Virus-mediated inhibition of the ppp(A2′p)n A system and its prevention by interferon

Encephalomyocarditis virus infection of mouse Ehrlich ascites tumour or L-cells or human HeLa cells inhibits the activation of the ppp(A2′p)_n A-dependent nuclease and prevents the binding of a radioactive analogue of ppp(A2′p)_n A to the ppp(A2′p)_n A binding protein. This loss or inactivation of the ppp(A2′p)_n A-dependent nuclease in response to virus infection is prevented by interferon pretreatment of the cells.     

Ontogeny of ppp(A2′p)nA-binding protein in mouse brain

Mouse brain tissue extracts at various stages of development show a drastic change in the specific activity of pp(A2′p)₂A-[³²P]pCp binding protein. Identification of the ppp(A2′p)₃A-[³²P]pCp binding protein was established by (i) binding to the specific ligand ppp(A2′p)₃A-[³²P]pCp, (ii) displacement of binding by nanomolar concentration of pppA(pA)₃, and (iii) affinity labeling techniques in which periodate oxidized ppp(A2′p)₃A-[³²P]pC was specifically cross-linked to a protein with a molecular weight of 86 000. These data suggest that the ppp(A2′p)₃A-[³²P]pCp protein is closely associated with the process of cellular proliferation and differentiation.     

Oligo(2'-5')adenylate synthetase in human lymphoblastoid cells

The enzyme oligo(2′–5′)adenylate synthetase, when activated by double-stranded RNA, polymerizes ATP into the novel oligonucleotide (2′–5′)ppp(Ap)_nA. We describe conditions for assay of this enzyme in crude extracts of a human lymphoblastoid cell line, Namalwa. The production of (2′–5′)ppp(Ap)_nA by Namalwa extracts was 3–5 times greater than the production by extracts of interferon pretreated mouse L cells, and 700 fold higher than the production by extracts of untreated mouse L cells. The relatively high level of oligo(2′–5′)adenylate synthetase in Namalwa cells was not attributable solely to their constitutive secretion of low levels of interferon. Analysis of the size distribution of the oligomers formed at different times suggested that the enzyme can add ATP to a free pppApA. Infection by Newcastle disease virus or treatment with interferon raised the apparent synthetase levels only marginally. Experiments that employed antibody to interferon suggested that the interferon must be externalized from the NDV-infected cell to induce maximal synthetase levels.     

The (gt)n(ga)m containing intron 2 of HLA-DRB alleles binds a zinc-dependent protein and forms non B-DNA structures

We studied protein binding and structural features of perfect and imperfect composite (gt)_n(ga)_m blocks from different HLA-DRB1 alleles in their original genomic and artificial environments. The major retarded protein/DNA complex of the genomic (gt)_n(ga)_m fragments comprises a zinc-dependent protein present in nuclear extracts from different cell types. The protein binding is characterized by moderate affinities independent of the polymorphic form of the physiological microsatellite allele. The binding affinity depends on the 5′ and 3′ adjacent single copy parts. DNase I footprinting of genome-derived fragments revealed that the 5′ adjacent sequence and the (gt)_n repeat are preferentially protected on the (gt)_n(ga)_m strand. Comparing three alleles, a regular pattern of footprints was not detectable in the (gt)_n part, indicating that the zinc-dependent protein recognizes structural rather than sequence-specific features in this region. Chemical probing resulted in a pattern characteristic for Z-DNA in the (gt)_n tract of the fragments. However, EMSA experiments using the Z-DNA specific monoclonal antibody mABZ-22 did not prove the presence of Z-DNA. As demonstrated by chemical modifications of the different (ga)_m targets, only one of three (gt)_n(ga)_m fragments formed intramolecular triplexes of the type H-y3 and H-y5. DNase I footprinting revealed only weak protection, if any, in the homopurine tract. Rather, the (tc)_m strands are hypersensitive for DNase I. This is probably due to structural conversions into intramolecular *H-triplexes after binding of HIZP.     

