in sizes and relative abundance of mRNAs and/or mRNA subtypes were observed, demonstrating that great diversity exists, which may reflect tissue and species variation in posttranscriptional processing of mRNA transcripts. When rat anterior pituitary cells were cultured in the presence of 8-bromo-cAMP (8-Br-cAMP), RII beta mRNA levels increased in a dose- and time-dependent manner to a maximum of about 4- to 5-fold the basal values after 5 h in the presence of 2 mM 8-Br-cAMP. Under the same conditions, the C alpha mRNA, already at high levels, further increased, but to a lesser extent (1.5-2 times compared to basal abundancy). Cholera toxin (6 nM) reproduced the effects of 8-Br-cAMP on both C alpha and RII beta mRNAs. These effects were completely abolished in the presence of actinomycin-D, suggesting that cAMP enhances RII beta and C alpha gene transcription. On the other hand, cell exposure to the phorbol ester 12-O-tetradecanoyl 13-phorbol acetate, a potent activator of protein kinase-C (PKC), readily induced a dose-dependent actinomycin-D-inhibited increase in the RII beta mRNA content to levels about 2-fold those in control unstimulated cells, whereas it depressed levels of C alpha mRNA by 25%. In conclusion, we have found that the six genes coding for the alpha- and beta-isoforms of PKA subunits are all expressed in the anterior pituitary, and that the expression of two of those genes (RII beta and C alpha) is regulated by cAMP and phorbol ester in a similar or opposite manner.(ABSTRACT TRUNCATED AT 400 WORDS)

Nucleotide sequence and analysis of the coliphage T3 S-adenosylmethionine hydrolase gene and its surrounding ribonuclease III processing sites.

To understand better the characteristics of the coliphage T3 S-adenosyl-L-methionine (AdoMet) hydrolase (AdoMetase, E.C. 3.3.1.2) and its expression in phage-infected Escherichia coli, we determined the DNA sequence of the cloned gene and its surrounding ribonuclease (RNase) III mRNA transcript processing sites. The AdoMetase gene contains two in-frame protein translation initiation sites specifying peptides 17105 and 13978 daltons in size. Both proteins terminate at the same ochre codon making the shorter peptide identical to the carboxy terminal 82% of the 17 kd protein. Our data explain the existence of two AdoMetase-related peptides in preparations of the purified enzyme as well as identify sequences that might serve to regulate the enzyme's expression. Comparisons between this T3 sequence and the homologous 0.3 gene region of the closely related coliphage T7 show both the nucleotide and amino acid sequences to be unrelated. The RNase III mRNA processing sites that bracket these genes in T3 and T7 are highly conserved in both their primary and secondary structures.