Comparison of the nuclear ribonucleoproteins containing the transcripts of adenovirus-2 and HeLa cell dna

Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle

Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.

Regulation of mRNA production by the adenoviral E1B 55-kDa and E4 Orf6 proteins

The E1B 55-kDa and E4 Orf6 proteins of human subgroup C adenoviruses both counter host cell defenses mediated by the cellular p53 protein and regulate viral late gene expression. A complex containing the two proteins has been implicated in induction of selective export of viral late mRNAs from the nucleus to the cytoplasm, with concomitant inhibition of export of the majority of newly synthesized cellular mRNAs. The molecular mechanisms by which these viral proteins subvert cellular pathways of nuclear export are not yet clear. Here, we review recent efforts to identify molecular and biochemical functions of the E1B 55-kDa and E4 Orf6 proteins required for regulation of mRNA export, the several difficulties and discrepancies that have been encountered in studies of these viral proteins, and evidence indicating that the reorganization of the infected cell nucleus and production of viral late mRNA at specific intra-nuclear sites are important determinants of selective mRNA export in infected cells. In our view, it is not yet possible to propose a coherent molecular model for regulation of mRNA export by the E1B 55-kDa and E4 Orf6 proteins. However, it should now be possible to address specific questions about the roles of potentially relevant properties of these viral proteins.

Altered levels of the Drosophila HRB87F/hrp36 hnRNP protein have limited effects on alternative splicing in vivo

The Drosophila melanogaster genes Hrb87F and Hrb98DE encode the fly proteins HRB87F and HRB98DE (also known as hrp36 and hrp38, respectively) that are most similar in sequence and function to mammalian A/B-type hnRNP proteins. Using overexpression and deletion mutants of Hrb87F, we have tested the hypothesis that the ratio of A/B hnRNP proteins to SR family proteins modulates certain types of alternative splice-site selection. In flies in which HRB87F/hrp36 had been overexpressed 10- to 15-fold above normal levels, aberrant internal exon skipping was induced in at least one endogenous transcript, the dopa decarboxylase (Ddc) pre-mRNA, which previously had been shown to be similarly affected by excess HRB98DE/hrp38. In a second endogenous pre-mRNA, excess HRB87F/hrp36 had no effect on alternative 3' splice-site selection, as expected from mammalian hnRNP studies. Immunolocalization of the excess hnRNP protein showed that it localized correctly to the nucleus, specifically to sites on or near chromosomes, and that the peak of exon-skipping activity in Ddc RNA correlated with the peak of chromosomally associated hnRNP protein. The chromosomal association and level of the SR family of proteins were not significantly affected by the large increase in hnRNP proteins during this time period. Although these results are consistent with a possible role for hnRNP proteins in alternative splicing, the more interesting finding was the failure to detect significant adverse effects on flies with a greatly distorted ratio of hnRNPs to SR proteins. Electron microscopic visualization of the general population of active genes in flies overexpressing hnRNP proteins also indicated that the great majority of genes seemed normal in terms of cotranscriptional RNA processing events, although there were a few abnormalities consistent with rare exon-skipping events. Furthermore, in a Hrb87F null mutant, which is viable, the normal pattern of Ddc alternative splicing was observed, indicating that HRB87F/hrp36 is not required for Ddc splicing regulation. Thus, although splice-site selection can be affected in at least a few genes by gross overexpression of this hnRNP protein, the combined evidence suggests that if it plays a general role in alternative splicing in vivo, the role can be provided by other proteins with redundant functions, and the role is independent of its concentration relative to SR proteins.

Modulation of alternative splicing of adenoviral E1A transcripts: factors involved in the early-to-late transition

The E1A pre-mRNA of adenovirus is spliced into three mRNA species (13S, 12S, and 9S mRNAs) by the use of three alternative 5'-splice sites. The 13S and 9S mRNAs predominate during the early and late periods of infection, respectively. With HeLa nuclear extracts isolated in early and late periods of infection, we were able to reproduce a 13S-9S modulation that resembles that occurring in infected cells. An in vitro analysis of the cis-acting parameters involved in the 13S-9S switch indicates that the 13S mRNA splicing inhibition is one of the first events of the late period and leads to the subsequent stimulation of the 9S mRNA reaction. The new abilities of the late nuclear extract for the 9S mRNA reaction were also confirmed by analyzing splicing of a major late transcript containing leaders 1 and 2 separated by the wild-type intervening sequence (IVS) of 1021 nucleotides. Complementation experiments show that the trans-acting factor(s) are micrococcal nuclease sensitive. They were partially characterized by induction experiments, and we show that the primary factors responsible for the 13S-9S modulation in vitro are viral RNAs of high molecular weight that accumulate late in infection. We postulate that the splicing modulation of E1A pre-mRNA results from an indirect mode of action for these viral RNAs, based on a sequestration of common splicing factors that are not present in vast excess in HeLa cells.

