Ability of tryptophan tRNA to hybridize with 35S RNA of avian myeloblastosis virus and to prime reverse transcription in vitro

Mechanistic differences between nucleic acid chaperone activities of the Gag proteins of Rous sarcoma virus and human immunodeficiency virus type 1 are attributed to the MA domain

Host cell tRNAs are recruited for use as primers to initiate reverse transcription in retroviruses. Human immunodeficiency virus type 1 (HIV-1) uses tRNA(Lys3) as the replication primer, whereas Rous sarcoma virus (RSV) uses tRNA(Trp). The nucleic acid (NA) chaperone function of the nucleocapsid (NC) domain of HIV-1 Gag is responsible for annealing tRNA(Lys3) to the genomic RNA (gRNA) primer binding site (PBS). Compared to HIV-1, little is known about the chaperone activity of RSV Gag. In this work, using purified RSV Gag containing an N-terminal His tag and a deletion of the majority of the protease domain (H6.Gag.3h), gel shift assays were used to monitor the annealing of tRNA(Trp) to a PBS-containing RSV RNA. Here, we show that similar to HIV-1 Gag lacking the p6 domain (GagΔp6), RSV H6.Gag.3h is a more efficient chaperone on a molar basis than NC; however, in contrast to the HIV-1 system, both RSV H6.Gag.3h and NC have comparable annealing rates at protein saturation. The NC domain of RSV H6.Gag.3h is required for annealing, whereas deletion of the matrix (MA) domain, which stimulates the rate of HIV-1 GagΔp6 annealing, has little effect on RSV H6.Gag.3h chaperone function. Competition assays confirmed that RSV MA binds inositol phosphates (IPs), but in contrast to HIV-1 GagΔp6, IPs do not stimulate RSV H6.Gag.3h chaperone activity unless the MA domain is replaced with HIV-1 MA. We conclude that differences in the MA domains are primarily responsible for mechanistic differences in RSV and HIV-1 Gag NA chaperone function. Importance: Mounting evidence suggests that the Gag polyprotein is responsible for annealing primer tRNAs to the PBS to initiate reverse transcription in retroviruses, but only HIV-1 Gag chaperone activity has been demonstrated in vitro. Understanding RSV Gag's NA chaperone function will allow us to determine whether there is a common mechanism among retroviruses. This report shows for the first time that full-length RSV Gag lacking the protease domain is a highly efficient NA chaperone in vitro, and NC is required for this activity. In contrast to results obtained for HIV-1 Gag, due to the weak nucleic acid binding affinity of the RSV MA domain, inositol phosphates do not regulate RSV Gag-facilitated tRNA annealing despite the fact that they bind to MA. These studies provide insight into the viral regulation of tRNA primer annealing, which is a potential target for antiretroviral therapy.

Inability of human immunodeficiency virus type 1 produced in murine cells to selectively incorporate primer formula

Attempts to use the mouse as a model system for studying AIDS are stymied by the multiple blocks to human immunodeficiency virus type 1 (HIV-1) replication that exist in mouse cells at the levels of viral entry, transcription, and Gag assembly and processing. In this report, we describe an additional block in the selective packaging of tRNA(3Lys) into HIV-1 produced in murine cells. HIV-1 and murine leukemia virus (MuLV) use tRNA(3Lys) and tRNA(Pro), respectively, as primers for reverse transcription. Selective packaging of tRNA(3Lys) into HIV-1 produced in human cells is much stronger than that for tRNA(Pro) incorporation into MuLV produced in murine cells, and different packaging mechanisms are used. Thus, both lysyl-tRNA synthetase and GagPol are required for tRNA(3Lys) packaging into HIV-1, but neither prolyl-tRNA synthetase nor GagPol is required for tRNA(Pro) packaging into MuLV. In this report, we show that when HIV-1 is produced in murine cells, the virus switches from an HIV-1-like incorporation of tRNA(3Lys) to an MuLV-like packaging of tRNA(Pro). The primer binding site in viral RNA remains complementary to tRNA(3Lys), resulting in a significant decrease in reverse transcription and infectivity. Reduction in tRNA(3Lys) incorporation occurs even though both murine lysyl-tRNA synthetase and HIV-1 GagPol are packaged into the HIV-1 produced in murine cells. Nevertheless, the murine cell is able to support the select incorporation of tRNA(3Lys) into another retrovirus that uses tRNA(3Lys) as a primer, the mouse mammary tumor virus.