Hydrolysis of some mRNA 5′-Cap Analogs Catalyzed by the Human Fhit Protein - and Lupin ApppA Hydrolases

Abstract

Hydrolysis of the following four cap analogs: m⁷G(5′)ppp(5′)A, m⁷G(5′)ppp(5′)m⁶A, m⁷G(5′)ppp(5′)m^2′OG and m⁷G(5′)ppp(5′)2′dG catalyzed by homogeneous human Fhit protein and yellow lupin Ap₃A hydrolase has been investigated. The hydrolysis products were identified by HPLC analysis and the K_m and V_max values calculated based on the data obtained by the fluorimetric method.     

Interaction of wheat protein synthesis elongation factor 1 with GTP analogs

Wheat protein synthesis elongation factor 1 was tested for binding to GTP analogs, including structures resembling “caps” that are present at the 5′-termini of most eukaryotic mRNAs. The interaction was assayed by determining the capacity of the analogs to inhibit the binding of [³H]GTP to elongation factor 1. Significant interaction of elongation factor 1 with G(5′)ppp(5′)G, G(5′)pppp(5′)G, and G(5′)ppp(5′)A was observed. Methylation of a ribose 2′-hydroxyl had very little effect, but methylation of the 7 position of guanosine greatly diminished the affinity of elongation factor 1 for these compounds. m⁷G(5′)ppp(5′)Cm, m⁷G(5′)ppp(5′)Um, and m⁷G(5′)ppp(5′)Am gave no detectable binding with EF1.     

Synthesis and Biological Activity of a Bis-Substituted 3′-Deoxyadenosine Analog of 2–5A

Abstract

The 5′-monophosphate, p5′(3′dA)2′p5′A2′5′(3′dA), was synthesized and found to bind to the 2–5A-dependent endonuclease of mouse L cells only two-three times less effectively than the parent p5′A2′p5′A2′p5′A. When evaluated for its ability to activate the 2–5A-dependent endonuclease, ppp5′(3′dA)2′p5′A2′p5′(3′dA) was found to be fifty times more effective than ppp5′A2′p5′(3′dA)2′p5′A and ten times less effective than 2–5A as an endonuclease activator     

Only One 3′-Hydroxyl Group Of ppp 5′A 2′p 5′A 2′p 5′A(2–5A) is Required for Activation of the Mouse 2–5A-Dependent Endonuclease

Abstract

The 3′-hydroxyl groups of each of the adenosines of 2–5A triraer (ppp5′A2′p5′A2′p5′A) were sequentially replaced by hydrogen through a phosphotriester synthetic approach. Biochemical evaluation of these analogs led to the conclusion that only the 3′-hydroxy group of the second adenosine is required for activation of RNase L.     

Biological activities of phosphodiester linkage isomers of 2-5A

To determine the relative importance of the 2',5'-phosphodiester bond of 2-5A in its binding to and activation of the 2-5A-dependent ribonuclease (RNase L, RNase F), a number of phosphodiester linkage isomers of 2-5A were prepared. These isomers were obtained either by lead ion-catalyzed polymerization of adenosine 5'-phosphorimidazolidate or by T4 polynucleotide kinase-catalyzed 5'-phosphorylation of adenylyl(3' leads to 5')adenylyl(3' leads to 5')adenosine followed by reaction of the corresponding phosphorimidazolidates with tri(n-butylammonium)pyrophosphate. The following 2-5A isomers thus were prepared: ppp5'A2'p5'A3'p5'A, ppp5'A3'p5'A2'p5'A, ppp5'A3'p5'A3'p5'A("3-5A"), ppp5'A2'p5'A3'p5'A2'p5'A,and ppp5'A3'p5'A2'p5'-A2'p5'A. The ability of these isomeric 2-5As to interact with the 2-5A-dependent endonuclease was ascertained by three different criteria: (i) ability to prevent the protein synthesis inhibitory effects of 2-5A, (ii) activity as an inhibitor of translation in encephalomyocarditis RNA-programmed L cell extracts, and (iii) ability to prevent binding of the radiolabeled probe, ppp5'A2'p5'A2'p5'A2'p5'A3'[32P]p5'Cp, to the endonuclease of L cell extracts. In certain experiments, degradation of oligonucleotide was minimized or eliminated by altering assay conditions, providing alternate phosphodiesterase substrates, or by using purified endoribonuclease of Ehrlich ascites cells. By all criteria, replacement of 2',5'-bond by a 3',5'-bond led to a substantial decrease in biological activity. Generally, replacement of just one 2',5'-phosphodiester bond with a 3',5'-linkage led to at least a one order of magnitude loss of activity. In accord with this trend, ppp5'A3'p5'A3'p5'A(3-5A) was greater than 10,000 less active than 2-5A in binding to the endonuclease or as an inhibitor of protein synthesis.     