The distribution of two hnRNP-associated proteins defined by a monoclonal antibody is altered in heat-shocked HeLa cells

A monoclonal antibody obtained after mice were immunized with hnRNP purified from HeLa cells recognizes two polypeptides of Mr 35,000 and 37,000. By immunocytofluorescence, these antigens can be visualized only in cells previously heat shocked at 45 degrees C for 5 or 10 min, although they are present at the same level in unstressed and stressed cells. The signal, which is mostly concentrated in the interchromatin space, where hnRNP fibrils are located, does not accumulate with time and disappears 4 to 5 h after heat shock. Discrimination between the two types of hnRNP substructures, the 30-50 S monoparticles and the nuclear matrix fibrils, based on differential sensitivity to salt or ribonuclease treatment, showed that in unstressed cells the antigens behave as monoparticle proteins. In contrast, in heat-shocked cells, most 35-37K antigens behave as nuclear matrix proteins. Thus, heat shock seems to induce a rapid and reversible switch of these two antigens from hnRNP monoparticles to the nuclear matrix. The data demonstrate that heat shock, which was previously shown not to alter the overall RNA: protein packaging ratio of hnRNP, induces subtle modifications of their substructure. Such modifications might be of importance since heat shock is known for instance to affect pre-mRNA processing.

Nuclear non-polyadenylated RNAs containing the first intervening sequence of the major late premessenger RNA from adenovirus-2: characterization and distribution in ribonucleoproteins

The nuclear non-polyadenylated RNA from HeLa cells infected with adenovirus-2 was examined for the presence of molecules containing the first intervening sequence (IVS1) of the major late premessenger RNA. Four molecules with the approximate size of free IVS1 in sucrose gradients (1021 nucleotides) were separated by polyacrylamide gel electrophoresis and characterized by complementary methods: S1 nuclease mapping, susceptibility to debranching enzyme, RNAase-H-directed cleavage. The results indicate that the most abundant RNA form is the excised lariat IVS1. We also find linear IVS1 and a randomly nicked lariat, the latter probably being made during RNA isolation. The fourth RNA is a leader 1-IVS1 molecule. No truncated IVS1 which might indicate that IVS1 is excised by several cycle of cleavage-ligation was detected. A study of the distribution of the four RNAs in hnRNP shows that they are part of RNPs of about 70 S. However, each RNP has distinct sedimentation characteristics and sensitivity to salt dissociation. Together, the results suggest that the excised lariat IVS1 is released from the large late premRNP under the form of a 70 S RNP, where it is linearized.

High Specificity of the cDNA-RNase Assay to Detect Accurate SplicingIn Vitro

e previously developed a splicing assay (Keohavong et al., 1982) that we designated as a cDNA-RNase assay to analyze the ligation reaction between exons of premessenger RNA during in vivo or in vitro splicing. It was important to determine the specificity of this splicing assay, since the accuracy of in vitro splicing must always be demonstrated clearly. To do this, we constructed DNA probes derived from adenovirus E1A cDNA carrying deletions or insertions of 2-6 bases. After hybridizing them to the wild-type mRNA, the ability of single-strand-specific RNases to detect small mismatches of the RNA-DNA hybrids was examined. The demonstration that an imprecision in the splicing reaction of as little as 2 nucleotides can be detected with an efficiency of 99% indicates the high specificity of the splicing assay and its usefulness for the verification of accurate splicing in in vitro systems.

Two 5S genes are expressed in chicken somatic cells

Two 5S RNA species were detected in chicken cells. 5S I RNA has the nucleotide sequence of chicken 5S RNA previously published by Brownlee et al. (1) and 5S II RNA differs from it by 10 mutations. The secondary structure of both species is compatible with that proposed for other eukaryotic 5S RNAs. 5S II RNA represents 50-60% of 5S I RNA. Both species were found in total chicken liver and brain and were present in polysomes in the same relative proportions. Only one 5S RNA species could be detected in rat liver and HeLa cells. Chicken is the first vertebrate described so far in which two 5S RNA genes are expressed in somatic cells.