Defective replication in human immunodeficiency virus type 1 when non-primers are used for reverse transcription

tRNA(3Lys), the primer for reverse transcriptase in human immunodeficiency virus type 1 (HIV-1), anneals to the primer binding site (PBS) in HIV-1 RNA. It has been shown that altering the PBS and U5 regions upstream of the PBS in HIV-1 so as to be complementary to sequences in tRNA(Met) or tRNA(His) will allow these tRNA species to be stably used as primers for reverse transcription. We have examined the replication of these mutant viruses in Sup-T1 cells. When Sup-T1 cells are infected by cocultivation with HIV-1-transfected 293T cells, viruses using tRNA(His) or tRNA(Met) are produced at rates that are approximately 1/10 or 1/100, respectively, of rates for wild-type virions that use tRNA(3Lys). When Sup-T1 cells are directly infected with equal amounts of these different viruses isolated from the culture supernatant of transfected 293T cells, virions using tRNA(Met) are produced at 1/100 the rate of wild-type viruses, and production of virions using tRNA(His) is not detected. Both wild-type and mutant virions selectively package tRNA(Lys) only, and examination of the ability of total viral RNA to prime reverse transcription in vitro indicates a >80% reduction in the annealing of tRNA(His) or tRNA(Met) to the mutant viral RNAs. PCR analysis of which of the three primer tRNAs is used indicates that only tRNA(3Lys) is detected as primer in wild-type virions and only tRNA(His) is detected as primer in virions containing a PBS complementary to tRNA(His), while the mutant viruses containing a PBS complementary to tRNA(Met) use both tRNA(Met) and tRNA(1,2Lys) as primer tRNAs.

Effect of altering the tRNA(Lys)(3) concentration in human immunodeficiency virus type 1 upon its annealing to viral RNA, GagPol incorporation, and viral infectivity

Human immunodeficiency virus type 1 (HIV-1) uses tRNA(Lys)(3) as a primer for reverse transcription and, during viral assembly, this tRNA is selectively packaged into the virus along with the other major tRNA(Lys), tRNA(Lys)(3). Increasing the cytoplasmic concentration of tRNA(Lys)(3) through transfection of cells with a plasmid containing both HIV-1 proviral DNA and a tRNA(Lys)(3) gene results in a greater incorporation of tRNA(Lys)(3) into virions, which is accompanied by increased annealing of tRNA(Lys)(3) to the viral genome and increased infectivity of the viral population. Increased viral tRNA(Lys)(3) is accompanied by decreased viral tRNA(Lys)(3), with the total tRNA(Lys)/virion and the GagPol/Gag ratios remaining unchanged. Viral tRNA(Lys) can be doubled, with increases in both tRNA(Lys)(3) and tRNA(Lys)(1,2) concentrations, by overexpressing lysyl tRNA synthetase. This also results in increased tRNA(Lys)(3) annealing to the viral RNA and increased viral infectivity but, again, no change in the GagPol/Gag ratio was observed. This result indicates that GagPol, whose interaction is required during packaging, is not a limiting factor during tRNA(Lys) incorporation into HIV-1, whereas LysRS is.

Incorporation of excess wild-type and mutant tRNA(3Lys) into human immunodeficiency virus type 1

Human immunodeficiency virus (HIV) particles produced in COS-7 cells transfected with HIV type 1 (HIV-1) proviral DNA contain 8 molecules of tRNA(3Lys) per 2 molecules of genomic RNA and 12 molecules of tRNA1,2Lys per 2 molecules of genomic RNA. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a human tRNA3Lys gene, there is a large increase in the amount of cytoplasmic tRNA3Lys per microgram of total cellular RNA, and the tRNA3Lys content in the virus increases from 8 to 17 molecules per 2 molecules of genomic RNA. However, the total number of tRNALys molecules per 2 molecules of genomic RNA remains constant at 20; i.e., the viral tRNA1,2Lys content decreases from 12 to 3 molecules per 2 molecules of genomic RNA. All detectable tRNA3Lys is aminoacylated in the cytoplasm of infected cells and deacylated in the virus. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a mutant amber suppressor tRNA3Lys gene (in which the anticodon is changed from TTT to CTA), there is also a large increase in the relative concentration of cytoplasmic tRNA3Lys, and the tRNA3Lys content in the virus increases from 8 to 15 molecules per 2 molecules of genomic RNA, with a decrease in viral tRNA1,2Lys from 12 to 5 molecules per 2 molecules of genomic RNA. Thus, the total number of molecules of tRNALys in the virion remains at 20. The alteration of the anticodon has little effect on the viral packaging of this mutant tRNA in spite of the fact that it no longer contains the modified base mcm 5s2U at position 34, and its ability to be aminoacylated is significantly impaired compared with that of wild-type tRNA3Lys. Viral particles which have incorporated either excess wild-type tRNA3Lys or mutant suppressor tRNA3Lys show no differences in viral infectivity compared with wild-type HIV-1.