Affinity labelling and characterization of the ppp(A2'p)nA-dependent endoribonuclease from different mammalian sources

The ppp(A2'p)nA-dependent endoribonucleases from a number of different mammalian sources have been investigated. The enzyme from reticulocyte lysates shows optimal activity of 50-150 mM KCl and requires the presence of Mg2+. Whilst the enzyme is inactivated after passage of reticulocyte lysates through Sephadex columns in the absence of ATP, it retains full activity provided ATP is included in the column buffer. The activity of the partially purified nuclease was unaffected by the addition of reticulocyte RNase inhibitor, which, in contrast, effectively inhibited other endogenous endonucleases. The ppp(A2'p)nA-dependent Rnase co-purified with a ppp(A2'p)nA-binding protein and with a protein which could be specifically covalently labelled with an oxidised radioactive analogue of ppp(A2'p)nA. This covalent labelling could be carried out either with the partially purified RNase or in crude extracts from rabbit reticulocytes, mouse Krebs and Ehrlich ascites tumour cells and human lymphoblastoid (Daudi) or HeLa cells. In each case the affinity labelled protein migrated to a position corresponding to a apparent molecular weight of about 85 000 on electrophoresis on dodecylsulphate/polyacrylamide gels. In all cases labelling could be prevented by the addition of an excess of unlabelled ppp(A2'p)nA but not, for example, by a similar excess of the biologically inactive dimer ppp(A2'p)'A. It is concluded that the RNase and ppp(A2'p)nA binding activities are likely to reside in the same molecule.     

The ppp(A2'p)nA and protein kinase systems in wild-type and interferon-resistant Daudi cells

Daudi cells, a human lymphoblastoid line, are exceptionally sensitive to the growth inhibitory effects of interferon, 1 unit/ml being sufficient to inhibit cell growth. In addition, interferon treatment of these cells severely inhibits the incorporation of exogenous thymidine into DNA and causes cells to accumulate in the G1(G0) at the expense of the S phase of the cell cycle. The possible involvement of ppp(A2'p)nA(n = 2 to less than or equal to 4) in these effects has been investigated. No (less than 1 nM) ppp(A2'p)nA or (A2'p)nA or alternative products of the ppp(A2'p)nA synthetase [e.g. NAD (2'pA)2] were detected in interferon-treated cells. In addition no evidence was obtained for the occurrence of ppp(A2'p)nA-mediated ribosomal RNA cleavage in these cells even after several days of treatment with relatively high doses of interferon. A line of Daudi cells which is resistant to all three of the above effects of interferon was selected. The wild type and resistant lines were compared with respect to the ppp(A2'p)nA and interferon and double-stranded RNA (dsRNA)-mediated protein kinase systems. The resistant line was not receptor-negative as it responded to interferon by the production of elevated levels of the ppp(A2'p)nA synthetase similar to those observed in extracts from wild-type cells. There was no detectable difference between the lines in the levels of the (2'-5')phosphodiesterase responsible for the degradation of ppp(A2'p)nA. There was, however, about a twofold increase in the ppp(A2'p)nA-dependent endoribonuclease activity in response to interferon with extracts from the wild-type but not the resistant cells. In addition, although the dsRNA-dependent protein kinase activity increased in both types of cell there was a striking reduction in the level of protein phosphorylation in general in response to interferon with material from the wild-type but not the resistant cells.     

Double-stranded RNA-stimulated enzyme activities isolated from human placental extracts