Synthesis and processing of simian virus 40-specific RNA in adenovirus-infected, simian virus 40-transformed human cells

Human simian virus 80 (SV80) cells transformed by simian virus 40 (SV40) synthesize substantial quantities of the SV40 large T-antigen (Henderson & Livingston, 1974; Tjian, 1978) and cytoplasmic, poly(A)-containing RNA species that exhibit spliced structures characteristic of the SV40, early messenger RNA species that encode both large and small T-antigens (Flint & Beltz, 1979). When SV80 cells were infected with type C adenovirus, both the synthesis of SV40 large T-antigen and the appearance in the cytoplasm of newly synthesized, SV40-specific RNA sequences were inhibited during the late phase of infection. The results of hybridization to SV40 DNA of SV80 nuclear RNA, prepared from mock- or adenovirus-infected cells after labeling for short periods in vivo or in vitro, indicated that transcription of integrated SV40 was, by contrast, not disrupted during the late phase of adenovirus infection. Poly(A)-containing, nuclear RNA species that hybridized to SV40 DNA sequences and exhibited the sizes of spliced, large and small T-antigen mRNA species were also synthesized in infected cells at a time when the corresponding mRNA sequences did not leave the nucleus. These results suggest that the failure of non-adenoviral mRNA sequences to enter the cytoplasm of adenovirus-infected cells does not reflect inhibition of either their transcription or the normal enzymatic processing reactions to which pre-mRNA species are subject. Several lines of evidence do, however, establish that nuclear, SV40-specific RNA sequences are less stable in adenovirus-infected compared to mock-infected SV80 cells.

An assessment of the evidence for the role of ribonucleoprotein particles in the maturation of eukaryote mRNA

This article has sought to draw together, on the one hand, what is known of mRNA processing and its control and, on the other hand, what is known of the structure and validity of hnRNP and snRNP particles. At the same time, it has attempted to synthesize these two themes into a critical assessment of the evidence which suggests that the particles are intimately involved in processing. It cannot be said that the case is proven. The evidence is compelling but circumstantial. The last few years have seen the development of the first in vitro splicing systems (Weingartner and Keller, 1981; Goldenberg and Raskus, 1981; Kole and Weissman, 1982), the isolation of monoclonal antibodies to defined snRNP (Lerner et al., 1981a; Billings et al., 1982) and hnRNP proteins (Hugle et al., 1982), and the ability to use artificial lipid vesicles to transfer antisera (Lenk et al., 1982) and radioactive snRNA (Gross and Cetron, 1982) into cells. It is to be hoped that further refinements of these and other techniques will allow us to solve this, one of the major outstanding problems of molecular biology.

The orderly splicing of the first three leaders of the adenovirus-2 major late transcript

A strategy based on the hybridization of labeled nucleoplasmic RNA to a short cloned cDNA probe was devised to study the ligation of the three first leader sequences (Le1, Le2, Le3) of the major late adenovirus-2 transcript. The hybridized RNA was subsequently fractionated by electrophoresis and identified with the aid of restriction fragments of the DNA probe. The ligations were shown to occur stepwise and in an orderly fashion. Le1 and Le2 were first ligated without detectable lag time. The tripartite leader was formed after a lag time of 10-15 min probably due, for a large part, to the stepwise excision of the intervening sequence between Le2 and Le3. The possible processing intermediate Le2-Le3 was not detected.

Adenoviral heterogeneous nuclear RNA is associated with host cell proteins

In this study irradiation of intact cells with 244-nm ultraviolet light was used to cross-link hnRNA to proteins that are closely associated with it. In this way proteins interacting specifically with hnRNA could be identified excluding the possibility of non-specific binding of proteins to the RNA during cell fractionation. In uninfected HeLa cells two polypeptides of 41500 and 43000 molecular weight can be cross-linked very efficiently to hnRNA. Other proteins, with molecular weights of 36000 and 37000, were covalently linked less effectively. Irradiation of adenovirus-infected cells results in the cross-linking of the same polypeptides to hnRNA. It was found, however, that hnRNA from adenovirus-infected cells contains both viral and host transcripts. Both classes of transcripts are quantitatively associated with the nuclear matrix and can be cross-linked by irradiation with equal efficiency. To determine whether both adenoviral and cellular transcripts are associated with the same proteins, the cross-linked adenoviral hnRNA-protein complexes were isolated by preparative hybridization to adenoviral DNA immobilized on Sepharose. The results show that the purified cross-linked adenoviral hnRNA-protein complexes also contain the host 41500-Mr and 43000-Mr proteins as major components. This suggests that in the infected cell adenoviral-specific hnRNA is associated with host proteins and that the structural organization of viral hnRNA-protein complexes in infected cells probably is similar to the organization of host hnRNA in uninfected cells.

The conformation of adenovirus VAI-RNA in solution

The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the structure. The results suggest that VAI-RNA in solution has a compact structure with a free energy of around -60 kcal with two stems and four bulge regions. The implication of this structure for the function of VAI-RNA is discussed.

Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs

U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in addition, differs from U4A and U4B RNAs at two internal positions. Thus, U4C RNA is encoded by another gene as U4A and U4B RNAs. Only one nucleotide substitution occurred between chicken and man showing that U4A, U4B and U4C RNAs have been extremely conserved throughout evolution. The three molecular species are capped, they contain three psi, a 2'-P methyl A and a m6A. An additional post-transcriptional modification close to the cap structure is observed in man. On the basis on an experimental study, two models of secondary structure may be proposed for U4 RNA. The 3'domain is the same in both models and is homologous to that of U1 and U5 RNAs. It consists of a single-stranded region, containing the sequence Py-(A)2-(U)n-Gp flanked by two stable hairpins probably involved in tertiary interactions. The 5' domain is less stable than the 3' domain and its structure is different in the two models. However, a long single-stranded pyrimidine region containing modified nucleotides is found in both models as in U1 and U5 RNAs. Several other nucleotide sequence homologies related to specific features of secondary structure suggest that U1, U4 and U5 RNAs derive from a common ancestor and may have common function.

Small RNAs in HnRNP fibrils and their possible function in splicing

Several arguments are in favor of a function of snRNA in the processing of premessenger RNA. A large fraction of snRNA is localized in hnRNP which are assumed to be the site of processing. The different snRNA species are not bound to hnRNP in a unique manner but are associated with both proteins and hnRNA which suggests the possibility of metabolic exchanges in the course of processing. There is approximately 1-2 molecules of snRNA per individual hnRNP. We reexamined the possibility that U1A RNA might serve for the alignment of the extremities of the intron sequences of premessenger RNA insuring correct condition for cutting and splicing. We found that only a UCCA (3' leads to 5') sequence at position 8-11 of U1A RNA was complementary to an AG-GU (5' leads to 3') around a putative splice point for 69 different introns sequenced so far. On the basis of secondary structure of U1A RNA, the UCCA sequence would be available for hybridization. The UCCA sequence is also present in U2 RNA and 4.5 S RNAI. It might associate with AG-GU in a manner similar to that of codon-anticodon, the stability of the complex being insured by the configuration of hnRNP. The possible formation of larger hybrids stable by themselves is unlikely upon examination of the nucleotide sequence of various introns adjacent to the splice point. As there is no direct experimental evidence for the function of snRNA in splicing, there considerations are speculative at the present time. The possibility that adenovirus encoded VA RNA would play a role in splicing was also examined. Various arguments suggest that this possibility is rather remote.

Nuclear ribonucleoprotein particles from adenovirus infected Hela cells

Heterogenous nuclear RNA-protein complexes (hnRNP) from adenovirus-2 (Ad-2) infected Hela cells contain most of the virus-specific RNA which is labeled in the nucleus during periods lasting from 45 seconds to 2 hours. Moreover, the percentage of RNA which is Ad-2 specific as monitored by filter hybridization increases progressively from early to late period where it accounts for as much as 50-60% of the labeled RNA. The Ad-2 sequences are found in heterogenous complexes sedimenting between 30 and 200 S the density of which in CsCl (rho approximately 1.39) as well as metrizamide (rho approximately 1.29) seems to be the same as that of the bulk particles. A more detailed analysis with restriction fragments shows that all regions of the Ad-2 genome are represented in these particles.

The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes

Preparations of chicken, rat and human nuclear 5S RNA contain two sets of molecules. The set with the lowest electrophoretic mobility (5Sa) contains RNAs identical or closely related to ribosomal 5S RNA from the corresponding animal species. In HeLa cells and rat brain, we only detected an RNA identical to the ribosomal 5S RNA. In hen brain and liver, we found other species differing by a limited number of substitutions. The results suggest that mutated 5S genes may be expressed differently according to the cell type. The set with the highest mobility corresponds to U5 RNA. In both rat brain and HeLa cells, U5 RNA was found to be composed of 4 and 5 different molecules respectively (U5A, U5B1-4) differing by a small number of substitutions or insertions. In hen brain, no U5B was detected but U5A' differing from U5A by the absence of the 3'-terminal adenosine. All the U5 RNAs contain the same set of modified nucleotides. They also have the same secondary structure which consists of two hairpins joined together by a 17 nucleotide long single-stranded region. The 3' half of the molecule has a compact conformation. Together, the results suggest that U5 RNAs are transcribed from a multigene family and that mutated genes may be expressed as far as secondary structure is conserved. The conformation of U5 RNA is likely to be related to its function and it is of interest to mention that several similarities of structure are found between U5 and U1A RNA.

Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man

The methods of enzymatic and chemical treatment of end-labeled RNA were applied to the determination of the nucleotide sequence of chicken and man U1A RNA and to the reexamination of that of rat U1A RNA. The chemical method allowed the easy demonstration of the cap structure. All three RNA were 165 nucleotide long. Two hitherto non described modified pyrimidines were detected close to the 5' end. Only 9 base substitutions were observed from chicken to man indicating high degree of conservation of U1A RNA through evolution.