Role of Pr160gag-pol in mediating the selective incorporation of tRNA(Lys) into human immunodeficiency virus type 1 particles

COS-7 cells transfected with human immunodeficiency virus type 1 (HIV-1) proviral DNA produce virus in which three tRNA species are most abundant in the viral tRNA population. These tRNAs have been identified through RNA sequencing techniques as tRNA(3Lys) the primer tRNA in HIV-1, and members of the tRNA(1,2Lys) isoacceptor family. These RNAs represent 60% of the low-molecular-weight RNA isolated from virus particles, while they represent only 6% of the low-molecular-weight RNA isolated from the COS cell cytoplasm. Thus, tRNA(Lys) is selectively incorporated into HIV-1 particles. We have measured the ratio of tRNA(3Lys) molecules to copies of genomic RNA in viral RNA samples and have calculated that HIV-1 contains approximately eight molecules of tRNA(3Lys) per two copies of genomic RNA. We have also obtained evidence that the Pr160gag-pol precursor is involved in primer tRNA(3Lys) incorporation into virus. First, selective tRNA(Lys) incorporation and wild-type amounts of tRNA(3Lys) were maintained in a protease-negative virus unable to process Pr55gag and Pr160gag-pol precursors, indicating that precursor processing was not required for primer tRNA incorporation. Second, viral particles containing only unprocessed Pr55gag protein did not selectively incorporate tRNA(Lys), while virions containing both unprocessed Pr55gag and Pr160gag-pol proteins demonstrated select tRNA(3Lys) packaging. Third, studies with a proviral mutant containing a deletion of most of the reverse transcriptase sequences and approximately one-third of the integrase sequence in the Pr160gag-pol precursor resulted in the loss of selective tRNA incorporation and an eightfold decrease in the amount of tRNA(3Lys) per two copies of genomic RNA. We have also confirmed herein finding of a previous study which indicated that the primer binding site is not required for the selective incorporation of tRNA(Lys).

3' truncated tRNAArg is essential for in vitro specific cleavage of partially synthesized mouse 18S rRNA

In vitro synthesized 5' portions of mouse 18S rRNA are cleaved efficiently at a specific site in partially purified extracts of mouse FM3A cells and several mouse tissues. This activity is composed of both protein and RNA, and can be reconstituted with the protein component in micrococcal nuclease-treated extracts and the RNA component in phenol-treated ones. The RNA component of about 65 nucleotides with the complementing activity was purified from total RNA in the partially purified FM3A cell extracts by polyacrylamide gel electrophoreses. Chemical sequencing of this RNA elucidated that it is tRNAArg lacking nine nucleotides from its 3' terminus. Ribonuclease H treatment directed by deoxyoligonucleotides complementary to tRNAArg completely abolishes the cleavage activity, supporting the above conclusion.

Identification of tRNAs incorporated into wild-type and mutant human immunodeficiency virus type 1

We have identified the tRNAs which are incorporated into both wild-type human immunodeficiency virus type 1 strain IIIB (HIV-1IIIB) produced in COS-7 cells transfected with HIV-1 proviral DNA and mutant, noninfectious HIV-1Lai particles produced in a genetically engineered Vero cell line. The mutant proviral DNA contains nucleotides 678 to 8944; i.e., both long terminal repeats and the primer binding site are absent. As analyzed by two-dimensional polyacrylamide gel electrophoresis, both mutant and wild-type HIV-1 contain four major-abundance tRNA species, which include tRNA(1,2Lys), tRNA(3Lys) (the putative primer for HIV-1 reverse transcriptase) and tRNA(Ile). Identification was accomplished by comparing the electrophoretic mobilities and RNase T1 digests with those of tRNA(3Lys) and tRNA(1,2Lys) purified from human placenta and comparing the partial nucleotide sequence at the 3' end of each viral tRNA species with published tRNA sequences. Thus, the absence of the primer binding site in the mutant virus does not affect tRNA(Lys) incorporation into HIV-1. However, only the wild-type virus contains tRNA(3Lys) tightly associated with the viral RNA genome. The identification of the tightly associated tRNA as tRNA(3Lys) is based upon an electrophoretic mobility identical to that of tRNA(3Lys) and the ability of this RNA to hybridize with a tRNA(3Lys)-specific DNA probe. In addition to the four wild-type tRNA species, the mutant HIV-1-like particle contains two tRNA(His) species and three tRNA-sized species that we have been unable to identify. Their absence in wild-type virus makes it unlikely that they are required for viral infectivity.

Characterization of the spermidine-dependent, sequence-specific endoribonuclease that requires transfer RNA for its activity

The spermidine-dependent, sequence-specific endoribonuclease (RNase 65) in mouse FM3A cells consists of protein and transfer RNA lacking its 3' terminus. In vitro properties of this enzyme were characterized using partially purified enzyme. The RNase 65 activity requires spermidine, which is not replaceable with spermine or Mg++. The enzyme cleaves an RNA substrate on the 3' side of the phosphodiester bond. The cleavage reaction has a temperature optimum around 50 degrees C and a pH optimum around 7.0. The optimum KCl concentration for the activity is around 10 mM. Relative cleavage efficiency of two differently folded RNA substrates with the common target sequence was analyzed at 37 degrees C and 50 degrees C. The results of this analysis suggest that unfolding of the target sequence is critical for recognition by RNase 65. Furthermore, in experiments using several point-mutated RNA substrates designed to form basically the same secondary structure as the wild type, one to three nucleotide substitutions in the target sequence all reduced cleavage efficiency. The RNase 65 activity is found only in cytosolic extracts, not in nuclear ones. Gel filtration analysis suggests that the native size of the endoribonuclease is approximately 150 kDa.

Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity

Chemical synthesis is described of a 77-nucleotide-long RNA molecule that has the sequence of an Escherichia coli Ado-47-containing tRNA(fMet) species in which the modified nucleosides have been substituted by their unmodified parent nucleosides. The sequence was assembled on a solid-phase, controlled-pore glass support in a stepwise manner with an automated DNA synthesizer. The ribonucleotide building blocks used were fully protected 5'-monomethoxytrityl-2'-silyl-3'-N,N-diisopropylaminophosphoram idites. p-Nitro-phenylethyl groups were used to protect the O6 of guanine residues. The fully deprotected tRNA analogue was characterized by polyacrylamide gel electrophoresis (sizing), terminal nucleotide analysis, sequencing, and total enzyme degradation, all of which indicated that the sequence was correct and contained only 3-5 linkages. The 77-mer was then assayed for amino acid acceptor activity by using E. coli methionyl-tRNA synthetase. The results indicated that the synthetic product, lacking modified bases, is a substrate for the enzyme and has an amino acid acceptance 11% of that of the major native species, tRNA(fMet) containing 7-methylguanosine at position 47.

Effect of zinc ions on tRNA structure. I. Reversed-phase chromatography

The effect of zinc on the chromatographic behavior of four tRNAs was examined on RPC-5 and Aminex A-28 columns. RPC-5 contains dichlorodifluoroethylene beads coated with a quaternary ammonium compound where the substituents are: R1 = methyl, and R2-4 = C8-10 hydrocarbons. Aminex A-28 contains quaternary ammonium covalently attached to styrene-divinylbenzene copolymer lattice and R1-3 are methyl groups. The retentions of tRNAVal, tRNAIle, and tRNALys of E. coli and yeast tRNAPhe on RPC-5 were all markedly increased by Zn2+ ions. In contrast, no increased retention due to Zn2+ was observed when tRNAPhe was chromatographed on Aminex A-28. A model for chromatography on RPC-5 is developed which treats the elution behavior of tRNAs from this matrix as the sum of ion-exchange and hydrophobic interactions. The chromatography of tRNA in the presence and absence of Zn2+ is interpreted in terms of this model and the effects of sodium chloride concentration, temperature, and pH were explored as the experimental variables. These experiments suggest that in the absence of Zn2+ tRNA does not interact appreciably with the hydrophobic surface of the column. The addition of Zn2+ has three effects on chromatography: a decrease in the number of anionic sites on the tRNA which interact with the positively charged ammonium ion, an increase in affinity of the tRNA for these ionic sites, and an increase in affinity of tRNA for hydrophobic sites on the column. All three effects were fully reversed by the addition of Cd2+ (10 mM) or Mg2+ (35 mM), but only partially reversed at lower concentrations of these competing ions. These results show that chromatography on RCP-5 can be a sensitive physical chemical technique for examination of the structure of tRNA, and probably for other nucleic acids as well.

Human glutamate tRNA forms stable hybrids in vitro with 28S ribosomal RNA

A human glutamate tRNA has been shown to form stable hybrids with 28S ribosomal RNA. This tRNA was purified from HeLa cell cytoplasmic RNA by RNA-RNA solution hybridization followed by the isolation of tRNA-28S rRNA complexes by hybridization-selection with ribosomal DNA or by recovery of the 28S peak from formamide-sucrose gradients. The single hybridizing tRNA species was identified as tRNAGluCUC by sequencing: pU-C-C-C-U-G-G-U-G-m2G-U-C-phi-A-G-U-G-G-D-phi-A-G-G-A-U-U- C-G-G-C-G-C-U-C-U-C-A-C-C-G-C-G-G-C-m5C-m5C-G-G-G-Tm-phi-C-G-A- U-U-C-C-C-G-G-U-C-A-G-G-G-A-A-C-C-AOH. Computer analysis located a nucleotide sequence near the middle of human 28S rRNA which is complementary to 15-26 nucleotides between residues 20 and 50 of this tRNA. An interaction between this tRNA and 28S rRNA suggests that tRNAGluCUC may have functions in the cell in addition to translation.

Nucleotide sequence analysis of endogenous murine leukemia virus-related proviral clones reveals primer-binding sites for glutamine tRNA

Nucleotide sequences of the region that corresponds to the site of tRNA primer binding for a functional retrovirus were determined in five murine leukemia virus-related sequence clones from mouse chromosomal DNA, which contain a unique 170 to 200-base-pair additional internal segment in the long terminal repeats. The 3'-terminal 18-nucleotide sequence of a major glutamine tRNA isoacceptor was found to match well with the putative primer binding site: 18 of 18 in three clones, 17 of 18 in one clone, and 16 of 18 in one clone. This implies that most of these endogenous proviral sequences of the mouse genome, if replicated as retroviruses, will be different from ecotropic murine leukemia viruses and most mammalian type C retroviruses in using glutamine tRNA, rather than proline tRNA, as a primer.