A (2′–5′)A_n synthetase activity was isolated from human placental extracts by affinity chromatography on poly(rI)·poly(rC)-agarose. The oligonucleotide (2′–5′)A_n was identified by (1) chromatography on PEI-cellulose and DEAE-cellulose, (2) inhibition of polypeptide synthesis in lysed rabbit reticulocytes (3) competition of the binding of pppA(pA)3,3′-[³²P]pCp to rabbit reticulocyte lysates, and (4) alkaline phosphatase digestion. The synthetase activity in most placental preparations is activated by natural or synthetic dsRNA. However, in a few placental synthetase preparations, dsRNA is only marginally stimulatory and only becomes effective by prior treatment of the enzyme preparations with the calcium-dependent micrococal nuclease. This suggeststhat there is an endogenous placental dsRNA contaminant in the enzyme preparations. In some synthetase preparations, a second dsRNA-stimulated product, tentatively identified as the nucleotide 5′-IMP, is also observed. Because the specific AMP deaminase inhibitor coformycin (10 μM) blocks the formation of IMP from ATP and causes a quantitative accumulation of AMP, and because the formation of IMp becomes independent of dsRNA when ADP or AMP is used in plase of ATP, the presence of a dsRNA-stimulated ATP phosphohydrolase (ATPase) activity in human placenta is suggested.     

Reactive column HPLC: rapid analysis on RPC-5 of oligoadenylates that differ at the 3'-terminus.

Oligoadenylates can be analyzed according to the type of 3′-terminus (A_nA, A_nAp, and A_nA > p, oligoadenylates that have at the 3′-terminus no phosphate, a 2′(3′)-monophosphate, and a 2′,3′-cyclic phosphate respectively) by hplc on RPC-5 support using a novel dual-column technique. The first column separates A_nAp plus A_nA > p from A_nA, and at the start of the second column a layer of bacterial alkaline phosphatase enzyme converts the A_nAp into A_nA. Hence this A_nA emerges separately from the original A_nA and from the A_nA > p. The technique can be used to analyze a three-component mixture for a single chain length or a mixture of A_nAp and A_nA > p of mixed chain lengths (n = 3 to 7). The presence of poly(U) does not interfere with the analysis.     

In Vitro Genetic Analysis of the RNA Binding Site of Vigilin, a Multi-KH-Domain Protein

The function(s) and RNA binding properties of vigilin, a ubiquitous protein with 14 KH domains, remain largely obscure. We recently showed that vigilin is the estrogen-inducible protein in polysome extracts which binds specifically to a segment of the 3′ untranslated region (UTR) of estrogen-stabilized vitellogenin mRNA. In order to identify consensus mRNA sequences and structures important in binding of vigilin to RNA, before vigilin was purified, we developed a modified in vitro genetic selection protocol. We subsequently validated our selection procedure, which employed crude polysome extracts, by testing natural and in vitro-selected RNAs with purified recombinant vigilin. Most of the selected up-binding mutants exhibited hypermutation of G residues leading to a largely unstructured, single-stranded region containing multiple conserved (A)_nCU and UC(A)_n motifs. All eight of the selected down-binding mutants contained a mutation in the sequence (A)_nCU. Deletion analysis indicated that approximately 75 nucleotides are required for maximal binding. Using this information, we predicted and subsequently identified a strong vigilin binding site near the 3′ end of human dystrophin mRNA. RNA sequences from the 3′ UTRs of transferrin receptor and estrogen receptor, which lack strong homology to the selected sequences, did not bind vigilin. These studies describe an aproach to identifying long RNA binding sites and describe sequence and structural requirements for interaction of vigilin with RNAs.     

Characterization and Localization of Adenosine A2 Receptors in Bovine Rod Outer Segments

Abstract: Previous work from this laboratory has shown that retinal adenosine A₂ binding sites are localized over outer and inner segments of photoreceptors in rabbit and mouse retinal sections. In the present study, adenosine receptor binding has been characterized and localized in membranes from bovine rod outer segments (ROS). Saturation studies with varying concentrations (10–150 nM) of 5′-(N-[2,8-³H]ethylcarboxamido)adenosine ([³H]NECA) and 100 μg of ROS membrane protein show a single site with a K_D of 103 nM and a B_max of 1.3 pM/mg of protein. Cold Scatchards, which used nonradiolabeled NECA (concentrations ranging from 10 nM to 250 nM) in competition with a fixed amount of [³H]NECA (30 nM), demonstrated the presence of a low-affinity site (K_D, 50 μM) in addition to the high-affinity site. To confirm the presence of A_2abinding sites, saturation analyses with 2-p-(2-[³H]-carboxyethyl)phenylamino-5′-N-ethylcarboxamido adenosine (0–80 nM) also revealed a single population of high-affinity A_2a receptors (K_D, 9.4 nM). The binding sites labeled by [³H]NECA appear to be A₂ receptor sites because binding was displaced by increasing concentrations of 5′-(N-methylcarboxamido)adenosine and 2-chloroadenosine. ROS were fractionated into plasma and disk membranes for localization studies. Receptor binding assays, used to determine specific binding, showed that the greatest concentration of A₂ receptors was on the plasma membranes. Therefore, adenosine A₂ receptors are in a position to respond to changes in the concentration of extracellular adenosine, which may exhibit a circadian rhythm.     

Multiple protein kinase activities in the dimorphic fungus Mucor rouxii. Comparison with a cyclic adenosine 3',5'-monophosphate binding protein.

Protein kinase and cyclic adenosine 3′,5′-monophosphate (cAMP) binding activities have been detected in cell extracts of the dimorphic fungus Mucor rouxii. The subcellular distribution of both activities indicates that most of the binding protein is in the high-speed supernatant (S₁₀₀), while about 70% of the total protein kinase activity remains in particulate fractions. S₁₀₀ preparations have been analyzed by diethylaminoethyl cellulose column chromatography. Binding activity can be resolved in two peaks (A and B) and protein kinase in three peaks (I, II, and III). Peaks I and II are casein dependent and insensitive to cAMP. Peak III utilizes histone as substrate and is activated (two- to fourfold) by cAMP. Theophylline strongly inhibits cAMP binding activity and mimics the effect of cAMP on cAMP-dependent protein kinase. The possible relationship between cAMP binding activity and cAMP-dependent protein kinase is suggested.     

Effect of 5′-terminal structure and base composition on polyribonucleotide binding to ribosomes

Ribopolymers of variable base composition and 5′-terminal structure were synthesized with polynucleotide phosphorylase. Under primer-dependent conditions, m⁷GpppGmpC (m⁷G-cap)², its alkali-treated m⁷G ring-opened derivative, GpppGpC and ppGpC but not m⁷GpppGmpCp, m⁷GpppGm or GpppG were incorporated as 5′-termini. The ribopolymers were compared with reovirus mRNA, which contains m⁷G-cap, for their ability to form initiation complexes with wheat germ 40 S ribosomal subunits and 80 S ribosomes. The presence of 5′-terminal m⁷G was required for stable complex formation by some ribopolymers while for others binding was increased by two- to fourfold. The final level of binding observed was similar to that with reovirus mRNA. In addition to 5′-terminal m⁷G, the base composition of the ribopolymers markedly influenced binding. Some ribopolymers including m⁷G-cap (A)_n did not bind significantly; m⁷G-cap (U)_n formed 40 S complexes while m⁷G-cap (A,U)_n bound to 80 S ribosomes. The ribopolymer m⁷G-cap (A₂,U₂,G)_n directed protein synthesis as measured by amino acid incorporation into polypeptides, methionine tRNA association with 40 S complexes, and puromycin reactivity of 80 S-associated methionine and, like reovirus mRNA, its binding to ribosomes was inhibited by 7-methylguanosine 5′-monophosphate.     

Effect of pyrimidine and ribose modifications on the antiviral activity of synthetic polynucleotides

Homo- and copolynucleotides derived from 3-methyluridine, 5,6-dihydrouridine and 2′-azido-2′-deoxyuridine (dUz) were prepared and evaluated for antiviral activity either as single strands or as double strands when complexed with complementary homopolynucleotides. The synthetic materials were not as active as (A)_n · (U)_n or (I)_n · (C)_n in inducing the interferon system. The antiviral activity of (A)_n · (dUz)_n was not affected by treatment with high concentrations of pancreatic RNase A, whereas this activity was totally abolished when (A)_n · (dUz)_n was digested with human serum.     

Characterization of Neurospora crassa polyadenylated messenger ribonucleic acid: structure of the 5'-terminus.

Polyadenylated (poly(A)⁺) mRNA from Neurospora crassa was isolated by affinity chromatography on poly(U) Sepharose and its structure was examined. Two 5′-terminal ·cap’ structures, m⁷G(5′)ppp(5′)Ap and m⁷G(5′)ppp(5′)Gp, occurring in a relative distribution of 75 and 25% were found. No evidence was obtained for 2′-O-methylation in a nucleotide adjacent to the 5′-terminal cap.