Structural features required for the binding of tRNATrp to avian myeloblastosis virus reverse transcriptase

The basis of the specific binding of tRNATrp by avian myeloblastosis virus reverse transcriptase was studied by chemical and enzymatic modification of the RNA. Binding does not depend on recognition of the tryptophan anticodon since molecules cleaved in the anticodon are stably bound by the enzyme. Modification of pseudouridine residues in the tRNA destroys binding to reverse transcriptase. These results are consistent with a model in which reverse transcriptase-tRNATrp interaction occurs not at the anticodon, but at regions in the tRNA which contain or are stabilized by pseudouridine residues.

Effect of polymerase mutations on packaging of primer tRNAPro during murine leukemia virus assembly

The role of reverse transcriptase in selective encapsidation of the murine leukemia virus (MuLV) tRNA primer, tRNAPro, was investigated by examining the tRNA composition of several nonconditional pol mutants. One mutant, clone 23, which contains an altered polymerase about 40% smaller than the wild-type enzyme (B. I. Gerwin et al., J. Virol. 31:741-751, 1979) had a typical viral tRNA pattern, including normal levels of tRNAPro in free and 70S-associated 4S RNA. Another class of mutants, produced by Moloney murine leukemia virus-infected cell clone M13 and subclone M13/1, does not contain any detectable polymerase protein (A. Shields et al., Cell 14:601-609, 1978) and was found to have reduced amounts of tRNAPro in free 4S RNA. However, the level of tRNAPro associated with the genome was normal in the mutant virions. These results suggest that the reverse transcriptase protein is involved in the initial selection of tRNA primer during virus assembly, but not in the subsequent association of this tRNA with genomic RNA.

Reverse transcriptase as the major determinant for selective packaging of tRNA's into Avian sarcoma virus particles

Mutants of avian sarcoma virus which lack a functional DNA polymerase were found to be nonselective in the incorporation of host cell tRNA's into virus particles. In contrast, mutants which possess a functional DNA polymerase but lack the viral genome RNA contained a specific subset of the host cell tRNA population, indistinguishable from that of the wild-type virus. Thus the reverse transcriptase, and not the viral RNA, is probably the major factor determining which tRNA's are incorporated into avian sarcoma virus particles. Supporting evidence was obtained in an in vitro binding assay between purified reverse transcriptase and unfractionated cellular tRNA's. However, the subset of tRNA's which associated with the genome in the 70S complex was determined primarily by the viral RNA. In the absence of DNA polymerase, the 70S RNA complex in mature virus particles contained the normal complement of associated tRNA's with the exception of tRNATrp, the primer for RNA-directed DNA synthesis.

Partial purification and characterization of a ribonucleic acid N2-guanine methyltransferase associated with avian myeloblastosis virus

A nucleic acid methylase, N2-guanine ribonucleic acid (RNA) methyltransferase, which is associated with type C RNA tumor viruses, has been purified from avian myeloblastosis virions by gel filtration on Sephadex G-200, followed by chromatography on hydroxylapatite. The molecular weight estimated by gel filtration is 220 000, and the methylase activity has a pH optimum of 7.6--7.9. Magnesium and ammonium ions both stimulate activity 1.5-fold at 9.5 mM and 0.36 M, respectively, but apparently neither is essential for activity. Both daunomycin and adriamycin, antineoplastic drugs, also increase activity 1.5-fold at 1 mM. The enzyme was purified 120-fold from the virions and the activity is partially stabilized by dithiothretiol, but large losses were sustained during 24-h dialysis. The purified enzyme retains 75% of its activity on storage at -25 degrees C for 2 months in buffer containing 50% glycerol. Escherichia coli tRNAPhe and tRNAVal are preferred substrates with methylation occurring at position 10 of E. coli tRNAPhe.

Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts

The lysine isoacceptor tRNAs differ in two aspects from the majority of the other mammalian tRNA species: they do not contain ribosylthymine (T) in loop IV, and a 'new' lysine tRNA, which is practically absent in non-dividing tissue, appears at elevated levels in proliferating cells. We have therefore purified the three major isoaccepting lysine tRNAs from rabbit liver and the 'new' lysine tRNA isolated from SV40-transformed mouse fibroblasts, and determined their nucleotide sequences. Our basic findings are as follows. a) The three major lysine tRNAs (species 1, 2 and 3) from rabbit liver contain 2'-O-methylribosylthymine (Tm) in place of T. tRNA1Lys and tRNA2Lys differ only by a single base pair in the middle of the anticodon stem; the anticodon sequence C-U-U is followed by N-threonyl-adenosine (t6A). TRNA3Lys has the anticodon S-U-U and contains two highly modified thionucleosides, S (shown to be 2-thio-5-carboxymethyl-uridine methyl ester) and a further modified derivative of t6 A (2-methyl-thio-N6-threonyl-adenosine) on the 3' side of the anticodon. tRNA3Lys differs in 14 and 16 positions, respectively, from the other two isoacceptors. b) Protein synthesis in vitro, using synthetic polynucleotides of defined sequence, showed that tRNA2Lys with anticodon C-U-U recognized A-A-G only, whereas tRNA3Lys, which contains thio-nucleotides in and next to the anticodon, decodes both lysine codons A-A-G and A-A-A, but with a preference for A-A-A. In a globin-mRNA-translating cell-free system from ascites cells, both lysine tRNAs donated lysine into globin. The rate and extent of lysine incorporation, however, was higher with tRNA2Lys than with tRNA3Lys, in agreement with the fact that alpha-globin and beta-globin mRNAs contain more A-A-G than A-A-A- codons for lysine. c) A comparison of the nucleotide sequences of lysine tRNA species 1, 2 and 3 from rabbit liver, with that of the 'new' tRNA4Lys from transformed and rapidly dividing cells showed that this tRNA is not the product of a new gene or group of genes, but is an undermodified tRNA derived exclusively from tRNA2Lys. Of the two dihydrouridines present in tRNA2Lys, one is found as U in tRNA4Lys; the purine next to the anticodon is as yet unidentified but is known not be t6 A. In addition we have found U, T and psi besides Tm as the first nucleoside in loop IV.

Initiation of DNA synthesis by the avian retrovirus reverse transcriptase in vitro: nature and location of the oligodeoxycytidylic acid primer binding site

We have investigated the use of oligodeoxycytidylic acid [oligo(dC)] as a primer for the initiation of DNA synthesis by the avian retrovirus reverse transcriptase in vitro, employing the viral RNA genome as template. The addition of oligo(dC)(12-18) to viral 35S RNA results in a stimulation of DNA synthesis by the viral RNA-directed DNA polymerase comparable to that observed when oligo(dT) is employed as a primer. Under similar conditions neither oligo(dA)(12-18) nor oligo(dG)(12-18) was active as primer for transcription of the avian retrovirus genome. Several different approaches have been employed to localize the oligo(dC)(12-18) binding site on the viral genome, including isolation of poly(A)-containing fragments, competition hybridization, and RNase H hydrolysis. These analyses indicate that oligo(dC)(12-18) binds to a site approximately 2,000 to 3,000 nucleotides from the 3' terminus of the genome of transforming strains of avian sarcoma viruses and approximately 700 to 1,000 nucleotides from the 3' terminus of nontransforming avian retroviruses. Therefore, the major site of initiation of DNA synthesis by oligo(dC)(12-18) appears to be in the vicinity of the 3' end of the env gene and the 5' end of the src gene, although the presence of minor initiation sites located elsewhere on the viral genome cannot be excluded by these data. Characterization of oligonucleotides after pancreatic RNase hydrolysis and poly(C)-Sepharose chromatography of viral RNA directly demonstrates the presence of oligoguanylic acid residues in the avian sarcoma virus genome. DNA sequences transcribed from the oligo(dC) primer appear to be conserved in all of the avian leukosis-sarcoma viruses tested. The use of oligo(dC) as a tool for the production of specific complementary DNA probes is discussed.

Selective packaging of host tRNA's by murine leukemia virus particles does not require genomic RNA

The 4S RNA contained in RNA tumor virus particles consists of a selected population of host tRNA's. However, the mechanism by which virions select host tRNA's has not been elucidated. We have considered a model which specifies that 35S genomic RNA determines which tRNA's are to be encapsidated as well as the relative amounts of these tRNA's within the virion. The model was tested by comparing the free 4S RNA composition of normal murine leukemia virus (MuLV) particles and noninfectious virions from actinomycin D (ActD)-treated cells, which are deficient in genomic RNA (ActD virions). Viral 4S RNA was analyzed by two-dimensional polyacrylamide gel electrophoresis. Surprisingly, the patterns obtained for control and ActD 4S RNA were identical to each other and were clearly distinct from the cell 4S RNA pattern. The viral patterns had three prominent areas of radioactivity. One of the spots was identified on the basis of its oligonucleotide fingerprint as tRNA (Pro), the primer for MuLV RNA-directed DNA synthesis. These results were obtained with two different MuLV strains, AKR and Moloney, each grown in SC-1 cells. The demonstration that ActD virions contain primer tRNA and in general exhibit the characteristic MuLV tRNA pattern rather than the complete representation of cell 4S RNA leads to the conclusion that genomic RNA is not the major determinant in selective packaging of host tRNA's. A possible role for one or more viral proteins, including reverse transcriptase, is suggested.

Inhibition of reverse transcription of 70S and 35S avian myeloblastosis RNAs by nonprimer tRNA's

We studied the kinetics of the reverse transcription of 70S and 35S RNA of avian myeloblastosis virus in the presence and absence of various tRNA's. All tRNA's inhibited synthesis. tRNA's from Escherichia coli and yeast exhibited a noncompetitive type of inhibition, i.e., they bound reversibly and randomly and did not alter the affinity of the viral RNA for the polymerase. Nonprimer tRNA's obtained from 70S RNA molecules produced a complex pattern of inhibition. The results show that the nonprimer tRNA's which bound to the reverse transcriptase decreased the affinity of the viral RNA for the enzyme. The maximum rate of synthesis with 70S RNA as the template was less than that with 35S RNA, presumably because the former contains nonprimer tRNA's which can interact with the polymerase.

Alterations in lysine transfer RNA during erythroid differentiation of the Friend cell

The proportion of lysine tRNA represented by the isoacceptor species lysine tRNA4 has previously been shown to be largest in cells with the greatest ability to proliferate. Using reverse phase chromatography (RPC-5), we have analyzed the changes in the relative quantities of lysine tRNA species which occur in different cellular states of the Friend cell, a transformed murine cell infected with Friend erythroleukemia virus complex. This cell undergoes erythroid differentiation when exposed to various chemicals. Lysine tRNA4 comprises 32% of the total lysine tRNA in rapidly dividing, uninduced Friend cells, but only 16% of the total lysine tRNA in uninducase. Friend cells undergoing erythroid differentiation divide more slowly than uninduced cells, and finally cease proliferation, but lysine tRNA4 becomes the major lysine tRNA species (greater than 50%). This does not appear to reflect erythroid properties of the cell, since the lysine tRNA of the mouse reticulocyte contains very little lysine tRNA4. The non-dividing erythroid Friend cell, therefore, represents an exception to the finding that non-dividing cells usually have little or no lysine tRNA4 present.

Persistent infection of primary human cell cultures with rubella variant carrying DNA Polymerase activity

Infection of primary human cells with a rubella variant carrying DNA polymerase activity resulted in persistent infection; infection with wild type virus caused death of the infected cells and a cytopathic effect.

Isolation and characterization of a new rubella variang with DNA polymerase activity

A rubella variant (HPV-RV) was isolated from high passage rubella virus preparations propagated at 37 degrees C in baby hamster kidney BHK21/WI-2 cells. HPV-RV formed clear plaques in HeLa cells and primary cells of the Rhesus monkey kidney although wild type rubella virus did not produce plaques in these cells. Cells persistently infected with rubella virus were insensitive to infection by HPV-RV at both 34 degrees and 39.5 degrees C. HPV-RV agglutinated one day old chick, human group O and sheep erythrocytes. This hemagglutinating activity was inhibited by anti-BHK latent virus serum but not by anti-rubella virus serum. The plaque forming ability of HPV-RV was neutralized by anti-BHK latent virus serum although the same antiserum did not affect the plaque forming ability of wild type rubella virus. Furthermore, HPV-RV was found to have the complement fixation antigen of rubella virus and DNA polymerase activity. From these findings, it is concluded that HPV-RV is a hybrid between rubella virus and a latent virus of BHK21/WI-2 cells.

Reverse transcriptase of RNA tumor viruses. V. In vitro proteolysis of reverse transcriptase from avian myeloblastosis virus and isolation of a polypeptide manifesting only RNase H activity

Purified avian myeloblastosis virus reverse transcriptase contains two subunits that are structurally related. The large subunit, beta (molecular weight, 95,000), was converted in vitro by chymotrypsin into a polypeptide of molecular weight 63,000. This polypeptide was indistinguishable from the small subunit, alpha (molecular weight, 65,000), in its chromatographic behavior on the phosphocellulose column and its tryptic peptide composition. During this proteolytic conversion, a polypeptide of molecular weight 32,000 (fragment B) was obtained. It was composed of tryptic peptides unique to beta and appeared to be derived from the portion of the beta subunit that was cleaved off during the conversion of beta into alpha. Upon continued proteolysis, a smaller polypeptide of molecular weight 24,000 (fragment A) was generated. This polypeptide manifested only RNase H activity and shared common amino acid sequences with beta and alpha subunits. Fragment A did not share any amino acid sequence homology with fragment B.

In vitro transcription of the avian retrovirus genome by the alpha form of the viral RNA-directed DNA polymerase

The nature of transcription of the avian retrovirus RNA genome by the alpha form of the viral RNA-directed DNA polymerase has been investigated. Transcription was most efficient when Mn2+ was provided as the divalent metal ion. The patterns of DNA transcription using 70S RNA, 35S RNA-tRNAtrp, or 35S RNA-oligo(dT)12-18 template-primer complexes by the alpha DNA polymerase were essentially identical to those obtained using the alphabeta form. The alpha DNA polymerase appears to be deficient in the synthesis of true duplex DNA but is able to synthesize hairpin-structured DNA initiated at the 5' terminus of the viral genome on the tRNAtrp primer molecule.

tRNATrp (bovine) binding to the reverse transcriptase of avian myeloblastosis virus and function as a heterologous primer

The primary structures for tTNATrp (bovine) and primer tRNATrp (avian) show only minor differences in nucleotide sequence. The heterologous tRNATrp (bovine) appears to have properties similar to the tRNATrp (avian) in its ability to bind the alphabeta from of RNA-dependent DNA nucleotidyltransferase of avian myeloblastosis virus. A stable enzyme-tRNA complex has been isolated by gel filtration. In addition, tRNATrp (bovine) can hydridize to the avian viral 35S RNA and act as a primer for transcription of the RNA. tRNATrp (bovine) can be obtained in larger amounts than the avian primer and can be used to study the interactions between the primer and the viral enzyme.

5.9-S RNA, a new RNA characterized in several mammalian cell lines

A new species of RNA has been isolated from several different cell lines, both oncornavirus producing and non-producing. This RNA, which we designate 5.9-S RNA is present in the cellular cytoplasmic fraction at very low concentration (approximately 1% of the quantity of 4-S RNA), but it accumulates to much higher levels in two murine oncornaviruses, Moloney murine sarcoma leukemia virus complex and Gross leukemia virus, where it represents as much as 10% of the low-molecular-weight RNA fraction associated with the 70-S RNA genome. The electrophoretic mobility and fingerprint analysis of T1 RNase digest products show that this species of RNA is approximately 160-165-residues long, and can be unequivocally distinguished from all previously described species of RNA in this size range.

Initiation sites of Rous sarcoma virus RNA-directed DNA synthesis in vitro

Rous sarcoma virus DNA synthesis in disrupted virions is initiated mainly at a site about 200 nucleotides or less from the 5' terminus, but other initiation sites throughtout the RNA seem to be used as well. No AUG triplet occurs within a 5' terminal segment of about 25 nucleotides.

Evidence for circularization of the avian oncornavirus RNA genome during proviral DNA synthesis from studies of reverse transcription in vitro

The RNA-directed DNA polymerase (deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase EC 2.7.7.7) of avian oncornavirus requires a tryptophan tRNA (tRNATrp) primer molecule located close to the 5' end of the viral RNA genome for the initiation of DNA synthesis in vitro. In this communication we demonstrate that the DNA product, transcribed from avian myeloblastosis virus (AMV) 35S RNA containing only tRNATrp as primer, is located also at the 5' end of the RNA genome. More importantly, we demonstrate that these 5' terminal DNA transcripts contain nucleotide sequences complementary to the 3' end of the genome. We have interpreted these results to mean that the genome. We have interpreted these results to mean that the 3' and 5' termini of the AMV 35S RNA genome become juxtaposed with each other either before or immediately after DNA synthesis has begun. These results are discussed in regard to the mechanism for synthesis of the circular forms of oncornavirus proviral DNA.

Initiation of DNA synthesis by the avian oncornavirus RNA-directed DNA polymerase: tryptophan tRNA as the major species of primer RNA

The major species of primer RNA required for the initiation of DNA synthesis by the Rous sarcoma virus RNA-directed DNA polymerase can be aminoacylated by tryptophan. Furthermore, an intact 3' terminus is required for the primer to function in the initiation of DNA synthesis.

E. coli tRNAs as inhibitors of viral reverse transcription in vitro

Reverse transcription of 70S AMV RNA by AMV reverse transcriptase has been studied in the presence of E. coli tRNAs. We have shown that inhibition of DNA synthesis occurs and that the tRNAs bind to the enzyme and not to the 70S RNA. The results have implications for the control of reverse transcription in vivo.

tRNA's associated with the 70S RNA of avian myeloblastosis virus

The distribtuion of various amino acid tRNA's in the 4S RNA components of avian myeloblastosis virus (AMV) and in 4S RNA prepared from chicken cmbryo cells, chicken myeloblasts, and chicken livers was determined. This was done by aminoacylating the 4S RNA samples with a mixture of 17 radioactive amino acids and subsequently identifying the tRNA-accepted amino acids on an amino acid analyzer after deacylation. In embryo cells, myeloblasts, and liver, tRNA's accepting all 1m amino acids were demonstrated. "Free" AMV 4S RNA was characterized by very low quantities of glutamate, valine, and tyrosine tRNA's. RNAs accepting all 17 amino acids, with the exception of tyrosine, were shown to be present in the "70S-associated" 4S RNA which dissociates at 60 C. The bulk of the 70S-associated 4S RNA was dissociated at 60 C at low ionic strength with a concomitant conversion of 70S RNA to 35S RNA. The residual associated 4S RNA was dissociated by further heating of the 35S RNA to 80 C; tryptophan tRNA accounted for greater than 90% of the total amino acid accepting activity in this fraction. The results support other studies in suggesting that tryptophan tRNA may serve as a primer for DNA synthesis in AMV, as has been shown in Rous sarcoma virus.